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

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

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

Genome plasticity in Candida albicans is driven by long repeat sequences

Todd, R. T., Wikoff, T. D., Forche, A., & Selmecki, A. (2019) · eLife · doi:10.7554/elife.45954 · Cited by 118

Rare pathogenic variants predispose to hepatocellular carcinoma in nonalcoholic fatty liver disease

Pelusi, S., Baselli, G., Pietrelli, A., Dongiovanni, P., Donati, B., McCain, M. V., Meroni, M., Fracanzani, A. L., Romagnoli, R., Petta, S., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-39998-2 · Cited by 125

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

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

Elongation Factor TFIIS Prevents Transcription Stress and R-Loop Accumulation to Maintain Genome Stability

Zatreanu, D., Han, Z., Mitter, R., Tumini, E., Williams, H., Gregersen, L., Dirac-Svejstrup, A. B., Roma, S., Stewart, A., Aguilera, A., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.07.037 · Cited by 124

Incorporation of a nucleoside analog maps genome repair sites in postmitotic human neurons

Reid, D. A., Reed, P. J., Schlachetzki, J. C. M., Nitulescu, I. I., Chou, G., Tsui, E. C., Jones, J. R., Chandran, S., Lu, A. T., McClain, C. A., et al. (2021) · Science · doi:10.1126/science.abb9032 · Cited by 121

Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA

Koh, K. D., Balachander, S., Hesselberth, J. R., & Storici, F. (2015) · Nature Methods · doi:10.1038/nmeth.3259 · Cited by 122

H3K4me1 Distribution Predicts Transcription State and Poising at Promoters

Bae, S., & Lesch, B. J. (2020) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2020.00289 · Cited by 120

Dynamics of the 4D Genome during in Vivo Lineage Specification and Differentiation

Oudelaar, A. M., Beagrie, R. A., Gosden, M., de Ornellas, S., Georgiades, E., Kerry, J., Hidalgo, D., Carrelha, J., Shivalingam, A., El-Sagheer, A. H., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16598-7 · Cited by 119

Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: diffTF

Berest, I., Arnold, C., Reyes-Palomares, A., Palla, G., Rasmussen, K. D., Giles, H., Bruch, P.-M., Huber, W., Dietrich, S., Helin, K., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.10.106 · Cited by 119

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

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

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

Genetic risk for Alzheimer’s disease is concentrated in specific macrophage and microglial transcriptional networks

Tansey, K. E., Cameron, D., & Hill, M. J. (2018) · Genome Medicine · doi:10.1186/s13073-018-0523-8 · Cited by 115

An ancestral recombination graph of human, Neanderthal, and Denisovan genomes

Schaefer, N. K., Shapiro, B., & Green, R. E. (2021) · Science Advances · doi:10.1126/sciadv.abc0776 · Cited by 106

Human retinoic acid–regulated CD161+ regulatory T cells support wound repair in intestinal mucosa

Povoleri, G. A. M., Nova-Lamperti, E., Scottà, C., Fanelli, G., Chen, Y.-C., Becker, P. D., Boardman, D., Costantini, B., Romano, M., Pavlidis, P., et al. (2018) · Nature Immunology · doi:10.1038/s41590-018-0230-z · Cited by 114

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

Frequency and complexity of de novo structural mutation in autism

Brandler, W. M., Antaki, D., Gujral, M., Noor, A., Rosanio, G., Chapman, T. R., Barrera, D. J., Lin, G. N., Malhotra, D., Watts, A. C., et al. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2016.02.018 · Cited by 104

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

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

Direct Regulation of Diurnal Drd3 Expression and Cocaine Reward by NPAS2

Ozburn, A. R., Falcon, E., Twaddle, A., Nugent, A. L., Gillman, A. G., Spencer, S. M., Arey, R. N., Mukherjee, S., Lyons-Weiler, J., Self, D. W., et al. (2015) · Biological Psychiatry · doi:10.1016/j.biopsych.2014.07.030 · Cited by 110

Mechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU.1

Pham, T.-H., Minderjahn, J., Schmidl, C., Hoffmeister, H., Schmidhofer, S., Chen, W., Längst, G., Benner, C., & Rehli, M. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt355 · Cited by 102

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

Liu, Z., Ji, Q., Ren, J., Yan, P., Wu, Z., Wang, S., Sun, L., Wang, Z., Li, J., Sun, G., et al. (2022) · Developmental Cell · doi:10.1016/j.devcel.2022.05.004 · 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

NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence

Parry, A. J., Hoare, M., Bihary, D., Hänsel-Hertsch, R., Smith, S., Tomimatsu, K., Mannion, E., Smith, A., D’Santos, P., Russell, I. A., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04283-9 · Cited by 102

A catalog of single nucleotide changes distinguishing modern humans from archaic hominins

Kuhlwilm, M., & Boeckx, C. (2019) · Scientific Reports · doi:10.1038/s41598-019-44877-x · Cited by 108

Enhancers Are Major Targets for Murine Leukemia Virus Vector Integration

De Ravin, S. S., Su, L., Theobald, N., Choi, U., Macpherson, J. L., Poidinger, M., Symonds, G., Pond, S. M., Ferris, A. L., Hughes, S. H., et al. (2014) · Journal of Virology · doi:10.1128/jvi.00011-14 · Cited by 103

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

Mutation rates, spectra, and genome-wide distribution of spontaneous mutations in mismatch repair deficient yeast.

Lang, G. I., Parsons, L., & Gammie, A. E. (2013) · G3 Genes Genomes Genetics · doi:10.1534/g3.113.006429 · Cited by 107

A reference genome of the Chinese hamster based on a hybrid assembly strategy

Rupp, O., MacDonald, M. L., Li, S., Dhiman, H., Polson, S., Griep, S., Heffner, K., Hernandez, I., Brinkrolf, K., Jadhav, V., et al. (2018) · Biotechnology and Bioengineering · doi:10.1002/bit.26722 · Cited by 107

KdmB, a Jumonji Histone H3 Demethylase, Regulates Genome-Wide H3K4 Trimethylation and Is Required for Normal Induction of Secondary Metabolism in Aspergillus nidulans

Gacek-Matthews, A., Berger, H., Sasaki, T., Wittstein, K., Gruber, C., Lewis, Z. A., & Strauss, J. (2016) · PLOS Genetics · doi:10.1371/journal.pgen.1006222 · Cited by 105

Yam genomics supports West Africa as a major cradle of crop domestication

Scarcelli, N., Cubry, P., Akakpo, R., Thuillet, A.-C., Obidiegwu, J., Baco, M. N., Otoo, E., Sonké, B., Dansi, A., Djedatin, G., et al. (2019) · Science Advances · doi:10.1126/sciadv.aaw1947 · Cited by 105

Epigenomic map of human liver reveals principles of zonated morphogenic and metabolic control

Brosch, M., Kattler, K., Herrmann, A., von Schönfels, W., Nordström, K., Seehofer, D., Damm, G., Becker, T., Zeissig, S., Nehring, S., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06611-5 · Cited by 98

The active enhancer network operated by liganded RXR supports angiogenic activity in macrophages

Daniel, B., Nagy, G., Hah, N., Horvath, A., Czimmerer, Z., Poliska, S., Gyuris, T., Keirsse, J., Gysemans, C., Van Ginderachter, J. A., et al. (2014) · Genes & Development · doi:10.1101/gad.242685.114 · Cited by 97

The interaction between cytosine methylation and processes of DNA replication and repair shape the mutational landscape of cancer genomes

Poulos, R. C., Olivier, J., & Wong, J. W. H. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx463 · Cited by 93

A reanalysis of mouse ENCODE comparative gene expression data

Gilad, Y., & Mizrahi-Man, O. (2015) · F1000Research · doi:10.12688/f1000research.6536.1 · Cited by 100

Genomic responses to selection for tame/aggressive behaviors in the silver fox ( Vulpes vulpes )

Wang, X., Pipes, L., Trut, L. N., Herbeck, Y., Vladimirova, A. V., Gulevich, R. G., Kharlamova, A. V., Johnson, J. L., Acland, G. M., Kukekova, A. V., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1800889115 · 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

Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort

Vockley, C. M., Guo, C., Majoros, W. H., Nodzenski, M., Scholtens, D. M., Hayes, M. G., Lowe, W. L., & Reddy, T. E. (2015) · Genome Research · doi:10.1101/gr.190090.115 · Cited by 99

Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5′ splice site strength

Wickramasinghe, V. O., Gonzàlez-Porta, M., Perera, D., Bartolozzi, A. R., Sibley, C. R., Hallegger, M., Ule, J., Marioni, J. C., & Venkitaraman, A. R. (2015) · Genome Biology · doi:10.1186/s13059-015-0749-3 · Cited by 91

Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia

Tucci, S., Vohr, S. H., McCoy, R. C., Vernot, B., Robinson, M. R., Barbieri, C., Nelson, B. J., Fu, W., Purnomo, G. A., Sudoyo, H., et al. (2018) · Science · doi:10.1126/science.aar8486 · Cited by 97

Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility

Meijer, M., Agirre, E., Kabbe, M., van Tuijn, C. A., Heskol, A., Zheng, C., Mendanha Falcão, A., Bartosovic, M., Kirby, L., Calini, D., et al. (2022) · Neuron · doi:10.1016/j.neuron.2021.12.034 · Cited by 98

Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic

Verfaillie, A., Svetlichnyy, D., Imrichova, H., Davie, K., Fiers, M., Kalender Atak, Z., Hulselmans, G., Christiaens, V., & Aerts, S. (2016) · Genome Research · doi:10.1101/gr.204149.116 · Cited by 82

HSV-1-induced disruption of transcription termination resembles a cellular stress response but selectively increases chromatin accessibility downstream of genes

Hennig, T., Michalski, M., Rutkowski, A. J., Djakovic, L., Whisnant, A. W., Friedl, M.-S., Jha, B. A., Baptista, M. A. P., L’Hernault, A., Erhard, F., et al. (2018) · PLOS Pathogens · doi:10.1371/journal.ppat.1006954 · Cited by 95

The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts

Saini, N., Roberts, S. A., Klimczak, L. J., Chan, K., Grimm, S. A., Dai, S., Fargo, D. C., Boyer, J. C., Kaufmann, W. K., Taylor, J. A., et al. (2016) · PLOS Genetics · doi:10.1371/journal.pgen.1006385 · Cited by 94

Succinylation of H3K122 destabilizes nucleosomes and enhances transcription

Zorro Shahidian, L., Haas, M., Le Gras, S., Nitsch, S., Mourão, A., Geerlof, A., Margueron, R., Michaelis, J., Daujat, S., & Schneider, R. (2021) · The EMBO Reports · doi:10.15252/embr.202051009 · Cited by 92

Hypermutation of the Inactive X Chromosome Is a Frequent Event in Cancer

Jäger, N., Schlesner, M., Jones, D. T. W., Raffel, S., Mallm, J.-P., Junge, K. M., Weichenhan, D., Bauer, T., Ishaque, N., Kool, M., et al. (2013) · Cell · doi:10.1016/j.cell.2013.09.042 · Cited by 90

LEDGF and HDGF2 relieve the nucleosome-induced barrier to transcription in differentiated cells

LeRoy, G., Oksuz, O., Descostes, N., Aoi, Y., Ganai, R. A., Kara, H. O., Yu, J.-R., Lee, C.-H., Stafford, J., Shilatifard, A., et al. (2019) · Science Advances · doi:10.1126/sciadv.aay3068 · Cited by 89

Genome structures resolve the early diversification of teleost fishes

Parey, E., Louis, A., Montfort, J., Bouchez, O., Roques, C., Iampietro, C., Lluch, J., Castinel, A., Donnadieu, C., Desvignes, T., et al. (2023) · Science · doi:10.1126/science.abq4257 · Cited by 87

SIRT7 mediates L1 elements transcriptional repression and their association with the nuclear lamina

Vazquez, B. N., Thackray, J. K., Simonet, N. G., Chahar, S., Kane-Goldsmith, N., Newkirk, S. J., Lee, S., Xing, J., Verzi, M. P., An, W., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz519 · Cited by 79

Haplotype-aware pantranscriptome analyses using spliced pangenome graphs

Sibbesen, J. A., Eizenga, J. M., Novak, A. M., Sirén, J., Chang, X., Garrison, E., & Paten, B. (2023) · Nature Methods · doi:10.1038/s41592-022-01731-9 · Cited by 83

TFAP2 paralogs regulate melanocyte differentiation in parallel with MITF

Seberg, H. E., Van Otterloo, E., Loftus, S. K., Liu, H., Bonde, G., Sompallae, R., Gildea, D. E., Santana, J. F., Manak, J. R., Pavan, W. J., et al. (2017) · PLOS Genetics · doi:10.1371/journal.pgen.1006636 · Cited by 85

Jpx RNA regulates CTCF anchor site selection and formation of chromosome loops

Oh, H. J., Aguilar, R., Kesner, B., Lee, H.-G., Kriz, A. J., Chu, H.-P., & Lee, J. T. (2021) · Cell · doi:10.1016/j.cell.2021.11.012 · Cited by 84

Quantifying the contribution of Neanderthal introgression to the heritability of complex traits

McArthur, E., Rinker, D. C., & Capra, J. A. (2021) · Nature Communications · doi:10.1038/s41467-021-24582-y · Cited by 71

The Evf2 ultraconserved enhancer lncRNA functionally and spatially organizes megabase distant genes in the developing forebrain

Cajigas, I., Chakraborty, A., Swyter, K. R., Luo, H., Bastidas, M., Nigro, M., Morris, E. R., Chen, S., VanGompel, M. J. W., Leib, D., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.07.024 · Cited by 82

Marked Diversity of Unique Cortical Enhancers Enables Neuron-Specific Tools by Enhancer-Driven Gene Expression

Blankvoort, S., Witter, M. P., Noonan, J., Cotney, J., & Kentros, C. (2018) · Current Biology · doi:10.1016/j.cub.2018.05.015 · Cited by 72

Activation of endogenous retroviruses during brain development causes an inflammatory response

Jönsson, M. E., Garza, R., Sharma, Y., Petri, R., Södersten, E., Johansson, J. G., Johansson, P. A., Atacho, D. A., Pircs, K., Madsen, S., et al. (2021) · The EMBO Journal · doi:10.15252/embj.2020106423 · Cited by 80

Neutralizing Gatad2a-Chd4-Mbd3/NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency

Mor, N., Rais, Y., Sheban, D., Peles, S., Aguilera-Castrejon, A., Zviran, A., Elinger, D., Viukov, S., Geula, S., Krupalnik, V., et al. (2018) · Cell Stem Cell · doi:10.1016/j.stem.2018.07.004 · Cited by 79

Dissecting Murine Muscle Stem Cell Aging through Regeneration Using Integrative Genomic Analysis

Shcherbina, A., Larouche, J., Fraczek, P., Yang, B. A., Brown, L. A., Markworth, J. F., Chung, C. H., Khaliq, M., de Silva, K., Choi, J. J., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107964 · Cited by 76

HNF1A recruits KDM6A to activate differentiated acinar cell programs that suppress pancreatic cancer

Kalisz, M., Bernardo, E., Beucher, A., Maestro, M. A., del Pozo, N., Millán, I., Haeberle, L., Schlensog, M., Safi, S. A., Knoefel, W. T., et al. (2020) · The EMBO Journal · doi:10.15252/embj.2019102808 · Cited by 77

Comparison of whole genome amplification techniques for human single cell exome sequencing

Borgström, E., Paterlini, M., Mold, J. E., Frisen, J., & Lundeberg, J. (2017) · PLOS ONE · doi:10.1371/journal.pone.0171566 · Cited by 77

TGFβ-induced fibroblast activation requires persistent and targeted HDAC-mediated gene repression

Jones, D. L., Haak, A. J., Caporarello, N., Choi, K. M., Ye, Z., Yan, H., Varelas, X., Ordog, T., Ligresti, G., & Tschumperlin, D. J. (2019) · Journal of Cell Science · doi:10.1242/jcs.233486 · Cited by 77

Proimmunogenic impact of MEK inhibition synergizes with agonist anti-CD40 immunostimulatory antibodies in tumor therapy

Baumann, D., Hägele, T., Mochayedi, J., Drebant, J., Vent, C., Blobner, S., Noll, J. H., Nickel, I., Schumacher, C., Boos, S. L., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15979-2 · Cited by 76

Nascent Transcript Folding Plays a Major Role in Determining RNA Polymerase Elongation Rates

Turowski, T. W., Petfalski, E., Goddard, B. D., French, S. L., Helwak, A., & Tollervey, D. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.06.002 · Cited by 75

A Cancer-Specific Ubiquitin Ligase Drives mRNA Alternative Polyadenylation by Ubiquitinating the mRNA 3′ End Processing Complex

Yang, S. W., Li, L., Connelly, J. P., Porter, S. N., Kodali, K., Gan, H., Park, J. M., Tacer, K. F., Tillman, H., Peng, J., et al. (2020) · Molecular Cell · doi:10.1016/j.molcel.2019.12.022 · Cited by 79

Integrated analysis of behavioral, epigenetic, and gut microbiome analyses in AppNL-G-F, AppNL-F, and wild type mice

Kundu, P., Torres, E. R. S., Stagaman, K., Kasschau, K., Okhovat, M., Holden, S., Ward, S., Nevonen, K. A., Davis, B. A., Saito, T., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-83851-4 · Cited by 75

Automated in situ chromatin profiling efficiently resolves cell types and gene regulatory programs

Janssens, D. H., Wu, S. J., Sarthy, J. F., Meers, M. P., Myers, C. H., Olson, J. M., Ahmad, K., & Henikoff, S. (2018) · Epigenetics & Chromatin · doi:10.1186/s13072-018-0243-8 · Cited by 73

Cabazitaxel versus abiraterone or enzalutamide in poor prognosis metastatic castration-resistant prostate cancer: a multicentre, randomised, open-label, phase II trial

Annala, M., Fu, S., Bacon, J. V. W., Sipola, J., Iqbal, N., Ferrario, C., Ong, M., Wadhwa, D., Hotte, S. J., Lo, G., et al. (2021) · Annals of Oncology · doi:10.1016/j.annonc.2021.03.205 · Cited by 73

Functional characterization of Alzheimer’s disease genetic variants in microglia

Yang, X., Wen, J., Yang, H., Jones, I. R., Zhu, X., Liu, W., Li, B., Clelland, C. D., Luo, W., Wong, M. Y., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01506-8 · Cited by 71

Tissue-resident memory CD8 + T cells cooperate with CD4 + T cells to drive compartmentalized immunopathology in the CNS

Vincenti, I., Page, N., Steinbach, K., Yermanos, A., Lemeille, S., Nunez, N., Kreutzfeldt, M., Klimek, B., Di Liberto, G., Egervari, K., et al. (2022) · Science Translational Medicine · doi:10.1126/scitranslmed.abl6058 · Cited by 70

Mutational signatures reveal the role of RAD52 in p53-independent p21-driven genomic instability

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Dedifferentiation and neuronal repression define familial Alzheimer’s disease

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