BEDTools: a flexible suite of utilities for comparing genomic features

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1. Intron retention is a widespread mechanism of tumor-suppressor inactivation
   Hyunchul Jung, Donghoon Lee, Jongkeun Lee, Donghyun Park, Yeon Jeong Kim, Woong‐Yang Park, Dongwan Hong, Peter J. Park, Eunjung Lee · 2015 · Nature Genetics
2. Developmental Acquisition of Regulomes Underlies Innate Lymphoid Cell Functionality
   Shih, Han-Yu, Sciumè, Giuseppe, Mikami, Yohei, Guo, Liying, Sun, Hong-Wei, Brooks, Stephen R., Urban, Joseph F., Davis, Fred P., Kanno, Yuka, O’Shea, John J. · 2016 · Cell
3. Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response
   HIPSCI Consortium, Alasoo, Kaur, Rodrigues, Julia, Mukhopadhyay, Subhankar, Knights, Andrew J., Mann, Alice L., Kundu, Kousik, Hale, Christine, Dougan, Gordon, Gaffney, Daniel J. · 2018 · Nature Genetics
4. The Cellular EJC Interactome Reveals Higher-Order mRNP Structure and an EJC-SR Protein Nexus
   Guramrit Singh, Alper Küçükural, Can Cenik, John Leszyk, Scott A. Shaffer, Zhiping Weng, Melissa J. Moore · 2012 · Cell
5. Genomic Variation in Natural Populations ofDrosophila melanogaster
   Charles H. Langley, Kristian Stevens, Charis Cardeno, Yuh Chwen G. Lee, Daniel R. Schrider, John E. Pool, Sasha A. Langley, Charlyn Suarez, Russell B Corbett-Detig, Bryan Kolaczkowski et al. · 2012 · Genetics
6. The Essential Genome of Escherichia coli K-12
   Emily C. A. Goodall, Ashley Robinson, Iain G. Johnston, Sara Jabbari, Keith A. Turner, Adam. F. Cunningham, Peter A. Lund, Jeffrey A. Cole, Ian R. Henderson · 2018 · mBio
7. Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks
   Rubin, Adam J., Parker, Kevin R., Satpathy, Ansuman T., Qi, Yanyan, Wu, Beijing, Ong, Alvin J., Mumbach, Maxwell R., Ji, Andrew L., Kim, Daniel S., Cho, Seung Woo et al. · 2019 · Cell
8. Parent-of-origin-specific signatures of de novo mutations
   Jakob M. Goldmann, Wendy S.W. Wong, Michele Pinelli, Terry Farrah, Dale L. Bodian, Anna Stittrich, Gustavo Glusman, Lisenka E.L.M. Vissers, Alexander Hoischen, Jared C. Roach et al. · 2016 · Nature Genetics
9. Loci associated with skin pigmentation identified in African populations
   Crawford, Nicholas G., Kelly, Derek E., Hansen, Matthew E. B., Beltrame, Marcia H., Fan, Shaohua, Bowman, Shanna L., Jewett, Ethan, Ranciaro, Alessia, Thompson, Simon, Lo, Yancy et al. · 2017 · Science
10. Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection
    ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants, Adam D. Ewing, Kathleen E. Houlahan, Yin Hu, Kyle Ellrott, Cristian Caloian, Takafumi N. Yamaguchi, J Christopher Bare, Christine P’ng, Daryl M. Waggott et al. · 2015 · Nature Methods
11. Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression
    Cuomo, Anna S. E., Seaton, Daniel D., McCarthy, Davis J., Martinez, Iker, Bonder, Marc Jan, Garcia-Bernardo, Jose, Amatya, Shradha, Madrigal, Pedro, Isaacson, Abigail, Buettner, Florian et al. · 2020 · Nature Communications
12. Interactome Maps of Mouse Gene Regulatory Domains Reveal Basic Principles of Transcriptional Regulation
    Kyong-Rim Kieffer-Kwon, Zhonghui Tang, Ewy A. Mathé, Jason Qian, Myong‐Hee Sung, Guoliang Li, Wolfgang Resch, Songjoon Baek, Nathanael D. Pruett, Lars Grøntved et al. · 2013 · Cell
13. N-methyladenine DNA Modification in Glioblastoma
    Qi Xie, Tao Wu, Ryan C. Gimple, Zheng Li, Briana C. Prager, Qiulian Wu, Yang Yu, Pengcheng Wang, Yinsheng Wang, David U. Gorkin et al. · 2018 · Cell
14. Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts
    Undiagnosed Diseases Network, Frésard, Laure, Care4Rare Canada Consortium, Smail, Craig, Ferraro, Nicole M., Teran, Nicole A., Li, Xin, Smith, Kevin S., Bonner, Devon, Kernohan, Kristin D. et al. · 2019 · Nature Medicine
15. High-resolution mycobiota analysis reveals dynamic intestinal translocation preceding invasive candidiasis
    Bing Zhai, Mihaela Ola, Thierry Rolling, Nicholas L. Tosini, Sari Joshowitz, Eric R. Littmann, Luigi A. Amoretti, Emily Fontana, Roberta J. Wright, Edwin Miranda et al. · 2020 · Nature Medicine
16. CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize
    Jonathan Isaiah Gent, Nathanael A. Ellis, Lin Guo, Alex Harkess, Yingyin Yao, Xiaoyu Zhang, R. Kelly Dawe · 2012 · Genome Research
17. The genetic prehistory of the New World Arctic
    Raghavan, Maanasa, DeGiorgio, Michael, Albrechtsen, Anders, Moltke, Ida, Skoglund, Pontus, Korneliussen, Thorfinn S., Grønnow, Bjarne, Appelt, Martin, Gulløv, Hans Christian, Friesen, T. Max et al. · 2014 · Science
18. On the origin and evolutionary consequences of gene body DNA methylation
    Adam J. Bewick, Lexiang Ji, Chad E. Niederhuth, Eva‐Maria Willing, Brigitte T. Hofmeister, Xiuling Shi, Li Wang, Zefu Lu, Nicholas A. Rohr, Benjamin Hartwig et al. · 2016 · Proceedings of the National Academy of Sciences
19. Establishment, maintenance, and recall of inflammatory memory
    Samantha B. Larsen, Christopher J. Cowley, Sairaj M. Sajjath, Douglas Barrows, Yihao Yang, Thomas S. Carroll, Elaine V. Fuchs · 2021 · Cell stem cell
20. Supplementation of Saturated Long-Chain Fatty Acids Maintains Intestinal Eubiosis and Reduces Ethanol-induced Liver Injury in Mice
    Chen, Peng, Torralba, Manolito, Tan, Justin, Embree, Mallory, Zengler, Karsten, Stärkel, Peter, van Pijkeren, Jan-Peter, DePew, Jessica, Loomba, Rohit, Ho, Samuel B. et al. · 2015 · Gastroenterology
21. Novel mutations in PIEZO1 cause an autosomal recessive generalized lymphatic dysplasia with non-immune hydrops fetalis
    Elisavet Fotiou, Silvia Martin‐Almedina, Michael A. Simpson, Shin Lin, Kristiana D. Gordon, Glen W. Brice, Giles Atton, Iona Jeffery, David C. Rees, Cyril Mignot et al. · 2015 · Nature Communications
22. LHX2- and LDB1-mediated trans interactions regulate olfactory receptor choice
    Kevin D. Monahan, Adan Horta, Stavros Lomvardas · 2019 · Nature
23. A complete telomere-to-telomere assembly of the maize genome
    Jian Chen, Zijian Wang, Kaiwen Tan, Wei Huang, Junpeng Shi, Tong Li, Jiang Yong Hu, Kai Wang, Chao Wang, Beibei Xin et al. · 2023 · Nature Genetics
24. lobSTR: A short tandem repeat profiler for personal genomes
    Melissa Gymrek, David Golan, Saharon Rosset, Yaniv Erlich · 2012 · Genome Research
25. Community-wide transcriptome of the oral microbiome in subjects with and without periodontitis
    Duran-Pinedo, Ana E, Chen, Tsute, Teles, Ricardo, Starr, Jacqueline R, Wang, Xiaoshan, Krishnan, Keerthana, Frias-Lopez, Jorge · 2014 · The ISME Journal
26. Neuropeptide CGRP Limits Group 2 Innate Lymphoid Cell Responses and Constrains Type 2 Inflammation
    Hiroyuki Nagashima, Tanel Mahlakõiv, Han‐Yu Shih, Fred P. Davis, Françoise Meylan, Yuefeng Huang, Oliver J. Harrison, Chen Yao, Yohei Mikami, Joseph F. Urban et al. · 2019 · Immunity
27. Species- and site-specific genome editing in complex bacterial communities
    Benjamin E. Rubin, Spencer Diamond, Brady F. Cress, Alexander Crits‐Christoph, Yue Clare Lou, Adair L. Borges, Haridha Shivram, Christine He, Michael Y. Xu, Zeyi Zhou et al. · 2021 · Nature Microbiology
28. A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae
    Nookaew, Intawat, Papini, Marta, Pornputtapong, Natapol, Scalcinati, Gionata, Fagerberg, Linn, Uhlén, Matthias, Nielsen, Jens · 2012 · Nucleic Acids Research
29. Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell level
    Andrew D Farmer, Sandra Thibivilliers, Kook Hui Ryu, John Schiefelbein, Marc Libault · 2021 · Molecular Plant
30. Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease
    Ralf Gilsbach, Sebastian Preißl, Björn Andreas Grüning, Tilman Schnick, Lukas Burger, Vladimı́r Beneš, Andreas Würch, Ulrike Bönisch, Stefan Günther, Rolf Backofen et al. · 2014 · Nature Communications
31. Altered Levels of Mitochondrial DNA Are Associated with Female Age, Aneuploidy, and Provide an Independent Measure of Embryonic Implantation Potential
    Elpida Fragouli, Katharina Späth, Samer Alfarawati, Fiona Kaper, Andrew Craig, Claude-Edouard Michel, Felix Kokocinski, Jacques Cohen, S. Munné, Dagan Wells · 2015 · PLoS Genetics
32. Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries
    Meredith L. Carpenter, Jason D. Buenrostro, Cristina E. Valdiosera, Hannes Schroeder, Morten E. Allentoft, Martin Sikora, Morten Rasmussen, Simon Gravel, Sonia E. Guillén, Georgi Nekhrizov et al. · 2013 · The American Journal of Human Genetics
33. Discrete functions of nuclear receptor Rev-erbα couple metabolism to the clock
    Yuxiang Zhang, Bin Fang, Matthew J. Emmett, Manashree Damle, Zheng Sun, Dan Feng, Sean M. Armour, Jarrett R. Remsberg, Jennifer Jager, Raymond E. Soccio et al. · 2015 · Science
34. Genome-wide Analysis Reveals SR Protein Cooperation and Competition in Regulated Splicing
    Shatakshi Pandit, Yu Zhou, Lily Shiue, Gabriela Coutinho-Mansfield, Hairi Li, Jinsong Qiu, Jie Sheng Huang, Gene Wei-Ming Yeo, Manuel Ares, Xiang‐Dong Fu · 2013 · Molecular Cell
35. Comparative genomics reveals the dynamics of chromosome evolution in Lepidoptera
    Charlotte J Wright, Lewis Stevens, Alexander Mackintosh, Mara Lawniczak, Mark Blaxter · 2024 · Nature Ecology & Evolution
36. Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes
    Zefu Lu, Brigitte T. Hofmeister, Christopher Vollmers, Rebecca M. DuBois, Robert J. Schmitz · 2016 · Nucleic Acids Research
37. CDK12 regulates DNA repair genes by suppressing intronic polyadenylation
    Dubbury, Sara J., Boutz, Paul L., Sharp, Phillip A. · 2018 · Nature
38. The Genome 10K Project: A Way Forward
    Koepfli, Klaus-Peter, Paten, Benedict, the Genome 10K Community of Scientists, O’Brien, Stephen J. · 2015 · Annual Review of Animal Biosciences
39. Social status alters immune regulation and response to infection in macaques
    Snyder-Mackler, Noah, Sanz, Joaquín, Kohn, Jordan N., Brinkworth, Jessica F., Morrow, Shauna, Shaver, Amanda O., Grenier, Jean-Christophe, Pique-Regi, Roger, Johnson, Zachary P., Wilson, Mark E. et al. · 2016 · Science
40. Performance evaluation for rapid detection of pan-cancer microsatellite instability with MANTIS
    Esko Antero Kautto, Russell Bonneville, Jharna Miya, Lianbo Yu, Melanie A. Krook, Julie W. Reeser, Sameek Roychowdhury · 2016 · Oncotarget
41. Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico
    Åshild J. Vågene‬, Alexander Herbig, Michael G. Campana, Nelly M. Robles García, Christina Warinner, Susanna J. Sabin, Maria A. Spyrou, Aida Andrades Valtueña, Daniel H. Huson, Noreen Tuross et al. · 2018 · Nature Ecology & Evolution
42. Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation
    Maria Pachiadaki, Eva Sintes, Kristin Bergauer, Julia M. Brown, Nicholas R. Record, Brandon K. Swan, Mary Elizabeth Mathyer, Steven Hallam, Purificación López‐García, Yoshihiro Takaki et al. · 2017 · Science
43. Identification of entacapone as a chemical inhibitor of FTO mediating metabolic regulation through FOXO1
    Shiming Peng, Wen Xiao, Dapeng Ju, Baofa Sun, Nannan Hou, Qianlan Liu, Yanli Wang, Haijiao Zhao, Chun‐Chun Gao, Song Zhang et al. · 2019 · Science Translational Medicine
44. Rhizobial tRNA-derived small RNAs are signal molecules regulating plant nodulation
    Bo Ren, Xutong Wang, Jingbo Duan, Jianxin Ma · 2019 · Science
45. Genotyping structural variants in pangenome graphs using the vg toolkit
    Hickey, Glenn, Heller, David, Monlong, Jean, Sibbesen, Jonas A., Sirén, Jouni, Eizenga, Jordan, Dawson, Eric T., Garrison, Erik, Novak, Adam M., Paten, Benedict · 2020 · Genome Biology
46. A gene–environment-induced epigenetic program initiates tumorigenesis
    Direna Alonso‐Curbelo, Yu-Jui Ho, Cassandra Burdziak, Jesper L.V. Mååg, John P. Morris, Rohit Chandwani, Hsuan-An Chen, Kaloyan M. Tsanov, Francisco M. Barriga, Wei Luan et al. · 2021 · Nature
47. Transcriptomic profiling of SARS-CoV-2 infected human cell lines identifies HSP90 as target for COVID-19 therapy
    Emanuel Wyler, Kirstin Mösbauer, Vedran Franke, Asija Diag, Lina Theresa Gottula, Roberto Arsiè, Filippos Klironomos, David Koppstein, Katja Hönzke, Salah Ayoub et al. · 2021 · iScience
48. Spatiotemporal Evolution of the Primary Glioblastoma Genome
    Jinkuk Kim, In‐Hee Lee, Hee Jin Cho, Chul‐Kee Park, Yang-Soon Jung, Yanghee Kim, So Hee Nam, Byung Sup Kim, Mark D. Johnson, Doo‐Sik Kong et al. · 2015 · Cancer Cell
49. A Genome-wide Map of CTCF Multivalency Redefines the CTCF Code
    Hirotaka Nakahashi, Kyong-Rim Kieffer, Wolfgang Resch, Laura Vian, Marei Dose, Diana A. Stavreva, Ofir Hakim, Nathanael D. Pruett, Steevenson Nelson, Arito Yamane et al. · 2013 · Cell Reports
50. GADD45A binds R-loops and recruits TET1 to CpG island promoters
    Khelifa Arab, Emil Karaulanov, Michael U. Musheev, Philipp Trnka, Andrea Schäfer, Ingrid Grummt, Christof Niehrs · 2018 · Nature Genetics
51. ImmGen report: sexual dimorphism in the immune system transcriptome
    Gal-Oz, Shani Talia, Maier, Barbara, Yoshida, Hideyuki, Seddu, Kumba, Elbaz, Nitzan, Czysz, Charles, Zuk, Or, Stranger, Barbara E., Ner-Gaon, Hadas, Shay, Tal · 2019 · Nature Communications
52. Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development
    Phanstiel, Douglas H., Van Bortle, Kevin, Spacek, Damek, Hess, Gaelen T., Shamim, Muhammad Saad, Machol, Ido, Love, Michael I., Aiden, Erez Lieberman, Bassik, Michael C., Snyder, Michael P. · 2017 · Molecular Cell
53. The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution
    Smith, Jeramiah J., Timoshevskaya, Nataliya, Ye, Chengxi, Holt, Carson, Keinath, Melissa C., Parker, Hugo J., Cook, Malcolm E., Hess, Jon E., Narum, Shawn R., Lamanna, Francesco et al. · 2018 · Nature Genetics
54. BRD4 assists elongation of both coding and enhancer RNAs by interacting with acetylated histones
    Tomohiko Kanno, Yuka Kanno, Gary LeRoy, Eric I. Campos, Hong‐Wei Sun, Stephen R. Brooks, Golnaz Vahedi, Tom D. Heightman, Benjamin Aaron Garcia, Danny Reinberg et al. · 2014 · Nature Structural & Molecular Biology
55. Enriching the ant tree of life: enhanced UCE bait set for genome‐scale phylogenetics of ants and other Hymenoptera
    Michael G. Branstetter, John T. Longino, Philip S. Ward, Brant C. Faircloth · 2017 · Methods in Ecology and Evolution
56. Transcriptional landscape of repetitive elements in normal and cancer human cells
    Steven W. Criscione, Yue Zhang, William Thompson, John M. Sedivy, Nicola Neretti · 2014 · BMC Genomics
57. SARS-CoV-2 genomic and subgenomic RNAs in diagnostic samples are not an indicator of active replication
    Alexandersen, Soren, Chamings, Anthony, Bhatta, Tarka Raj · 2020 · Nature Communications
58. Transcriptome variation in human tissues revealed by long-read sequencing
    Dafni A. Glinos, Garrett Garborcauskas, Paul Hoffman, Nava Ehsan, Lihua Jiang, Alper Gokden, Xiaoguang Dai, François Aguet, Kathleen L. Brown, Kiran V. Garimella et al. · 2022 · Nature
59. Genome-wide Mapping of Transcriptional Start Sites Defines an Extensive Leaderless Transcriptome in Mycobacterium tuberculosis
    Cortes, Teresa, Schubert, Olga T., Rose, Graham, Arnvig, Kristine B., Comas, Iñaki, Aebersold, Ruedi, Young, Douglas B. · 2013 · Cell Reports
60. Deep-sequencing of human Argonaute-associated small RNAs provides insight into miRNA sorting and reveals Argonaute association with RNA fragments of diverse origin
    Alexander Maxwell Burroughs, Yoshinari Ando, Michiel de Hoon, Yasuhiro Tomaru, Harukazu Suzuki, Yoshihide Hayashizaki, Carsten O. Daub · 2011 · RNA Biology
61. The effects of death and post-mortem cold ischemia on human tissue transcriptomes
    Pedro Gabriel Ferreira, Manuel Muñoz-Aguirre, Ferrán Reverter, Caio De SĂĄ Godinho, Abel Sousa, Alicia Amadoz, Reza Sodaei, Marta R. Hidalgo, Dmitri Davidovich Pervouchine, José Carbonell‐Caballero et al. · 2018 · Nature Communications
62. Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes
    Amanda M. Ackermann, Zhiping Paul Wang, Jonathan Schug, Ali Naji, Klaus H. Kaestner · 2016 · Molecular Metabolism
63. An intrinsic S/G 2 checkpoint enforced by ATR
    Joshua C. Saldivar, Stephan Hamperl, Michael J. Bocek, Mingyu Chung, Thomas E. Bass, Fernanda Cisneros-Soberanis, Kumiko Samejima, Linfeng Xie, James R. Paulson, William C. Earnshaw et al. · 2018 · Science
64. GRID-seq reveals the global RNA–chromatin interactome
    Xiao Li, Bing Zhou, Liang Chen, Lan‐Tao Gou, Hairi Li, Xiang‐Dong Fu · 2017 · Nature Biotechnology
65. Transcriptional addiction in cancer cells is mediated by YAP/TAZ through BRD4
    Francesca Zanconato, Giusy Battilana, Mattia Forcato, Letizia Filippi, Luca Azzolin, Andrea Manfrin, Erika Giorgia Quaranta, Daniele Di Biagio, Gianluca Sigismondo, Vincenza Guzzardo et al. · 2018 · Nature Medicine
66. Transcriptome and epigenome landscape of human cortical development modeled in organoids
    Anahita Amiri, Gianfilippo Coppola, Soraya Scuderi, Feinan Wu, Tanmoy Roychowdhury, Fuchen Liu, Sirisha Pochareddy, Yurae Shin, Alexias Safi, Lingyun Song et al. · 2018 · Science
67. Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance
    Patrick Munk, Christian Brinch, Frederik Duus Møller, Thomas Nordahl Petersen, René S. Hendriksen, Anne Mette Seyfarth, Jette Sejer Kjeldgaard, Christina Aaby Svendsen, Bram A. D. van Bunnik, Fanny Berglund et al. · 2022 · Nature Communications
68. Codon identity regulates mRNA stability and translation efficiency during the maternal‐to‐zygotic transition
    Ariel Bazzini, Florencia Del Viso, Miguel A. Moreno-Mateos, Timothy G. Johnstone, Charles E. Vejnar, Yidan Qin, Jun Yao, Mustafa Kezar Khokha, Antonio J. Giráldez · 2016 · The EMBO Journal
69. Deficiency of terminal ADP‐ribose protein glycohydrolase TARG1/C6orf130 in neurodegenerative disease
    Reza Sharifi, Rosa Morra, C. Denise Appel, Michael Tallis, Barry A. Chioza, Gytis Jankevicius, Michael A. Simpson, Ivan Matić, Ege Sackey, Barbara Golia et al. · 2013 · The EMBO Journal
70. –Omic and Electronic Health Record Big Data Analytics for Precision Medicine
    Po-Yen Wu, Chih‐Wen Cheng, Chanchala D. Kaddi, Janani Venugopalan, Ryan Hoffman, May Dongmei Wang · 2016 · IEEE Transactions on Biomedical Engineering
71. Integrative genomic and transcriptomic analysis of leiomyosarcoma
    Priya Chudasama, Sadaf Shabbir Mughal, Mathijs Arnoud Sanders, Daniel Hübschmann, Inn Chung, Katharina I. Deeg, Siao-Han Wong, Sophie Rabe, Mario Hlevnjak, Marc Zapatka et al. · 2018 · Nature Communications
72. Dynamic methylome of internal mRNA N7-methylguanosine and its regulatory role in translation
    Lionel Malbec, Ting Zhang, Yusheng Chen, Ying Zhang, Baofa Sun, Boyang Shi, Yongliang Zhao, Ying Yang, Yun‐Gui Yang · 2019 · Cell Research
73. Construction of a chromosome-scale long-read reference genome assembly for potato
    Gina M. Pham, John P. Hamilton, Joshua C. Wood, Joseph T Burke, Hainan Zhao, Brieanne Vaillancourt, Shujun Ou, Jiming Jiang, C. Robin Buell · 2020 · GigaScience
74. Improved peak-calling with MACS2
    John M. Gaspar · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
75. Uridylation by TUT4 and TUT7 Marks mRNA for Degradation
    Jaechul Lim, Minju Ha, Hyeshik Chang, S. Chul Kwon, Dhirendra K. Simanshu, Dinshaw J. Patel, V Narry Kim · 2014 · Cell
76. EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species
    Tianshun Gao, Jiang X. Qian · 2019 · Nucleic Acids Research
77. Immune regulation by fungal strain diversity in inflammatory bowel disease
    Xin V. Li, Irina Leonardi, Gregory Putzel, Alexa Semon, William D. Fiers, Takato Kusakabe, Woan-Yu Lin, Iris Hanxing Gao, Itai Doron, Alejandra Gutiérrez-Guerrero et al. · 2022 · Nature
78. Evolutionary changes in promoter and enhancer activity during human corticogenesis
    Reilly, Steven K., Yin, Jun, Ayoub, Albert E., Emera, Deena, Leng, Jing, Cotney, Justin, Sarro, Richard, Rakic, Pasko, Noonan, James P. · 2015 · Science
79. Genomic Landscape and Mutational Signatures of Deafness-Associated Genes
    Héla Azaiez, Kevin T. A. Booth, Sean S. Ephraim, Bradley Crone, E. Ann Black-Ziegelbein, Robert J. Marini, Aiden Eliot Shearer, Christina Sloan-Heggen, Diana L. Kolbe, Thomas L. Casavant et al. · 2018 · The American Journal of Human Genetics
80. GALLO: An R package for genomic annotation and integration of multiple data sources in livestock for positional candidate loci
    Pablo Augusto de Souza Fonseca, Aroa Suárez‐Vega, Gabriele Marras, Ángela Cánovas · 2020 · GigaScience
81. Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer
    Tamara Ouspenskaia, Travis E. Law, Karl R. Clauser, Susan Klaeger, Siranush Sarkizova, François Aguet, Bo Li, Elena Christian, Binyamin A. Knisbacher, Phuong M. Le et al. · 2021 · Nature Biotechnology
82. Social environment is associated with gene regulatory variation in the rhesus macaque immune system
    Tung, Jenny, Barreiro, Luis B., Johnson, Zachary P., Hansen, Kasper D., Michopoulos, Vasiliki, Toufexis, Donna, Michelini, Katelyn, Wilson, Mark E., Gilad, Yoav · 2012 · Proceedings of the National Academy of Sciences
83. The transcriptional landscape of mouse beta cells compared to human beta cells reveals notable species differences in long non-coding RNA and protein-coding gene expression
    Benner, Christopher, van der Meulen, Talitha, Cacéres, Elena, Tigyi, Kristof, Donaldson, Cynthia J, Huising, Mark O · 2014 · BMC Genomics
84. Natural regulatory mutations elevate the fetal globin gene via disruption of BCL11A or ZBTB7A binding
    Martyn, Gabriella E., Wienert, Beeke, Yang, Lu, Shah, Manan, Norton, Laura J., Burdach, Jon, Kurita, Ryo, Nakamura, Yukio, Pearson, Richard C. M., Funnell, Alister P. W. et al. · 2018 · Nature Genetics
85. Use Model-Based Analysis of ChIP-Seq (MACS) to Analyze Short Reads Generated by Sequencing Protein–DNA Interactions in Embryonic Stem Cells
    Tao Liu · 2014 · Methods in molecular biology
86. Global spread of three multidrug-resistant lineages of Staphylococcus epidermidis
    Jean Y. H. Lee, Ian R. Monk, Anders Gonçalves da Silva, Torsten Seemann, Kyra Chua, Angela Kearns, Robert Hill, Neil Woodford, Mette Damkjær Bartels, Birgit Strommenger et al. · 2018 · Nature Microbiology
87. Histone H3.3 K27M Accelerates Spontaneous Brainstem Glioma and Drives Restricted Changes in Bivalent Gene Expression
    Jon D. Larson, Lawryn H. Kasper, Barbara S. Paugh, Hongjian Jin, Gang Wu, Chang-Hyuk Kwon, Yiping Fan, Timothy I. Shaw, André Bortolini Silveira, Chunxu Qu et al. · 2018 · Cancer Cell
88. Nucleotide excision repair is impaired by binding of transcription factors to DNA
    Radhakrishnan Sabarinathan, Loris Mularoni, Jordi Deu-Pons, Abel González-Pérez, Núria López-Bigas · 2016 · Nature
89. 5-Hydroxymethylcytosine signatures in cell-free DNA provide information about tumor types and stages
    Chun‐Xiao Song, Senlin Yin, Li Ma, Amanda Wheeler, Yu Chen, Yan Zhang, Bin Liu, Junjie Xiong, Weihan Zhang, Jian‐Kun Hu et al. · 2017 · Cell Research
90. Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline
    Nicolás Rascovan, Karl-Göran Sjögren, Kristian Kristiansen, Rasmus Nielsen, Eske Willerslev, Christelle Desnues, Simon Rasmussen · 2018 · Cell
91. Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling
    Caleb A. Lareau, Leif S. Ludwig, Christoph Muus, Satyen Harish Gohil, Tongtong Zhao, Zachary Chiang, Karin Pelka, Jeffrey M. Verboon, Wendy Luo, Elena Christian et al. · 2020 · Nature Biotechnology
92. Insulator function and topological domain border strength scale with architectural protein occupancy
    Kevin Van Bortle, Michael H. Nichols, Li Li, Chin‐Tong Ong, Naomi Takenaka, Zhaohui Steve Qin, Victor G. Corces · 2014 · Genome biology
93. Establishment of mouse expanded potential stem cells
    Jian Ping Yang, David John Ryan, Wei Wang, Jason Cheuk-Ho Tsang, Guocheng Lan, Hideki Masaki, Xuefei Gao, Liliana Antunes, Yong Yu, Zhexin Zhu et al. · 2017 · Nature
94. The Augmented R-Loop Is a Unifying Mechanism for Myelodysplastic Syndromes Induced by High-Risk Splicing Factor Mutations
    Liang Chen, Jiayu Chen, Yi-Jou Huang, Ying Gu, Jinsong Qiu, Hao Qian, Changwei Shao, Xuan Zhang, Jing Hu, Hairi Li et al. · 2018 · Molecular Cell
95. Landscape and Regulation of m6A and m6Am Methylome across Human and Mouse Tissues
    June Liu, Kai Li, Jiabin Cai, Mingchang Zhang, Xiaoting Zhang, Xushen Xiong, Haowei Meng, Xizhan Xu, Zhibin Huang, Jinying Peng et al. · 2019 · Molecular Cell
96. Epigenetic patterns in a complete human genome
    Gershman, Ariel, Sauria, Michael E. G., Guitart, Xavi, Vollger, Mitchell R., Hook, Paul W., Hoyt, Savannah J., Jain, Miten, Shumate, Alaina, Razaghi, Roham, Koren, Sergey et al. · 2022 · Science
97. Discovery of stimulation-responsive immune enhancers with CRISPR activation
    Simeonov, Dimitre R., Gowen, Benjamin G., Boontanrart, Mandy, Roth, Theodore L., Gagnon, John D., Mumbach, Maxwell R., Satpathy, Ansuman T., Lee, Youjin, Bray, Nicolas L., Chan, Alice Y. et al. · 2017 · Nature
98. Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa
    M. Gallego-Llorente, Eppie R. Jones, Anders Eriksson, Veronika Siska, Kathryn Weedman Arthur, J. W. Arthur, Matthew C. Curtis, Jay T. Stock, Mauro Coltorti, Pierluigi Pieruccini et al. · 2015 · Science
99. Epigenetic therapy induces transcription of inverted SINEs and ADAR1 dependency
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100. Polyamine metabolism is a central determinant of helper T cell lineage fidelity
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