Xuegong Zhang

Xuegong Zhang

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Aspirin inhabits proliferation and promotes apoptosis of pancreatic cancer cells via PI3K/Akt/mTOR signaling pathway.

Panminerva Med 2019 Sep 24. Epub 2019 Sep 24.

Department of Hepatobiliary Surgery, Affiliated Hospital of Binzhou Medical College, Binzhou, China -

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http://dx.doi.org/10.23736/S0031-0808.19.03752-2DOI Listing
September 2019

Tongue coating microbiome as a potential biomarker for gastritis including precancerous cascade.

Protein Cell 2019 Jul 26;10(7):496-509. Epub 2018 Nov 26.

MOE Key Laboratory of Bioinformatics and TCM-X center/Bioinformatics Division, BNRist/Department of Automation, Tsinghua University, Beijing, 100084, China.

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http://link.springer.com/10.1007/s13238-018-0596-6
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http://dx.doi.org/10.1007/s13238-018-0596-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6588651PMC
July 2019

Estimating the total genome length of a metagenomic sample using k-mers.

BMC Genomics 2019 Apr 4;20(Suppl 2):183. Epub 2019 Apr 4.

MOE Key Laboratory of Bioinformatics Division and Center for Synthetic & System Biology, BNRIST, Beijing, 100084, China.

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http://dx.doi.org/10.1186/s12864-019-5467-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456951PMC
April 2019

A new statistic for efficient detection of repetitive sequences.

Bioinformatics 2019 Apr 16. Epub 2019 Apr 16.

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

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https://academic.oup.com/bioinformatics/advance-article/doi/
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http://dx.doi.org/10.1093/bioinformatics/btz262DOI Listing
April 2019

Super-enhancers are transcriptionally more active and cell type-specific than stretch enhancers.

Epigenetics 2018 11;13(9):910-922. Epub 2018 Oct 11.

b Key Lab of Bioinformatics/Bioinformatics Division, BNRIST (Beijing National Research Center for Information Science and Technology), Department of Automation , Tsinghua University , Beijing , China.

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http://dx.doi.org/10.1080/15592294.2018.1514231DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6284781PMC
March 2019

Integrative modeling reveals key chromatin and sequence signatures predicting super-enhancers.

Sci Rep 2019 Feb 27;9(1):2877. Epub 2019 Feb 27.

MOE Key Lab of Bioinformatics/Bioinformatics Division, BNRIST (Beijing National Research Center for Information Science and Technology), Department of Automation, Tsinghua University, Beijing, 100084, China.

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http://dx.doi.org/10.1038/s41598-019-38979-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6393462PMC
February 2019

DEsingle for detecting three types of differential expression in single-cell RNA-seq data.

Bioinformatics 2018 09;34(18):3223-3224

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

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http://dx.doi.org/10.1093/bioinformatics/bty332DOI Listing
September 2018

Multiple domains of bacterial and human Lon proteases define substrate selectivity.

Emerg Microbes Infect 2018 Aug 17;7(1):149. Epub 2018 Aug 17.

Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China.

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http://dx.doi.org/10.1038/s41426-018-0148-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6098112PMC
August 2018

Characterization of kinase gene expression and splicing profile in prostate cancer with RNA-Seq data.

BMC Genomics 2018 Aug 13;19(Suppl 6):564. Epub 2018 Aug 13.

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

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http://dx.doi.org/10.1186/s12864-018-4925-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6101066PMC
August 2018

Making genome browsers portable and personal.

Genome Biol 2018 07 18;19(1):93. Epub 2018 Jul 18.

Key Lab of Bioinformatics/Bioinformatics Division, BNRIST (Beijing National Research Center for Information Science and Technology), Department of Automation, Tsinghua University, Beijing, 100084, China.

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http://dx.doi.org/10.1186/s13059-018-1470-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6050684PMC
July 2018

Precise temporal regulation of alternative splicing during neural development.

Nat Commun 2018 06 6;9(1):2189. Epub 2018 Jun 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.

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http://dx.doi.org/10.1038/s41467-018-04559-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5989265PMC
June 2018

SEASTAR: systematic evaluation of alternative transcription start sites in RNA.

Nucleic Acids Res 2018 05;46(8):e45

Department of Microbiology, Immunology, & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.

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http://dx.doi.org/10.1093/nar/gky053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5934623PMC
May 2018

Effect of high WDR5 expression on the hepatocellular carcinoma prognosis.

Oncol Lett 2018 May 20;15(5):7864-7870. Epub 2018 Mar 20.

Department of General Surgery, People's Hospital of Rizhao, Rizhao, Shandong 276800, P.R. China.

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http://dx.doi.org/10.3892/ol.2018.8298DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5921231PMC
May 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.

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

The identification of switch-like alternative splicing exons among multiple samples with RNA-Seq data.

PLoS One 2017 25;12(5):e0178320. Epub 2017 May 25.

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

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0178320PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5444801PMC
September 2017

Computational operon prediction in whole-genomes and metagenomes.

Brief Funct Genomics 2017 Jul;16(4):181-193

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http://dx.doi.org/10.1093/bfgp/elw034DOI Listing
July 2017

Systematic identification of cancer-related long noncoding RNAs and aberrant alternative splicing of quintuple-negative lung adenocarcinoma through RNA-Seq.

Lung Cancer 2017 07 21;109:21-27. Epub 2017 Apr 21.

Informatics, MSD China R&D, Beijing, China; Global Research IT, MRL-IT, Merck & Co., Inc., Boston, MA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.lungcan.2017.04.009DOI Listing
July 2017

ulfasQTL: an ultra-fast method of composite splicing QTL analysis.

BMC Genomics 2017 01 25;18(Suppl 1):963. Epub 2017 Jan 25.

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

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http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864
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http://dx.doi.org/10.1186/s12864-016-3258-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5310271PMC
January 2017

Precision Medicine: What Challenges Are We Facing?

Genomics Proteomics Bioinformatics 2016 10 13;14(5):253-261. Epub 2016 Oct 13.

CAS Key Laboratory of Genome Sciences and Information, Chinese Academy of Sciences, Beijing 100101, China. Electronic address:

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http://dx.doi.org/10.1016/j.gpb.2016.10.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5093857PMC
October 2016

The Influence of the Global Gene Expression Shift on Downstream Analyses.

PLoS One 2016 19;11(4):e0153903. Epub 2016 Apr 19.

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

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0153903PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4836657PMC
September 2016

Erratum to: A survey of best practices for RNA-seq data analysis.

Genome Biol 2016 Aug 26;17(1):181. Epub 2016 Aug 26.

Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697-2300, USA.

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http://dx.doi.org/10.1186/s13059-016-1047-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5000515PMC
August 2016

dbSUPER: a database of super-enhancers in mouse and human genome.

Nucleic Acids Res 2016 Jan 4;44(D1):D164-71. Epub 2015 Oct 4.

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

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http://dx.doi.org/10.1093/nar/gkv1002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702767PMC
January 2016

Computational prediction of CRISPR cassettes in gut metagenome samples from Chinese type-2 diabetic patients and healthy controls.

BMC Syst Biol 2016 Jan 11;10 Suppl 1. Epub 2016 Jan 11.

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

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http://dx.doi.org/10.1186/s12918-015-0248-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4895601PMC
January 2016

Annual periodicity in planktonic bacterial and archaeal community composition of eutrophic Lake Taihu.

Sci Rep 2015 Oct 27;5:15488. Epub 2015 Oct 27.

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

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http://dx.doi.org/10.1038/srep15488DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4621408PMC
October 2015

mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA-sequencing data.

Nat Commun 2015 Aug 3;6:7816. Epub 2015 Aug 3.

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

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http://www.nature.com/articles/ncomms8816
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http://dx.doi.org/10.1038/ncomms8816DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4523900PMC
August 2015

dslice: an R package for nonparametric testing of associations with application in QTL and gene set analysis.

Bioinformatics 2015 Jun 20;31(11):1842-4. Epub 2015 Jan 20.

MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Department of Automation, Tsinghua University, Beijing 100084, China, Department of Statistics, Harvard University, Cambridge, MA 02138, USA, School of Life Sciences, Tsinghua University, Beijing 100084, China and Center of Statistics, Tsinghua University, Beijing 100084, China MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Department of Automation, Tsinghua University, Beijing 100084, China, Department of Statistics, Harvard University, Cambridge, MA 02138, USA, School of Life Sciences, Tsinghua University, Beijing 100084, China and Center of Statistics, Tsinghua University, Beijing 100084, China.

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http://dx.doi.org/10.1093/bioinformatics/btv021DOI Listing
June 2015

qDNAmod: a statistical model-based tool to reveal intercellular heterogeneity of DNA modification from SMRT sequencing data.

Nucleic Acids Res 2014 Dec 17;42(22):13488-99. Epub 2014 Nov 17.

MOE Key Lab of Bioinformatics, Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing 100084, China

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http://dx.doi.org/10.1093/nar/gku1097DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4267614PMC
December 2014

Improvement of Dscam homophilic binding affinity throughout Drosophila evolution.

BMC Evol Biol 2014 Aug 27;14:186. Epub 2014 Aug 27.

State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.

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http://dx.doi.org/10.1186/s12862-014-0186-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4243935PMC
August 2014

RNAseqViewer: visualization tool for RNA-Seq data.

Bioinformatics 2014 Mar 8;30(6):891-2. Epub 2013 Nov 8.

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

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http://dx.doi.org/10.1093/bioinformatics/btt649DOI Listing
March 2014

Short read mapping for exome sequencing.

Methods Mol Biol 2013 ;1038:93-111

Bioinformatics Division, Tsinghua National Laboratory of Information Science and Technology, Beijing, China.

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http://dx.doi.org/10.1007/978-1-62703-514-9_6DOI 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.

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

Sequence signatures of genes with accompanying antisense transcripts in Saccharomyces cerevisiae.

Sci China Life Sci 2014 Jan 26;57(1):52-8. Epub 2013 Dec 26.

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

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http://dx.doi.org/10.1007/s11427-013-4597-7DOI Listing
January 2014

Network-based differential gene expression analysis suggests cell cycle related genes regulated by E2F1 underlie the molecular difference between smoker and non-smoker lung adenocarcinoma.

BMC Bioinformatics 2013 Dec 17;14:365. Epub 2013 Dec 17.

Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Mount Sinai School of Medicine, New York, NY, USA.

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http://dx.doi.org/10.1186/1471-2105-14-365DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3878503PMC
December 2013

Identifying potential cancer driver genes by genomic data integration.

Sci Rep 2013 Dec 18;3:3538. Epub 2013 Dec 18.

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

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http://www.nature.com/articles/srep03538
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http://dx.doi.org/10.1038/srep03538DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3866686PMC
December 2013

Opportunities and methods for studying alternative splicing in cancer with RNA-Seq.

Cancer Lett 2013 Nov 27;340(2):179-91. Epub 2012 Nov 27.

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

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https://linkinghub.elsevier.com/retrieve/pii/S03043835120065
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http://dx.doi.org/10.1016/j.canlet.2012.11.010DOI Listing
November 2013

Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic.

PLoS Comput Biol 2013 14;9(3):e1002935. Epub 2013 Mar 14.

Tsinghua National Laboratory for Information Science and Technology, and Department of Automation, Tsinghua University, Beijing, China.

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http://dx.doi.org/10.1371/journal.pcbi.1002935DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3597545PMC
November 2013

Prioritizing genes responsible for host resistance to influenza using network approaches.

BMC Genomics 2013 Nov 21;14:816. Epub 2013 Nov 21.

Department of Biochemistry, The University of Hong Kong, Hong Kong, China.

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http://dx.doi.org/10.1186/1471-2164-14-816DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4046670PMC
November 2013

Alignment-free supervised classification of metagenomes by recursive SVM.

BMC Genomics 2013 Sep 22;14:641. Epub 2013 Sep 22.

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

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http://dx.doi.org/10.1186/1471-2164-14-641DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3849074PMC
September 2013

Computational prediction of associations between long non-coding RNAs and proteins.

BMC Genomics 2013 Sep 24;14:651. Epub 2013 Sep 24.

Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.

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http://dx.doi.org/10.1186/1471-2164-14-651DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3827931PMC
September 2013

NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data.

BMC Bioinformatics 2013 Jul 10;14:220. Epub 2013 Jul 10.

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

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http://dx.doi.org/10.1186/1471-2105-14-220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3717102PMC
July 2013

Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome.

Sci Rep 2012 6;2:936. Epub 2012 Dec 6.

Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing 100084, China.

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http://dx.doi.org/10.1038/srep00936DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3515809PMC
May 2013

Identifying differentially spliced genes from two groups of RNA-seq samples.

Gene 2013 Apr 8;518(1):164-70. Epub 2012 Dec 8.

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

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http://dx.doi.org/10.1016/j.gene.2012.11.045DOI Listing
April 2013

Common variants in the ATP2B1 gene are associated with hypertension and arterial stiffness in Chinese population.

Mol Biol Rep 2013 Feb 19;40(2):1867-73. Epub 2012 Oct 19.

State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.

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http://dx.doi.org/10.1007/s11033-012-2242-3DOI Listing
February 2013

Comparison of metagenomic samples using sequence signatures.

BMC Genomics 2012 Dec 27;13:730. Epub 2012 Dec 27.

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

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http://dx.doi.org/10.1186/1471-2164-13-730DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3549735PMC
December 2012

Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite.

BMC Syst Biol 2011 14;5 Suppl 2:S3. Epub 2011 Dec 14.

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

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https://pdfs.semanticscholar.org/866d/2374de79824ed0f4f77b1d
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http://link.springer.com/content/pdf/10.1186/1752-0509-5-S2-
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http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0
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http://dx.doi.org/10.1186/1752-0509-5-S2-S3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287483PMC
November 2012

Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes.

BMC Bioinformatics 2012 Jul 28;13:182. Epub 2012 Jul 28.

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

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-13-182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3464615PMC
July 2012

Characterization and prediction of lysine (K)-acetyl-transferase specific acetylation sites.

Mol Cell Proteomics 2012 Jan 30;11(1):M111.011080. Epub 2011 Sep 30.

Department of Biomedical Informatics, Peking University Health Science Center, Beijing 100191, China.

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http://dx.doi.org/10.1074/mcp.M111.011080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3270103PMC
January 2012

Observations on novel splice junctions from RNA sequencing data.

Biochem Biophys Res Commun 2011 Jun 7;409(2):299-303. Epub 2011 May 7.

College of Computer Science and Technology, Jilin University, Changchun 130012, China.

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http://dx.doi.org/10.1016/j.bbrc.2011.05.005DOI Listing
June 2011

Network-based group variable selection for detecting expression quantitative trait loci (eQTL).

BMC Bioinformatics 2011 Jun 30;12:269. Epub 2011 Jun 30.

Mathematics and Physics, School of Sciences, Tsinghua University, Beijing 100084, China.

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http://dx.doi.org/10.1186/1471-2105-12-269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3152919PMC
June 2011

Sequence alignment as hypothesis testing.

J Comput Biol 2011 May;18(5):677-91

MOE Key Lab of Bioinformatics and Bioinformatics Division of TNLIST/Department of Automation, Tsinghua University, Beijing, P.R. China.

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http://dx.doi.org/10.1089/cmb.2010.0328DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3122928PMC
May 2011

Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq.

Bioinformatics 2011 Feb 17;27(4):502-8. Epub 2010 Dec 17.

TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China.

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http://dx.doi.org/10.1093/bioinformatics/btq696DOI Listing
February 2011

Isoform abundance inference provides a more accurate estimation of gene expression levels in RNA-seq.

J Bioinform Comput Biol 2010 Dec;8 Suppl 1:177-92

MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing, P R China.

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December 2010

Global network analysis of lipid-raft-related proteins reveals their centrality in the network and their roles in multiple biological processes.

J Mol Biol 2010 Oct 13;402(4):761-73. Epub 2010 Aug 13.

MOE Key Laboratory of Bioinformatics, State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Bioinformatics and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.

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http://dx.doi.org/10.1016/j.jmb.2010.08.014DOI Listing
October 2010

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.

Authors:
Leming Shi Gregory Campbell Wendell D Jones Fabien Campagne Zhining Wen Stephen J Walker Zhenqiang Su Tzu-Ming Chu Federico M Goodsaid Lajos Pusztai John D Shaughnessy André Oberthuer Russell S Thomas Richard S Paules Mark Fielden Bart Barlogie Weijie Chen Pan Du Matthias Fischer Cesare Furlanello Brandon D Gallas Xijin Ge Dalila B Megherbi W Fraser Symmans May D Wang John Zhang Hans Bitter Benedikt Brors Pierre R Bushel Max Bylesjo Minjun Chen Jie Cheng Jing Cheng Jeff Chou Timothy S Davison Mauro Delorenzi Youping Deng Viswanath Devanarayan David J Dix Joaquin Dopazo Kevin C Dorff Fathi Elloumi Jianqing Fan Shicai Fan Xiaohui Fan Hong Fang Nina Gonzaludo Kenneth R Hess Huixiao Hong Jun Huan Rafael A Irizarry Richard Judson Dilafruz Juraeva Samir Lababidi Christophe G Lambert Li Li Yanen Li Zhen Li Simon M Lin Guozhen Liu Edward K Lobenhofer Jun Luo Wen Luo Matthew N McCall Yuri Nikolsky Gene A Pennello Roger G Perkins Reena Philip Vlad Popovici Nathan D Price Feng Qian Andreas Scherer Tieliu Shi Weiwei Shi Jaeyun Sung Danielle Thierry-Mieg Jean Thierry-Mieg Venkata Thodima Johan Trygg Lakshmi Vishnuvajjala Sue Jane Wang Jianping Wu Yichao Wu Qian Xie Waleed A Yousef Liang Zhang Xuegong Zhang Sheng Zhong Yiming Zhou Sheng Zhu Dhivya Arasappan Wenjun Bao Anne Bergstrom Lucas Frank Berthold Richard J Brennan Andreas Buness Jennifer G Catalano Chang Chang Rong Chen Yiyu Cheng Jian Cui Wendy Czika Francesca Demichelis Xutao Deng Damir Dosymbekov Roland Eils Yang Feng Jennifer Fostel Stephanie Fulmer-Smentek James C Fuscoe Laurent Gatto Weigong Ge Darlene R Goldstein Li Guo Donald N Halbert Jing Han Stephen C Harris Christos Hatzis Damir Herman Jianping Huang Roderick V Jensen Rui Jiang Charles D Johnson Giuseppe Jurman Yvonne Kahlert Sadik A Khuder Matthias Kohl Jianying Li Li Li Menglong Li Quan-Zhen Li Shao Li Zhiguang Li Jie Liu Ying Liu Zhichao Liu Lu Meng Manuel Madera Francisco Martinez-Murillo Ignacio Medina Joseph Meehan Kelci Miclaus Richard A Moffitt David Montaner Piali Mukherjee George J Mulligan Padraic Neville Tatiana Nikolskaya Baitang Ning Grier P Page Joel Parker R Mitchell Parry Xuejun Peng Ron L Peterson John H Phan Brian Quanz Yi Ren Samantha Riccadonna Alan H Roter Frank W Samuelson Martin M Schumacher Joseph D Shambaugh Qiang Shi Richard Shippy Shengzhu Si Aaron Smalter Christos Sotiriou Mat Soukup Frank Staedtler Guido Steiner Todd H Stokes Qinglan Sun Pei-Yi Tan Rong Tang Zivana Tezak Brett Thorn Marina Tsyganova Yaron Turpaz Silvia C Vega Roberto Visintainer Juergen von Frese Charles Wang Eric Wang Junwei Wang Wei Wang Frank Westermann James C Willey Matthew Woods Shujian Wu Nianqing Xiao Joshua Xu Lei Xu Lun Yang Xiao Zeng Jialu Zhang Li Zhang Min Zhang Chen Zhao Raj K Puri Uwe Scherf Weida Tong Russell D Wolfinger

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