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Fast and accurate short read alignment with Burrows-Wheeler transform

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The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

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Fast and accurate long-read alignment with Burrows-Wheeler transform.

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A framework for variation discovery and genotyping using next-generation DNA sequencing data

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Integrating common and rare genetic variation in diverse human populations

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An ensemble approach to accurately detect somatic mutations using SomaticSeq

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Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes

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Transcriptome Association Identifies Regulators of Wheat Spike Architecture

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Genomic architecture of phenotypic extremes in a wild cervid

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Biallelic Variants in UBA5 Link Dysfunctional UFM1 Ubiquitin-like Modifier Pathway to Severe Infantile-Onset Encephalopathy

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Evolutionary engineering reveals divergent paths when yeast is adapted to different acidic environments

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Exome-capture RNA sequencing of decade-old breast cancers and matched decalcified bone metastases

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Phylogenetics of a Fungal Invasion: Origins and Widespread Dispersal of White-Nose Syndrome

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Nationwide germline whole genome sequencing of 198 consecutive pediatric cancer patients reveals a high incidence of cancer prone syndromes

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The drug-induced phenotypic landscape of colorectal cancer organoids

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Exome sequencing of lymphomas from three dog breeds reveals somatic mutation patterns reflecting genetic backgroundPreprint

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Accuracy and efficiency of germline variant calling pipelines for human genome data

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Patterns of Genomic Variation in the Opportunistic Pathogen Candida glabrata Suggest the Existence of Mating and a Secondary Association with Humans

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Loss-of-Function Mutations in the WNT Co-receptor LRP6 Cause Autosomal-Dominant Oligodontia

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Transversions have larger regulatory effects than transitions

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Genome-wide analyses as part of the international FTLD-TDP whole-genome sequencing consortium reveals novel disease risk factors and increases support for immune dysfunction in FTLD

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Genetic load has potential in large populations but is realized in small inbred populations

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Performant Mutation Identification Using Targeted Next-Generation Sequencing of 14 Thoracic Aortic Aneurysm Genes

Proost, D., Vandeweyer, G., Meester, J., Salemink, S., Kempers, M. J. E., Ingram, C., Peeters, N., Saenen, J. B., Vrints, C. J., Lacro, R. V., et al. (2015) · Human Mutation · doi:10.1002/humu.22802 · Cited by 116

A modifier of Huntington's disease onset at the MLH1 locus

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Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator

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Alliance A071401: Phase II Trial of Focal Adhesion Kinase Inhibition in Meningiomas With Somatic NF2 Mutations

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Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn’s disease

Douglas, G. M., Hansen, R., Jones, C. M. A., Dunn, K. A., Comeau, A., Bielawski, J. P., Tayler, R., El-Omar, E. M., Russell, R. K., Hold, G. L., et al. (2018) · Microbiome · doi:10.1186/s40168-018-0398-3 · Cited by 124

Cross-species oncogenic signatures of breast cancer in canine mammary tumors

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Targeted genomic analysis of Müllerian adenosarcoma

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SNP Discovery Using a Pangenome: Has the Single Reference Approach Become Obsolete?

Hurgobin, B., & Edwards, D. (2017) · Biology · doi:10.3390/biology6010021 · Cited by 113

A pilot study of ultra-deep targeted sequencing of plasma DNA identifies driver mutations in hepatocellular carcinoma

Labgaa, I., Villacorta-Martín, C., D’Avola, D., Craig, A. J., von Felden, J., Martins-Filho, S. N., Sia, D., Stueck, A., Ward, S. C., Fiel, M. I., et al. (2018) · Oncogene · doi:10.1038/s41388-018-0206-3 · Cited by 117

Copy-number variants in clinical genome sequencing: deployment and interpretation for rare and undiagnosed disease

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Low genetic variation is associated with low mutation rate in the giant duckweed

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Population genetic analysis of the DARC locus (Duffy) reveals adaptation from standing variation associated with malaria resistance in humans

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The impact of antimalarial resistance on the genetic structure of Plasmodium falciparum in the DRC

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The patterns of deleterious mutations during the domestication of soybean

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REC114 Partner ANKRD31 Controls Number, Timing, and Location of Meiotic DNA Breaks

Boekhout, M., Karasu, M. E., Wang, J., Acquaviva, L., Pratto, F., Brick, K., Eng, D. Y., Xu, J., Camerini‐Otero, R. D., Patel, D. J., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.03.023 · Cited by 114

The Evolutionary History of Wild, Domesticated, and Feral Brassica oleracea (Brassicaceae)

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The mutational signatures of formalin fixation on the human genome

Guo, Q., Lakatos, E., Bakir, I. A., Curtius, K., Graham, T. A., & Mustonen, V. (2022) · Nature Communications · doi:10.1038/s41467-022-32041-5 · Cited by 116

Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing informationPreprint

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SNP genotyping and population genomics from expressed sequences – current advances and future possibilities

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A demonstration of unsupervised machine learning in species delimitation

Derkarabetian, S., Castillo, S., Koo, P. K., Ovchinnikov, S., & Hedin, M. C. (2019) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2019.106562 · Cited by 109

Insights into variation in meiosis from 31,228 human sperm genomes

Bell, A. D., Mello, C. J., Nemesh, J. C., Brumbaugh, S. A., Wysoker, A., & McCarroll, S. A. (2020) · Nature · doi:10.1038/s41586-020-2347-0 · Cited by 111

Deficient H2A.Z deposition is associated with genesis of uterine leiomyoma

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Loss-of-function CARD8 mutation causes NLRP3 inflammasome activation and Crohn’s disease

Mao, L., Kitani, A., Similuk, M. N., Oler, A. J., Albenberg, L. G., Kelsen, J. R., Aktay, A., Quezado, M., Yao, M. D., Montgomery-Recht, K., et al. (2018) · Journal of Clinical Investigation · doi:10.1172/jci98642 · Cited by 111

Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis

Lees, J. A., Ferwerda, B., Kremer, P. H. C., Wheeler, N. E., Serón, M. V., Croucher, N. J., Gladstone, R. A., Bootsma, H. J., Rots, N. Y., Wijmenga‐Monsuur, A. J., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09976-3 · Cited by 113

Large-scale pathway specific polygenic risk and transcriptomic community network analysis identifies novel functional pathways in Parkinson disease

Bandrés‐Ciga, S., Sáez-Atiénzar, S., Kim, J., Makarious, M. B., Faghri, F., Díez-Fairén, M., Iwaki, H., Leonard, H. L., Botía, J. A., Ryten, M., et al. (2020) · Acta Neuropathologica · doi:10.1007/s00401-020-02181-3 · Cited by 113

Comprehensive Genomic Profiling of Neuroendocrine Carcinomas of the Gastrointestinal System

Yachida, S., Totoki, Y., Noë, M., Nakatani, Y., Horie, M., Kawasaki, K., Nakamura, H. K., Saito-Adachi, M., Suzuki, M., Takai, E., et al. (2022) · Utrecht University Repository (Utrecht University) · Cited by 112

Genome assembly and annotation of Arabidopsis halleri , a model for heavy metal hyperaccumulation and evolutionary ecology

Briskine, R. V., Paape, T. D., Shimizu‐Inatsugi, R., Nishiyama, T., Akama, S., Sese, J., & Shimizu, K. K. (2016) · Molecular Ecology Resources · doi:10.1111/1755-0998.12604 · Cited by 112

A domestication history of dynamic adaptation and genomic deterioration in Sorghum

Smith, O., Nicholson, W. V., Kistler, L., Mace, E., Clapham, A., Rose, P., Stevens, C., Ware, R., Samavedam, S., Barker, G., et al. (2019) · Nature Plants · doi:10.1038/s41477-019-0397-9 · Cited by 106

Proteome Instability Is a Therapeutic Vulnerability in Mismatch Repair-Deficient Cancer

McGrail, D. J., Garnett, J., Yin, J., Dai, H., Shih, D. J. H., Lam, T., Li, Y., Sun, C., Li, Y., Schmandt, R. E., et al. (2020) · Cancer Cell · doi:10.1016/j.ccell.2020.01.011 · Cited by 109

PGRNseq

GORDON, A. S., Fulton, R. S., Qin, X., Mardis, E. R., Nickerson, D. A., & Scherer, S. (2016) · Pharmacogenetics and Genomics · doi:10.1097/fpc.0000000000000202 · Cited by 111

Temperate phages both mediate and drive adaptive evolution in pathogen biofilms

Davies, E. V., James, C. E., Williams, D. F., O’Brien, S., Fothergill, J. L., Haldenby, S. T., Paterson, S., Winstanley, C., & Brockhurst, M. A. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1520056113 · Cited by 110

Comparative genomics and transcriptomics of Pichia pastoris

Love, K. R., Shah, K., Whittaker, C. A., Wu, J., Matthews, C. B., Ma, D., Leeson, R. L., Priest, M., Borowsky, J. H., Young, S., et al. (2016) · BMC Genomics · doi:10.1186/s12864-016-2876-y · Cited by 110

Runs of homozygosity have utility in mammalian conservation and evolutionary studies

Brüniche–Olsen, A., Kellner, K. F., Anderson, C. J., & DeWoody, J. A. (2018) · Conservation Genetics · doi:10.1007/s10592-018-1099-y · Cited by 108

Genomic epidemiology of syphilis reveals independent emergence of macrolide resistance across multiple circulating lineages

Beale, M. A., Marks, M., Sahi, S. K., Tantalo, L. C., Nori, A., French, P., Lukehart, S. A., Marra, C. M., & Thomson, N. R. (2019) · Nature Communications · doi:10.1038/s41467-019-11216-7 · Cited by 109

Population genomics of Fusarium graminearum reveals signatures of divergent evolution within a major cereal pathogen

Kelly, A. C., & Ward, T. J. (2018) · PLoS ONE · doi:10.1371/journal.pone.0194616 · Cited by 116

Landscape of genomic alterations in high-grade serous ovarian cancer from exceptional long- and short-term survivors

Yang, S. Y. C., Lheureux, S., Karakasis, K., Burnier, J. V., Bruce, J. P., Clouthier, D., Danesh, A., Quevedo, R., Dowar, M., Hanna, Y., et al. (2018) · Genome Medicine · doi:10.1186/s13073-018-0590-x · Cited by 111

Leishmania Genome Dynamics during Environmental Adaptation Reveal Strain-Specific Differences in Gene Copy Number Variation, Karyotype Instability, and Telomeric Amplification

Bussotti, G., Gouzelou, E., Boité, M. C., Djenad, I. K., Harrat, Z., Eddaikra, N., Mottram, J. C., Αντωνίου, Μ., Christodoulou, V., Bali, A., et al. (2018) · mBio · doi:10.1128/mbio.01399-18 · Cited by 108

Exaggerated heterochiasmy in a fish with sex-linked male coloration polymorphisms

Bergero, R., Gardner, J., Bader, B., Yong, L., & Charlesworth, D. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1818486116 · Cited by 102

The genomic landscape of Mongolian hepatocellular carcinoma

Candia, J., Bayarsaikhan, E., Tandon, M., Budhu, A., Forgues, M., Товуу, Л.-О., Tudev, U., Lack, J., Chao, A., Chinburen, J., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18186-1 · Cited by 112

A reference genome of the Chinese hamster based on a hybrid assembly strategy

Rupp, O., MacDonald, M. L., Li, S., Dhiman, H., Polson, S., Griep, S., Heffner, K., Hernandez, I., Brinkrolf, K., Jadhav, V., et al. (2018) · Biotechnology and Bioengineering · doi:10.1002/bit.26722 · Cited by 107

Canine Brachycephaly Is Associated with a Retrotransposon-Mediated Missplicing of SMOC2

Marchant, T. W., Johnson, E. J., McTeir, L., Johnson, C. I., Gow, A. G., Liuti, T., Kuehn, D., Svenson, K. L., Bermingham, M. L., Drögemüller, M., et al. (2017) · Current Biology · doi:10.1016/j.cub.2017.04.057 · Cited by 112

Sorghum Dw2 Encodes a Protein Kinase Regulator of Stem Internode Length

Hilley, J., Weers, B. D., Truong, S. K., McCormick, R. F., Mattison, A. J., McKinley, B. A., Morishige, D. T., & Mullet, J. E. (2017) · Scientific Reports · doi:10.1038/s41598-017-04609-5 · Cited by 107

Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes

Numanagić, I., Malikić, S., Ford, M., Qin, X., Toji, L. H., Radovich, M., Skaar, T. C., Pratt, V. M., Berger, B., Scherer, S., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-03273-1 · Cited by 105

Codon usage influences fitness through RNA toxicity

Mittal, P., Brindle, J., Stephen, J. O., Plotkin, J. B., & Kudla, G. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1810022115 · Cited by 100

Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci

Onuchic, V., Lurie, E., Carrero, I., Pawliczek, P., Patel, R. Y., Rozowsky, J. S., Galeev, T. R., Huang, Z., Altshuler, R. C., Zhang, Z., et al. (2018) · Science · doi:10.1126/science.aar3146 · Cited by 103

Bladder cancer organoids as a functional system to model different disease stages and therapy response

Minoli, M., Cantore, T., Hanhart, D., Kiener, M., Fedrizzi, T., Manna, F. L., Karkampouna, S., Chouvardas, P., Genitsch, V., Rodríguez-Calero, A., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-37696-2 · Cited by 112

Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia

Schrider, D. R., Ayroles, J. F., Matute, D. R., & Kern, A. D. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007341 · Cited by 112

Strand-selective base editing of human mitochondrial DNA using mitoBEs

Yi, Z., Zhang, X., Tang, W., Yu, Y. F., Wei, X., Zhang, X., & Wei, W. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01791-y · Cited by 112

A comparison of single nucleotide polymorphism and microsatellite markers for analysis of parentage and kinship in a cooperatively breeding bird

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Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries

Zekavat, S. M., Ruotsalainen, S., Handsaker, R. E., Alver, M., Bloom, J., Poterba, T., Seed, C., Ernst, J., Chaffin, M., Engreitz, J., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04668-w · Cited by 98

Clinical sequencing: From raw data to diagnosis with lifetime value

Caspar, S. M., Dubacher, N., Kopps, A. M., Meienberg, J., Henggeler, C., & Mátyás, G. (2017) · Clinical Genetics · doi:10.1111/cge.13190 · Cited by 109

Systematic comparison of germline variant calling pipelines cross multiple next-generation sequencers

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Disentangling the role of Africa in the global spread of H5 highly pathogenic avian influenza

Fusaro, A., Zecchin, B., Vrancken, B., Abolnik, C., Ademun, R., Alassane, A., Arafa, A.-S., Awuni, J. A., Couacy‐Hymann, E., Coulibaly, M., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-13287-y · Cited by 105

How array design creates SNP ascertainment bias

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A high-risk retinoblastoma subtype with stemness features, dedifferentiated cone states and neuronal/ganglion cell gene expression

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