Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Identification of common molecular subsequences

Smith, T. F., & Waterman, M. S. (1981) · Journal of Molecular Biology · doi:10.1016/0022-2836(81)90087-5 · Cited by 9,962

Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy AssessmentPreprint

Ewing, B., Hillier, L., Wendl, M. C., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.175 · Cited by 6,993

Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities

Ewing, B., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.186 · Cited by 5,439

Accurate whole human genome sequencing using reversible terminator chemistry

Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684

SOAP: Short oligonucleotide alignment program

Li, R., Li, Y., Kristiansen, K., & Wang, J. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn025 · Cited by 3,597

Genome-Wide Mapping of in Vivo Protein-DNA Interactions

Johnson, D. S., Mortazavi, A., Myers, R. M., & Wold, B. (2007) · Science · doi:10.1126/science.1141319 · Cited by 2,927

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

Marioni, J. C., Mason, C. E., Mane, S. M., Stephens, M., & Gilad, Y. (2008) · Genome Research · doi:10.1101/gr.079558.108 · Cited by 2,771

Mapping short DNA sequencing reads and calling variants using mapping quality scores

Li, H., Ruan, J., & Durbin, R. (2008) · Genome Research · doi:10.1101/gr.078212.108 · Cited by 2,638

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

Nagalakshmi, U., Wang, Z., Waern, K., Shou, C., Raha, D., Gerstein, M., & Snyder, M. (2008) · Science · doi:10.1126/science.1158441 · Cited by 2,479

A Block-sorting Lossless Data Compression Algorithm

Burrows, M. T., & Wheeler, D. J. (1994) · Cited by 2,333

In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse

Morselli, M., Pastor, W. A., Montanini, B., Nee, K., Ferrari, R., Fu, K., Bonora, G., Rubbi, L., Clark, A. T., Ottonello, S., et al. (2015) · eLife · doi:10.7554/elife.06205 · Cited by 167

Evolution at two levels of gene expression in yeast

Artieri, C. G., & Fraser, H. B. (2014) · Genome Research · doi:10.1101/gr.165522.113 · Cited by 138

Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells

Menendez, D., Nguyen, T.-A., Freudenberg, J. M., Mathew, V. J., Anderson, C. W., Jothi, R., & Resnick, M. A. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt504 · Cited by 154

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

Global Regulation of Promoter Melting in Naive Lymphocytes

Kouzine, F., Wojtowicz, D., Yamane, A., Resch, W., Kieffer-Kwon, K.-R., Bandle, R., Nelson, S., Nakahashi, H., Awasthi, P., Feigenbaum, L., et al. (2013) · Cell · doi:10.1016/j.cell.2013.04.033 · Cited by 154

KrasG12D and Nkx2-1 haploinsufficiency induce mucinous adenocarcinoma of the lung

Maeda, Y., Tsuchiya, T., Hao, H., Tompkins, D. H., Xu, Y., Mucenski, M. L., Du, L., Keiser, A. R., Fukazawa, T., Naomoto, Y., et al. (2012) · Journal of Clinical Investigation · doi:10.1172/jci64048 · Cited by 163

Positively selected enhancer elements endow osteosarcoma cells with metastatic competence

Morrow, J. J., Bayles, I., Funnell, A. P. W., Miller, T. E., Saiakhova, A., Lizardo, M. M., Bartels, C. F., Kapteijn, M. Y., Hung, S., Mendoza, A., et al. (2018) · Nature Medicine · doi:10.1038/nm.4475 · Cited by 161

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

The hypersensitive glucocorticoid response specifically regulates period 1 and expression of circadian genes

Reddy, T. E., Gertz, J., Crawford, G. E., Garabedian, M. J., & Myers, R. M. (2012) · Molecular and Cellular Biology · doi:10.1128/mcb.00062-12 · Cited by 149

Evolutionary insight from whole‐genome sequencing of experimentally evolved microbes

DETTMAN, J. R., RODRIGUE, N., MELNYK, A. H., WONG, A., BAILEY, S. F., & KASSEN, R. (2012) · Molecular Ecology · doi:10.1111/j.1365-294x.2012.05484.x · Cited by 160

Functional Dynamics of the Gut Microbiome in Elderly People during Probiotic Consumption

Eloe-Fadrosh, E. A., Brady, A., Crabtree, J., Drabek, E. F., Ma, B., Mahurkar, A., Ravel, J., Haverkamp, M., Fiorino, A.-M., Botelho, C., et al. (2015) · mBio · doi:10.1128/mbio.00231-15 · Cited by 160

Polony gels enable amplifiable DNA stamping and spatial transcriptomics of chronic pain

Fu, X., Sun, L., Dong, R., Chen, J. Y., Silakit, R., Condon, L. F., Lin, Y., Lin, S., Palmiter, R. D., & Gu, L. (2022) · Cell · doi:10.1016/j.cell.2022.10.021 · Cited by 161

Long-range single-molecule mapping of chromatin accessibility in eukaryotes

Shipony, Z., Marinov, G. K., Swaffer, M. P., Sinnott-Armstrong, N. A., Skotheim, J. M., Kundaje, A., & Greenleaf, W. J. (2020) · Nature Methods · doi:10.1038/s41592-019-0730-2 · Cited by 160

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

TET1 regulates hypoxia-induced epithelial-mesenchymal transition by acting as a co-activator

Tsai, Y.-P., Chen, H.-F., Chen, S.-Y., Cheng, W.-C., Wang, H.-W., Shen, Z.-J., Song, C., Teng, S.-C., He, C., & Wu, K.-J. (2014) · Genome biology · doi:10.1186/s13059-014-0513-0 · Cited by 152

24 hours in the life of HIV-1 in a T cell line

Mohammadi, P., Desfarges, S., Bartha, I., Joos, B., Zangger, N., Muñoz, M., Günthard, H. F., Beerenwinkel, N., Telenti, A., & Ciuffi, A. (2013) · PLoS Pathogens · doi:10.1371/journal.ppat.1003161 · Cited by 155

The Functional Proximal Proteome of Oncogenic Ras Includes mTORC2

Kovalski, J. R., Bhaduri, A., Zehnder, A. M., Neela, P. H., Che, Y., Wozniak, G. G., & Khavari, P. A. (2019) · Molecular Cell · doi:10.1016/j.molcel.2018.12.001 · Cited by 154

HIV-1 Integrase Binds the Viral RNA Genome and Is Essential during Virion Morphogenesis

Kessl, J. J., Kutluay, S. B., Townsend, D., Rebensburg, S., Slaughter, A., Larue, R. C., Shkriabai, N., Bakouche, N., Fuchs, J. R., Bieniasz, P. D., et al. (2016) · Cell · doi:10.1016/j.cell.2016.07.044 · Cited by 152

GATA3-dependent cellular reprogramming requires activation-domain dependent recruitment of a chromatin remodeler

Takaku, M., Grimm, S. A., Shimbo, T., Perera, L., Menafra, R., Stunnenberg, H. G., Archer, T. K., Machida, S., Kurumizaka, H., & Wade, P. A. (2016) · Genome Biology · doi:10.1186/s13059-016-0897-0 · Cited by 151

Toward the human cellular microRNAome

McCall, M. N., Kim, M.-S., Adil, M., Patil, A. H., Lu, Y., Mitchell, C. J., Leal-Rojas, P., Xu, J., Kumar, M., Dawson, V. L., et al. (2017) · Genome Research · doi:10.1101/gr.222067.117 · Cited by 151

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

Cell fitness screens reveal a conflict between LINE-1 retrotransposition and DNA replication

Ardeljan, D., Steranka, J. P., Liu, C., Li, Z., Taylor, M. S., Payer, L. M., Gorbounov, M., Sarnecki, J. S., Deshpande, V., Hruban, R. H., et al. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-0372-1 · Cited by 135

The PhoP-Dependent ncRNA Mcr7 Modulates the TAT Secretion System in Mycobacterium tuberculosis

Solans, L., Gonzalo-Asensio, J., Sala, C., Benjak, A., Uplekar, S., Rougemont, J., Guilhot, C., Malaga, W., Martín, C., & Cole, S. T. (2014) · PLoS Pathogens · doi:10.1371/journal.ppat.1004183 · Cited by 147

Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling

Łabaj, P. P., Leparc, G. G., Linggi, B. E., Markillie, L. M., Wiley, H. S., & Kreil, D. P. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr247 · Cited by 141

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

Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs

Weingarten-Gabbay, S., Klaeger, S., Sarkizova, S., Pearlman, L. R., Chen, D.-Y., Gallagher, K. M. E., Bauer, M. R., Taylor, H. B., Dunn, W. A., Tarr, C., et al. (2021) · Cell · doi:10.1016/j.cell.2021.05.046 · Cited by 147

Multi-omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency

Yang, P., Humphrey, S. J., Cinghu, S., Pathania, R., Oldfield, A. J., Kumar, D., Perera, D., Yang, J. Y. H., James, D. E., Mann, M., et al. (2019) · Cell Systems · doi:10.1016/j.cels.2019.03.012 · Cited by 146

RNA-sequence analysis of human B-cells

Toung, J. M., Morley, M., Li, M., & Cheung, V. G. (2011) · Genome Research · doi:10.1101/gr.116335.110 · Cited by 142

Placing the HIRA Histone Chaperone Complex in the Chromatin Landscape

Pchelintsev, N. A., McBryan, T., Rai, T. S., van Tuyn, J., Ray-Gallet, D., Almouzni, G., & Adams, P. D. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.03.026 · Cited by 143

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

OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds

Wu, J., Anczuków, O., Krainer, A. R., Zhang, M. Q., & Zhang, C. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt216 · Cited by 123

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

Sources of bias in measures of allele-specific expression derived from RNA-seq data aligned to a single reference genome

Stevenson, K. R., Coolon, J. D., & Wittkopp, P. J. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-536 · Cited by 140

Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism

Belda, E., Voland, L., Tremaroli, V., Falony, G., Adriouch, S., Assmann, K. E., Prifti, E., Aron-Wisnewsky, J., Debédat, J., Le Roy, T., et al. (2022) · Gut · doi:10.1136/gutjnl-2021-325753 · Cited by 140

Stabilization of the Max Homodimer with a Small Molecule Attenuates Myc-Driven Transcription

Struntz, N. B., Chen, A., Deutzmann, A., Wilson, R. M., Stefan, E., Evans, H. L., Ramirez, M. A., Liang, T., Caballero, F., Wildschut, M. H. E., et al. (2019) · Cell Chemical Biology · doi:10.1016/j.chembiol.2019.02.009 · Cited by 130

MYC Recruits SPT5 to RNA Polymerase II to Promote Processive Transcription Elongation

Baluapuri, A., Hofstetter, J., Dudvarski Stankovic, N., Endres, T., Bhandare, P., Vos, S. M., Adhikari, B., Schwarz, J. D., Narain, A., Vogt, M., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.02.031 · Cited by 138

Identification of neurodegenerative factors using translatome–regulatory network analysis

Brichta, L., Shin, W., Jackson-Lewis, V., Blesa, J., Yap, E.-L., Walker, Z., Zhang, J., Roussarie, J.-P., Alvarez, M. J., Califano, A., et al. (2015) · Nature Neuroscience · doi:10.1038/nn.4070 · Cited by 118

ZFHX4 Interacts with the NuRD Core Member CHD4 and Regulates the Glioblastoma Tumor-Initiating Cell State

Chudnovsky, Y., Kim, D., Zheng, S., Whyte, W. A., Bansal, M., Bray, M.-A., Gopal, S., Theisen, M. A., Bilodeau, S., Thiru, P., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2013.12.032 · Cited by 136

Functional assessment of human enhancer activities using whole-genome STARR-sequencing

Liu, Y., Yu, S., Dhiman, V. K., Brunetti, T., Eckart, H., & White, K. P. (2017) · Genome Biology · doi:10.1186/s13059-017-1345-5 · Cited by 136

Dysregulation of MicroRNAs and Target Genes Networks in Peripheral Blood of Patients With Sporadic Amyotrophic Lateral Sclerosis.

Liguori, M., Nuzziello, N., Introna, A., Consiglio, A., Licciulli, F., D’Errico, E., Scarafino, A., Distaso, E., & Simone, I. L. (2018) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2018.00288 · Cited by 131

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

Ribosome stalling during selenoprotein translation exposes a ferroptosis vulnerability

Li, Z., Ferguson, L., Deol, K. K., Roberts, M. A., Magtanong, L., Hendricks, J. M., Mousa, G. A., Kilinc, S., Schaefer, K., Wells, J. A., et al. (2022) · Nature Chemical Biology · doi:10.1038/s41589-022-01033-3 · Cited by 134

Neuropathological and transcriptomic characteristics of the aged brain

Miller, J. A., Guillozet-Bongaarts, A., Gibbons, L. E., Postupna, N., Renz, A., Beller, A. E., Sunkin, S. M., Ng, L., Rose, S. E., Smith, K. A., et al. (2017) · eLife · doi:10.7554/elife.31126 · Cited by 134

Transcription factors lhx1/5-1 and pitx are required for the maintenance and regeneration of serotonergic neurons in planarians

Currie, K. W., & Pearson, B. J. (2013) · Development · doi:10.1242/dev.098590 · Cited by 131

MicroRNA Expression and Regulation in Human, Chimpanzee, and Macaque Brains

Hu, H. Y., Guo, S., Xi, J., Yan, Z., Fu, N., Zhang, X., Menzel, C., Liang, H., Yang, H., Zhao, M., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002327 · Cited by 130

Small RNA sequencing revealed dysregulated piRNAs in Alzheimer's disease and their probable role in pathogenesis

Roy, J., Sarkar, A., Parida, S., Ghosh, Z., & Mallick, B. (2017) · Molecular BioSystems · doi:10.1039/c6mb00699j · Cited by 130

Transcriptional programs in transient embryonic zones of the cerebral cortex defined by high-resolution mRNA sequencing

Ayoub, A. E., Oh, S., Xie, Y., Leng, J., Cotney, J., Dominguez, M. H., Noonan, J. P., & Rakic, P. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1112213108 · Cited by 129

K63-polyubiquitinated HAUSP deubiquitinates HIF-1α and dictates H3K56 acetylation promoting hypoxia-induced tumour progression

Wu, H.-T., Kuo, Y.-C., Hung, J.-J., Huang, C.-H., Chen, W.-Y., Chou, T.-Y., Chen, Y., Chen, Y.-J., Chen, Y.-J., Cheng, W.-C., et al. (2016) · Nature Communications · doi:10.1038/ncomms13644 · Cited by 129

Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq

Sheynkman, G. M., Shortreed, M. R., Frey, B. L., & Smith, L. M. (2013) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o113.028142 · Cited by 128

Lkb1 inactivation drives lung cancer lineage switching governed by Polycomb Repressive Complex 2

Zhang, H., Fillmore Brainson, C., Koyama, S., Redig, A. J., Chen, T., Li, S., Gupta, M., Garcia-de-Alba, C., Paschini, M., Herter-Sprie, G. S., et al. (2017) · Nature Communications · doi:10.1038/ncomms14922 · Cited by 127

Refinement of the androgen response element based on ChIP-seq in androgen-insensitive and androgen-responsive prostate cancer cell lines

Wilson, S., Qi, J., & Filipp, F. V. (2016) · Scientific Reports · doi:10.1038/srep32611 · Cited by 126

Transcription factor PU.1 represses and activates gene expression in early T cells by redirecting partner transcription factor binding

Hosokawa, H., Ungerbäck, J., Wang, X., Matsumoto, M., Nakayama, K. I., Cohen, S. M., Tanaka, T., & Rothenberg, E. V. (2018) · Immunity · doi:10.1016/j.immuni.2018.04.024 · Cited by 116

Targeting Processive Transcription Elongation via SEC Disruption for MYC-Induced Cancer Therapy

Liang, K., Smith, E. R., Aoi, Y., Stoltz, K. L., Katagi, H., Woodfin, A. R., Rendleman, E. J., Marshall, S. A., Murray, D. C., Wang, L., et al. (2018) · Cell · doi:10.1016/j.cell.2018.09.027 · Cited by 124

LRPPRC-mediated folding of the mitochondrial transcriptome

Siira, S. J., Spåhr, H., Shearwood, A.-M. J., Ruzzenente, B., Larsson, N.-G., Rackham, O., & Filipovska, A. (2017) · Nature Communications · doi:10.1038/s41467-017-01221-z · Cited by 123

The dynamic epigenetic regulation of the inactive X chromosome in healthy human B cells is dysregulated in lupus patients

Pyfrom, S., Paneru, B., Knox, J. J., Cancro, M. P., Posso, S., Buckner, J. H., & Anguera, M. C. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2024624118 · Cited by 126

Somatic and Germline Mutation Periodicity Follow the Orientation of the DNA Minor Groove around Nucleosomes

Pich, O., Muiños, F., Sabarinathan, R., Reyes-Salazar, I., Gonzalez-Perez, A., & Lopez-Bigas, N. (2018) · Cell · doi:10.1016/j.cell.2018.10.004 · Cited by 123

Transcriptional cofactors display specificity for distinct types of core promoters

Haberle, V., Arnold, C. D., Pagani, M., Rath, M., Schernhuber, K., & Stark, A. (2019) · Nature · doi:10.1038/s41586-019-1210-7 · Cited by 123

Human Trace Amine-Associated Receptor TAAR5 Can Be Activated by Trimethylamine

Wallrabenstein, I., Kuklan, J., Weber, L., Zborala, S., Werner, M., Altmüller, J., Becker, C., Schmidt, A., Hatt, H., Hummel, T., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0054950 · Cited by 122

FoxP1 orchestration of ASD-relevant signaling pathways in the striatum

Araujo, D. J., Anderson, A. G., Berto, S., Runnels, W., Harper, M., Ammanuel, S., Rieger, M. A., Huang, H.-C., Rajkovich, K., Loerwald, K. W., et al. (2015) · Genes & Development · doi:10.1101/gad.267989.115 · Cited by 111

MLV integration site selection is driven by strong enhancers and active promoters

LaFave, M. C., Varshney, G. K., Gildea, D. E., Wolfsberg, T. G., Baxevanis, A. D., & Burgess, S. M. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1399 · Cited by 114

In vivo selection of a computationally designed SCHEMA AAV library yields a novel variant for infection of adult neural stem cells in the SVZ

Ojala, D. S., Sun, S., Santiago-Ortiz, J. L., Shapiro, M. G., Romero, P. A., & Schaffer, D. V. (2018) · Molecular Therapy · doi:10.1016/j.ymthe.2017.09.006 · Cited by 97

Cryptococcal Titan Cell Formation Is Regulated by G-Protein Signaling in Response to Multiple Stimuli

Okagaki, L. H., Wang, Y., Ballou, E. R., O'Meara, T. R., Bahn, Y.-S., Alspaugh, J. A., Xue, C., & Nielsen, K. (2011) · Eukaryotic Cell · doi:10.1128/ec.05179-11 · Cited by 117

Evidence for additive and synergistic action of mammalian enhancers during cell fate determination

Choi, J., Lysakovskaia, K., Stik, G., Demel, C., Söding, J., Tian, T. V., Graf, T., & Cramer, P. (2021) · eLife · doi:10.7554/elife.65381 · Cited by 117

Transcript and protein expression decoupling reveals RNA binding proteins and miRNAs as potential modulators of human aging

Wei, Y.-N., Hu, H.-Y., Xie, G.-C., Fu, N., Ning, Z.-B., Zeng, R., & Khaitovich, P. (2015) · Genome Biology · doi:10.1186/s13059-015-0608-2 · Cited by 117

RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and GTPase binding in bipolar disorder

Akula, N., Barb, J., Jiang, X., Wendland, J. R., Choi, K. H., Sen, S. K., Hou, L., Chen, D. T. W., Laje, G., Johnson, K., et al. (2014) · Molecular Psychiatry · doi:10.1038/mp.2013.170 · Cited by 116

p53 induces transcriptional and translational programs to suppress cell proliferation and growth

Loayza-Puch, F., Drost, J., Rooijers, K., Lopes, R., Elkon, R., & Agami, R. (2013) · Genome Biology · doi:10.1186/gb-2013-14-4-r32 · Cited by 114

Large scale loss of data in low-diversity Illumina sequencing libraries can be recovered by deferred cluster calling

Krueger, F., Andrews, S. R., & Osborne, C. S. (2011) · PLoS ONE · doi:10.1371/journal.pone.0016607 · Cited by 102

The genomic landscape of cohesin-associated chromatin interactions

DeMare, L. E., Leng, J., Cotney, J., Reilly, S. K., Yin, J., Sarro, R., & Noonan, J. P. (2013) · Genome Research · doi:10.1101/gr.156570.113 · Cited by 114

Complete regression of advanced pancreatic ductal adenocarcinomas upon combined inhibition of EGFR and C-RAF

Blasco, M. T., Navas, C., Martín-Serrano, G., Graña-Castro, O., Lechuga, C. G., Martín-Díaz, L., Djurec, M., Li, J., Morales-Cacho, L., Esteban-Burgos, L., et al. (2019) · Cancer Cell · doi:10.1016/j.ccell.2019.03.002 · Cited by 115

The transcriptional response to tumorigenic polarity loss in Drosophila

Bunker, B. D., Nellimoottil, T. T., Boileau, R. M., Classen, A. K., & Bilder, D. (2015) · eLife · doi:10.7554/elife.03189 · Cited by 114

Identification of in vivo DNA-binding mechanisms of Pax6 and reconstruction of Pax6-dependent gene regulatory networks during forebrain and lens development

Sun, J., Rockowitz, S., Xie, Q., Ashery-Padan, R., Zheng, D., & Cvekl, A. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv589 · Cited by 113

Active DNA demethylation promotes cell fate specification and the DNA damage response

Wang, D., Wu, W., Callen, E., Pavani, R., Zolnerowich, N., Kodali, S., Zong, D., Wong, N., Noriega, S., Nathan, W. J., et al. (2022) · Science · doi:10.1126/science.add9838 · Cited by 113

A limited capacity for microglial repopulation in the adult brain

Najafi, A. R., Crapser, J., Jiang, S., Ng, W., Mortazavi, A., West, B. L., & Green, K. N. (2018) · Glia · doi:10.1002/glia.23477 · Cited by 99

Adjunctive Probiotic Lactobacillus rhamnosus Probio-M9 Administration Enhances the Effect of Anti-PD-1 Antitumor Therapy via Restoring Antibiotic-Disrupted Gut Microbiota

Gao, G., Ma, T., Zhang, T., Jin, H., Li, Y., Kwok, L.-Y., Zhang, H., & Sun, Z. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.772532 · Cited by 111

Tools for experimental and computational analyses of off-target editing by programmable nucleases

Bao, X. R., Pan, Y., Lee, C. M., Davis, T. H., & Bao, G. (2021) · Nature Protocols · doi:10.1038/s41596-020-00431-y · Cited by 106

Dynamic changes in the Streptococcus pneumoniae transcriptome during transition from biofilm formation to invasive disease upon influenza A virus infection

Pettigrew, M. M., Marks, L. R., Kong, Y., Gent, J. F., Roche-Hakansson, H., & Hakansson, A. P. (2014) · Infection and Immunity · doi:10.1128/iai.02225-14 · Cited by 110

A KRAB/KAP1-miRNA Cascade Regulates Erythropoiesis Through Stage-Specific Control of Mitophagy

Barde, I., Rauwel, B., Marin-Florez, R. M., Corsinotti, A., Laurenti, E., Verp, S., Offner, S., Marquis, J., Kapopoulou, A., Vanicek, J., et al. (2013) · Science · doi:10.1126/science.1232398 · Cited by 111

Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis

Gillespie, M. A., Palii, C. G., Sanchez-Taltavull, D., Shannon, P., Longabaugh, W. J. R., Downes, D. J., Sivaraman, K., Espinoza, H. M., Hughes, J. R., Price, N. D., et al. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.03.031 · Cited by 110

Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions

Pugacheva, E. M., Rivero-Hinojosa, S., Espinoza, C. A., Méndez-Catalá, C. F., Kang, S., Suzuki, T., Kosaka-Suzuki, N., Robinson, S., Nagarajan, V., Ye, Z., et al. (2015) · Genome biology · doi:10.1186/s13059-015-0736-8 · Cited by 110

Lysosomal Signaling Licenses Embryonic Stem Cell Differentiation via Inactivation of Tfe3

Villegas, F., Lehalle, D., Mayer, D., Rittirsch, M., Stadler, M. B., Zinner, M., Olivieri, D., Vabres, P., Duplomb-Jego, L., De Bont, E. S. J. M., et al. (2019) · Cell Stem Cell · doi:10.1016/j.stem.2018.11.021 · Cited by 110

Differential transcriptome analysis of glandular and filamentous trichomes in Artemisia annua

Soetaert, S. S., Van Neste, C. M., Vandewoestyne, M. L., Head, S. R., Goossens, A., Van Nieuwerburgh, F. C., & Deforce, D. L. (2013) · BMC Plant Biology · doi:10.1186/1471-2229-13-220 · Cited by 109

The lipid elongation enzyme ELOVL2 is a molecular regulator of aging in the retina

Chen, D., Chao, D. L., Rocha, L., Kolar, M., Nguyen Huu, V. A., Krawczyk, M., Dasyani, M., Wang, T., Jafari, M., Jabari, M., et al. (2020) · Aging Cell · doi:10.1111/acel.13100 · Cited by 109

PRRX1 is a master transcription factor of stromal fibroblasts for myofibroblastic lineage progression

Lee, K.-W., Yeo, S.-Y., Gong, J.-R., Koo, O.-J., Sohn, I., Lee, W. Y., Kim, H. C., Yun, S. H., Cho, Y. B., Choi, M.-A., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30484-4 · Cited by 103

Whole transcriptome sequencing of the aging rat brain reveals dynamic RNA changes in the dark matter of the genome

Wood, S. H., Craig, T., Li, Y., Merry, B., & de Magalhães, J. P. (2013) · AGE · doi:10.1007/s11357-012-9410-1 · Cited by 105

Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads

Li, W., & Jiang, T. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts559 · Cited by 97

Profiling the genetic determinants of chromatin accessibility with scalable single-cell CRISPR screens

Liscovitch-Brauer, N., Montalbano, A., Deng, J., Méndez-Mancilla, A., Wessels, H.-H., Moss, N. G., Kung, C.-Y., Sookdeo, A., Guo, X., Geller, E., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-00902-x · Cited by 107

Accelerating next generation sequencing data analysis: an evaluation of optimized best practices for Genome Analysis Toolkit algorithms

Franke, K. R., & Crowgey, E. L. (2020) · Genomics & Informatics · doi:10.5808/gi.2020.18.1.e10 · Cited by 95

Re‐annotation, improved large‐scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus

Cormier, A., Avia, K., Sterck, L., Derrien, T., Wucher, V., Andres, G., Monsoor, M., Godfroy, O., Lipinska, A., Perrineau, M., et al. (2017) · New Phytologist · doi:10.1111/nph.14321 · Cited by 103

TERT activation targets DNA methylation and multiple aging hallmarks

Shim, H. S., Iaconelli, J., Shang, X., Li, J., Lan, Z. D., Jiang, S., Nutsch, K., Beyer, B. A., Lairson, L. L., Boutin, A. T., et al. (2024) · Cell · doi:10.1016/j.cell.2024.05.048 · Cited by 104

The male germ cell gene regulator CTCFL is functionally different from CTCF and binds CTCF-like consensus sites in a nucleosome composition-dependent manner

Sleutels, F., Soochit, W., Bartkuhn, M., Heath, H., Dienstbach, S., Bergmaier, P., Franke, V., Rosa-Garrido, M., van de Nobelen, S., Caesar, L., et al. (2012) · Epigenetics & Chromatin · doi:10.1186/1756-8935-5-8 · Cited by 96

Evidence for epigenetic regulation of pro-inflammatory cytokines, interleukin-12 and interferon gamma, in peripheral blood mononuclear cells from PTSD patients

Bam, M., Yang, X., Zhou, J., Ginsberg, J. P., Leyden, Q., Nagarkatti, P. S., & Nagarkatti, M. (2016) · Journal of Neuroimmune Pharmacology · doi:10.1007/s11481-015-9643-8 · Cited by 103

Gain-of-function mutation of microRNA-140 in human skeletal dysplasia

Grigelioniene, G., Suzuki, H. I., Taylan, F., Mirzamohammadi, F., Borochowitz, Z. U., Ayturk, U. M., Tzur, S., Horemuzova, E., Lindstrand, A., Weis, M. A., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0353-2 · Cited by 103

Genome-wide CRISPR screen for PARKIN regulators reveals transcriptional repression as a determinant of mitophagy

Potting, C., Crochemore, C., Moretti, F., Nigsch, F., Schmidt, I., Manneville, C., Carbone, W., Knehr, J., DeJesus, R., Lindeman, A., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1711023115 · Cited by 93

RNA Pol II Dynamics Modulate Co-transcriptional Chromatin Modification, CTD Phosphorylation, and Transcriptional Direction

Fong, N., Saldi, T., Sheridan, R. M., Cortazar, M. A., & Bentley, D. L. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.04.016 · Cited by 98

Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype

Wu, Y., Fletcher, M., Gu, Z., Wang, Q., Costa, B., Bertoni, A., Man, K.-H., Schlotter, M., Felsberg, J., Mangei, J., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-20225-w · Cited by 101

A Histone Deacetylase Adjusts Transcription Kinetics at Coding Sequences during Candida albicans Morphogenesis

Hnisz, D., Bardet, A. F., Nobile, C. J., Petryshyn, A., Glaser, W., Schöck, U., Stark, A., & Kuchler, K. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1003118 · Cited by 100

Analytical tools and current challenges in the modern era of neuroepigenomics

Maze, I., Shen, L., Zhang, B., Garcia, B. A., Shao, N., Mitchell, A., Sun, H., Akbarian, S., Allis, C. D., & Nestler, E. J. (2014) · Nature Neuroscience · doi:10.1038/nn.3816 · Cited by 100

Global DNA Hypermethylation in Down Syndrome Placenta

Jin, S., Lee, Y. K., Lim, Y. C., Zheng, Z., Lin, X. M., Ng, D. P. Y., Holbrook, J. D., Law, H. Y., Kwek, K. Y. C., Yeo, G. S. H., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003515 · Cited by 99

Transformation of a text T,

Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2015)

Fast gapped-read alignment with Bowtie 2

Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400

SOAP2: an improved ultrafast tool for short read alignment

Li, R., Yu, C., Li, Y., Lam, T., Yiu, S., Kristiansen, K., & Wang, J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp336 · Cited by 3,763

Fast and memory efficient approach for mapping NGS reads to a reference genome

Kumar, S., Agarwal, S., & Ranvijay (2019) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s0219720019500082 · Cited by 27

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