BetterScholar BetterScholar
9
Role
Title
Level Year L/R
🐜 Lineage-specific dynamic and pre-established enhancer–promoter contacts cooperate in terminal differentiation
19 auth. Adam J. Rubin, Brook C. Barajas, M. Furlan-Magaril, V. Lopez-Pajares, Maxwell R Mumbach, Imani Howard, Daniel S. Kim, Lisa D. Boxer, Jonathan M. Cairns, M. Spivakov, ... S. Wingett, Minyi Shi, Zhixin Zhao, W. Greenleaf, A. Kundaje, M. Snyder, Howard Y. Chang, P. Fraser, P. Khavari
8 2017
8
🐜
🐜 Perspectives on ENCODE
501 auth. F. Abascal, Reyes Acosta, Nicholas J. Addleman, Jessika Adrian, Veena Afzal, Bronwen L. Aken, Rizi Ai, J. Akiyama, O. A. Jammal, Henry Amrhein, S. Anderson, Gregory Andrews, I. Antoshechkin, K. Ardlie, J. Armstrong, ... Matthew Astley, Budhaditya Banerjee, Amira A. Barkal, If H. A. Barnes, I. Barozzi, D. Barrell, Gemma Barson, Daniel Bates, Ulugbek K. Baymuradov, C. Bazile, Michael A. Beer, Samantha P. Beik, M. Bender, Ruth Bennett, L. Bouvrette, Bradley E. Bernstein, Andrew E. Berry, A. Bhaskar, A. Bignell, S. Blue, D. Bodine, C. Boix, Nathan Boley, Tyler Borrman, Beatrice Borsari, A. Boyle, Laurel A. Brandsmeier, A. Breschi, E. Bresnick, Jason A. Brooks, Michael Buckley, C. Burge, Rachel Byron, Eileen W. Cahill, Lingling Cai, Lulu Cao, Mark Carty, R. Castanon, Andres Castillo, H. Chaib, Esther T. Chan, Daniel R. Chee, Sora Chee, Huaming Chen, Jia-Yu Chen, Songjie Chen, J. M. Cherry, S. Chhetri, J. Choudhary, Jacqueline Chrast, Dongjun Chung, Declan Clarke, Neal A. L. Cody, Candice J. Coppola, J. Coursen, A. D'Ippolito, S. Dalton, Cassidy Danyko, C. Davidson, J. DÑvila-Velderrain, Carrie A. Davis, J. Dekker, A. Deran, Gilberto Desalvo, Gloria Despacio-Reyes, Colin N. Dewey, D. Dickel, Morgan Diegel, M. Diekhans, V. Dileep, Bo Ding, S. Djebali, A. Dobin, Daniel Dominguez, S. Donaldson, J. Drenkow, T. Dreszer, Y. Drier, M. Duff, D. Dunn, Catharine L. Eastman, J. Ecker, Matthew D. Edwards, Nicole C. El-Ali, Shaimae I. Elhajjajy, Keri Elkins, A. Emili, C. Epstein, Rachel C. Evans, Iakes Ezkurdia, K. Fan, P. Farnham, Nina P. Farrell, E. Feingold, Anne-Maud Ferreira, Katherine I. Fisher-Aylor, Stephen Fitzgerald, Paul Flicek, Chuan-Sheng Foo, K. Fortier, A. Frankish, Peter Freese, Shaliu Fu, Xiang-Dong Fu, Yu Fu, Yoko Fukuda-Yuzawa, M. Fulciniti, Alister P. W. Funnell, I. Gabdank, Timur Galeev, M. Gao, C. G. Girón, Tyler H. Garvin, C. Gelboin-Burkhart, G. Georgolopoulos, M. Gerstein, B. Giardine, D. Gifford, D. Gilbert, Daniel A. Gilchrist, Shawn M. Gillespie, T. Gingeras, Peng Gong, Alvaro J. GonzÑlez, J. Gonzalez, P. Good, A. Goren, David U. Gorkin, B. Graveley, Michael Gray, J. Greenblatt, Ed Griffiths, M. Groudine, Fabian Grubert, Mengting Gu, R. Guigó, Hongbo Guo, Gamze Gursoy, M. Gutierrez-Arcelus, J. Halow, R. Hardison, Matthew Hardy, M. Hariharan, A. Harmanci, Anne N. Harrington, J. Harrow, Tatsunori B. Hashimoto, R. Hasz, Meital Hatan, E. Haugen, J. Hayes, Peng He, Yupeng He, Nastaran Heidari, David Hendrickson, Elisabeth F. Heuston, J. Hilton, B. Hitz, Abigail Hochman, Cory Holgren, Lei Hou, Shuyu Hou, Y. Hsiao, Shan-Chun Hsu, Hui Huang, T. Hubbard, Jack Huey, Timothy R. Hughes, T. Hunt, S. Ibarrientos, Robbyn Issner, M. Iwata, Osagie G. Izuogu, T. Jaakkola, Nader Jameel, Camden Jansen, Lixia Jiang, Peng Jiang, Audra K. Johnson, Rory Johnson, Irwin Jungreis, Madhura Kadaba, Maya Kasowski, M. Kasparian, Momoe Kato, R. Kaul, T. Kawli, M. Kay, Judy C. Keen, S. Keleş, C. Keller, D. Kelley, Manolis Kellis, Pouya Kheradpour, Daniel S. Kim, Anthony Kirilusha, R. Klein, B. Knoechel, Samantha Kuan, M. Kulik, Sushant Kumar, A. Kundaje, T. Kutyavin, Julien Lagarde, B. Lajoie, Nicole J. Lambert, John E Lazar, Ah Young Lee, Donghoon Lee, Elizabeth Lee, Jin-Wook Lee, Kristen Lee, C. Leslie, Shawn E. Levy, Bin Li, Hai-Ri Li, Nan Li, Shantao Li, Xiangrui Li, Yining Li, Jin Lian, Maxwell W. Libbrecht, Shin Lin, Y. Lin, Dianbo Liu, Jason Liu, Peng Liu, Tingting Liu, X. Liu, Yaping Liu, Maria Long, S. Lou, J. Loveland, Aiping Lu, Yuheng Lu, Eric Lécuyer, Lijia Ma, M. Mackiewicz, B. Mannion, M. Mannstadt, Deepa Manthravadi, G. Marinov, Fergal J. Martin, E. Mattei, Kenneth McCue, Megan McEown, G. McVicker, Sarah K. Meadows, A. Meissner, E. Mendenhall, C. L. Messer, W. Meuleman, Clifford A. Meyer, Steve Miller, Matthew G. Milton, Tejaswini Mishra, Dianna E. Moore, H. M. Moore, Samuel H. Moore, Jennifer R. Moran, A. Mortazavi, Jonathan M. Mudge, N. Munshi, Rabi Murad, R. Myers, V. Nandakumar, Preetha Nandi, A. Narasimha, Aditi K. Narayanan, H. Naughton, FÑbio C. P. Navarro, P. Navas, Jurijs Nazarovs, Jemma Nelson, Shane J. Neph, Fidencio J. Neri, Joseph R. Nery, Amy R. Nesmith, J. S. Newberry, Kimberly M. Newberry, Vu Ngo, R. Nguyen, Tung Nguyen, Andrew Nishida, W. S. Noble, Catherine S. Novak, E. Novoa, Briana Nuñez, C. W. O'Donnell, S. Olson, Kathrina C. Onate, Ericka Otterman, Hakan Ozadam, Michael Pagan, T. Palden, X. Pan, Yongjin P. Park, E. Partridge, B. Paten, Florencia Pauli-Behn, M. Pazin, Baikang Pei, L. Pennacchio, Alexander R. Perez, Emily Perry, D. Pervouchine, Nishigandha Phalke, Quan T. Pham, D. H. Phanstiel, I. Plajzer-Frick, G. Pratt, H. Pratt, S. Preissl, J. Pritchard, Y. Pritykin, Michael J. Purcaro, Qian Qin, Giovanni Quinones-Valdez, Ines Rabano, Ernest Radovani, Anil Raj, N. Rajagopal, Oren Ram, L. Ramírez, Ricardo N. Ramirez, D. Rausch, S. Raychaudhuri, Joseph Raymond, Rozita Razavi, Timothy E. Reddy, Thomas M. Reimonn, Bing Ren, A. Reymond, Alex P. Reynolds, S. Rhie, Johannes Rinn, Miguel Rivera, J. Rivera-Mulia, Brian S. Roberts, J. Rodríguez, J. Rozowsky, Russell Ryan, Eric Rynes, Denis Salins, R. Sandstrom, Takayo Sasaki, S. Sathe, D. Savic, A. Scavelli, J. Scheiman, Christoph N. Schlaffner, J. Schloss, F. Schmitges, L. See, A. Sethi, M. Setty, A. Shafer, Shuo Shan, Eilon Sharon, Quan Shen, Yin Shen, R. Sherwood, Minyi Shi, Sunyoung Shin, N. Shoresh, Kyle T. Siebenthall, Cristina Sisu, T. Slifer, C. A. Sloan, Anna M. Smith, V. Snetkova, Michael P. Snyder, D. Spacek, Sharanya Srinivasan, R. Srivas, G. Stamatoyannopoulos, J. Stamatoyannopoulos, Rebecca Stanton, D. Steffan, Sandra Stehling-Sun, J. Strattan, Amanda Su, B. Sundararaman, M. Suner, Tahin Syed, Matt Szynkarek, Forrest Tanaka, D. Tenen, Mingxiang Teng, Jeffrey A. Thomas, David E. Toffey, M. Tress, Diane Trout, G. Trynka, J. Tsuji, S. Upchurch, Oana Ursu, Barbara Uszczynska-Ratajczak, Mia C. Uziel, A. Valencia, B. V. Biber, A. van der Velde, Eric L. Van Nostrand, Yekaterina Vaydylevich, Jesús VÑzquez, Alec Victorsen, J. Vielmetter, J. Vierstra, A. Visel, A. Vlasova, Christopher M. Vockley, S. Volpi, Shinny Vong, Hao Wang, Mengchi Wang, Qin Wang, Ruth Wang, Tao Wang, Wen Wang, Xiao-feng Wang, Yanli Wang, N. Watson, Xintao Wei, Zhijie Wei, Hendrik Weisser, S. Weissman, Rene Welch, R. Welikson, Z. Weng, H. Westra, J. Whitaker, Collin G. White, Kevin P. White, Andre Wildberg, B. Williams, D. Wine, Heather Witt, B. Wold, Maxim Y Wolf, J. Wright, Rui Xiao, Xinshu Xiao, Jie Xu, Jinrui Xu, Koon-Kiu Yan, Yongqi Yan, Hongbo Yang, Xinqiong Yang, Yi-Wen Yang, G. Yardımcı, Brian A. Yee, Gene W. Yeo, Taylor Young, Tianxiong Yu, Feng Yue, C. Zaleski, C. Zang, Haoyang Zeng, Weihua Zeng, D. Zerbino, J. Zhai, L. Zhan, Y. Zhan, Bo Zhang, Jialing Zhang, Jing Zhang, Kaijie Zhang, Lijun Zhang, Peng Zhang, Qi Zhang, Xiao-ou Zhang, Yanxiao Zhang, Zhizhuo Zhang, Yuan Zhao, Ye Zheng, Guoqing Zhong, Xiao-Qiao Zhou, Yun Zhu, Jared Zimmerman, Michael P. Snyder, Bing Ren, R. Hardison, J. M. Cherry, Bradley E. Bernstein, E. Mendenhall, Paul Flicek
6 2020
6
🐜
🐜 The Kipoi repository accelerates community exchange and reuse of predictive models for genomics
13 auth. Ε½iga Avsec, Roman Kreuzhuber, Johnny Israeli, Nancy Xu, Jun Cheng, Avanti Shrikumar, Abhimanyu Banerjee, Daniel S. Kim, T. Beier, L. Urban, ... A. Kundaje, O. Stegle, J. Gagneur
6 2019
6
🐜
🦁 The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation
20 auth. Daniel S. Kim, Viviana I. Risca, D. Reynolds, James Chappell, Adam J. Rubin, N. Jung, L. Donohue, V. Lopez-Pajares, Arwa S. Kathiria, Minyi Shi, ... Zhixin Zhao, Harsh Deep, Mahfuza Sharmin, Deepti S Rao, Shin Lin, Howard Y. Chang, Michael P. Snyder, W. Greenleaf, A. Kundaje, P. Khavari
5 2020
5
🦁
🐬 Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts
Surag Nair, Daniel S. Kim, Jacob Perricone, A. Kundaje
5 2019
5
🐬
🐜 The ENCODE Uniform Analysis Pipelines
60 auth. B. Hitz, Jin-Wook Lee, Otto Jolanki, Meenakshi S. Kagda, Keenan Graham, Paul Sud, I. Gabdank, J. Seth Strattan, C. A. Sloan, T. Dreszer, Laurence D. Rowe, Nikhil R. Podduturi, V. Malladi, Esther T. Chan, Jean M. Davidson, ... Marcus Ho, S. Miyasato, Matt Simison, Forrest Tanaka, Yunhai Luo, Ian Whaling, Eurie L. Hong, Brian T. Lee, R. Sandstrom, Eric Rynes, Jemma Nelson, Andrew Nishida, A. Ingersoll, Michael Buckley, M. Frerker, Daniel S. Kim, Nathan Boley, Diane Trout, A. Dobin, Sorena Rahmanian, D. Wyman, Gabriela Balderrama-Gutierrez, Fairlie Reese, Neva C. Durand, O. Dudchenko, D. Weisz, Suhas S. P. Rao, Alyssa Blackburn, Dimos Gkountaroulis, Mahdi Sadr, M. Olshansky, Yossi Eliaz, D. Nguyen, Ivan D. Bochkov, M. Shamim, Ragini Mahajan, Erez Lieberman Aiden, T. Gingeras, S. Heath, M. Hirst, W. James Kent, A. Kundaje, A. Mortazavi, B. Wold, J. Cherry
5 2023
5
🐜
🐜 Kipoi: accelerating the community exchange and reuse of predictive models for genomics
12 auth. Ε½iga Avsec, Roman Kreuzhuber, Johnny Israeli, Nancy Xu, Jun Cheng, Avanti Shrikumar, ... Abhimanyu Banerjee, Daniel S. Kim, L. Urban, A. Kundaje, O. Stegle, J. Gagneur
5 2018
5
🐜
🐜 A cis-regulatory lexicon of DNA motif combinations mediating cell-type-specific gene regulation
12 auth. L. Donohue, M. Guo, Yang Zhao, N. Jung, Rose T. Bussat, Daniel S. Kim, ... Poornima H. Neela, Laura N. Kellman, Omar S. Garcia, R. Meyers, R. Altman, P. Khavari
3 2022
3
🐜
🐜 Single-Cell and Spatial Transcriptomic Analysis of Human Skin Delineates Intercellular Communication and Pathogenic Cells.
23 auth. K. Thrane, M. Winge, Hongyu Wang, Larry Chen, M. Guo, Alma Andersson, X. Abalo, Xue Yang, Daniel S. Kim, Sophia K. Longo, ... Brian Y. Soong, Jordan M Meyers, D. Reynolds, A. McGeever, D. Demircioglu, Dan Hasson, R. Mirzazadeh, Adam J. Rubin, Gordon H. Bae, Jim Karkanias, K. Rieger, J. Lundeberg, A. Ji
3 2023
3
🐜