Cited by ..

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

Stewart MacArthur, Xiao-Yong Li, Jingyi Li, James B Brown, Hou Cheng Chu, Lucy Zeng, Brandi P Grondona, Aaron Hechmer, Lisa Simirenko, Soile VE Keränen, David W Knowles, Mark Stapleton, Peter Bickel, Mark D Biggin, Michael B Eisen

Genome Biol. 2009; 10(7): R80. Published online 2009 July 23. doi: 10.1186/gb-2009-10-7-r80

PMCID:: PMC2728534

Abstract Full Text PDF–1.7M Supplementary Material

Is Cited by the Following 43 Articles in this Archive:

A Conserved Developmental Patterning Network Produces Quantitatively Different Output in Multiple Species of Drosophila

Charless C. Fowlkes, Kelly B. Eckenrode, Meghan D. Bragdon, Miriah Meyer, Zeba Wunderlich, Lisa Simirenko, Cris L. Luengo Hendriks, Soile V. E. Keränen, Clara Henriquez, David W. Knowles, Mark D. Biggin, Michael B. Eisen, Angela H. DePace

PLoS Genet. 2011 October; 7(10): e1002346. Published online 2011 October 27. doi: 10.1371/journal.pgen.1002346

PMCID:: PMC3203197

Abstract Full Text PDF–8.2M Supplementary Material

Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition

Melissa M. Harrison, Xiao-Yong Li, Tommy Kaplan, Michael R. Botchan, Michael B. Eisen

PLoS Genet. 2011 October; 7(10): e1002266. Published online 2011 October 20. doi: 10.1371/journal.pgen.1002266

PMCID:: PMC3197655

Abstract Full Text PDF–1.1M Supplementary Material

Temporal Coordination of Gene Networks by Zelda in the Early Drosophila Embryo

Chung-Yi Nien, Hsiao-Lan Liang, Stephen Butcher, Yujia Sun, Shengbo Fu, Tenzin Gocha, Nikolai Kirov, J. Robert Manak, Christine Rushlow

PLoS Genet. 2011 October; 7(10): e1002339. Published online 2011 October 20. doi: 10.1371/journal.pgen.1002339

PMCID:: PMC3197689

Abstract Full Text PDF–8.0M Supplementary Material

Cooperative transcription factor associations discovered using regulatory variation

Konrad J. Karczewski, Nicholas P. Tatonetti, Stephen G. Landt, Xinqiong Yang, Teri Slifer, Russ B. Altman, Michael Snyder

Proc Natl Acad Sci U S A. 2011 August 9; 108(32): 13353–13358. Published online 2011 July 26. doi: 10.1073/pnas.1103105108

PMCID:: PMC3156166

Abstract Full Text PDF–418K Supplementary Material

Integrated Genome-Scale Prediction of Detrimental Mutations in Transcription Networks

Mirko Francesconi, Rob Jelier, Ben Lehner

PLoS Genet. 2011 May; 7(5): e1002077. Published online 2011 May 26. doi: 10.1371/journal.pgen.1002077

PMCID:: PMC3102745

Abstract Full Text PDF–1001K Supplementary Material

Genome surveyor 2.0: cis-regulatory analysis in Drosophila

Majid Kazemian, Michael H. Brodsky, Saurabh Sinha

Nucleic Acids Res. 2011 July 1; 39(Web Server issue): W79–W85. Published online 2011 May 18. doi: 10.1093/nar/gkr291

PMCID:: PMC3125742

Abstract Full Text PDF–7.7M

Dynamic reprogramming of chromatin accessibility during Drosophila embryo development

Sean Thomas, Xiao-Yong Li, Peter J Sabo, Richard Sandstrom, Robert E Thurman, Theresa K Canfield, Erika Giste, William Fisher, Ann Hammonds, Susan E Celniker, Mark D Biggin, John A Stamatoyannopoulos

Genome Biol. 2011; 12(5): R43. Published online 2011 May 11. doi: 10.1186/gb-2011-12-5-r43

PMCID:: PMC3219966

Abstract Full Text PDF–1.5M Supplementary Material

Hairless is a cofactor for Runt-dependent transcriptional regulation

Pegine B. Walrad, Saiyu Hang, J. Peter Gergen

Mol Biol Cell. 2011 April 15; 22(8): 1364–1374. doi: 10.1091/mbc.E10-06-0483

PMCID:: PMC3078061

Abstract Full Text PDF–1.4M

The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding

Xiao-Yong Li, Sean Thomas, Peter J Sabo, Michael B Eisen, John A Stamatoyannopoulos, Mark D Biggin

Genome Biol. 2011; 12(4): R34. Published online 2011 April 7. doi: 10.1186/gb-2011-12-4-r34

PMCID:: PMC3218860

Abstract Full Text PDF–787K Supplementary Material

Genome-Wide Tissue-Specific Occupancy of the Hox Protein Ultrabithorax and Hox Cofactor Homothorax in Drosophila

Matthew Slattery, Lijia Ma, Nicolas Négre, Kevin P. White, Richard S. Mann

PLoS One. 2011; 6(4): e14686. Published online 2011 April 5. doi: 10.1371/journal.pone.0014686

PMCID:: PMC3071676

Abstract Full Text PDF–1.8M Supplementary Material

Genome-Wide Analysis of the Binding of the Hox Protein Ultrabithorax and the Hox Cofactor Homothorax in Drosophila

Siew Woh Choo, Robert White, Steven Russell

PLoS One. 2011; 6(4): e14778. Published online 2011 April 5. doi: 10.1371/journal.pone.0014778

PMCID:: PMC3071696

Abstract Full Text PDF–1.8M Supplementary Material

High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation

Anil Ozdemir, Katherine I. Fisher-Aylor, Shirley Pepke, Manoj Samanta, Leslie Dunipace, Kenneth McCue, Lucy Zeng, Nobuo Ogawa, Barbara J. Wold, Angelike Stathopoulos

Genome Res. 2011 April; 21(4): 566–577. doi: 10.1101/gr.104018.109

PMCID:: PMC3065704

Abstract Full Text PDF–1.7M

A Cis-Regulatory Map of the Drosophila Genome

Nicolas Nègre, Christopher D. Brown, Lijia Ma, Christopher Aaron Bristow, Steven W. Miller, Ulrich Wagner, Pouya Kheradpour, Matthew L. Eaton, Paul Loriaux, Rachel Sealfon, Zirong Li, Haruhiko Ishii, Rebecca F. Spokony, Jia Chen, Lindsay Hwang, Chao Cheng, Richard P. Auburn, Melissa B. Davis, Marc Domanus, Parantu K. Shah, Carolyn A. Morrison, Jennifer Zieba, Sarah Suchy, Lionel Senderowicz, Alec Victorsen, Nicholas A. Bild, A. Jason Grundstad, David Hanley, David M. MacAlpine, Mattias Mannervik, Koen Venken, Hugo Bellen, Robert White, Steven Russell, Robert L. Grossman, Bing Ren, Mark Gerstein, James W. Posakony, Manolis Kellis, Kevin P. White

Nature. Author manuscript; available in PMC 2011 September 23.

Published in final edited form as: Nature. 2011 March 24; 471(7339): 527–531. doi: 10.1038/nature09990

PMCID:: PMC3179250

Abstract Full Text PDF–1.2M Supplementary Material

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

Roger Pique-Regi, Jacob F. Degner, Athma A. Pai, Daniel J. Gaffney, Yoav Gilad, Jonathan K. Pritchard

Genome Res. 2011 March; 21(3): 447–455. doi: 10.1101/gr.112623.110

PMCID:: PMC3044858

Abstract Full Text PDF–1.4M

Quantitative Models of the Mechanisms That Control Genome-Wide Patterns of Transcription Factor Binding during Early Drosophila Development

Tommy Kaplan, Xiao-Yong Li, Peter J. Sabo, Sean Thomas, John A. Stamatoyannopoulos, Mark D. Biggin, Michael B. Eisen

PLoS Genet. 2011 February; 7(2): e1001290. Published online 2011 February 3. doi: 10.1371/journal.pgen.1001290

PMCID:: PMC3033374

Abstract Full Text PDF–2.2M Supplementary Material

Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin

Nicole C. Riddle, Aki Minoda, Peter V. Kharchenko, Artyom A. Alekseyenko, Yuri B. Schwartz, Michael Y. Tolstorukov, Andrey A. Gorchakov, Jacob D. Jaffe, Cameron Kennedy, Daniela Linder-Basso, Sally E. Peach, Gregory Shanower, Haiyan Zheng, Mitzi I. Kuroda, Vincenzo Pirrotta, Peter J. Park, Sarah C.R. Elgin, Gary H. Karpen

Genome Res. 2011 February; 21(2): 147–163. doi: 10.1101/gr.110098.110

PMCID:: PMC3032919

Abstract Full Text PDF–2.1M

Genome-wide analysis of promoter architecture in Drosophila melanogaster

Roger A. Hoskins, Jane M. Landolin, James B. Brown, Jeremy E. Sandler, Hazuki Takahashi, Timo Lassmann, Charles Yu, Benjamin W. Booth, Dayu Zhang, Kenneth H. Wan, Li Yang, Nathan Boley, Justen Andrews, Thomas C. Kaufman, Brenton R. Graveley, Peter J. Bickel, Piero Carninci, Joseph W. Carlson, Susan E. Celniker

Genome Res. 2011 February; 21(2): 182–192. doi: 10.1101/gr.112466.110

PMCID:: PMC3032922

Abstract Full Text PDF–900K

Whole-Genome Analysis Reveals That Active Heat Shock Factor Binding Sites Are Mostly Associated with Non-Heat Shock Genes in Drosophila melanogaster

Sarah E. Gonsalves, Alan M. Moses, Zak Razak, Francois Robert, J. Timothy Westwood

PLoS One. 2011; 6(1): e15934. Published online 2011 January 14. doi: 10.1371/journal.pone.0015934

PMCID:: PMC3021535

Abstract Full Text PDF–1.4M Supplementary Material

Co-regulatory expression quantitative trait loci mapping: method and application to endometrial cancer

Kenneth S Kompass, John S Witte

BMC Med Genomics. 2011; 4: 6. Published online 2011 January 12. doi: 10.1186/1755-8794-4-6

PMCID:: PMC3032645

Abstract Full Text PDF–565K Supplementary Material

Shape-based peak identification for ChIP-Seq

Valerie Hower, Steven N Evans, Lior Pachter

BMC Bioinformatics. 2011; 12: 15. Published online 2011 January 12. doi: 10.1186/1471-2105-12-15

PMCID:: PMC3032669

Abstract Full Text PDF–766K

Genomic Differentiation Between Temperate and Tropical Australian Populations of Drosophila melanogaster

Bryan Kolaczkowski, Andrew D. Kern, Alisha K. Holloway, David J. Begun

Genetics. 2011 January; 187(1): 245–260. doi: 10.1534/genetics.110.123059

PMCID:: PMC3018305

Abstract Full Text PDF–5.7M

A Widespread Distribution of Genomic CeMyoD Binding Sites Revealed and Cross Validated by ChIP-Chip and ChIP-Seq Techniques

Haiyan Lei, Tetsunari Fukushige, Wei Niu, Mihail Sarov, Valerie Reinke, Michael Krause

PLoS One. 2010; 5(12): e15898. Published online 2010 December 29. doi: 10.1371/journal.pone.0015898

PMCID:: PMC3012110

Abstract Full Text PDF–747K Supplementary Material

Comprehensive analysis of the chromatin landscape in Drosophila

Peter V. Kharchenko, Artyom A. Alekseyenko, Yuri B. Schwartz, Aki Minoda, Nicole C. Riddle, Jason Ernst, Peter J. Sabo, Erica Larschan, Andrey A. Gorchakov, Tingting Gu, Daniela Linder-Basso, Annette Plachetka, Gregory Shanower, Michael Y. Tolstorukov, Lovelace J. Luquette, Ruibin Xi, Youngsook L. Jung, Richard W. Park, Eric P. Bishop, Theresa P. Canfield, Richard Sandstrom, Robert E. Thurman, David M. MacAlpine, John A. Stamatoyannopoulos, Manolis Kellis, Sarah C. R. Elgin, Mitzi I. Kuroda, Vincenzo Pirrotta, Gary H. Karpen, Peter J. Park

Nature. Author manuscript; available in PMC 2011 September 24.

Published in final edited form as: Nature. 2011 March 24; 471(7339): 480–485. Published online 2010 December 22. doi: 10.1038/nature09725

PMCID:: PMC3109908

Abstract Full Text PDF–1.0M Supplementary Material

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

Mark B. Gerstein, Zhi John Lu, Eric L. Van Nostrand, Chao Cheng, Bradley I. Arshinoff, Tao Liu, Kevin Y. Yip, Rebecca Robilotto, Andreas Rechtsteiner, Kohta Ikegami, Pedro Alves, Aurelien Chateigner, Marc Perry, Mitzi Morris, Raymond K. Auerbach, Xin Feng, Jing Leng, Anne Vielle, Wei Niu, Kahn Rhrissorrakrai, Ashish Agarwal, Roger P. Alexander, Galt Barber, Cathleen M. Brdlik, Jennifer Brennan, Jeremy Jean Brouillet, Adrian Carr, Ming-Sin Cheung, Hiram Clawson, Sergio Contrino, Luke O. Dannenberg, Abby F. Dernburg, Arshad Desai, Lindsay Dick, Andréa C. Dosé, Jiang Du, Thea Egelhofer, Sevinc Ercan, Ghia Euskirchen, Brent Ewing, Elise A. Feingold, Reto Gassmann, Peter J. Good, Phil Green, Francois Gullier, Michelle Gutwein, Mark S. Guyer, Lukas Habegger, Ting Han, Jorja G. Henikoff, Stefan R. Henz, Angie Hinrichs, Heather Holster, Tony Hyman, A. Leo Iniguez, Judith Janette, Morten Jensen, Masaomi Kato, W. James Kent, Ellen Kephart, Vishal Khivansara, Ekta Khurana, John K. Kim, Paulina Kolasinska-Zwierz, Eric C. Lai, Isabel Latorre, Amber Leahey, Suzanna Lewis, Paul Lloyd, Lucas Lochovsky, Rebecca F. Lowdon, Yaniv Lubling, Rachel Lyne, Michael MacCoss, Sebastian D. Mackowiak, Marco Mangone, Sheldon McKay, Desirea Mecenas, Gennifer Merrihew, David M. Miller, III, Andrew Muroyama, John I. Murray, Siew-Loon Ooi, Hoang Pham, Taryn Phippen, Elicia A. Preston, Nikolaus Rajewsky, Gunnar Rätsch, Heidi Rosenbaum, Joel Rozowsky, Kim Rutherford, Peter Ruzanov, Mihail Sarov, Rajkumar Sasidharan, Andrea Sboner, Paul Scheid, Eran Segal, Hyunjin Shin, Chong Shou, Frank J. Slack, Cindie Slightam, Richard Smith, William C. Spencer, E. O. Stinson, Scott Taing, Teruaki Takasaki, Dionne Vafeados, Ksenia Voronina, Guilin Wang, Nicole L. Washington, Christina M. Whittle, Beijing Wu, Koon-Kiu Yan, Georg Zeller, Zheng Zha, Mei Zhong, Xingliang Zhou, modENCODE Consortium, Julie Ahringer, Susan Strome, Kristin C. Gunsalus, Gos Micklem, X. Shirley Liu, Valerie Reinke, Stuart K. Kim, LaDeana W. Hillier, Steven Henikoff, Fabio Piano, Michael Snyder, Lincoln Stein, Jason D. Lieb, Robert H. Waterston

Science. Author manuscript; available in PMC 2011 July 24.

Published in final edited form as: Science. 2010 December 24; 330(6012): 1775–1787. Published online 2010 December 22. doi: 10.1126/science.1196914

PMCID:: PMC3142569

Abstract Full Text PDF–3.0M Supplementary Material

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

The modENCODE Consortium, Sushmita Roy, Jason Ernst, Peter V. Kharchenko, Pouya Kheradpour, Nicolas Negre, Matthew L. Eaton, Jane M. Landolin, Christopher A. Bristow, Lijia Ma, Michael F. Lin, Stefan Washietl, Bradley I. Arshinoff, Ferhat Ay, Patrick E. Meyer, Nicolas Robine, Nicole L. Washington, Luisa Di Stefano, Eugene Berezikov, Christopher D. Brown, Rogerio Candeias, Joseph W. Carlson, Adrian Carr, Irwin Jungreis, Daniel Marbach, Rachel Sealfon, Michael Y. Tolstorukov, Sebastian Will, Artyom A. Alekseyenko, Carlo Artieri, Benjamin W. Booth, Angela N. Brooks, Qi Dai, Carrie A. Davis, Michael O. Duff, Xin Feng, Andrey A. Gorchakov, Tingting Gu, Jorja G. Henikoff, Philipp Kapranov, Renhua Li, Heather K. MacAlpine, John Malone, Aki Minoda, Jared Nordman, Katsutomo Okamura, Marc Perry, Sara K. Powell, Nicole C. Riddle, Akiko Sakai, Anastasia Samsonova, Jeremy E. Sandler, Yuri B. Schwartz, Noa Sher, Rebecca Spokony, David Sturgill, Marijke van Baren, Kenneth H. Wan, Li Yang, Charles Yu, Elise Feingold, Peter Good, Mark Guyer, Rebecca Lowdon, Kami Ahmad, Justen Andrews, Bonnie Berger, Steven E. Brenner, Michael R. Brent, Lucy Cherbas, Sarah C. R. Elgin, Thomas R. Gingeras, Robert Grossman, Roger A. Hoskins, Thomas C. Kaufman, William Kent, Mitzi I. Kuroda, Terry Orr-Weaver, Norbert Perrimon, Vincenzo Pirrotta, James W. Posakony, Bing Ren, Steven Russell, Peter Cherbas, Brenton R. Graveley, Suzanna Lewis, Gos Micklem, Brian Oliver, Peter J. Park, Susan E. Celniker, Steven Henikoff, Gary H. Karpen, Eric C. Lai, David M. MacAlpine, Lincoln D. Stein, Kevin P. White, Manolis Kellis

Science. Author manuscript; available in PMC 2011 October 13.

Published in final edited form as: Science. 2010 December 24; 330(6012): 1787–1797. Published online 2010 December 22. doi: 10.1126/science.1198374