C
C. Shou
Researcher at Yale University
Publications - 10
Citations - 4014
C. Shou is an academic researcher from Yale University. The author has contributed to research in topics: Gene & Genome. The author has an hindex of 8, co-authored 10 publications receiving 3781 citations.
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Journal ArticleDOI
The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing
Ugrappa Nagalakshmi,Zhong Wang,Karl Waern,C. Shou,Debasish Raha,Mark Gerstein,Michael Snyder +6 more
TL;DR: A quantitative sequencing-based method is developed for mapping transcribed regions, in which complementary DNA fragments are subjected to high-throughput sequencing and mapped to the genome, and it is demonstrated that most (74.5%) of the nonrepetitive sequence of the yeast genome is transcribed.
Journal ArticleDOI
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
Mark Gerstein,Zhi John Lu,Eric L. Van Nostrand,Chao Cheng,Bradley I. Arshinoff,Tao Liu,Kevin Y. Yip,R. Robilotto,Andreas Rechtsteiner,Kohta Ikegami,P. Alves,A. Chateigner,Marc D. Perry,Mitzi Morris,Raymond K. Auerbach,X. Feng,Jing Leng,A. Vielle,Wei Niu,Kahn Rhrissorrakrai,Ashish Agarwal,Roger P. Alexander,Galt P. Barber,Cathleen M. Brdlik,J. Brennan,Jeremy Brouillet,Adrian Carr,Ming Sin Cheung,Hiram Clawson,Sergio Contrino,Luke Dannenberg,Abby F. Dernburg,Arshad Desai,L. Dick,Andréa C. Dosé,Jiang Du,Thea A. Egelhofer,Sevinc Ercan,Ghia Euskirchen,Brent Ewing,Elise A. Feingold,Reto Gassmann,Peter J. Good,Philip Green,Francois Gullier,M. Gutwein,Mark S. Guyer,Lukas Habegger,Ting Han,Jorja G. Henikoff,Stefan R. Henz,Angie S. Hinrichs,H. Holster,Tony Hyman,A. Leo Iniguez,J. Janette,M. Jensen,Masaomi Kato,W. James Kent,E. Kephart,Vishal Khivansara,Ekta Khurana,John Kim,P. Kolasinska-Zwierz,Eric C. Lai,Isabel J. Latorre,Amber Leahey,Suzanna E. Lewis,Paul Lloyd,Lucas Lochovsky,Rebecca F. Lowdon,Yaniv Lubling,Rachel Lyne,Michael J. MacCoss,Sebastian D. Mackowiak,Marco Mangone,Sheldon J. McKay,D. Mecenas,Gennifer E. Merrihew,David M. Miller,A. Muroyama,John I. Murray,Siew Loon Ooi,Hoang Pham,T. Phippen,Elicia Preston,Nikolaus Rajewsky,Gunnar Rätsch,Heidi Rosenbaum,Joel Rozowsky,Kim Rutherford,P. Ruzanov,Mihail Sarov,Rajkumar Sasidharan,Andrea Sboner,P. Scheid,Eran Segal,Hyunjin Shin,C. Shou,Frank J. Slack,C. Slightam,Richard J.H. Smith,William C. Spencer,Eo Stinson,S. Taing,Teruaki Takasaki,D. Vafeados,Ksenia Voronina,Guilin Wang,Nicole L. Washington,Christina M. Whittle,Beijing Wu,Koon-Kiu Yan,Georg Zeller,Z. Zha,Mei Zhong,Xingliang Zhou,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 +130 more
TL;DR: These studies identified regions of the nematode and fly genomes that show highly occupied targets (or HOT) regions where DNA was bound by more than 15 of the transcription factors analyzed and the expression of related genes were characterized, providing insights into the organization, structure, and function of the two genomes.
Journal ArticleDOI
Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization
Yuichiro Mishima,Cei Abreu-Goodger,Alison A Staton,Carlos Stahlhut,C. Shou,Chao Cheng,Mark Gerstein,Anton J. Enright,Antonio J. Giraldez +8 more
TL;DR: Results suggest thatmiR-1 and miR-133 actively shape gene expression patterns in muscle tissue, where they regulate sarcomeric actin organization.
Journal ArticleDOI
A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets
Chao Cheng,Koon-Kiu Yan,Kevin Y. Yip,Kevin Y. Yip,Joel Rozowsky,Roger P. Alexander,C. Shou,Mark Gerstein +7 more
TL;DR: A statistical framework is developed to study the relationship between chromatin features and gene expression that can be used to predict gene expression of protein coding genes, as well as microRNAs, including modENCODE worm datasets.
Journal ArticleDOI
Measuring the evolutionary rewiring of biological networks.
C. Shou,Nitin Bhardwaj,Hugo Y. K. Lam,Koon-Kiu Yan,Philip M. Kim,Michael Snyder,Mark Gerstein +6 more
TL;DR: A formalism based on analogy to simple models of sequence evolution was developed and used to conduct a systematic study of network rewiring on all the currently available biological networks, and it was found that, similar to sequences, biological networks show a decreased rate of change at large time divergences.