BEDTools: a flexible suite of utilities for comparing genomic features

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

Improved tools for biological sequence comparison.

Pearson, W. R., & Lipman, D. J. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.8.2444 · Cited by 11,227

The Human Genome Browser at UCSC

Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D. (2002) · Genome Research · doi:10.1101/gr.229102 · Cited by 10,400

Galaxy: a platform for interactive large-scale genome analysis.Preprint

Giardine, B., Riemer, C., Hardison, R., Burhans, R. C., Elnitski, L., Shah, P., Zhang, Y., Blankenberg, D., Albert, I., Taylor, J., et al. (2005) · Genome Research · doi:10.1101/gr.4086505 · Cited by 2,217

The variation and evolution of complete human centromeres

Logsdon, G. A., Rozanski, A. N., Ryabov, F., Potapova, T., Shepelev, V. A., Catacchio, C. R., Porubskỳ, D., Mao, Y., Yoo, D., Rautiainen, M., et al. (2024) · Nature · doi:10.1038/s41586-024-07278-3 · Cited by 207

Efficient site-specific integration of large genes in mammalian cells via continuously evolved recombinases and prime editing

Pandey, S., Gao, X. D., Krasnow, N. A., McElroy, A. N., Tao, Y., Duby, J. E., Steinbeck, B. J., McCreary, J., Pierce, S. E., Tolar, J., et al. (2024) · Nature Biomedical Engineering · doi:10.1038/s41551-024-01227-1 · Cited by 218

Discovery of target genes and pathways at GWAS loci by pooled single-cell CRISPR screens

Morris, J. A., Caragine, C., Daniloski, Z., Domingo, J., Barry, T., Lu, L., Davis, K., Ziosi, M., Glinos, D. A., Hao, S., et al. (2023) · Science · doi:10.1126/science.adh7699 · Cited by 208

The myokine decorin is regulated by contraction and involved in muscle hypertrophy

Kanzleiter, T., Rath, M., Görgens, S. W., Jensen, J., Tangen, D. S., Kolnes, A. J., Kolnes, K. J., Lee, S., Eckel, J., Schürmann, A., et al. (2014) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2014.06.123 · Cited by 209

i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules

Herrmann, C., de Sande, B. V., Potier, D., & Aerts, S. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks543 · Cited by 211

Global DNA Methylation Remodeling Accompanies CD8 T Cell Effector Function

Scharer, C. D., Barwick, B. G., Youngblood, B., Ahmed, R., & Boss, J. M. (2013) · The Journal of Immunology · doi:10.4049/jimmunol.1301395 · Cited by 212

DAF-16 employs the chromatin remodeller SWI/SNF to promote stress resistance and longevity

Riedel, C. G., Dowen, R. H., Lourenco, G. F., Kirienko, N. V., Heimbucher, T., West, J. A., Bowman, S. K., Kingston, R. E., Dillin, A., Asara, J. M., et al. (2013) · Nature Cell Biology · doi:10.1038/ncb2720 · Cited by 207

Genomic legacy of the African cheetah, Acinonyx jubatus

Dobrynin, P., Liu, S., Tamazian, G., Xiong, Z., Yurchenko, A. A., Krasheninnikova, K., Kliver, S., Schmidt-Küntzel, A., Koepfli, K.-P., Johnson, W., et al. (2015) · Genome Biology · doi:10.1186/s13059-015-0837-4 · Cited by 204

Ribose-Map: a bioinformatics toolkit to map ribonucleotides embedded in genomic DNA

Gombolay, A. L., Vannberg, F. O., & Storici, F. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky874 · Cited by 204

A TCF4-dependent gene regulatory network confers resistance to immunotherapy in melanoma

Pozniak, J., Pedri, D., Landeloos, E., Van Herck, Y., Antoranz, A., Vanwynsberghe, L., Nowosad, A., Roda, N., Makhzami, S., Bervoets, G., et al. (2024) · Cell · doi:10.1016/j.cell.2023.11.037 · Cited by 199

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads

Human Genome Structural Variation Consortium, Porubsky, D., Ebert, P., Audano, P. A., Vollger, M. R., Harvey, W. T., Marijon, P., Ebler, J., Munson, K. M., Sorensen, M., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-0719-5 · Cited by 203

cGAS-mediated induction of type I interferon due to inborn errors of histone pre-mRNA processing

Uggenti, C., Lepelley, A., Depp, M., Badrock, A. P., Rodero, M. P., El-Daher, M.-T., Rice, G. I., Dhir, S., Wheeler, A. P., Dhir, A., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-00737-3 · Cited by 192

Identification, Characterization, and Heritability of Murine Metastable Epialleles: Implications for Non-genetic Inheritance

Kazachenka, A., Bertozzi, T. M., Sjoberg-Herrera, M. K., Walker, N., Gardner, J., Gunning, R., Pahita, E., Adams, S., Adams, D., & Ferguson-Smith, A. C. (2018) · Cell · doi:10.1016/j.cell.2018.09.043 · Cited by 181

Detecting and correcting systematic variation in large-scale RNA sequencing data

Li, S., Łabaj, P. P., Zumbo, P., Sykacek, P., Shi, W., Shi, L., Phan, J., Wu, P.-Y., Wang, M., Wang, C., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.3000 · Cited by 175

RYBP and Cbx7 define specific biological functions of polycomb complexes in mouse embryonic stem cells

Morey, L., Aloia, L., Cozzuto, L., Benitah, S. A., & Di Croce, L. (2013) · Cell Reports · doi:10.1016/j.celrep.2012.11.026 · Cited by 201

Genome-wide DNA methylation profiling in the superior temporal gyrus reveals epigenetic signatures associated with Alzheimer’s disease

Watson, C. T., Roussos, P., Garg, P., Ho, D. J., Azam, N., Katsel, P. L., Haroutunian, V., & Sharp, A. J. (2016) · Genome Medicine · doi:10.1186/s13073-015-0258-8 · Cited by 201

Noncoding RNA transcription targets AID to divergently transcribed loci in B cells

Pefanis, E., Wang, J., Rothschild, G., Lim, J., Chao, J., Rabadan, R., Economides, A. N., & Basu, U. (2014) · Nature · doi:10.1038/nature13580 · Cited by 201

The chromatin accessibility signature of human immune aging stems from CD8+ T cells

Ucar, D., Márquez, E. J., Chung, C.-H., Marches, R., Rossi, R. J., Uyar, A., Wu, T.-C., George, J., Stitzel, M. L., Palucka, A. K., et al. (2017) · Journal of Experimental Medicine · doi:10.1084/jem.20170416 · Cited by 200

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

Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts

PDXNET Consortium, Woo, X. Y., EurOPDX Consortium, Giordano, J., Srivastava, A., Zhao, Z.-M., Lloyd, M. W., de Bruijn, R., Suh, Y.-S., Patidar, R., et al. (2021) · Nature Genetics · doi:10.1038/s41588-020-00750-6 · Cited by 190

High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human

Wang, X., He, L., Goggin, S. M., Saadat, A., Wang, L., Sinnott-Armstrong, N., Claussnitzer, M., & Kellis, M. (2018) · Nature Communications · doi:10.1038/s41467-018-07746-1 · Cited by 159

Spatially resolved epigenomic profiling of single cells in complex tissues

Lu, T., Ang, C. E., & Zhuang, X. (2022) · Cell · doi:10.1016/j.cell.2022.09.035 · Cited by 197

Co-transcriptional splicing regulates 3′ end cleavage during mammalian erythropoiesis

Reimer, K. A., Mimoso, C. A., Adelman, K., & Neugebauer, K. M. (2021) · Molecular Cell · doi:10.1016/j.molcel.2020.12.018 · Cited by 180

2000 Years of Parallel Societies in Stone Age Central Europe

Bollongino, R., Nehlich, O., Richards, M. P., Orschiedt, J., Thomas, M. G., Sell, C., Fajkošová, Z., Powell, A., & Burger, J. (2013) · Science · doi:10.1126/science.1245049 · Cited by 195

Super-enhancers include classical enhancers and facilitators to fully activate gene expression

Blayney, J. W., Francis, H., Rampasekova, A., Camellato, B., Mitchell, L., Stolper, R., Cornell, L., Babbs, C., Boeke, J. D., Higgs, D. R., et al. (2023) · Cell · doi:10.1016/j.cell.2023.11.030 · Cited by 196

Genome-wide, integrative analysis implicates microRNA dysregulation in autism spectrum disorder

Wu, Y. E., Parikshak, N. N., Belgard, T. G., & Geschwind, D. H. (2016) · Nature Neuroscience · doi:10.1038/nn.4373 · Cited by 195

Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex

Mich, J. K., Graybuck, L. T., Hess, E. E., Mahoney, J. T., Kojima, Y., Ding, Y., Somasundaram, S., Miller, J. A., Kalmbach, B. E., Radaelli, C., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.108754 · Cited by 193

Histone variant H2A.J accumulates in senescent cells and promotes inflammatory gene expression

Contrepois, K., Coudereau, C., Benayoun, B. A., Schuler, N., Roux, P.-F., Bischof, O., Courbeyrette, R., Carvalho, C., Thuret, J.-Y., Ma, Z., et al. (2017) · Nature Communications · doi:10.1038/ncomms14995 · Cited by 191

Autophagy Regulation of Metabolism Is Required for CD8+ T Cell Anti-tumor Immunity

DeVorkin, L., Pavey, N., Carleton, G., Comber, A., Ho, C., Lim, J., McNamara, E., Huang, H., Kim, P., Zacharias, L. G., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.03.037 · Cited by 185

Pan-cancer analysis identifies tumor-specific antigens derived from transposable elements

Shah, N. M., Jang, H. J., Liang, Y., Maeng, J. H., Tzeng, S.-C., Wu, A., Basri, N. L., Qu, X., Fan, C., Li, A., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01349-3 · Cited by 175

Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil

Voloch, C. M., Silva F, R. D., de Almeida, L. G. P., Cardoso, C. C., Brustolini, O. J., Gerber, A. L., Guimarães, A. P. D. C., Mariani, D., Costa, R. M. D., Ferreira, O. C., et al. (2020) · doi:10.1101/2020.12.23.20248598 · Cited by 372

DNA methylation enables transposable element-driven genome expansion

Zhou, W., Liang, G., Molloy, P. L., & Jones, P. A. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1921719117 · Cited by 181

A Comprehensive Mouse Transcriptomic BodyMap across 17 Tissues by RNA-seq

Li, B., Qing, T., Zhu, J., Wen, Z., Yu, Y., Fukumura, R., Zheng, Y., Gondo, Y., & Shi, L. (2017) · Scientific Reports · doi:10.1038/s41598-017-04520-z · Cited by 184

Mutations in SLC12A5 in epilepsy of infancy with migrating focal seizures

Stödberg, T., McTague, A., Ruiz, A. J., Hirata, H., Zhen, J., Long, P., Farabella, I., Meyer, E., Kawahara, A., Vassallo, G., et al. (2015) · Nature Communications · doi:10.1038/ncomms9038 · Cited by 184

An atlas of gene regulatory elements in adult mouse cerebrum

Li, Y. E., Preissl, S., Hou, X., Zhang, Z., Zhang, K., Qiu, Y., Poirion, O. B., Li, B., Chiou, J., Liu, H., et al. (2021) · Nature · doi:10.1038/s41586-021-03604-1 · Cited by 185

Comparison of village dog and wolf genomes highlights the role of the neural crest in dog domestication

Pendleton, A. L., Shen, F., Taravella, A. M., Emery, S., Veeramah, K. R., Boyko, A. R., & Kidd, J. M. (2018) · BMC Biology · doi:10.1186/s12915-018-0535-2 · Cited by 156

DNA methylation in lung cells is associated with asthma endotypes and genetic risk

Nicodemus-Johnson, J., Myers, R. A., Sakabe, N. J., Sobreira, D. R., Hogarth, D. K., Naureckas, E. T., Sperling, A. I., Solway, J., White, S. R., Nobrega, M. A., et al. (2016) · JCI Insight · doi:10.1172/jci.insight.90151 · Cited by 180

The transcription factor ZEB2 drives the formation of age-associated B cells

Dai, D., Gu, S., Han, X., Ding, H., Jiang, Y., Zhang, X., Yao, C., Hong, S., Zhang, J., Shen, Y., et al. (2024) · Science · doi:10.1126/science.adf8531 · Cited by 178

FOXA2 drives lineage plasticity and KIT pathway activation in neuroendocrine prostate cancer

Han, M., Li, F., Zhang, Y., Dai, P., He, J., Li, Y., Zhu, Y., Zheng, J., Huang, H., Bai, F., et al. (2022) · Cancer Cell · doi:10.1016/j.ccell.2022.10.011 · Cited by 166

Reorganization of chromosome architecture in replicative cellular senescence

Criscione, S. W., De Cecco, M., Siranosian, B., Zhang, Y., Kreiling, J. A., Sedivy, J. M., & Neretti, N. (2016) · Science Advances · doi:10.1126/sciadv.1500882 · Cited by 164

Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution

Arnold, C. D., Gerlach, D., Spies, D., Matts, J. A., Sytnikova, Y. A., Pagani, M., Lau, N. C., & Stark, A. (2014) · Nature Genetics · doi:10.1038/ng.3009 · Cited by 175

Truncation and constitutive activation of the androgen receptor by diverse genomic rearrangements in prostate cancer

Henzler, C., Li, Y., Yang, R., McBride, T., Ho, Y., Sprenger, C., Liu, G., Coleman, I., Lakely, B., Li, R., et al. (2016) · Nature Communications · doi:10.1038/ncomms13668 · Cited by 173

A comparative atlas of single-cell chromatin accessibility in the human brain

Li, Y. E., Preissl, S., Miller, M., Johnson, N. D., Wang, Z., Jiao, H., Zhu, C., Wang, Z., Xie, Y., Poirion, O., et al. (2023) · Science · doi:10.1126/science.adf7044 · Cited by 173

Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly

Karcher, N., Nigro, E., Punčochář, M., Blanco-Míguez, A., Ciciani, M., Manghi, P., Zolfo, M., Cumbo, F., Manara, S., Golzato, D., et al. (2021) · Genome Biology · doi:10.1186/s13059-021-02427-7 · Cited by 159

The Landscape of L1 Retrotransposons in the Human Genome Is Shaped by Pre-insertion Sequence Biases and Post-insertion Selection

Sultana, T., van Essen, D., Siol, O., Bailly-Bechet, M., Philippe, C., Zine El Aabidine, A., Pioger, L., Nigumann, P., Saccani, S., Andrau, J.-C., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.02.036 · Cited by 154

Single-cell chromatin accessibility landscape identifies tissue repair program in human regulatory T cells

Delacher, M., Simon, M., Sanderink, L., Hotz-Wagenblatt, A., Wuttke, M., Schambeck, K., Schmidleithner, L., Bittner, S., Pant, A., Ritter, U., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.03.007 · Cited by 164

Transcriptional response to stress is pre-wired by promoter and enhancer architecture

Vihervaara, A., Mahat, D. B., Guertin, M. J., Chu, T., Danko, C. G., Lis, J. T., & Sistonen, L. (2017) · Nature Communications · doi:10.1038/s41467-017-00151-0 · Cited by 164

Bridge RNAs direct programmable recombination of target and donor DNA

Durrant, M. G., Perry, N. T., Pai, J. J., Jangid, A. R., Athukoralage, J. S., Hiraizumi, M., McSpedon, J. P., Pawluk, A., Nishimasu, H., Konermann, S., et al. (2024) · Nature · doi:10.1038/s41586-024-07552-4 · Cited by 163

Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D

Viñuela, A., Varshney, A., van de Bunt, M., Prasad, R. B., Asplund, O., Bennett, A., Boehnke, M., Brown, A. A., Erdos, M. R., Fadista, J., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18581-8 · Cited by 152

The HUSH complex is a gatekeeper of type I interferon through epigenetic regulation of LINE-1s

Tunbak, H., Enriquez-Gasca, R., Tie, C. H. C., Gould, P. A., Mlcochova, P., Gupta, R. K., Fernandes, L., Holt, J., van der Veen, A. G., Giampazolias, E., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19170-5 · Cited by 162

Immediate and deferred epigenomic signatures of in vivo neuronal activation in mouse hippocampus

Fernandez-Albert, J., Lipinski, M., Lopez-Cascales, M. T., Rowley, M. J., Martin-Gonzalez, A. M., del Blanco, B., Corces, V. G., & Barco, A. (2019) · Nature Neuroscience · doi:10.1038/s41593-019-0476-2 · Cited by 166

Comprehensive identification and annotation of cell type-specific and ubiquitous CTCF-binding sites in the human genome

Chen, H., Tian, Y., Shu, W., Bo, X., & Wang, S. (2012) · PLoS ONE · doi:10.1371/journal.pone.0041374 · Cited by 161

FoxO maintains a genuine muscle stem-cell quiescent state until geriatric age

García-Prat, L., Perdiguero, E., Alonso-Martín, S., Dell’Orso, S., Ravichandran, S., Brooks, S. R., Juan, A. H., Campanario, S., Jiang, K., Hong, X., et al. (2020) · Nature Cell Biology · doi:10.1038/s41556-020-00593-7 · Cited by 161

5-hydroxymethylcytosine accumulation in postmitotic neurons results in functional demethylation of expressed genes

Mellén, M., Ayata, P., & Heintz, N. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1708044114 · Cited by 151

The transcription factor p53: Not a repressor, solely an activator.

Fischer, M., Steiner, L., & Engeland, K. (2014) · Cell Cycle · doi:10.4161/15384101.2014.949083 · Cited by 153

Origins of De Novo Genes in Human and Chimpanzee

Ruiz-Orera, J., Hernandez-Rodriguez, J., Chiva, C., Sabidó, E., Kondova, I., Bontrop, R., Marqués-Bonet, T., & Albà, M. M. (2015) · PLOS Genetics · doi:10.1371/journal.pgen.1005721 · Cited by 160

HIV-1 replication complexes accumulate in nuclear speckles and integrate into speckle-associated genomic domains

Francis, A. C., Marin, M., Singh, P. K., Achuthan, V., Prellberg, M. J., Palermino-Rowland, K., Lan, S., Tedbury, P. R., Sarafianos, S. G., Engelman, A. N., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17256-8 · Cited by 159

IVT-seq reveals extreme bias in RNA sequencing

Lahens, N. F., Kavakli, I. H., Zhang, R., Hayer, K., Black, M. B., Dueck, H., Pizarro, A., Kim, J., Irizarry, R., Thomas, R. S., et al. (2014) · Genome Biology · doi:10.1186/gb-2014-15-6-r86 · Cited by 158

3DSNP: a database for linking human noncoding SNPs to their three-dimensional interacting genes

Lu, Y., Quan, C., Chen, H., Bo, X., & Zhang, C. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1022 · Cited by 133

Cell-specific histone modification maps in the human frontal lobe link schizophrenia risk to the neuronal epigenome

Girdhar, K., Hoffman, G. E., Jiang, Y., Brown, L., Kundakovic, M., Hauberg, M. E., Francoeur, N. J., Wang, Y.-C., Shah, H., Kavanagh, D. H., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0187-0 · Cited by 139

Single-cell multi-omics identifies chronic inflammation as a driver of TP53-mutant leukemic evolution

Rodriguez-Meira, A., Norfo, R., Wen, S., Chédeville, A. L., Rahman, H., O’Sullivan, J., Wang, G., Louka, E., Kretzschmar, W. W., Paterson, A., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01480-1 · Cited by 158

Dichotomous engagement of HDAC3 activity governs inflammatory responses

Nguyen, H. C. B., Adlanmerini, M., Hauck, A. K., & Lazar, M. A. (2020) · Nature · doi:10.1038/s41586-020-2576-2 · Cited by 150

The genetic and biochemical determinants of mRNA degradation rates in mammals

Agarwal, V., & Kelley, D. R. (2022) · Genome Biology · doi:10.1186/s13059-022-02811-x · Cited by 155

Deletions of chromosomal regulatory boundaries are associated with congenital disease

Ibn-Salem, J., Köhler, S., Love, M. I., Chung, H.-R., Huang, N., Hurles, M. E., Haendel, M., Washington, N. L., Smedley, D., Mungall, C. J., et al. (2014) · Genome Biology · doi:10.1186/s13059-014-0423-1 · Cited by 143

Integrative epigenetic taxonomy of primary prostate cancer

Stelloo, S., Nevedomskaya, E., Kim, Y., Schuurman, K., Valle-Encinas, E., Lobo, J., Krijgsman, O., Peeper, D. S., Chang, S. L., Feng, F. Y.-C., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-07270-2 · Cited by 154

Targeting Piezo1 unleashes innate immunity against cancer and infectious disease

Aykut, B., Chen, R., Kim, J. I., Wu, D., Shadaloey, S. A. A., Abengozar, R., Preiss, P., Saxena, A., Pushalkar, S., Leinwand, J., et al. (2020) · Science Immunology · doi:10.1126/sciimmunol.abb5168 · Cited by 154

Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma

Grosso, A. R., Leite, A. P., Carvalho, S., Matos, M. R., Martins, F. B., Vítor, A. C., Desterro, J. M., Carmo-Fonseca, M., & de Almeida, S. F. (2015) · eLife · doi:10.7554/elife.09214 · Cited by 152

miR-10b-5p expression in Huntington’s disease brain relates to age of onset and the extent of striatal involvement

Hoss, A. G., Labadorf, A., Latourelle, J. C., Kartha, V. K., Hadzi, T. C., Gusella, J. F., MacDonald, M. E., Chen, J.-F., Akbarian, S., Weng, Z., et al. (2015) · BMC Medical Genomics · doi:10.1186/s12920-015-0083-3 · Cited by 151

Comprehensive genome and epigenome characterization of CHO cells in response to evolutionary pressures and over time

Feichtinger, J., Hernández, I., Fischer, C., Hanscho, M., Auer, N., Hackl, M., Jadhav, V., Baumann, M., Krempl, P. M., Schmidl, C., et al. (2016) · Biotechnology and Bioengineering · doi:10.1002/bit.25990 · Cited by 148

Chromatin accessibility maps of chronic lymphocytic leukaemia identify subtype-specific epigenome signatures and transcription regulatory networks

Rendeiro, A. F., Schmidl, C., Strefford, J. C., Walewska, R., Davis, Z., Farlik, M., Oscier, D., & Bock, C. (2016) · Nature Communications · doi:10.1038/ncomms11938 · Cited by 146

KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription factors

Feng, C., Song, C., Liu, Y., Qian, F., Gao, Y., Ning, Z., Wang, Q., Jiang, Y., Li, Y., Li, M., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkz881 · Cited by 147

Click chemistry enables preclinical evaluation of targeted epigenetic therapies

Tyler, D. S., Vappiani, J., Cañeque, T., Lam, E. Y. N., Ward, A., Gilan, O., Chan, Y.-C., Hienzsch, A., Rutkowska, A., Werner, T., et al. (2017) · Science · doi:10.1126/science.aal2066 · Cited by 146

Combined mutation in Vhl, Trp53 and Rb1 causes clear cell renal cell carcinoma in mice

Harlander, S., Schönenberger, D., Toussaint, N. C., Prummer, M., Catalano, A., Brandt, L., Moch, H., Wild, P. J., & Frew, I. J. (2017) · Nature Medicine · doi:10.1038/nm.4343 · Cited by 143

Transcriptional consequences of 16p11.2 deletion and duplication in mouse cortex and multiplex autism families

Blumenthal, I., Ragavendran, A., Erdin, S., Klei, L., Sugathan, A., Guide, J. R., Manavalan, P., Zhou, J. Q., Wheeler, V. C., Levin, J. Z., et al. (2014) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.05.004 · Cited by 145

Improved plant cytosine base editors with high editing activity, purity, and specificity

Ren, Q., Sretenovic, S., Liu, G., Zhong, Z., Wang, J., Huang, L., Tang, X., Guo, Y., Liu, L., Wu, Y., et al. (2021) · Plant Biotechnology Journal · doi:10.1111/pbi.13635 · Cited by 131

Increased virulence of the oral microbiome in oral squamous cell carcinoma revealed by metatranscriptome analyses

Yost, S., Stashenko, P., Choi, Y., Kukuruzinska, M., Genco, C. A., Salama, A., Weinberg, E. O., Kramer, C. D., & Frias-Lopez, J. (2018) · International Journal of Oral Science · doi:10.1038/s41368-018-0037-7 · Cited by 144

ZnuA and zinc homeostasis in Pseudomonas aeruginosa

Pederick, V. G., Eijkelkamp, B. A., Begg, S. L., Ween, M. P., McAllister, L. J., Paton, J. C., & McDevitt, C. A. (2015) · Scientific Reports · doi:10.1038/srep13139 · Cited by 138

Adeno-to-squamous transition drives resistance to KRAS inhibition in LKB1 mutant lung cancer

Tong, X., Patel, A. S., Kim, E., Li, H., Chen, Y., Li, S., Liu, S., Dilly, J., Kapner, K. S., Zhang, N., et al. (2024) · Cancer Cell · doi:10.1016/j.ccell.2024.01.012 · Cited by 142

The rise and fall of African rice cultivation revealed by analysis of 246 new genomes

Cubry, P., Tranchant-Dubreuil, C., Thuillet, A.-C., Monat, C., Ndjiondjop, M.-N., Labadie, K., Cruaud, C., Engelen, S., Scarcelli, N., Rhoné, B., et al. (2018) · Current Biology · doi:10.1016/j.cub.2018.05.066 · Cited by 142

Machine-guided design of cell-type-targeting cis-regulatory elements

Gosai, S. J., Castro, R. I., Fuentes, N., Butts, J. C., Mouri, K., Alasoadura, M., Kales, S., Nguyen, T. T. L., Noche, R. R., Rao, A. S., et al. (2024) · Nature · doi:10.1038/s41586-024-08070-z · Cited by 142

SNES: single nucleus exome sequencing

Leung, M. L., Wang, Y., Waters, J., & Navin, N. E. (2015) · Genome Biology · doi:10.1186/s13059-015-0616-2 · Cited by 112

Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila

Ciabrelli, F., Comoglio, F., Fellous, S., Bonev, B., Ninova, M., Szabo, Q., Xuéreb, A., Klopp, C., Aravin, A., Paro, R., et al. (2017) · Nature Genetics · doi:10.1038/ng.3848 · Cited by 129

Heterogeneity and interplay of the extracellular vesicle small RNA transcriptome and proteome

Sork, H., Corso, G., Krjutskov, K., Johansson, H. J., Nordin, J. Z., Wiklander, O. P. B., Lee, Y. X. F., Westholm, J. O., Lehtiö, J., Wood, M. J. A., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-28485-9 · Cited by 140

SCAF4 and SCAF8, mRNA Anti-Terminator Proteins

Gregersen, L. H., Mitter, R., Ugalde, A. P., Nojima, T., Proudfoot, N. J., Agami, R., Stewart, A., & Svejstrup, J. Q. (2019) · Cell · doi:10.1016/j.cell.2019.04.038 · Cited by 140

Dnmt3a restrains mast cell inflammatory responses

Leoni, C., Montagner, S., Rinaldi, A., Bertoni, F., Polletti, S., Balestrieri, C., & Monticelli, S. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1616420114 · Cited by 138

High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development

Wilderman, A., VanOudenhove, J., Kron, J., Noonan, J. P., & Cotney, J. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.03.129 · Cited by 139

Transcriptomic analyses reveal rhythmic and CLOCK-driven pathways in human skeletal muscle

Perrin, L., Loizides-Mangold, U., Chanon, S., Gobet, C., Hulo, N., Isenegger, L., Weger, B. D., Migliavacca, E., Charpagne, A., Betts, J. A., et al. (2018) · eLife · doi:10.7554/elife.34114 · Cited by 139

Structural basis for retroviral integration into nucleosomes

Maskell, D. P., Renault, L., Serrao, E., Lesbats, P., Matadeen, R., Hare, S., Lindemann, D., Engelman, A. N., Costa, A., & Cherepanov, P. (2015) · Nature · doi:10.1038/nature14495 · Cited by 138

Ovarian Cancers Harboring Inactivating Mutations in CDK12 Display a Distinct Genomic Instability Pattern Characterized by Large Tandem Duplications

Popova, T., Manié, E., Boeva, V., Battistella, A., Goundiam, O., Smith, N. K., Mueller, C. R., Raynal, V., Mariani, O., Sastre-Garau, X., et al. (2016) · Cancer Research · doi:10.1158/0008-5472.can-15-2128 · Cited by 130

Insights into the biogenesis and potential functions of exonic circular RNA

Ragan, C., Goodall, G. J., Shirokikh, N. E., & Preiss, T. (2019) · Scientific Reports · doi:10.1038/s41598-018-37037-0 · Cited by 137

Biased Allelic Expression in Human Primary Fibroblast Single Cells

Borel, C., Ferreira, P. G., Santoni, F., Delaneau, O., Fort, A., Popadin, K. Y., Garieri, M., Falconnet, E., Ribaux, P., Guipponi, M., et al. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.12.001 · Cited by 120

DNA methylation in the gene body influences MeCP2-mediated gene repression

Kinde, B., Wu, D. Y., Greenberg, M. E., & Gabel, H. W. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1618737114 · Cited by 118

Mechanisms governing the pioneering and redistribution capabilities of the non-classical pioneer PU.1

Minderjahn, J., Schmidt, A., Fuchs, A., Schill, R., Raithel, J., Babina, M., Schmidl, C., Gebhard, C., Schmidhofer, S., Mendes, K., et al. (2020) · Nature Communications · doi:10.1038/s41467-019-13960-2 · Cited by 136

Introns Protect Eukaryotic Genomes from Transcription-Associated Genetic Instability

Bonnet, A., Grosso, A. R., Elkaoutari, A., Coleno, E., Presle, A., Sridhara, S. C., Janbon, G., Géli, V., de Almeida, S. F., & Palancade, B. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.07.002 · Cited by 135

Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis

Beale, M. A., Marks, M., Cole, M. J., Lee, M.-K., Pitt, R., Ruis, C., Balla, E., Crucitti, T., Ewens, M., Fernández-Naval, C., et al. (2021) · Nature Microbiology · doi:10.1038/s41564-021-01000-z · Cited by 135

Recombination between heterologous human acrocentric chromosomes

Guarracino, A., Buonaiuto, S., de Lima, L. G., Potapova, T., Rhie, A., Koren, S., Rubinstein, B., Fischer, C., Human Pangenome Reference Consortium, Abel, H. J., et al. (2023) · Nature · doi:10.1038/s41586-023-05976-y · Cited by 134

BioID identifies novel c-MYC interacting partners in cultured cells and xenograft tumors

Dingar, D., Kalkat, M., Chan, P.-K., Srikumar, T., Bailey, S. D., Tu, W. B., Coyaud, E., Ponzielli, R., Kolyar, M., Jurisica, I., et al. (2015) · Journal of Proteomics · doi:10.1016/j.jprot.2014.09.029 · Cited by 131

A unique role for DNA (hydroxy)methylation in epigenetic regulation of human inhibitory neurons

Kozlenkov, A., Li, J., Apontes, P., Hurd, Y. L., Byne, W. M., Koonin, E. V., Wegner, M., Mukamel, E. A., & Dracheva, S. (2018) · Science Advances · doi:10.1126/sciadv.aau6190 · Cited by 103

FOXA1 mutations reveal distinct chromatin profiles and influence therapeutic response in breast cancer

Arruabarrena-Aristorena, A., Maag, J. L. V., Kittane, S., Cai, Y., Karthaus, W. R., Ladewig, E., Park, J., Kannan, S., Ferrando, L., Cocco, E., et al. (2020) · Cancer Cell · doi:10.1016/j.ccell.2020.08.003 · Cited by 130

Genome-wide de novo L1 Retrotransposition Connects Endonuclease Activity with Replication

Flasch, D. A., Macia, Á., Sánchez, L., Ljungman, M., Heras, S. R., García-Pérez, J. L., Wilson, T. E., & Moran, J. V. (2019) · Cell · doi:10.1016/j.cell.2019.02.050 · Cited by 127

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

Neph, S. J., Kuehn, M. S., Reynolds, A. P., Haugen, E., Thurman, R. E., Johnson, A., Rynes, E., Maurano, M. T., Vierstra, J. D., Thomas, S., et al. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts277 · Cited by 971

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