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122 Article(s) on File
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Chd5 orchestrates chromatin remodelling during sperm development
Li W,
Wu J,
Kim SY,
Zhao M,
Hearn SA,
Zhang MQ,
Meistrich ML,
Mills AA

Nat Commun
  5 (0): 3812; May 13 2014   Nlm
[Abstract]
[DOI] [Full Text]

Chd5 orchestrates chromatin remodelling during sperm development
Li W,
Wu J,
Kim SY,
Zhao M,
Hearn SA,
Zhang MQ,
Meistrich ML,
Mills AA

Nature Communications
  5 (0): May 13 2014   NLM
[DOI] [Full Text]

Assessment of transcript reconstruction methods for RNA-seq
Steijger T,
Abril JF,
Engström PG,
Kokocinski F,
Akerman M,
Alioto T,
Ambrosini G,
Antonarakis SE,
Behr J,
Bertone P,
Bohnert R,
Bucher P,
Cloonan N,
Derrien T,
Djebali S,
Du J,
Dudoit S,
Gerstein M,
Gingeras TR,
Gonzalez D,
Grimmond SM,
Guigó R,
Habegger L,
Harrow J,
Hubbard TJ,
Iseli C,
Jean G,
Kahles A,
Lagarde J,
Leng J,
Lefebvre G,
Lewis S,
Mortazavi A,
Niermann P,
Rätsch G,
Reymond A,
Ribeca P,
Richard H,
Rougemont J,
Rozowsky J,
Sammeth M,
Sboner A,
Schulz MH,
Searle SM,
Solorzano ND,
Solovyev V,
Stanke M,
Stevenson BJ,
Stockinger H,
Valsesia A,
Weese D,
White S,
Wold BJ,
Wu J,
Wu TD,
Zeller G,
Zerbino D,
Zhang MQ

Nature Methods
  10 (12): 1177-1184; Nov 2013  
[Abstract]
[DOI] [Full Text]

The transcription factor Foxo1 controls central-memory CD8+ T cell responses to infection
Kim MV,
Ouyang W,
Liao W,
Zhang MQ,
Li MO

Immunity
  39 (2): 286-97; Aug 22 2013   Nlm
[Abstract]
[DOI] [Full Text]

The effects of carbon dioxide and temperature on microRNA expression in Arabidopsis development
May P,
Liao W,
Wu Y,
Shuai B,
McCombie WR,
Zhang MQ,
Liu QA

Nature Communications
  4 (0): Jul 31 2013   NLM
[DOI] [Full Text]

OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds
Wu J,
Anczukow O,
Krainer AR,
Zhang MQ,
Zhang C

Nucleic Acids Res
  16 (6): 5149-5163; Apr 9 2013   NLM
[Abstract]
[DOI] [Full Text]

Major chromosomal breakpoint intervals in breast cancer co-localize with differentially methylated regions
Tang MH,
Varadan V,
Kamalakaran S,
Zhang MQ,
Dimitrova N,
Hicks J

Frontiers in Oncology
  2 (0): 197; Dec 27 2012   NLM
[Abstract]
[DOI] [Full Text]

A novel Bayesian change-point algorithm for genome-wide analysis of diverse ChIPseq data types
Xing H,
Liao W,
Mo Y,
Zhang MQ

Journal of Visualized Experiments
  (70): Dec 10 2012  
[DOI] [Full Text]

Novel Foxo1-dependent transcriptional programs control T reg cell function
Ouyang W,
Liao W,
Luo CT,
Yin N,
Huse M,
Kim MV,
Peng M,
Chan P,
Ma Q,
Mo Y,
Meijer D,
Zhao K,
Rudensky AY,
Atwal G,
Zhang MQ,
Li MO

Nature
  491 (7425): 554-559; Nov 22 2012  
[Abstract]
[DOI] [Full Text]

Genome-Wide Localization of Protein-DNA Binding and Histone Modification by a Bayesian Change-Point Method with ChIP-seq Data
Xing H,
Mo Y,
Liao W,
Zhang MQ

PLoS Comput Biol
  8 (7): e1002613; Jul 26 2012   Nlm
[Abstract]
[DOI] [Full Text]

H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence
Chicas A,
Kapoor A,
Wang XW,
Aksoy O,
Evertts AG,
Zhang MQ,
Garcia BA,
Bernstein E,
Lowe SW

Proceedings of the National Academy of Sciences of the United States of America
  109 (23): 8971-8976; Jun 5 2012  
[Abstract]
[DOI] [Full Text]

Cell-Type-Based Analysis of MicroRNA Profiles in the Mouse Brain
He M,
Liu Y,
Wang X,
Zhang MQ,
Hannon GJ,
Huang ZJ

Neuron
  73 (1): 35-48; Jan 12 2012   NLM
[Abstract]
[DOI] [Full Text]

Identification of Tumor Suppressors and Oncogenes from Genomic and Epigenetic Features in Ovarian Cancer
Wrzeszczynski KO,
Varadan V,
Byrnes J,
Lum E,
Kamalakaran S,
Levine DA,
Dimitrova N,
Zhang MQ,
Lucito R

PLoS ONE
  6 (12): Dec 2011  
[Abstract]
[DOI] [Full Text]

Direct cloning of double-stranded RNAs from RNase protection analysis reveals processing patterns of C/D box snoRNAs and provides evidence for widespread antisense transcript expression
Shen ML,
Eyras E,
Wu J,
Khanna A,
Josiah S,
Rederstorff M,
Zhang MQ,
Stamm S

Nucleic Acids Research
  39 (22): 9720-9730; Dec 2011  
[Abstract]
[DOI] [Full Text]

Identification of Novel Androgen-Regulated Pathways and mRNA Isoforms through Genome-Wide Exon-Specific Profiling of the LNCaP Transcriptome
Rajan P,
Dalgliesh C,
Carling PJ,
Buist T,
Zhang CL,
Grellscheid SN,
Armstrong K,
Stockley J,
Simillion C,
Gaughan L,
Kalna G,
Zhang MQ,
Robson CN,
Leung HY,
Elliott DJ

PLoS ONE
  6 (12): Dec 2011  
[Abstract]
[DOI] [Full Text]

SpliceTrap: a method to quantify alternative splicing under single cellular conditions
Wu J,
Akerman M,
Sun S,
McCombie WR,
Krainer AR,
Zhang MQ

Bioinformatics
  27 (21): 3010-3016 ; Nov 2011   PMC3198574
[Abstract]
[DOI]

Study of FoxA Pioneer Factor at Silent Genes Reveals Rfx-Repressed Enhancer at Cdx2 and a Potential Indicator of Esophageal Adenocarcinoma Development
Watts JA,
Zhang CL,
Klein-Szanto AJ,
Kormish JD,
Fu J,
Zhang MQ,
Zaret KS

PLoS Genetics
  7 (9): Sep 2011   PMC3174211
[Abstract]
[DOI] [Full Text]

Functional Mutation of SMAC/DIABLO, Encoding a Mitochondrial Proapoptotic Protein, Causes Human Progressive Hearing Loss DFNA64
Cheng J,
Zhu Y,
He S,
Lu Y,
Chen J,
Han B,
Petrillo M,
Wrzeszczynski K,
Yang S,
Dai P,
Zhai S,
Han D,
Zhang MQ,
Li W,
Liu X,
Li H,
Chen ZY,
Yuan H

The American Journal of Human Genetics
  89 (1): 56-66; Jul 15 2011   PMC3135809
[Abstract]
[DOI]

Transcriptome Study for Early Hematopoiesis-Achievement, Challenge and New Opportunity
Wang SM,
Zhang MQ

Journal of Cellular Physiology
  223 (3): 549-552; Jun 2010   PMCID: PMC2875260
[Abstract]
[DOI] [Full Text] [PDF]

Dissecting the Unique Role of the Retinoblastoma Tumor Suppressor during Cellular Senescence
Chicas A,
Wang X,
Zhang C,
McCurrach ME,
Zhao Z,
Mert O,
Dickins RA,
Narita M,
Zhang MQ,
Lowe SW

Cancer Cell
  17 (4): 376-387; Apr 12 2010   PMCID: PMC2889489
[Abstract]
[DOI] [Full Text] [PDF]

SFSSClass: an integrated approach for miRNA based tumor classification
Mitra R,
Bandyopadhyay S,
Maulik U,
Zhang MQ

BMC Bioinformatics
  11(Su (0): Jan 18 2010   PMCID: PMC3009493
[Abstract]
[DOI] [Full Text] [PDF]

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
Harris RA,
Wang T,
Coarfa C,
Nagarajan RP,
Hong C,
Downey SL,
Johnson BE,
Fouse SD,
Delaney A,
Zhao Y,
Olshen A,
Ballinger T,
Zhou X,
Forsberg KJ,
Gu J,
Echipare L,
OGeen H,
Lister R,
Pelizzola M,
Xi Y,
Epstein CB,
Bernstein BE,
Hawkins RD,
Ren B,
Chung WY,
Gu H,
Bock C,
Gnirke A,
Zhang MQ,
Haussler D,
Ecker JR,
Li W,
Farnham PJ,
Waterland RA,
Meissner A,
Marra MA,
Hirst M,
Milosavljevic A,
Costello JF

Nature Biotechnology
  28 (10): 1097-1105; 2010   PMCID: PMC2955169
[Abstract]
[DOI] [Full Text] [PDF]

Updates to the RMAP short-read mapping software
Smith AD,
Chung WY,
Hodges E,
Kendall JT,
Hannon GJ,
Hicks JB,
Xuan Z,
Zhang MQ

Bioinformatics
  25 (21): 2841-2842; Nov 1 2009   PMCID: PMC2895571
[Abstract]
[DOI] [Full Text] [PDF]

High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing Dup removed 04/2012
Hodges E,
Smith AD,
Kendall JT,
Xuan Z,
Ravi K,
Rooks M,
Zhang MQ,
Ye K,
Bhattacharjee A,
Brizuela L,
McCombie WR,
Wigler MH,
Hannon GJ,
Hicks JB

Genome Res
  19 (9): 1593-1605; Sep 2009   PMCID: PMC2752124
[Abstract]
[DOI] [Full Text] [PDF]

An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia
Benita Y,
Kikuchi H,
Smith AD,
Zhang MQ,
Chung DC,
Xavier RJ

Nucleic Acids Res
  37 (14): 4587–4602; Aug 2009   PMCID: PMC2724271
[Abstract]
[DOI] [Full Text] [PDF]

The transcriptome of human CD34+ hematopoietic stem-progenitor cells
Kim YC,
Wu Q,
Chen J,
Xuan Z,
Jung Y,
Zhang MQ,
Rowley JD,
Wang SM

Proc Natl Acad Sci U S A
  106 (20): 8278-8283; May 19 2009   PMCID: PMC2688877
[Abstract]
[DOI] [Full Text] [PDF]

Determination of enriched histone modifications in non-genic portions of the human genome
Rosenfeld JA,
Wang Z,
Schones DE,
Zhao K,
DeSalle R,
Zhang MQ

BMC Genomics
  10 (1): 143; Mar 31 2009   PMCID: PMC2667539
[Abstract]
[DOI] [Full Text] [PDF]

Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development
Li T,
Huang J,
Jiang Y,
Zeng Y,
He F,
Zhang MQ,
Han Z,
Zhang X

Genomics
  93 (3): 235-242; Mar 2009   PMCID: PMC2995988
[Abstract]
[DOI] [Full Text] [PDF]

Gene set-based module discovery in the breast cancer transcriptome
Niida A,
Smith AD,
Imoto S,
Aburatani H,
Zhang MQ,
Akiyama T

BMC Bioinformatics
  10 (0): 71; Feb 26 2009   PMCID: PMC2674431
[Abstract]
[DOI] [Full Text] [PDF]

High-resolution human core-promoter prediction with CoreBoost_HM
Wang X,
Xuan Z,
Zhao X,
Li Y,
Zhang MQ

Genome Res
  19 (2): 266-75; Feb 2009   PMCID: PMC2652208
[Abstract]
[DOI] [Full Text] [PDF]

The seventh Asia Pacific bioinformatics conference (APBC2009)
Zhang MQ,
Waterman MS,
Zhang X

BMC Bioinformatics
  10 (0): Jan 30 2009   PMCID: PMC2648764
[DOI] [Full Text] [PDF]

Challenges in understanding genome-wide DNA methylation
Zhang MQ,
Smith AD

Journal of Computer Science and Technology
  25 (1): 26-34; 2009  
[Abstract]
[DOI] [Full Text]

ZOOM! Zillions of oligos mapped
Lin H,
Zhang Z,
Zhang MQ,
Ma B,
Li M

Bioinformatics
  24 (21): 2431-7; Nov 1 2008  
[Abstract]
[DOI] [Full Text] [PDF]

Regulation of the PDK4 isozyme by the Rb-E2F1 complex
Hsieh MC,
Das D,
Sambandam N,
Zhang MQ,
Nahle Z

J Biol Chem
  283 (41): 27410-7; Oct 10 2008  
[Abstract]
[DOI] [Full Text] [PDF]

Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells
Niida A,
Smith AD,
Imoto S,
Tsutsumi S,
Aburatani H,
Zhang MQ,
Akiyama T

Bmc Bioinformatics
  9 (0): 404; Sep 29 2008   PMCID: PMC2572072
[Abstract]
[DOI] [Full Text] [PDF]

Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2
Zhang C,
Zhang Z,
Castle J,
Sun S,
Johnson J,
Krainer AR,
Zhang MQ

Genes Dev
  22 (18): 2550-63; Sep 15 2008   PMCID: PMC2546699
[Abstract]
[DOI] [Full Text] [PDF]

Histone methylation marks play important roles in predicting the methylation status of CpG islands
Fan S,
Zhang MQ,
Zhang X

Biochemical and Biophysical Research Communications
  374 (3): 559-564; Sep 2008  
[Abstract]
[DOI] [Full Text] [PDF]

Poly A- transcripts expressed in HeLa cells
Wu Q,
Kim YC,
Lu J,
Xuan ZY,
Chen J,
Zheng Y,
Zhou T,
Zhang MQ,
Wu CI,
Wang SM

PLoS ONE
  3 (7): e2803; Jul 30 2008   PMCID: PMC2481391
[Abstract]
[DOI] [Full Text] [PDF]

Combinatorial patterns of histone acetylations and methylations in the human genome
Wang Z,
Zang C,
Rosenfeld JA,
Schones DE,
Barski A,
Cuddapah S,
Cui K,
Roh TY,
Peng W,
Zhang MQ,
Zhao K

Nat Genet
  40 (7): 897-903; Jul 2008   PMCID: PMC2769248
[Abstract]
[DOI] [Full Text] [PDF]

Multiobjective fuzzy biclustering in microarray data: Method and a new performance measure
Maulik U,
Mukhopadhyay A,
Bandyopadhyay S,
Zhang MQ,
Zhang X

2008 IEEE Congress on Evolutionary Computation, CEC 2008
  1536-1543; Jun 2008  
[Abstract]
[DOI] [Full Text]

CD36-dependent Regulation of Muscle FoxO1 and PDK4 in the PPAR{delta}/{beta}-mediated Adaptation to Metabolic Stress
Nahle Z,
Hsieh M,
Pietka T,
Coburn CT,
Grimaldi PA,
Zhang MQ,
Das D,
Abumrad NA

J Biol Chem
  283 (21): 14317-26; May 23 2008   PMCID: PMC2386936
[Abstract]
[DOI] [Full Text] [PDF]

Scanning the human genome at kilobase resolution
Chen J,
Kim YC,
Jung YC,
Xuan ZY,
Dworkin G,
Zhang YM,
Zhang MQ,
Wang SM

Genome Res
  18 (5): 751-762; May 2008   PMCID: PMC2336809
[Abstract]
[DOI] [Full Text] [PDF]

RNA landscape of evolution for optimal exon and intron discrimination
Zhang C,
Li WH,
Krainer AR,
Zhang MQ

Proc Natl Acad Sci U S A
  105 (15): 5797-5802 ; Apr 15 2008   PMCID: PMC2311341
[Abstract]
[DOI] [Full Text] [PDF]

Using quality scores and longer reads improves accuracy of Solexa read mapping
Smith AD,
Xuan ZY,
Zhang MQ

Bmc Bioinformatics
  9 (128): Feb 2008   PMCID: PMC2335322
[Abstract]
[DOI] [Full Text] [PDF]

Network-based global inference of human disease genes
Wu X,
Jiang R,
Zhang MQ,
Li S

Mol Syst Biol
  4 (0): 189; 2008   PMCID: PMC2424293
[Abstract]
[DOI] [Full Text] [PDF]

Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species
Wang XW,
Gu J,
Zhang MQ,
Li YD

Bioinformatics
  24 (2): 165-171; Jan 2008  
[Abstract]
[Full Text] [PDF]

Interferon regulatory factors are transcriptional regulators of adipogenesis
Eguchi J,
Yan QW,
Schones DE,
Karnal M,
Hsu CH,
Zhang MQ,
Crawford GE,
Rosen ED

Cell Metabolism
  7 (1): 86-94; Jan 2008   PMCID: PMC2278019
[Abstract]
[DOI] [Full Text] [PDF]

Identification of synaptic targets of Drosophila Pumilio
Chen G,
Li W,
Zhang Q,
Regulski MR,
Sinha N,
Barditch J,
Tully T,
Krainer AR,
Zhang MQ,
Dubnau JT

PLoS computational biology
  4 (2): e1000026 ; 2008  
[Full Text]

Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs
Barrera LO,
Li Z,
Smith AD,
Arden KC,
Cavenee WK,
Zhang MQ,
Green RD,
Ren B

Genome Res
  18 (1): 46-59; Jan 2008   PMCID: PMC2134779
[Abstract]
[DOI] [Full Text] [PDF]

OSCAR: one-class SVM for accurate recognition of cis-elements
Jiang B,
Zhang MQ,
Zhang X

Bioinformatics
  23 (21): 2823-8; Nov 1 2007  
[Abstract]
[Full Text] [PDF]

Evolutionary impact of limited splicing fidelity in mammalian genes
Zhang C,
Krainer AR,
Zhang MQ

Trends Genet
  23 (10): 484-488; Oct 2007  
[Abstract]
[DOI] [Full Text] [PDF]

Computational analyses of eukaryotic promoters
Zhang MQ

Bmc Bioinformatics
  8 Sup (0): S3; Sep 27 2007   PMCID: PMC1995544
[Abstract]
[DOI] [Full Text] [PDF]

Neural Potential of a Stem Cell Population in the Hair Follicle
Mignone JL,
Roig-Lopez JL,
Fedtsova N,
Schones DE,
Manganas LN,
Maletic-Savatic M,
Keyes WM,
Mills AA,
Gleiberman A,
Zhang MQ,
Enikolopov GN

Cell Cycle
  6 (17): 2161 - 2170 ; Sep 1 2007  
[Abstract]
[Full Text] [PDF]

A highly conserved regulatory element controls hematopoietic expression of GATA-2 in zebrafish
Yang Z,
Jiang H,
Zhao F,
Shankar DB,
Sakamoto KM,
Zhang MQ,
Lin S

Bmc Developmental Biology
  7 (0): Aug 2007  
[DOI] [Full Text] [PDF]

Critical roles for Dicer in the female germline
Murchison EP,
Stein P,
Xuan ZY,
Pan H,
Zhang MQ,
Schultz RM,
Hannon GJ

Genes Dev
  21 (6): 682-93; Mar 15 2007  
[Abstract]
[DOI] [Full Text] [PDF]

Computing exact P-values for DNA motifs
Zhang J,
Jiang B,
Li M,
Tromp J,
Zhang XG,
Zhang MQ

Bioinformatics
  23 (5): 531-537; Mar 2007  
[Abstract]
[DOI] [Full Text] [PDF]

Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome
Kim TH,
Abdullaev ZK,
Smith AD,
Ching KA,
Loukinov DI,
Green RD,
Zhang MQ,
Lobanenkov VV,
Ren B

Cell
  128 (6): 1231-1245; Mar 2007  
[Abstract]
[DOI] [Full Text] [PDF]

Boosting with stumps for predicting transcription start sites
Zhao X,
Xuan ZY,
Zhang MQ

Genome Biol
  8 (2): R17; Feb 2 2007  
[Abstract]
[DOI] [Full Text] [PDF]

Tissue-specific regulatory elements in mammalian promoters
Smith AD,
Sumazin P,
Zhang MQ

Molecular Systems Biology
  3 (0): Jan 2007  
[Abstract]
[DOI] [Full Text] [PDF]

Statistical significance of cis-regulatory modules
Schones DE,
Smith AD,
Zhang MQ

Bmc Bioinformatics
  8 (0): 16; Jan 2007   1796902
[Abstract]
[DOI] [Full Text] [PDF]

Computational prediction of novel components of lung transcriptional networks
Martinez MJ,
Smith AD,
Li BL,
Zhang MQ,
Harrod KS

Bioinformatics
  23 (1): 21-29; Jan 2007  
[Abstract]
[DOI] [Full Text] [PDF]

TRED: a transcriptional regulatory element database, new entries and other development
Jiang C,
Xuan ZY,
Zhao F,
Zhang MQ

Nucleic Acids Res
  35 (0): D137-D140; Jan 2007   PMCID: PMC1899102
[DOI] [Full Text] [PDF]

Computational prediction of methylation status in human genomic sequences
Das R,
Dimitrova N,
Xuan ZY,
Rollins RA,
Haghighi F,
Edwards JR,
Ju JY,
Bestor TH,
Zhang MQ

Proc Natl Acad Sci U S A
  103 (28): 10713-6; Jul 11 2006  
[Abstract]
[DOI] [Full Text] [PDF]

Adaptively inferring human transcriptional subnetworks
Das D,
Nahlé Z,
Zhang MQ

Mol Syst Biol
  2 (0): 2006.0029; Jun 6 2006  
[Abstract]
[DOI] [Full Text] [PDF]

A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome
Zhang C,
Xuan ZY,
Otto S,
Hover JR,
McCorkle SR,
Mandel G,
Zhang MQ

Nucleic Acids Res
  34 (8): 2238-46; 2006  
[Abstract]
[DOI] [Full Text] [PDF]

Predicting methylation status of CpG islands in the human brain
Fang F,
Fan S,
Zhang X,
Zhang MQ

Bioinformatics
  22 (18): 2204-2209; 2006  
[Abstract]
[DOI] [Full Text] [PDF]

Profiling alternatively spliced mRNA isoforms for prostate cancer classification
Zhang C,
Li HR,
Fan JB,
Wang-Rodriguez J,
Downs T,
Fu X,
Zhang MQ

BMC Bioinformatics
  7 (0): 202; 2006  
[Abstract]
[DOI] [Full Text] [PDF]

Regulating gene expression through RNA nuclear retention
Prasanth KV,
Prasanth SG,
Xuan ZY,
Hearn S,
Freier SM,
Bennett CF,
Zhang MQ,
Spector DL

Cell
  123 (2): 249-263; Oct 2005  
[Abstract]
[DOI] [Full Text] [PDF]

Using CorePromoter to find human core promoters
Zhang MQ

Curr Protoc Bioinformatics
  Chapt (0): Unit 2.9; Jul 2005  
[Abstract]
[DOI] [Full Text] [PDF]

Mining ChIP-chip data for transcription factor and cofactor binding sites
Smith AD,
Sumazin P,
Das D,
Zhang MQ

Bioinformatics
  21 Su (0): i403-12; Jun 2005  
[Abstract]
[DOI] [Full Text]

Identifying tissue-selective transcription factor binding sites in vertebrate promoters
Smith AD,
Sumazin P,
Zhang MQ

Proc Natl Acad Sci U S A
  102 (5): 1560-5; Feb 1 2005  
[Abstract]
[DOI] [Full Text]

Similarity of position frequency matrices for transcription factor binding sites
Schones DE,
Sumazin P,
Zhang MQ

Bioinformatics
  21 (3): 307-13; Feb 1 2005  
[Abstract]
[DOI]

Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes
Wang J,
Smith PJ,
Krainer AR,
Zhang MQ

Nucleic Acids Res
  33 (16): 5053-62; 2005  
[Abstract]
[DOI]

DWE: discriminating word enumerator
Sumazin P,
Chen G,
Hata N,
Smith AD,
Zhang T,
Zhang MQ

Bioinformatics
  21 (1): 31-8; Jan 1 2005  
[Abstract]
[DOI]

From worm to human: bioinformatics approaches to identify FOXO target genes
Xuan Z,
Zhang MQ

Mech Ageing Dev
  126 (1): 209-15; Jan 2005  
[Abstract]
[DOI]

The mouse genome: experimental examination of gene predictions and transcriptional start sites
Dike S,
Balija VS,
Nascimento LU,
Xuan Z,
Ou J,
Zutavern T,
Palmer LE,
Hannon G,
Zhang MQ,
McCombie WR

Genome Res
  14 (12): 2424-9; Dec 2004  
[Abstract]
[DOI]

Interacting models of cooperative gene regulation
Das D,
Banerjee N,
Zhang MQ

Proc Natl Acad Sci U S A
  101 (46): 16234-9; Nov 16 2004  
[Abstract]
[DOI]

Evidence and characteristics of putative human alpha recombination hotspots
Zhang J,
Li F,
Li J,
Zhang MQ,
Zhang XG

Human Molecular Genetics
  13 (22): 2823-2828; Nov 2004  
[Abstract]
[Full Text]

Identifying combinatorial regulation of transcription factors and binding motifs
Kato M,
Hata N,
Banerjee N,
Futcher B,
Zhang MQ

Genome Biology
  5 (8): 2004  
[Abstract]
[Full Text]

Transcription factor binding element detection using functional clustering of mutant expression data
Chen G,
Hata N,
Zhang MQ

Nucleic Acids Res
  32 (8): 2362-71; 2004  
[Abstract]
[DOI]

Identifying cooperativity among transcription factors controlling the cell cycle in yeast
Banerjee N,
Zhang MQ

Nucleic Acids Research
  31 (23): 7024-7031; Dec 2003  
[Abstract]
[Full Text]

ESEfinder: a web resource to identify exonic splicing enhancers
Cartegni L,
Wang JH,
Zhu ZW,
Zhang MQ,
Krainer AR

Nucleic Acids Research
  31 (13): 3568-3571; Jul 2003  
[Abstract]
[Full Text]

A global transcriptional regulatory role for c-Myc in Burkitts lymphoma cells
Li ZR,
Van Calcar S,
Qu CX,
Cavenee WK,
Zhang MQ,
Ren B

Proceedings of the National Academy of Sciences of the United States of America
  100 (14): 8164-8169; Jul 2003  
[Abstract]
[Full Text]

Computational comparison of two mouse draft genomes and the human golden path
Xuan Z,
Wang J,
Zhang MQ

Genome Biol
  4 (1): R1; 2003  
[Abstract]
[DOI] [Full Text]

Prediction, annotation, and analysis of human promoters
Zhang MQ

Cold Spring Harbor Symposia on Quantitative Biology LXVIII: The genome of Homo Sapiens
  68 217-25; 2003  
[DOI]

The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis
Carmell MA,
Xuan ZY,
Zhang MQ,
Hannon GJ

Genes Development
  16 (21): 2733-2742; Nov 2002  
[Full Text]

Extracting functional information from microarrays: A challenge for functional genomics
Zhang MQ

Proceedings of the National Academy of Sciences of the United States of America
  99 (20): 12509-12511; Oct 2002  
[DOI] [Full Text]

Gene expression profiling in developing human hippocampus
Zhang Y,
Mei PC,
Lou R,
Zhang MQ,
Wu GY,
Qiang BQ,
Zhang ZG,
Shen Y

Journal of Neuroscience Research
  70 (2): 200-208; Oct 2002  
[Full Text]

Computational prediction of eukaryotic protein-coding genes
Zhang MQ

Nature Reviews Genetics
  3 (9): 698-709; Sep 2002  
[DOI] [Full Text] [PDF]

GFScan: A gene family search tool at genomic DNA level
Xuan ZY,
McCombie WR,
Zhang MQ

Genome Research
  12 (7): 1142-1149; Jul 2002  
[Full Text]

Predicting full-length transcripts
Zhang MQ

Trends in Biotechnology
  20 (7): 275-275; Jul 2002  
[Full Text]

Evaluation and comparison of clustering algorithms in analyzing es cell gene expression data
Chen GX,
Jaradat SA,
Banerjee N,
Tanaka TS,
Ko MS,
Zhang MQ

Statistica Sinica
  12 (1): 241-262; Jan 2002  
[Full Text]

Using MZEF to find internal coding exons
Zhang MQ

Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]
  Chapt (0): Unit 4.2 ; 2002  
[Abstract]


Computational identification of promoters and first exons in the human genome
Davuluri RV,
Grosse I,
Zhang MQ

Nature Genetics
  29 (4): 412-417; Dec 2001  
[Abstract]
[DOI] [Full Text]

Use of chromatin immunoprecipitation to clone novel E2F target promoters
Weinmann AS,
Bartley SM,
Zhang T,
Zhang MQ,
Farnham PJ

Molecular and Cellular Biology
  21 (20): 6820-6832; Oct 2001  
[Abstract]
[Full Text]

Aberrant alternative splicing of thyroid hormone receptor in a TSH-secreting pituitary tumor is a mechanism for hormone resistance
Ando S,
Sarlis NJ,
Krishnan J,
Feng X,
Refetoff S,
Zhang MQ,
Oldfield EH,
Yen PM

Molecular Endocrinology
  15 (9): 1529-1538; Sep 2001  
[Abstract]
[Full Text] [PDF]

Identifying the 3 -terminal exon human DNA
Tabaska JE,
Davuluri RV,
Zhang MQ

Bioinformatics
  17 (7): 602-607; Jul 2001  
[Abstract]
[Full Text]

Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors
Kel AE,
Kel-Margoulis OV,
Farnham PJ,
Bartley SM,
Wingender E,
Zhang MQ

Journal of Molecular Biology
  309 (1): 99-120; May 2001  
[Abstract]
[Full Text]

Comparative DNA sequence analysis of mouse and human protocadherin gene clusters
Wu Q,
Zhang T,
Cheng JF,
Kim Y,
Grimwood J,
Schmutz J,
Dickson M,
Noonan JP,
Zhang MQ,
Myers RM,
Maniatis T

Genome Research
  11 (3): 389-404; Mar 2001  
[Abstract]
[Full Text]

A mechanism for exon skipping caused by nonsense or missense mutations in BRCA1 and other genes
Liu HX,
Cartegni L,
Zhang MQ,
Krainer AR

Nature Genetics
  27 (1): 55-58; Jan 2001  
[Abstract]
[DOI] [Full Text]

An alternative-exon database and its statistical analysis
Stamm S,
Zhu J,
Nakai K,
Stoilov P,
Stoss O,
Zhang MQ

DNA and Cell Biology
  19 (12): 739-756; Dec 2000  
[Abstract]
[Full Text]

Discriminant analysis and its application in DNA sequence motif recognition
Zhang MQ

Brief Bioinform
  1 (4): 331-42; Nov 2000  
[Abstract]
[DOI] [Full Text]

CART classification of human 5 UTR sequences
Davuluri RV,
Suzuki Y,
Sugano S,
Zhang MQ

Genome Research
  10 (11): 1807-1816; Nov 2000  
[Abstract]
[Full Text]

Large-scale human promoter mapping using CpG islands
Ioshikhes IP,
Zhang MQ

Nature Genetics
  26 (1): 61-63; Sep 2000  
[Abstract]
[Full Text]

Super-paramagnetic clustering of yeast gene expression profiles
Getz G,
Levine E,
Domany E,
Zhang MQ

Physica A
  279 (1): 457-464; May 2000  
[Abstract]
[Full Text]

Exonic splicing enhancer motif recognized by human SC35 under splicing conditions
Liu HX,
Chew SL,
Cartegni L,
Zhang MQ,
Krainer AR

Molecular and Cellular Biology
  20 (3): 1063-1071; Feb 2000  
[Abstract]
[Full Text]

Cluster, function and promoter: analysis of yeast expression array
Zhu J,
Zhang MQ

Pacific Symposium on Biocomputing
  479-90; Jan 4 2000  
[Abstract]
[Full Text] [PDF]

A 38 kb segment containing the cdc2 gene from the left arm of fission yeast chromosome II: sequence analysis and characterization of the genomic DNA and cDNAs encoded on the segment
Machida M,
Yamazaki S,
Kunihiro S,
Tanaka T,
Kushida N,
Jinno K,
Haikawa Y,
Yamazaki J,
Yamamoto S,
Sekine M,
Oguchi A,
Nagai Y,
Sakai M,
Aoki K,
Ogura K,
Kudoh Y,
Kikuchi H,
Zhang MQ,
Yanagida M

Yeast
  16 (1): 71-80; Jan 2000  
[Abstract]
[Full Text]

Large-scale gene expression data analysis: a new challenge to computational biologists
Zhang MQ

Genome Res
  9 (8): 681-8; Aug 1999  
[Abstract]
[Full Text]

SCPD: a promoter database of the yeast Saccharomyces cerevisiae
Zhu J,
Zhang MQ

Bioinformatics
  15 (7): 607-11; Jul-Aug 1999  
[Abstract]
[Full Text]

Promoter analysis of co-regulated genes in the yeast genome
Zhang MQ

Comput Chem
  23 (3): 233-50; Jun 15 1999  
[Abstract]
[Full Text]

Detection of polyadenylation signals in human DNA sequences
Tabaska JE,
Zhang MQ

Gene
  231 (1): 77-86; Apr 29 1999  
[Abstract]
[Full Text]

Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure
Ioshikhes I,
Trifonov EN,
Zhang MQ

Proc Natl Acad Sci U S A
  96 (6): 2891-5; Mar 16 1999  
[Abstract]
[Full Text]

Identification of protein-coding regions in Arabidopsis thaliana genome based on quadratic discriminant analysis
Zhang MQ

Plant Mol Biol
  37 (5): 803-6; Jul 1998  
[Abstract]
[Full Text]

Statistical features of human exons and their flanking regions
Zhang MQ

Hum Mol Genet
  7 (5): 919-32; May 1998  
[Abstract]
[Full Text]

Identification of human gene core promoters in silico
Zhang MQ

Genome Res
  8 (3): 319-26; Mar 1998  
[Abstract]
[Full Text]

A discrimination study of human core-promoters
Zhang MQ

Pac Symp Biocomput
  (0): 240-51; 1998  
[Abstract]
[Full Text]

Identification of protein coding regions in the human genome by quadratic discriminant analysis
Zhang MQ

Proc Natl Acad Sci U S A
  94 (2): 565-8; Jan 21 1997  
[Abstract]
[Full Text]

A sequence compilation and comparison of exons that are alternatively spliced in neurons
Stamm S,
Zhang MQ,
Marr TG,
Helfman DM

Nucleic Acids Res
  22 (9): 1515-26; May 11 1994  
[Abstract]
[DOI] [Full Text]

Fission yeast gene structure and recognition
Zhang MQ,
Marr TG

Nucleic Acids Res
  22 (9): 1750-9; May 11 1994  
[Abstract]
[DOI] [Full Text]

Genome Mapping by Random Anchoring - a Discrete Theoretical-Analysis
Zhang MQ,
Marr TG

Journal of Statistical Physics
  73 (3): 611-623; Nov 1993  
[Abstract]
[Full Text]

A weight array method for splicing signal analysis
Zhang MQ,
Marr TG

Comput Appl Biosci
  9 (5): 499-509; Oct 1993  
[Abstract]



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