deepTools2: a next generation web server for deep-sequencing data analysis

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

Integrative analysis of 111 reference human epigenomes

Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature · doi:10.1038/nature14248 · Cited by 6,368

Comprehensive Integration of Single-Cell Data

Stuart, T., Butler, A., Hoffman, P., Hafemeister, C., Papalexi, E., Mauck, W. M., Hao, Y., Stoeckius, M., Smibert, P., & Satija, R. (2019) · Cell · doi:10.1016/j.cell.2019.05.031 · Cited by 15,453

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

Afgan, E., Baker, D., Batut, B., van den Beek, M., Bouvier, D., Čech, M., Chilton, J., Clements, D., Coraor, N., Grüning, B. A., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky379 · Cited by 3,662

Impact of cytosine methylation on DNA binding specificities of human transcription factors

Yin, Y., Morgunova, E., Jolma, A., Kaasinen, E., Sahu, B., Khund-Sayeed, S., Das, P. K., Kivioja, T., Dave, K., Zhong, F., et al. (2017) · Science · doi:10.1126/science.aaj2239 · Cited by 1,257

TOX is a critical regulator of tumour-specific T cell differentiation

Scott, A. C., Dündar, F., Zumbo, P., Chandran, S. S., Klebanoff, C. A., Shakiba, M., Trivedi, P., Menocal, L., Appleby, H., Camara, S., et al. (2019) · Nature · doi:10.1038/s41586-019-1324-y · Cited by 1,106

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

Cusanovich, D. A., Hill, A. J., Aghamirzaie, D., Daza, R. M., Pliner, H. A., Berletch, J. B., Filippova, G. N., Huang, X., Christiansen, L., DeWitt, W. S., et al. (2018) · Cell · doi:10.1016/j.cell.2018.06.052 · Cited by 759

Comparative cellular analysis of motor cortex in human, marmoset and mouse

Bakken, T. E., Jorstad, N. L., Hu, Q., Lake, B. B., Tian, W., Kalmbach, B. E., Crow, M., Hodge, R. D., Krienen, F. M., Sorensen, S. A., et al. (2021) · Nature · doi:10.1038/s41586-021-03465-8 · Cited by 812

Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing

Nuñez, J. K., Chen, J., Pommier, G. C., Cogan, J. Z., Replogle, J. M., Adriaens, C., Ramadoss, G. N., Shi, Q., Hung, K. L., Samelson, A. J., et al. (2021) · Cell · doi:10.1016/j.cell.2021.03.025 · Cited by 760

Decoding myofibroblast origins in human kidney fibrosis

Kuppe, C., Ibrahim, M. M., Kranz, J., Zhang, X., Ziegler, S., Perales-Patón, J., Jansen, J., Reimer, K. C., Smith, J. R., Dobie, R., et al. (2021) · Nature · doi:10.1038/s41586-020-2941-1 · Cited by 769

Loss of epigenetic information as a cause of mammalian aging

Yang, J.-H., Hayano, M., Griffin, P. T., Amorim, J. A., Bonkowski, M. S., Apostolides, J. K., Salfati, E. L., Blanchette, M., Munding, E. M., Bhakta, M., et al. (2023) · Cell · doi:10.1016/j.cell.2022.12.027 · Cited by 643

Thiol-linked alkylation for the metabolic sequencing of RNA

Herzog, V. A., Reichholf, B., Neumann, T., Rescheneder, P., Bhat, P., Burkard, T. R., Wlotzka, W., von Haeseler, A., Zuber, J., & Ameres, S. L. (2017) · doi:10.1101/177642 · Cited by 622

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

Hansen, A. S., Pustova, I., Cattoglio, C., Tjian, R., & Darzacq, X. (2017) · eLife · doi:10.7554/elife.25776 · Cited by 613

Persistence of a regeneration-associated, transitional alveolar epithelial cell state in pulmonary fibrosis

Kobayashi, Y., Tata, A., Konkimalla, A., Katsura, H., Lee, R. F., Ou, J., Banovich, N. E., Kropski, J. A., & Tata, P. R. (2020) · Nature Cell Biology · doi:10.1038/s41556-020-0542-8 · Cited by 559

Treatment-Induced Tumor Dormancy through YAP-Mediated Transcriptional Reprogramming of the Apoptotic Pathway

Kurppa, K. J., Liu, Y., To, C., Zhang, T., Fan, M., Vajdi, A., Knelson, E. H., Xie, Y., Lim, K., Cejas, P., et al. (2020) · Cancer Cell · doi:10.1016/j.ccell.2019.12.006 · Cited by 475

Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues

Bartosovic, M., Kabbe, M., & Castelo-Branco, G. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-00869-9 · Cited by 483

Direct promoter repression by BCL11A controls the fetal to adult hemoglobin switch

Liu, N., Hargreaves, V. V., Zhu, Q., Kurland, J. V., Hong, J., Kim, W., Sher, F., Macias-Trevino, C., Rogers, J. M., Kurita, R., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.016 · Cited by 478

From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

Hoyt, S. J., Storer, J. M., Hartley, G. A., Grady, P. G. S., Gershman, A., de Lima, L. G., Limouse, C., Halabian, R., Wojenski, L., Rodriguez, M., et al. (2022) · Science · doi:10.1126/science.abk3112 · Cited by 411

Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation

Preissl, S., Fang, R., Huang, H., Zhao, Y., Raviram, R., Gorkin, D. U., Zhang, Y., Sos, B. C., Afzal, V., Dickel, D. E., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0079-3 · Cited by 332

Hypoxia induces rapid changes to histone methylation and reprograms chromatin

Batie, M., Frost, J., Frost, M., Wilson, J. W., Schofield, P., & Rocha, S. (2019) · Science · doi:10.1126/science.aau5870 · Cited by 385

Mitochondrial Reprogramming Underlies Resistance to BCL-2 Inhibition in Lymphoid Malignancies

Guièze, R., Liu, V. M., Rosebrock, D., Jourdain, A. A., Hernández-Sánchez, M., Martinez Zurita, A., Sun, J., Ten Hacken, E., Baranowski, K., Thompson, P. A., et al. (2019) · Cancer Cell · doi:10.1016/j.ccell.2019.08.005 · Cited by 361

Acetate Promotes T Cell Effector Function during Glucose Restriction

Qiu, J., Villa, M., Sanin, D. E., Buck, M. D., O’Sullivan, D., Ching, R., Matsushita, M., Grzes, K. M., Winkler, F., Chang, C.-H., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.04.022 · Cited by 342

MCM2 promotes symmetric inheritance of modified histones during DNA replication

Petryk, N., Dalby, M., Wenger, A., Stromme, C. B., Strandsby, A., Andersson, R., & Groth, A. (2018) · Science · doi:10.1126/science.aau0294 · Cited by 294

Impaired death receptor signaling in leukemia causes antigen-independent resistance by inducing CAR T-cell dysfunction

Singh, N., Lee, Y. G., Shestova, O., Ravikumar, P., Hayer, K. E., Hong, S. J., Lu, X. M., Pajarillo, R., Agarwal, S., Kuramitsu, S., et al. (2020) · Cancer Discovery · doi:10.1158/2159-8290.cd-19-0813 · Cited by 295

A bacterial bile acid metabolite modulates Treg activity through the nuclear hormone receptor NR4A1

Li, W., Hang, S., Fang, Y., Bae, S., Zhang, Y., Zhang, M., Wang, G., McCurry, M. D., Bae, M., Paik, D., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.07.013 · Cited by 306

Epigenetic patterns in a complete human genome

Gershman, A., Sauria, M. E. G., Guitart, X., Vollger, M. R., Hook, P. W., Hoyt, S. J., Jain, M., Shumate, A., Razaghi, R., Koren, S., et al. (2022) · Science · doi:10.1126/science.abj5089 · Cited by 297

p21 produces a bioactive secretome that places stressed cells under immunosurveillance

Sturmlechner, I., Zhang, C., Sine, C. C., van Deursen, E.-J., Jeganathan, K. B., Hamada, N., Grasic, J., Friedman, D., Stutchman, J. T., Can, I., et al. (2021) · Science · doi:10.1126/science.abb3420 · Cited by 295

Pathological priming causes developmental gene network heterochronicity in autistic subject-derived neurons

Schafer, S. T., Paquola, A. C. M., Stern, S., Gosselin, D., Ku, M., Pena, M., Kuret, T. J. M., Liyanage, M., Mansour, A. A., Jaeger, B. N., et al. (2019) · Nature Neuroscience · doi:10.1038/s41593-018-0295-x · Cited by 288

Reciprocal Signaling between Glioblastoma Stem Cells and Differentiated Tumor Cells Promotes Malignant Progression

Wang, X., Prager, B. C., Wu, Q., Kim, L. J. Y., Gimple, R. C., Shi, Y., Yang, K., Morton, A. R., Zhou, W., Zhu, Z., et al. (2018) · Cell Stem Cell · doi:10.1016/j.stem.2018.03.011 · Cited by 285

Distinct structural classes of activating FOXA1 alterations in advanced prostate cancer

Parolia, A., Cieslik, M., Chu, S.-C., Xiao, L., Ouchi, T., Zhang, Y., Wang, X., Vats, P., Cao, X., Pitchiaya, S., et al. (2019) · Nature · doi:10.1038/s41586-019-1347-4 · Cited by 284

Methods for ChIP-seq analysis: A practical workflow and advanced applications

Nakato, R., & Sakata, T. (2021) · Methods · doi:10.1016/j.ymeth.2020.03.005 · Cited by 267

Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF

Hansen, A. S., Hsieh, T.-H. S., Cattoglio, C., Pustova, I., Saldaña-Meyer, R., Reinberg, D., Darzacq, X., & Tjian, R. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.07.039 · Cited by 279

KDM5B promotes immune evasion by recruiting SETDB1 to silence retroelements

Zhang, S.-M., Cai, W. L., Liu, X., Thakral, D., Luo, J., Chan, L. H., McGeary, M. K., Song, E., Blenman, K. R. M., Micevic, G., et al. (2021) · Nature · doi:10.1038/s41586-021-03994-2 · Cited by 272

Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells

Sabbagh, M. F., Heng, J. S., Luo, C., Castanon, R. G., Nery, J. R., Rattner, A., Goff, L. A., Ecker, J. R., & Nathans, J. (2018) · eLife · doi:10.7554/elife.36187 · Cited by 245

Inflammatory macrophage dependence on NAD+ salvage is a consequence of reactive oxygen species–mediated DNA damage

Cameron, A. M., Castoldi, A., Sanin, D. E., Flachsmann, L. J., Field, C. S., Puleston, D. J., Kyle, R. L., Patterson, A. E., Hässler, F., Buescher, J. M., et al. (2019) · Nature Immunology · doi:10.1038/s41590-019-0336-y · Cited by 269

Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries

Sun, J. H., Zhou, L., Emerson, D. J., Phyo, S. A., Titus, K. R., Gong, W., Gilgenast, T. G., Beagan, J. A., Davidson, B. L., Tassone, F., et al. (2018) · Cell · doi:10.1016/j.cell.2018.08.005 · Cited by 249

KMT2D Deficiency Impairs Super-Enhancers to Confer a Glycolytic Vulnerability in Lung Cancer

Alam, H., Tang, M., Maitituoheti, M., Dhar, S. S., Kumar, M., Han, C. Y., Ambati, C. R., Amin, S. B., Gu, B., Chen, T.-Y., et al. (2020) · Cancer Cell · doi:10.1016/j.ccell.2020.03.005 · Cited by 243

NFIA is a gliogenic switch enabling rapid derivation of functional human astrocytes from pluripotent stem cells

Tchieu, J., Calder, E. L., Guttikonda, S. R., Gutzwiller, E. M., Aromolaran, K. A., Steinbeck, J. A., Goldstein, P. A., & Studer, L. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0035-0 · Cited by 231

Neuronal enhancers are hotspots for DNA single-strand break repair

Wu, W., Kargbo-Hill, S. E., Nathan, W. J., Paiano, J., Callen, E., Wang, D., Shinoda, K., van Wietmarschen, N., Colón-Mercado, J. M., Zong, D., et al. (2021) · Nature · doi:10.1038/s41586-021-03468-5 · Cited by 223

A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing

Petti, A. A., Williams, S. R., Miller, C. A., Fiddes, I. T., Srivatsan, S. N., Chen, D. Y., Fronick, C. C., Fulton, R. S., Church, D. M., & Ley, T. J. (2019) · Nature Communications · doi:10.1038/s41467-019-11591-1 · Cited by 215

Smooth Muscle Cell Reprogramming in Aortic Aneurysms

Chen, P.-Y., Qin, L., Li, G., Malagon-Lopez, J., Wang, Z., Bergaya, S., Gujja, S., Caulk, A. W., Murtada, S.-I., Zhang, X., et al. (2020) · Cell Stem Cell · doi:10.1016/j.stem.2020.02.013 · Cited by 214

CoBATCH for High-Throughput Single-Cell Epigenomic Profiling

Wang, Q., Xiong, H., Ai, S., Yu, X., Liu, Y., Zhang, J., & He, A. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.07.015 · Cited by 213

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

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

Multimodal analysis of cell-free DNA whole-genome sequencing for pediatric cancers with low mutational burden

Peneder, P., Stütz, A. M., Surdez, D., Krumbholz, M., Semper, S., Chicard, M., Sheffield, N. C., Pierron, G., Lapouble, E., Tötzl, M., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23445-w · Cited by 200

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

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

Warburg-like metabolic transformation underlies neuronal degeneration in sporadic Alzheimer’s disease

Traxler, L., Herdy, J. R., Stefanoni, D., Eichhorner, S., Pelucchi, S., Szücs, A., Santagostino, A., Kim, Y., Agarwal, R. K., Schlachetzki, J. C. M., et al. (2022) · Cell Metabolism · doi:10.1016/j.cmet.2022.07.014 · Cited by 179

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

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

Decoding gene regulation in the fly brain

Janssens, J., Aibar, S., Taskiran, I. I., Ismail, J. N., Spanier, K. I., Bravo González-Blas, C., Quan, X. J., Papasokrati, D., Hulselmans, G., Makhzami, S., et al. (2021) · doi:10.1101/2021.08.11.454937 · Cited by 170

Tet2 and Tet3 cooperate with B-lineage transcription factors to regulate DNA modification and chromatin accessibility

Lio, C.-W., Zhang, J., González-Avalos, E., Hogan, P. G., Chang, X., & Rao, A. (2016) · eLife · doi:10.7554/elife.18290 · Cited by 170

Decoding gene regulation in the fly brain

Janssens, J., Aibar, S., Taskiran, I. I., Ismail, J. N., Gomez, A. E., Aughey, G., Spanier, K. I., De Rop, F. V., González-Blas, C. B., Dionne, M., et al. (2022) · Nature · doi:10.1038/s41586-021-04262-z · Cited by 170

Targeted degradation of the enhancer lysine acetyltransferases CBP and p300

Vannam, R., Sayilgan, J., Ojeda, S., Karakyriakou, B., Hu, E., Kreuzer, J., Morris, R., Herrera Lopez, X. I., Rai, S., Haas, W., et al. (2021) · Cell Chemical Biology · doi:10.1016/j.chembiol.2020.12.004 · Cited by 177

The Polycomb-Dependent Epigenome Controls β Cell Dysfunction, Dedifferentiation, and Diabetes

Lu, T. T.-H., Heyne, S., Dror, E., Casas, E., Leonhardt, L., Boenke, T., Yang, C.-H., Sagar, Arrigoni, L., Dalgaard, K., et al. (2018) · Cell Metabolism · doi:10.1016/j.cmet.2018.04.013 · Cited by 151

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

Hi-C analyses with GENOVA: a case study with cohesin variants

van der Weide, R. H., van den Brand, T., Haarhuis, J. H. I., Teunissen, H., Rowland, B. D., & de Wit, E. (2021) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqab040 · Cited by 161

Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation

Baek, S., & Lee, I. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.06.012 · Cited by 151

Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression

Beagan, J. A., Pastuzyn, E. D., Fernandez, L. R., Guo, M. H., Feng, K., Titus, K. R., Chandrashekar, H., Shepherd, J. D., & Phillips-Cremins, J. E. (2020) · Nature Neuroscience · doi:10.1038/s41593-020-0634-6 · Cited by 143

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

Profiling chromatin states using single-cell itChIP-seq

Ai, S., Xiong, H., Li, C. C., Luo, Y., Shi, Q., Liu, Y., Yu, X., Li, C., & He, A. (2019) · Nature Cell Biology · doi:10.1038/s41556-019-0383-5 · Cited by 140

Inhibition of CGAS-STING by JQ1 Alleviates Oxidative Stress-Induced Retina Inflammation and Degeneration

Zou, M., Ke, Q., Nie, Q., Qi, R., Zhu, X., Liu, W., Hu, X., Sun, Q., Fu, J.-L., Tang, X., et al. (2022) · Cell Death & Differentiation · doi:10.1038/s41418-022-00967-4 · Cited by 138

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

Histone deacetylase (HDAC) 1 and 2 complexes regulate both histone acetylation and crotonylation in vivo

Kelly, R. D. W., Chandru, A., Watson, P. J., Song, Y., Blades, M., Robertson, N. S., Jamieson, A. G., Schwabe, J. W. R., & Cowley, S. M. (2018) · Scientific Reports · doi:10.1038/s41598-018-32927-9 · Cited by 138

Highly efficient and rapid generation of human pluripotent stem cells by chemical reprogramming.

Liuyang, S., Wang, G., Wang, Y., He, H., Lyu, Y., Cheng, L., Yang, Z., Guan, J., Fu, Y., Zhu, J., et al. (2023) · Cell Stem Cell · doi:10.1016/j.stem.2023.02.008 · Cited by 136

Kupffer-cell-derived IL-6 is repurposed for hepatocyte dedifferentiation via activating progenitor genes from injury-specific enhancers

Li, L., Cui, L., Lin, P., Liu, Z., Bao, S., Ma, X., Nan, H., Zhu, W., Cen, J., Mao, Y., et al. (2023) · Cell Stem Cell · doi:10.1016/j.stem.2023.01.009 · Cited by 134

Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis

Poetsch, A. R., Boulton, S. J., & Luscombe, N. M. (2018) · Genome Biology · doi:10.1186/s13059-018-1582-2 · Cited by 132

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

Widespread activation of developmental gene expression characterized by PRC1-dependent chromatin looping

Loubiere, V., Papadopoulos, G. L., Szabo, Q., Martinez, A.-M., & Cavalli, G. (2020) · Science Advances · doi:10.1126/sciadv.aax4001 · Cited by 126

FBXO44 promotes DNA replication-coupled repetitive element silencing in cancer cells

Shen, J. Z., Qiu, Z., Wu, Q., Finlay, D., Garcia, G., Sun, D., Rantala, J., Barshop, W., Hope, J. L., Gimple, R. C., et al. (2021) · Cell · doi:10.1016/j.cell.2020.11.042 · Cited by 113

IL-33-PU.1 Transcriptome Reprogramming Drives Functional State Transition and Clearance Activity of Microglia in Alzheimer’s Disease

Lau, S.-F., Chen, C., Fu, W.-Y., Qu, J. Y., Cheung, T. H., Fu, A. K. Y., & Ip, N. Y. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107530 · Cited by 114

Niche stiffening compromises hair follicle stem cell potential during ageing by reducing bivalent promoter accessibility

Koester, J., Miroshnikova, Y. A., Ghatak, S., Chacón-Martínez, C. A., Morgner, J., Li, X., Atanassov, I., Altmüller, J., Birk, D. E., Koch, M., et al. (2021) · Nature Cell Biology · doi:10.1038/s41556-021-00705-x · Cited by 117

Cross-species analysis of enhancer logic using deep learning

Minnoye, L., Taskiran, I. I., Mauduit, D., Fazio, M., Van Aerschot, L., Hulselmans, G., Christiaens, V., Makhzami, S., Seltenhammer, M., Karras, P., et al. (2020) · Genome Research · doi:10.1101/gr.260844.120 · Cited by 116

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

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

Large-scale chromatin reorganization reactivates placenta-specific genes that drive cellular aging

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A tissue injury sensing and repair pathway distinct from host pathogen defense

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