From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline

The Sequence Alignment/Map format and SAMtools

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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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On a Test of Whether one of Two Random Variables is Stochastically Larger than the Other

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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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A map of human genome variation from population-scale sequencing.

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dbSNP: the NCBI database of genetic variation

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Integrating common and rare genetic variation in diverse human populations

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RNA-Seq Data for Reliable SNP Detection and Genotype Calling: Interest for Coding Variant Characterization and Cis-Regulation Analysis by Allele-Specific Expression in Livestock Species

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Integrated proteogenomic characterization of medullary thyroid carcinoma

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Indica rice genome assembly, annotation and mining of blast disease resistance genes

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Depolarization of sperm membrane potential is a common feature of men with subfertility and is associated with low fertilization rate at IVF

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Whole Genome Sequencing of Mycobacterium bovis Isolated From Livestock in the United States, 1989–2018

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Genomic signatures of domestication in Old World camels

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Genetic evaluation of dementia with Lewy bodies implicates distinct disease subgroups

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Genomic data reveals potential for hybridization, introgression, and incomplete lineage sorting to confound phylogenetic relationships in an adaptive radiation of narrow‐mouth frogs

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High prevalence of TP53 mutations is associated with poor survival and an EMT signature in gliosarcoma patients

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Germline and sporadic mTOR pathway mutations in low-grade oncocytic tumor of the kidney

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Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants

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A reliable method for the detection of BRCA1 and BRCA2 mutations in fixed tumour tissue utilising multiplex PCR-based targeted next generation sequencing

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Rare variants in axonogenesis genes connect three families with sound–color synesthesia

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Targeted gene sequencing in 6994 individuals with neurodevelopmental disorder with epilepsy

Heyne, H., Artomov, M., Battke, F., Bianchini, C., Smith, D. R., Liebmann, N., Tadigotla, V. R., Stanley, C. M., Lal, D., Rehm, H. L., et al. (2019) · Genetics in Medicine · doi:10.1038/s41436-019-0531-0 · Cited by 65

Evolutionary history of human Plasmodium vivax revealed by genome-wide analyses of related ape parasites

Loy, D. E., Plenderleith, L. J., Sundararaman, S. A., Liu, W., Gruszczyk, J., Chen, Y.-J., Trimboli, S., Learn, G. H., MacLean, O. A., Morgan, A. L. K., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1810053115 · Cited by 64

Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility

Lee, H. J., Hou, Y., Chen, Y., Dailey, Z. Z., Riddihough, A., Jang, H. J., Wang, T., & Johnson, S. L. (2020) · Genome biology · doi:10.1186/s13059-020-1948-0 · Cited by 64

Genome-Wide Identification of a Regulatory Mutation in BMP15 Controlling Prolificacy in Sheep

Chantepie, L., Bodin, L., Sarry, J., Woloszyn, F., Plisson‐Petit, F., Ruesche, J., Drouilhet, L., & Fabre, S. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00585 · Cited by 64

Synthetic Lethal Interaction between the ESCRT Paralog Enzymes VPS4A and VPS4B in Cancers Harboring Loss of Chromosome 18q or 16q

Neggers, J. E., Paolella, B. R., Asfaw, A., Rothberg, M. V., Skipper, T. A., Yang, A., Kalekar, R. L., Krill-Burger, J. M., Dharia, N. V., Kugener, G., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.108493 · Cited by 62

Next-generation sequencing of 34 genes in sudden unexplained death victims in forensics and in patients with channelopathic cardiac diseases

HERTZ, C. L., Christiansen, S. L., Ferrero‐Miliani, L., Fordyce, S. L., Dahl, M., Holst, A. G., Ottesen, G. L., Frank-Hansen, R., Bundgaard, H., & Morling, N. (2014) · International Journal of Legal Medicine · doi:10.1007/s00414-014-1105-y · Cited by 64

Somatic Mutations in NEK9 Cause Nevus Comedonicus

Levinsohn, J. L., Sugarman, J. L., McNiff, J. M., Antaya, R. J., & Choate, K. A. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2016.03.019 · Cited by 64

Molecular diagnosis of patients with epilepsy and developmental delay using a customized panel of epilepsy genes

Ortega-Moreno, L., Giráldez, B. G., Insuga, V. M. S., Pozo, R. L.-D., Rodrigo-Moreno, M., Alarcón-Morcillo, C., Sánchez‐Martín, G., Díaz-Gómez, E., Guerrero, R., Serratosa, J. M., et al. (2017) · PLoS ONE · doi:10.1371/journal.pone.0188978 · Cited by 65

Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica

Paape, T. D., Briskine, R. V., Halstead-Nussloch, G., Lischer, H. E. L., Shimizu‐Inatsugi, R., Hatakeyama, M., Kenta, T., Nishiyama, T., Sabirov, R. N., Sese, J., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06108-1 · Cited by 64

Divergent Fine-Scale Recombination Landscapes between a Freshwater and Marine Population of Threespine Stickleback Fish

Shanfelter, A. F., Archambeault, S., & White, M. A. (2019) · Genome Biology and Evolution · doi:10.1093/gbe/evz090 · Cited by 66

Congruence and Conflict in the Higher-Level Phylogenetics of Squamate Reptiles: An Expanded Phylogenomic Perspective

Singhal, S., Colston, T. J., Grundler, M. R., Smith, S. A., Costa, G. C., Colli, G. R., Moritz, C. C., Pyron, R. A., & Rabosky, D. L. (2020) · Systematic Biology · doi:10.1093/sysbio/syaa054 · Cited by 64

Clonal Hematopoiesis: Somatic Mutations in Blood Cells and Atherosclerosis

Natarajan, P., Jaiswal, S., & Kathiresan, S. (2018) · Circulation Genomic and Precision Medicine · doi:10.1161/circgen.118.001926 · Cited by 63

Systematic benchmark of ancient DNA read mapping

Oliva, A., Tobler, R., Cooper, A., Llamas, B., & Souilmi, Y. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab076 · Cited by 63

Accounting for uncertainty in DNA sequencing data

O'Rawe, J., Ferson, S. A., & Lyon, G. J. (2015) · Trends in Genetics · doi:10.1016/j.tig.2014.12.002 · Cited by 63

Genomic Diversity, Virulence, and Antimicrobial Resistance ofKlebsiella pneumoniaeStrains from Cows and Humans

Yang, Y., Higgins, C. H., Rehman, I., Galvão, K. N., Brito, I., Bicalho, M. L. S., Song, J., Wang, H., & Bicalho, R. C. (2019) · Applied and Environmental Microbiology · doi:10.1128/aem.02654-18 · Cited by 63

Whole exome sequencing identified ATP6V1C2 as a novel candidate gene for recessive distal renal tubular acidosis

Jobst‐Schwan, T., Klämbt, V., Tarsio, M., Heneghan, J. F., Majmundar, A. J., Shril, S., Buerger, F., Ottlewski, I., Shmukler, B. E., Topaloğlu, R., et al. (2019) · Kidney International · doi:10.1016/j.kint.2019.09.026 · Cited by 63

DGCR8 microprocessor defect characterizes familial multinodular goiter with schwannomatosis

Rivera, B., Nadaf, J., Fahiminiya, S., Apellániz-Ruiz, M., Saskin, A., Chong, A., Sharma, S., Wagener, R., Revil, T., Condello, V., et al. (2019) · Journal of Clinical Investigation · doi:10.1172/jci130206 · Cited by 63

Interaction of two MADS-box genes leads to growth phenotype divergence of all-flesh type of tomatoes

Huang, B., Hu, G., Wang, K., Frasse, P., Maza, É., Djari, A., Deng, W., Pirrello, J., Burlat, V., Pons, C., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-27117-7 · Cited by 63

Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history

Patiranage, D. S. R., Rey, E., Emrani, N., Wellman, G. B., Schmid, K., Schmöckel, S. M., Tester, M. A., & Jung, C. (2022) · eLife · doi:10.7554/elife.66873 · Cited by 62

The Chromosome-Encoded Hypothetical Protein TC0668 Is an Upper Genital Tract Pathogenicity Factor of Chlamydia muridarum

Conrad, T., Gong, S., Yang, Z., Matulich, P., Keck, J., Beltrami, N., Chen, C., Zhou, Z., Dai, J. M., & Zhong, G. (2015) · Infection and Immunity · doi:10.1128/iai.01171-15 · Cited by 63

Revisiting a classic case of introgression: hybridization and gene flow in Californian sunflowers

Owens, G. L., Baute, G. J., & Rieseberg, L. H. (2016) · Molecular Ecology · doi:10.1111/mec.13569 · Cited by 59

Common and Low Frequency Variants in MERTK Are Independently Associated with Multiple Sclerosis Susceptibility with Discordant Association Dependent upon HLA-DRB1*15:01 Status

Binder, M. D., Fox, A. D., Merlo, D., Johnson, L., Giuffrida, L., Calvert, S. E., Akkermann, R., Ma, G. Z. M., ANZgene, Perera, A. A., et al. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1005853 · Cited by 63

Directional Selection from Host Plants Is a Major Force Driving Host Specificity in Magnaporthe Species

Zhong, Z., Norvienyeku, J., Chen, M., Bao, J., Lin, L., Chen, L., Lin, Y., Wu, X., Cai, Z., Zhang, Q., et al. (2016) · Scientific Reports · doi:10.1038/srep25591 · Cited by 63

Empirical evaluation of variant calling accuracy using ultra-deep whole-genome sequencing data

Kishikawa, T., Momozawa, Y., Ozeki, T., Mushiroda, T., Inohara, H., Kamatani, Y., Kubo, M., & Okada, Y. (2019) · Scientific Reports · doi:10.1038/s41598-018-38346-0 · Cited by 61

Long-term taxonomic and functional divergence from donor bacterial strains following fecal microbiota transplantation in immunocompromised patients

Moss, E. L., Falconer, S. B., Ei, T., Wang, M., Systrom, H. K., Mahabamunuge, J., Relman, D. A., Hohmann, E. L., & Bhatt, A. S. (2017) · PLoS ONE · doi:10.1371/journal.pone.0182585 · Cited by 63

Analytical and Clinical Validation of Expressed Variants and Fusions From the Whole Transcriptome of Thyroid FNA Samples

Angell, T. E., Wirth, L. J., Cabanillas, M. E., Shindo, M. L., Cibas, E. S., Babiarz, J., Hao, Y., Kim, S. Y., Walsh, P. S., Huang, J., et al. (2019) · Frontiers in Endocrinology · doi:10.3389/fendo.2019.00612 · Cited by 63

A novel high-throughput molecular counting method with single base-pair resolution enables accurate single-gene NIPT

Tsao, D., Silas, S., Landry, B. P., Itzep, N. P., Nguyen, A. B., Greenberg, S., Kanne, C. K., Sheehan, V., Sharma, R., Shukla, R., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-50378-8 · Cited by 62

Distinct molecular etiologies of male and female hepatocellular carcinoma

Natri, H. M., Wilson, M. A., & Buetow, K. H. (2019) · BMC Cancer · doi:10.1186/s12885-019-6167-2 · Cited by 63

Uracil Accumulation and Mutagenesis Dominated by Cytosine Deamination in CpG Dinucleotides in Mice Lacking UNG and SMUG1

Alsøe, L., Sarno, A., Carracedo, S., Domańska, D., Dingler, F. A., Lirussi, L., SenGupta, T., Tekin, N. B., Jobert, L., Alexandrov, L. B., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-07314-5 · Cited by 62

Evolution of genomic variation in the burrowing owl in response to recent colonization of urban areas

Mueller, J. C., Kuhl, H., Boerno, S. T., Tella, J. L., Carrete, M., & Kempenaers, B. (2018) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2018.0206 · Cited by 65

Genetically diverse uropathogenic Escherichia coli adopt a common transcriptional program in patients with UTIs

Sintsova, A., Frick-Cheng, A. E., Smith, S. N., Pirani, A. M., Subashchandrabose, S., Snitkin, E. S., & Mobley, H. L. T. (2019) · eLife · doi:10.7554/elife.49748 · Cited by 59

Comparative genome‐scale analysis of Pichia pastoris variants informs selection of an optimal base strain

Brady, J. R., Whittaker, C. A., Tan, M. C., Kristensen, D. L., Ma, D., Dalvie, N. C., Love, K. R., & Love, J. C. (2019) · Biotechnology and Bioengineering · doi:10.1002/bit.27209 · Cited by 62

Rare genetic variants in interleukin-37 link this anti-inflammatory cytokine to the pathogenesis and treatment of gout

Klück, V., van Deuren, R. C., Cavalli, G., Shaukat, A., Arts, P., Cleophas, M. C. P., Crișan, T. O., Tausche, A., Riches, P. L., Dalbeth, N., et al. (2020) · Annals of the Rheumatic Diseases · doi:10.1136/annrheumdis-2019-216233 · Cited by 62

Heterogeneity and transcriptome changes of human CD8+ T cells across nine decades of life

Lü, J., Ahmad, R., Nguyen, T. B. V., Cifello, J., Hemani, H., Li, J., Chen, J., Li, S., Wang, J., Achour, A., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-32869-x · Cited by 64

From high masked to high realized genetic load in inbred Scandinavian wolves

Smeds, L., & Ellegren, H. (2022) · Molecular Ecology · doi:10.1111/mec.16802 · Cited by 65

Mitochondrial complex I deficiency stratifies idiopathic Parkinson’s disease

Flønes, I. H., Toker, L., Sandnes, D. A., Castelli, M., Mostafavi, S., Lura, N. G., Shadad, O., Fernández‐Vizarra, E., Painous, C., Pérez‐Soriano, A., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-47867-4 · Cited by 67

Illuminating Choices for Library Prep: A Comparison of Library Preparation Methods for Whole Genome Sequencing of Cryptococcus neoformans Using Illumina HiSeq

Rhodes, J. L., Beale, M. A., & Fisher, M. C. (2014) · PLoS ONE · doi:10.1371/journal.pone.0113501 · Cited by 62

From Wet‐Lab to Variations: Concordance and Speed of Bioinformatics Pipelines for Whole Genome and Whole Exome Sequencing

Laurie, S., Fernández-Callejo, M., Marco‐Sola, S., Trotta, J.-R., Camps, J., Chacón, A., Espinosa, A., Gut, M., Gut, I. G., Heath, S. C., et al. (2016) · Human Mutation · doi:10.1002/humu.23114 · Cited by 62

A systems genetics resource and analysis of sleep regulation in the mouse

Diessler, S., Jan, M., Emmenegger, Y., Guex, N., Middleton, B., Skene, D. J., Ibberson, M. R., Burdet, F., Götz, L., Pagni, M., et al. (2018) · PLoS Biology · doi:10.1371/journal.pbio.2005750 · Cited by 63

Identification of Pathogen Genomic Differences That Impact Human Immune Response and Disease during Cryptococcus neoformans Infection

Gerstein, A. C., Jackson, K. M., McDonald, T. R., Wang, Y., Lueck, B. D., Bohjanen, S., Smith, K. D., Akampurira, A., Meya, D. B., Xue, C., et al. (2019) · mBio · doi:10.1128/mbio.01440-19 · Cited by 61

A high-quality cucumber genome assembly enhances computational comparative genomics

Osipowski, P., Pawełkowicz, M. E., Wojcieszek, M., Skarzyńska, A., Przybecki, Z., & Pląder, W. (2019) · Molecular Genetics and Genomics · doi:10.1007/s00438-019-01614-3 · Cited by 62

Comparison of Read Mapping and Variant Calling Tools for the Analysis of Plant NGS Data

Schilbert, H. M., Rempel, A., & Pucker, B. (2020) · Plants · doi:10.3390/plants9040439 · Cited by 61

Exome sequencing of oral leukoplakia and oral squamous cell carcinoma implicates DNA damage repair gene defects in malignant transformation

Farah, C. S., Jessri, M., Bennett, N. J., Dalley, A. J., Shearston, K., & Fox, S. A. (2019) · Oral Oncology · doi:10.1016/j.oraloncology.2019.07.005 · Cited by 62

Genomic Evidence for Local Adaptation of Hunter-Gatherers to the African Rainforest

Lopez, M., Choin, J., Sikora, M., Siddle, K. J., Harmant, C., Costa, H. A., Silvert, M., Mouguiama-Daouda, P., Hombert, J.-M., Froment, A., et al. (2019) · Current Biology · doi:10.1016/j.cub.2019.07.013 · Cited by 62

Reverse Transcriptase Inhibition Disrupts Repeat Element Life Cycle in Colorectal Cancer.

Rajurkar, M., Parikh, A. R., Solovyov, A., You, E., Kulkarni, A. S., Chu, C., Xu, K. H., Jaicks, C., Taylor, M. S., Wu, C., et al. (2022) · Cancer Discovery · doi:10.1158/2159-8290.cd-21-1117 · Cited by 61

Immunogenetics associated with severe coccidioidomycosis

Hsu, A. P., Korzeniowska, A., Aguilar, C. C., Gu, J., Karlins, E., Oler, A. J., Chen, G., Reynoso, G. V., Davis, J., Chaput, A., et al. (2022) · JCI Insight · doi:10.1172/jci.insight.159491 · Cited by 67

Navigating bottlenecks and trade-offs in genomic data analysis

Berger, B., & Yu, Y. W. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00551-z · Cited by 62

Dysregulation and Epigenetic Reprogramming of NRF2 Signaling Axis Promote Acquisition of Cisplatin Resistance and Metastasis in Head and Neck Squamous Cell Carcinoma

Osman, A. A., Arslan, E., Bartels, M. D., Michikawa, C., Lindemann, A., Tomczak, K. J., Yu, W., Sandulache, V. C., Ma, W., Shen, L., et al. (2023) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-22-2747 · Cited by 63

Effect of lossy compression of quality scores on variant calling

Ochoa, I., Hernáez, M., Goldfeder, R. L., Weissman, T., & Ashley, E. A. (2016) · Briefings in Bioinformatics · doi:10.1093/bib/bbw011 · Cited by 61

Whole‐exome sequencing reveals critical genes underlying metastasis in oesophageal squamous cell carcinoma

Dai, W., Ko, J. M. Y., Choi, S. S. A., Yu, Z., Ning, L., Zheng, H., Gopalan, V., Chan, K. T., Lee, N. P. Y., Chan, K. W., et al. (2017) · The Journal of Pathology · doi:10.1002/path.4925 · Cited by 60

Cutaneous Non-Neural Granular Cell Tumors Harbor Recurrent ALK Gene Fusions

Cohen, J. N., Yeh, I., Jordan, R. C., Wolsky, R. J., Horvai, A., McCalmont, T. H., & LeBoit, P. E. (2018) · The American Journal of Surgical Pathology · doi:10.1097/pas.0000000000001122 · Cited by 61

Genetic variants in components of the NALCN–UNC80–UNC79 ion channel complex cause a broad clinical phenotype (NALCN channelopathies)

Bramswig, N. C., Bertoli‐Avella, A. M., Albrecht, B., Aqeel, A. I. A., Alhashem, A. M., Al-Sannaa, N. A., Bah, M. G., Bröhl, K., Depienne, C., Dorison, N., et al. (2018) · Human Genetics · doi:10.1007/s00439-018-1929-5 · Cited by 61

Germline pathogenic variants identified in women with ovarian tumors

Carter, N. J., Marshall, M. L., Susswein, L. R., Zorn, K. K., Hiraki, S. C., Arvai, K. J., Torene, R. I., McGill, A. K., Yackowski, L., Murphy, P. D., et al. (2018) · Gynecologic Oncology · doi:10.1016/j.ygyno.2018.09.030 · Cited by 62

Next-Generation Sequencing of Uveal Melanoma for Detection of Genetic Alterations Predicting Metastasis

Afshar, A. R., Damato, B. E., Stewart, J. M., Zablotska, L. B., Roy, R., Olshen, A. B., Joseph, N. M., & Bastian, B. C. (2019) · Translational Vision Science & Technology · doi:10.1167/tvst.8.2.18 · Cited by 61

Genome-wide analyses of ADHD identify 27 risk loci, refine the genetic architecture and implicate several cognitive domainsPreprint

Demontis, D., Walters, G. B., Athanasiadis, G. I., Walters, R. K., Therrien, K., Farajzadeh, L., Voloudakis, G., Bendl, J. M., Zeng, B., Zhang, W., et al. (2022) · medRxiv · doi:10.1101/2022.02.14.22270780 · Cited by 61

An efficient genotyper and star-allele caller for pharmacogenomicsPreprint

Hari, A., Zhou, Q., Gonzaludo, N., Harting, J., Scott, S. A., Qin, X., Scherer, S., Şahinalp, S. C., & Numanagić, I. (2023) · Genome Research · doi:10.1101/gr.277075.122 · Cited by 60

Imputation from SNP chip to sequence: a case study in a Chinese indigenous chicken population

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New insights into the associations among feed efficiency, metabolizable efficiency traits and related QTL regions in broiler chickens

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