BEDTools: a flexible suite of utilities for comparing genomic features

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1. Genomic atlas of the plasma metabolome prioritizes metabolites implicated in human diseases
   Yiheng Chen, Tianyuan Lu, U. Pettersson, Isobel D. Stewart, Guillaume Butler‐Laporte, Tomoko Nakanishi, Agustin Cerani, Kevin Y. H. Liang, Satoshi Yoshiji, Julian Willett et al. · 2023 · Nature Genetics
2. The power of genetic diversity in genome-wide association studies of lipids
   Graham, Sarah E., Clarke, Shoa L., Wu, Kuan-Han H., Kanoni, Stavroula, Zajac, Greg J. M., Ramdas, Shweta, Surakka, Ida, Ntalla, Ioanna, Vedantam, Sailaja, Winkler, Thomas W. et al. · 2021 · Nature
3. Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing
   Zhang, Jianjun, Fujimoto, Junya, Zhang, Jianhua, Wedge, David C., Song, Xingzhi, Zhang, Jiexin, Seth, Sahil, Chow, Chi-Wan, Cao, Yu, Gumbs, Curtis et al. · 2014 · Science
4. The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut
   David J. Bertioli, Steven B. Cannon, Lutz Froenicke, Guodong Huang, Andrew D Farmer, Ethalinda K. S. Cannon, Xin Liu, Dongying Gao, Josh Paul Clevenger, Sudhansu Dash et al. · 2016 · Nature Genetics
5. Chromatin states define tumour-specific T cell dysfunction and reprogramming
   Philip, Mary, Fairchild, Lauren, Sun, Liping, Horste, Ellen L., Camara, Steven, Shakiba, Mojdeh, Scott, Andrew C., Viale, Agnes, Lauer, Peter, Merghoub, Taha et al. · 2017 · Nature
6. Zc3h13 Regulates Nuclear RNA m6A Methylation and Mouse Embryonic Stem Cell Self-Renewal
   Jing Wen, Ruitu Lyu, Honghui Ma, Hongjie Shen, Chenxi He, Jiahua Wang, Fangfang Jiao, Hang Liu, Pengyuan Yang, Li Tan et al. · 2018 · Molecular Cell
7. Control of somatic tissue differentiation by the long non-coding RNA TINCR
   M. Kretz, Z. Siprashvili, C. Chu, D. Webster, A. Zehnder, Kun Qu, Carolyn S. Lee, R. Flockhart, A. Groff, Jennifer M. Chow et al. · 2012 · Nature
8. Cicero predicts cis-regulatory DNA interactions from single-cell chromatin accessibility data
   Pliner, Hannah A., Packer, Jonathan S., McFaline-Figueroa, José L., Cusanovich, Darren A., Daza, Riza M., Aghamirzaie, Delasa, Srivatsan, Sanjay, Qiu, Xiaojie, Jackson, Dana, Minkina, Anna et al. · 2018 · Molecular Cell
9. Joint profiling of chromatin accessibility and gene expression in thousands of single cells
   Cao, Junyue, Cusanovich, Darren A., Ramani, Vijay, Aghamirzaie, Delasa, Pliner, Hannah A., Hill, Andrew J., Daza, Riza M., McFaline-Figueroa, Jose L., Packer, Jonathan S., Christiansen, Lena et al. · 2018 · Science
10. Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms
    Rolf Sommer Kaas, Pimlapas Leekitcharoenphon, Frank M. Aarestrup, Ole Lund · 2014 · PLoS ONE
11. Therapeutic targeting of BET bromodomain proteins in castration-resistant prostate cancer
    Irfan Ahmed Asangani, Vijaya L. Dommeti, Xiaoju Wang, Rohit Malik, Marcin P. Cieslik, Rendong Yang, June F Escara-Wilke, Kari Wilder-Romans, Sudheer Dhanireddy, Carl G. Engelke et al. · 2014 · Nature
12. HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease
    Lucas D. Ward, M Kellis · 2015 · Nucleic Acids Research
13. The cohesin release factor WAPL restricts chromatin loop extension
    Haarhuis, Judith H.I., van der Weide, Robin H., Blomen, Vincent A., Yáñez-Cuna, J. Omar, Amendola, Mario, van Ruiten, Marjon S., Krijger, Peter H.L., Teunissen, Hans, Medema, René H., van Steensel, Bas et al. · 2017 · Cell
14. Braveheart, a Long Noncoding RNA Required for Cardiovascular Lineage Commitment
    Carla Klattenhoff, Johanna C. Scheuermann, Lauren E. Surface, Robert K. Bradley, Paul Fields, Matthew L. Steinhauser, Huiming Ding, Vincent L. Butty, Lillian Torrey Sosa, Simon F. Haas et al. · 2013 · Cell
15. Integrative functional genomic analysis of human brain development and neuropsychiatric risks
    Li, Mingfeng, Santpere, Gabriel, Imamura Kawasawa, Yuka, Evgrafov, Oleg V., Gulden, Forrest O., Pochareddy, Sirisha, Sunkin, Susan M., Li, Zhen, Shin, Yurae, Zhu, Ying et al. · 2018 · Science
16. Rapid and precise alignment of raw reads against redundant databases with KMA
    Philip T. L. C. Clausen, Frank M. Aarestrup, Ole Lund · 2018 · BMC Bioinformatics
17. A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility
    Cusanovich, Darren A., Hill, Andrew J., Aghamirzaie, Delasa, Daza, Riza M., Pliner, Hannah A., Berletch, Joel B., Filippova, Galina N., Huang, Xingfan, Christiansen, Lena, DeWitt, William S. et al. · 2018 · Cell
18. ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases
    Li Shen, Ning‐Yi Shao, Xiaochuan Liu, Eric J. Nestler · 2014 · BMC Genomics
19. Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression
    Fairfax, Benjamin P., Humburg, Peter, Makino, Seiko, Naranbhai, Vivek, Wong, Daniel, Lau, Evelyn, Jostins, Luke, Plant, Katharine, Andrews, Robert, McGee, Chris et al. · 2014 · Science
20. Genomically Recoded Organisms Expand Biological Functions
    Marc J. Lajoie, Alexis J. Rovner, Daniel Bryan Goodman, Hans R. Aerni, Adrian D. Haimovich, Gleb Kuznetsov, Jaron A. M. Mercer, Harris H. Wang, Peter A. Carr, Joshua A. Mosberg et al. · 2013 · Science
21. Gene expression across mammalian organ development
    Cardoso-Moreira, Margarida, Halbert, Jean, Valloton, Delphine, Velten, Britta, Chen, Chunyan, Shao, Yi, Liechti, Angélica, Ascenção, Kelly, Rummel, Coralie, Ovchinnikova, Svetlana et al. · 2019 · Nature
22. Gateways to the FANTOM5 promoter level mammalian expression atlas
    Lizio, Marina, Harshbarger, Jayson, Shimoji, Hisashi, Severin, Jessica, Kasukawa, Takeya, Sahin, Serkan, Abugessaisa, Imad, Fukuda, Shiro, Hori, Fumi, Ishikawa-Kato, Sachi et al. · 2015 · Genome Biology
23. ChIP‐Atlas: a data‐mining suite powered by full integration of public ChIP‐seq data
    Oki, Shinya, Ohta, Tazro, Shioi, Go, Hatanaka, Hideki, Ogasawara, Osamu, Okuda, Yoshihiro, Kawaji, Hideya, Nakaki, Ryo, Sese, Jun, Meno, Chikara · 2018 · The EMBO Reports
24. Prediction of acute myeloid leukaemia risk in healthy individuals
    Abelson, Sagi, Collord, Grace, Ng, Stanley W. K., Weissbrod, Omer, Mendelson Cohen, Netta, Niemeyer, Elisabeth, Barda, Noam, Zuzarte, Philip C., Heisler, Lawrence, Sundaravadanam, Yogi et al. · 2018 · Nature
25. G&T-seq: parallel sequencing of single-cell genomes and transcriptomes
    Macaulay, Iain C, Haerty, Wilfried, Kumar, Parveen, Li, Yang I, Hu, Tim Xiaoming, Teng, Mabel J, Goolam, Mubeen, Saurat, Nathalie, Coupland, Paul, Shirley, Lesley M et al. · 2015 · Nature Methods
26. A high-fidelity Cas9 mutant delivered as a ribonucleoprotein complex enables efficient gene editing in human hematopoietic stem and progenitor cells
    Vakulskas, Christopher A., Dever, Daniel P., Rettig, Garrett R., Turk, Rolf, Jacobi, Ashley M., Collingwood, Michael A., Bode, Nicole M., McNeill, Matthew S., Yan, Shuqi, Camarena, Joab et al. · 2018 · Nature Medicine
27. Tracking Cancer Evolution Reveals Constrained Routes to Metastases: TRACERx Renal
    Samra Turajlic, Hang Xu, Kevin Litchfield, Andrew Rowan, Tim Chambers, Jose Ignacio Lopez, David L. Nicol, Tim O’Brien, James Larkin, Stuart D. Horswell et al. · 2018 · Cell
28. Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects
    Bin Shen, Wensheng Zhang, Jun Zhang, Jiankui Zhou, Jian-Ying Wang, Li Chen, Lu Wang, Alex Hodgkins, Vivek Iyer, Xingxu Huang et al. · 2014 · Nature Methods
29. Marine DNA Viral Macro- and Microdiversity from Pole to Pole
    Ann Gregory, Ahmed A. Zayed, Nádia Conceição‐Neto, Ben Temperton, Benjamin Bolduc, Adriana Alberti, Mathieu Ardyna, Ksenia Arkhipova, Margaux Carmichael, Corinne Cruaud et al. · 2019 · Cell
30. Genetics of 35 blood and urine biomarkers in the UK Biobank
    Sinnott-Armstrong, Nasa, Tanigawa, Yosuke, Amar, David, Mars, Nina, Benner, Christian, Aguirre, Matthew, Venkataraman, Guhan Ram, Wainberg, Michael, Ollila, Hanna M., Kiiskinen, Tuomo et al. · 2021 · Nature Genetics
31. Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma
    David Jones, Barbara Hutter, Natalie Jäger, Andrey Korshunov, Marcel Kool, Hans-Jörg Warnatz, Thomas Zichner, Sally R. Lambert, Marina Vladimirovna Ryzhova, Dong-Anh Khuong-Quang et al. · 2013 · Nature Genetics
32. Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato
    Michael Alonge, Xingang Wang, Matthias Benoit, Sebastian Soyk, Lara Pereira, Lei Zhang, Hamsini Suresh, Srividya Ramakrishnan, Florian Maumus, Danielle Ciren et al. · 2020 · Cell
33. Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease
    Kuscu, Cem, Arslan, Sevki, Singh, Ritambhara, Thorpe, Jeremy, Adli, Mazhar · 2014 · Nature Biotechnology
34. In vivo CRISPR base editing of PCSK9 durably lowers cholesterol in primates
    Musunuru, Kiran, Chadwick, Alexandra C., Mizoguchi, Taiji, Garcia, Sara P., DeNizio, Jamie E., Reiss, Caroline W., Wang, Kui, Iyer, Sowmya, Dutta, Chaitali, Clendaniel, Victoria et al. · 2021 · Nature
35. Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
    Rapaport, Franck, Khanin, Raya, Liang, Yupu, Pirun, Mono, Krek, Azra, Zumbo, Paul, Mason, Christopher E, Socci, Nicholas D, Betel, Doron · 2013 · Genome Biology
36. A Unified Model for the Function of YTHDF Proteins in Regulating m6A-Modified mRNA
    Sara Zaccara, Samie R. Jaffrey · 2020 · Cell
37. 5-methylcytosine promotes pathogenesis of bladder cancer through stabilizing mRNAs
    Xin Chen, Ang Li, Bao-Fa Sun, Ying Yang, Ya-Nan Han, Xun Yuan, Ri-Xin Chen, Wen-Su Wei, Yanchao Liu, Chun‐Chun Gao et al. · 2019 · Nature Cell Biology
38. The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution
    Hélène Badouin, Jérôme Gouzy, Christopher J. Grassa, Florent Murat, S. Evan Staton, Ludovic Cottret, Christine Lelandais‐Brière, Gregory L. Owens, Sébastien Carrère, Baptiste Mayjonade et al. · 2017 · Nature
39. Organoid single-cell genomic atlas uncovers human-specific features of brain development
    Sabina Kanton, Michael James Boyle, Zhisong He, Małgorzata Santel, Anne Weigert, Fátima Sanchís-Calleja, Patricia Guijarro, Leila Sidow, Jonas Simon Fleck, Dingding Han et al. · 2019 · Nature
40. Metabolic Induction of Trained Immunity through the Mevalonate Pathway
    Siroon Bekkering, Rob J.W. Arts, Boris Novakovic, Ioannis Kourtzelis, Charlotte D.C.C. van der Heijden, Yang Li, Călin D. Popa, Rob ter Horst, Julia van Tuijl, Romana Teodora Netea-Maier et al. · 2018 · Cell
41. Loss of furin cleavage site attenuates SARS-CoV-2 pathogenesis
    Johnson, Bryan A., Xie, Xuping, Bailey, Adam L., Kalveram, Birte, Lokugamage, Kumari G., Muruato, Antonio, Zou, Jing, Zhang, Xianwen, Juelich, Terry, Smith, Jennifer K. et al. · 2021 · Nature
42. The Stress Granule Transcriptome Reveals Principles of mRNA Accumulation in Stress Granules
    Anthony Khong, Tyler Matheny, Saumya Jain, Sarah F. Mitchell, Joshua Wheeler, Roy Parker · 2017 · Molecular Cell
43. An atlas of genetic influences on osteoporosis in humans and mice
    23andMe Research Team, Morris, John A., Kemp, John P., Youlten, Scott E., Laurent, Laetitia, Logan, John G., Chai, Ryan C., Vulpescu, Nicholas A., Forgetta, Vincenzo, Kleinman, Aaron et al. · 2019 · Nature Genetics
44. Complex multi-enhancer contacts captured by genome architecture mapping
    Beagrie, Robert A., Scialdone, Antonio, Schueler, Markus, Kraemer, Dorothee C. A., Chotalia, Mita, Xie, Sheila Q., Barbieri, Mariano, de Santiago, Inês, Lavitas, Liron-Mark, Branco, Miguel R. et al. · 2017 · Nature
45. Erratum: Corrigendum: KLF4-dependent phenotypic modulation of smooth muscle cells has a key role in atherosclerotic plaque pathogenesis
    Laura S. Shankman, Delphine A Gomez, Olga A Cherepanova, Morgan Salmon, Gabriel F. Alencar, Ryan M. Haskins, Pamela Swiatlowska, Alexandra A. C. Newman, Elizabeth S. Greene, Adam C. Straub et al. · 2016 · Nature Medicine
46. RETRACTED ARTICLE: Molecular characterization of LC3-associated phagocytosis reveals distinct roles for Rubicon, NOX2 and autophagy proteins
    Martinez, Jennifer, Malireddi, R. K. Subbarao, Lu, Qun, Cunha, Larissa Dias, Pelletier, Stephane, Gingras, Sebastien, Orchard, Robert, Guan, Jun-Lin, Tan, Haiyan, Peng, Junmin et al. · 2015 · Nature Cell Biology · Retracted
47. Temporal Control of Mammalian Cortical Neurogenesis by m6A Methylation
    Ki‐Jun Yoon, Francisca Rojas, Caroline B. Vissers, Fadi Jacob, Michael J. Pokrass, Dennisse V. Jimenez, Yijing Su, Nam-Shik Kim, Yunhua Zhu, Lily Zheng et al. · 2017 · Cell
48. HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
    Sergey Nurk, Brian P. Walenz, Arang Rhie, Mitchell Robert Vollger, Glennis A. Logsdon, Robert Grothe, Karen H. Miga, Evan E. Eichler, Adam M. Phillippy, Sergey Koren · 2020 · Genome Research
49. Systematic mapping of functional enhancer–promoter connections with CRISPR interference
    Fulco, Charles P., Munschauer, Mathias, Anyoha, Rockwell, Munson, Glen, Grossman, Sharon R., Perez, Elizabeth M., Kane, Michael, Cleary, Brian, Lander, Eric S., Engreitz, Jesse M. · 2016 · Science
50. A long noncoding RNA protects the heart from pathological hypertrophy
    Pei Han, Wei Li, Chiou-Hong Lin, Jin Yang, Ching Shang, Sylvia Nürnberg, Kevin Kai Jin, Weihong Xu, Chieh‐Yu Lin, Chieh‐Yu Lin et al. · 2014 · Nature
51. Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.
    Ji-Sen Zhang, Xing-Tan Zhang, Hai-Bao Tang, Qing Zhang, Xiu-Ting Hua, Xiao-Kai Ma, Fan Zhu, Tyler C. Jones, Xin-Guang Zhu, J. Bowers et al. · 2018 · Nature Genetics
52. Mapping genome-wide transcription-factor binding sites using DAP-seq
    Anna Bartlett, Ronan C. O’Malley, Shao‐shan Carol Huang, Mary Galli, Joseph R. Nery, Andrea Gallavotti, Joseph R. Ecker · 2017 · Nature Protocols
53. Variant PRC1 Complex-Dependent H2A Ubiquitylation Drives PRC2 Recruitment and Polycomb Domain Formation
    Neil P. Blackledge, Anca M. Farcas, Takashi Kondo, Hamish W. King, Joanna F. McGouran, Lars L.P. Hanssen, Shinsuke Ito, Sarah Cooper, Kaori Kondo, Yoko Koseki et al. · 2014 · Cell
54. Widespread intron retention in mammals functionally tunes transcriptomes
    Braunschweig, Ulrich, Barbosa-Morais, Nuno L., Pan, Qun, Nachman, Emil N., Alipanahi, Babak, Gonatopoulos-Pournatzis, Thomas, Frey, Brendan, Irimia, Manuel, Blencowe, Benjamin J. · 2014 · Genome Research
55. The genome of Chenopodium quinoa
    David E. Jarvis, Yung Shwen Ho, Damien J. Lightfoot, Sandra M. Schmöckel, Bo Li, Theo J. A. Borm, Hajime Ohyanagi, Katsuhiko Mineta, Craig Michell, Noha Saber et al. · 2017 · Nature
56. A Compendium of Mutational Signatures of Environmental Agents
    Kucab, Jill E., Zou, Xueqing, Morganella, Sandro, Joel, Madeleine, Nanda, A. Scott, Nagy, Eszter, Gomez, Celine, Degasperi, Andrea, Harris, Rebecca, Jackson, Stephen P. et al. · 2019 · Cell
57. Cistrome: an integrative platform for transcriptional regulation studies
    Tao Liu, Jorge A Ortiz, Len Taing, Clifford A. Meyer, Bernett Teck Kwong Lee, Yong Zhang, Hyunjin Shin, Swee Seong Wong, Jian Ma, Ying Lei et al. · 2011 · Genome biology
58. <i>N</i> ⁶ -methyladenosine of chromosome-associated regulatory RNA regulates chromatin state and transcription
    Liu, Jun, Dou, Xiaoyang, Chen, Chuanyuan, Chen, Chuan, Liu, Chang, Xu, Meng Michelle, Zhao, Siqi, Shen, Bin, Gao, Yawei, Han, Dali et al. · 2020 · Science
59. Transcriptome-wide mapping of N6-methyladenosine by m6A-seq based on immunocapturing and massively parallel sequencing
    Dan Dominissini, Sharon Moshitch-Moshkovitz, Mali Salmon‐Divon, Ninette Amariglio, Gideon Rechavi · 2013 · Nature Protocols
60. Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice
    Jin, Shuai, Zong, Yuan, Gao, Qiang, Zhu, Zixu, Wang, Yanpeng, Qin, Peng, Liang, Chengzhi, Wang, Daowen, Qiu, Jin-Long, Zhang, Feng et al. · 2019 · Science
61. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes
    Matthew B. Hufford, Arun Somwarpet Seetharam, Margaret Roth Woodhouse, Kapeel M. Chougule, Shujun Ou, Jianing Liu, William A. Ricci, Tingting Guo, Andrew J. Olson, Yinjie Qiu et al. · 2021 · Science
62. Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding
    Hsieh, Tsung-Han S., Cattoglio, Claudia, Slobodyanyuk, Elena, Hansen, Anders S., Rando, Oliver J., Tjian, Robert, Darzacq, Xavier · 2020 · Molecular Cell
63. Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas
    Hou, Yu, Guo, Huahu, Cao, Chen, Li, Xianlong, Hu, Boqiang, Zhu, Ping, Wu, Xinglong, Wen, Lu, Tang, Fuchou, Huang, Yanyi et al. · 2016 · Cell Research
64. Haplotype-resolved diverse human genomes and integrated analysis of structural variation
    Ebert, Peter, Audano, Peter A., Zhu, Qihui, Rodriguez-Martin, Bernardo, Porubsky, David, Bonder, Marc Jan, Sulovari, Arvis, Ebler, Jana, Zhou, Weichen, Serra Mari, Rebecca et al. · 2021 · Science
65. A DNA methylation atlas of normal human cell types
    Loyfer, Netanel, Magenheim, Judith, Peretz, Ayelet, Cann, Gordon, Bredno, Joerg, Klochendler, Agnes, Fox-Fisher, Ilana, Shabi-Porat, Sapir, Hecht, Merav, Pelet, Tsuria et al. · 2023 · Nature
66. The impact of sex on gene expression across human tissues
    Meritxell Oliva, Manuel Muñoz-Aguirre, Sarah Kim-Hellmuth, Valentin Wucher, Ariel DH Gewirtz, Daniel J. Cotter, Princy Parsana, Silva Kasela, Brunilda Balliu, Ana Viñuela et al. · 2020 · Science
67. Enhancer redundancy provides phenotypic robustness in mammalian development
    Osterwalder, Marco, Barozzi, Iros, Tissières, Virginie, Fukuda-Yuzawa, Yoko, Mannion, Brandon J., Afzal, Sarah Y., Lee, Elizabeth A., Zhu, Yiwen, Plajzer-Frick, Ingrid, Pickle, Catherine S. et al. · 2018 · Nature
68. RaGOO: fast and accurate reference-guided scaffolding of draft genomes
    Michael Alonge, Sebastian Soyk, Srividya Ramakrishnan, Xingang Wang, Sara Goodwin, Fritz Joachim Sedlazeck, Zachary B. Lippman, Michael C. Schatz · 2019 · Genome biology
69. Erratum: Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean
    Zhengkui Zhou, Yu Jiang, Zheng Wang, Zhiheng Gou, Jun Lyu, Weiyu Li, Yanjun Yu, Liping Shu, Yingjun Zhao, Yanming Ma et al. · 2016 · Nature Biotechnology
70. β-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance
    Boris Novakovic, Ehsan Habibi, Shuang-Yin Wang, Rob J.W. Arts, Robab Davar, Wout Megchelenbrink, Bowon Kim, Tatyana Kuznetsova, Matthijs Kox, Jelle Zwaag et al. · 2016 · Cell
71. Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs
    Kapusta, Aurélie, Kronenberg, Zev, Lynch, Vincent J., Zhuo, Xiaoyu, Ramsay, LeeAnn, Bourque, Guillaume, Yandell, Mark, Feschotte, Cédric · 2013 · PLoS Genetics
72. Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements
    Katariina M. M. Pärnänen, Antti Karkman, Jenni Hultman, Christina Lyra, Johan Bengtsson‐Palme, D. G. Joakim Larsson, Samuli Rautava, Erika Isolauri, Seppo Salminen, Himanshu Kumar et al. · 2018 · Nature Communications
73. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens
    Gasperini, Molly, Hill, Andrew J., McFaline-Figueroa, José L., Martin, Beth, Kim, Seungsoo, Zhang, Melissa D., Jackson, Dana, Leith, Anh, Schreiber, Jacob, Noble, William S. et al. · 2019 · Cell
74. Mitochondrial double-stranded RNA triggers antiviral signalling in humans
    Dhir, Ashish, Dhir, Somdutta, Borowski, Lukasz S., Jimenez, Laura, Teitell, Michael, Rötig, Agnès, Crow, Yanick J., Rice, Gillian I., Duffy, Darragh, Tamby, Christelle et al. · 2018 · Nature
75. Atlas of Subcellular RNA Localization Revealed by APEX-Seq
    Furqan M. Fazal, Shuo Han, Kevin R. Parker, Pornchai Kaewsapsak, Jin Xu, Alistair Nicol Boettiger, Howard Y. Chang, Alice Y. Ting · 2019 · Cell
76. Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal
    Samra Turajlic, Hang Xu, Kevin Litchfield, Andrew Rowan, Stuart D. Horswell, Tim Chambers, Tim O’Brien, Jose Ignacio Lopez, Thomas B.K. Watkins, David L. Nicol et al. · 2018 · Cell
77. The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut
    Ann Gregory, Olivier Zablocki, Ahmed A. Zayed, Anna Howell, Benjamin Bolduc, Matthew B. Sullivan · 2020 · Cell Host & Microbe
78. Common genetic variation drives molecular heterogeneity in human iPSCs
    Kilpinen, Helena, Goncalves, Angela, Leha, Andreas, Afzal, Vackar, Alasoo, Kaur, Ashford, Sofie, Bala, Sendu, Bensaddek, Dalila, Casale, Francesco Paolo, Culley, Oliver J. et al. · 2017 · Nature
79. The histone deacetylase SIRT6 is a tumor suppressor that controls cancer metabolism
    Sebastián, Carlos, Zwaans, Bernadette M.M., Silberman, Dafne M., Gymrek, Melissa, Goren, Alon, Zhong, Lei, Ram, Oren, Truelove, Jessica, Guimaraes, Alexander R., Toiber, Debra et al. · 2012 · Cell
80. lncRNA-dependent mechanisms of androgen-receptor-regulated gene activation programs
    Liuqing Yang, Chunru Lin, Chunyu Jin, Joy C. Yang, Bogdan Tanasă, Wenbo Li, Daria Merkurjev, Kenneth A. Ohgi, Da Meng, Jie Zhang et al. · 2013 · Nature
81. Transcription-Replication Conflict Orientation Modulates R-Loop Levels and Activates Distinct DNA Damage Responses
    Stephan Hamperl, Michael J. Bocek, Joshua C. Saldivar, Tomek Swigut, Karlene A. Cimprich · 2017 · Cell
82. Loss of epigenetic information as a cause of mammalian aging
    Yang, Jae-Hyun, Hayano, Motoshi, Griffin, Patrick T., Amorim, João A., Bonkowski, Michael S., Apostolides, John K., Salfati, Elias L., Blanchette, Marco, Munding, Elizabeth M., Bhakta, Mital et al. · 2023 · Cell
83. Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals
    Battle, Alexis, Mostafavi, Sara, Zhu, Xiaowei, Potash, James B., Weissman, Myrna M., McCormick, Courtney, Haudenschild, Christian D., Beckman, Kenneth B., Shi, Jianxin, Mei, Rui et al. · 2014 · Genome Research
84. Extensive introgression in a malaria vector species complex revealed by phylogenomics
    Michaël C. Fontaine, James B. Pease, Aaron Steele, Robert Michael Waterhouse, Daniel E. Neafsey, Igor V. Sharakhov, Xiaofang Jiang, Andrew Brantley Hall, Flaminia Catteruccia, Evdoxia G. Kakani et al. · 2014 · Science
85. Heterochromatin-Driven Nuclear Softening Protects the Genome against Mechanical Stress-Induced Damage
    Michele M. Nava, Yekaterina A. Miroshnikova, Leah C. Biggs, Daniel B. Whitefield, Franziska Metge, Jorge Bouças, Helena Vihinen, Eija Jokitalo, Xinping Li, Juan Manuel GARCIA ARCOS et al. · 2020 · Cell
86. High-frequency, precise modification of the tomato genome
    Tomáš Čermák, Nicholas J. Baltes, Radim Čegan, Yong Zhang, Daniel F. Voytas · 2015 · Genome biology
87. Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease
    Gjoneska, Elizabeta, Pfenning, Andreas R., Mathys, Hansruedi, Quon, Gerald, Kundaje, Anshul, Tsai, Li-Huei, Kellis, Manolis · 2015 · Nature
88. Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma
    Northcott, Paul A., Lee, Catherine, Zichner, Thomas, Stütz, Adrian M., Erkek, Serap, Kawauchi, Daisuke, Shih, David J. H., Hovestadt, Volker, Zapatka, Marc, Sturm, Dominik et al. · 2014 · Nature
89. Improved data analysis for the MinION nanopore sequencer
    Miten Jain, Ian T. Fiddes, Karen H. Miga, Hugh E. Olsen, Benedict Paten, Mark A. Akeson · 2015 · Nature Methods
90. CDK7 Inhibition Suppresses Super-Enhancer-Linked Oncogenic Transcription in MYCN-Driven Cancer
    Edmond Chipumuro, Eugenio Marco, Camilla Laulund Christensen, Nicholas P. Kwiatkowski, Tinghu Zhang, Clark M. Hatheway, Brian J. Abraham, Bandana Sharma, Caleb Matthew Yeung, Abigail B. Altabef et al. · 2014 · Cell
91. Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome
    Derek M. Bickhart, Benjamin D. Rosen, Sergey Koren, Brian L Sayre, Alex R. Hastie, Saki Chan, Joyce Lee, Ernest T. Lam, Ivan Liachko, Shawn T Sullivan et al. · 2017 · Nature Genetics
92. Base-resolution models of transcription-factor binding reveal soft motif syntax
    Avsec, Žiga, Weilert, Melanie, Shrikumar, Avanti, Krueger, Sabrina, Alexandari, Amr, Dalal, Khyati, Fropf, Robin, McAnany, Charles, Gagneur, Julien, Kundaje, Anshul et al. · 2021 · Nature Genetics
93. Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre
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94. Coordinated circRNA Biogenesis and Function with NF90/NF110 in Viral Infection
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