Publications by authors named "Zhidong Tu"

30Publications

Transcriptome analysis reveals the difference between "healthy" and "common" aging and their connection with age-related diseases.

Aging Cell 2020 03 19;19(3):e13121. Epub 2020 Feb 19.

Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.

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http://dx.doi.org/10.1111/acel.13121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7059150PMC
March 2020

Human geroprotector discovery by targeting the converging subnetworks of aging and age-related diseases.

Geroscience 2020 02 21;42(1):353-372. Epub 2019 Oct 21.

Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York City, USA.

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http://dx.doi.org/10.1007/s11357-019-00106-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7031474PMC
February 2020

A probabilistic multi-omics data matching method for detecting sample errors in integrative analysis.

Gigascience 2019 07;8(7)

Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA.

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http://dx.doi.org/10.1093/gigascience/giz080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6615984PMC
July 2019

Temporal genetic association and temporal genetic causality methods for dissecting complex networks.

Nat Commun 2018 09 28;9(1):3980. Epub 2018 Sep 28.

Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.

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http://dx.doi.org/10.1038/s41467-018-06203-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6162292PMC
September 2018

Human Pancreatic β Cell lncRNAs Control Cell-Specific Regulatory Networks.

Cell Metab 2017 02 29;25(2):400-411. Epub 2016 Dec 29.

Section of Epigenomics and Disease, Department of Medicine, Imperial College London, London W12 0NN, United Kingdom; Genomic Programming of Beta Cells Laboratory, Institut d'Investigacions Biomediques August Pi I Sunyer (IDIBAPS), Barcelona 08036, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid 28029, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.cmet.2016.11.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5300904PMC
February 2017

Discover the network underlying the connections between aging and age-related diseases.

Sci Rep 2016 09 1;6:32566. Epub 2016 Sep 1.

Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, NY, 10029, USA.

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http://dx.doi.org/10.1038/srep32566DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5007654PMC
September 2016

Inter-tissue coexpression network analysis reveals DPP4 as an important gene in heart to blood communication.

Genome Med 2016 Feb 9;8(1):15. Epub 2016 Feb 9.

Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.

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http://dx.doi.org/10.1186/s13073-016-0268-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4746932PMC
February 2016

New Method for Joint Network Analysis Reveals Common and Different Coexpression Patterns among Genes and Proteins in Breast Cancer.

J Proteome Res 2016 Mar 2;15(3):743-54. Epub 2016 Feb 2.

Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai , 770 Lexington Avenue, 14th Floor, NewYork, New York 10065, United States.

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http://dx.doi.org/10.1021/acs.jproteome.5b00925DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4782177PMC
March 2016

Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases.

Sci Rep 2015 Oct 19;5:15145. Epub 2015 Oct 19.

Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, NY, 10029, USA.

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http://dx.doi.org/10.1038/srep15145DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4609956PMC
October 2015

Integrative random forest for gene regulatory network inference.

Bioinformatics 2015 Jun;31(12):i197-205

Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv268DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542785PMC
June 2015

Integrative analysis of DNA methylation and gene expression data identifies EPAS1 as a key regulator of COPD.

PLoS Genet 2015 Jan 8;11(1):e1004898. Epub 2015 Jan 8.

Institute of Genomics and Multiscale Biology, Mount Sinai School of Medicine, New York, New York, United States of America; Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1004898DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4287352PMC
January 2015

Baf250a orchestrates an epigenetic pathway to repress the Nkx2.5-directed contractile cardiomyocyte program in the sinoatrial node.

Cell Res 2014 Oct 22;24(10):1201-13. Epub 2014 Aug 22.

1] Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA [2] Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA.

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http://dx.doi.org/10.1038/cr.2014.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4185344PMC
October 2014

MODMatcher: multi-omics data matcher for integrative genomic analysis.

PLoS Comput Biol 2014 Aug 14;10(8):e1003790. Epub 2014 Aug 14.

Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003790DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4133046PMC
August 2014

Multifaceted roles of miR-1s in repressing the fetal gene program in the heart.

Cell Res 2014 Mar 31;24(3):278-92. Epub 2014 Jan 31.

Mindich Child Health and Development Institute, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1040, New York, NY 10029, USA.

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http://dx.doi.org/10.1038/cr.2014.12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3945888PMC
March 2014

The role of Hepatitis C Virus in the dynamic protein interaction networks of hepatocellular cirrhosis and carcinoma.

Int J Comput Biol Drug Des 2011 18;4(1):5-18. Epub 2011 Feb 18.

Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.

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http://dx.doi.org/10.1504/IJCBDD.2011.038654DOI Listing
May 2011

A network-based integrative approach to prioritize reliable hits from multiple genome-wide RNAi screens in Drosophila.

BMC Genomics 2009 May 12;10:220. Epub 2009 May 12.

Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA.

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http://dx.doi.org/10.1186/1471-2164-10-220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2697172PMC
May 2009

Integrating siRNA and protein-protein interaction data to identify an expanded insulin signaling network.

Genome Res 2009 Jun 4;19(6):1057-67. Epub 2009 Mar 4.

Rosetta Inpharmatics, a wholly owned subsidiary of Merck & Co., Inc., Seattle, Washington 98109, USA.

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http://dx.doi.org/10.1101/gr.087890.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694478PMC
June 2009

An integrative approach for causal gene identification and gene regulatory pathway inference.

Bioinformatics 2006 Jul;22(14):e489-96

Molecular and Computational Biology Program, University of Southern California, Los Angeles, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl234DOI Listing
July 2006

Network motif identification in stochastic networks.

Proc Natl Acad Sci U S A 2006 Jun 12;103(25):9404-9. Epub 2006 Jun 12.

Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA.

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http://dx.doi.org/10.1073/pnas.0507841103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1480420PMC
June 2006

Diffusion kernel-based logistic regression models for protein function prediction.

OMICS 2006 ;10(1):40-55

Department of Computer Science, University of Southern California, Los Angeles, 90089, USA.

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http://dx.doi.org/10.1089/omi.2006.10.40DOI Listing
September 2006

Further understanding human disease genes by comparing with housekeeping genes and other genes.

BMC Genomics 2006 Feb 21;7:31. Epub 2006 Feb 21.

Molecular and Computational Biology Program, University of Southern California, Los Angeles, California 90089, USA.

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http://dx.doi.org/10.1186/1471-2164-7-31DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1397819PMC
February 2006

Mapping Gene Ontology to proteins based on protein-protein interaction data.

Bioinformatics 2004 Apr 29;20(6):895-902. Epub 2004 Jan 29.

Department of Biological Sciences, Molecular and Computational Biology Program, University of Southern California, 1042 West 36th Place, Los Angeles, CA 90089-1113, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg500DOI Listing
April 2004