BEDTools: a flexible suite of utilities for comparing genomic features

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The Human Genome Browser at UCSC

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Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1

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Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements

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Hemimetabolous genomes reveal molecular basis of termite eusociality

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Predicting 3D genome folding from DNA sequence with Akita

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The presence of extra chromosomes leads to genomic instability

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Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment

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Mutational signatures reveal the dynamic interplay of risk factors and cellular processes during liver tumorigenesis

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Molecular Evolution of Early-Onset Prostate Cancer Identifies Molecular Risk Markers and Clinical Trajectories

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FTO mediates LINE1 m 6 A demethylation and chromatin regulation in mESCs and mouse development

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The Sweden Cancerome Analysis Network - Breast (SCAN-B) Initiative: a large-scale multicenter infrastructure towards implementation of breast cancer genomic analyses in the clinical routine

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Negative regulation of ABA signaling by WRKY33 is critical for Arabidopsis immunity towards Botrytis cinerea 2100

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High-quality genome assembly of the silkworm, Bombyx mori

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Hominoid-Specific Transposable Elements and KZFPs Facilitate Human Embryonic Genome Activation and Control Transcription in Naive Human ESCs

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An RNA thermoswitch regulates daytime growth in Arabidopsis

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METTL3-mediated m6A modification is required for cerebellar development

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The evening complex coordinates environmental and endogenous signals in Arabidopsis

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Functional partitioning of transcriptional regulators by patterned charge blocks

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Nm-seq maps 2′-O-methylation sites in human mRNA with base precision

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Bioinformatics-Based Identification of Expanded Repeats: A Non-reference Intronic Pentamer Expansion in RFC1 Causes CANVAS

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Reconstructing de novo silencing of an active plant retrotransposon

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HAL: a hierarchical format for storing and analyzing multiple genome alignments

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A Collinearity-Incorporating Homology Inference Strategy for Connecting Emerging Assemblies in the Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era

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eccDNAs are apoptotic products with high innate immunostimulatory activity

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Dynamic Reorganization of Chromatin Accessibility Signatures during Dedifferentiation of Secretory Precursors into Lgr5+ Intestinal Stem Cells

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Short poly(A) tails are a conserved feature of highly expressed genes

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Potential for primary productivity in a globally-distributed bacterial phototroph

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Transposable elements are the primary source of novelty in primate gene regulationPreprint

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TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools

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NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets

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Open chromatin reveals the functional maize genome

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Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus

Hurgobin, B., Golicz, A. A., Bayer, P. E., Chan, C. K., Tirnaz, S., Dolatabadian, A., Schießl, S., Samans, B., Montenegro, J. D., Parkin, I. A. P., et al. (2017) · Plant Biotechnology Journal · doi:10.1111/pbi.12867 · Cited by 291

The Implication of Early Chromatin Changes in X Chromosome Inactivation

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The stepwise assembly of the neonatal virome is modulated by breastfeeding

Liang, G., Zhao, C., Zhang, H., Mattei, L. M., Sherrill-Mix, S. A., Bittinger, K. L., Kessler, L. R., Wu, G. D., Baldassano, R. N., DeRusso, P. A., et al. (2020) · Nature · doi:10.1038/s41586-020-2192-1 · Cited by 283

Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis

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Stalled developmental programs at the root of pediatric brain tumors

Jessa, S., Blanchet-Cohen, A., Krug, B., Vladoiu, M. C., Coutelier, M., Faury, D., Poreau, B., Jay, N. D., Hébert, S., Monlong, J., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0531-7 · Cited by 301

Rare driver mutations in head and neck squamous cell carcinomas converge on NOTCH signaling

Loganathan, S. K., Schleicher, K., Malik, A., Quevedo, R., Langille, E. R., Teng, K., Oh, R. H., Rathod, B., Tsai, R., Samavarchi‐Tehrani, P., et al. (2020) · Science · doi:10.1126/science.aax0902 · Cited by 285

Precursors for Nonlymphoid-Tissue Treg Cells Reside in Secondary Lymphoid Organs and Are Programmed by the Transcription Factor BATF

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DNA Breaks and End Resection Measured Genome-wide by End Sequencing

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Evaluation of Algorithm Performance in ChIP-Seq Peak Detection

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Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy

Campanaro, S., Treu, L., Kougias, P., Francisci, D. D., Valle, G., & Angelidaki, İ. (2016) · Biotechnology for Biofuels · doi:10.1186/s13068-016-0441-1 · Cited by 293

Global RNA recognition patterns of post‐transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo

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The histone H3.3K36M mutation reprograms the epigenome of chondroblastomas

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Convergent regulatory evolution and loss of flight in paleognathous birds

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High-resolution, strand-specific R-loop mapping via S9.6-based DNA–RNA immunoprecipitation and high-throughput sequencing

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Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut

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High-resolution interrogation of functional elements in the noncoding genome

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Decoding the epitranscriptional landscape from native RNA sequences

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Genome-wide mapping and assembly of structural variant breakpoints in the mouse genomePreprint

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Predicting mRNA Abundance Directly from Genomic Sequence Using Deep Convolutional Neural Networks

Agarwal, V., & Shendure, J. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107663 · Cited by 243

DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of enhancers

de Almeida, B. P., Reiter, F., Pagani, M., & Stark, A. (2021) · doi:10.1101/2021.10.05.463203 · Cited by 284

The loss of RNA N6-adenosine methyltransferase Mettl14 in tumor-associated macrophages promotes CD8+ T cell dysfunction and tumor growth

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DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers

de Almeida, B. P., Reiter, F., Pagani, M., & Stark, A. (2022) · Nature Genetics · doi:10.1038/s41588-022-01048-5 · Cited by 283

Genome-wide DNA-methylation landscape defines specialization of regulatory T cells in tissues

Delacher, M., Imbusch, C. D., Weichenhan, D., Breiling, A., Hotz-Wagenblatt, A., Träger, U., Hofer, A.-C., Kägebein, D., Wang, Q., Frauhammer, F., et al. (2017) · Nature Immunology · doi:10.1038/ni.3799 · Cited by 282

Weight Loss after Gastric Bypass Surgery in Human Obesity Remodels Promoter Methylation

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Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes

Miguel-Escalada, I., Bonàs‐Guarch, S., Cebola, I., Ponsa-Cobas, J., Mendieta-Esteban, J., Atla, G., Javierre, B. M., Rolando, D., Farabella, I., Morgan, C. C., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0457-0 · Cited by 269

Genome-wide map of regulatory interactions in the human genome

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Epigenome-wide differences in pathology-free regions of multiple sclerosis–affected brains

Huynh, J. L., Garg, P., Thin, T. H., Yoo, S., Dutta, R., Trapp, B. D., Haroutunian, V. H., Zhu, J., Donovan, M. J., Sharp, A. J., et al. (2013) · Nature Neuroscience · doi:10.1038/nn.3588 · Cited by 282

Exome sequencing identifies NBEAL2 as the causative gene for gray platelet syndrome

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Advanced Applications of RNA Sequencing and Challenges

Han, Y., Gao, S., Muegge, K., Zhang, W., & Zhou, B. (2015) · Bioinformatics and Biology Insights · doi:10.4137/bbi.s28991 · Cited by 303

Rapid evolutionary response to a transmissible cancer in Tasmanian devils

Epstein, B., Jones, M. E., Hamede, R., Hendricks, S. A., McCallum, H. I., Murchison, E. P., Schönfeld, B., Wiench, C., Hohenlohe, P. A., & Storfer, A. T. (2016) · Nature Communications · doi:10.1038/ncomms12684 · Cited by 281

The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants

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De Novo Mutations in MLL Cause Wiedemann-Steiner Syndrome

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Rapid magnetic isolation of extracellular vesicles via lipid-based nanoprobes

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Genome hypermobility by lateral transduction

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Cisplatin-induced immune modulation in ovarian cancer mouse models with distinct inflammation profiles

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Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED

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Transcription factors interact with RNA to regulate genes

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Prophage-mediated defence against viral attack and viral counter-defence

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Epigenetic control of innate and adaptive immune memory

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Adaptive introgression enables evolutionary rescue from extreme environmental pollution

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Resetting histone modifications during human parental-to-zygotic transition

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Single-Cell Multiomics Sequencing Reveals Prevalent Genomic Alterations in Tumor Stromal Cells of Human Colorectal Cancer

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Reverse-transcribed SARS-CoV-2 RNA can integrate into the genome of cultured human cells and can be expressed in patient-derived tissues

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Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression

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Static and Evolving Norovirus Genotypes: Implications for Epidemiology and Immunity

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The impact of short tandem repeat variation on gene expression

Feupe, S. F., Margoliash, J., Wang, C., Saini, S., Yanicky, R., Shleizer-Burko, S., Goren, A., & Gymrek, M. (2019) · Nature Genetics · doi:10.1038/s41588-019-0521-9 · Cited by 279

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

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RNA Sequencing of Laser-Capture Microdissected Compartments of the Maize Kernel Identifies Regulatory Modules Associated with Endosperm Cell Differentiation

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Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa , document novel gene space of aus and indica

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Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data

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TERRA RNA Antagonizes ATRX and Protects Telomeres

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The SS18-SSX Fusion Oncoprotein Hijacks BAF Complex Targeting and Function to Drive Synovial Sarcoma

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The histone chaperone CAF-1 safeguards somatic cell identity

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An interactive environment for agile analysis and visualization of ChIP-sequencing data

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HCV-Induced Epigenetic Changes Associated With Liver Cancer Risk Persist After Sustained Virologic Response

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The aryl hydrocarbon receptor AhR links atopic dermatitis and air pollution via induction of the neurotrophic factor artemin

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Evaluation of Hybridization Capture Versus Amplicon‐Based Methods for Whole‐Exome Sequencing

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The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres

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Analysis of Circulating Cell-Free DNA Identifies Multiclonal Heterogeneity of BRCA2 Reversion Mutations Associated with Resistance to PARP Inhibitors

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MYRF is a membrane-associated transcription factor that autoproteolytically cleaves to directly activate myelin genes

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Ancestral Origins and Genetic History of Tibetan Highlanders

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Identification of the m6Am Methyltransferase PCIF1 Reveals the Location and Functions of m6Am in the Transcriptome

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Whole exome sequencing study identifies novel rare and common Alzheimer’s-Associated variants involved in immune response and transcriptional regulation

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Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development

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Peroxisome Proliferator-Activated Receptor γ and C/EBPα Synergistically Activate Key Metabolic Adipocyte Genes by Assisted Loading

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Antigen Identification for Orphan T Cell Receptors Expressed on Tumor-Infiltrating Lymphocytes

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The AREB1 Transcription Factor Influences Histone Acetylation to Regulate Drought Responses and Tolerance in Populus trichocarpa

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BEDTools: The Swiss‐Army Tool for Genome Feature Analysis

Quinlan, A. R. (2014) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi1112s47 · Cited by 2,286

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

Dale, R., Pedersen, B. S., & Quinlan, A. R. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr539 · Cited by 507

BEDOPS: high-performance genomic feature operations

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bedtools: interval arithmetic for genomes

Quinlan, A. (2020) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.3834603

Bedtoolsr: An R package for genomic data analysis and manipulation.

Phanstiel, D. H., Patwardhan, M. N., Davis, E. S., & Wenger, C. D. (2024) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/sbzm-zc31