Y
Yu Zhang
Researcher at Pennsylvania State University
Publications - 60
Citations - 2883
Yu Zhang is an academic researcher from Pennsylvania State University. The author has contributed to research in topics: Epigenomics & Gene. The author has an hindex of 20, co-authored 58 publications receiving 2424 citations.
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Journal ArticleDOI
In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features
TL;DR: Global comparison of several structural features between these two categories shows that the mRNAs associated with stress responses tend to have more single-strandedness, longer maximal loop length and higher free energy per nucleotide, features that may allow these RNAs to undergo conformational changes in response to environmental conditions.
Journal ArticleDOI
Complete Khoisan and Bantu genomes from southern Africa
Stephan C. Schuster,Webb Miller,Aakrosh Ratan,Lynn P. Tomsho,Belinda Giardine,Lindsay R. Kasson,Robert S. Harris,Desiree C. Petersen,Fangqing Zhao,Ji Qi,Can Alkan,Jeffrey M. Kidd,Yazhou Sun,Daniela I. Drautz,Pascal Bouffard,Donna M. Muzny,Jeffrey G. Reid,Lynne V. Nazareth,Qingyu Wang,Richard Burhans,Cathy Riemer,Nicola E. Wittekindt,Priya Moorjani,Elizabeth A. Tindall,Charles G. Danko,Wee Siang Teo,Anne M. Buboltz,Zhenhai Zhang,Qianyi Ma,Arno Oosthuysen,Abraham W. Steenkamp,Hermann Oostuisen,Philippus Venter,John P. Gajewski,Yu Zhang,B. Franklin Pugh,Kateryna D. Makova,Anton Nekrutenko,Elaine R. Mardis,Nick Patterson,Tom H. Pringle,Francesca Chiaromonte,James C. Mullikin,Evan E. Eichler,Ross C. Hardison,Richard A. Gibbs,Timothy T. Harkins,Vanessa M. Hayes +47 more
TL;DR: The extent of whole-genome and exome diversity among the five men, reporting 1.3 million novel DNA differences genome-wide, including 13,146 novel amino acid variants, suggests the Bushmen seem to be more different from each other than, for example, a European and an Asian.
Journal ArticleDOI
Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression
Yong Cheng,Weisheng Wu,Swathi Ashok Kumar,Duonan Yu,Wulan Deng,Tamara Tripic,David C. King,Kuan Bei Chen,Ying Zhang,Daniela I. Drautz,Belinda Giardine,Stephan C. Schuster,Webb Miller,Francesca Chiaromonte,Yu Zhang,Gerd A. Blobel,Mitchell J. Weiss,Ross C. Hardison +17 more
TL;DR: The data expand the repertoire of Gata1 action in erythropoiesis by defining a new cohort of target genes and determining the spatial distribution of cis-regulatory modules throughout the genome, and begin to establish functional criteria and mechanisms that distinguish GATA1 activation from repression at specific target genes.
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Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil).
Webb Miller,Vanessa M. Hayes,Vanessa M. Hayes,Aakrosh Ratan,Desiree C. Petersen,Desiree C. Petersen,Nicola E. Wittekindt,Jason R. Miller,Brian P. Walenz,James W. Knight,Ji Qi,Fangqing Zhao,Qingyu Wang,Oscar C. Bedoya-Reina,Neerja Katiyar,Lynn P. Tomsho,Lindsay Mc Clellan Kasson,Rae-Anne Hardie,Paula Woodbridge,Elizabeth A. Tindall,Mads F. Bertelsen,Dale Dixon,Stephen Pyecroft,Kristofer M. Helgen,Arthur M. Lesk,Thomas H. Pringle,Nick Patterson,Yu Zhang,Alexandre Kreiss,Gregory M. Woods,Menna E. Jones,Stephan C. Schuster +31 more
TL;DR: Analysis of 14 complete mitochondrial genomes from current and museum specimens, as well as mitochondrial and nuclear SNP markers in 175 animals, suggests that the observed low genetic diversity in today's population preceded the Devil Facial Tumor Disease disease outbreak by at least 100 y.
Journal ArticleDOI
Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration.
Weisheng Wu,Yong Cheng,Cheryl A. Keller,Jason Ernst,Jason Ernst,Swathi Ashok Kumar,Tejaswini Mishra,Christapher S. Morrissey,Christine M. Dorman,Kuan-Bei Chen,Daniela I. Drautz,Belinda Giardine,Yoichiro Shibata,Lingyun Song,Maxim Pimkin,Gregory E. Crawford,Terrence S. Furey,Manolis Kellis,Manolis Kellis,Webb Miller,James Taylor,Stephan C. Schuster,Yu Zhang,Francesca Chiaromonte,Gerd A. Blobel,Mitchell J. Weiss,Ross C. Hardison +26 more
TL;DR: The results indicate that during erythroid differentiation, the broad features of chromatin states are established at the stage of lineage commitment, largely independently of GATA1, which determine permissiveness for expression, with subsequent induction or repression mediated by distinctive combinations of transcription factors.