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

The Sequence Alignment/Map format and SAMtools

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041

Fast and accurate short read alignment with Burrows-Wheeler transform

Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607

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

McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895

ggplot2: Elegant Graphics for Data Analysis

Wickham, H. (2009) · doi:10.1007/978-0-387-98141-3 · Cited by 14,447

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

Mann, H. B., & Whitney, D. R. (1947) · The Annals of Mathematical Statistics · doi:10.1214/aoms/1177730491 · Cited by 14,320

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

Li, H., & Durbin, R. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp698 · Cited by 12,063

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

DePristo, M. A., Banks, E., Poplin, R. E., Garimella, K. V., Maguire, J., Hartl, C., Philippakis, A., del Angel, G., Rivas, M. A., Hanna, M., et al. (2011) · Nature Genetics · doi:10.1038/ng.806 · Cited by 11,457

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

The 1000 Genomes Project Consortium (2010) · Nature · doi:10.1038/nature09534 · Cited by 7,877

dbSNP: the NCBI database of genetic variation

Sherry, S. T. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.308 · Cited by 7,502

Integrating common and rare genetic variation in diverse human populations

The International HapMap 3 Consortium (2010) · Nature · doi:10.1038/nature09298 · Cited by 3,026

Evolutionary determinants of genome-wide nucleotide composition

Long, H., Sung, W., Küçükyıldırım, S., Williams, E., Miller, S. F., Guo, W., Patterson, C. E., Gregory, C., Strauss, C., Stone, C., et al. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0425-y · Cited by 188

The Genome Landscape of Tibetan Sheep Reveals Adaptive Introgression from Argali and the History of Early Human Settlements on the Qinghai–Tibetan Plateau

Hu, X., Yang, J. H., Xie, X.-L., Lv, F., Cao, Y.-H., Li, W., Liu, M., Wang, Y., Li, J., Liu, Y., et al. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy208 · Cited by 193

A multi-task convolutional deep neural network for variant calling in single molecule sequencing

Luo, R., Sedlazeck, F. J., Lam, T., & Schatz, M. C. (2019) · Nature Communications · doi:10.1038/s41467-019-09025-z · Cited by 188

Iranome: A catalog of genomic variations in the Iranian population

Fattahi, Z., Beheshtian, M., Mohseni, M., Poustchi, H., Sellars, E., Nezhadi, S. H., Amini, A., Arzhangi, S., Jalalvand, K., Jamali, P., et al. (2019) · Human Mutation · doi:10.1002/humu.23880 · Cited by 197

A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response

Luo, Y., Kanai, M., Choi, W., Li, X., Sakaue, S., Yamamoto, K., Ogawa, K., Gutiérrez‐Arcelus, M., Gregersen, P. K., Stuart, P. E., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00935-7 · Cited by 177

De Novo Coding Variants Are Strongly Associated with Tourette Disorder

Willsey, A. J., Fernandez, T. V., Yu, D., King, R. A., Dietrich, A., Xing, J., Sanders, S. J., Mandell, J. D., Huang, A. Y., Richer, P., et al. (2017) · Neuron · doi:10.1016/j.neuron.2017.04.024 · Cited by 187

Distinct mutational signatures characterize concurrent loss of polymerase proofreading and mismatch repair

Haradhvala, N. J., Kim, J., Maruvka, Y. E., Polak, P. P., Rosebrock, D., Livitz, D. G., Hess, J. M., Leshchiner, I., Kamburov, A., Mouw, K. W., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04002-4 · Cited by 181

The genome of oil-Camellia and population genomics analysis provide insights into seed oil domestication

Lin, P., Wang, K., Wang, Y., Hu, Z., Yan, C., Huang, H., Ma, X., Cao, Y., Long, W., Liu, W., et al. (2022) · Genome biology · doi:10.1186/s13059-021-02599-2 · Cited by 184

Genomic Epidemiology: Whole-Genome-Sequencing–Powered Surveillance and Outbreak Investigation of Foodborne Bacterial Pathogens

Deng, X., den Bakker, H. C., & Hendriksen, R. S. (2016) · Annual Review of Food Science and Technology · doi:10.1146/annurev-food-041715-033259 · Cited by 195

Dynamic regulation of RNA editing in human brain development and disease

Hwang, T., Park, C., Leung, A. K. L., Gao, Y., Hyde, T. M., Kleinman, J. E., Rajpurohit, A., Tao, R., Shin, J. H., & Weinberger, D. R. (2016) · Nature Neuroscience · doi:10.1038/nn.4337 · Cited by 184

Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese

Okada, Y., Momozawa, Y., Sakaue, S., Kanai, M., Ishigaki, K., Akiyama, M., Kishikawa, T., Arai, Y., Sasaki, T., Kosaki, K., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-03274-0 · Cited by 182

Rapid and repeated local adaptation to climate in an invasive plant

van Boheemen, L. A., Atwater, D. Z., & Hodgins, K. A. (2018) · New Phytologist · doi:10.1111/nph.15564 · Cited by 185

Deep-coverage whole genome sequences and blood lipids among 16,324 individuals

Natarajan, P., Peloso, G. M., Zekavat, S. M., Montasser, M. E., Ganna, A., Chaffin, M. D., Khera, A. V., Zhou, W., Bloom, J. M., Engreitz, J., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-05747-8 · Cited by 183

Whole genome sequencing in clinical practice

Bagger, F. O., Borgwardt, L. G., Jespersen, A. S., Hansen, A. R., Bertelsen, B., Kodama, M., & Nielsen, F. C. (2024) · BMC Medical Genomics · doi:10.1186/s12920-024-01795-w · Cited by 210

Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel

Gerdol, M., Moreira, R., Cruz, F., Gómez‐Garrido, J., Vlasova, A. V., Rosani, U., Venier, P., Naranjo-Ortíz, M. A., Murgarella, M., Greco, S., et al. (2020) · Genome biology · doi:10.1186/s13059-020-02180-3 · Cited by 204

Whole-exome sequencing identifies multiple loss-of-function mutations of NF-κB pathway regulators in nasopharyngeal carcinoma

Zheng, H., Dai, W., Cheung, A. K. L., Ko, J. M. Y., Kan, R., Wong, B. W. Y., Leong, M. M., Deng, M., Kwok, T. C. T., Chan, J. Y. W., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1607606113 · Cited by 187

Habitat suitability is a poor proxy for landscape connectivity during dispersal and mating movements

Keeley, A. T. H., Beier, P., Keeley, B. W., & Fagan, M. E. (2017) · Landscape and Urban Planning · doi:10.1016/j.landurbplan.2017.01.007 · Cited by 173

Persistent anthrax as a major driver of wildlife mortality in a tropical rainforest

Hoffmann, C., Zimmermann, F., Biek, R., Kuehl, H., Nowak, K., Mundry, R., Agbor, A., Angedakin, S., Arandjelovic, M., Blankenburg, A., et al. (2017) · Nature · doi:10.1038/nature23309 · Cited by 180

Mutations disrupting neuritogenesis genes confer risk for cerebral palsy

Jin, S. C., Lewis, S. A., Bakhtiari, S., Zeng, X. Q., Sierant, M. C., Shetty, S., Nordlie, S. M., Elie, A., Corbett, M. A., Norton, B. Y., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0695-1 · Cited by 178

Big Data Analytics for Genomic Medicine

He, K., Ge, D., & He, M. M. (2017) · International Journal of Molecular Sciences · doi:10.3390/ijms18020412 · Cited by 194

Genomic analyses implicate noncoding de novo variants in congenital heart disease

Richter, F., Morton, S. U., Kim, S. W., Kitaygorodsky, A., Wasson, L. K., Chen, K., Zhou, J., Qi, H., Patel, N., DePalma, S. R., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0652-z · Cited by 180

Best practices for evaluating single nucleotide variant calling methods for microbial genomics

Olson, N. D., Lund, S. P., Colman, R. E., Foster, J. T., Sahl, J. W., Schupp, J. M., Keim, P., Morrow, J. B., Salit, M., & Zook, J. M. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00235 · Cited by 177

The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencingPreprint

Cieslik, M. P., Chugh, R. K., Wu, Y.-M., Wu, M., Brennan, C. A., Lonigro, R. J., Su, F., Wang, R., Siddiqui, J., Mehra, R., et al. (2015) · Genome Research · doi:10.1101/gr.189621.115 · Cited by 174

Burden Testing of Rare Variants Identified through Exome Sequencing via Publicly Available Control Data

Guo, M. H., Plummer, L., Chan, Y.-M., Hirschhorn, J. N., & Lippincott, M. F. (2018) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2018.08.016 · Cited by 180

Sequencing Degraded DNA from Non-Destructively Sampled Museum Specimens for RAD-Tagging and Low-Coverage Shotgun Phylogenetics

Tin, M. M. Y., Economo, E. P., & Mikheyev, A. S. (2014) · PLoS ONE · doi:10.1371/journal.pone.0096793 · Cited by 174

An intronic GAA repeat expansion in FGF14 causes the autosomal-dominant adult-onset ataxia SCA27B/ATX-FGF14

Rafehi, H., Read, J. L., Szmulewicz, D. J., Davies, K. C., Snell, P., Fearnley, L. G., Scott, L., Thomsen, M., Gillies, G., Pope, K., et al. (2022) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2022.11.015 · Cited by 175

The Stone Age Plague and Its Persistence in Eurasia

Valtueña, A. A., Mittnik, A., Key, F. M., Haak, W., Allmäe, R., Belinskij, A. B., Daubaras, M., Feldman, M., Jankauskas, R., Janković, I., et al. (2017) · Current Biology · doi:10.1016/j.cub.2017.10.025 · Cited by 182

Independent impacts of aging on mitochondrial DNA quantity and quality in humans

Zhang, R., Wang, Y., Ye, K., Picard, M. A., & Gu, Z. (2017) · BMC Genomics · doi:10.1186/s12864-017-4287-0 · Cited by 178

De Novo Insertions and Deletions of Predominantly Paternal Origin Are Associated with Autism Spectrum Disorder

Dong, S., Walker, M. F., Carriero, N. J., DiCola, M. J., Willsey, A. J., Ye, A. Y., Waqar, Z., González, L. E., Overton, J. D., Frahm, S., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.08.068 · Cited by 175

Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios

Besenbacher, S., Liu, S. M., Izarzugaza, J. M. G., Grove, J., Belling, K., Bork‐Jensen, J., Huang, S., Als, T. D., Li, S., Yadav, R., et al. (2015) · Nature Communications · doi:10.1038/ncomms6969 · Cited by 169

Radiation-related genomic profile of papillary thyroid carcinoma after the Chernobyl accident

Morton, L. M., Karyadi, D. M., Stewart, C., Ti, B., Dawson, E. T., Steinberg, M. K., Dai, J., Hartley, S. W., Schonfeld, S. J., Sampson, J. N., et al. (2021) · Science · doi:10.1126/science.abg2538 · Cited by 178

Methods and models for unravelling human evolutionary history

Schraiber, J. G., & Akey, J. M. (2015) · Nature Reviews Genetics · doi:10.1038/nrg4005 · Cited by 171

Resistance to malaria through structural variation of red blood cell invasion receptors

Leffler, E. M., Band, G., Busby, G., Kivinen, K., Le, S. Q., Clarke, G. M., Bojang, K., Conway, D. J., Jallow, M., Sisay-Joof, F., et al. (2017) · Science · doi:10.1126/science.aam6393 · Cited by 169

Regenerative Metaplastic Clones in COPD Lung Drive Inflammation and Fibrosis

Rao, W. H., Wang, S., Dulęba, M., Niroula, S., Göller, K., Xie, J., Mahalingam, R., Neupane, R., Liew, A.-A., Vincent, M., et al. (2020) · Cell · doi:10.1016/j.cell.2020.03.047 · Cited by 176

Genomic incompatibilities in the diploid and tetraploid offspring of the goldfish × common carp cross

Liu, S., Luo, J., Chai, J., Ren, L., Zhou, Y., Huang, F., Liu, X., Chen, Y., Zhang, C., Tao, M., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1512955113 · Cited by 165

Assembly of the threespine stickleback Y chromosome reveals convergent signatures of sex chromosome evolution

Peichel, C. L., McCann, S. R., Ross, J. A., Naftaly, A. F. S., Urton, J. R., Cech, J. N., Grimwood, J., Schmutz, J., Myers, R., Kingsley, D. M., et al. (2020) · Genome biology · doi:10.1186/s13059-020-02097-x · Cited by 163

Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia

Bryois, J., Garrett, M. E., Song, L., Safi, A., Giusti-Rodriguez, P., Johnson, G. D., Shieh, A. W., Buil, A., Fullard, J. F., Roussos, P., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-05379-y · Cited by 167

Detection of aberrant gene expression events in RNA sequencing data

Yépez, V. A., Mertes, C., Müller, M., Klaproth-Andrade, D., Wachutka, L., Frésard, L., Gušić, M., Scheller, I. F., Goldberg, P. F., Prokisch, H., et al. (2021) · Nature Protocols · doi:10.1038/s41596-020-00462-5 · Cited by 163

Reducing INDEL calling errors in whole genome and exome sequencing data

Fang, H., Wu, Y., Narzisi, G., O'Rawe, J., Barrón, L. T. J., Rosenbaum, J., Ronemus, M., Iossifov, I. H., Schatz, M. C., & Lyon, G. J. (2014) · Genome Medicine · doi:10.1186/s13073-014-0089-z · Cited by 170

MSH6 and PMS2 germ-line pathogenic variants implicated in Lynch syndrome are associated with breast cancer

Roberts, M. E., Jackson, S. A., Susswein, L. R., Zeinomar, N., Ma, X., Marshall, M. L., Stettner, A. R., Milewski, B., Xu, Z., Solomon, B. D., et al. (2018) · Genetics in Medicine · doi:10.1038/gim.2017.254 · Cited by 166

Actionable Activating Oncogenic ERBB2/HER2 Transmembrane and Juxtamembrane Domain Mutations

Pahuja, K. B., Nguyen, T. T., Jaiswal, B. S., Prabhash, K., Thaker, T. M., Senger, K., Chaudhuri, S., Kljavin, N. M., Antony, A., Phalke, S., et al. (2018) · Cancer Cell · doi:10.1016/j.ccell.2018.09.010 · Cited by 167

NANS-mediated synthesis of sialic acid is required for brain and skeletal development

van Karnebeek, C. D. M., Bonafé, L., Wen, X.-Y., Tarailo-Graovac, M., Balzano, S., Royer-Bertrand, B., Ashikov, A., Garavelli, L., Mammi, I., Turolla, L., et al. (2016) · Nature Genetics · doi:10.1038/ng.3578 · Cited by 164

Small-molecule targeting of brachyury transcription factor addiction in chordoma

Sharifnia, T., Wawer, M. J., Chen, T., Huang, Q., Weir, B. A., Sizemore, A. E., Lawlor, M. A., Goodale, A. B., Cowley, G. S., Vázquez, F., et al. (2019) · Nature Medicine · doi:10.1038/s41591-018-0312-3 · Cited by 159

Evolutionary genomic dynamics of Peruvians before, during, and after the Inca Empire

Harris, D., Song, W., Shetty, A. C., Levano, K. S., Cáceres, O., Padilla, C., Borda, V., Tarazona, D. D., Trujillo, O., Sánchez, C., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1720798115 · Cited by 166

Germline Elongator mutations in Sonic Hedgehog medulloblastoma

Waszak, S. M., Robinson, G. W., Gudenas, B. L., Smith, K. S., Forget, A., Kojic, M., García-López, J., Hadley, J. L., Hamilton, K. V., Indersie, É., et al. (2020) · Nature · doi:10.1038/s41586-020-2164-5 · Cited by 170

Standing genetic variation fuels rapid adaptation to ocean acidification

(2019) · doi:10.1038/s41467-019-13767-1 · Cited by 162

Local emergence in Amazonia of Plasmodium falciparum k13 C580Y mutants associated with in vitro artemisinin resistance

Mathieu, L., Cox, H., Early, A. M., Mok, S., Lazrek, Y., Paquet, J.-C., Ade, M. P., Lucchi, N. W., Grant, Q., Udhayakumar, V., et al. (2020) · eLife · doi:10.7554/elife.51015 · Cited by 161

Anti-tumour immunity induces aberrant peptide presentation in melanoma

Bartok, O., Pataskar, A., Nagel, R., Laos, M., Goldfarb, E., Hayoun, D., Levy, R., Körner, P.-R., Kreuger, I. Z. M., Champagne, J., et al. (2020) · Nature · doi:10.1038/s41586-020-03054-1 · Cited by 170

Reprogramming of the FOXA1 cistrome in treatment-emergent neuroendocrine prostate cancer

Baca, S. C., Takeda, D. Y., Seo, J.-H., Hwang, J. H., Ku, S., Arafeh, R., Arnoff, T. E., Agarwal, S., Bell, C. A., O’Connor, E. P., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-22139-7 · Cited by 163

Heterozygous Loss-of-Function SEC61A1 Mutations Cause Autosomal-Dominant Tubulo-Interstitial and Glomerulocystic Kidney Disease with Anemia

Bolar, N. A., Golzio, C., Živná, M., Hayot, G., Hemelrijk, C. V., Schepers, D., Vandeweyer, G., Hoischen, A., Huyghe, J. R., Raes, A. M., et al. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2016.05.028 · Cited by 161

Low number of fixed somatic mutations in a long-lived oak tree

Schmid-Siegert, E., Sarkar, N., Iseli, C., Calderon, S., Gouhier-Darimont, C., Chrast, J., Cattaneo, P., Schütz, F., Farinelli, L., Pagni, M., et al. (2017) · Nature Plants · doi:10.1038/s41477-017-0066-9 · Cited by 161

Prognostic genome and transcriptome signatures in colorectal cancers

Nunes, L., Li, F., Wu, M., Luo, T., Hammarström, K., Torell, E., Ljuslinder, I., Mezheyeuski, A., Edqvist, P.-H. D., Löfgren‐Burström, A., et al. (2024) · Nature · doi:10.1038/s41586-024-07769-3 · Cited by 179

Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells

DeBoever, C., Li, H., Jakubosky, D. A., Benaglio, P., Reyna, J., Olson, K. M., Huang, H., Biggs, W., Sandoval, E., D’Antonio, M., et al. (2017) · Cell stem cell · doi:10.1016/j.stem.2017.03.009 · Cited by 167

Exome Sequencing in Children With Pulmonary Arterial Hypertension Demonstrates Differences Compared With Adults

Zhu, N., Gonzaga-Jauregui, C. G., Welch, C. L., Ma, L., Qi, H., King, A. K., Krishnan, U., Rosenzweig, E. B., Ivy, D. D., Austin, E. D., et al. (2018) · Circulation Genomic and Precision Medicine · doi:10.1161/circgen.117.001887 · Cited by 162

Patient-derived organoids and orthotopic xenografts of primary and recurrent gliomas represent relevant patient avatars for precision oncology

Golebiewska, A., Hau, A., Oudin, A., Stieber, D., Yabo, Y. A., Baus, V., Barthelemy, V., Klein, E., Bougnaud, S., Keunen, O., et al. (2020) · Acta Neuropathologica · doi:10.1007/s00401-020-02226-7 · Cited by 161

Systematic analysis of binding of transcription factors to noncoding variants

Yan, J., Qiu, Y., dos Santos, A. M. R., Yin, Y., Li, Y. E., Vinckier, N., Nariai, N., Benaglio, P., Raman, A., Li, X., et al. (2021) · Nature · doi:10.1038/s41586-021-03211-0 · Cited by 163

A novel canine reference genome resolves genomic architecture and uncovers transcript complexity

Wang, C., Wallerman, O., Arendt, M. L., Sundström, E., Karlsson, Å., Nordin, J., Mäkeläinen, S., Pielberg, G., Hanson, J., Ohlsson, Å., et al. (2021) · Communications Biology · doi:10.1038/s42003-021-01698-x · Cited by 176

Whole-genome sequencing of 1,171 elderly admixed individuals from Brazil

Naslavsky, M. S., Scliar, M. O., Yamamoto, G. L., Wang, J. Y. T., Zverinova, S., Karp, T., Nunes, K., Ceroni, J. R. M., de Carvalho, D. L., Simões, C. E. D. S., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28648-3 · Cited by 168

A map of gene expression in neutrophil-like cell lines

Rincón, E., Rocha-Gregg, B. L., & Collins, S. R. (2018) · BMC Genomics · doi:10.1186/s12864-018-4957-6 · Cited by 160

Intronic ATTTC repeat expansions in STARD7 in familial adult myoclonic epilepsy linked to chromosome 2

Corbett, M. A., Kroes, T., Veneziano, L., Bennett, M. F., Florian, R. T., Schneider, A., Coppola, A., Licchetta, L., Franceschetti, S., Suppa, A., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-12671-y · Cited by 159

Rare variants in SOX17 are associated with pulmonary arterial hypertension with congenital heart disease

Zhu, N., Welch, C. L., Wang, J., Allen, P. M., Gonzaga-Jauregui, C. G., Ma, L., King, A. K., Krishnan, U., Rosenzweig, E. B., Ivy, D. D., et al. (2018) · Genome Medicine · doi:10.1186/s13073-018-0566-x · Cited by 162

TBCRC 032 IB/II Multicenter Study: Molecular Insights to AR Antagonist and PI3K Inhibitor Efficacy in Patients with AR+ Metastatic Triple-Negative Breast Cancer

Lehmann, B. D., Abramson, V. G., Sanders, M. E., Mayer, E. L., Haddad, T. C., Nanda, R., Poznak, C. H. V., Storniolo, A. M., Nangia, J. R., Ericsson, P. I. G., et al. (2019) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-19-2170 · Cited by 159

Genomic predictors of response to PD-1 inhibition in children with germline DNA replication repair deficiency

Das, A., Sudhaman, S., Morgenstern, D. A., Coblentz, A. C., Chung, J., Stone, S. C., Alsafwani, N. S., Liu, Z. A., Karsaneh, O. A. A., Soleimani, S., et al. (2022) · Nature Medicine · doi:10.1038/s41591-021-01581-6 · Cited by 165

Failure of human rhombic lip differentiation underlies medulloblastoma formation

Hendrikse, L. D., Haldipur, P., Saulnier, O., Millman, J., Sjoboen, A. H., Erickson, A. W., Ong, W., Gordon, V. D., Coudière-Morrison, L., Mercier, A. L., et al. (2022) · Nature · doi:10.1038/s41586-022-05215-w · Cited by 167

SMCHD1 mutations associated with a rare muscular dystrophy can also cause isolated arhinia and Bosma arhinia microphthalmia syndrome

Shaw, N. D., Brand, H., Kupchinsky, Z. A., Bengani, H., Plummer, L., Jones, T. I., Erdin, S., Williamson, K. A., Rainger, J., Stortchevoi, A., et al. (2017) · Nature Genetics · doi:10.1038/ng.3743 · Cited by 154

Sex-Based Analysis of De Novo Variants in Neurodevelopmental Disorders

Turner, T. N., Wilfert, A. B., Bakken, T. E., Bernier, R. A., Pepper, M. R., Zhang, Z., Torene, R. I., Retterer, K., & Eichler, E. E. (2019) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2019.11.003 · Cited by 159

Exome sequencing implicates genetic disruption of prenatal neuro-gliogenesis in sporadic congenital hydrocephalus

Jin, S. C., Dong, W., Kundishora, A. J., Panchagnula, S., Moreno-De-Luca, A., Furey, C. G., Allocco, A. A., Walker, R. L., Nelson-Williams, C. J., Smith, H. L., et al. (2020) · Nature Medicine · doi:10.1038/s41591-020-1090-2 · Cited by 154

Emergence and interstate spread of highly pathogenic avian influenza A(H5N1) in dairy cattle in the United States

Nguyen, T.-Q., Hutter, C. R., Markin, A., Thomas, M. N., Lantz, K., Killian, M. L., Janzen, G. M., Vijendran, S., Wagle, S., Inderski, B., et al. (2025) · Science · doi:10.1126/science.adq0900 · Cited by 277

The genome-wide effects of ionizing radiation on mutation induction in the mammalian germline

Adewoye, A. B., Lindsay, S., Dubrova, Y. E., & Hurles, M. E. (2015) · Nature Communications · doi:10.1038/ncomms7684 · Cited by 155

Intestinal PPARα Protects Against Colon Carcinogenesis via Regulation of Methyltransferases DNMT1 and PRMT6

Luo, Y., Xie, C., Brocker, C. N., Fan, J., Wu, X., Feng, L., Wang, Q., Zhao, J., Lu, D., Tandon, M., et al. (2019) · Gastroenterology · doi:10.1053/j.gastro.2019.05.057 · Cited by 155

ketu mutant mice uncover an essential meiotic function for the ancient RNA helicase YTHDC2

Jain, D., Puno, M. R., Meydan, C., Lailler, N., Mason, C. E., Lima, C. D., Anderson, K. V., & Keeney, S. (2018) · eLife · doi:10.7554/elife.30919 · Cited by 159

STRetch: detecting and discovering pathogenic short tandem repeat expansions

Dashnow, H., Lek, M., Phipson, B., Halman, A., Sadedin, S., Lonsdale, A., Davis, M. R., Lamont, P. J., Clayton, J. S., Laing, N. G., et al. (2018) · Genome biology · doi:10.1186/s13059-018-1505-2 · Cited by 160

Evolution of the RNA N6-Methyladenosine Methylome Mediated by Genomic Duplication

Miao, Z., Zhang, T., Qi, Y., Song, J., Han, Z., & Ma, C. (2019) · PLANT PHYSIOLOGY · doi:10.1104/pp.19.00323 · Cited by 155

Radiotherapy is associated with a deletion signature that contributes to poor outcomes in patients with cancer

Kocakavuk, E., Anderson, K. J., Varn, F. S., Johnson, K. C., Amin, S. B., Sulman, E. P., Lolkema, M. P., Barthel, F. P., & Verhaak, R. G. W. (2021) · Nature Genetics · doi:10.1038/s41588-021-00874-3 · Cited by 153

Neoantigen-specific CD4+ T cells in human melanoma have diverse differentiation states and correlate with CD8+ T cell, macrophage, and B cell function

Veatch, J. R., Lee, S. M., Shasha, C., Singhi, N., Szeto, J. L., Moshiri, A. S., Kim, T. S., Smythe, K. S., Kong, P., Fitzgibbon, M., et al. (2022) · Cancer Cell · doi:10.1016/j.ccell.2022.03.006 · Cited by 159

De Novo Mutation in Genes Regulating Neural Stem Cell Fate in Human Congenital Hydrocephalus

Furey, C. G., Choi, J., Jin, S. C., Zeng, X. Q., Timberlake, A. T., Nelson-Williams, C. J., Mansuri, M. S., Lu, Q., Durán, D., Panchagnula, S., et al. (2018) · Neuron · doi:10.1016/j.neuron.2018.06.019 · Cited by 148

Clinically relevant molecular subtypes and genomic alteration-independent differentiation in gynecologic carcinosarcoma

Gotoh, O., Sugiyama, Y., Takazawa, Y., Kato, K., Tanaka, N., Omatsu, K., Takeshima, N., Nomura, H., Hasegawa, K., Fujiwara, K., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-12985-x · Cited by 152

Integrated exome and RNA sequencing of TFE3-translocation renal cell carcinoma

Sun, G., Chen, J., Liang, J., Yin, X., Zhang, M., Yao, J., He, N., Armstrong, C. M., Zheng, L., Zhang, X., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25618-z · Cited by 155

A first-generation pediatric cancer dependency map

Dharia, N. V., Kugener, G., Guenther, L. M., Malone, C. F., Durbin, A. D., Hong, A. L., Howard, T. P., Bandopadhayay, P., Wechsler, C. S., Fung, I., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00819-w · Cited by 153

GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments

Herten, K., Hestand, M. S., Vermeesch, J. R., & Houdt, J. K. J. V. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0514-3 · Cited by 157

Human Semaphorin 3 Variants Link Melanocortin Circuit Development and Energy Balance

van der Klaauw, A. A., Croizier, S., de Oliveira, E. M., Stadler, L. K. J., Park, S., Kong, Y., Banton, M. C., Tandon, P., Hendricks, A. E., Keogh, J. M., et al. (2019) · Cell · doi:10.1016/j.cell.2018.12.009 · Cited by 159

POWR1 is a domestication gene pleiotropically regulating seed quality and yield in soybean

Goettel, W., Zhang, H., Li, Y., Qiao, Z., Jiang, H., Hou, D., Song, Q., Pantalone, V. R., Song, B., Yu, D., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30314-7 · Cited by 153

Next-Generation Diagnostics: Gene Panel, Exome, or Whole Genome?

Sun, Y., Ruivenkamp, C. A. L., Hoffer, M. J. V., Vrijenhoek, T., Kriek, M., van Asperen, C. J., den Dunnen, J. T., & Santen, G. W. E. (2015) · Human Mutation · doi:10.1002/humu.22783 · Cited by 151

Human TBK1 deficiency leads to autoinflammation driven by TNF-induced cell death

Taft, J., Markson, M., Legarda, D., Patel, R., Chan, M., Malle, L., Richardson, A., Gruber, C., Martín-Fernández, M., Mancini, G. M. S., et al. (2021) · Cell · doi:10.1016/j.cell.2021.07.026 · Cited by 151

GNA14 Somatic Mutation Causes Congenital and Sporadic Vascular Tumors by MAPK Activation

Lim, Y. H., Bacchiocchi, A., Qiu, J., Straub, R., Bruckner, A. L., Bercovitch, L. G., Narayan, D., McNiff, J. M., Ko, C. J., Robinson‐Bostom, L., et al. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2016.06.010 · Cited by 151

The critically endangered vaquita is not doomed to extinction by inbreeding depression

Robinson, J. A., Kyriazis, C. C., Nigenda‐Morales, S. F., Beichman, A. C., Rojas‐Bracho, L., Robertson, K. M., Fontaine, M. C., Wayne, R. K., Lohmueller, K. E., Taylor, B. L., et al. (2022) · Science · doi:10.1126/science.abm1742 · Cited by 151

Rare truncating variants in the sarcomeric protein titin associate with familial and early-onset atrial fibrillation

Ahlberg, G., Refsgaard, L., Lundegaard, P. R., Andreasen, L., Ranthe, M. F., Linscheid, N., Nielsen, J. B., Melbye, M., Haunsø, S., Sajadieh, A., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06618-y · Cited by 144

Uniform genomic data analysis in the NCI Genomic Data Commons

Zhang, Z., Hernandez, K. M., Savage, J. H., Li, S., Miller, D. P., Agrawal, S., Ortuño, F. M., Staudt, L. M., Heath, A. P., & Grossman, R. L. (2021) · Nature Communications · doi:10.1038/s41467-021-21254-9 · Cited by 149

Rapid Targeted Genomics in Critically Ill Newborns

van Diemen, C. C., Kerstjens‐Frederikse, W. S., Bergman, K. A., de Koning, T. J., Sikkema‐Raddatz, B., van der Velde, J. K., Abbott, K. M., Herkert, J. C., Löhner, K., Rump, P., et al. (2017) · PEDIATRICS · doi:10.1542/peds.2016-2854 · Cited by 148

Whole-Exome Sequencing of Cell-Free DNA Reveals Temporo-spatial Heterogeneity and Identifies Treatment-Resistant Clones in Neuroblastoma

Chicard, M., Daage, L. C., Clément, N., Danzon, A., Bohec, M., Bernard, V., Baulande, S., Bellini, A., Deveau, P., Pierron, G., et al. (2017) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-17-1586 · Cited by 150

Fine-mapping and functional studies highlight potential causal variants for rheumatoid arthritis and type 1 diabetes

Westra, H.-J., Martínez‐Bonet, M., Önengüt-Gümüşcü, S., Lee, A., Luo, Y., Teslovich, N. C., Worthington, J., Martin, J. J., Huizinga, T. W. J., Klareskog, L., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0216-7 · Cited by 147

Enhancer release and retargeting activates disease-susceptibility genes

Oh, S., Shao, J., Mitra, J., Xiong, F., D’Antonio, M., Wang, R., Garcia-Bassets, I., Ma, Q., Zhu, X., Lee, J.-H., et al. (2021) · Nature · doi:10.1038/s41586-021-03577-1 · Cited by 148

Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzziiPreprint

The Anopheles gambiae 1000 Genomes Consortium, Clarkson, C. S., Miles, A., Harding, N. J., Lucas, E. R., Battey, C. J., Amaya-Romero, J. E., Kern, A. D., Fontaine, M. C., Donnelly, M. J., et al. (2020) · Genome Research · doi:10.1101/gr.262790.120 · Cited by 134

Microbiome composition shapes rapid genomic adaptation of Drosophila melanogaster

Rudman, S. M., Greenblum, S. I., Hughes, R. C., Rajpurohit, S., Kiratli, O. L. Z., Lowder, D. B., Lemmon, S. G., Petrov, D. A., Chaston, J. M., & SCHMIDT, P. S. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1907787116 · Cited by 145

Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte Genus

Meleshko, O., Martin, M. D., Korneliussen, T. S., Schröck, C., Lamkowski, P., Schmutz, J., Healey, A. L., Piatkowski, B. T., Shaw, A. J., Weston, D. J., et al. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab063 · Cited by 150

Integrase-Deficient Lentiviral Vector as an All-in-One Platform for Highly Efficient CRISPR/Cas9-Mediated Gene Editing

Ortinski, P. I., O’Donovan, B., Dong, X., & Kantor, B. (2017) · Molecular Therapy - Methods & Clinical Development · doi:10.1016/j.omtm.2017.04.002 · Cited by 146

The wild species genome ancestry of domestic chickens

Lawal, R. A., Martin, S. H., Vanmechelen, K., Vereijken, A., Silva, P., Al-Atiyat, R. M., Aljumaah, R. S., Mwacharo, J. M., Wu, D., Zhang, Y., et al. (2020) · BMC Biology · doi:10.1186/s12915-020-0738-1 · Cited by 168

Predicting dynamic cellular protein–RNA interactions by deep learning using in vivo RNA structures

Sun, L., Xu, K., Huang, W., Yang, Y., Li, P., Tang, L., Xiong, T., & Zhang, Q. C. (2021) · Cell Research · doi:10.1038/s41422-021-00476-y · Cited by 145

Comprehensive Genomic Profiling of Neuroendocrine Carcinomas of the Gastrointestinal System

Yachida, S., Totoki, Y., Noë, M., Nakatani, Y., Horie, M., Kawasaki, K., Nakamura, H., Saito-Adachi, M., Suzuki, M., Takai, E., et al. (2021) · Cancer Discovery · doi:10.1158/2159-8290.cd-21-0669 · Cited by 161

Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours

Kukekova, A. V., Johnson, J. L., Xiang, X., Feng, S., Liu, S., Rando, H. M., Kharlamova, A. V., Herbeck, Y., Serdyukova, N. A., Xiong, Z., et al. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0611-6 · Cited by 145

GATK Variant Discovery Pipeline

He, C., & Liu, S. (2024) · BIO-PROTOCOL · doi:10.21769/bioprotoc.5068

Validation and assessment of variant calling pipelines for next-generation sequencing

Pirooznia, M., Kramer, M., Parla, J. S., Goes, F. S., Potash, J. B., McCombie, W. R., & Zandi, P. P. (2014) · Human Genomics · doi:10.1186/1479-7364-8-14 · Cited by 132

Variant Calling from RNA-seq Data Using the GATK Joint Genotyping Workflow

Brouard, J., & Bissonnette, N. (2012) · Methods in molecular biology · doi:10.1007/978-1-0716-2293-3_13 · Cited by 34

xGAP: a python based efficient, modular, extensible and fault tolerant genomic analysis pipeline for variant discovery

Gorla, A., Jew, B., Zhang, L., & Sul, J. H. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btaa1097 · Cited by 2

MapCaller – An integrated and efficient tool for short-read mapping and variant calling using high-throughput sequenced dataPreprint

Lin, H.-N., & Hsu, W. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/783605 · Cited by 6