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Key Publications

Kanagal-Shamanna Lab

MD Anderson Cancer Center

Leukemia, August 1, 2022

doi: https://doi.org/10.1038/s41375-022-01652-8

Key Points:
  • 101 consecutive MDS samples were evaluated with traditional cytogenetic methods (karyotyping, FISH, CMA), an 81-gene NGS panel, and OGM
  • OGM found nearly double the number of clinically relevant pathogenic variants compared to traditional cytogenetics
  • OGM findings could inform different prognostic risk classification or identify important additional variants in 28% of study participants
  • Changes to CCSS and IPSS-R risk scores in 21% and 17% of subjects, respectively.
  • Additional 13% of samples had additional alternations researchers suggest could be used for therapy selection/response and disease monitoring
  • The combination of OGM and NGS resulted in the detection of at least one clinically significant clonal abnormality in 97 of 101 samples
View Publication

Kolhe Lab

Augusta University

medRxiv, Preprint: May 16, 2022

doi: https://doi.org/10.1101/2022.05.11.22274975

Key Points:
  • Retrospective validation study analyzing 94 unique amniocentesis samples previously characterized with karyotyping, FISH, and/or CMA
  • OGM was 100% concordant with findings from traditional cytogenetics across multiple types of chromosomal aberrations (aneuploidies, triploidy, deletions, duplications, translocations, isochromosomes, markers, AOH)
  • OGM detected 64 additional reportable SVs in 43 samples
View Publication

Adam C. Smith — University Health Network, Toronto, Rashmi Kanagal-Shamanna — MD Anderson, Kornelia Neveling — Radboud UMC

Am J Hematol, May 12, 2022;1-8.

doi: https://doi.org/10.1002/ajh.26587

Key Points:
  • Highlights the performance of OGM in acute myeloid leukemia, myelodysplastic syndromes, and B cell acute lymphoblastic leukemia
  • Illustrates how the OGM workflow can solve common challenges in testing for hematologic malignancies
  • Discusses the strengths and weaknesses of OGM compared to traditional methods
View Publication

Malan Lab

Hôpital Necker-Enfants Malades

Eur J Hum Genet, April 30, 2022:712-720.

doi: https://doi.org/10.1038/s41431-022-01094-x

Key Points:
  • Report of two unrelated subjects with a de novo 16p13.11p11.2 triplication associated with a 16p11.2 duplication, detected by CMA
  • Short-read WGS could not map any of the breakpoints
  • OGM determined the relative orientation of the triplicated and duplicated segments as well as the genomic positions of the breakpoints
  • Insights from OGM allowed authors to unravel the mechanism of these complex chromosomal rearrangements involving segmental duplications, propose a mechanism, and report a new clinically recognizable genomic disorder”
View Publication

Xiaochuan Wang Lab

Children’s Hospital of Fudan University

Research Square, Preprint: February 22, 2022

doi: https://doi.org/10.21203/rs.3.rs-1290086/v1

Key Points:
  • Case series evaluating three subjects with clinically confirmed chronic granulomatous disease that were negative by NGS (panel and WES)
  • OGM was performed and identified a novel pathogenic ~1.5 kbp deletion in a causative gene in 1/3 subjects
  • Demonstrates ability to identify disease-causing variants missed by sequencing technologies”
View Publication

Dewaele Lab

University Hospitals Leuven

Am J Hematol, April 2022;97:548-561.

doi: https://doi.org/10.1002/ajh.26487

Key Points:
  • Evaluated 41 samples of acute lymphoblastic leukemia (ALL): 29 B-ALL; 12 T-ALL
  • OGM detected all recurrent CNVs and SVs as well as additional recurrent SVs and resulting fusions
  • While traditional techniques (karyotype, FISH, MLPA, array) could assign only 23 samples to a major cytogenetic risk group, researchers conclude that OGM data would allow assignment of 32 subjects, potentially improving risk stratification
View Publication

Nguyen and Vangala Labs

Ruhr-University BochumInt

J Cancer, January 22, 2022;150(12);1998-2011.

doi: https://doi.org/10.1002/ijc.33942

Key Points:
  • Evaluated OGM performance in 27 samples from subjects with AML or MDS who underwent routine cytogenetic diagnostics (karyotype, FISH and RT-PCR when indicated)
  • OGM detected 31% more European Leukemia Net (ELN) and recurrent myeloid abnormalities compared to karyotyping and FISH
  • OGM also found abnormalities in 35% more samples than karyotyping, and in 67% of samples, the karyotype could be redefined by OGM. OGM refinement of the karyotype resulted in putative changes to the ELN risk classifications used in determining treatment plans
View Publication

Kolhe Lab

Augusta University

medRxiv, Preprint: Jan 17, 2022

doi: https://doi.org/10.1101/2022.01.15.22269355

Key Points:
  • Evaluated the use of OGM and a 523-gene NGS panel for genomic profiling of 15 myeloid tumors and compared results to karyotyping, FISH, and a 54-gene NGS panel
  • Results demonstrated 100% analytical concordance of OGM and the 523-gene NGS panel for variants found with traditional methods
  • In addition, OGM better characterized structural variants (SVs) previously reported by karyotyping in five samples and identified additional translocations and 11 CNVs
  • Demonstrated the combination of OGM and NGS is beneficial for comprehensive genomic profiling of myeloid neoplasm and NxClinical software enables simultaneous visualization and CNV confirmation
View Publication

Multicenter: University of Rochester, Medical College of Wisconsin, Columbia University, Greenwood Genetic Center, Augusta University, Praxis Genomics, University of Iowa

medRxiv, Preprint: Dec 27, 2022

doi: https://doi.org/10.1101/2021.12.27.21268432

Key Points:
  • Interim readout of an ongoing multisite study comparing the performance of OGM in postnatal samples with known genetic aberrations from prior testing with karyotype, FISH, and/or CMA
  • OGM had full concordance with previous findings in 97.7% (214/219) and partial concordance in 2.3% (5/219) of samples with multiple CNVs
  • Additional metrics establish strong technical performance, with a first-pass success rate of 94% (311/331 samples), a final pass rate of 99.1%, a reproducibility of analytical QC of 98.8% (171/173 replicates), and an inter-site reproducibility of pathogenic variant calls of 100% (16/16 replicates)
View Publication

Gläser Lab

University of Freiburg

Genes, Nov 21, 2022;12(11):1836.

doi: https://doi.org/10.3390/genes12111836

Key Points:
  • Case report of a family with clinically diagnosed Marfan syndrome with no pathogenic variants identified on NGS analysis of FBN1 gene, but with a reciprocal balanced translocation between chromosomes 2 and 15
  • OGM was performed and mapped the breakpoint within the FBN1 gene on chromosome 15 — later confirmed by targeted sequencing — disrupting the gene and likely explaining the observed phenotype
  • First report of a reciprocal translocation in the FBN1 gene associated with a typical Marfan syndrome presentation”
View Publication

Shieh, Penon-Portmann, and Wong Labs

University of California – San Francisco

Genom Med, Sept 23, 2021;6(77)

doi: https://doi.org/10.1038/s41525-021-00241-5

Key Points:
  • Describes a Full-Genome Analysis (FGA) approach using NGS linked-read sequencing and OGM to evaluate full spectrum of genetic variation in inherited genetic disorders
  • FGA was used in 50 subjects previously undiagnosed by either trio whole exome sequencing (23/50) and/or array (43/50)
  • FGA demonstrated an overall rate of detecting pathogenic variants of 40% (20/50) and identified candidate variants in 60% (18/30) of the remaining subjects. Lastly, FGA identified SVs and small variants in 8 of the 23 subjects missed by trio WES”
View Publication

Sabatella and Kuiper Labs

Princess Maxima Centre for Pediatric Oncology, Radboud University Medical Center

J Pathol, October 2021;255:202–211.

doi: https://doi.org/10.1002/path.5755

Key Points:
  • Case report of a family with two siblings born from healthy parents who were both neonatally diagnosed with atypical teratoid rhabdoid tumor (ATRT), associated with acquired homozygosity of SMARCB1
  • WES and WGS failed to identify germline or somatic SMARCB1 pathogenic mutations• OGM detected an insertion of ~2.8 kb within intron 2 of SMARCB1
  • Further characterization with long-read sequencing identified this insertion to be a SINE-VNTR-Alu, subfamily E (SVA-E) retrotransposon element, which was present in a mosaic state in the mother
  • Demonstrates the power of OGM and long-read sequencing to identify genomic variations in high-risk cancer-predisposing genes that are refractory to detection with traditional techniques”
View Publication

El Khattabi and Hoischen Labs

Université de Paris, Hôpital Cochin, Radboud University Medical Center

Am J Hum Genet, August 5, 2022;108:1409-1422.

doi: https://doi.org/10.1016/j.ajhg.2021.05.012

Key Points:
  • 85 constitutional samples with known chromosomal aberrations in the context of developmental and reproductive disorders
  • OGM had 100% concordance with traditional cytogenetic methods of karyotyping, FISH, and chromosomal microarray, detecting 99/99 aberrations
  • Aberration types included 7 aneuploidies, 19 deletions, 20 duplications, 34 translocations, 6 inversions, 2 insertions, 6 isochromosomes, 1 ring chromosome and 4 complex rearrangements”
View Publication

Hoischen Lab

Radboud University Medical Center

Am J Hum Genet, Aug 5, 2021;108(8):1423-1435.

doi: https://doi.org/10.1016/j.ajhg.2021.06.001

Key Points:
  • Evaluated OGM performance in 52 myeloid and lymphoid samples with clinically relevant aberrations detected with karyotyping, FISH, and/or CMA (36 simple; 16 complex)
  • Found 100% concordance of OGM in samples that traditional methods characterized as simple (46/46 aberrations in 36 samples)
  • Also found full concordance in 14/16 samples that traditional methods characterized as complex, with the remaining 2 cases largely concordant, while revealing additional new structural variants, gene fusion events, and greater detail about the structure of previously observed variants
  • OGM identified 15 additional candidate balanced translocations in 8 samples (4 simple; 4 complex) leading to potential gene fusion
View Publication

Shashi Lab

Duke University Medical Center (part of the Undiagnosed Diseases Network)

Mol Genet Genomic Med, Jul 2021;9(7):e1665.

doi: https://doi.org/10.1002/mgg3.1665

Key Points:
  • Case report of a 4-year-old male with an epileptic encephalopathy of undiagnosed molecular origin
  • Extensive prior metabolic and genetic testing had been non-diagnostic, including chromosome analysis, CMA (Affymetrix Cytoscan HD array), an infantile epilepsy panel (sequencing and deletion/duplication analysis of 38 genes), mitochondrial genome sequencing, trio WES, and trio WGS
  • OGM identified a mosaic, de novo 90 kb deletion and inversion on the X chromosome disrupting the CDKL5gene, resulting in a diagnosis of X-linked dominant early infantile epileptic encephalopathy-2 after confirmation in a clinical laboratory
  • Demonstrates the use of OGM to identify a mosaic structural variant missed by other techniques
View Publication

Multicenter: Columbia University, Mayo Clinic, Penn State, PathGroup, Legacy Health, Augusta University, Fred Hutchinson and MD Anderson Cancer Centers

medRxiv, Preprint: November 10, 2022.

doi: https://doi.org/10.1101/2020.11.07.20227728

Key Points:
  • Evaluated OGM performance in 100 AML samples previously evaluated with karyotyping and FISH
  • OGM detected 100% of all clinically relevant SVs and CNVs previously detected by traditional methods
  • OGM provided important incremental data in 24% of cases: additional clinically relevant SVs above and beyond traditional methods in 11% of samples and refinement of the genomic structure analysis in another 13%
  • Researchers illustrated how OGM consolidated techniques recommended by clinical guidelines (WHO, ELN, NCCN) for detection of hallmark AML SVs
View Publication
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Animal/Plant
Oncology
Covid-19
Solid tumors
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Technology development
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All Publications

Title Date Authors Journal
Optical Genome Mapping Identifies Novel Recurrent Structural Alterations in Childhood ETV6::RUNX1+ and High Hyperdiploid Acute Lymphoblastic Leukemia September 21, 2023 Brandes, Danielle, Yasin, et al. HemaSphere
Assembly of 43 diverse human Y chromosomes reveals extensive complexity and variation June 12, 2023 Pille Hallast, Peter Ebert, Mark Loftus, et al. bioRxiv
Babesia duncani multi-omics identifies virulence factors and drug targets April 13, 2023 Pallavi Singh, Stefano Lonardi, Qihua Liang, et al. Nature Microbiology
X-linked hypophosphatemia in 4 generations due to an exon 13–15 duplication in PHEX, in the absence of the c.*231A>G variant April 13, 2023 Julio Soto Barros, Sabrina I. Sanchez, Kristin Cabral, et al. Bone
FOXI3 pathogenic variants cause one form of craniofacial microsomia April 11, 2023 Ke Mao, Christelle Borel, Muhammad Ansar, et al. Nature Communications
Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species April 6, 2023 Ning Li, Qiang He, Juan Wang, et al. Nature Genetics
Abstract 214: Patient-specific mapping of oncogenic structural changes in pediatric osteosarcoma April 4, 2023 Andrew S. Clugston, Megan Ostrowski, Coco Wu, et al. Cancer Research (AACR)
Abstract 95: Uncommitted cells and phenotypic plasticity elucidate the complexity of the epithelial-mesenchymal molecular gradient of pleural mesothelioma April 4, 2023 David T. Severson, Samuel Freyaldenhoven, Benjamin Wadowski, et al. Cancer Research (AACR)
Abstract 2227: Streamlined workflow for analyzing and reporting hematological malignancies in Bionano VIATM software April 4, 2023 Benjamin Clifford, Jen Hauenstien, Andy Wing Chun Pang, et al. Cancer Research (AACR)
Abstract 240: Comprehensive analytical solution to measure HRD genomic scars from SNP arrays, pan-cancer NGS panels, and optical genome mapping (OGM) April 4, 2023 Daniel Saul, Megan Roytman, Viren Wasnikar, et al. Cancer Research (AACR)
Abstract 2224: Applying optical genome mapping to detect genomic biomarkers and use for residual disease monitoring in hematologic malignancies April 4, 2023 Alex Chitsazan, Andy Pang, Alex Hastie, et al. Cancer Research (AACR)
Abstract 6539: Application of optical genome mapping to identify samples with homologous recombination deficiency April 4, 2023 Andy Wing Chun Pang, Kelsea Chang, Nikhil Sahajpal, et al. Cancer Research (AACR)
Abstract 2074: Genome Integrity assessment and verification by optical genome mapping for cell manufacturing/bioprocessing applications April 4, 2023 Alex R. Hastie Cancer Research (AACR)
Abstract 2053: Structural variants detected by optical genome mapping in acute lymphoblastic leukemia patient-derived xenografts models April 4, 2023 Yueying Wang, Mengting Qin, JinPing Liu, et al. Cancer Research (AACR)
Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions April 3, 2023 Geoffrey C. Waldbieser, Shikai Liu, Zihao Yuan, et al. BMC Biology
Optical Genome Mapping in Routine Cytogenetic Diagnosis of Acute Leukemia April 3, 2023 Gwendoline Soler, Zangbéwendé Guy Ouedraogo, Carole Goumy, et al. Cancers
Making Reference Genomes Useful: Annotation April 1, 2023 Miguel García-Sancho & James Lowe Communities and Projects
Biallelic variants in CRIPT cause a Rothmund-Thomson-like syndrome with increased cellular senescence March 31, 2023 Luisa Averdunk, Maxim A Huetzen, Daniel Moreno-Andrés, et al. Genetics in Medicine
Case report: Optical genome mapping revealed double rearrangements in a male undergoing preimplantation genetic testing March 31, 2023 Jun Ren, Yuezhi Keqie, Yutong Li, et al. Frontiers in Genetics
Hidden Compositional Heterogeneity of Fish Chromosomes in the Era of Polished Genome Assemblies March 30, 2023 Marta Vohnoutová, Lucia Zifčáková, Radka Symonová, et al. Fishes
A complete gap-free diploid genome in Saccharum complex and the genomic footprints of evolution in the highly polyploid Saccharum genus March 30, 2023 Tianyou Wang, Baiyu Wang, Xiuting Hua, et al. Nature Plants
An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes March 28, 2023 Nataliya Timoshevskaya, Kaan I Eşkut, Vladimir A Timoshevskiy, et al. Cell Reports
The genomics of linkage drag in inbred lines of sunflower March 27, 2023 Kaichi Huang, Mojtaba Jahani, Jérôme Gouzy, et al. Proceedings of the National Academy of Sciences
Chiropterans are a hotspot for horizontal transfer of DNA transposons in Mammalia March 23, 2023 Nicole S Paulat, Jessica M Storer, Diana D Moreno-Santillán, et al. bioRxiv
Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice March 21, 2023 Yong Zhou, Zhichao Yu, Dmytro Chebotarov, et al. Nature Communications
The NLRomes of Zea mays NAM founder lines and Zea luxurians display presence-absence variation, integrated domain diversity, and mobility March 16, 2023 Shawn Thatcher, Mark Jung, Gayathri Panangipalli, et al. Molecular Plant Pathology
Deciphering a novel complex inversion affecting F8 in a family with severe haemophilia A by optical genome mapping March 10, 2023 Somayyeh Fahiminiya, Spyros Oikonomopoulos, Georges-Etienne Rivard, et al. Haemophilia
An improved assembly of the pearl millet reference genome using Oxford Nanopore long reads and optical mapping March 9, 2023 Marine Salson, Julie Orjuela, Cédric Mariac, et al. G3 (Bethseda)
Optical Genome Mapping for Cytogenetic Diagnostics in AML March 9, 2023 Verena Nilius-Eliliwi, Wanda M. Gerding, Roland Schroers, et al. Cancers
A chromosome-assigned Mongolian gerbil genome with sequenced centromeres provides evidence of a new chromosome March 6, 2023 Thomas D Brekke, Alexander ST Papadopulos, Eva Julia, et al. bioRxiv
Perspectives on the Application of Cytogenomic Approaches in Chronic Lymphocytic Leukaemia March 3, 2023 Wan Mohamad Zamri, Wan Norizzati, Nazihah Mohd Yunus, et al. Diagnostics
Helical coiling of metaphase chromatids March 2, 2023 Ivona Kubalová, Amanda Souza Câmara, Petr Cápal, et al. Nucleic Acids Research
A high-quality reference genome for the critically endangered Aeolian wall lizard, Podarcis raffonei March 2, 2023 Maëva Gabrielli, Andrea Benazzo, Roberto Biello, et al. Journal of Heredity
Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet March 2, 2023 Haidong Yan, Min Sun, Zhongren Zhang, et al. Nature Genetics
Next generation cytogenetics-optical mapping for comprehensive structural variant detection in hematological malignancies and beyond March 1, 2023 Alexander Hoischen 2023 Korean Society of Hematology International Conference
The allotetraploid Nicotiana tabacum genome and GenBank genomics highlight the genomic features, genetic diversity and regulation of morphological, metabolic and disease-resistance traits February 28, 2023 Yanjun Zan, Shuai Chen, Min Ren, et al. bioRxiv
Stepwise use of genomics and transcriptomics technologies increases diagnostic yield in Mendelian disorders February 28, 2023 Estelle Colin, Yannis Duffourd, Martin Chevarin, et al. Frontiers in Cell and Developmental Biology
Optical Genome Mapping as an Alternative to FISH-Based Cytogenetic Assessment in Chronic Lymphocytic Leukemia February 27, 2023 Andriana Valkama, Sandra Vorimo, Timo A. Kumpula, et al. Cancers
Design and Validation of a Custom Next-Generation Sequencing Panel in Pediatric Acute Lymphoblastic Leukemia February 23, 2023 José Vicente Gil, Esperanza Such, Claudia Sargas, et al. International Journal of Molecular Sciences
GenBank genomics highlight the genomic features, genetic diversity and regulation of morphological, metabolic and disease-resistance traits in Nicotiana tabacum February 23, 2023 Yanjun Zan, Shuai Chen, Min Ren, et al. bioRxiv
Multisite Assessment of Optical Genome Mapping for Analysis of Structural Variants in Constitutional Postnatal Cases February 22, 2023 M Anwar Iqbal, Ulrich Broeckel, Brynn Levy, et al. Journal of Molecular Diagnostics
Crane fly semiochemical overrules plant control over cyanobiont in Azolla symbioses February 21, 2023 Erbil Güngör, Jérôme Savary, Kelvin Adema, et al. bioRxiv
Genome assembly and genetic dissection of a prominent drought-resistant maize germplasm February 20, 2023 Tian Tian, Shuhui Wang, Shiping Yang, et al. Nature Genetics
DUX4 double whammy: The transcription factor that causes a rare muscular dystrophy also kills the precursors of the human nose February 17, 2023 Kaoru Inoue, Hamed Bostan, MaKenna R Browne, et al. Science Advances
Rare structural variants, aneuploidies, and mosaicism in individuals with Mullerian aplasia detected by optical genome mapping February 17, 2023 Soumia Brakta, Zoe A Hawkins, Nikhil Sahajpal, et al. Human Genetics
Putative signals of generalist plant species adaptation to local pollinator communities and abiotic factors February 16, 2023 L Frachon, L Arrigo, Q Rusman, et al. Molecular Biology and Evolution
Genomic, genetic and phylogenetic evidence for a new falcon species using chromosome-level genome assembly of the gyrfalcon and population genomics February 13, 2023 Farooq Omar Al-Ajli, Giulio Formenti, Olivier Fedrigo, et al. bioRxiv
Chronic Lymphocytic Leukemia: Current Knowledge and Future Advances in Cytogenomic Testing February 8, 2023 Lauren M Wainman, Wahab A Kahn, Prabhjot Kaur, et al. Advancements in Cancer Research
Optical Genome Mapping: a Novel Approach to Identifying Structural Variants in Metastatic Neuroendocrine Tumors February 6, 2023 Daniel M. DePietro, Isabela Gatmaytan, BA, et al. Endocrine Abstracts
Chromosome-level genome assembly of goose provides insight into the adaptation and growth of local goose breeds February 3, 2023 Qiqi Zhao, Zhenping Lin, Junpeng Chen, et al. Gigascience
Multiple chicken (Gallus gallus) genome references to advance genetic variation studies. Single haplotype chicken genome assemblies January 30, 2023 Wesley Warren*, Olivier Fedrigo, Alan Tracey, et al. Edinburgh Research Explorer
Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and is Associated with Worse Outcomes January 30, 2023 Lorinc Sandor Pongor, Christopher W Schultz, Lorenzo Rinaldi, et al. Cancer Discovery
Cross-species transcriptomic analysis identifies mitochondrial dysregulation as a functional consequence of the schizophrenia-associated 3q29 deletion January 28, 2023 Ryan H. Purcell, Esra Sefik, Erica Werner, et al. bioRxiv
The Australasian dingo archetype: De novo chromosome-length genome assembly, DNA methylome, and cranial morphology January 27, 2023 J. William O. Ballard, Matt A. Field, Richard J. Edwards, et al. bioRxiv
Comparative benchmarking of optical genome mapping and chromosomal microarray reveals high technological concordance in CNV identification and structural variant refinement January 22, 2023 Hayk Barseghyan, Andy Pang, Ben Clifford, et al. medRxiv
High-quality Fagopyrum esculentum genome provides insights into the flavonoid accumulation among different tissues and self-incompatibility January 21, 2023 Qiang He, Dan Ma, Wei Li, et al. Journal of Integrative Plant Biology
Genome assembly of the hybrid grapevine Vitis ‘Chambourcin’ January 20, 2023 Sagar Patel, Zachary N. Harris, Jason P. Londo, et al. bioRxiv
Testing for Facioscapulohumeral Muscular Dystrophy with Optical Genome Mapping January 17, 2023 Pratik Koppikar, Suresh Shenoy, Naga Guruju, et al. Current Protocols
De novo genome assembly and analyses of 12 founder inbred lines provide insights into maize heterosis January 16, 2023 Baobao Wang, Mei Hou, Junpeng Shi, et al. Nature Genetics
Structural Refinement by Direct Mapping Reveals Assembly Inconsistencies near Hi-C Junctions January 10, 2023 Luca Marcolungo, Leonardo Vincenzi, Matteo Ballottari, et al. Plants
Genetic Predisposition to Neurological Complications in Patients with COVID-19 January 9, 2023 Nikhil Shri Sahajpal, Alex R Hastie, Maximilian Schieck, et al. Biomolecules
A strongly improved assembly of the pearl millet reference genome using Oxford Nanopore long reads and optical mapping January 6, 2023 Marine Salson, Julie Orjuela, Cédric Mariac, et al. bioRxiv
Precision oncology using organoids of a secretory carcinoma of the salivary gland treated with TRK-inhibitors January 5, 2023 Gerben Lassche, Adriana C.H. van Engen - van Grunsven, Onnovan Hooij, et al. Oral Oncology
Draft genome sequencing and assembly of Risso’s dolphin, Grampus griseus January 1, 2023 Jayan D.M. Senevirathna, Ryo Yonezawa, Taiki Saka, et al. Journal of Genomics
Chromosome-scale genome assembly of a Japanese chili pepper landrace, Capsicum annuum ‘Takanotsume’ December 25, 2022 Kenta Shirasawa, Munetaka Hosokawa, Yasuo Yasui, et al. DNA Research
Optical Genome Mapping for detecting Homologous Recombination Deficiency (HRD) in human breast cancers December 24, 2022 Sandra Vanhuele, Youlia Kirova, Anne-Sophie Hamy-Petit, et al. bioRxiv
Detection of Transgene Location in the CYP2A13/2B6/2F1-transgenic Mouse Model using Optical Genome Mapping Technology December 21, 2022 Xinxin Ding, John Han, Laura S. Van Winkle, et al. ASPET
Optical Genome Mapping for Comprehensive Assessment of Chromosomal Aberrations and Discovery of New Fusion Genes in Pediatric B-Acute Lymphoblastic Leukemia December 21, 2022 Huixia Gao, Hanli Xu, Chanjuan Wang, et al. Cancers
Optical genome mapping and revisiting short-read genome sequencing data reveal previously overlooked structural variants disrupting retinal disease−associated genes December 16, 2022 Suzanne E.de Bruijn, Kim Rodenburg, Jordi Corominas, et al. Genetics in Medicine
Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies December 13, 2022 Keyur Talsania, Tsai-wei Shen, Xiongfong Chen, et al. Genome Biology
The Gossypium herbaceum L. Wagad genome as a resource for understanding cotton domestication December 1, 2022 Thiruvarangan Ramaraj, Corrinne E Grover, Azalea C Mendoza, et al. G3
Use of Bionano Optical Genome Mapping in a multi-platform structural variation analysis of a cancer reference cell line November 26, 2022 Andy Wing Chun Pang, Ben Kellman, Alex Hastie, et al. Cancer Genetics
Identification of novel genomic structural variations in Angiosarcoma by Optical Genome Mapping November 26, 2022 Thuy Phung, Wa Du, Joyce Lee, et al. Cancer Genetics
Optical genome mapping workflow for Somatic Abnormality detection in Multiple Solid Tumor types November 26, 2022 Benjamin Clifford, Andy Wing Chun Pang, Mark Oldakowski, et al. Cancer Genetics
Comparison of optical genome mapping, CMA, and 523-gene NGS panel for Homologous Recombination Deficiency calculation November 26, 2022 Nikhil Sahajpal, Ashis Mondal, Daniel Saul, et al. Cancer Genetics
Optical Genome Mapping workflow for identification and analysis of variants in Hematological Malignancies November 26, 2022 James Yu, Hayk Barseghyan, Jen Hauenstein, et al. Cancer Genetics
Optical genome mapping and 523-gene sequencing panel for comprehensive genomic evaluation of myeloid cancers November 26, 2022 Nikhil Sahajpal, Ashis Mondal, Sudha Ananth, et al. Cancer Genetics
Optical Genome Mapping: Clinical validation and diagnostic utility for cytogenomic analysis of Hematological Neoplasms November 26, 2022 Nikhil Sahajpal, Ashis Mondal, Tatiana Tvrdik, et al. Cancer Genetics
International working group recommendations for the implementation of optical genome mapping in Hematologic Malignancies November 26, 2022 Adam Smith, Rashmi Kanagal Shamanna, Barbara Dewaele, et al. Cancer Genetics
Optical Genome Mapping in MDS and AML as tool for structural variant profiling—comment and data update on Yang et al.: “High-resolution structural variant profiling of myelodysplastic syndromes by optical genome mapping uncovers cryptic aberrations of prognostic and therapeutic significance” November 24, 2022 Deepak B. Vangala, Verena Nilius-Eliliwi, Wanda M. Gerding, et al. Leukemia
A dynamic Campylobacterales epibiont community associated with the bone eating worm Osedax November 16, 2022 Shana Goffredi, Balig Panossian, Camille Brzechffa, et al. bioRxiv
Homologous Recombination Deficiency (HRD) in Hematological Malignancies November 15, 2022 Nikhil Sahajpal, Vamsi K. Kota, Anand P. Jillella, et al. Blood
Incremental Clinically Relevant Information in 70 CLL Cases with Optical Genome Mapping: Going Beyond Karyotype and FISH November 15, 2022 Nikhil Sahajpal, Anand P. Jillella, Ashis Mondal, et al. Blood
Unraveling Gene Fusions with Optical Genome Mapping in Hematological Malignancies: The Unexplored Terrain November 15, 2022 Nikhil Sahajpal, Vamsi K. Kota, Anand P. Jillella, et al. Blood
Pilot Inter-Laboratory Comparison Study of Optical Genome Mapping Analysis for Cytogenomic Characterization of Hematological Malignancies: A Spanish Multicentric Study November 15, 2022 Anna Puiggros, Mar Mallo, Marta Salido, et al. Blood
Combined Structural Variant and Mutation Profiling for Comprehensive Characterization of Chromoanagenesis and TP53 Mutations in Myelodysplastic Syndromes with Complex Karyotype November 15, 2022 Hui Yang, Guillermo Garcia-Manero, Yue Wei, et al. Blood
Optical Genome Mapping and Comprehensive Next Generation Sequencing Panel for Myeloid Cancers: New Era of Complimentary Profiling November 15, 2022 Nikhil Sahajpal, Ashis Mondal, Anand P. Jillella, et al. Blood
Deciphering the Somatic and Germline Structural Variation Landscape in Pediatric B-Cell Precursor Acute Lymphoblastic Leukemia By Whole Genome Optical Mapping November 15, 2022 Danielle Brandes, Triantafyllia Brozou, Karin Nebral, et al. Blood
DeepOM: Single-molecule optical genome mapping via deep learning November 13, 2022 Yevgeni Nogin, Tahir Detinis Zur, Sapir Margalit, et al. bioRxiv
The 22q11.2 Low Copy Repeats November 11, 2022 Lisanne Vervoort, Joris Robert Vermeesch Genes
Genomic technologies to improve variation identification in undiagnosed diseases November 9, 2022 Joseph TC Shieh Pediatric Neonatology
Diagnostic analysis of the highly complex OPN1LW/OPN1MW gene cluster using long-read sequencing and MLPA November 9, 2022 Lonneke Haer-Wigman, Amber den Ouden, Maria M. van Genderen, et al. NPJ Genomic Medicine
Chromosome-scale scaffolding of the fungus gnat genome (Diptera: Bradysia coprophila) November 4, 2022 John M. Urban, Susan A. Gerbi, Allan C. Spradling, et al. bioRxiv
Reclassification of DMD Duplications as Benign: Recommendations for Cautious Interpretation of Variants Identified in Prenatal Screening October 28, 2022 Wenbin He, Guiquan Meng, Xiao Hu, et al. Genes
Chromosome-scale genome assemblies of five different Brassica oleracea morphotypes provide insights in intraspecific diversification October 28, 2022 Chengcheng Cai, Johan Bucher, View ORCID ProfileRichard Finkers, et al. bioRxiv
Arctic introgression and chromatin regulation facilitated rapid Qinghai-Tibet Plateau colonization by an avian predator October 27, 2022 Li Hu, Juan Long, Yi Lin, et al. Nature Communications
A Complex Genomic Rearrangement Resulting in Loss of Function of SCN1A and SCN2A in a Patient with Severe Developmental and Epileptic Encephalopathy October 26, 2022 Valeria Orlando, Silvia Di Tommaso, Viola Alesi, et al. International Journal of Molecular Sciences
Whole-genome optical mapping to elucidate myeloid/lymphoid neoplasms with eosinophilia and tyrosine kinase gene fusions October 21, 2022 Benjamin Podvin, Pauline Roynard, Augustin Boudry, et al. Leukemia Research
The genome of Lactuca saligna, a wild relative of lettuce, provides insight into non-host resistance to the downy mildew Bremia lactucae October 21, 2022 Wei Xiong, Lidija Berke, Richard Michelmore, et al. bioRxiv
Semi-automated assembly of high-quality diploid human reference genomes October 19, 2022 Erich D. Jarvis, Giulio Formenti, Arang Rhie, et al. Nature
Born with intronless ERF transcriptional factors: C4 photosynthesis inherits a legacy dating back 450 million years October 18, 2022 Ming-Ju Amy Lyu, Huilong Du, Hongyan Yao, et al. bioRxiv
A chromosome-scale assembly of Brassica carinata (BBCC) accession HC20 containing resistance to multiple pathogens and an early generation assessment of introgressions into B. juncea (AABB) October 17, 2022 Kumar Paritosh, Sivasubramanian Rajarammohan, Satish Kumar Yadava, et al. bioRxiv
Optical Mapping Compendium of structural variants across global cattle breeds October 13, 2022 A. Talenti, J. Powell, D. Wragg, et al. Scientific Data
ATTCT and ATTCC repeat expansions in the ATXN10 gene affect disease penetrance of spinocerebellar ataxia type 10 October 13, 2022 C Alejandra Morato Torres, Faria Zafar, Yu-Chih Tsai, et al. HGG Advances
Optical Genome and Epigenome Mapping of Clear Cell Renal Cell Carcinoma October 13, 2022 Sapir Margalit, Zuzana Tulpová, Yael Michaeli, et al. bioRxiv
The snapdragon genomes reveal the evolutionary dynamics of the S locus supergene October 10, 2022 Sihui Zhu, Yu'e Zhang, Lucy Copsey, et al. bioRxiv
Molecular and genetic mechanisms conferring dissolution of dioecy in Diospyros oleifera Cheng October 9, 2022 Peng Sun Jr., Soichiro Nishiyama Jr., Huawei Li Jr., et al. bioRxiv
Optical genome mapping identifies clinically relevant genomic rearrangements in prostate cancer biopsy sample October 8, 2022 Yeeun Shim, Jongsoo Lee, Jieun Seo, et al. Cancer Cell International
A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.) October 8, 2022 J Mitchell McGrath, Andrew Funk, Paul Galewski, et al. DNA Research
DNA in nanochannels – Theory and applications October 7, 2022 Karolin Krykholm, Vilhelm Muller, KK Sriram, et al. Quarterly Reviews of Biophysics
Inversion polymorphism in a complete human genome assembly October 6, 2022 David Porubsky, William T. Harvey, Allison N. Rozanski, et al. bioRxiv
Identification and characterization of two DMD pedigrees with large inversion mutations based on a long-read sequencing pipeline October 5, 2022 Chang Geng, Ciliu Zhang, Pidong Li, et al. EJHG
Chromosome-scale genome assembly of a Japanese chili pepper landrace, Capsicum annuum ‘Takanotsume’ September 30, 2022 Kenta Shirasawa, Munetaka Hosokawa, Yasuo Yasui, et al. bioRxiv
The generation of the first chromosome-level de-novo genome assembly and the development and validation of a 50K SNP array for North American Atlantic salmon September 29, 2022 Guangtu Gao, Geoffrey C. Waldbieser, Ramey C. Youngblood, et al. bioRxiv
Quartet DNA reference materials and datasets for comprehensively evaluating germline variants calling performance September 28, 2022 Luyao Ren, Xiaoke Duan, Lianghua Dong, et al. bioRxiv
The genomes of medicinal skullcaps reveal the polyphyletic origins of clerodane diterpene biosynthesis in the family Lamiaceae September 26, 2022 Haixiu Li, Song Wu, Ruoxi Lin, et al. bioRxiv
The origin of a new chromosome in gerbils September 22, 2022 Thomas D. Brekke, Alexander S. T. Papadopulos, Eva Julià, et al. bioRxiv
Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics September 22, 2022 Tao Yang, Rong Liu, Yingfeng Luo, et al. Nature Genetics
Identification of a familial complex chromosomal rearrangement by optical genome mapping September 21, 2022 Yang Yang, Wang Hao Molecular Cytogenetics
Copy number analysis in cancer diagnostic testing September 20, 2022 Tara Spence, Adrian M Dubuc Clinics in Laboratory Medicine
Annelid functional genomics reveal the origins of bilaterian life cycles. September 19, 2022 Yan Liang, Francisco M. Martín-Zamora, Kero Guynes, et al. bioRxiv
High-quality Chromosome-scale Genomes Facilitate Effective Identification of Large Structural Variations in Hot and Sweet Peppers  September 19, 2022 Joung-Ho Lee, Jelli Venkatesh, Jinkwan Jo, et al. Horticulture Research
A Novel Non-Allelic Homologous Recombination Event in a Parent with an 11;22 Reciprocal Translocation Leading to 22q11.2 Deletion Syndrome September 17, 2022 Steven Pastor, Oanh Tran, Daniel E. McGinn, et al. Genes
“Omics” data unveil early molecular response underlying limb regeneration in the Chinese mitten crab, Eriocheir sinensis September 16, 2022 Jun Wang, Xiaowen Chen, Xin Hou, et al. Science Advances
Reference quality genome sequence of Indian pomegranate cv. ‘Bhagawa’ ( Punica granatum L.) September 15, 2022 P Roopa Sowjanya, Parashuram Shilpa, Goudappa Prakash Patil, et al. Frontiers in Plant Science
Integration of multi-omics data reveals cis-regulatory variants that are associated with phenotypic differentiation of eastern from western pigs September 14, 2022 Yuwen Liu, Yang Fu, Yalan Yang, et al. Genetics Selection Evolution
A high-quality chromosome-level genome assembly of rohu carp, Labeo rohita, and its utilization in SNP-based exploration of gene flow and sex determination September 12, 2022 Mark A. Arick II, Corrinne E. Grover, Chuan-Yu Hsu, et al. bioRxiv
Broad genomic workup including optical genome mapping uncovers a DDX3X: MLLT10 gene fusion in acute myeloid leukemia September 9, 2022 Verena Nilius-Eliliwi, Marco Tembrink, Wanda Maria Gerding, et al. Frontiers in Oncology
Human papillomavirus integration strictly correlates with global genome instability in head and neck cancer September 2, 2022 Brandon Labarge, Max Hennessy, Lijun Zhang, et al. Molecular Cancer Research
Optical genome mapping refines cytogenetic diagnostics, prognostic stratification and provides new molecular insights in adult MDS/AML patients September 2, 2022 Estelle Balducci, Sophie Kaltenbach, Patrick Villarese, et al. Blood Cancer Journal
Comparative phylotranscriptomics reveals a 110 million years-old symbiotic program September 2, 2022 Cyril Libourel, Jean Keller, Lukas Brichet, et al. bioRxiv
A survey of current methods to detect and genotype inversions September 1, 2022 Vincent C. T. Hanlon, Peter M. Lansdorp, Victor Guryev, et al. Human Mutation
Genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley August 29, 2022 Wenying Zhang, Cong Tan, Haifei Hu, et al. Plant Biotechnology Journal
Restriction Site Detection in Optical Mapping Data August 17, 2022 Vít Doleží, Petr Gajdoš, Marek Běhálek, et al. Advances in Intelligent Networking and Collaborative Systems
Destabilized 3’UTR ARE therapeutically degrades ERBB2 in drug-resistant ERBB2+ cancer models August 15, 2022 Chidiebere U Awah, Yana Glemaud, Fayola Levine, et al. bioRxiv
Genomic analyses of Pamir argali, Tibetan sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation August 10, 2022 Xin Li , San-Gang He, Wen-Rong Li, et al. Genome Research
Genomic local adaptation of a generalist plant species to pollinator communities and abiotic factors August 5, 2022 L. Frachon, L. Arrigo, Q. Rusman, et al. bioRxiv
Repeat-based holocentromeres influence genome architecture and karyotype evolution August 3, 2022 Paulo G Hofstatter, Gokilavani Thangavel, Thomas Lux, et al. Cell
Repeat expansions nested within tandem CNVs: A unique structural change in GLS exemplifies the diagnostic challenges of non-coding pathogenic variation August 1, 2022 Sarah Fazal, Matt C Danzi, André B P van Kuilenburg, et al. Human Molecular Genetics
High-resolution structural variant profiling of myelodysplastic syndromes by optical genome mapping uncovers cryptic aberrations of prognostic and therapeutic significance August 1, 2022 Hui Yang, Guillermo Garcia-Manero, Koji Sasaki, et al. Leukemia
TP53 Abnormalities Are Underlying the Poor Outcome Associated with Chromothripsis in Chronic Lymphocytic Leukemia Patients with Complex Karyotype July 29, 2022 Silvia Ramos-Campoy, Anna Puiggros, Joanna Kamaso, et al. Cancers
Intragenic inversions in NF1 gene as pathogenic mechanism in neurofibromatosis type 1 July 26, 2022 Viola Alesi, Francesca Romana Lepri, Maria Lisa Dentici, et al. EJHG
Prevalence of intronic repeat expansions in RFC1 in Dutch patients with CANVAS and adult-onset ataxia July 21, 2022 Fatemeh Ghorbani, Jelkje de Boer-Bergsma, Corien C Verschuuren-Bemelmans, et al. Journal of Neurology
Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex-predation July 21, 2022 Harsh Shukla, Kushal Suryamohan, Anubhab Khan, et al. bioRxiv
A Chromosome-Length Assembly of the Hawaiian Monk Seal ( Neomonachus schauinslandi): A History of “Genetic Purging” and Genomic Stability July 18, 2022 David W Mohr, Stephen J Gaughran, Justin Paschall, et al. Genes
New genomic resources provide insights into the recent evolutionary adaptation of Antirrhinum lineage and multiomics investigation of S-locus July 18, 2022 Sihui Zhu, Yu’e Zhang, Dongfeng Zheng, et al. bioRxiv
Multipartite super-enhancers function in an orientation-dependent manner July 14, 2022 Mira T. Kassouf, Helena S. Francis, Matthew Gosden, et al. bioRxiv
Helical metaphase chromatid coiling is conserved July 14, 2022 Ivona Kubalová, Amanda Souza Câmara, Petr Cápal, et al. bioRxiv
Chromosome-scale assembly and annotation of the perennial ryegrass genome July 12, 2022 Istvan Nagy, Elisabeth Veeckman, Chang Liu, et al. BMC Genomics
A Draft Human Pangenome Reference July 9, 2022 Wen-Wei Liao, Mobin Asri, Jana Ebler, et al. bioRxiv
A chromosome-level assembly of the Japanese eel genome: Insights into gene duplication and chromosomal reorganization July 1, 2022 Hongbo Wang, Hin Ting Wan, Bin Wu, et al. bioRxiv
Genome sequence assembly evaluation using long-range sequencing data June 30, 2022 Dengfeng Guan,   Shane A. McCarthy,   Jonathan M. D. Wood, et al. bioRxiv
Genome sequence of Gossypium anomalum facilitates interspecific introgression breeding June 22, 2022 Zhenzhen Xu, Jiedan Chen, Shan Meng, et al. Plant Communications
Genome and transcriptome architecture of allopolyploid okra (Abelmoschus esculentus) June 17, 2022 Ronald Nieuwenhuis, Thamara Hesselink, Hetty C. van den Broeck, et al. bioRxiv
Detection of cryptic balanced chromosomal rearrangements using high-resolution optical genome mapping June 16, 2022 Shuo Zhang, Zhenle Pei, Caixia Lei, et al. Journal of Medical Genetics
Next-Generation Sequencing Technologies: Approaches and Applications for Crop Improvement June 14, 2022 Anupam Singh, Goriparthi Ramakrishna, Tanvi Kaila, et al.
Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice (Oryza sativa) June 13, 2022 Yong Zhou, Zhichao Yu, Dmytro Chebotarov, et al. bioRxiv
Genomics of cold adaptations in the Antarctic notothenioid fish radiation June 9, 2022 Iliana Bista, Jonathan M. D. Wood, Thomas Desvignes, et al. bioRxiv
Scrutinizing pathogenicity of the USH2A c.2276 G > T; p.(Cys759Phe) variant June 7, 2022 André Weber, Thomas Liehr, Ahmed Al-Rikabi, et al. NPJ Genomic Medicine
Scrutinizing pathogenicity of the USH2A c.2276 G > T; p.(Cys759Phe) variant June 7, 2022 Janine Reurink, Erik de Vrieze, Catherina H Z Li, et al. NPJ Genomic Medicine
The genomics of linkage drag in sunflower June 7, 2022 Kaichi Huang, Mojtaba Jahani, Jérôme Gouzy, et al. bioRxiv
Neurogenetic Variant Analysis by Optical Genome Mapping for Structural Variation Detection-Balanced Genomic Rearrangements, Copy Number Variants, and Repeat Expansions/Contractions June 1, 2022 Hayk Barseghyan, Andy W. C. Pang, Yang Zhang, et al. Genomic Structural Variants in Nervous System Disorders
The immunogenomic landscape of cattle June 1, 2022 Ting-Ting Li, Tian Xia, Jia-Qi Wu, et al. bioRxiv
Allele-aware chromosome-level genome assembly of Artemisia annua reveals the correlation between ADS expansion and artemisinin yield June 1, 2022 Baosheng Liao, Xiaofeng Shen, Li Xiang, et al. Molecular Plant
The evolution of two transmissible cancers in Tasmanian devils May 28, 2022 Maximilian R. Stammnitz, Kevin Gori, Young Mi Kwon, et al. bioRxiv
Generation of hypoimmunogenic induced pluripotent stem cells by CRISPR-Cas9 system and detailed evaluation for clinical application May 25, 2022 Yuko Kitano, Sayaka Nishimura, Tomoaki M. Kato, et al.
Primary mediastinal large B-cell lymphoma is characterized by large-scale copy-neutral loss of heterozygosity May 25, 2022 Stefania Tuveri, Koen Debackere, Lukas Marcelis, et al. Chromosomes & Cancer
Emerging technologies in the study of the virome May 25, 2022 Sophie E Smith, Wanqi Huang, Kawtar Tiamani, et al. Current Opinion in Virology
Optical Genome Mapping Identifies a Novel Pediatric Embryonal Tumor Subtype with a ZNF532-NUTMI Fusion May 23, 2022 Miriam Bornhorst, Augustine Eze, Surajit Bhattacharya, et al. medRxiv
Optical mapping compendium of structural variants across global cattle breeds May 16, 2022 A. Talenti, J. Powell, D. Wragg, et al. bioRxiv
Clinical validation and diagnostic utility of optical genome mapping in prenatal diagnostic testing May 16, 2022 Nikhil Shri Sahajpal, Ashis K Mondal, Timothy Fee, et al. medRxiv
ATTCT and ATTCC repeat expansions in the ATXN10 gene affect disease penetrance of spinocerebellar ataxia type 10 May 16, 2022 C. Alejandra Morato Torres, Faria Zafar, Yu-Chih Tsai, et al. medRxiv
Dynamic Features of Chromosomal Instability during Culture of Induced Pluripotent Stem Cells May 15, 2022 Casey O. Dubose, John R. Daum, Christopher L. Sansam, et al. bioRxiv
Tissue and cell-type specific molecular and functional signatures of 16p11.2 reciprocal genomic disorder across mouse brain and human neuronal models May 13, 2022 Derek J.C. Tai, Parisa Razaz, Serkan Erdin, et al. bioRxiv
Optical genome mapping for structural variation analysis in hematologic malignancies May 12, 2022 Adam C. Smith, Kornelia Neveling, Rashmi Kanagal-Shamanna, et al. American Journal of Hematology
The first neocentric, discontinuous, and complex small supernumerary marker chromosome composed of 7 euchromatic blocks derived from 5 different chromosomes May 10, 2022 André Weber, Thomas Liehr, Ahmed Al-Rikabi, et al.
Decoding The Nuclear Genome of The Human Pathogen Babesia duncani Shed Light on its Virulence, Drug Susceptibility and Evolution among Apicomplexa May 9, 2022 Stefano Lonardi, Pallavi Singh, Qihua Liang, et al. bioRxiv
Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders May 6, 2022 David Porubsky, Wolfram Höps, Hufsah Ashraf, et al. Cell
Efficacy and initial clinical evaluation of optical genome mapping in the diagnosis of structural variations May 6, 2022 N Hao, J Zhou, M M Li, et al.
Assembly of complete diploid phased chromosomes from draft genome sequences May 2, 2022 Andrea Minio, Noé Cochetel, Amanda Vondras, et al. bioRxiv
Copy Number Analysis in a Large Cohort Suggestive of Inborn Errors of Immunity Indicates a Wide Spectrum of Relevant Chromosomal Losses and Gains April 29, 2022 Rensheng Wan, Maximilian Schieck, Andrés Caballero-Oteyza, et al. Journal of Clinical Immunology
Multiplex structural variant detection by whole-genome mapping and nanopore sequencing April 20, 2022 Lahari Uppuluri, Yilin Wang, Eleanor Young, et al. Scientific Reports
CD34+CD19-CD22+ B-cell progenitors might underlie phenotypic escape in patients treated with CD19-directed therapies April 18, 2022 Clara Bueno, Susana Barrera, Alex Bataller, et al. Blood
Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection April 16, 2022 Aurélie Canaguier, Romane Guilbaud, Erwan Denis, et al. bioRxiv
Optical genome mapping capability expanded to enable detection of absence of heterozygosity April 8, 2022 —, Aliz Raksi, Ernest T Lam, et al.
16p13.11p11.2 triplication syndrome: a new recognizable genomic disorder characterized by optical genome mapping and whole genome sequencing April 7, 2022 Romain Nicolle, Karine Siquier-Pernet, Marlène Rio, et al. EJHG
Evaluation of optical genome mapping for detecting chromosomal translocation in clinical cytogenetics April 6, 2022 Peng Dai, Xiaofan Zhu, Yanzheng Pei, et al. Molecular Genetics and Genomic Medicine
Comprehensive Structural Variant Detection: From Mosaic to Population-Level April 5, 2022 Mortiz Smolka, Luis F Paulin, Christopher M Grochowski, et al. bioRxiv
Molecular characterization of myotonic dystrophy fibroblast cell lines for use in small molecule screening April 4, 2022 Jana R Jenquin, Alana P O’Brien, Kiril Poukalov, et al.
Monitoring of Leukemia Clones in B-cell Acute Lymphoblastic Leukemia at Diagnosis and During Treatment by Single-cell DNA Amplicon Sequencing April 2, 2022 Sarah Meyers, Llucia Alberti-Servera, Olga Gielen, et al.
A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta) April 1, 2022 Marc Palmada-Flores, Joseph D Orkin, Bettina Haase, et al. Gigascience
A chromosome-length assembly of the Hawaiian Monk seal (Neomonarchus schauinslandi) confirms genomic stability in the Pinnipeds and a prolonged history of “genetic purging” March 31, 2022 David W Mohr, Stephen J Gaughran, Justin Paschall, et al. bioRxiv
Barcode aware adaptive sampling for GridION and PromethION Oxford Nanopore sequencers March 30, 2022 Alexander Payne, Rory Munro, Nadine Holmes, et al. bioRxiv
Pangenomics provides insights into the role of synanthropy in barn swallow evolution March 29, 2022 Simona Secomandi, Guido Roberto Gallo, Marcella Sozzoni, et al. bioRxiv
Construction of a new chromosome-scale, long-read reference genome assembly of the Syrian hamster, Mesocricetus auratus March 23, 2022 R. Alan Harris, Muthuswamy Raveendran, Dustin T. Lyfoung, et al. bioRxiv
Whole-genome sequence and methylome profiling of the almond (Prunus dulcis [Mill.] D.A.Webb) cultivar ‘Nonpareil’ March 23, 2022 Katherine M D'Amico-Willman, Wilberforce Z Ouma, Tea Meulia, et al. G3 (Bethseda)
Draft genome sequence of Indian mulberry (Morus indica) provides a resource for functional and translational genomics March 21, 2022 Mukesh Jain, Juhi Bansal, Mohan Singh Rajkumar, et al. Genomics
A t(6;14;9)(p22;q22;q34) three-way translocation: Description of a cytogeneetically visible variant t(6;9) in acute myeloid leukemia March 17, 2022 —, Adam C. Smith, Dawn Maze, et al.
A t(6;14;9)(p22;q22;q34) three-way translocation: Description of a cytogenetically visible variant t(6;9) in acute myeloid leukemia March 16, 2022 Adam C Smith, Dawn Maze, Daniel Xia, et al. American Journal of Hematology
Optical Genome Mapping: Clinical Validation and Diagnostic Utility for Enhanced Cytogenomic Analysis of Hematological Neoplasms March 15, 2022 Nikhil Shri Sahajpal, Ashis K Mondal, Tatiana Tvrdik, et al. medRxiv
Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning March 14, 2022 Naveenkumar Athiyannan, Michael Abrouk, Willem H. P. Boshoff, et al. Nature Genetics
Familial long-read sequencing increases yield of de novo mutations March 14, 2022 Michelle D Noyes, William T Harvey, David Porubsky, et al. AJHG
Multi-omics comparison of malignant and normal uveal melanocytes reveals novel molecular features of uveal melanoma March 11, 2022 David Gentien,  Elnaz Saberi-Ansari,  Nicolas Servant, et al. bioRxiv
Genomic consequences of domestication of the Siamese fighting fish March 9, 2022 Young Mi Kwon, Nathan Vranken, Carla Hoge, et al. Science Advances
A happy accident: a novel turfgrass reference genome March 9, 2022 Alyssa R. Phillips, Arun S. Seetharam, Taylor AuBuchon-Elder, et al. bioRxiv
Automated assembly of high-quality diploid human reference genomes. March 8, 2022 Erich D. Jarvis, Giulio Formenti, Arang Rhie, et al. bioRxiv
Characterization of PAX5 Intragenic Tandem Multiplication in Pediatric B-Lymphoblastic Leukemia by Optical Genome Mapping March 5, 2022 Jeffrey Jean, Alexandra E Kovach, Andrew Doan, et al. Blood Advances
From Tiny Samples to Big Findings: Highly automated workflows and compact laboratory systems boost output and conserve resources, facilitating discovery and diagnostics. March 2, 2022 Kathy Liszewski Genetic Engineering and Biotechnology News
eP333: Tracking the emergence of SARS-CoV-2 variants of concern in vaccinated and unvaccinated patients March 2, 2022 —, Alec Vest, Holly Houdeshell, et al.
Sex-specific changes in autosomal methylation rate in ageing common terns. February 26, 2022 Britta Meyer, Maria Moiron, Calvinna Caswara, et al. Authorea
Structure, dynamics and impact of replication stress-induced structural variants in hepatocellular carcinoma. February 25, 2022 Quentin Bayard, Pierre Cordier, Camille Peneau, et al. Cancer Research
Caecilian genomes reveal molecular basis of adaptation and convergent evolution of limblessness in snakes and caecilians. February 25, 2022 Vladimir Ovchinnikov, Marcela Uliano-Silva, Mark Wilkinson, et al. bioRxiv
‘Nebbiolo’ genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.) February 24, 2022 Simone Maestri, Giorgio Gambino, Giulia Lopatriello, et al. BMC Genomics
Optical Genome Mapping Improves Genetic Diagnosis in Chronic Granulomatous Diseases. February 22, 2022 Xiaoying Hui, Jingmin Yang, Wenjie Wang, et al. Research Square
Broadening the genomic landscape of sensory disorders February 18, 2022 Jeroen J Smits, Suzanne E de Bruijn, Cornelis P Lanting, et al. Radboud Respository
A genomic toolkit for ‘the soybean of the tropics’ – winged bean (Psophocarpus tetragonolobus). February 18, 2022 Wai Kuan Ho, Alberto Tanzi, Fei Sang, et al. Research Square
A cattle graph genome incorporating global breed diversity February 17, 2022 A Talenti, J Powell, J D Hemmink, et al. Nature Communications
Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes. February 16, 2022 Fernando A. Rabanal, Maike Gräff, Christa Lanz, et al. bioRxiv
Guiding the Global Evolution of Cytogenetic Testing for Hematologic Malignancies. February 15, 2022 Yassmine M. N. Akkari, Linda B. Baughn, Adrian M. Dubuc, et al. Blood
Methods to Improve Molecular Diagnosis in Genomic Cold Cases in Pediatric Neurology February 11, 2022 Magda K. Kadlubowska and Isabelle Schrauwen Genes (Basel)
Curated variation benchmarks for challenging medically relevant autosomal genes. February 7, 2022 Justin Wagner, Nathan D. Olson, Lindsay Harris, et al. Nature Biotechnology
Optical Genome Mapping And Single Nucleotide Polymorphism Microarray: An Integrated Approach For Investigating Challenging Cases Of Products Of Conception. February 6, 2022 Nikhil S Sahajpal, Ashis K Mondal, Sudha Ananth, et al. medRxiv
Optimizing the diagnostic workflow for acute lymphoblastic leukemia by optical genome mapping. February 4, 2022 Katrina Rack, Jolien De Bie, Geneviève Ameye, et al. American Journal of Hematology
Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding. February 3, 2022 Jean-Marc Aury, Stefan Engelen, Benjamin Istace, et al. bioRxiv
Structural Variation Detection of Adolescent Thyroid Cancer Using Optical Mapping. January 31, 2022 Lei Yang, Shaochang Wu, Baosheng Liao, et al. Research Square
Epigenomic and structural events preclude recombination in Brassica napus January 28, 2022 Franz Boideau, Gautier Richard, Olivier Coriton, et al.
Genome biology of the Darkedged Splitfin, Girardinichthys multiradiatus, and the evolution of sex chromosomes and placentation. January 26, 2022 Kang Du, Martin Pippel, Susanne Kneitz, et al. Genome Research
Erratum for CD44-positive cells are responsible for gemcitabine resistance in pancreatic cancer cells. January 25, 2022 —, Hong SP, Wen J, et al.
Type IV pili is a critical virulence factor in clinical isolates of Paenibacillus thiaminolyticus. January 24, 2022 Christine Hehnly, Aiqin Shi, Paddy Ssentongo, et al. bioRxiv
Optical genome mapping reveals additional prognostic information compared to conventional cytogenetics in AML/MDS patients January 22, 2022 Wanda M. Gerding, Marco Tembrink, Verena Nilius-Eliliwi, et al. Cancer Genetics and Epigenetics
MDS/MPN-Unclassifiable with t(X;17)(q28;q21) and KANSL1-MTCP1/CMC4 Fusion Gene. January 17, 2022 Peter Molony, Adam C Smith, Shamini Selvarajah, et al. Cytogenetic and Genome Research
Clinical Utility of Combined Optical Genome Mapping and 523-gene Next Generation Sequencing Panel For Comprehensive Evaluation of Myeloid Cancers. January 17, 2022 Nikhil Shri Sahajpal, Ashis K Mondal, Sudha Ananth, et al. medRxiv
OptiDiff: structural variation detection from single optical mapping reads. January 11, 2022 Mehmet Akdel, Dick de Ridder bioRxiv
Optical genome mapping identifies rare structural variations as predisposition factors associated with severe COVID-19. January 10, 2022 Nikhil Shri Sahajpal, Chi-Yu Jill Lai, Alex Hastie, et al. ISCIENCE
Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates January 6, 2022 Adam Nunn, Isaac Rodríguez-Arévalo, Zenith Tandukar, et al. Plant Biotechnology Journal
Applications of Optical Mapping for Plant Genome Assembly and Structural Variation Detection. January 1, 2022 Yuxuan Yuan Plant Bioinformatics
Recent applications of CRISPR-Cas9 in Genome Mapping and Sequencing (Chapter 2). January 1, 2022 Dharma Varapula, Lahari Uppuluri, Ming Xiao, et al. CRC Press
Multi-site Technical Performance and Concordance of Optical Genome Mapping: Constitutional Postnatal Study for SV, CNV, and Repeat Array Analysis. December 30, 2021 M. Anwar Iqbal, Ulrich Broeckel, Brynn Levy, et al. medRxiv
A Rare Moment? Advances Spurring Rare Disease Diagnosis and Treatment. December 29, 2021 Malorye Allison Branca Clinical OMICs
Recombination suppression and selection affect local ancestries in genomes of a migratory songbird. December 23, 2021 Jun Ishigohoka, Karen Bascón-Cardozo, Andrea Bours, et al. bioRxiv
A high-quality Genome and Comparison of Short versus Long Read Transcriptome of the Palaearctic duck Aythya fuligula (Tufted Duck) December 20, 2021 Ralf C Mueller, Patrik Ellström, Kerstin Howe, et al. Gigascience
Haplotype-resolved inversion landscape reveals hotspots of mutational recurrence associated with genomic disorders. December 20, 2021 David Porubsky, Wolfram Höps, Hufsah Ashraf, et al. bioRxiv
A high-continuity and annotated tomato reference genome December 15, 2021 Xiao Su, Baoan Wang, Xiaolin Geng, et al. BMC Genomics
The blackgrass genome reveals patterns of divergent evolution of non-target site resistance to herbicides. December 15, 2021 Lichun Cai, David Comont, Dana MacGregor, et al. bioRxiv
Constitutional chromothripsis of the APC locus as a cause of genetic predisposition to colon cancer. December 14, 2021 Florentine Scharf, Rafaela Magalhaes Leal Silva, Monika Morak, et al.
Chromosome-level genome assembly of the functionally extinct northern white rhinoceros (Ceratotherium simum cottoni). December 11, 2021 Gaojianyong Wang, Björn Brändl, Christian Rohrandt, et al. bioRxiv
A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes. December 10, 2021 H. Toh, C. Yang, G. Formenti, et al. bioRxiv
De Novo Assembly of the Nearly Complete Fathead Minnow Reference Genome Reveals a Repetitive but Compact Genome. December 10, 2021 John W. Martinson, David C. Bencic, Gregory P. Toth, et al. Environmental Toxicology and Chemistry
Optical genome mapping in routine human genetic diagnostics—Its advantages and limitations December 8, 2021 Paul Dremsek , Thomas Schwarz, Beatrix Weil, et al. Genes
Acute myeloid leukemia with t (X; 6) 9p11; q23); MYB-GATA1 and female sex: GATA1 insufficiency may be insufficient for pathogenesis December 4, 2021 Alexandra E Kovach, Elena Zerkalenkova, Ludmila Zemtsova, et al. Cancer Genetics
African-specific prostate cancer molecular taxonomy. December 1, 2021 Vanessa Hayes, Weerachai Jaratlerdsiri, Jue Jiang, et al. Research Square
Barcode aware adaptive sampling for Oxford Nanopore sequencers. December 1, 2021 Alexander Payne, Rory Munro, Nadine Holmes, et al. bioRxiv
Combining dense and sparse labeling in optical DNA mapping. November 29, 2021 Erik Torstensson, Gaurav Goyal, Anna Johnning, et al. PLOS One
Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH. November 29, 2021 King L. Hung, Jens Luebeck, Siavash R. Dehkordi, et al. bioRxiv
Breaking the vicious circle: Extrachromosomal circular DNA as an emerging player in tumour evolution. November 29, 2021 Matius Robert, Karen Crasta Seminars in Cell & Developmental Biology
Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences. November 29, 2021 Terence Gall-Duncan, Nozomu Sato, Ryan K.C. Yuen, et al. Genome Research
High-Throughput Characterization of Cytogenomic Heterogeneity of MDS Using High-Resolution Optical Genome Mapping. November 23, 2021 Hui Yang, Guillermo Garcia-Manero, Guillermo Montalban-Bravo, et al. Blood
Evaluation of copy number variants for genetic hearing loss: a review of current approaches and recent findings. November 22, 2021 Wafaa Abbasi, Courtney E. French, Shira Rockowitz, et al. Human Genetics
Marfan Syndrome Caused by Disruption of the FBN1 Gene due to A Reciprocal Chromosome Translocation November 21, 2021 Anna Clara Schnause, Katalin Komlosi, Barbara Herr, et al. Genes
Multi-modal investigation of the schizophrenia-associated 3q29 genomic interval reveals global genetic diversity with unique haplotypes and segments that increase the risk for non-allelic homologous recombination NAHR November 15, 2021 Feyza Yilmaz, Umamaheswaran Gurusamy, Trenell J. Mosley, et al. medRxiv
Long-read assembly of the Chinese indigenous Ningxiang pig genome and identification of genetic variations in fat metabolism among different breeds November 10, 2021 Haiming Ma, Juan Jiang, Jun He, et al. Molecular Ecology Resources
Prospects of telomere-to-telomere assembly in barley: analysis of sequence gaps in the MorexV3 reference genome November 10, 2021 Pavla Navrátilová, Helena Toegelová, Zuzana Tulpová, et al. bioRxiv
Extrachromosomal DNA: An emerging hallmark in human cancer November 9, 2021 Sihan Wu, Vineet Bafna, Howard Y. Chang, et al. Annual Review of Pathology: Mechanisms of Disease
Genome editing reveals that pSCL4 is required for chromosome linearity in Streptomyces clavuligerus November 8, 2021 Juan Pablo Gomez-Escribano, Lis Algora Gallardo, Kenan A. J. Bozhüyük, et al. Microbial Genomics
Real time, in-line optical mapping of single molecules of DNA November 7, 2021 Franziska M Esmeka, Tim Erichlandwehr, Dennis HB Morsa, et al. Biosensors and Bioelectronics:X
A giant NLR gene confers broad-spectrum resistance to Phytophthora sojae in soybean November 5, 2021 Weidong Wang, Liyang Chen, Kevin Fengler, et al. Nature Communications
The landscape of extrachromosomal circular DNA in medulloblastoma November 1, 2021 Owen S Chapman, Jens Luebeck, Sameena Wani, et al. bioRxiv
Applications of Optical Genome Mapping in Next-Generation Cytogenetics and Genomics November 1, 2021 Wahab A Kahn, Diana M Toledo Advances in Molecular Pathology
Whole-genome sequence and methylome profiling of the almond (Prunus dulcis [Mill.] D.A.Webb) cultivar ‘Nonpareil’ November 1, 2021 —, —, 2021 —, et al.
Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph October 30, 2021 Bin Huang, Guozheng Wei, Bing Wang, et al. BMC Bioinformatics
Unexpected post-glacial colonisation route explains the white colour of barn owls (Tyto alba) from the British Isles October 25, 2021 Ana Paula Machado, Tristan Cumer, Christian Iseli, et al. Molecular Ecology
The genome sequence of the common frog, Rana temporaria Linnaeus 1758 [version 1; peer review: awaiting peer review] October 22, 2021 Jeffrey W Streicher Wellcome Open Research
The genome sequence of the common toad, Bufo bufo (Linnaeus, 1758) [version 1; peer review: 1 approved] October 20, 2021 Jeffrey W Streicher Wellcome Open Research
Long read technologies identify a hidden inverted duplication in a family with choroideremia October 14, 2021 Zeinab Fadaie, Kornelia Neveling, Tuomo Mantere, et al.
Towards a Comprehensive Variation Benchmark for Challenging Medically-Relevant Autosomal Genes October 4, 2021 —, —, 2021 —, et al.
Two Gap-free Reference Genomes and a Global View of the Centromere Architecture in Rice October 4, 2021 Jia-Ming Song, Wen-Zhao Xie, Shuo Wang, et al. Molecular Plant
The Streptochaeta genome and the evolution of the grasses October 4, 2021 Arun S. Seetharam, Yunqing Yu, Sébastien Bélanger, et al. Frontiers in Plant Science
Towards a Comprehensive Variation Benchmark for Challenging Medically-Relevant Autosomal Genes October 1, 2021 Justin Wagner, Nathan D Olson, Lindsay Harris, et al. bioRxiv
Optical Mapping of the Fusarium oxysporum f. sp. melongenae Genome September 24, 2021 Duygu Ates, Hacer H Altinok, Muhammed Bahattin Tanyolac, et al. Research Square
Application of full-genome analysis to diagnose rare monogenic disorders September 23, 2021 Joseph T Shieh, Monica Penon-Portmann, Karen HY Wong, et al. NPJ Genomic Medicine
Avian neo-sex chromosomes reveal dynamics of recombination suppression and W degeneration September 20, 2021 Hanna Sigeman, Maria Strandh, Estelle Proux-Wéra, et al. Molecular Biology and Evolution
Characterization of full-length LINE-1 insertions in 154 genomes September 15, 2021 Jessica S Wonga, Tanaya Jadhava, Eleanor Young, et al. Genomics
The Impact of Whole Genome Data on Therapeutic Decision-Making in Metastatic Prostate Cancer September 14, 2021 —, —, 2021 —, et al.
Genomic and transcriptomic analyses reveal a tandem amplification unit of 11 genes and mutations of mismatch repair genes in methotrexate-resistant HT-29 cells September 14, 2021 Ahreum Kim, Jong-Yeon Shin, Jeong-Sun Seo, et al. Experimental and Molecular Medicine
GABOLA: A Reliable Gap-Filling Strategy for de novo Chromosome-Level Assembly September 8, 2021 Wei-Hsuan Chuang, Hsueh-Chien Cheng, Yu-Jung Chang, et al. bioRxiv
Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing September 7, 2021 Caroline Belser, Franc-Christophe Baurens, Benjamin Noel, et al. Communications Biology
Multiplatform discovery and regulatory function analysis of structural variations in non-small cell lung carcinoma September 7, 2021 Lin Xia, Zhoufeng Wang, Xinyue Wu, et al. Cell Reports
Single-molecule sequencing of long DNA molecules allows high contiguity de novo genome assembly for the fungus fly, Sciara coprophila September 6, 2021 John M. Urban, Michael S. Foulk, Jacob E. Bliss, et al. BMC Genomics
Introgression among North American wild grapes (Vitis) fuels biotic and abiotic adaptation September 3, 2021 Abraham Morales-Cruz, Jonas A Aguirre-Liguori, Yongfeng Zhou, et al. Genome Biology
Insights into angiosperm evolution, floral development and chemical biosynthesis from the Aristolochia fimbriata genome September 2, 2021 Liuyu Qin, Yiheng Hu, Jinpeng Wang, et al. Nature Plants
A high-quality chromosome-scale assembly of the centipedegrass [Eremochloa ophiuroides (Munro) Hack.] genome provides insights into chromosomal structural evolution and prostrate growth habit September 1, 2021 Jingjing Wang, Hailing Zi, Rui Wang, et al. Horticulture Research
The clinical utility of optical genome mapping for the assessment of genomic aberrations in acute lymphoblastic leukemia August 30, 2021 Jonathan Lukas Lühmann, Marie Stelter, Marie Wolter, et al. Cancers
Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves higher resolution for research and breeding August 24, 2021 Jean-Marc Aury, Stefan Engelen, Benjamin Istace, et al. bioRxiv
Expanding the conservation genomics toolbox: Incorporating structural variants to enhance genomic studies for species of conservation concern August 23, 2021 Jana Wold, Klaus-Peter Koepfli, Stephanie J. Galla, et al. Molecular Ecology
Pan-genome of Raphanus highlights genetic variation and introgression among domesticated, wild and weedy radishes August 10, 2021 Xiaohui Zhang, Tongjin Liu, Jinglei Wang, et al. Nature Plants
Validation of Optical Genome Mapping for the Molecular Diagnosis of Facioscapulohumeral Muscular Dystrophy (FSHD) August 9, 2021 —, Aaron A.StenceJon G.ThomasonJonathan A.PruessnerRamakrishna R.SompallaeAnthony N.SnowDeqinMaSteven A.MooreAaron D.Bossler 1 Department of Pathology, [&hellip, et al.
Validation of Optical Genome Mapping for the Molecular Diagnosis of Facioscapulohumeral Muscular Dystrophy August 9, 2021 Aaron A Stence, Jon G Thomason, Jonathan A Pruessner, et al. Journal of Molecular Diagnostics
De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes August 6, 2021 Matthew B. Hufford, Arun S. Seetharam, Margaret R. Woodhouse, et al. Science
Using de novo assembly to identify structural variation of complex immune system gene regions August 3, 2021 Jia-Yuan Zhang, Hannah Roberts, David S. C. Flores, et al. PLOS Computational Biology
Inside AJHG: A Chat with Laïla El Khattabi and Alexander Hoischen August 3, 2021 —, Each month, the editors of The American Journal of Human Genetics interview an author [&hellip, et al.
The promise of next generation cytogenetics: Optical genome mapping July 31, 2021 Yasmine Akkari
Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case July 30, 2021 Benjamin Istace, Caroline Belser, Cyril Falentin, et al. Biology
Extensive variation in the intelectin gene family in laboratory and wild mouse strains July 30, 2021 Faisal Almalki, Eric B. Nonnecke, Patricia A. Castillo, et al. Scientific Reports
Optical genome mapping identifies a germline retrotransposon insertion in SMARCB1 in two siblings with atypical teratoid rhabdoid tumors July 29, 2021 Mariangela Sabatella, Tuomo Mantere, Esmé Waanders, et al. Journal of Pathology
The genome sequence of the European turtle dove, Streptopelia turtur Linnaeus July 27, 2021 Jenny C. Dunn, Keith C. Hamer, Antony J. Morris, et al. Wellcome Open Research
Genomic rearrangements have consequences for introgression breeding as revealed by genome assemblies of wild and cultivated lentil species July 24, 2021 Larissa Ramsay, Chu Shin Koh, Sateesh Kagale, et al. bioRxiv
A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis July 23, 2021 Zirlane Portugal Costa, Alessandro Mello Varani, Luiz Augusto Cauz-Santos, et al. The Plant Genome
Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing July 20, 2021 Hollis A. Dahn, Jacquelyn Mountcastle, Jennifer Balacco, et al. bioRxiv
Whole-genome optical mapping of bone-marrow myeloma cells reveals association of extramedullary multiple myeloma with chromosome 1 abnormalities July 19, 2021 Eva Kriegova, Regina Fillerova, Jiri Minarik, et al. Scientific Reports
Return of the Lemnaceae: Duckweed as a model plant system in the genomics and post-genomics era July 17, 2021 Kenneth Acosta, Klaus J Appenroth, Ljudmilla Borisjuk, et al. The Plant Cell
Genome-Wide Mapping of Human DNA Replication by Optical Replication Mapping Supports a Stochastic Model of Eukaryotic Replication Timing July 15, 2021 Weitao Wang, Kyle N. Klein, Karel Proesmans, et al. Molecular Cell
Phylogeny and Sex Chromosome Evolution of Palaeognathae July 13, 2021 Zongji Wang, Jilin Zhange, Xiaoman Xua, et al. Journal of Genetics and Genomics
Long Reads Capture Simultaneous Enhancer-Promoter Methylation Status for Cell-type Deconvolution July 12, 2021 Sapir Margalit, Yotam Abramson, Hila Sharim, et al. Bioinformatics
A reference-grade genome identifies salt-tolerance genes from the salt-secreting mangrove species Avicennia marina July 8, 2021 Purushothaman Natarajan, Ashok Kumar Murugesan, Ganesan Govindan, et al. Communications Biology
Simple Quantification of Epigenetic DNA Modifications and DNA Damage on Multi-Well Slides July 7, 2021 —, Yael Michaeli Sapir Margalit Sigal Avraham Hila Erez Noa Gilat Zuzana Tulpová Yuval Ebenstein —, 2021 —, et al.
A full molecular picture of F8 intron 1 inversion created with optical genome mapping July 7, 2021 —, Somayyeh Fahiminiya,  Georges-Etienne Rivard, et al.
Multicolor Whole-Genome Mapping in Nanochannels for Genetic Analysis July 7, 2021 Lahari Uppuluri, Tanaya Jadhav, Yilin Wang, et al. Analytical Chemistry
Optical genome mapping enables constitutional chromosomal aberration detection July 7, 2021 Tuomo Mantere, Kornelia Neveling, Celine Pebrel-Richard, et al. AJHG
Next-generation cytogenetics: Comprehensive assessment of 52 hematological malignancy genomes by optical genome mapping July 7, 2021 Kornelia Neveling, Tuomo Mantere, Ssan Vermeulen, et al. AJHG
A full molecular picture of F8 intron 1 inversion created with optical genome mapping July 7, 2021 Somayyeh Fahiminiya, Georges-Etienne Rivard, Patrick Scott, et al. Haemophilia
De Novo Sequencing and High-Contiguity Genome Assembly of Moniezia expansa Reveals Its Specific Fatty Acid Metabolism and Reproductive Stem Cell Regulatory Network July 6, 2021 Yi Liu, Zhengrong Wang, Wanlong Huang, et al. Frontiers in Cellular and Infection Microbiology
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies July 2, 2021 Ann M. Mc Cartney, Kishwar Shafin, Michael Alonge, et al. bioRxiv
Identification of unique variants as the underlying cause of IRD in pedigrees that remained unresolved after initial whole genome sequence analysis June 30, 2021 —, Pooja Biswas,  Berzhan Kurmanov, et al.
Population genomics of apricots unravels domestication history and adaptive events June 25, 2021 Alexis Groppi, Shuo Liu, Amandine Cornille, et al. Nature Communications
The genome sequence of the European water vole, Arvicola amphibius Linnaeus 1758 [version 1; peer review: awaiting peer review] June 24, 2021 Angus I. Carpenter, Michelle Smith, Craig Corton, et al. Wellcome Open Research
Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations June 24, 2021 Peng Qin, Hongwei Lu, Huilong Du, et al. Cell
A cattle graph genome incorporating global breed diversity June 23, 2021 —, A. Talenti,  J. Powell, et al.
Two SMARCAD1 Variants Causing Basan Syndrome in a Canadian and a Dutch Family June 14, 2021 Youssef Elhaji, Tessa M.A. van Henten, Claudia A.L. Ruivenkamp, et al. JID Innovations
Chromosome-level Genome Assembly of a Regenerable Maize Inbred Line A188 June 9, 2021 Guifang Lin, Cheng He, Jun Zheng, et al. Genome Biology
A pair of effectors encoded on a conditionally dispensable chromosome of Fusarium oxysporum suppress host-specific immunity June 9, 2021 Yu Ayukawa, Shuta Asai, Pamela Gan, et al. Communications Biology
Hi-C scaffolded short- and long-read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution June 7, 2021 Claire R. Peart, Christina Williams, Saurabh D. Pophaly, et al. Molecular Ecology Resources
Improved genome assembly and pan-genome provide key insights on eggplant domestication and breeding June 5, 2021 Lorenzo Barchi, Mark Timothy Rabanus-Wallace, Jaime Prohens, et al. Plant Journal
Exploring the missing heritability in subjects with hearing loss, enlarged vestibular aqueducts, and a single or no pathogenic SLC26A4 variant (Chapter 5). June 4, 2021 Jeroen J. Smits, Suzanne E. de Bruijn, Cornelis P. Lanting, et al. Human Genetics
Exploring the Missing Heritability in Subjects With Hearing Loss, Enlarged Vestibular Aqueducts, and A Single or No Pathogenic SLC26A4 Variant June 4, 2021 —, Jeroen Smits, Suzanne E. de Bruijn, et al.
Towards improved genetic diagnosis of human differences of sex development June 3, 2021 Emmanuèle C. Délot, Eric Vilain Nature Reviews Genetics
Transposable element accumulation drives size differences among polymorphic Y chromosomes in Drosophila June 3, 2021 Alison H. Nguyen, Doris Bachtrog bioRxiv
Signal-based optical map alignment June 2, 2021 Mehmet Akdel, Henri van de Geest, Elio Schijlen, et al. bioRxiv
Parameter exploration improves the accuracy of long-read genome assembly May 30, 2021 Anurag Priyam, Alicja Witwicka, Anindita Brahma, et al. bioRxiv
Introgressing the Aegilops tauschii genome into wheat as a basis for cereal improvement May 27, 2021 Yun Zhou, Shenglong Bai, Hao Li, et al. Nature Plants
Re-examination of two diatom reference genomes using long-read sequencing May 24, 2021 Gina V. Filloramo, Bruce A. Curtis, Emma Blanche, et al. BMC Genomics
Adoption of Optical Genome Mapping in Clinical Cancer Cytogenetic Laboratory: A Stepwise Approach May 24, 2021 Victoria Stinnett, Liqun Jiang, Lisa Haley, et al. Journal of Equine Veterinary Science
37   Genomic improvement of the horse X chromosome and characterization of the pseudoautosomal boundary May 24, 2021 M. Jevit, B. Davis, A. Hillhouse, et al. Journal of Equine Veterinary Science
Golden pompano genome resource enables discovery of valuable gene determining growth traits May 22, 2021 Honglin Luo, Yongde Zhang, Changmian Ji, et al. bioRxiv
Extensive variation within the pan-genome of cultivated and wild sorghum May 20, 2021 Yongfu Tao, Hong Luo, Jiabao Xu, et al. Nature Plants
The genome sequence of the Norway rat, Rattus norvegicus Berkenhout 1769 [version 1; peer review: awaiting peer review] May 18, 2021 Kerstin Howe, Melinda Dwinell, Mary Shimoyama, et al. Wellcome Open Research
The genetic architecture of phenotypic diversity in the betta fish (Betta splendens) May 17, 2021 Wanchang Zhang, Hongru Wang, Débora Y. C. Brandt, et al. bioRxiv
The genome sequence of the European golden eagle, Aquila chrysaetos chrysaetos Linnaeus 1758 [version 1; peer review: awaiting peer review] May 14, 2021 Dan Mead, Rob Ogden, Anna Meredith, et al. Wellcome Open Research
The First High-Quality Reference Genome of Sika Deer Provides Insights for High-Tannin Adaptation May 14, 2021 Xiumei Xing, Cheng Ai, Tianjiao Wang, et al. bioRxiv
FaNDOM: Fast nested distance-based seeding of optical maps May 14, 2021 Siavash Raeisi Dehkordi, Jens Luebeck, Vineet Bafna, et al. Patterns
Determining Optical Mapping Errors by Simulations May 13, 2021 Michal Vašinek, Marek Běhálek, Petr Gajdoš, et al. Bioinformatics
Comparison of structural variants detected by optical mapping with long-read next-generation sequencing May 13, 2021 Jakub Savara, Tomáš Novosád, Petr Gajdoš, et al. Bioinformatics
Optical genome mapping, a promising alternative to gold standard cytogenetic approaches in a series of acute lymphoblastic leukemias May 13, 2021 Valentin Lestringant, Nicolas Duployez, Dominique Penther, et al. Chromosomes and Cancer
The genome sequence of the brown trout, Salmo trutta Linnaeus 1758 [version 1; peer review: awaiting peer review] May 13, 2021 Tom Hansen, Per Gunnar Fjelldal, Sigbjørn Lien, et al. Wellcome Open Research
Subtelomeric assembly of a multi-gene pathway for antimicrobial defense compounds in cereals May 7, 2021 Yan Li, Aymeric Leveau, Qiang Zhao, et al. Nature Communications
Detection of a mosaic CDKL5 deletion and inversion by optical genome mapping ends an exhaustive diagnostic odyssey May 6, 2021 Heidi Cope, Hayk Barseghyan, Surajit Bhattacharya, et al. Molecular Genetics and Genomic Medicine
A high-quality bonobo genome refines the analysis of hominid evolution May 5, 2021 Yafei Mao, Claudia R Catacchio, LaDeana W Hillier, et al. Nature
The genome of the warm-season turfgrass African bermudagrass (Cynodon transvaalensis) May 1, 2021 Fengchao Cui, Geli Taier, Manli Li, et al. Horticulture Research
Sequence of the supernumerary B chromosome of maize provides insight into its drive mechanism and evolution April 29, 2021 Nicolas Blavet, Hua Yang, Handong Su, et al. PNAS
Universal nomenclature for oxytocin–vasotocin ligand and receptor families April 28, 2021 Constantina Theofanopoulou, Gregory Gedman, James A. Cahill, et al. Nature
Evolutionary and biomedical insights from a marmoset diploid genome assembly April 28, 2021 Chentao Yang, Yang Zhou, Stephanie Marcus, et al. Nature
Towards complete and error-free genome assemblies of all vertebrate species April 28, 2021 Arang Rhie, Shane A. McCarthy, Olivier Fedrigo, et al.
Optical maps refine the bread wheat Triticum aestivum cv Chinese Spring genome assembly April 24, 2021 Tingting Zhu, Le Wang, Hélène Rimbert, et al. The Plant Journal
Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection April 16, 2021 —, Background Structural Variations (SVs) are very diverse genomic rearrangements. In the past, their [&hellip, et al.
Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale April 16, 2021 Jonathan Jeffet, Sapir Margalit, Yael Michaeli, et al. Essays in Biochemistry
False gene and chromosome losses affected by assembly and sequence errors April 9, 2021 Juwan Kim, Chul Lee, Byung June Ko, et al. bioRxiv
Widespread false gene gains caused by duplication errors in genome assemblies April 9, 2021 Byung June Ko, Chul Lee, Juwan Kim, et al. bioRxiv
Haplotype-resolved diverse human genomes and integrated analysis of structural variation April 2, 2021 PETER EBERT, PETER A. AUDANO, HUI ZHU, et al. Science
Construction of whole genomes from scaffolds using single cell strand-seq data March 31, 2021 Mark Hills, Ester Falconer, Kieran O’Neill, et al. International Journal of Molecular Sciences
Novelty and convergence in adaptation to whole genome duplication March 30, 2021 Magdalena Bohutínská, Mark Alston, Patrick Monnahan, et al. Molecular Biology and Evolution
Genomic variation and recent population histories of spotted (Strix occidentalis) and barred (S. varia) owls March 25, 2021 Naoko T Fujito, Zachary R Hanna, Michal Levy-Sakin, et al. Genome Biology and Evolution
Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential March 18, 2021 M. Timothy Rabanus-Wallace, Bernd Hackauf, Martin Mascher, et al. Nature Genetics
Long-read sequence assembly: a technical evaluation in barley March 12, 2021 Martin Mascher, Thomas Wicker, Jerry Jenkins, et al. The Plant Cell
Optical Genome Mapping as a Next-Generation Cytogenomic Tool for Detection of Structural and Copy Number Variations for Prenatal Genomic Analyses March 11, 2021 Nikhil Shri Sahajpal, Hayk Barseghyan, Ravindra Kolhe, et al. Genes
Chromosome level reference of Atlantic halibut Hippoglossushippoglossus provides insight into the evolution of sexual determination systems March 2, 2021 Anthony L. Einfeldt, Tony Kess, Amber Messmer, et al.
Sorghum breeding in the genomic era: opportunities and challenges March 2, 2021 Huaiqing Hao, Zhigang Li, Chuanyuan Leng, et al.
Robust Benchmark Structural Variant Calls of An Asian Using the State-of-Art Long Fragment Sequencing Technologies March 2, 2021 Xiao Du, Lili Li, Fan Liang, et al. and Bioinformatics
Genome editing reveals fitness effects of a gene for sexual dichromatism in Sulawesian fishes March 1, 2021 Satoshi Ansai, Koji Mochida, Shingo Fujimoto, et al. Nature Communications
The genome of Tripterygium wilfordii and characterization of the celastrol biosynthesis pathway February 28, 2021 Tianlin Pei, Mengxiao Yan, Yu Kong, et al. Gigabyte
De novo assembly and annotation of a highly contiguous reference genome of the fathead minnow (Pimephales promelas) reveals an AT-rich repetitive genome with compact gene structure February 25, 2021 John Martinson, David C. Bencic, Gregory P. Toth, et al. bioRxiv
Chemoenzymatic labeling of DNA methylation patterns for single-molecule epigenetic mapping February 24, 2021 —, DNA methylation, specifically, et al.
Chemoenzymatic labeling of DNA methylation patterns for single-molecule epigenetic mapping February 24, 2021 Tslil Gabrieli, Yael Michaeli, Sigal Avraham, et al. bioRxiv
Genome assembly and population genomic analysis provide insights into the evolution of modern sweet corn February 23, 2021 Ying Hu, Vincent Colantonio, Bárbara S. F. Müller, et al. Nature Communications
A long reads-based de-novo assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout February 22, 2021 Guangtu Gao, Susana Magadan, Geoffrey C Waldbieser, et al. G3 Genes Genomes Genetics
Genome sequences of Tropheus moorii and Petrochromis trewavasae, two eco-morphologically divergent cichlid fishes endemic to Lake Tanganyika February 22, 2021 C. Fischer, S. Koblmüller, C. Börger, et al. Scientific Reports
Genomics Armed With Diversity Leads the Way in Brassica Improvement in a Changing Global Environment February 18, 2021 Nur Shuhadah Mohd Saad, Anita A. Severn-Ellis, Aneeta Pradhan, et al. Frontiers in Genetics
Identification of Somatic Structural Variants in Solid Tumors By Optical Genome Mapping February 18, 2021 David Y. Goldrich, Brandon LaBarge, Scott Chartrand, et al. Journal of Personalized Medicine
Optical Mapping of the Fusarium oxysporum f. sp. melongenae Genome February 16, 2021 Duygu Ates, Hacer H Altinok, Muhammed Bahattin Tanyolac, et al. Journal of Basic Microbiology
long-read-tools.org: an interactive catalogue of analysis methods for long-read sequencing data February 16, 2021 Shanika L Amarasinghe, Matthew E Ritchie, Quentin Gouil, et al. Gigascience
Whole‐Genome Sequence of Synthesized Allopolyploids in Cucumis Reveals Insights into the Genome Evolution of Allopolyploidization February 15, 2021 Xiaqing Yu, Panqiao Wang, Ji Li, et al. Advanced Science
Extensive introgression among North American wild grapes (Vitis) fuels biotic and abiotic adaptation February 12, 2021 Abraham Morales-Cruz, Jonas Aguirre-Liguori, Yongfeng Zhou, et al. bioRxiv
Chromosome-level reference genome of the Soursop (Annona muricata), a new resource for Magnoliid research and tropical pomology February 11, 2021 Joeri S. Strijk, Damien D. Hinsinger, Mareike M. Roeder, et al. Molecular Ecology Resources
Hepatitis B virus integrations promote local and distant oncogenic driver alterations in hepatocellular carcinoma February 9, 2021 Camille Péneau, Sandrine Imbeaud, Tiziana La Bella, et al. Hepatology
Skewed X inactivation in genetically diverse mice is associated with recurrent copy number changes at the Xce locus February 5, 2021 Kathie Y Sun, Daniel Oreper, Sarah A Schoenrock, et al. bioRxiv
Diploid chromosome-scale assembly of the Muscadinia rotundifolia genome supports chromosome fusion and disease resistance gene expansion during Vitis and Muscadinia divergence February 5, 2021 Noé Cochetel, Andrea Minio, Mélanie Massonnet, et al. G3 Genes Genomes Genetics
Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control February 3, 2021 Todd P. Michael, Evan Ernst, Nolan Hartwick, et al. Genome Research
Genome assembly of the maize inbred line A188 provides a new reference genome for functional genomics February 1, 2021 Fei Ge, Jingtao Qu, Peng Liu, et al. bioRxiv
Fine structure and transcription dynamics of bread wheat ribosomal DNA loci deciphered by a multi-omics approach. January 29, 2021 Zuzana Tulpová, Aleš Kovařík, Helena Toegelová, et al.
Chromosome‐level assembly of Southern catfish (Silurus meridionalis) provides insights into visual adaptation to the nocturnal and benthic lifestyles January 27, 2021 Shuqing Zheng, Feng Shao, Wenjing Tao, et al. Molecular Ecology Resources
The genome of Shanputao (Vitis amurensis) provides a new insight into cold tolerance of grapevine January 21, 2021 Yi Wang, Haiping Xin, Peige Fan, et al. The Plant Journal
Transcriptome Alterations in Myotonic Dystrophy Frontal Cortex January 19, 2021 Brittney A Otero, Kiril Poukalov, Ryan P Hildebrandt, et al. Cell Reports
Improved Spirodela polyrhiza genome and proteomic analyses reveal a conserved chromosomal structure with high abundance of chloroplastic proteins favoring energy production January 17, 2021 Alex Harkess, Fionn McLoughlin, Natasha Bilkey, et al. Journal of Experimental Botany
Application of Optical Genome Mapping For Comprehensive Assessment of Chromosomal Structural Variants for Clinical Evaluation of Myelodysplastic Syndromes January 15, 2021 Hui Yang, Guillermo Garcia-Manero, Diana Rush, et al. medRxiv
Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis January 15, 2021 Amit Rai, Hideki Hirakawa, Ryo Nakabayashi, et al. Nature Communications
Construction and Integration of Three De Novo Japanese Human Genome Assemblies toward a Population-Specific Reference January 11, 2021 Jun Takayama, Shu Tadaka , Kenji Yano, et al. Nature Communications
A large genome with chromosome‐scale assembly sheds light on the evolutionary success of a true toad (Bufo gargarizans) January 11, 2021 Bin Lu, Jianping Jiang, Hua Wu, et al. Molecular Ecology Resources
Host genome analysis of structural variations by Optical Genome Mapping provides clinically valuable insights into genes implicated in critical immune, viral infection, and viral replication pathways in patients with severe COVID-19 January 8, 2021 Nikhil Shri Sahajpal, Chi-Yu Jill Lai, Alex Hastie, et al. medRxiv
A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals January 6, 2021 Jing Li, Jilin Zhang, Jing Liu, et al. Gigascience
nanotatoR: A tool for enhanced annotation of genomic structural variants January 6, 2021 Surajit Bhattacharya, Hayk Barseghyan, Emmanuèle C. Délot, et al. BMC Genomics
Genomic regions associated with microdeletion/microduplication syndromes exhibit extreme diversity of structural variation January 6, 2021 Yulia Mostovoy, Feyza Yilmaz, Stephen K Chow, et al. Genetics
Platypus and echidna genomes reveal mammalian biology and evolution January 6, 2021 Yang Zhou, Linda Shearwin-Whyatt, Jing Li, et al. Nature
Pan-genome Analysis in Sorghum Highlights the Extent of Genomic Variation and Sugarcane Aphid Resistance Genes January 4, 2021 Bo Wang, Yinping Jiao, Kapeel Chougule, et al. bioRxiv
Assembly and Validation of Two Gap-free Reference Genomes for Xian/indica Rice Reveals Insights into Plant Centromere Architecture January 1, 2021 Jia-Ming Song, Wen-Zhao Xie, Shuo Wang, et al. bioRxiv
A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes December 30, 2020 Kumar Paritosh, Satish Kumar Yadava, Priyansha Singh, et al. Plant Biotechnology Journal
Characterization of an unbalanced translocation causing 3q28qter duplication and 10q26.2qter deletion in a patient with global developmental delay and self-injury December 17, 2020 Ikeoluwa A Osei-Owusu, Alexis L Norris, Anya T Joynt, et al. Cold Spring Harbor Molecular Case Studies
Long-read assembly of the Brassica napus reference genome Darmor-bzh December 15, 2020 Mathieu Rousseau-Gueutin, Caroline Belser, Corinne Da Silva, et al. Gigascience
The iron-responsive genome of the chiton Acanthopleura granulata December 15, 2020 Rebecca M Varney, Daniel I Speiser, Carmel McDougall, et al. Genome Biology Evolution
Hybrid sequencing resolves two germline ultra-complex chromosomal rearrangements consisting of 137 breakpoint junctions in a single carrier December 14, 2020 Jesper Eisfeldt , Maria Pettersson, Anna Petri, et al. Human Genetics
The comparative genomic landscape of adaptive radiation in crater lake cichlid fishes December 11, 2020 Peiwen Xiong, C. Darrin Hulsey, Carmelo Fruciano, et al. Molecular Ecology
A highly contiguous genome assembly of Brassica nigra (BB) and revised nomenclature for the pseudochromosomes December 11, 2020 Kumar Paritosh, Akshay Kumar Pradhan, Deepak Pental, et al. BMC Genomics
The changing face of genome assemblies: guidance on achieving high-quality reference genomes December 11, 2020 Annabel Whibley, Joanna L Kelley, Shawn R Narum, et al. Molecular Ecology Resources
Single-molecule telomere length characterization by optical mapping in nano-channel array: Perspective and Review on Telomere Length Measurement December 10, 2020 Lahari Uppuluri, Dharma Varapula, Eleanor Young, et al. Environmental Toxicology and Pharmacology
Unbiased optical mapping of telomere-integrated endogenous human herpesvirus 6 December 8, 2020 Darren J Wight, Giulia Aimola, Amr Aswad, et al. PNAS
Accurate assembly of the olive baboon (Papio anubis) genome using long-read and Hi-C data December 7, 2020 Sanjit Singh Batra, Michal Levy-Sakin, Jacqueline Robinson, et al. Gigascience
Customized optical mapping by CRISPR-Cas9 mediated DNA labeling with multiple sgRNAs November 24, 2020 Heba Z Abid, Eleanor Young, Jennifer McCaffrey, et al. Nucleic Acids Research
A National Multicenter Evaluation of the Clinical Utility of Optical Genome Mapping for Assessment of Genomic Aberrations in Acute Myeloid Leukemia November 10, 2020 Brynn Levy, Linda B. Baughn, Scott Chartrand, et al. medRxiv
BiSCoT: Improving large eukaryotic genome assemblies with optical maps November 5, 2020 Benjamin Istace​, Caroline Belser, Jean-Marc Aury, et al. Bioinformatics
Human-specific expansion of 22q11.2 low copy repeats November 4, 2020 Lisanne Vervoort, Nicolas Dierckxsens, Zjef Pereboom, et al. bioRxiv
The evolutionary origin and domestication history of goldfish (Carassius auratus) November 2, 2020 Duo Chen, Qing Zhang, Weiqi Tang, et al. PNAS
Towards a reference genome that captures global genetic diversity October 30, 2020 Karen H. Y. Wong, Walfred Ma, Chun-Yu Wei, et al. Nature Communications
Contrasting signatures of genomic divergence during sympatric speciation October 28, 2020 Andreas F. Kautt, Claudius F. Kratochwil, Alexander Nater, et al. Nature
Genomic structural variation in ‘Nebbiolo’ grapevines at the individual, clonal and cultivar levels October 27, 2020 Simone Maestri, Giorgio Gambino, Andrea Minio, et al. bioRxiv
Reference genome and demographic history of the most endangered marine mammal, the vaquita October 22, 2020 Phillip A. Morin, Frederick I. Archer, Catherine D. Avila, et al. Molecular Ecology Resources
A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism October 22, 2020 Reuben M. Buckley, Brian W. Davis, Wesley A. Brashear, et al. PLOS Genetics
Genome mapping of a LYST mutation in corn snakes indicates that vertebrate chromatophore vesicles are lysosome-related organelles October 20, 2020 Asier Ullate-Agote, Ingrid Burgelin, Adrien Debry, et al. PNAS
A multi-platform reference for somatic structural variation detection October 16, 2020 Jose Espejo Valle-Inclan, Nicolle J.M. Besselink, Ewart de Bruijn, et al. bioRxiv
Discovery of novel functions of minor ZGA gene on heart and vascular regulation in Golden pompano genome provides clues for anti-cancer therapeutic strategies October 9, 2020 Honglin Luo, Yongde Zhang, Changmian Ji, et al. bioRxiv
Two New Aspergillus flavus Reference Genomes Reveal a Large Insertion Potentially Contributing to Isolate Stress Tolerance and Aflatoxin Production October 5, 2020 Jake C Fountain, Josh P Clevenger, Brian Nadon, et al. G3 Genes Genomes Genetics
Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs October 1, 2020 Kevin Hadi, Xiaotong Yao, Julie M Behr, et al. Cell
Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate September 8, 2020 Michael Abrouk, Hanin Ibrahim Ahmed, Philippe Cubry, et al. Nature Communications
Long-read sequencing for non-small-cell lung cancer genomes September 4, 2020 Yoshitaka Sakamoto, Liu Xu, Masahide Seki, et al. Genome Research
Fully Phased Sequence of a Diploid Human Genome Determined de Novo from the DNA of a Single Individual September 1, 2020 llya Soifer, Nicole L Fong, Nelda Yi, et al. G3 Genes Genomes Genetics
The Beginning of the End: A Chromosomal Assembly of the New World Malaria Mosquito Ends with a Novel Telomere September 1, 2020 Austin Compton, Jiangtao Liang, Chujia Chen, et al. G3 Genes Genomes Genetics
AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications September 1, 2020 Jens Luebeck, Ceyda Coruh, Siavash R. Dehkordi, et al. Nature Communications
Anatomy and transcription dynamics of wheat ribosomal RNA loci revealed by optical mapping and RNA sequencing August 31, 2020 —, Three out of four RNA components of ribosomes are encoded by 45S [&hellip, ], et al.
Chromosome-level genome assembly of the female western mosquitofish (Gambusia affinis) August 27, 2020 Feng Shao, Arne Ludwig, Yang Mao, et al. Gigascience
3D Printing-Enabled DNA Extraction for Long-Read Genomics August 25, 2020 Paridhi Agrawal, Jeffrey G. Reifenberger, Kevin D. Dorfman, et al. ACS Omega
A Practical Guide for Structural Variation Detection in the Human Genome August 19, 2020 Lixing Yang Current Protocols in Human Genetics
Karyotypic Evolution of Sauropsid Vertebrates Illuminated by Optical and Physical Mapping of the Painted Turtle and Slider Turtle Genomes August 12, 2020 Ling Sze Lee, Beatriz M. Navarro-Domínguez, Zhiqiang Wu, et al. Genes
Identification of a likely pathogenic structural variation in the LAMA1 gene by Bionano optical mapping August 12, 2020 Min Chen, Min Zhang, Yeqing Qian, et al. NPJ Genomic Medicine
A chromosome‐scale reference genome and genome‐wide genetic variations elucidate adaptation in yak August 3, 2020 Qiu-mei Ji, Jin-wei Xin, Zhi-xin Chai, et al.
Advances in optical mapping for genomic research August 1, 2020 Yuxuan Yuan, Claire Yik-Lok Chung, Ting-Fung Chan, et al. Computational and Structural Biotechnology Journal
A chromosome-level genome assembly of the wild rice Oryza rufipogon facilitates tracing the origins of Asian cultivated rice July 28, 2020 Xianrong Xie, Huilong Du, Huiwu Tang, et al. Science China Life Sciences
Long-reads assembly of the Brassica napus reference genome, Darmor-bzh July 22, 2020 —, The combination of long-reads and long-range information to produce genome assemblies is [&hellip, ], et al.
Optical mapping of the 22q11.2DS region reveals complex repeat structures and preferred locations for non-allelic homologous recombination (NAHR) July 22, 2020 Steven Pastor, Oanh Tran, Andrea Jin, et al. Scientific Reports
Next generation cytogenetics: genome-imaging enables comprehensive structural variant detection for 100 constitutional chromosomal aberrations in 85 samples July 17, 2020 —, Chromosomal aberrations and structural variations are a major cause of human genetic [&hellip, ], et al.
Single-molecule analysis of subtelomeres and telomeres in Alternative Lengthening of Telomeres (ALT) cells July 15, 2020 Heba Z. Abid, Jennifer McCaffrey, Kaitlin Raseley, et al. BMC Genomics
Telomere-to-telomere assembly of a complete human X chromosome July 14, 2020 Karen H. Miga, Sergey Koren, Arang Rhie, et al. Nature
Pan-Genome of Wild and Cultivated Soybeans July 9, 2020 Yucheng Liu, Huilong Du, Pengcheng Li, et al. Cell
Discovery and population genomics of structural variation in a songbird genus July 7, 2020 Matthias H. Weissensteiner, Ignas Bunikis, Ana Catalán, et al. Nature Communications
Optical map guided genome assembly July 6, 2020 Miika Leinonen, Leena Salmela BMC Bioinformatics
A chromosome-scale reference genome of Aquilegia oxysepala var. kansuensis July 1, 2020 Jinghe Xie, Haifeng Zhao, Kunpeng Li, et al. Horticulture Research
The genome sequence of the channel bull blenny, Cottoperca gobio (Günther, 1861) June 24, 2020 Iliana Bista, Shane A. McCarthy, Jonathan Wood, et al. Wellcome Open Research
Recurrent inversion toggling and great ape genome evolution June 15, 2020 David Porubsky, Ashley D. Sanders, Wolfram Höps, et al. Nature Biotechnology
A robust benchmark for detection of germline large deletions and insertions June 15, 2020 Justin M. Zook, Nancy F. Hansen, Nathan D. Olson, et al. Nature Biotechnology
Long-read human genome sequencing and its applications June 5, 2020 Glennis A. Logsdon, Mitchell R. Vollger, Evan E. Eichler, et al. Nature Reviews Genetics
From asymmetrical to balanced genomic diversification during rediploidization: Subgenomic evolution in allotetraploid fish May 27, 2020 JING LUO, JING CHAI, YANLING WEN, et al. Science Advances
Towards complete and error-free genome assemblies of all vertebrate species May 24, 2020 —, High-quality and complete reference genome assemblies are fundamental for the application of [&hellip, ], et al.
Gapless assembly of maize chromosomes using long-read technologies May 20, 2020 Jianing Liu, Arun S. Seetharam, Kapeel Chougule, et al. Genome Biology
AnAms1.0: A high-quality chromosome-scale assembly of a domestic cat Felis catus of American Shorthair breed May 19, 2020 Sachiko Isobe, Yuki Matsumoto, Claire Chung, et al. bioRxiv
Chromosome‐level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of Nanopore Sequencing, Bionano and Hi‐C technology May 17, 2020 Lina Sun, Tian Gao, Feilong Wang, et al. Molecular Ecology Resources
Sequencing smart: De novo sequencing and assembly approaches for non-model mammals. May 12, 2020 Graham J Etherington, Darren Heavens, David Baker, et al. Gigascience
The Impact of Whole Genome Data on Therapeutic Decision-Making in Metastatic Prostate Cancer: A Retrospective Analysis May 7, 2020 Megan Crumbaker, Eva K. F. Chan, Tingting Gong, et al. Cancers (Basel)
Genome sequencing sheds light on the contribution of structural variants to Brassica oleracea diversification May 5, 2020 Ning Guo, Shenyun Wang, Lei Gao, et al. BMC Biology
The Gossypium longicalyx Genome as a Resource for Cotton Breeding and Evolution May 1, 2020 Corrinne E Grover, Mengqiao Pan, Daojun Yuan, et al. G3 Genes Genomes Genetics
Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle April 29, 2020 Wai Yee Low, Rick Tearle, Ruijie Liu, et al. Nature Communications
Chromosome-Scale Assembly of Winter Oilseed Rape Brassica napus April 28, 2020 HueyTyng Lee, Harmeet Singh Chawla, Christian Obermeier, et al. Frontiers in Plant Science
Comprehensive phenotyping of neuropsychiatric traits in a multiplex 3q29 deletion family: a case report April 22, 2020 Melissa M. Murphy, T. Lindsey Burrell, Joseph F. Cubells, et al. BMC Psychiatry
Precise breakpoint detection in a patient with 9p– syndrome April 21, 2020 Jeffrey Ng, Eleanor Sams, Dustin Baldridge, et al. Cold Spring Harbor Molecular Case Studies
Complete Genome Sequences of the Human Pathogen Paenibacillus thiaminolyticus Mbale and Type Strain P. thiaminolyticus NRRL B-4156 April 9, 2020 Christine Hehnly, Lijun Zhang, Joseph N. Paulson, et al. Microbiology Resource Announcements
Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection April 9, 2020 Peter D. Olson, Alan Tracey, Andrew Baillie, et al. BMC Biology
OMGS: Optical Map-Based Genome Scaffolding April 8, 2020 Weihua Pan, Tao Jiang, Stefano Lonardi, et al. Journal of Computational Biology
The structure, function, and evolution of a complete human chromosome 8 April 7, 2020 Glennis A. Logsdon, Mitchell R. Vollger, PingHsun Hsieh, et al. Nature
Twelve Platinum-Standard Reference Genomes Sequences (PSRefSeq) that complete the full range of genetic diversity of Asian rice April 7, 2020 Yong Zhou, Dmytro Chebotarov, Dave Kudrna, et al. Scientific Data
Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C April 1, 2020 Matt A Field, Benjamin D Rosen, Olga Dudchenko, et al. Gigascience
De novo assembly of the cattle reference genome with single-molecule sequencing March 19, 2020 Benjamin D Rosen, Derek M Bickhart, Robert D Schnabel, et al. Gigascience
Integrated analysis of optical mapping and whole-genome sequencing reveals intratumoral genetic heterogeneity in metastatic lung squamous cell carcinoma March 17, 2020 Yizhou Peng, Chongze Yuan, Xiaoting Tao, et al. Translational Lung Cancer Research
Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages March 9, 2020 Yufeng Fang, Marco A. Coelho, Haidong Shu, et al. PLOS Genetics
Population sequencing enhances understanding of tea plant evolution March 7, 2020 Xinchao Wang, Hu Feng, Yuxiao Chang, et al. Nature Communications
Gene presence-absence variation associates with quantitative Verticillium longisporum disease resistance in Brassica napus March 5, 2020 Iulian Gabur, Harmeet Singh Chawla, Daniel Teshome Lopisso, et al. Scientific Reports
A chromosome level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution March 4, 2020 Wesley C. Warren, Tyler E. Boggs, Richard Borowsky, et al. Nature Communications
Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing March 4, 2020 Daniela C. Soto, Colin Shew, Mira Mastoras, et al. Genes
Chromosome-Scale Genome Assembly Provides Insights into Speciation of Allotetraploid and Massive Biomass Accumulation of Elephant Grass (Pennisetum purpureum Schum.) March 2, 2020 Shengkui Zhang, Zhiqiang Xia, Wenqing Zhang, et al. bioRxiv
Chromosomal-level assembly of Juglans sigillata genome using Nanopore, BioNano, and Hi-C analysis February 26, 2020 De-Lu Ning, Tao Wu, Liang-Jun Xiao, et al. Gigascience
Next generation cytogenetics: comprehensive assessment of 48 leukemia genomes by genome imaging February 8, 2020 —, Kornelia Neveling, Tuomo Mantere, et al.
Analysis of balanced reciprocal translocations in patients with subfertility using single-molecule optical mapping. February 5, 2020 Hui Wang, Zhengjun Jia, Aiping Mao, et al. Journal of Assisted Reproduction and Genetics
The genome sequence of the Eurasian red squirrel, Sciurus vulgaris Linnaeus 1758 February 3, 2020 Daniel Mead, Kathryn Fingland, Rachel Cripps, et al. Wellcome Open Research
Genomic novelty versus convergence in the basis of adaptation to whole genome duplication February 2, 2020 —, Magdalena Bohutínská, Mark Alston, et al.
Comprehensive Analysis of Human Subtelomeres by Whole Genome Mapping. January 27, 2020 Eleanor Young, Heba Z. Abid, Pui-Yan Kwok, et al. PLOS Genetics
A Catalog of Structural and Gene Copy Number Variations of Cultivated Rice January 27, 2020 Peng Qin, Hongwei Lu, Huilong Du, et al. Cell
High-quality genome sequence of white lupin provides insight into soil exploration and seed quality January 24, 2020 Bárbara Hufnagel, André Marques, Alexandre Soriano, et al. Nature Communications
Building near-complete plant genomes January 22, 2020 Todd P Michael, Robert Van Buren
Enhanced genome assembly and a new official gene set for Tribolium castaneum January 14, 2020 Nicolae Herndon, Jennifer Shelton, Lizzy Gerischer, et al. BMC Genomics
Natural copy number differences of tandemly repeated small nucleolar RNAs in the Prader-Willi syndrome genomic region regulate individual behavioral responses in mammals January 13, 2020 Maryam Keshavarz, Rebecca Krebs-Wheaton, Peter Refki, et al. bioRxiv
Significantly improving the quality of genome assemblies through curation January 9, 2020 Kerstin Howe, William Chow, Joanna Collins, et al. Gigascience
The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins January 6, 2020 Kushal Suryamohan, Sajesh P. Krishnankutty, Joseph Guillory, et al. Nature Genetics
Structural variant identification and characterization January 6, 2020 Parithi Balachandran, Christine R. Beck Chromosome Research
First near complete haplotype phased genome assembly of River buffalo (Bubalus bubalis) January 2, 2020 Sudhakar Ananthasayanam, Harish Kothandaraman, Nilesh Nayee, et al. bioRxiv
The Driver of Extreme Human-Specific Olduvai Repeat Expansion Remains Highly Active in the Human Genome January 1, 2020 Ilea E Heft, Yulia Mostovoy, Michal Levy-Sakin, et al. Genetics
Challenges in identifying large germline structural variants for clinical use by long read sequencing December 23, 2019 Barbara Jenko Bizjana, Theodora Katsilab, Tine Tesovnika, et al.
Comprehensive Detection of Germline and Somatic Structural Mutation in Cancer Genomes by Bionano Genomics Optical Mapping December 20, 2019 —, In cancer genetics, the ability to identify constitutive and low-allelic fraction structural [&hellip, et al.
The genetic basis of sex determination in grapevines (Vitis spp.) December 12, 2019 Mélanie Massonnet, Noé Cochetel, Andrea Minio, et al. bioRxiv
Pseudo-chromosome-length genome assembly of a double haploid “Bartlett” pear (Pyrus communis L.) December 9, 2019 Gareth Linsmith, Stephane Rombauts, Sara Montanari, et al. Gigascience
The Genome Sequence of Gossypioides kirkii Illustrates a Descending Dysploidy in Plants November 27, 2019 Joshua A. Udall, Evan Long, Thiruvarangan Ramaraj, et al.
WENGAN: Efficient and high quality hybrid de novo assembly of human genomes November 25, 2019 Alex Di Genova, Elena Buena-Atienza, Stephan Ossowski, et al. bioRxiv
Circular ecDNA promotes accessible chromatin and high oncogene expression November 20, 2019 Sihan Wu, Kristen M. Turner, Nam Nguyen, et al. Nature
Long walk to genomics: History and current approaches to genome sequencing and assembly. November 17, 2019 Alice Maria Giani, Guido Roberto Gallo, Luca Gianfranceschi , et al. Computational and Structural Biotechnology Journal
Validating Gene Fusion as the Source of Chimeric RNAs November 15, 2019 Sachin Kumar Gupta, Jocelyn Duen-Ya Jea, Laising Yen, et al. Chimeric RNA
Rapid prenatal diagnosis of Facioscapulohumeral Muscular Dystrophy 1 by combined Bionano optical mapping and karyomapping November 11, 2019 Yuting Zheng, Lingrong Kong, Hui Xu, et al. Prenatal Diagnosis
Diversity, dynamics and effects of LTR retrotransposons in the model grass Brachypodium distachyon November 2, 2019 Christoph Stritt, Michele Wyler, Elena L. Gimmi, et al. New Phytologist
Genomic Structure of Hstx2 Modifier of Prdm9-Dependent Hybrid Male Sterility in Mice November 1, 2019 Diana Lustyk, Slavomír Kinský, Kristian Karsten Ullrich, et al. Genetics
Genome rearrangements induce biofilm formation in Escherichia coli C, an old model organism with a new application in biofilm research October 22, 2019 Jarosław E. Król, Donald C. Hall Jr, Sergey Balashov, et al. BMC Genomics
Golden pompano genome and embryo transcriptome shed light on regulation of minor ZGA gene on heart and vascular development October 17, 2019 —, Whole-genome duplication (WGD) event affects embryo development in teleosts1–3. Although minor zygotic [&hellip, ], et al.
The chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis October 16, 2019 Lisong Hu, Zhongping Xu, Maojun Wang, et al. Nature Communications
An Improved Genome Assembly of the European Aspen Populus tremula October 15, 2019 Bastian Schiffthaler, Nicolas Delhomme, Carolina Bernhardsson, et al. bioRxiv
Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes October 11, 2019 Gavin M Douglas, Morgan G I Langille Genome Biology Evolution
A chromosome-level genome assembly of Pyropia haitanensis (Bangiales, Rhodophyta) October 10, 2019 Min Cao, Kuipeng Xu, Xinzi Yu, et al. Molecular Ecology Resources
Extension distribution for DNA confined in a nanochannel near the Odijk regime September 18, 2019 Hui-Min Chuang, Jeffrey G. Reifenberger, Aditya Bikram Bhandari, et al. Journal of Chemical Physics
Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars September 18, 2019 Joel-E. Kuon, Weihong Qi, Pascal Schläpfer, et al. BMC Biology
Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants September 17, 2019 Yaoxi He, Xin Luo, Bin Zhou, et al. Nature Communications
Chromosome-scale de novo assembly and phasing of a Chinese indigenous pig genome September 14, 2019 Yalan Yang, Jinmin Lian, Bingkun Xie, et al. bioRxiv
An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps September 14, 2019 Prashant S. Hosmani, Mirella Flores-Gonzalez, Henri van de Geest, et al. bioRxiv
Single-molecule optical mapping enables quantitative measurement of D4Z4 repeats in facioscapulohumeral muscular dystrophy (FSHD) September 10, 2019 Yi Dai, Pidong Li, Zhiqiang Wang, et al. Journal of Medical Genetics
Genome sequencing of the Australian wild diploid species Gossypium australe highlights disease resistance and delayed gland morphogenesis September 3, 2019 Yingfan Cai, Xiaoyan Cai, Qinglian Wang, et al. Plant Biotechnology Journal
De novo assembly of a Tibetan genome and identification of novel structural variants associated with high altitude adaptation September 2, 2019 Ouzhuluobu, Yaoxi He, Haiyi Lou, et al. bioRxiv
De Novo Genome Sequence Assemblies of Gossypium raimondii and Gossypium turneri August 28, 2019 Joshua A Udall, Evan Long, Chris Hanson, et al. G3 Genes Genomes Genetics
A high-quality genome assembly for the endangered golden snub-nosed monkey (Rhinopithecus roxellana) August 22, 2019 Lu Wang, Jinwei Wu, Xiaomei Liu, et al. Gigascience
Construction and comparison of three reference-quality genome assemblies for soybean August 21, 2019 Babu Valliyodan, Steven B. Cannon, Philipp E. Bayer, et al. The Plant Journal
Hybrid assembly of the genome of the entomopathogenic nematode Steinernema carpocapsae identifies the X-chromosome August 1, 2019 Lorrayne Serra, Marissa Macchietto, Aide Macias-Muñoz, et al. G3 Genes Genomes Genetics
MapOptics: A light-weight, cross-platform visualisation tool for optical mapping alignment August 1, 2019 Josephine Burgin, Corentin Molitor, Fady Mohareb, et al. Bioinformatics
De novo assembly of a wild pear (Pyrus betuleafolia) genome. August 1, 2019 Xingguang Dong, Zheng Wang, Luming Tian, et al.
Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards July 29, 2019 Abigail L. Lind, Yvonne Y. Y. Lai, Yulia Mostovoy, et al. Nature Ecology and Evolution
The 22q11 low copy repeats are characterized by unprecedented size and structure variability July 24, 2019 Wolfram Demaerel, Yulia Mostovoy, Feyza Yilmaz, et al. Genome Research
Six new reference-quality bat genomes illuminate the molecular basis and evolution of bat adaptations July 22, 2019 David Jebb, Zixia Huang, Martin Pippel, et al. Nature
SVCurator: A Crowdsourcing app to visualize evidence of structural variants for the human genome July 18, 2019 Lesley M. Chapman, Noah Spies, Patrick Pai, et al. PLOS Computational Biology
OMMA enables population-scale analysis of complex genomic features and phylogenomic relationships from nanochannel-based optical maps. July 9, 2019 Alden King-Yung Leung, Melissa Chun-Jiao Liu, Le Li, et al. Gigascience
The genome assembly and annotation of yellowhorn (Xanthoceras sorbifolium Bunge) June 26, 2019 Qiang Liang, Huayang Li, Shouke Li, et al. Gigascience
Whole Genome Analyses of Chinese Population and De Novo Assembly of A Northern Han Genome June 5, 2019 Zhenglin Du, Liang Ma, Hongzhu Qu, et al. Genomics Proteomics Bioinformatics
The genome of C57BL/6J “Eve”, the mother of the laboratory mouse genome reference strain June 1, 2019 Vishal Kumar Sarsani, Narayanan Raghupathy, Ian T Fiddes, et al. G3 Genes Genomes Genetics
Accessing a Russian Wheat Aphid Resistance Gene in Bread Wheat by Long-Read Technologies June 1, 2019 Zuzana Tulpová, Helena Toegelová, Nora L V Lapitan, et al. Plant Genome
The Dark Matter of Large Cereal Genomes: Long Tandem Repeats. May 20, 2019 https://www.mdpi.com/1422-0067/20/10/2483 International Journal of Molecular Sciences
The soursop genome and comparative genomics of basal angiosperms provide new insights on evolutionary incongruence May 17, 2019 Joeri S. Strijk, Damien D. Hinsinger, Mareike M. Roeder, et al. bioRxiv
Single-Scaffold Genome Sequence of Probiotic Strain Bifidobacterium breve BR03 (DSM 16604), Obtained by Combining Hybrid Sequencing and Optical Mapping. May 16, 2019 F. Fracchetti, A. Del Casale, M. Tebaldi, et al. Microbiology Resource Announcements
Effect of Sequence Depth and Length in Long-read Assembly of the Maize Inbred NC358 May 8, 2019 Shujun Ou, Jianing Liu, Kapeel M. Chougule, et al. Nature Communications
The genome of cowpea (Vigna unguiculata [L.] Walp.) April 24, 2019 Stefano Lonardi, María Muñoz-Amatriaín, Qihua Liang, et al. The Plant Journal
Multi-platform discovery of haplotype-resolved structural variation in human genomes April 16, 2019 Mark J. P. Chaisson, Ashley D. Sanders, Xuefang Zhao, et al. Nature Communications
Bionano Genome Mapping: High-Throughput, Ultra-Long Molecule Genome Analysis System for Precision Genome Assembly and Haploid-Resolved Structural Variation Discovery. April 10, 2019 Sven Bocklandt, Alex Hastie, Han Cao, et al. Single Molecule and Single Cell Sequencing
A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds April 8, 2019 Andreas Wallberg, Ignas Bunikis, Olga Vinnere Pettersson, et al. BMC Genomics
A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour. April 2, 2019 Liyi Zhang, Jiang Hu, Xiaolei Han, et al. Nature Communications
Reproducible integration of multiple sequencing datasets to form high-confidence SNP, indel, and reference calls for five human genome reference materials April 1, 2019 Justin M. Zook, Jennifer McDaniel, Nathan D. Olson, et al. Nature Biotechnology
Genomic inversions and GOLGA core duplicons underlie disease instability at the 15q25 locus March 27, 2019 Flavia A. M. Maggiolini, Stuart Cantsilieris, Pietro D’Addabbo, et al. PLOS Genetics
Sequencing a Juglans regia × J. microcarpa hybrid yields high-quality genome assemblies of parental species March 25, 2019 Tingting Zhu, Le Wang, Frank M. You, et al. Horticulture Research
Translating genomics to the clinical diagnosis of disorders/differences of sex development March 20, 2019 Abhinav Parivesh, Hayk Barseghyan, Emmanuèle Délotab, et al. Current Topics in Developmental Biology
Application of Karyomapping for the prenatal diagnosis of five families affected with facioscapulohumerial muscular dystrophy type 1 March 10, 2019 Yuting Zheng, Lingrong Kong, Hui Xu, et al.
Long-read single-molecule maps of the functional methylome March 7, 2019 Hila Sharim, Assaf Grunwald, Tslil Gabrieli, et al. Genome Research
Genome maps across 26 human populations reveal population-specific patterns of structural variation March 4, 2019 Michal Levy-Sakin, Steven Pastor, Yulia Mostovoy, et al. Nature Communications
An Integrated Framework for Genome Analysis Reveals Numerous Previously Unrecognizable Structural Variants in Leukemia Patients’ Samples February 28, 2019 Jie Xu, Fan Song, Emily Schleicher, et al. bioRxiv
Comprehensive structural variation genome map of individuals carrying complex chromosomal rearrangements February 8, 2019 Jesper Eisfeldt, Maria Pettersson, Francesco Vezzi, et al. PLOS Genetics
Chromosome conformation capture resolved near complete genome assembly of broomcorn millet January 25, 2019 Junpeng Shi, Xuxu Ma, Jihong Zhang, et al. Nature Communications
Clinical application of single‐molecule optical mapping to a multigeneration FSHD1 pedigree January 21, 2019 Qian Zhang, Xueqin Xu, Lirong Ding, et al. Molecular Genetics and Genomic Medicine
A critical comparison of technologies for a plant genome sequencing project. January 9, 2019 Pirita Paajanen, George Kettleborough, Elena López-Girona, et al. Gigascience
Improved Genome Sequence of Wild Emmer Wheat Zavitan with the Aid of Optical Maps January 8, 2019 G3 Genes Genomes Genetics
Genome Assembly and Annotation of the Trichoplusia ni Tni-FNL Insect Cell Line Enabled by Long-Read Technologies January 1, 2019 Keyur Talsania, Monika Mehta, Castle Raley, et al. Genes
Degenerative expansion of a young supergene December 21, 2018 Eckart Stolle, Rodrigo Pracana, Philip Howard, et al. Molecular Biology and Evolution
Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense December 3, 2018 Maojun Wang, Lili Tu, Daojun Yuan, et al. Nature Genetics
SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica) November 29, 2018 Giulio Formenti, Matteo Chiara, Lucy Poveda, et al. Gigascience
The genome of the tegu lizard Salvator merianae: combining Illumina, PacBio, and optical mapping data to generate a highly contiguous assembly November 27, 2018 Juliana G Roscito, Katrin Sameith, Martin Pippel, et al. Gigascience
A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping November 19, 2018 Stéphane Deschamps, Yun Zhang, Victor Llaca, et al. Nature Communications
Improved reference genome of Aedes aegypti informs arbovirus vector control November 14, 2018 Benjamin J. Matthews, Olga Dudchenko, Sarah B. Kingan, et al. Nature
Isolation of High Molecular Weight DNA from Insects November 10, 2018 Susan J. Brown, Michelle Coleman Insect Genomics
Ongoing human chromosome end extension revealed by analysis of Bionano and nanopore data November 9, 2018 Haojing Shao, Chenxi Zhou, Minh Duc Cao, et al. Scientific Reports
Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps November 2, 2018 Caroline Belser, Benjamin Istace, Erwan Denis, et al. Nature Genetics
De novo assembly of two Swedish genomes reveals missing segments from the human GRCh38 reference and improves variant calling of population-scale sequencing data October 9, 2018 Adam Ameur, Huiwen Che, Marcel Martin, et al. Genes
Copy number variants in clinical WGS: deployment and interpretation for rare and undiagnosed disease October 8, 2018 Andrew M. Gross PhD, Subramanian S. Ajay PhD, Vani Rajan MS, et al.
Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing October 1, 2018 Edwin A Solares, Mahul Chakraborty, Danny E Miller, et al.
Discovery of multi-megabase polymorphic inversions by chromosome conformation capture sequencing in large-genome plant species. September 26, 2018 Axel Himmelbach, Alevtina Ruban, Ines Walde, et al. The Plant Journal
Measuring the wall depletion length of nanoconfined DNA. September 12, 2018 Aditya Bikram Bhandari, Jeffrey G. Reifenberger, Hui-Min Chuang, et al. Journal of Chemical Physics
An Integrative Framework For Detecting Structural Variations In Cancer Genomes September 10, 2018 Jesse R. Dixon, Jie Xu, Vishnu Dileep, et al. Nature Genetics
Detecting Large Indels Using Optical Map Data September 9, 2018 Xian Fan, Jie Xu, Luay Nakhleh, et al. RECOMB International Conference on Comparative Genomics
A tandem duplication of BRCA1 exons 1-19 through DHX8 exon 2 in four families with hereditary breast and ovarian cancer syndrome. September 6, 2018 Chen Du, Dorothea Mark, Barbara Wappenschmidt, et al. Breast Cancer Research and Treatment
scanPAV: a pipeline for extracting presence– absence variations in genome pairs September 1, 2018 Francesca Giordano, Maximilian R Stammnitz, Elizabeth P Murchison, et al. Bioinformatics
Reassessment of the evolution of wheat chromosomes 4A, 5A, and 7B. August 23, 2018 Jan Dvorak, Le Wang, Tingting Zhu, et al. Theoretical and Applied Genetics
Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome. August 17, 2018 Gabriel Keeble-Gagnère, Philippe Rigault, Josquin Tibbits, et al. Genome Biology
Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies August 15, 2018 Lei Zhang, Xu Cai, Jian Wu, et al.
Genomic Structural Variations Within Five Continental Populations of Drosophila melanogaster August 15, 2018 Evan Long, Carrie Evans, John Chaston, et al. G3 Genes Genomes Genetics
Draft genome of Glyptosternon maculatum, an endemic fish from Tibet Plateau August 14, 2018 Haiping Liu, Qiyong Liu, Zhiqiang Chen, et al. Gigascience
Accurate Detection of Chimeric Contigs via Bionano Optical Maps. August 8, 2018 Weihua Pan, Stefano Lonardi Bioinformatics
De novo assembly of a young Drosophila Y chromosome using Single-Molecule sequencing and Chromatin Conformation capture July 30, 2018 Shivani Mahajan, Kevin H.-C. Wei, Matthew J. Nalley, et al. PLOS One
Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes July 30, 2018 Silong Sun, Yingsi Zhou, Jian Chen, et al. Nature Genetics
The maize W22 genome provides a foundation for functional genomics and transposon biology July 30, 2018 Nathan M. Springer, Sarah N. Anderson, Carson M. Andorf, et al. Nature Genetics
Generating a high-confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping and Oxford Nanopore technologies July 28, 2018 Phuong N.T. Hoang, Todd P. Michael, Sarah Gilbert, et al. The Plant Journal
De novo assembly of a Chinese soybean genome July 27, 2018 Yanting Shen, Jing Liu, Haiying Geng, et al. Science China Life Sciences
Structural Variation Detection and Analysis Using Bionano Optical Mapping July 24, 2018 Saki Chan, Ernest Lam, Michael Saghbini, et al. Copy Number Variants
CRISPR-bind: a simple, custom CRISPR/dCas9-mediated labeling of genomic DNA for mapping in nanochannel arrays July 19, 2018 Denghong Zhang, Saki Chan, Kenneth Sugerman, et al. bioRxiv
Large-Scale Structural Variation Detection in Subterranean Clover Subtypes Using Optical Mapping July 17, 2018 Yuxuan Yuan, Zbyněk Milec, Philipp E. Bayer, et al. Frontiers in Plant Science
Genome-Wide Characterization and Expression Analyses of Pleurotus ostreatus MYB Transcription Factors during Developmental Stages and under Heat Stress Based on de novo Sequenced Genome. July 14, 2018 Lining Wang, Wei Gao, Xiangli Wu, et al. International Journal of Molecular Sciences
Adaptation and conservation insights from the koala genome July 2, 2018 Rebecca N. Johnson, Denis O’Meally, Zhiliang Chen, et al. Nature Genetics
Epigenetic Optical Mapping of 5-Hydroxymethylcytosine in Nanochannel Arrays June 20, 2018 Tslil Gabrieli, Hila Sharim, Gil Nifker, et al. ACS Nano
Genome of an allotetraploid wild peanut Arachis monticola: a de novo assembly June 19, 2018 Dongmei Yin, Changmian Ji, Xingli Ma, et al. Gigascience
New technologies to uncover the molecular basis of disorders of sex development June 15, 2018 Hayk Barseghyan, Emmanuèle C.Délot, Eric Vilain, et al. Molecular and Cellular Endocrinology
Modelling Bionano optical data and simulation study of genome map assembly June 11, 2018 Ping Chen, Xinyun Jing, Jian Ren, et al. Bioinformatics
Analysis of Brachypodium genomes with genome-wide optical maps June 8, 2018 Tingting Zhu, Zhaorong Hu, Juan C. Rodriguez, et al. Genome
High-resolution comparative analysis of great ape genomes May 29, 2018 Ronnie de Jonge, Malaika K. Ebert, Callie R. Huitt-Roehl, et al. PNAS
Conservation of a gene cluster reveals novel cercosporin biosynthetic mechanisms and extends production to the genus Colletotrichum May 29, 2018 Ronnie de Jonge, Malaika K. Ebert, Callie R. Huitt-Roehl, et al. PNAS
Error correcting optical mapping data May 25, 2018 Kingshuk Mukherjee, Darshan Washimkar, Martin D Muggli, et al. Gigascience
Structural variation and rates of genome evolution in the grass family seen through comparison of sequences of genomes greatly differing in size May 16, 2018 Jan Dvorak, Le Wang, Tingting Zhu, et al. The Plant Journal
De novo genome assembly of the red silk cotton tree (Bombax ceiba) May 10, 2018 Yong Gao, Haibo Wang, Chao Liu, et al. Gigascience
Genome sequence of the progenitor of wheat A subgenome Triticum urartu May 9, 2018 Hong-Qing Ling, Bin Ma, Xiaoli Shi, et al. Nature
Comparative genomics of the wheat fungal pathogen Pyrenophora tritici-repentis reveals chromosomal variations and genome plasticity April 23, 2018 Paula Moolhuijzen, Pao Theen See, James K. Hane, et al. BMC Genomics
Chromosome‐scale pseudomolecules refined by optical, physical and genetic maps in flax April 22, 2018 Frank M. You, Jin Xiao, Pingchuan Li, et al. The Plant Journal
Intact DNA purified from flow-sorted nuclei unlocks the potential of next-generation genome mapping and assembly in Solanum species April 10, 2018 Paola Gaiero, Hana Šimková, Jan Vrána, et al. MethodsX
A guide to sequence your favorite plant genomes March 30, 2018 Fay-Wei Li, Alex Harkess Applications in Plant Sciences
Dynamic Evolution of α-Gliadin Prolamin Gene Family in Homeologous Genomes of Hexaploid Wheat March 26, 2018 Naxin Huo, Tingting Zhu, Susan Altenbach, et al. Scientific Reports
Improving Nelumbo nucifera genome assemblies using high‐resolution genetic maps and Bionano genome mapping reveals ancient chromosome rearrangements March 25, 2018 Songtao Gui, Jing Peng, Xiaolei Wang, et al. The Plant Journal
Optical mapping reveals a higher level of genomic architecture of chained fusions in cancer March 21, 2018 Eva K.F. Chan, Daniel L. Cameron, Desiree C. Petersen, et al. Genome Research
The hardy rubber tree genome provides insights into the evolution of polyisoprene biosynthesis March 5, 2018 Ta-na Wuyun, Lin Wang, Huimin Liu, et al. Molecular Plant
Human copy number variants are enriched in regions of low mappability February 21, 2018 Jean Monlong, Patrick Cossette, Caroline Meloche, et al. Nucleic Acids Research
Complete Genome Sequence of the Model Oleaginous Alga Nannochloropsis gaditana CCMP1894. February 15, 2018 Ariel S Schwartz, Rob Brown, Imad Ajjawi, et al. Genome Announcements
High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell February 7, 2018 Todd P. Michael, Florian Jupe, Felix Bemm, et al. Nature Communications
Integrated physical map of bread wheat chromosome arm 7DS to facilitate gene cloning and comparative studies January 25, 2018 ZuzanaTulpová, Ming-Cheng Luo, Helena Toegelová, et al. New Biotechnology
Odijk excluded volume interactions during the unfolding of DNA confined in a nanochannel January 24, 2018 Jeffrey G. Reifenberger, Han Cao, and Kevin D. Dorfman, et al.
The axolotl genome and the evolution of key tissue formation regulators January 24, 2018 Sergej Nowoshilow, Siegfried Schloissnig, Ji-Feng Fei, et al. Nature
The complex architecture of plant transgene insertions January 18, 2018 Florian Jupe, Angeline C. Rivkin, Todd P. Michael, et al. bioRxiv
Genome-scale sequence disruption following biolistic transformation in rice and maize January 16, 2018 Jianing Liu, Natalie J. Nannas, Fang-fang Fu, et al. The Plant Cell
High-Quality Complete and Draft Genome Sequences for Three Escherichia spp. and Three Shigella spp. Generated with Pacific Biosciences and Illumina Sequencing and Optical Mapping January 4, 2018 Max R Schroeder, Phalasy Juieng, Dhwani Batra, et al. Genome Announcements
Genome Sequencing and Assembly by Long Reads in Plants December 28, 2017 Changsheng Li, Feng Lin, Dong An, et al. Genes
Is it ordered correctly? Validating genome assemblies by optical mapping December 20, 2017 Joshua A. Udall, R. Kelly Dawe The Plant Cell
Extensive hidden genetic variation shapes the structure of functional elements in Drosophila December 18, 2017 Mahul Chakraborty, Nicholas W. VanKuren, Roy Zhao, et al. Nature Genetics
Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity December 13, 2017 Patrick P Edger, Robert VanBuren, Marivi Colle, et al.
Current advances in genome sequencing of common wheat and its ancestral species December 8, 2017 Xiaoli Shia, Hong-Qing Ling The Crop Journal
OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps December 1, 2017 Le Li, Alden King-Yung Leung, Tsz-Piu Kwok, et al. Genome Biology
Sequence-Dependent Persistence Length of Long DNA November 29, 2017 Hui-Min Chuang, Jeffrey G. Reifenberger, Han Cao, et al. Physical Review Letters
Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus) November 16, 2017 Peter A. Larsen, R. Alan Harris, Yue Liu, et al. BMC Biology
Comparative genome analysis of programmed DNA elimination in nematodes November 8, 2017 Jianbin Wang, Shenghan Gao, Yulia Mostovoy, et al. Genome Research
Genome-Wide Identification of Early-Firing Human Replication Origins by Optical Replication Mapping November 6, 2017 Kyle Klein, Weitao Wang, Tyler Borrman, et al. bioRxiv
The asparagus genome sheds light on the origin and evolution of a young Y chromosome November 2, 2017 Alex Harkess, Jinsong Zhou, Chunyan Xu, et al. Nature Communications
Genome sequence of the progenitor of the wheat D genome Aegilops tauschii November 1, 2017 Ming-Cheng Luo, Yong Q. Gu, Daniela Puiu, et al. Nature
Next-generation mapping: a novel approach for detection of pathogenic structural variants with a potential utility in clinical diagnosis October 25, 2017 Hayk Barseghyan, Wilson Tang, Richard T. Wang, et al. Genome Research
High-throughput single-molecule telomere characterization October 12, 2017 Jennifer McCaffrey, Eleanor Young, Katy Lassahn, et al. Genome Research
Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop September 5, 2017 Masaomi Hatakeyama, Sirisha Aluri, Mathi Thumilan Balachadran, et al. DNA Research
The Tartary Buckwheat Genome Provides Insights into Rutin Biosynthesis and Abiotic Stress Tolerance August 31, 2017 Lijun Zhang, Xiuxiu Li, Bin Ma, et al. Molecular Plant
A Step-by-Step Guide to Assemble a Reptilian Genome August 15, 2017 Asier Ullate-Agote, Yingguang Frank Chan, Athanasia C. Tzika, et al. Avian and Reptilian Developmental Biology
High-throughput optical mapping of replicating DNA August 6, 2017 Francesco De Carli, Nikita Menezes, Wahiba Berrabah, et al. Small Methods
Strategies for optimizing Bionano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula August 4, 2017 Karen M Moll, Peng Zhou, Thiruvarangan Ramaraj, et al. BMC Genomics
Sequencing and de novo assembly of 150 genomes from Denmark as a population reference July 26, 2017 Lasse Maretty, Jacob Malte Jensen, Bent Petersen, et al. Nature
Modeling the relaxation of internal DNA segments during genome mapping in nanochannels July 23, 2017 Aashish Jain, Julian Sheats, Jeffrey G. Reifenberger, et al. Bioinformatics
Irys Extract July 11, 2017 Rani Arielly, Yuval Ebenstein Bioformatics
BionanoAnalyst: a visualisation tool to assess genome assembly quality using Bionano data June 30, 2017 Yuxuan Yuan, Philipp E. Bayer, Armin Scheben, et al. BMC Bioinformatics
A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency June 19, 2017 K. D. Edwards, N. Fernandez-Pozo, K. Drake-Stowe, et al. BMC Genomics
Improved maize reference genome with single-molecule technologies June 12, 2017 Yinping Jiao, Paul Peluso, Jinghua Shi, et al. Nature
runBNG: A software package for Bionano genomic analysis on the command line June 9, 2017 Yuxuan Yuan, Philipp E Bayer, Huey-Tyng Lee, et al. Bioformatics
Wild tobacco genomes reveal the evolution of nicotine biosynthesis June 6, 2017 Shuqing Xu, Thomas Brockmöller, Aura Navarro-Quezada, et al. PNAS
High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development June 5, 2017 Nicolas Daccord, Jean-Marc Celton, Gareth Linsmith, et al. Nature Genetics
Draft genome of spinach and transcriptome diversity of 120 Spinacia accessions May 24, 2017 Chenxi Xu, Chen Jiao, Honghe Sun, et al. Nature Communications
Evolution of a Biomass-Fermenting Bacterium To Resist Lignin Phenolics May 17, 2017 Tristan Cerisy, Tiffany Souterre, Ismael Torres-Romero, et al. Applied and Environmental Microbiology
Sequencing and de novo assembly of a near complete indica rice genome May 4, 2017 Huilong Du, Ying Yu, Yanfei Ma, et al. Nature Communications
OMSim: a simulator for optical map data. May 3, 2017 Giles Miclotte, Stéphane Plaisance, Stephane Rombauts, et al. Bioinformatics
Construction of a map-based reference genome sequence for barley, Hordeum vulgare L. April 27, 2017 Sebastian Beier, Axel Himmelbach, Christian Colmsee, et al. Scientific Data
A chromosome conformation capture ordered sequence of the barley genome. April 26, 2017 Martin Mascher, Heidrun Gundlach, Axel Himmelbach, et al. Nature
Improved de novo Genome Assembly: Linked-Read Sequencing Combined with Optical Mapping Produce a High Quality Mammalian Genome at Relatively Low Cost April 19, 2017 DW Mohr, A Naguib, NI Weisenfeld, et al. bioRxiv
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly April 10, 2017 Valerie A. Schneider, Tina Graves-Lindsay, Kerstin Howe, et al. Genome Research
Genomic innovation for crop improvement March 16, 2017 Michael W. Bevan, Cristobal Uauy, Brande B. H. Wulff, et al. Nature
Improvements in Genomic Technologies: Application to Crop Genomics March 9, 2017 Yuxuan Yuan, Philipp E.Bayer, Jacqueline Batley, et al. Trends in Biotechnology
Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome March 6, 2017 Derek M Bickhart, Benjamin D Rosen, Sergey Koren, et al. Nature Genetics
Reduced representation optical methylation mapping (R2OM2). March 6, 2017 Assaf Grunwald, Hila Sharim, Tslil Gabrieli, et al. bioRxiv
Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications March 3, 2017 Matthias H. Weissensteiner, Andy W.C. Pang, Ignas Bunikis, et al. Genome Research
Next Generation Mapping Reveals Novel Large Genomic Rearrangements in Prostate Cancer March 1, 2017 Weerachai Jaratlerdsiri, Eva K.F. Chan, Desiree C. Petersen, et al. Oncotarget
Cas9-Assisted Targeting of CHromosome segments (CATCH) for targeted nanopore sequencing and optical genome mapping March 1, 2017 Tslil Gabrieli, Hila Sharim, Yael Michaeli, et al. bioRxiv
Genome sequencing supports a multi-vertex model for Brassiceae species February 24, 2017 Feng Cheng, Jianli Liang, Chengcheng Cai, et al. Current Opinion in Plant Biology
ABySS 2.0: Resource-efficient assembly of large genomes using a Bloom filter February 23, 2017 Shaun D Jackman, Benjamin P Vandervalk, Hamid Mohamadi, et al. Genome Research
Rapid Automated Large Structural Variation Detection in a Diploid Genome by NanoChannel Based Next-Generation Mapping February 14, 2017 Alex R Hastie, Ernest T Lam, Andy Wing Chun Pang, et al. bioRxiv
High-throughput single-molecule mapping links subtelomeric variants and long-range haplotypes with specific telomeres February 9, 2017 Eleanor Young, Steven Pastor, Ramakrishnan Rajagopalan, et al. Nucleic Acids Research
The genome of Chenopodium quinoa February 8, 2017 David E. Jarvis, Yung Shwen Ho, Damien J. Lightfoot, et al. Nature
Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data February 3, 2017 Wen-Biao Jiao, Gonzalo Garcia Accinelli, Benjamin Hartwig, et al. Genome Research
A Review of Genome Sequencing in the Largest Cereal Genome, Triticum aestivum L. February 1, 2017 Anandi Bierman, Anna-Maria Botha Agricultural Sciences
Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm January 27, 2017 Aleksey V. Zimin, Daniela Puiu, Ming-Cheng Luo, et al. Genome Research
Building and Improving Reference Genome Assemblies January 27, 2017 Karyn Meltz Steinberg, Valerie A. Schneider, Can Alkan, et al. Proceedings of the IEEE
An advanced reference genome of Trifolium subterraneum L. reveals genes related to agronomic performance January 23, 2017 Parwinder Kaur, Philipp E. Bayer, Zbyněk Milec, et al. Plant Biotechnology Journal
Sequencing and comparative analyses of Aegilops tauschii chromosome arm 3DS reveal rapid evolution of Triticeae genomes January 20, 2017 Jingzhong Xie, Naxin Huo, Shenghui Zhou, et al. Journal of Genetics and Genomics
Ancient duplication and horizontal transfer of a toxin gene cluster reveals novel mechanisms in the cercosporin biosynthesis pathway January 16, 2017 —, Ronnie de Jonge, Malaika K Ebert, et al.
Comprehensive definition of genome features in Spirodela polyrhiza by high-depth physical mapping and short-read DNA sequencing strategies October 18, 2016 Todd P. Michael, Douglas Bryant, Ryan Gutierrez, et al. The Plant Journal
De novo assembly and phasing of a Korean human genome October 5, 2016 Jeong-Sun Seo, Arang Rhie, Junsoo Kim, et al. Nature
OMBlast: alignment tool for optical mapping using a seed-and-extend approach. September 30, 2016 Alden King-Yung Leung, Tsz-Piu Kwok, Raymond Wan, et al. Bioformatics
Super-Resolution Genome Mapping in Silicon Nanochannels September 19, 2016 Jonathan Jeffet, Asaf Kobo, Tianxiang Su, et al. ACS Nano
The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection September 5, 2016 Jinghua Yang, Dongyuan Liu, Xiaowu Wang, et al. Nature Genetics
Genome Mapping in Plant Comparative Genomics September 1, 2016 Lindsay Chaney, Aaron R Sharp, Carrie R Evans, et al. Trends in Plant Science
Improvement of the threespine stickleback (Gasterosteus aculeatus) genome using a Hi-C-based Proximity-Guided Assembly method August 3, 2016 Catherine L Peichel, Shawn T Sullivan, Ivan Liachko, et al. Journal of Heredity
High-Quality Assembly of an Individual of Yoruban Descent August 2, 2016 Karyn Meltz Steinberg, Tina Graves Lindsay, Valerie A. Schneider, et al. bioRxiv
Analysis of tandem gene copies in maize chromosomal regions reconstructed from long sequence reads July 19, 2016 Jiaqiang Dong, Yaping Feng, Dibyendu Kumar, et al. PNAS
Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions July 14, 2016 Taiji Kawakatsu, Shao-Shan Carol Huang, Florian Jupe, et al. Cell
Long-read sequencing and de novo assembly of a Chinese genome June 30, 2016 Lingling Shi, Yunfei Guo, Chengliang Dong, et al. Nature Communications
Extensive sequencing of seven human genomes to characterize benchmark reference materials June 7, 2016 Justin M. Zook, David Catoe, Jennifer McDaniel, et al. Scientific Data
A hybrid approach for de novo human genome sequence assembly and phasing. May 9, 2016 Yulia Mostovoy, Michal Levy-Sakin, Jessica Lam, et al. Nature Methods
Third-generation sequencing and the future of genomics April 13, 2016 Hayan Lee, James Gurtowski, Shinjae Yoo, et al. bioRxiv
Improvement of the banana “Musa acuminata” reference sequence using NGS data and semi-automated bioinformatics methods March 16, 2016 Guillaume Martin, Franc-Christophe Baurens, Gaëtan Droc, et al. BMC Genomics
The Amaranth Genome: Genome, Transcriptome, and Physical Map Assembly March 1, 2016 J. W. Clouse, D. Adhikary, J. T. Page, et al. The Plant Genome
Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius February 2, 2016 Jeffrey A. Rosenfeld, Darryl Reeves, Mercer R. Brugler, et al. Nature Communications
Bionano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes January 23, 2016 Helena Staňková, Alex R. Hastie, Saki Chan, et al.
Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays January 1, 2016 Angel C Y Mak, Yvonne Y Y Lai, Ernest T Lam, et al. Genetics
Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum November 21, 2015 Robert VanBuren, Doug Bryant, Patrick P. Edger, et al. Nature
CRISPR-CAS9 D10A nickase target-specific fluorescent labeling of double strand DNA for whole genome mapping and structural variation analysis October 19, 2015 Jennifer McCaffrey, Justin Sibert, Bin Zhang, et al. Nucleic Acids Research
Bacteriophage strain typing by rapid single molecule analysis. October 10, 2015 Assaf Grunwald, Moran Dahan, Anna Giesbertz, et al. Nucleic Acids Research
The genome and methylome of a beetle with complex social behavior, Nicrophorus vespilloides (Coleoptera: Silphidae) October 9, 2015 Christopher B. Cunningham, Lexiang Ji, R. Axel W. Wiberg, et al.
Tools and pipelines for Bionano data: molecule assembly pipeline and FASTA super scaffolding tool. September 29, 2015 Jennifer M. Shelton, Michelle C. Coleman, Nic Herndon, et al. BMC Genomics
Rapid construction of genome map for large yellow croaker (Larimichthys crocea) by the whole-genome mapping in Bionano Genomics Irys system. September 3, 2015 Shijun Xiao, Jiongtang Li, Fengshou Ma, et al. BMC Genomics
Optical Nano-mapping and Analysis of Plant Genomes August 11, 2015 Ming-Cheng Luo, Karin R. Deal, Armond Murray, et al. Plant Cytogenetics
Assembly and diploid architecture of an individual human genome via single-molecule technologies. June 29, 2015 Matthew Pendleton, Robert Sebra, Andy Wing Chun Pang, et al. Nature Methods
Structural forms of the human amylase locus and their relationships to SNPs, haplotypes and obesity. June 22, 2015 Christina L Usher, Robert E Handsaker, Tõnu Esko, et al. Nature Genetics
Assessing structural variation in a personal genome—towards a human reference diploid genome. April 11, 2015 Adam C English, William J Salerno, Oliver A Hampton, et al. BMC Genomics
Re-replication Origins in Sciara DNA Puffs Revealed by New and Old Genomic Technologies including Nanopore Sequencing April 7, 2015 John Urban, Ali Bashir, Robert Sebra, et al. The FASEB Journal
Using optical mapping data for the improvement of vertebrate genome assemblies March 18, 2015 Kerstin Howe, Jonathan MD Wood Gigascience
Discoveries and Advances in Plant and Animal Genomics. March 13, 2015 Rudi Appels, Johan Nystrom, Hollie Webster, et al. Functional and Integrative Genomics
Whole-genome mutational burden analysis of three pluripotency induction methods February 19, 2015 Kunal Bhutani, Kristopher L. Nazor, Roy Williams, et al. Nature Communications
Rapid Detection of Structural Variation in a Human Genome using Nanochannel-based Genome Mapping Technology. December 20, 2014 Hongzhi Cao, Alex R Hastie, Dandan Cao, et al. Gigascience
Single Haplotype Assembly of the Human Genome from a Hydatidiform Mole. November 4, 2014 Karyn Meltz Steinberg, Valerie A. Schneider, Tina A. Graves-Lindsay, et al. Genome Research
Finished Sequence and Assembly of the DUF1220-rich 1q21 Region Using a Haploid Human Genome. May 20, 2014 Majesta O’Bleness, Veronica B Searles, C Michael Dickens, et al. BMC Genomics
Genomics via Optical Mapping (I): 0-1 Laws for Mapping with Single Molecules November 22, 2013 Thomas Anantharaman, Bud Mishra bioRxiv
Genome mapping on Nanochannel arrays for structural variation analysis and sequence assembly. November 4, 2013 Ernest T Lam, Alex Hastie, Chin Lin, et al. Nature Biotechnology
Rapid Genome Mapping in Nanochannel Arrays for Highly Complete and Accurate De Novo Sequence Assembly of the Complex Aegilops tauschii Genome. February 6, 2013 Alex R. Hastie, Lingli Dong, Alexis Smith, et al. PLOS One
Multicolor super-resolution DNA imaging for genetic analysis. July 11, 2012 Murat Baday, Aaron Cravens, Alex Hastie, et al. Nucleic Acids Research
Single molecule linear analysis of DNA in nano-channel labeled with sequence specific fluorescent probes. August 10, 2010 Somes K. Das, Michael D. Austin, Matthew C. Akana, et al. Nucleic Acids Research
Single-molecule denaturation mapping of DNA in nanofluidic channels. July 27, 2010 Walter Reisner, Niels B Larsen, Asli Silahtaroglu, et al. PNAS
DNA in Nanochannels – directly visualizing genomic information. January 25, 2010 Fredrik Persson, Jonas O Tegenfeldt Chemical Society Reviews
Rapid DNA mapping by fluorescent single molecule detection. December 24, 2006 Ming Xiao, Angie Phong, Connie Ha, et al. Nucleic Acids Research
Restriction mapping in nanofluidic devices. July 19, 2005 Robert Riehn, Manchun Lu, Yan-Mei Wang, et al. PNAS
Single-molecule studies of repressor-DNA interactions show long-range interactions. June 30, 2005 Y M Wang, Jonas O Tegenfeldt, W Reisner, et al. PNAS
Statics and dynamics of single DNA molecules confined in Nanochannels. May 20, 2005 Walter Reisner, Keith J Morton, Robert Riehn, et al. Physical Review Letters
The dynamics of genomic-length DNA molecules in 100-nm channels. July 27, 2004 Jonas O Tegenfeldt, Christelle Prinz, Han Cao, et al. PNAS
Micro- and nanofluidics for DNA analysis. March 5, 2004 Jonas O Tegenfeldt, Christelle Prinz, Han Cao, et al. Analytical and Bioanalytical Chemistry
Fabrication of Gradient Fluidic Structures Interfacing Microfluidics and Nanofluidics. August 26, 2002 Han Cao, Jonas O Tegenfeldt, Robert H Austin, et al. Applied Physics Letters
Fabrication of 10nm Enclosed Nanofluidic Channels. July 1, 2002 Han Cao, Zhaoning Yu, Jian Wang, et al. Applied Physics Letters
Scanning the Controls: Genomics and Nanotechnology. March 1, 2002 Robert H Austin, Jonas O Tegenfeldt, Han Cao, et al. IEEE Transactions and Nanotechnology

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