Michael Q Zhang

Michael Q Zhang

UNVERIFIED PROFILE

Are you Michael Q Zhang?   Register this Author

Register author
Michael Q Zhang

Michael Q Zhang

Publications by authors named "Michael Q Zhang"

Are you Michael Q Zhang?   Register this Author

100Publications

3083Reads

12Profile Views

A large-scale CRISPR screen and identification of essential genes in cellular senescence bypass.

Aging (Albany NY) 2019 06;11(12):4011-4031

MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic and Systems Biology, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.18632/aging.102034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6628988PMC
June 2019

Integrating Hi-C and FISH data for modeling of the 3D organization of chromosomes.

Nat Commun 2019 05 3;10(1):2049. Epub 2019 May 3.

Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, 100084, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-019-10005-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6499832PMC
May 2019

Global transcriptional activity dynamics reveal functional enhancer RNAs.

Genome Res 2018 12 23;28(12):1799-1811. Epub 2018 Oct 23.

Department of Biological Sciences and Center for Systems Biology, University of Texas at Dallas, Richardson, Texas 75080, USA.

View Article

Download full-text PDF

Source
http://genome.cshlp.org/lookup/doi/10.1101/gr.233486.117
Publisher Site
http://dx.doi.org/10.1101/gr.233486.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6280751PMC
December 2018

HiCDB: a sensitive and robust method for detecting contact domain boundaries.

Nucleic Acids Res 2018 11;46(21):11239-11250

MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, BNRist, Department of Automation, Tsinghua University, Beijing 100084, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gky789DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6265446PMC
November 2018

Polarization-based super-resolution imaging of surface-enhanced Raman scattering nanoparticles with orientational information.

Nanoscale 2018 Nov;10(42):19757-19765

Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.

View Article

Download full-text PDF

Source
http://xlink.rsc.org/?DOI=C8NR04808H
Publisher Site
http://dx.doi.org/10.1039/c8nr04808hDOI Listing
November 2018

CAPTURE: In Situ Analysis of Chromatin Composition of Endogenous Genomic Loci by Biotinylated dCas9.

Curr Protoc Mol Biol 2018 07 19;123(1):e64. Epub 2018 Jun 19.

Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas.

View Article

Download full-text PDF

Source
http://doi.wiley.com/10.1002/cpmb.64
Publisher Site
http://dx.doi.org/10.1002/cpmb.64DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6028316PMC
July 2018

Regulatory RNA binding proteins contribute to the transcriptome-wide splicing alterations in human cellular senescence.

Aging (Albany NY) 2018 Jun;10(6):1489-1505

Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing, 100084, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.18632/aging.101485DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6046225PMC
June 2018

MTGIpick allows robust identification of genomic islands from a single genome.

Brief Bioinform 2018 05;19(3):361-373

Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bib/bbw118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6454522PMC
May 2018

Co-inhibitory Molecule B7 Superfamily Member 1 Expressed by Tumor-Infiltrating Myeloid Cells Induces Dysfunction of Anti-tumor CD8 T Cells.

Immunity 2018 04 3;48(4):773-786.e5. Epub 2018 Apr 3.

Institute for Immunology and School of Medicine, Tsinghua University, Beijing 100084, China; Beijing Key Lab for Immunological Research on Chronic Diseases, Beijing 100084, China. Electronic address:

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S10747613183011
Publisher Site
http://dx.doi.org/10.1016/j.immuni.2018.03.018DOI Listing
April 2018

CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data.

Bioinformatics 2018 02;34(3):381-387

State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btx595DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6454434PMC
February 2018

Alterations of specific chromatin conformation affect ATRA-induced leukemia cell differentiation.

Cell Death Dis 2018 02 8;9(2):200. Epub 2018 Feb 8.

MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, School of Medicine, Tsinghua University, Beijing, 100084, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41419-017-0173-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5833835PMC
February 2018

FIND: difFerential chromatin INteractions Detection using a spatial Poisson process.

Genome Res 2018 Feb 12. Epub 2018 Feb 12.

MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.212241.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5848619PMC
February 2018

NONCODEV5: a comprehensive annotation database for long non-coding RNAs.

Nucleic Acids Res 2018 01;46(D1):D308-D314

Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkx1107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753287PMC
January 2018

Network embedding-based representation learning for single cell RNA-seq data.

Nucleic Acids Res 2017 Nov;45(19):e166

MOE Key Laboratory of Bioinformatics, TNLIST Bioinformatics Division/Center for Synthetic & System Biology, Department of Automation, Tsinghua University, Beijing 100084, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkx750DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737094PMC
November 2017

BL-Hi-C is an efficient and sensitive approach for capturing structural and regulatory chromatin interactions.

Nat Commun 2017 11 20;8(1):1622. Epub 2017 Nov 20.

MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; School of Medicine, Tsinghua University, Beijing, 100084, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-017-01754-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5696378PMC
November 2017

Stochastic fluctuations can reveal the feedback signs of gene regulatory networks at the single-molecule level.

Sci Rep 2017 11 22;7(1):16037. Epub 2017 Nov 22.

Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-017-15464-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5700158PMC
November 2017

Emergent Lévy behavior in single-cell stochastic gene expression.

Phys Rev E 2017 Oct 18;96(4-1):040402. Epub 2017 Oct 18.

Department of Applied Mathematics, University of Washington, Seattle, Washington 98195, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevE.96.040402DOI Listing
October 2017

PAF1 regulation of promoter-proximal pause release via enhancer activation.

Science 2017 09 31;357(6357):1294-1298. Epub 2017 Aug 31.

Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.aan3269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6055228PMC
September 2017

In Situ Capture of Chromatin Interactions by Biotinylated dCas9.

Cell 2017 Aug;170(5):1028-1043.e19

Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cell.2017.08.003DOI Listing
August 2017

Web3DMol: interactive protein structure visualization based on WebGL.

Nucleic Acids Res 2017 07;45(W1):W523-W527

MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Department of Automation, Tsinghua University, Beijing 100084, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkx383DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570197PMC
July 2017

Allelic reprogramming of 3D chromatin architecture during early mammalian development.

Nature 2017 07;547(7662):232-235

Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature23263DOI Listing
July 2017

Reconstructing cell cycle pseudo time-series via single-cell transcriptome data.

Nat Commun 2017 06 19;8(1):22. Epub 2017 Jun 19.

MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Department of Computer Sciences, State Key Lab of Intelligent Technology and Systems, Tsinghua University, Beijing, 100084, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-017-00039-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5476636PMC
June 2017

Super-resolution imaging of a 2.5 kb non-repetitive DNA in the nuclear genome using molecular beacon probes.

Elife 2017 05 9;6. Epub 2017 May 9.

Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.7554/eLife.21660DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5433842PMC
May 2017

HCSGD: An integrated database of human cellular senescence genes.

J Genet Genomics 2017 May 29;44(5):227-234. Epub 2017 Apr 29.

Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 100084, China; Bioinformatics Division, Tsinghua National Laboratory for Information Science and Technology, Beijing 100084, China. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jgg.2017.04.001DOI Listing
May 2017

Recurrently deregulated lncRNAs in hepatocellular carcinoma.

Nat Commun 2017 02 13;8:14421. Epub 2017 Feb 13.

MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms14421DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5316832PMC
February 2017

ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis.

Nucleic Acids Res 2017 01 12;45(1):e4. Epub 2016 Sep 12.

MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing 100084, China

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkw809DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5224499PMC
January 2017

Analysis of C. elegans muscle transcriptome using trans-splicing-based RNA tagging (SRT).

Nucleic Acids Res 2016 12 23;44(21):e156. Epub 2016 Aug 23.

MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkw734DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5137427PMC
December 2016

Super-resolution dipole orientation mapping via polarization demodulation.

Light Sci Appl 2016 Oct 21;5(10):e16166. Epub 2016 Oct 21.

Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/lsa.2016.166DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6059828PMC
October 2016

FAT10 Is Critical in Influenza A Virus Replication by Inhibiting Type I IFN.

J Immunol 2016 08 27;197(3):824-33. Epub 2016 Jun 27.

State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Tsinghua University, Beijing 100005, China; State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610000, China

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4049/jimmunol.1501563DOI Listing
August 2016

Mammalian non-CG methylations are conserved and cell-type specific and may have been involved in the evolution of transposon elements.

Sci Rep 2016 08 30;6:32207. Epub 2016 Aug 30.

The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, People's Republic of China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/srep32207DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5004121PMC
August 2016

Engineering EMT using 3D micro-scaffold to promote hepatic functions for drug hepatotoxicity evaluation.

Biomaterials 2016 Jun 9;91:11-22. Epub 2016 Mar 9.

Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, 100084, PR China; China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, Zhejiang, 310058, PR ​China. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.biomaterials.2016.03.001DOI Listing
June 2016

De novo deciphering three-dimensional chromatin interaction and topological domains by wavelet transformation of epigenetic profiles.

Nucleic Acids Res 2016 06 7;44(11):e106. Epub 2016 Apr 7.

Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX 75080, USA MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST/Department Automation, Tsinghua University, Beijing 100084, China

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkw225DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4914103PMC
June 2016

NONCODE 2016: an informative and valuable data source of long non-coding RNAs.

Nucleic Acids Res 2016 Jan 19;44(D1):D203-8. Epub 2015 Nov 19.

CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkv1252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702886PMC
January 2016

Reconfigurable hybrid interface for molecular marker diagnostics and in-situ reporting.

Biosens Bioelectron 2015 Dec 17;74:744-50. Epub 2015 Jul 17.

Bioengineering Department, The University of Texas at Dallas, 800 West Campbell Road, Richardson, TX 75080, USA; Electrical Engineering Department, The University of Texas at Dallas, 800 West Campbell Road, Richardson, TX 75080, USA; Center for Systems Biology, The University of Texas at Dallas, 800 West Campbell Road, Richardson, TX 75080, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bios.2015.07.035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4549190PMC
December 2015

MICC: an R package for identifying chromatin interactions from ChIA-PET data.

Bioinformatics 2015 Dec 31;31(23):3832-4. Epub 2015 Jul 31.

MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China and.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btv445DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4653385PMC
December 2015

Long non-coding RNA expression profiles of hepatitis C virus-related dysplasia and hepatocellular carcinoma.

Oncotarget 2015 Dec;6(41):43770-8

Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.18632/oncotarget.6087DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4791265PMC
December 2015

Fast dimension reduction and integrative clustering of multi-omics data using low-rank approximation: application to cancer molecular classification.

BMC Genomics 2015 Dec 1;16:1022. Epub 2015 Dec 1.

MOE Key Laboratory of Bioinformatics, TNLIST Bioinformatics Division & Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing, 100084, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-015-2223-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4667498PMC
December 2015

3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process.

Genome Biol 2015 Dec 22;16:288. Epub 2015 Dec 22.

MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing, 100084, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13059-015-0851-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4716632PMC
December 2015

Histone Deacetylases Positively Regulate Transcription through the Elongation Machinery.

Cell Rep 2015 Nov 5;13(7):1444-1455. Epub 2015 Nov 5.

Department of Biological Sciences and Center for Systems Biology, The University of Texas at Dallas, Richardson, TX 75080, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.celrep.2015.10.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4934896PMC
November 2015

Genome-wide analysis of the response to nitric oxide in uropathogenic CFT073.

Microb Genom 2015 Oct 13;1(4):e000031. Epub 2015 Oct 13.

Department of Biological Sciences, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1099/mgen.0.000031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5320621PMC
October 2015

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function.

Cell 2015 Aug;162(4):900-10

Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, Institute of Systems Biomedicine, Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, SJTU, Shanghai 200240, China; Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (MOE), Bio-X Center, School of Life Sciences and Biotechnology, SJTU, Shanghai 200240, China. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cell.2015.07.038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4642453PMC
August 2015

ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks.

Nucleic Acids Res 2015 Jul 27;43(W1):W264-9. Epub 2015 Apr 27.

Centre for Genomic Sciences and Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, Guangdong 518057, China

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkv398DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489297PMC
July 2015

Genome Modification in Enterococcus faecalis OG1RF Assessed by Bisulfite Sequencing and Single-Molecule Real-Time Sequencing.

J Bacteriol 2015 Jun 30;197(11):1939-51. Epub 2015 Mar 30.

Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/JB.00130-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4420909PMC
June 2015

Design and bioinformatics analysis of genome-wide CLIP experiments.

Nucleic Acids Res 2015 Jun 9;43(11):5263-74. Epub 2015 May 9.

Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkv439DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4477666PMC
June 2015

Model-guided quantitative analysis of microRNA-mediated regulation on competing endogenous RNAs using a synthetic gene circuit.

Proc Natl Acad Sci U S A 2015 Mar 23;112(10):3158-63. Epub 2015 Feb 23.

Ministry of Education Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and Systems Biology, Tsinghua National Laboratory for Information Science and Technology/Department of Automation, Tsinghua University, Beijing 100084, China; and

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1413896112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4364186PMC
March 2015

Integrative analysis of 111 reference human epigenomes.

Nature 2015 Feb;518(7539):317-30

1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature14248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4530010PMC
February 2015

Epigenetic modification of MiR-429 promotes liver tumour-initiating cell properties by targeting Rb binding protein 4.

Gut 2015 Jan 26;64(1):156-67. Epub 2014 Feb 26.

International Co-operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military Medical University, Shanghai, China National Center for Liver Cancer, Shanghai, China National Laboratory for Oncogenes and Related Genes, Cancer Institute, Ruijing Hospital, Shanghai Jiao Tong University, Shanghai, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1136/gutjnl-2013-305715DOI Listing
January 2015

A common set of distinct features that characterize noncoding RNAs across multiple species.

Nucleic Acids Res 2015 Jan 12;43(1):104-14. Epub 2014 Dec 12.

MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gku1316DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4288202PMC
January 2015

ModuleRole: a tool for modulization, role determination and visualization in protein-protein interaction networks.

PLoS One 2014 1;9(5):e94608. Epub 2014 May 1.

Department of Molecular and Cell Biology, Center for Systems Biology, the University of Texas at Dallas, Richardson, Texas, United States of America; MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Department of Automation, Tsinghua University, Beijing, People's Republic of China.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0094608PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4006751PMC
December 2014

Genome-wide map of regulatory interactions in the human genome.

Genome Res 2014 Dec 16;24(12):1905-17. Epub 2014 Sep 16.

Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.176586.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4248309PMC
December 2014

Gene module based regulator inference identifying miR-139 as a tumor suppressor in colorectal cancer.

Mol Biosyst 2014 Dec 7;10(12):3249-54. Epub 2014 Oct 7.

MOE Key Laboratory of Bioinformatics, TNLIST Bioinformatics Division & Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 100084, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1039/c4mb00329bDOI Listing
December 2014

Genome Wide Mapping of Foxo1 Binding-sites in Murine T Lymphocytes.

Genom Data 2014 Dec;2:280-281

Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.gdata.2014.08.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4185926PMC
December 2014

Hsa-miR-1246, hsa-miR-320a and hsa-miR-196b-5p inhibitors can reduce the cytotoxicity of Ebola virus glycoprotein in vitro.

Sci China Life Sci 2014 Oct 13;57(10):959-72. Epub 2014 Sep 13.

State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; Department of Biochemistry and Molecular Biology, Peking Union Medical College, Tsinghua University, Beijing, 100005, China.

View Article

Download full-text PDF

Source
http://link.springer.com/content/pdf/10.1007/s11427-014-4742
Web Search
http://link.springer.com/10.1007/s11427-014-4742-y
Publisher Site
http://dx.doi.org/10.1007/s11427-014-4742-yDOI Listing
October 2014

Murine Memory T Cell Differentiation.

Bio Protoc 2014 Jul;4(13)

Department of Immunobiology, Yale University School of Medicine, New Haven, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.21769/BioProtoc.1171DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5669376PMC
July 2014

Murine CD8 T Cell Killing Assay.

Bio Protoc 2014 Jul;4(13)

Department of Immunology, Memorial Sloan Kettering Cancer Center (MSKCC), New York, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.21769/BioProtoc.1172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5697738PMC
July 2014

FastDMA: an infinium humanmethylation450 beadchip analyzer.

PLoS One 2013 5;8(9):e74275. Epub 2013 Sep 5.

Bioinformatics Division/Center for Synthetic and Systems Biology, Tsinghua National Laboratory for Information Science and Technology (TNLIST), Department of Automation, Tsinghua University, Beijing, China.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0074275PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3764200PMC
June 2014

MIROR: a method for cell-type specific microRNA occupancy rate prediction.

Mol Biosyst 2014 Jun 25;10(6):1377-84. Epub 2014 Mar 25.

Bioinformatics Division, Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1039/c3mb70610aDOI Listing
June 2014

Nucleosome eviction and multiple co-factor binding predict estrogen-receptor-alpha-associated long-range interactions.

Nucleic Acids Res 2014 Jun 29;42(11):6935-44. Epub 2014 Apr 29.

MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas, Dallas 800 West Campbell Road, RL11 Richardson, TX 75080-3021, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gku327DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4066761PMC
June 2014

Assembly and validation of versatile transcription activator-like effector libraries.

Sci Rep 2014 May 6;4:4857. Epub 2014 May 6.

1] Bioengineering Department, The University of Texas at Dallas, 800 West Campbell Road, Richardson TX 75080 USA [2] Center for Systems Biology, The University of Texas at Dallas, 800 West Campbell Road, Richardson TX 75080 USA [3] Electrical Engineering Department, The University of Texas at Dallas, 800 West Campbell Road, Richardson TX 75080 USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/srep04857DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4010924PMC
May 2014

Chd5 orchestrates chromatin remodelling during sperm development.

Nat Commun 2014 May 13;5:3812. Epub 2014 May 13.

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.

View Article

Download full-text PDF

Source
http://www.nature.com/articles/ncomms4812
Publisher Site
http://dx.doi.org/10.1038/ncomms4812DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4151132PMC
May 2014

Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells.

Nucleic Acids Res 2014 Mar 16;42(5):3009-16. Epub 2013 Dec 16.

Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Tsinghua University, Beijing 100084, China, Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX 75080, USA, LMAM, School of Mathematical Sciences, Peking University, Beijing 100871, China, Center for Theoretical Biology, Peking University, Beijing 100871, China and Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkt1306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3950701PMC
March 2014

HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism.

Cell Rep 2014 Mar 6;6(6):1139-1152. Epub 2014 Mar 6.

Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA. Electronic address:

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S22111247140008
Publisher Site
http://dx.doi.org/10.1016/j.celrep.2014.02.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3992522PMC
March 2014

The effects of carbon dioxide and temperature on microRNA expression in Arabidopsis development.

Nat Commun 2013 ;4:2145

Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 avenue des Hauts-Fourneaux, Esch sur-Alzette L-4362, Luxembourg.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms3145DOI Listing
February 2014

Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630.

Nucleic Acids Res 2014 Jan 22;42(2):1052-64. Epub 2013 Oct 22.

National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China, University of the Chinese Academy of Sciences, Beijing 100049, China, Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, Department of Histology and Embryology, University of South China, Hengyang Hunan Province 421001, China, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China, School of Applied Mathematics, Central University of Finance and Economics, Beijing 102206, China, Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas at Dallas, Dallas, TX 75083-0688, USA, Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Corrensstrasse 3, D-48149 Münster, Germany, Environmental Sciences Department, King Abdulaziz University, Jeddah 21589, Saudi Arabia, Department of Anatomy and Molecular Cell Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa, Nagoya 466-8550, Japan and School of Life Sciences, La Trobe University, Melbourne, Victoria, 3086, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkt932DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3902926PMC
January 2014

CDKN2A/p16 inactivation mechanisms and their relationship to smoke exposure and molecular features in non-small-cell lung cancer.

J Thorac Oncol 2013 Nov;8(11):1378-88

*Hamon Center for Therapeutic Oncology Research and †Division of Biostatistics, University of Texas Southwestern Medical Center, Dallas, Texas; ‡Department of Integrative Oncology, British Columbia Cancer Agency Research Centre, Vancouver, B.C., Canada; §Texas Scottish Rite Hospital for Children, Dallas, Texas; ‖Department of Surgery, Biochemistry, and Molecular Biology, Keck School of Medicine, USC/Norris Comprehensive Cancer Center, Los Angeles, California; ¶Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; #Oncology Biomarker Development, Genentech Inc., South San Francisco, California; **Department of Molecular and Cell Biology, Center for Systems Biology, University of Texas at Dallas, Dallas, Texas; and ††Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1097/JTO.0b013e3182a46c0cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3951422PMC
November 2013

BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data.

BMC Genomics 2013 Nov 10;14:774. Epub 2013 Nov 10.

Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2164-14-774DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3840619PMC
November 2013

Population dynamics of cancer cells with cell state conversions.

Quant Biol 2013 Sep;1(3):201-208

Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX 75080, USA ; MOE Key Laboratory of Bioinformatics; Bioinformatics Division/Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing 100084, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s40484-013-0014-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4467561PMC
September 2013

The transcription factor Foxo1 controls central-memory CD8+ T cell responses to infection.

Immunity 2013 Aug 8;39(2):286-97. Epub 2013 Aug 8.

Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.immuni.2013.07.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3809840PMC
August 2013

Computational identification of active enhancers in model organisms.

Genomics Proteomics Bioinformatics 2013 Jun 17;11(3):142-50. Epub 2013 May 17.

CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.gpb.2013.04.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4357786PMC
June 2013

DNA methylation data analysis and its application to cancer research.

Epigenomics 2013 Jun;5(3):301-16

Department of Molecular & Cell Biology, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX 75080, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.2217/epi.13.26DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4525706PMC
June 2013

OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds.

Nucleic Acids Res 2013 May 9;41(10):5149-63. Epub 2013 Apr 9.

Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkt216DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3664805PMC
May 2013

Genome-wide localization of protein-DNA binding and histone modification by a Bayesian change-point method with ChIP-seq data.

PLoS Comput Biol 2012 26;8(7):e1002613. Epub 2012 Jul 26.

Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1002613DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3406014PMC
January 2013

Major chromosomal breakpoint intervals in breast cancer co-localize with differentially methylated regions.

Front Oncol 2012 27;2:197. Epub 2012 Dec 27.

Cold Spring Harbor Laboratory Cold Spring Harbor, NY, USA ; Department of Oncology, Clinical Sciences, Lund University Lund, Sweden.

View Article

Download full-text PDF

Source
http://journal.frontiersin.org/article/10.3389/fonc.2012.001
Publisher Site
http://dx.doi.org/10.3389/fonc.2012.00197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530719PMC
January 2013

A novel Bayesian change-point algorithm for genome-wide analysis of diverse ChIPseq data types.

J Vis Exp 2012 Dec 10(70):e4273. Epub 2012 Dec 10.

Department of Applied Mathematics & Statistics, Stony Brook University.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3791/4273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3565849PMC
December 2012

Bivalent-like chromatin markers are predictive for transcription start site distribution in human.

PLoS One 2012 29;7(6):e38112. Epub 2012 Jun 29.

Department of Molecular Cell Biology, Center for Systems Biology, University of Texas at Dallas, Richardson, Texas, United States of America.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038112PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3387189PMC
November 2012

Novel Markov model of induced pluripotency predicts gene expression changes in reprogramming.

BMC Syst Biol 2011 14;5 Suppl 2:S8. Epub 2011 Dec 14.

MOE Key Laboratory of Bioinformatics and Bioinformatics Div, TNLIST /Department of Automation, Tsinghua University, Beijing 100084, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1752-0509-5-S2-S8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287488PMC
November 2012

Chromatin state and microRNA determine different gene expression dynamics responsive to TNF stimulation.

Genomics 2012 Nov 21;100(5):297-302. Epub 2012 Jul 21.

MOE Key Laboratory of Bioinformatics and Bioinformatics Div, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China.

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S08887543120014
Publisher Site
http://dx.doi.org/10.1016/j.ygeno.2012.07.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3771509PMC
November 2012

Regulatory elements of Caenorhabditis elegans ribosomal protein genes.

BMC Genomics 2012 Aug 28;13:433. Epub 2012 Aug 28.

Bioinformatics Division, Center for Synthetic and Systems Biology, Tsinghua National Laboratory for Information Science and Technology, Tsinghua University, Beijing, China.

View Article

Download full-text PDF

Source
http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
Publisher Site
http://dx.doi.org/10.1186/1471-2164-13-433DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575287PMC
August 2012

Cell-type-based analysis of microRNA profiles in the mouse brain.

Neuron 2012 Jan;73(1):35-48

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Genetics Program, State University of New York, Stony Brook, NY 11790, USA.

View Article

Download full-text PDF

Source
http://linkinghub.elsevier.com/retrieve/pii/S089662731101009
Publisher Site
http://dx.doi.org/10.1016/j.neuron.2011.11.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3270494PMC
January 2012