Works by Deyou Zheng

Results: 99

Spatiotemporal Gene Coexpression and Regulation in Mouse Cardiomyocytes of Early Cardiac Morphogenesis.

Published in:

2019

By:

Yang Liu;
Pengfei Lu;
Yidong Wang;
Morrow, Bernice E.;
Bin Zhou;
Deyou Zheng;
Liu, Yang;
Lu, Pengfei;
Wang, Yidong;
Zhou, Bin;
Zheng, Deyou

Publication type:

journal article

Advances in the development of gene therapy, noncoding RNA, and exosome-based treatments for tendinopathy.

Published in:

Annals of the New York Academy of Sciences, 2021, v. 1490, p. 3, doi. 10.1111/nyas.14382

By:

Ilaltdinov, Angela Wang;
Yubao Gong;
Leong, Daniel J.;
Gruson, Konrad I.;
Deyou Zheng;
Fung, David T.;
Li Sun;
Sun, Hui B.

Publication type:

Article

Letter to the Editor: 1H, 13C and 15N resonance assignments for methionine sulfoxide reductase B from Bacillus subtilis.

Published in:

Journal of Biomolecular NMR, 2003, v. 27, n. 2, p. 183, doi. 10.1023/A:1024991310929

By:

Zheng, Deyou;
Cort, John R.;
Chiang, YiWen;
Acton, Thomas;
Kennedy, Michael A.;
Montelione, Gaetano T.

Publication type:

Article

Fine-tuning spatial-temporal dynamics and surface receptor expression support plasma cell-intrinsic longevity.

Published in:

eLife, 2024, p. 1, doi. 10.7554/eLife.89712

By:

Zhixin Jing;
Galbo, Phillip;
Ovando, Luis;
Demouth, Megan;
Welte, Skylar;
Rosa Park;
Chandran, Kartik;
Yinghao Wu;
MacCarthy, Thomas;
Deyou Zheng;
Fooksman, David

Publication type:

Article

Dissection of Merkel cell formation in hairy and glabrous skin reveals a common requirement for FGFR2‐mediated signalling.

Published in:

Experimental Dermatology, 2019, v. 28, n. 4, p. 374, doi. 10.1111/exd.13901

By:

Nguyen, Minh Binh;
Valdes, Victor Julian;
Cohen, Idan;
Pothula, Venu;
Zhao, Dejian;
Zheng, Deyou;
Ezhkova, Elena

Publication type:

Article

Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation.

Published in:

Nucleic Acids Research, 2007, v. 35, p. d55, doi. 10.1093/nar/gkl851

By:

Karro, John E.;
Yan, Yangpan;
Zheng, Deyou;
Zhang, Zhaolei;
Carriero, Nicholas;
Cayting, Philip;
Harrrison, Paul;
Gerstein, Mark

Publication type:

Article

Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability.

Published in:

Nucleic Acids Research, 2005, v. 33, n. 8, p. 2374, doi. 10.1093/nar/gki531

By:

Harrison, Paul M.;
Zheng, Deyou;
Zhang, Zhaolei;
Carriero, Nicholas;
Gerstein, Mark

Publication type:

Article

SPINE 2: a system for collaborative structural proteomics within a federated database framework.

Published in:

Nucleic Acids Research, 2003, v. 31, n. 11, p. 2833, doi. 10.1093/nar/gkg397

By:

Goh, Chern‐Sing;
Lan, Ning;
Echols, Nathaniel;
Douglas, Shawn M.;
Milburn, Duncan;
Bertone, Paul;
Xiao, Rong;
Ma, Li‐Chung;
Zheng, Deyou;
Wunderlich, Zeba;
Acton, Tom;
Montelione, Gaetano T.;
Gerstein, Mark

Publication type:

Article

SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics.

Published in:

Nucleic Acids Research, 2001, v. 29, n. 13, p. 2884, doi. 10.1093/nar/29.13.2884

By:

Bertone, Paul;
Kluger, Yuval;
Lan, Ning;
Zheng, Deyou;
Christendat, Dinesh;
Yee, Adelinda;
Edwards, Aled M.;
Arrowsmith, Cheryl H.;
Montelione, Gaetano T.;
Gerstein, Mark

Publication type:

Article

Retraction Note: REST regulates the cell cycle for cardiac development and regeneration.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-46055-8

By:

Zhang, Donghong;
Wang, Yidong;
Lu, Pengfei;
Wang, Ping;
Yuan, Xinchun;
Yan, Jianyun;
Cai, Chenleng;
Chang, Ching-Pin;
Zheng, Deyou;
Wu, Bingruo;
Zhou, Bin

Publication type:

Article

Protective effects of macrophage-specific integrin α5 in myocardial infarction are associated with accentuated angiogenesis.

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-43369-x

By:

Li, Ruoshui;
Chen, Bijun;
Kubota, Akihiko;
Hanna, Anis;
Humeres, Claudio;
Hernandez, Silvia C.;
Liu, Yang;
Ma, Richard;
Tuleta, Izabela;
Huang, Shuaibo;
Venugopal, Harikrishnan;
Zhu, Fenglan;
Su, Kai;
Li, Jun;
Zhang, Jinghang;
Zheng, Deyou;
Frangogiannis, Nikolaos G.

Publication type:

Article

VISTA Emerges as a Promising Target against Immune Evasion Mechanisms in Medulloblastoma.

Published in:

Cancers, 2024, v. 16, n. 15, p. 2629, doi. 10.3390/cancers16152629

By:

Muñoz Perez, Natalia;
Pensabene, Juliana M.;
Galbo Jr., Phillip M.;
Sadeghipour, Negar;
Xiu, Joanne;
Moziak, Kirsten;
Yazejian, Rita M.;
Welch, Rachel L.;
Bell, W. Robert;
Sengupta, Soma;
Aulakh, Sonikpreet;
Eberhart, Charles G.;
Loeb, David M.;
Eskandar, Emad;
Zheng, Deyou;
Zang, Xingxing;
Martin, Allison M.

Publication type:

Article

Cytosine methylation changes in enhancer regions of core pro-fibrotic genes characterize kidney fibrosis development.

Published in:

Genome Biology, 2013, v. 14, n. 10, p. R108, doi. 10.1186/gb-2013-14-10-r108

By:

Yi-An Ko;
Mohtat, Davoud;
Suzuki, Masako;
Deok Park, Ae Seo;
Izquierdo, Maria Concepcion;
Sang Youb Han;
Hyun Mi Kang;
Han Si;
Hostetter, Thomas;
Pullman, James M.;
Fazzari, Melissa;
Verma, Amit;
Deyou Zheng;
Greally, John M.;
Susztak, Katalin

Publication type:

Article

Regulation of ERα-dependent breast cancer metastasis by a miR-29a signaling.

Published in:

Journal of Experimental & Clinical Cancer Research (17569966), 2023, v. 42, n. 1, p. 1, doi. 10.1186/s13046-023-02665-6

By:

Lü, Jinhui;
Zhao, Qian;
Guo, Yuefan;
Li, Danni;
Xie, Heying;
Liu, Cuicui;
Hu, Xin;
Liu, Suling;
Hou, Zhaoyuan;
wei, Xunbin;
Zheng, Deyou;
Pestell, Richard G.;
Yu, Zuoren

Publication type:

Article

scDAPP: a comprehensive single-cell transcriptomics analysis pipeline optimized for cross-group comparison.

Published in:

NAR Genomics & Bioinformatics, 2024, v. 6, n. 4, p. 1, doi. 10.1093/nargab/lqae134

By:

Ferrena, Alexander;
Zheng, Xiang Yu;
Jackson, Kevyn;
Hoang, Bang;
Morrow, Bernice E;
Zheng, Deyou

Publication type:

Article

In vivo transcriptional governance of hair follicle stem cells by canonical Wnt regulators.

Published in:

Nature Cell Biology, 2014, v. 16, n. 2, p. 179, doi. 10.1038/ncb2903

By:

Lien, Wen-Hui;
Polak, Lisa;
Lin, Mingyan;
Lay, Kenneth;
Zheng, Deyou;
Fuchs, Elaine

Publication type:

Article

REST regulates the cell cycle for cardiac development and regeneration.

Published in:

Nature Communications, 2017, v. 8, n. 1, p. 1, doi. 10.1038/s41467-017-02210-y

By:

Donghong Zhang;
Yidong Wang;
Pengfei Lu;
Ping Wang;
Xinchun Yuan;
Jianyun Yan;
3Chenleng Cai;
Ching-Pin Chang;
Deyou Zheng;
Bingruo Wu;
Bin Zhou

Publication type:

Article

Evolutionary Origins of Pax6 Control of Crystallin Genes.

Published in:

Genome Biology & Evolution, 2017, v. 9, n. 8, p. 2075, doi. 10.1093/gbe/evx153

By:

Cvekl, Ales;
Yilin Zhao;
McGreal, Rebecca;
Qing Xie;
Xun Gu;
Deyou Zheng

Publication type:

Article

CHARGE syndrome-associated CHD7 acts at ISL1-regulated enhancers to modulate second heart field gene expression.

Published in:

Cardiovascular Research, 2023, v. 119, n. 11, p. 2089, doi. 10.1093/cvr/cvad059

By:

Stathopoulou, Athanasia;
Wang, Ping;
Thellier, Charlotte;
Kelly, Robert G;
Zheng, Deyou;
Scambler, Peter J

Publication type:

Article

Integrative transcriptome network analysis of iPSC-derived neurons from schizophrenia and schizoaffective disorder patients with 22q11.2 deletion.

Published in:

BMC Systems Biology, 2016, v. 10, p. 1, doi. 10.1186/s12918-016-0366-0

By:

Mingyan Lin;
Pedrosa, Erika;
Hrabovsky, Anastasia;
Jian Chen;
Puliafito, Benjamin R.;
Gilbert, Stephanie R.;
Deyou Zheng;
Lachman, Herbert M.

Publication type:

Article

Comprehensive transcriptional landscape of aging mouse liver.

Published in:

BMC Genomics, 2015, v. 16, p. 1, doi. 10.1186/s12864-015-2061-8

By:

White, Ryan R.;
Milholland, Brandon;
MacRae, Sheila L.;
Mingyan Lin;
Deyou Zheng;
Vijg, Jan

Publication type:

Article

Comparison of REST Cistromes across Human Cell Types Reveals Common and Context-Specific Functions.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 6, p. 1, doi. 10.1371/journal.pcbi.1003671

By:

Rockowitz, Shira;
Lien, Wen-Hui;
Pedrosa, Erika;
Wei, Gang;
Lin, Mingyan;
Zhao, Keji;
Lachman, Herbert M.;
Fuchs, Elaine;
Zheng, Deyou

Publication type:

Article

Small RNAs Originated from Pseudogenes: cis- or trans- Acting?

Published in:

PLoS Computational Biology, 2009, v. 5, n. 7, p. 1, doi. 10.1371/journal.pcbi.1000449

By:

Xingyi Guo;
Zhaolei Zhang;
Gerstein, Mark B.;
Deyou Zheng

Publication type:

Article

ETV1 is a lineage survival factor that cooperates with KIT in gastrointestinal stromal tumours.

Published in:

Nature, 2010, v. 467, n. 7317, p. 849, doi. 10.1038/nature09409

By:

Ping Chi;
Yu Chen;
Lei Zhang;
Xingyi Guo;
Wongvipat, John;
Shamu, Tambudzai;
Fletcher, Jonathan A.;
Dewell, Scott;
Maki, Robert G.;
Deyou Zheng;
Antonescu, Cristina R.;
Allis, C. David;
Sawyers, Charles L.

Publication type:

Article

Deletion size analysis of 1680 22q11.2DS subjects identifies a new recombination hotspot on chromosome 22q11.2.

Published in:

Human Molecular Genetics, 2018, v. 27, n. 7, p. 1150, doi. 10.1093/hmg/ddy028

By:

Tingwei Guo;
Diacou, Alexander;
Hiroko Nomaru;
McDonald-McGinn, Donna M.;
Hestand, Matthew;
Demaerel, Wolfram;
Liangtian Zhang;
Yingjie Zhao;
Ujueta, Francisco;
Jidong Shan;
Montagna, Cristina;
Deyou Zheng;
Crowley, Terrence B.;
Kushan-Wells, Leila;
Bearden, Carrie E.;
Kates, Wendy R.;
Gothelf, Doron;
Schneider, Maude;
Eliez, Stephan;
Breckpot, Jeroen

Publication type:

Article

Reduced CYFIP1 in Human Neural Progenitors Results in Dysregulation of Schizophrenia and Epilepsy Gene Networks.

Published in:

PLoS ONE, 2016, v. 11, n. 1, p. 1, doi. 10.1371/journal.pone.0148039

By:

Nebel, Rebecca A.;
Zhao, Dejian;
Pedrosa, Erika;
Kirschen, Jill;
Lachman, Herbert M.;
Zheng, Deyou;
Abrahams, Brett S.

Publication type:

Article

Disruption of Interneuron Neurogenesis in Premature Newborns and Reversal with Estrogen Treatment.

Published in:

Journal of Neuroscience, 2018, v. 38, n. 5, p. 1100, doi. 10.1523/JNEUROSCI.1875-17.2017

By:

Tibrewal, Mahima;
Bokun Cheng;
Dohare, Preeti;
Furong Hu;
Mehdizadeh, Rana;
Ping Wang;
Deyou Zheng;
Ungvari, Zoltan;
Ballabh, Praveen

Publication type:

Article

Characteristics of allelic gene expression in human brain cells from single-cell RNA-seq data analysis.

Published in:

BMC Genomics, 2017, v. 18, p. 1, doi. 10.1186/s12864-017-4261-x

By:

Dejian Zhao;
Mingyan Lin;
Pedrosa, Erika;
Lachman, Herbert M.;
Deyou Zheng

Publication type:

Article

SMARTcleaner: identify and clean off-target signals in SMART ChIP-seq analysis.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2577-4

By:

Zhao, Dejian;
Zheng, Deyou

Publication type:

Article

Drosophila RpS12 controls translation, growth, and cell competition through Xrp1.

Published in:

PLoS Genetics, 2019, v. 15, n. 12, p. 1, doi. 10.1371/journal.pgen.1008513

By:

Ji, Zhejun;
Kiparaki, Marianthi;
Folgado, Virginia;
Kumar, Amit;
Blanco, Jorge;
Rimesso, Gerard;
Chuen, Jacky;
Liu, Yang;
Zheng, Deyou;
Baker, Nicholas E.

Publication type:

Article

Screening of Combination of Flumetralin and Fungicide to Control Cotton Fusarium wilt.

Published in:

Journal of Agricultural Science & Technology (1008-0864), 2024, v. 26, n. 1, p. 119, doi. 10.13304/j.nykjdb.2022.0884

By:

ZHENG Deyou;
ZUO Dongyun;
WANG Qiaolian;
LYU Limin;
CHENG Hailiang;
GU Aixing;
SONG Guoli

Publication type:

Article

Profiling of chromatin accessibility and identification of general cis-regulatory mechanisms that control two ocular lens differentiation pathways.

Published in:

Epigenetics & Chromatin, 2019, v. 12, n. 1, p. N.PAG, doi. 10.1186/s13072-019-0272-y

By:

Zhao, Yilin;
Zheng, Deyou;
Cvekl, Ales

Publication type:

Article

Pax6 associates with H3K4-specific histone methyltransferases Mll1, Mll2, and Set1a and regulates H3K4 methylation at promoters and enhancers.

Published in:

Epigenetics & Chromatin, 2016, v. 8, p. 1, doi. 10.1186/s13072-016-0087-z

By:

Jian Sun;
Yilin Zhao;
McGreal, Rebecca;
Cohen-Tayar, Yamit;
Rockowitz, Shira;
Wilczek, Carola;
Ashery-Padan, Ruth;
Shechter, David;
Deyou Zheng;
Cvekl, Ales

Publication type:

Article

ETS factors reprogram the androgen receptor cistrome and prime prostate tumorigenesis in response to PTEN loss.

Published in:

Nature Medicine, 2013, v. 19, n. 8, p. 1023, doi. 10.1038/nm.3216

By:

Chen, Yu;
Chi, Ping;
Rockowitz, Shira;
Iaquinta, Phillip J;
Shamu, Tambudzai;
Shukla, Shipra;
Gao, Dong;
Sirota, Inna;
Carver, Brett S;
Wongvipat, John;
Scher, Howard I;
Zheng, Deyou;
Sawyers, Charles L

Publication type:

Article

Reduced dosage of β-catenin provides significant rescue of cardiac outflow tract anomalies in a Tbx1 conditional null mouse model of 22q11.2 deletion syndrome.

Published in:

PLoS Genetics, 2017, v. 13, n. 3, p. 1, doi. 10.1371/journal.pgen.1006687

By:

Racedo, Silvia E.;
Hasten, Erica;
Lin, Mingyan;
Devakanmalai, Gnanapackiam Sheela;
Guo, Tingwei;
Ozbudak, Ertugrul M.;
Cai, Chen-Leng;
Zheng, Deyou;
Morrow, Bernice E.

Publication type:

Article

Pioneer factors govern super-enhancer dynamics in stem cell plasticity and lineage choice.

Published in:

Nature, 2015, v. 521, n. 7552, p. 366, doi. 10.1038/nature14289

By:

Adam, Rene C.;
Yang, Hanseul;
Rockowitz, Shira;
Larsen, Samantha B.;
Nikolova, Maria;
Oristian, Daniel S.;
Polak, Lisa;
Kadaja, Meelis;
Asare, Amma;
Zheng, Deyou;
Fuchs, Elaine

Publication type:

Article

Transcriptome analysis of microglia in a mouse model of Rett syndrome: differential expression of genes associated with microglia/macrophage activation and cellular stress.

Published in:

Molecular Autism, 2017, v. 8, p. 1, doi. 10.1186/s13229-017-0134-z

By:

Dejian Zhao;
Mokhtari, Ryan;
Pedrosa, Erika;
Birnbaum, Rayna;
Deyou Zheng;
Lachman, Herbert M.

Publication type:

Article

CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in cerebral organoids derived from iPS cells.

Published in:

Molecular Autism, 2017, v. 8, p. 1, doi. 10.1186/s13229-017-0124-1

By:

Ping Wang;
Mokhtari, Ryan;
Pedrosa, Erika;
Kirschenbaum, Michael;
Bayrak, Can;
Deyou Zheng;
Lachman, Herbert M.

Publication type:

Article

CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in neurodevelopment.

Published in:

Molecular Autism, 2015, v. 6, p. 1, doi. 10.1186/s13229-015-0048-6

By:

Ping Wang;
Mingyan Lin;
Pedrosa, Erika;
Hrabovsky, Anastasia;
Zheng Zhang;
Wenjun Guo;
Lachman, Herbert M.;
Deyou Zheng

Publication type:

Article

Polycomb repressive complex 2 in adult hair follicle stem cells is dispensable for hair regeneration.

Published in:

PLoS Genetics, 2021, v. 17, n. 12, p. 1, doi. 10.1371/journal.pgen.1009948

By:

Flora, Pooja;
Li, Meng-Yen;
Galbo Jr., Phillip M.;
Astorkia, Maider;
Zheng, Deyou;
Ezhkova, Elena

Publication type:

Article

PseudoPipe: an automated pseudogene identification pipeline.

Published in:

Bioinformatics, 2006, v. 22, n. 12, p. 1437, doi. 10.1093/bioinformatics/btl116

By:

Zhaolei Zhang;
Nicholas Carriero;
Deyou Zheng;
John Karro;
Paul M. Harrison;
Mark Gerstein

Publication type:

Article

KIR3DL3-HHLA2 is a human immunosuppressive pathway and a therapeutic target.

Published in:

Science Immunology, 2021, v. 6, n. 61, p. 1, doi. 10.1126/sciimmunol.abf9792

By:

Wei, Yao;
Ren, Xiaoxin;
Galbo Jr., Phillip M.;
Moerdler, Scott;
Wang, Hao;
Sica, R. Alejandro;
Etemad-Gilbertson, Bijan;
Shi, Lei;
Zhu, Liqiang;
Tang, Xudong;
Lin, Qi;
Peng, Mou;
Guan, Fangxia;
Zheng, Deyou;
Chinai, Jordan M.;
Zang, Xingxing

Publication type:

Article

Proton sensitivity of ASIC1 appeared with the rise of fishes by changes of residues in the region that follows TM1 in the ectodomain of the channel.

Published in:

Journal of Physiology, 2005, v. 568, n. 3, p. 725, doi. 10.1113/jphysiol.2005.087734

By:

Coric, Tatjana;
Deyou Zheng;
Gerstein, Mark;
Canessa, Cecilia M.

Publication type:

Article

Identification of ultra-rare genetic variants in pediatric acute onset neuropsychiatric syndrome (PANS) by exome and whole genome sequencing.

Published in:

Scientific Reports, 2022, v. 12, n. 1, p. 1, doi. 10.1038/s41598-022-15279-3

By:

Trifiletti, Rosario;
Lachman, Herbert M.;
Manusama, Olivia;
Zheng, Deyou;
Spalice, Alberto;
Chiurazzi, Pietro;
Schornagel, Allan;
Serban, Andreea M.;
van Wijck, Rogier;
Cunningham, Janet L.;
Swagemakers, Sigrid;
van der Spek, Peter J.

Publication type:

Article

An optimized approach for multiplexing single-nuclear ATAC-seq using oligonucleotide-conjugated antibodies.

Published in:

Epigenetics & Chromatin, 2023, v. 16, n. 1, p. 1, doi. 10.1186/s13072-023-00486-7

By:

Bera, Betelehem Solomon;
Thompson, Taylor V.;
Sosa, Eric;
Nomaru, Hiroko;
Reynolds, David;
Dubin, Robert A.;
Maqbool, Shahina B.;
Zheng, Deyou;
Morrow, Bernice E.;
Greally, John M.;
Suzuki, Masako

Publication type:

Article

Dynamic changes in whole genome DNA methylation, chromatin and gene expression during mouse lens differentiation.

Published in:

Epigenetics & Chromatin, 2023, v. 16, n. 1, p. 1, doi. 10.1186/s13072-023-00478-7

By:

Chang, William;
Zhao, Yilin;
Rayêe, Danielle;
Xie, Qing;
Suzuki, Masako;
Zheng, Deyou;
Cvekl, Ales

Publication type:

Article

Metabolite differences between glutamate carboxypeptidase II gene knockout mice and their wild-type littermates after traumatic brain injury: a 7-tesla 1H-MRS study.

Published in:

2018

By:

Wu, Wenbo;
Xu, Siyi;
Wang, Jialin;
Zhang, Kuiming;
Zhang, Mingkun;
Cao, Yang;
Ren, Hongqing;
Zheng, Deyou;
Zhong, Chunlong

Publication type:

journal article

HSMotifDiscover: identification of motifs in sequences composed of non-single-letter elements.

Published in:

Bioinformatics, 2022, v. 38, n. 16, p. 4036, doi. 10.1093/bioinformatics/btac437

By:

Singh, Vinod Kumar;
Misra, Rohan;
Almo, Steven C;
Steidl, Ulrich G;
Bülow, Hannes E;
Zheng, Deyou

Publication type:

Article

Stereo3D: using stereo images to enrich 3D visualization.

Published in:

Bioinformatics, 2020, v. 36, n. 14, p. 4189, doi. 10.1093/bioinformatics/btaa521

By:

Liu, Yang;
Singh, Vinod Kumar;
Zheng, Deyou

Publication type:

Article

Enriched expression of genes associated with autism spectrum disorders in human inhibitory neurons.

Published in:

Translational Psychiatry, 2018, v. 8, n. 1, p. 1, doi. 10.1038/s41398-017-0058-6

By:

Wang, Ping;
Zhao, Dejian;
Lachman, Herbert M.;
Zheng, Deyou

Publication type:

Article