PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.

Christine E. Horak, Michael Snyder, ChIP-chip: a genomic approach for identifying transcription factor binding sites. Methods in Enzymology. ,vol. 350, pp. 469- 483 ,(2002) , 10.1016/S0076-6879(02)50979-4

G. M. Euskirchen, J. S. Rozowsky, C.-L. Wei, W. H. Lee, Z. D. Zhang, S. Hartman, O. Emanuelsson, V. Stolc, S. Weissman, M. B. Gerstein, Y. Ruan, M. Snyder, Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies Genome Research. ,vol. 17, pp. 898- 909 ,(2007) , 10.1101/GR.5583007

Vishwanath R Iyer, Christine E Horak, Charles S Scafe, David Botstein, Michael Snyder, Patrick O Brown, None, Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF Nature. ,vol. 409, pp. 533- 538 ,(2001) , 10.1038/35054095

Jeffrey M. Kidd, Gregory M. Cooper, William F. Donahue, Hillary S. Hayden, Nick Sampas, Tina Graves, Nancy Hansen, Brian Teague, Can Alkan, Francesca Antonacci, Eric Haugen, Troy Zerr, N. Alice Yamada, Peter Tsang, Tera L. Newman, Eray Tüzün, Ze Cheng, Heather M. Ebling, Nadeem Tusneem, Robert David, Will Gillett, Karen A. Phelps, Molly Weaver, David Saranga, Adrianne Brand, Wei Tao, Erik Gustafson, Kevin McKernan, Lin Chen, Maika Malig, Joshua D. Smith, Joshua M. Korn, Steven A. McCarroll, David A. Altshuler, Daniel A. Peiffer, Michael Dorschner, John Stamatoyannopoulos, David Schwartz, Deborah A. Nickerson, James C. Mullikin, Richard K. Wilson, Laurakay Bruhn, Maynard V. Olson, Rajinder Kaul, Douglas R. Smith, Evan E. Eichler, Mapping and sequencing of structural variation from eight human genomes Nature. ,vol. 453, pp. 56- 64 ,(2008) , 10.1038/NATURE06862

Nava Whiteford, Niall Haslam, Gerald Weber, Adam Prügel-Bennett, Jonathan W Essex, Peter L Roach, Mark Bradley, Cameron Neylon, An analysis of the feasibility of short read sequencing Nucleic Acids Research. ,vol. 33, ,(2005) , 10.1093/NAR/GNI170

Antonio Piccolboni, Victor Sementchenko, Jill Cheng, Alan J Williams, Raymond Wheeler, Brant Wong, Jorg Drenkow, Mark Yamanaka, Sandeep Patel, Shane Brubaker, Hari Tammana, Gregg Helt, Kevin Struhl, Thomas R Gingeras, Simon Cawley, Stefan Bekiranov, Huck H Ng, Philipp Kapranov, Edward A Sekinger, Dione Kampa, Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell. ,vol. 116, pp. 499- 509 ,(2004) , 10.1016/S0092-8674(04)00127-8

Gordon Robertson, Martin Hirst, Matthew Bainbridge, Misha Bilenky, Yongjun Zhao, Thomas Zeng, Ghia Euskirchen, Bridget Bernier, Richard Varhol, Allen Delaney, Nina Thiessen, Obi L Griffith, Ann He, Marco Marra, Michael Snyder, Steven Jones, Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing Nature Methods. ,vol. 4, pp. 651- 657 ,(2007) , 10.1038/NMETH1068

Management Group Liefer Laura A. 51 Wetterstrand Kris A. 51 Good Peter J. 51 Feingold Elise A. 51 Guyer Mark S. 51 Collins Francis S. 52, Baylor College of Medicine Human Genome Sequencing Center*, Washington University Genome Sequencing Center*, Broad Institute*, Children’s Hospital Oakland Research Institute*, Mark Gerstein, Stylianos E Antonarakis, Serafim Batzoglou, Nick Goldman, Ross C Hardison, David Haussler, Webb Miller, Lior Pachter, Eric D Green, Arend Sidow, Zhiping Weng, Nathan D Trinklein, Yutao Fu, Zhengdong D Zhang, Ulaş Karaöz, Leah Barrera, Rhona Stuart, Deyou Zheng, Srinka Ghosh, Paul Flicek, David C King, James Taylor, Adam Ameur, Stefan Enroth, Mark C Bieda, Christoph M Koch, Heather A Hirsch, Chia-Lin Wei, Jill Cheng, Jonghwan Kim, Akshay A Bhinge, Paul G Giresi, Nan Jiang, Jun Liu, Fei Yao, Wing-Kin Sung, Kuo Ping Chiu, Vinsensius B Vega, Charlie WH Lee, Patrick Ng, Atif Shahab, Edward A Sekinger, Annie Yang, Zarmik Moqtaderi, Zhou Zhu, Xiaoqin Xu, Sharon Squazzo, Matthew J Oberley, David Inman, Michael A Singer, Todd A Richmond, Kyle J Munn, Alvaro Rada-Iglesias, Ola Wallerman, Jan Komorowski, Gayle K Clelland, Sarah Wilcox, Shane C Dillon, Robert M Andrews, Joanna C Fowler, Phillippe Couttet, Keith D James, Gregory C Lefebvre, Alexander W Bruce, Oliver M Dovey, Peter D Ellis, Pawandeep Dhami, Cordelia F Langford, Nigel P Carter, David Vetrie, Philipp Kapranov, David A Nix, Ian Bell, Sandeep Patel, Joel Rozowsky, Ghia Euskirchen, Stephen Hartman, Jin Lian, Jiaqian Wu, Alexander E Urban, Peter Kraus, Sara Van Calcar, Nate Heintzman, Tae Hoon Kim, Kun Wang, Chunxu Qu, Gary Hon, Rosa Luna, Christopher K Glass, M Geoff Rosenfeld, Shelley Force Aldred, Sara J Cooper, Anason Halees, Jane M Lin, Hennady P Shulha, Xiaoling Zhang, Mousheng Xu, Jaafar NS Haidar, Yong Yu, Ewan Birney*, Sherman Weissman, Yijun Ruan, Jason D Lieb, Vishwanath R Iyer, Roland D Green, Thomas R Gingeras, Claes Wadelius, Ian Dunham, Kevin Struhl, Ross C Hardison, Mark Gerstein, Peggy J Farnham, Richard M Myers, Bing Ren, Michael Snyder, Daryl J Thomas, Kate Rosenbloom, Rachel A Harte, Angie S Hinrichs, Heather Trumbower, Hiram Clawson, Jennifer Hillman-Jackson, Ann S Zweig, Kayla Smith, Archana Thakkapallayil, Galt Barber, Robert M Kuhn, Donna Karolchik, David Haussler, W James Kent, Emmanouil T Dermitzakis, Lluis Armengol, Christine P Bird, Taane G Clark, Gregory M Cooper, Paul IW de Bakker, Andrew D Kern, Nuria Lopez-Bigas, Joel D Martin, Barbara E Stranger, None, Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Nature. ,vol. 447, pp. 799- 816 ,(2007) , 10.1038/NATURE05874

John D. Storey, A direct approach to false discovery rates Journal of The Royal Statistical Society Series B-statistical Methodology. ,vol. 64, pp. 479- 498 ,(2002) , 10.1111/1467-9868.00346

Yoav Benjamini, Yosef Hochberg, Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing Journal of the Royal Statistical Society: Series B (Methodological). ,vol. 57, pp. 289- 300 ,(1995) , 10.1111/J.2517-6161.1995.TB02031.X