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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ggplot2: Elegant Graphics for Data Analysis

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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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Hidden Complexity of Yeast Adaptation under Simple Evolutionary Conditions

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Whole-Genome Sequencing of the NARO World Rice Core Collection (WRC) as the Basis for Diversity and Association Studies

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Comprehensive and Functional Analysis of Horizontal Gene Transfer Events in Diatoms

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Sensitive, Highly Multiplexed Sequencing of Microhaplotypes From the Plasmodium falciparum Heterozygome

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The genomic landscape across 474 surgically accessible epileptogenic human brain lesions

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Ancient homomorphy of molluscan sex chromosomes sustained by reversible sex-biased genes and sex determiner translocation

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Passage-dependent accumulation of somatic mutations in mesenchymal stromal cells during in vitro culture revealed by whole genome sequencing

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Ploidy Variation in Kluyveromyces marxianus Separates Dairy and Non-dairy Isolates

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Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial

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Mitochondrial DNA variants modulate N-formylmethionine, proteostasis and risk of late-onset human diseases

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Rare De Novo Missense Variants in RNA Helicase DDX6 Cause Intellectual Disability and Dysmorphic Features and Lead to P-Body Defects and RNA Dysregulation

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Model‐based genotype and ancestry estimation for potential hybrids with mixed‐ploidy

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Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs ( Occidozyga laevis )

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Patient similarity network of newly diagnosed multiple myeloma identifies patient subgroups with distinct genetic features and clinical implications

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Thrice out of Asia and the adaptive radiation of the western honey bee

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Epigenetic regulator genes direct lineage switching in MLL/AF4 leukemia

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Distinct Mechanisms of Mismatch Repair Deficiency Delineate Two Modes of Response to PD-1 Immunotherapy in Endometrial Carcinoma

Chow, R. D.-W., Michaels, T., Bellone, S., Hartwich, T. M. P., Bonazzoli, E., Iwasaki, A., Song, E., & Santin, A. D. (2022) · Cancer Discovery · doi:10.1158/2159-8290.cd-22-0686 · Cited by 78

Genome-wide association study using whole-genome sequencing identifies risk loci for Parkinson’s disease in Chinese population

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A 3.4-kb Copy-Number Deletion near EPAS1 Is Significantly Enriched in High-Altitude Tibetans but Absent from the Denisovan Sequence

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Characterisation of the British honey bee metagenome

Regan, T. W., Barnett, M. W., Laetsch, D. R., Bush, S. J., Wragg, D., Budge, G. E., Highet, F., Dainat, B., de Miranda, J. R., Watson, M., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-07426-0 · Cited by 72

Patterns of Z chromosome divergence among Heliconius species highlight the importance of historical demography

Belleghem, S. M. V., Baquero, M., Papa, R., Salazar, C. A., McMillan, W. O., Counterman, B. A., Jiggins, C. D., & Martin, S. H. (2018) · Molecular Ecology · doi:10.1111/mec.14560 · Cited by 70

Acquired amphotericin B resistance leads to fitness trade-offs that can be mitigated by compensatory evolution in Candida auris

Carolus, H., Sofras, D., Boccarella, G., Sephton-Clark, P., Biriukov, V., Cauldron, N. C., Lobo Romero, C., Vergauwen, R., Yazdani, S., Pierson, S., et al. (2024) · Nature Microbiology · doi:10.1038/s41564-024-01854-z · Cited by 72

Identification of donor microbe species that colonize and persist long term in the recipient after fecal transplant for recurrent Clostridium difficile

Kumar, R., Yi, N., Zhi, D., Eipers, P. G., Goldsmith, K. T., Dixon, P. B., Crossman, D. K., Crowley, M. R., Lefkowitz, E. J., Rodriguez, J. M., et al. (2017) · npj Biofilms and Microbiomes · doi:10.1038/s41522-017-0020-7 · Cited by 72

Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus)

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DICER1 mutations are frequent in müllerian adenosarcomas and are independent of rhabdomyosarcomatous differentiation

Bean, G. R., Anderson, J. A., Sangoi, A. R., Krings, G., & Garg, K. (2018) · Modern Pathology · doi:10.1038/s41379-018-0132-5 · Cited by 71

The Mutationathon highlights the importance of reaching standardization in estimates of pedigree-based germline mutation rates

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Ultraviolet radiation shapes dendritic cell leukaemia transformation in the skin

Griffin, G. K., Booth, C. A. G., Togami, K., Chung, S. S., Ssozi, D., Verga, J. A., Bouyssou, J., Lee, Y. S., Shanmugam, V., Hornick, J. L., et al. (2023) · Nature · doi:10.1038/s41586-023-06156-8 · Cited by 70

Exome sequencing of 20,979 individuals with epilepsy reveals shared and distinct ultra-rare genetic risk across disorder subtypes

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Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2

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De Novo Mutations in PPP3CA Cause Severe Neurodevelopmental Disease with Seizures

Myers, C. T., Stong, N., Mountier, E. I., Helbig, K. L., Freytag, S., Sullivan, J. E., Zeev, B. B., Nissenkorn, A., Tzadok, M., Heimer, G., et al. (2017) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2017.08.013 · Cited by 72

Genome analysis and knowledge-driven variant interpretation with TGex

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Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D

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A systematic comparison of pharmacogene star allele calling bioinformatics algorithms: a focus on CYP2D6 genotyping

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Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility

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Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis

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Polyclonal-to-monoclonal transition in colorectal precancerous evolution

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Genetic and epigenetic variation in 5S ribosomal RNA genes reveals genome dynamics in Arabidopsis thaliana

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Identification of high-risk human papillomavirus and Rb/E2F pathway genomic alterations in mutually exclusive subsets of colorectal neuroendocrine carcinoma

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Somatic mutations substantially increase the per-generation mutation rate in the conifer Picea sitchensis

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Coding and noncoding drivers of mantle cell lymphoma identified through exome and genome sequencing

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Entire plastid phylogeny of the carrot genus (Daucus, Apiaceae): Concordance with nuclear data and mitochondrial and nuclear DNA insertions to the plastid

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Characterizing temporal genomic heterogeneity in pediatric high-grade gliomas

Salloum, R., McConechy, M. K., Mikael, L. G., Fuller, C. E., Drissi, R., DeWire, M. D., Nikbakht, H., Jay, N. D., Yang, X., Boué, D. R., et al. (2017) · Acta Neuropathologica Communications · doi:10.1186/s40478-017-0479-8 · Cited by 71

De novo assembly of white poplar genome and genetic diversity of white poplar population in Irtysh River basin in China

Liu, Y., Wang, X., & Zeng, Q. (2019) · Science China Life Sciences · doi:10.1007/s11427-018-9455-2 · Cited by 69

Loss of ADAMTS19 causes progressive non-syndromic heart valve disease

Wünnemann, F., Ta‐Shma, A., Preuß, C., Leclerc, S., Vliet, P. P. V., Oneglia, A., Thibeault, M., Nordquist, E., Lincoln, J., Scharfenberg, F., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0536-2 · Cited by 72

The Medical Genome Reference Bank contains whole genome and phenotype data of 2570 healthy elderly

Pinese, M., Lacaze, P., Rath, E. M., Stone, A., Brion, M.-J., Ameur, A., Nagpal, S., Puttick, C., Husson, S., Degrave, D., et al. (2020) · Nature Communications · doi:10.1038/s41467-019-14079-0 · Cited by 70

Plasma cell-free RNA profiling distinguishes cancers from pre-malignant conditions in solid and hematologic malignancies

Roskams-Hieter, B., Kim, H. J., Anur, P., Wagner, J. T., Callahan, R. L., Spiliotopoulos, E., Kirschbaum, C. W., Çivitçi, F., Spellman, P. T., Thompson, R. F., et al. (2022) · npj Precision Oncology · doi:10.1038/s41698-022-00270-y · Cited by 72

Selection against admixture and gene regulatory divergence in a long-term primate field study

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Whole-genome doubling drives oncogenic loss of chromatin segregation

Lambuta, R. A., Nanni, L., Liu, Y., Díaz-Miyar, J., Iyer, A., Tavernari, D., Katanayeva, N., Ciriello, G., & Oricchio, E. (2023) · Nature · doi:10.1038/s41586-023-05794-2 · Cited by 74

Mapping of Craniofacial Traits in Outbred Mice Identifies Major Developmental Genes Involved in Shape Determination

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Suppressors and activators of JAK-STAT signaling at diagnosis and relapse of acute lymphoblastic leukemia in Down syndrome

Schwartzman, O., Savino, A. M., Gombert, M., Palmi, C., Cario, G., Schrappe, M., Eckert, C., von Stackelberg, A., Huang, J.-Y., Hameiri-Grossman, M., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1702489114 · Cited by 69

Evolution of novel mimicry rings facilitated by adaptive introgression in tropical butterflies

Enciso‐Romero, J., Pardo‐Díaz, C., Martin, S. H., Arias, C. F., Linares, M., McMillan, W. O., Jiggins, C. D., & Salazar, C. A. (2017) · Molecular Ecology · doi:10.1111/mec.14277 · Cited by 66

Uncommon Filaggrin Variants Are Associated with Persistent Atopic Dermatitis in African Americans

Margolis, D. J., Mitra, N., Gochnauer, H. R., Wubbenhorst, B. S., D'Andrea, K. P., Kraya, A., Hoffstad, O., Gupta, J., Kim, B., Yan, A. C., et al. (2018) · Journal of Investigative Dermatology · doi:10.1016/j.jid.2018.01.029 · Cited by 72

A recurrent point mutation in PRKCA is a hallmark of chordoid gliomas

Rosenberg, S., Simeonova, I., Bielle, F., Verreault, M., Bance, B., Roux, I. L., Daniau, M., Nadaradjane, A. A., Gleize, V., Paris, S., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04622-w · Cited by 68

The Sustained Induction of c-MYC Drives Nab-Paclitaxel Resistance in Primary Pancreatic Ductal Carcinoma Cells

Parasido, E., Avetian, G. S., Naeem, A., Graham, G. T., Pishvaian, M. J., Glasgow, E. F., Mudambi, S., Lee, Y., Ihemelandu, C. U., Choudhry, M. U., et al. (2019) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-19-0191 · Cited by 68

Comprehensive analysis of cutaneous and uveal melanoma liver metastases

Hoefsmit, E. P., Rozeman, E. A., Van, T. M., Dimitriadis, P., Krijgsman, O., Conway, J. W., da Silva, I. P., van der Wal, J. E., Ketelaars, S. L. C., Bresser, K., et al. (2020) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2020-001501 · Cited by 69

Resistance to pirimiphos-methyl in West African Anopheles is spreading via duplication and introgression of the Ace1 locus

Grau‐Bové, X., Lucas, E. R., Pipini, D., Rippon, E. J., Hof, A. E. V., Edi, C., Dadzie, S., Egyir-Yawson, A., Essandoh, J., Chabi, J., et al. (2021) · PLoS Genetics · doi:10.1371/journal.pgen.1009253 · Cited by 63

Use of Whole-Genome Sequencing for Mitochondrial Disease Diagnosis

Davis, R. L., Kumar, K. R., Puttick, C., Liang, C., Ahmad, K. E., Edema‐Hildebrand, F., Park, J., Minoche, A. E., Gayevskiy, V., Mallawaarachchi, A. C., et al. (2022) · Neurology · doi:10.1212/wnl.0000000000200745 · Cited by 69

Widespread somatic L1 retrotransposition in normal colorectal epithelium

Nam, C. H., Youk, J., Kim, J. Y., Lim, J., Park, J. W., Oh, S. A., Lee, H. J., Won, H., Won, H., Lee, D.-S., et al. (2023) · Nature · doi:10.1038/s41586-023-06046-z · Cited by 71

Constitutive activation of DIA1 (DIAPH1) via C‐terminal truncation causes human sensorineural hearing loss

Ueyama, T., Ninoyu, Y., Nishio, S., Miyoshi, T., Torii, H., Nishimura, K., Sugahara, K., Sakata, H., Thumkeo, D., Sakaguchi, H., et al. (2016) · EMBO Molecular Medicine · doi:10.15252/emmm.201606609 · Cited by 69

Cis- and Trans-regulatory Effects on Gene Expression in a Natural Population of Drosophila melanogaster

Osada, N., Miyagi, R., & Takahashi, A. (2017) · Genetics · doi:10.1534/genetics.117.201459 · Cited by 70

On the path to extinction: Inbreeding and admixture in a declining grey wolf population

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Avian influenza H9N2 subtype in Ghana: virus characterization and evidence of co-infection

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Somatic inactivating PTPRJ mutations and dysregulated pathways identified in canine malignant melanoma by integrated comparative genomic analysis

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Melanocytic tumors with MAP3K8 fusions: report of 33 cases with morphological-genetic correlations

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Branched evolution and genomic intratumor heterogeneity in the pathogenesis of cutaneous T-cell lymphoma

Iyer, A., Hennessey, D., O’Keefe, S. L., Patterson, J., Wang, W., Wong, G. K., & Gniadecki, R. (2020) · Blood Advances · doi:10.1182/bloodadvances.2020001441 · Cited by 70

Molecular autopsy by trio exome sequencing (ES) and postmortem examination in fetuses and neonates with prenatally identified structural anomalies

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Recommendations for performance optimizations when using GATK3.8 and GATK4

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Induced pluripotent stem cell modelling of HLHS underlines the contribution of dysfunctional NOTCH signalling to impaired cardiogenesis

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Blacklisting variants common in private cohorts but not in public databases optimizes human exome analysis

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Genetic Polymorphisms in the Long Noncoding RNA MIR2052HG Offer a Pharmacogenomic Basis for the Response of Breast Cancer Patients to Aromatase Inhibitor Therapy

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