Peggy Farnham
Active 1980–2024
- 117
- Papers
- 55,083
- Citations
- 92
- h-index
- 117
- i10-index
Citations
Citation sources
Countries
Institutions
Fields
- Biochemistry, Genetics and Molecular Biology74.6%
- Medicine14.1%
- Immunology and Microbiology4%
- Agricultural and Biological Sciences2.6%
- Neuroscience2.5%
- Computer Science0.6%
- Other1.6%
Topics
- Genomics and Chromatin Dynamics8.3%
- Epigenetics and DNA Methylation6.7%
- RNA modifications and cancer6.3%
- RNA Research and Splicing5.4%
- Cancer-related molecular mechanisms research5.3%
- RNA and protein synthesis mechanisms3%
- Other65%
Coauthors
- Henriette O’Geen18
- Victor X. Jin13
- Suhn K. Rhie10
- Roland Green9
- Seth Frietze8
- Stephanie M. Bartley8
- Benjamin P. Berman6
- Jill E. Slansky6
- Julie Wells6
- Lijing Yao6
- Mark Gerstein6
- Xiaoqin Xu6
- Andrew Perez5
- Anshul Kundaje5
- Charles M. Nicolet5
- Chibo Hong5
- Heather Witt5
- Mark Bieda5
- Martin Hirst5
- Sushma Iyengar5
- Zhifei Luo5
- Amy S. Weinmann4
- B Bernstein4
- Danny Reinberg4
All papers
- An integrated encyclopedia of DNA elements in the human genome
Authors: Ian Dunham, Ewan Birney, Javier Herrero, Steven P. Wilder, Damian Keefe, Kathryn Beal, Paul Flicek, Nathan Johnson, Daniel Sobral, Anshul Kundaje, Serafim Batzoglou, Nadine Hussami, Sofia Kyriazopoulou-Panagiotopoulou, Max W. Libbrecht, Marc A. Schaub, Shelley F. Aldred, Patrick Collins, Nathan D. Trinklein, Carrie A. Davis, Felix Schlesinger, T Gingeras, Alex Dobin, Wei Lin, Chenghai Xue, Chris Zaleski, Michael T. Baer, Philippe Batut, Kimberly Bell, Sudipto Chakrabortty, Jörg Drenkow, Megan Fastuca, Kata Fejes-Toth, Assaf Gordon, Sonali Jha, Jonathan Preall, Kimberly Presaud, Lei-Hoon See, Huaien Wang, Gregory J. Hannon, Francis Doyle, Scott A. Tenenbaum, Charles B. Epstein, Noam Shoresh, B Bernstein, Tarjei S. Mikkelsen, Alon Goren, Oren Ram, Xiaolan Zhang, Li Wang, Robbyn Issner, Michael J. Coyne, Timothy Durham, Manching Ku, Thanh Truong, Seth Frietze, Peggy Farnham, Heather Witt, Jennifer Harrow, Timothy J. Hubbard, Felix Kokocinski, Bronwen Aken, Daniel Barrell, Gemma Barson, Andrew Berry, Alexandra Bignell, Veronika Boychenko, Claire Davidson, Gloria Despacio-Reyes, Adam Frankish, James Gilbert, José M. González, Ed Griffiths, Toby Hunt, Mike Kay, Jane Loveland, Deepa Manthravadi, Jonathan Mudge, Gaurab Mukherjee, Gary Saunders, Stephen Searle, Catherine Snow, Charlie Steward, Electra Tapanari, Laurens Wilming, Amonida Zadissa, Rajinder Kaul, Jainab Khatun, Morgan C. Giddings, John Wrobel, Brian A. Risk, Bryan R. Lajoie, Amartya Sanyal, Job Dekker, Gaurav Jain, Stephen G. Landt, M Snyder, Nick Addleman, Keith Bettinger, Alan P. Boyle, Philip Cayting - Nature 2012 cited by 19,606
- ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
Authors: Stephen G. Landt, Georgi K. Marinov, Anshul Kundaje, Pouya Kheradpour, Florencia Pauli, Serafim Batzoglou, B Bernstein, Peter J. Bickel, James B. Brown, Philip Cayting, Yiwen Chen, Gilberto DeSalvo, Charles B. Epstein, Katherine Fisher-Aylor, Ghia Euskirchen, Mark Gerstein, Jason Gertz, Alexander J. Hartemink, Michael M. Hoffman, Vishwanath R. Iyer, Youngsook L. Jung, Subhradip Karmakar, Manolis Kellis, Peter V. Kharchenko, Qunhua Li, Tao Liu, X. Shirley Liu, Lijia Ma, Aleksandar Milosavljevic, R Myers, Peter J. Park, Michael J. Pazin, Marc D. Perry, Debasish Raha, Timothy E. Reddy, Joel Rozowsky, Noam Shoresh, Arend Sidow, Matthew Slattery, J Stamatoyannopoulos, Michael Tolstorukov, Kevin P. White, Simon Xi, Peggy Farnham, Jason D. Lieb, B Wold, M Snyder - Genome Research 2012 cited by 2,223
- Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs
Authors: John L. Rinn, Michael A. Kertesz, Jordon K. Wang, Sharon L. Squazzo, Xiao Xu, Samantha A. Brugmann, L. Henry Goodnough, Jill A. Helms, Peggy Farnham, Eran Segal, Howard Y. Chang - Cell 2007 cited by 4,299
- The NIH Roadmap Epigenomics Mapping Consortium
Authors: B Bernstein, J Stamatoyannopoulos, J Costello, Bing Ren, Aleksandar Milosavljevic, Alexander Meissner, Manolis Kellis, Marco A. Marra, Arthur L. Beaudet, Joseph R. Ecker, Peggy Farnham, Martin Hirst, Eric S. Lander, Tarjei S. Mikkelsen, James A. Thomson - Nature Biotechnology 2010 cited by 2,046
- Shared molecular neuropathology across major psychiatric disorders parallels polygenic overlap
Authors: Michael J. Gandal, Jillian R. Haney, Neelroop Parikshak, Virpi Leppä, Gokul Ramaswami, Christopher Hartl, Andrew J. Schork, Vivek Appadurai, Alfonso Buil, Thomas Werge, Chunyu Liu, Kevin P. White, iPSYCH-BROAD Working Group, Steve Horvath, Daniel H. Geschwind, Nenad Šestan, Flora M. Vaccarino, Mark Gerstein, Sherman M. Weissman, Sirisha Pochareddy, Matthew W. State, James A. Knowles, Peggy Farnham, Schahram Akbarian, Dalila Pinto, Harm Van Baekl, Stella Dracheva, Andrew E. Jaffe, Thomas M. Hyde, Peter P. Zandi, Gregory E. Crawford, Pat Sullivan, Wesley K. Thompson, Preben Bo Mortensen, Esben Agerbo, Marianne Giørtz Pedersen, Carsten Bøcker Pedersen, Ole Mors, Anders D. Børglum, Merete Nordentoft, David M. Hougaard, Jonas Bybjerg‐Grauholm, Marie Bækvad‐Hansen, Alicia R. Martin, Ashley Dumont, Christine Stevens, Claire Churchhouse, Daniel P. Howrigan, Duncan S. Palmer, Elise Robinson, Kyle Satterstrom, Felecia Cerrato, Hailiang Huang, Jacqueline I. Goldstein, Jennifer L. Moran, Joanna Martin Julian, M. Alonge Kimberly, C. Seed Patrick, Patrick Turley, Raymond K. Walters, Rich Belliveau, Stephan Ripke, Timothy Poterba, Mark J. Daly, Benjamin M. Neale, Menachem Fromer, Panos Roussos, Jessica Johnson, Hardik Shah, Milind Mahajan, Eric E. Schadt, Vahram Haroutunian, Douglas M. Ruderfer, Joseph D. Buxbaum, Solveig K. Sieberts, Kristen K. Dang, Ben Logsdon, Lara M. Mangravite, Mette A. Peters, Raquel E. Gur, Chang-Gyu Hahn, Bernie Devlin, Lambertus Klei, David A. Lewis, Barbara K. Lipska, Keisuke Hirai, Hiroyoshi Toyoshiba, Enrico Domenici - Science 2018 cited by 1,177
- Architecture of the human regulatory network derived from ENCODE data
Authors: Mark Gerstein, Anshul Kundaje, Manoj Hariharan, Stephen G. Landt, Koon‐Kiu Yan, Chao Cheng, Xinmeng Jasmine Mu, Ekta Khurana, Joel Rozowsky, Roger P. Alexander, Renqiang Min, Pedro Alves, Alexej Abyzov, Nick Addleman, Nitin Bhardwaj, Alan P. Boyle, Philip Cayting, Alexandra Charos, David Ziyou Chen, Yong Cheng, Declan Clarke, Catharine Eastman, Ghia Euskirchen, Seth Frietze, Yao Fu, Jason Gertz, Fabian Grubert, Arif Harmanci, Preti Jain, Maya Kasowski, Phil Lacroute, Jing Leng, Jin Lian, Hannah Monahan, Henriette O’Geen, Zhengqing Ouyang, E. Christopher Partridge, Dorrelyn Patacsil, Florencia Pauli, Debasish Raha, Lucı́a Ramı́rez, Timothy E. Reddy, Brian D. Reed, Minyi Shi, Teri Slifer, Jing Wang, Linfeng Wu, Xinqiong Yang, Kevin Y. Yip, Gili Zilberman-Schapira, Serafim Batzoglou, Arend Sidow, Peggy Farnham, R Myers, Sherman M. Weissman, M Snyder - Nature 2012 cited by 1,561
- The PsychENCODE project
Authors: Schahram Akbarian, Chunyu Liu, James A. Knowles, Flora M. Vaccarino, Peggy Farnham, Gregory E. Crawford, Andrew E. Jaffe, Dalila Pinto, Stella Dracheva, Daniel H. Geschwind, Jonathan Mill, Angus C. Nairn, Alexej Abyzov, Sirisha Pochareddy, Shyam Prabhakar, Sherman M. Weissman, Patrick F. Sullivan, Matthew W. State, Zhiping Weng, Mette A. Peters, Kevin P. White, Mark Gerstein, Anahita Amiri, Chris Armoskus, Allison E. Ashley‐Koch, Taejeong Bae, Andrea Beckel‐Mitchener, Benjamin P. Berman, Gerhard A. Coetzee, Gianfilippo Coppola, Nancy Francoeur, Menachem Fromer, Robert Gao, Kay Grennan, Jennifer Herstein, David H. Kavanagh, Nikolay A. Ivanov, Yan Jiang, Robert R. Kitchen, Alexey Kozlenkov, Marija Kundaković, Mingfeng Li, Zhen Li, Shuang Liu, Lara M. Mangravite, Eugenio Mattei, Eirene Markenscoff-Papadimitriou, Fábio C. P. Navarro, Nicole North, Larsson Omberg, David M. Panchision, Neelroop Parikshak, Jérémie Poschmann, Amanda J. Price, Michael Purcaro, Timothy E. Reddy, Panos Roussos, Shannon Schreiner, Soraya Scuderi, Robert Sebra, Mikihito Shibata, Annie W. Shieh, Mario Škarica, Wenjie Sun, Vivek Swarup, Amber Thomas, Junko Tsuji, Harm van Bakel, Daifeng Wang, Yongjun Wang, Kai Wang, Donna M. Werling, A. Jeremy Willsey, Heather Witt, Hyejung Won, Chloe C. Y. Wong, Gregory A. Wray, Emily Wu, Xuming Xu, Lijing Yao, Geetha Senthil, Thomas Lehner, Pamela Sklar, Nenad Šestan - Nature Neuroscience 2015 cited by 488
- dCas9-based epigenome editing suggests acquisition of histone methylation is not sufficient for target gene repression
Authors: Henriette O’Geen, Chonghua Ren, Charles M. Nicolet, Andrew Perez, Julian Halmai, Victoria M. Le, Joel P. Mackay, Peggy Farnham, David J. Segal - Nucleic Acids Research 2017 cited by 256
- Transcriptome and epigenome landscape of human cortical development modeled in organoids
Authors: Anahita Amiri, Gianfilippo Coppola, Soraya Scuderi, Feinan Wu, Tanmoy Roychowdhury, Fuchen Liu, Sirisha Pochareddy, Yurae Shin, Alexias Safi, Lingyun Song, Ying Zhu, André M. M. Sousa, Mark Gerstein, Gregory E. Crawford, Nenad Šestan, Alexej Abyzov, Flora M. Vaccarino, Schahram Akbarian, Joon‐Yong An, Christoper Armoskus, Allison E. Ashley‐Koch, Thomas G. Beach, Judson Belmont, Jaroslav Bendl, Tyler Borrman, Leanne Brown, Miguel Brown, Mimi Brown, Tonya M. Brunetti, Julien Bryois, Emily E. Burke, Adrian Camarena, Becky C. Carlyle, Yooree Chae, Alexander W. Charney, Chao Chen, Lijun Cheng, Adriana Cherskov, Jinmyung Choi, Declan Clarke, Leonardo Collado‐Torres, Rujia Dai, Luis de la Torre-Ubieta, Diane M. Del Valle, Olivia Devillers, Stella Dracheva, Prashant S. Emani, Oleg V. Evgrafov, Peggy Farnham, Dominic Fitzgerald, Elie Flatow, Nancy Francoeur, John F. Fullard, Michael J. Gandal, Tianliuyun Gao, Melanie E. Garrett, Daniel H. Geschwind, Gina Giase, Kiran Girdhar, Paola Giusti‐Rodríguez, Fernando S. Goes, Thomas Goodman, Kay Grennan, Mengting Gu, Gamze Gürsoy, Evi Hadjimichael, Chang-Gyu Hahn, Vahram Haroutunian, Mads E. Hauberg, Gabriel E. Hoffman, Jack Huey, Thomas M. Hyde, Nikolay A. Ivanov, Rivka Jacobov, Andrew E. Jaffe, Yan Jiang, Yi Jiang, Graham D. Johnson, Bibi Kassim, Amira Kefi, Yunjung Kim, Robert R. Kitchen, Joel E. Kleiman, James A. Knowles, Alexey Kozlenkov, Mingfeng Li, Zhen Li, Barbara K. Lipska, Chunyu Liu, Shuang Liu, Lara M. Mangravite, Jessica Mariani, Eugenio Mattei, Daniel J. Miller, J. Russell Moore, Angus C. Nairn, Fábio C. P. Navarro, Royce Park, Mette A. Peters, Dalila Pinto and 47 more - Science 2018 cited by 315
- Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability
Authors: Alex de Mendoza, Trung Viet Nguyen, Ethan Ford, Daniel Poppe, Sam Buckberry, Jahnvi Pflueger, Matthew Grimmer, Sabine Stolzenburg, Ozren Bogdanović, Alicia Oshlack, Peggy Farnham, Pilar Blancafort, Ryan Lister - Genome biology 2022 cited by 120
- Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome
Authors: Yu Gyoung Tak, Peggy Farnham - Epigenetics & Chromatin 2015 cited by 379
- Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner
Authors: Henriette O’Geen, Sofie Bates, Sakereh S. Carter, Karly Nisson, Julian Halmai, Kyle D. Fink, Suhn K. Rhie, Peggy Farnham, David J. Segal - Epigenetics & Chromatin 2019 cited by 176
- Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
Authors: R. Alan Harris, Ting Wang, Cristian Coarfa, Raman P. Nagarajan, Chibo Hong, Sara L. Downey, Brett Johnson, Shaun D. Fouse, Allen Delaney, Yongjun Zhao, Adam B. Olshen, Tracy Ballinger, Xin Zhou, Kevin J. Forsberg, Junchen Gu, Lorigail Echipare, Henriette O’Geen, Ryan Lister, Mattia Pelizzola, Yuanxin Xi, Charles B Epstein, B Bernstein, R. David Hawkins, Bing Ren, Wen‐Yu Chung, Hongcang Gu, Christoph Bock, Andreas Gnirke, Michael Q. Zhang, David Haussler, Joseph R. Ecker, Wei Li, Peggy Farnham, Robert A. Waterland, Alexander Meissner, Marco A. Marra, Martin Hirst, Aleksandar Milosavljevic, J Costello - Nature Biotechnology 2010 cited by 739
- KAP1 Protein: An Enigmatic Master Regulator of the Genome
Authors: Sushma Iyengar, Peggy Farnham - Journal of Biological Chemistry 2011 cited by 383
- An integrated encyclopedia of DNA elements in the human genome
Authors: Ian Dunham, Anshul Kundaje, Shelley Force Aldred, Patrick Collins, Carrie Davis, Francis Doyle, Charles B. Epstein, Seth Frietze, Jennifer Harrow, Rajinder Kaul, Jainab Khatun, Bryan R. Lajoie, Stephen G. Landt, Bumkyu Lee, Florencia Pauli, Kate R. Rosenbloom, Peter J. Sabo, Alexias Safi, Amartya Sanyal, Noam Shoresh, Jeremy M. Simon, Lingyun Song, Nathan D. Trinklein, Robert C. Altshuler, Ewan Birney, James B. Brown, Chao Cheng, Sarah Djebali, Xianjun Dong, Jason Ernst, Terrence S. Furey, Mark Gerstein, Belinda Giardine, Melissa C. Greven, Ross C. Hardison, Robert S. Harris, Javier Herrero, Michael M. Hoffman, Sowmya Iyer, Manolis Kellis, Pouya Kheradpour, Timo Lassmann, Qunhua Li, Xin-Ying Lin, Georgi K. Marinov, Angelika Merkel, A Mortazavi, Stephen C.J. Parker, Timothy E. Reddy, Joel Rozowsky, Felix Schlesinger, Robert E. Thurman, Jie Wang, Lucas D. Ward, Troy W. Whitfield, Steven P. Wilder, Wei-Sheng Wu, Hualin Simon Xi, Kevin Y. Yip, Jiali Zhuang, B Bernstein, Eric D. Green, Chris Gunter, M Snyder, Michael J. Pazin, Rebecca F. Lowdon, Laura A. L. Dillon, Leslie B. Adams, Caroline J. Kelly, Julia Zhang, Judith R. Wexler, Peter J. Good, Elise A. Feingold, Gregory E. Crawford, Job Dekker, Laura Elnitski, Peggy Farnham, Morgan C. Giddings, T Gingeras, Roderic Guigó, Timothy J. Hubbard, W. James Kent, Jason D. Lieb, Elliott H. Margulies, R Myers, J Stamatoyannopoulos, Scott A. Tenenbaum, Zhiping Weng, Kevin P. White, B Wold, Yanbao Yu, John A. Wrobel, Brian A. Risk, Harsha P. Gunawardena, Heather Kuiper, Christopher Maier, Ling Xie, Xian Chen, Tarjei S. Mikkelsen, Shawn Gillespie and 343 more - 2012 cited by 2,783
- A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome
Authors: Suhn K. Rhie, Andrew Perez, Fides D. Lay, Shannon Schreiner, Jiani Shi, Jenevieve Polin, Peggy Farnham - Nature Communications 2019 cited by 144
- T-bet Regulates the Terminal Maturation and Homeostasis of NK and Vα14i NKT Cells
Authors: Michael J. Townsend, Amy S. Weinmann, Jennifer L. Matsuda, Rachelle Salomon, Peggy Farnham, Christine A. Biron, Laurent Gapin, Laurie H. Glimcher - Immunity 2004 cited by 706
- Defining functional DNA elements in the human genome
Authors: Manolis Kellis, B Wold, M Snyder, B Bernstein, Anshul Kundaje, Georgi K. Marinov, Lucas D. Ward, Ewan Birney, Gregory E. Crawford, Job Dekker, Ian Dunham, Laura Elnitski, Peggy Farnham, Elise A. Feingold, Mark Gerstein, Morgan C. Giddings, David M. Gilbert, T Gingeras, Eric D. Green, Roderic Guigó, Tim Hubbard, Jim Kent, Jason D. Lieb, R Myers, Michael J. Pazin, Bing Ren, J Stamatoyannopoulos, Zhiping Weng, Kevin P. White, Ross C. Hardison - National Academy of Sciences, Proceedings of the National Academy of Sciences 2014 cited by 749
- DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape
Authors: Mingchao Xie, Chibo Hong, Bo Zhang, Rebecca F. Lowdon, Xiaoyun Xing, Daofeng Li, Xin Zhou, Hyung Joo Lee, Cécile L. Maire, Keith L. Ligon, Philippe Gascard, Mahvash Sigaroudinia, Thea D. Tlsty, Theresa A. Kadlecek, Arthur Weiss, Henriette O’Geen, Peggy Farnham, Pamela A. F. Madden, Andrew J. Mungall, Angela Tam, Baljit Kamoh, Stephanie Cho, Richard A. Moore, Martin Hirst, Marco A. Marra, J Costello, Ting Wang - Nature Genetics 2013 cited by 250
- Inferring regulatory element landscapes and transcription factor networks from cancer methylomes
Authors: Lijing Yao, Hui Shen, Peter W. Laird, Peggy Farnham, Benjamin P. Berman - Genome Biology 2015 cited by 219
- Using ChIP-Seq Technology to Generate High-Resolution Profiles of Histone Modifications
Authors: Henriette O’Geen, Lorigail Echipare, Peggy Farnham - Methods in molecular biology 2011 cited by 174
- Characterization of the ZFX family of transcription factors that bind downstream of the start site of CpG island promoters
Authors: Stephanie W. Ni, Andrew Perez, Shannon Schreiner, Charles M. Nicolet, Peggy Farnham - Nucleic Acids Research 2020 cited by 51
- The Human Epigenome Browser at Washington University
Authors: Xin Zhou, Brett Maricque, Mingchao Xie, Daofeng Li, Vasavi Sundaram, Eric A Martin, Brian C. Koebbe, Cydney Nielsen, Martin Hirst, Peggy Farnham, Robert M. Kuhn, Jingchun Zhu, Ivan Smirnov, W. James Kent, David Haussler, Pamela A. F. Madden, J Costello, Ting Wang - Nature Methods 2011 cited by 327
- Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
Authors: Bo Zhang, Yan Zhou, Nan Lin, Rebecca F. Lowdon, Chibo Hong, Raman P. Nagarajan, Jeffrey B. Cheng, Daofeng Li, Michael Stevens, Hyung Joo Lee, Xiaoyun Xing, Jia Zhou, Vasavi Sundaram, GiNell Elliott, Junchen Gu, Taoping Shi, Philippe Gascard, Mahvash Sigaroudinia, Thea D. Tlsty, Theresa A. Kadlecek, Arthur Weiss, Henriette O’Geen, Peggy Farnham, Cécile L. Maire, Keith L. Ligon, Pamela A. F. Madden, Angela Tam, Richard A. Moore, Martin Hirst, Marco A. Marra, Baoxue Zhang, J Costello, Ting Wang - Genome Research 2013 cited by 203
