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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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Integrating common and rare genetic variation in diverse human populations

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Whole-Genome Sequencing Reveals Elevated Tumor Mutational Burden and Initiating Driver Mutations in African Men with Treatment-Naïve, High-Risk Prostate Cancer

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Single nucleus sequencing reveals evidence of inter-nucleus recombination in arbuscular mycorrhizal fungi

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Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell type

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Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential

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Rare variant analysis of 4241 pulmonary arterial hypertension cases from an international consortium implicates FBLN2, PDGFD, and rare de novo variants in PAH

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Somatic variants in diverse genes leads to a spectrum of focal cortical malformations

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An Immunogenic Model of KRAS-Mutant Lung Cancer Enables Evaluation of Targeted Therapy and Immunotherapy Combinations

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Clinical isolates of Candida auris with enhanced adherence and biofilm formation due to genomic amplification of ALS4

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DNA mismatch repair preferentially protects genes from mutationPreprint

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Genetic landscape of sporadic vestibular schwannoma

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Genomic data recover previously undetectable fragmentation effects in an endangered amphibian

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TRPV4 and KRAS and FGFR1 gain-of-function mutations drive giant cell lesions of the jaw

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Phylogenomic delineation of Physcomitrium (Bryophyta: Funariaceae) based on targeted sequencing of nuclear exons and their flanking regions rejects the retention of Physcomitrella, Physcomitridium and Aphanorrhegma

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A polyploid admixed origin of beer yeasts derived from European and Asian wine populations

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Signatures of TOP1 transcription-associated mutagenesis in cancer and germline

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A Fast, Reproducible, High-throughput Variant Calling Workflow for Population Genomics

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A novel POLE mutation associated with cancers of colon, pancreas, ovaries and small intestine

Hansen, M. F., Johansen, J. A., Bjørnevoll, I., Sylvander, A. E., Steinsbekk, K. S., Sætrom, P., Sandvik, A. K., Drabløs, F., & Sjursen, W. (2015) · Familial Cancer · doi:10.1007/s10689-015-9803-2 · Cited by 83

Pseudogenization and Resurrection of a Speciation Gene

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Congenital Myasthenic Syndrome Type 19 Is Caused by Mutations in COL13A1, Encoding the Atypical Non-fibrillar Collagen Type XIII α1 Chain

Logan, C. V., Cossins, J., Cruz, P. M. R., Parry, D. A., Maxwell, S., Martínez‐Martínez, P., Riepsaame, J., Abdelhamed, Z. A., Lake, A. V. R., Moran, M., et al. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.10.017 · Cited by 82

The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology

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The molecular genetic basis of herbivory between butterflies and their host plants

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The Mitogenome of Norway Spruce and a Reappraisal of Mitochondrial Recombination in Plants

Sullivan, A. R., Eldfjell, Y., Schiffthaler, B., Delhomme, N., Asp, T., Hebelstrup, K. H., Keech, O., Öberg, L., Møller, I. M., Arvestad, L., et al. (2019) · Genome Biology and Evolution · doi:10.1093/gbe/evz263 · Cited by 80

Temporal evolution of cellular heterogeneity during the progression to advanced AR-negative prostate cancer

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Co-existence of BRAF and NRAS driver mutations in the same melanoma cells results in heterogeneity of targeted therapy resistance

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Candida auris Invasive Infections during a COVID-19 Case Surge

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Clinical utility of genomic analysis in adults with idiopathic liver disease

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Haploid selection within a single ejaculate increases offspring fitness

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Hypoxia-inducible factor-1α plays roles in Epstein-Barr virus’s natural life cycle and tumorigenesis by inducing lytic infection through direct binding to the immediate-early BZLF1 gene promoter

Kraus, R. J., Yu, X., Cordes, B.-L. A., Sathiamoorthi, S., Iempridee, T., Nawandar, D. M., Ma, S., Romero-Masters, J. C., McChesney, K., Lin, Z. N., et al. (2017) · PLoS Pathogens · doi:10.1371/journal.ppat.1006404 · Cited by 79

Hunt for the tipping point during endocrine resistance process in breast cancer by dynamic network biomarkers

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Genome‐wide association study identified novel candidate loci affecting wood formation in Norway spruce

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Exome Sequencing Identifies Genes and Gene Sets Contributing to Severe Childhood Obesity, Linking PHIP Variants to Repressed POMC Transcription

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IDH2 stabilizes HIF‐1α‐induced metabolic reprogramming and promotes chemoresistance in urothelial cancer

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Comparative genome analysis of Mycoplasma pneumoniae

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Population genomic analysis uncovers African and European admixture in Drosophila melanogaster populations from the south‐eastern United States and Caribbean Islands

Kao, J. Y., Zubair, A., Salomon, M. P., Nuzhdin, S. V., & Campo, D. (2015) · Molecular Ecology · doi:10.1111/mec.13137 · Cited by 77

Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage

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The genotype–phenotype landscape of familial amyotrophic lateral sclerosis in Australia

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Breeding history and candidate genes responsible for black skin of Xichuan black-bone chicken

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The pan-genome of Aspergillus fumigatus provides a high-resolution view of its population structure revealing high levels of lineage-specific diversity driven by recombination

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RIG: Recalibration and Interrelation of Genomic Sequence Data with the GATK

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Crop wild relative populations of Beta vulgaris allow direct mapping of agronomically important genes

Capistrano-Gossmann, G. G., Ries, D., Holtgräwe, D., Minoche, A. E., Kraft, T., Frerichmann, S. L. M., Sörensen, T. R., Dohm, J. C., González, I., Schilhabel, M. B., et al. (2017) · Nature Communications · doi:10.1038/ncomms15708 · Cited by 80

Pervasive gene conversion in chromosomal inversion heterozygotes

Korunes, K. L., & Noor, M. A. F. (2018) · Molecular Ecology · doi:10.1111/mec.14921 · Cited by 79

Mutations in Chromatin Modifier and Ephrin Signaling Genes in Vein of Galen Malformation

Durán, D., Zeng, X. Q., Jin, S. C., Choi, J., Nelson-Williams, C. J., Yatsula, B. A., Gaillard, J. R., Furey, C. G., Lu, Q., Timberlake, A. T., et al. (2018) · Neuron · doi:10.1016/j.neuron.2018.11.041 · Cited by 78

High-resolution QTL mapping in Tetranychus urticae reveals acaricide-specific responses and common target-site resistance after selection by different METI-I acaricides

Snoeck, S., Kurlovs, A. H., Bajda, S., Feyereisen, R., Greenhalgh, R., Perez, E. V., Kosterlitz, O., Dermauw, W., Clark, R. M., & Leeuwen, T. V. (2019) · Insect Biochemistry and Molecular Biology · doi:10.1016/j.ibmb.2019.04.011 · Cited by 79

The Lupus Susceptibility Locus Sgp3 Encodes the Suppressor of Endogenous Retrovirus Expression SNERV

Treger, R. S., Pope, S. D., Kong, Y., Tokuyama, M., Taura, M., & Iwasaki, A. (2019) · Immunity · doi:10.1016/j.immuni.2018.12.022 · Cited by 74

Genome Editing in Patient iPSCs Corrects the Most Prevalent USH2A Mutations and Reveals Intriguing Mutant mRNA Expression Profiles

Sanjurjo-Soriano, C., Erkilic, N., Baux, D., Mamaeva, D. V., Hamel, C., Meunier, I., Roux, A., & Kalatzis, V. (2019) · Molecular Therapy — Methods & Clinical Development · doi:10.1016/j.omtm.2019.11.016 · Cited by 82

Hormonal Suppression of Stem Cells Inhibits Symmetric Cell Division and Gastric Tumorigenesis

Chang, W., Wang, H., Kim, W., Liu, Y., Deng, H., Liu, H., Jiang, Z., Niu, Z., Sheng, W., Companioni, O., et al. (2020) · Cell stem cell · doi:10.1016/j.stem.2020.01.020 · Cited by 79

Genetic characterization of a unique neuroendocrine transdifferentiation prostate circulating tumor cell-derived eXplant model

Faugeroux, V., Pailler, E., Oulhen, M., Déas, O., Brullé, L., Hervieu, C., Marty, V., Alexandrova, K., Andree, K., Stoecklein, N. H., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15426-2 · Cited by 87

Complex evolution of novel red floral color inPetunia

Berardi, A. E., Esfeld, K., Jäggi, L., Mandel, T., Cannarozzi, G. M., & Kuhlemeier, C. J. (2021) · The Plant Cell · doi:10.1093/plcell/koab114 · Cited by 79

Genetic Defects in DNAH2 Underlie Male Infertility With Multiple Morphological Abnormalities of the Sperm Flagella in Humans and Mice

Hwang, J. Y., Nawaz, S., Choi, J., Wang, H., Hussain, S., Nawaz, M., López‐Giráldez, F., Jeong, K., Dong, W., Oh, J., et al. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.662903 · Cited by 82

Second-Hit, Postzygotic PMVK and MVD Mutations in Linear Porokeratosis

Atzmony, L., Khan, H., Lim, Y. H., Paller, A. S., Levinsohn, J. L., Holland, K. E., Mirza, F. N., Yin, E. S., Ko, C. J., Leventhal, J. S., et al. (2019) · JAMA Dermatology · doi:10.1001/jamadermatol.2019.0016 · Cited by 79

Covalent Plasmodium falciparum-selective proteasome inhibitors exhibit a low propensity for generating resistance in vitro and synergize with multiple antimalarial agents

Stokes, B. H., Yoo, E., Murithi, J. M., Luth, M. R., Afanasyev, P., da Fonseca, P. C. A., Winzeler, E. A., Ng, C. L., Bogyo, M. S., & Fidock, D. A. (2019) · PLoS Pathogens · doi:10.1371/journal.ppat.1007722 · Cited by 83

Genomic profiling of malignant phyllodes tumors reveals aberrations in FGFR1 and PI-3 kinase/RAS signaling pathways and provides insights into intratumoral heterogeneity

Liu, S.-Y., Joseph, N. M., Ravindranathan, A., Stohr, B. A., Greenland, N., Vohra, P., Hosfield, E. M., Yeh, I., Talevich, E., Onodera, C. S., et al. (2016) · Modern Pathology · doi:10.1038/modpathol.2016.97 · Cited by 78

Frequent GNAQ and GNA14 Mutations in Hepatic Small Vessel Neoplasm

Joseph, N. M., Brunt, E. M., Marginean, C. E., Nalbantoglu, I., Snover, D. C., Thung, S. N., Yeh, M. M., Umetsu, S. E., Ferrell, L. D., & Gill, R. M. (2018) · The American Journal of Surgical Pathology · doi:10.1097/pas.0000000000001110 · Cited by 78

Using single nucleotide variations in single-cell RNA-seq to identify subpopulations and genotype-phenotype linkage

Poirion, O., Zhu, X., Ching, T. H., & Garmire, L. X. (2018) · Nature Communications · doi:10.1038/s41467-018-07170-5 · Cited by 79

An integrated molecular profile of endometrioid ovarian cancer

Pierson, W. E., Peters, P., Chang, M. T., Chen, L.-M., Quigley, D. A., Ashworth, A., & Chapman, J. S. (2020) · Gynecologic Oncology · doi:10.1016/j.ygyno.2020.02.011 · Cited by 78

Natural Selection Shapes Variation in Genome-wide Recombination Rate in Drosophila pseudoobscura

Samuk, K., Manzano‐Winkler, B., Ritz, K. R., & Noor, M. A. F. (2020) · Current Biology · doi:10.1016/j.cub.2020.03.053 · Cited by 78

Comparative analysis of 7 short-read sequencing platforms using the Korean Reference Genome: MGI and Illumina sequencing benchmark for whole-genome sequencing

Kim, H., Jeon, S., Chung, O., Jun, J. H., Kim, H.-S., Blažytė, A., Lee, H.-Y., Yu, Y., Cho, Y. S., Bolser, D. M., et al. (2021) · GigaScience · doi:10.1093/gigascience/giab014 · Cited by 78

Differences in the genetic architecture of common and rare variants in childhood, persistent and late-diagnosed attention-deficit hyperactivity disorder

Rajagopal, V. M., Duan, J., Vilar‐Ribó, L., Grove, J., Zayats, T., Ramos‐Quiroga, J. A., Satterstrom, F. K., Artigas, M. S., Bybjerg‐Grauholm, J., Bækvad‐Hansen, M., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01143-7 · Cited by 81

Clinical genetic testing using a custom-designed steroid-resistant nephrotic syndrome gene panel: analysis and recommendations

Sen, E. S., Dean, P., Yarram-Smith, L., Bierżyńska, A., Woodward, G., Buxton, C., Dennis, G., Welsh, G. I., Williams, M., & Saleem, M. A. (2017) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2017-104811 · Cited by 78

Core Genome Multilocus Sequence Typing and Single Nucleotide Polymorphism Analysis in the Epidemiology of Brucella melitensis Infections

Janowicz, A., Massis, F. D., Ancora, M., Cammà, C., Patavino, C., Battisti, A., Prior, K., Harmsen, D., Scholz, H. C., Zilli, K., et al. (2018) · Journal of Clinical Microbiology · doi:10.1128/jcm.00517-18 · Cited by 78

The Evolutionary History of Nebraska Deer Mice: Local Adaptation in the Face of Strong Gene Flow

Pfeifer, S. P., Laurent, S., Sousa, V. C., Linnen, C. R., Foll, M., Excoffier, L., Hoekstra, H. E., & Jensen, J. D. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy004 · Cited by 75

Comparison of whole genome amplification techniques for human single cell exome sequencing

Borgström, E., Paterlini, M., Mold, J. E., Frisen, J., & Lundeberg, J. (2017) · PLOS ONE · doi:10.1371/journal.pone.0171566 · Cited by 77

DNA capture reveals transoceanic gene flow in endangered river sharks

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Extremely low genetic diversity across mangrove taxa reflects past sea level changes and hints at poor future responses

Guo, Z., Li, X., He, Z., Yang, Y., Wang, W., Zhong, C., Greenberg, A. J., Wu, C., Duke, N. C., & Shi, S. (2017) · Global Change Biology · doi:10.1111/gcb.13968 · Cited by 79

Bioinformatics for precision oncology

Singer, J., Irmisch, A., Ruscheweyh, H., Singer, F., Toussaint, N. C., Levesque, M. P., Stekhoven, D. J., & Beerenwinkel, N. (2017) · Briefings in Bioinformatics · doi:10.1093/bib/bbx143 · Cited by 81

Genetic selection of athletic success in sport-hunting dogs

Kim, J., Williams, F. J., Dreger, D. L., Plassais, J., Davis, B. W., Parker, H. G., & Ostrander, E. A. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1800455115 · Cited by 79

Similarities and differences between variants called with human reference genome HG19 or HG38

Pan, B., Kusko, R. L., Xiao, W., Zheng, Y., Liu, Z., Xiao, C., Sakkiah, S., Guo, W., Gong, P., Zhang, C., et al. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-2620-0 · Cited by 77

De Novo Genome Sequence Assembly of Dwarf Coconut (Cocos nucifera L. ‘Catigan Green Dwarf’) Provides Insights into Genomic Variation Between Coconut Types and Related Palm Species

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APOL1 C-Terminal Variants May Trigger Kidney Disease through Interference with APOL3 Control of Actomyosin

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