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Zhang Z, Lin
H, Zhang MQ, Ma B, Li M, (2008)
ZOOM! Zillions of oligos mapped. Bioinformatics, In press.
Watts JA, Zhang C,
Kormish JD, Zhang MQ, Zaret K,
(2008) Cryptic pathway of genetic regulation of Cdx2 revealed by genome
location analysis of FoxA2 at silent genes. Submitted.
Fan S, Zhang MQ,
Zhang X (2008) Histone Methylation Marks Play Important Roles in Predicting
the Methylation Status of CpG
Islands. BBRC, In
press.
Zhang C, Li
W-H, Krainer AR, Zhang
MQ (2008) An RNA landscape of evolution for optimal exon and intron
discrimination. PNAS, 105:5797-802.
PDF.
Niida A, Smith AD,
Imoto S, Tsutsumi S, Aburatani H, Zhang
MQ, Akiyama T (2008) Integrative bioinformatics analysis of
transcriptional regulatory programs in breast cancer cells. Submitted.
Zhao X, Yoon S, Zhang MQ, Ye K, Geschwind DH, Sebat J, Iakoucheva LM (2008)
High Connectivity among Autism Gene Candidates in Biological Networks:
Evidence for Common Pathways. Submitted.
Smith AD, Xuan Z,
Zhang MQ (2008) Using quality scores and longer reads improves accuracy
of Solexa read mapping. MBC Bioinformatics, BMC Bioinformatics, 9:128.
Chen
J, Kim YC, Jung Y-C, Xuan Z,
Dworkin G, Zhang Y, Zhang MQ,
Wang SM (2008) Scanning the human genome at kilobase resolution. Genome Res. 18:751-62.
PDF.
Nahle Z, Hsieh M, Pietka T, Coburn CC,
Grimaldi PA, Zhang MQ, Das D, Abumrad NA. (2008) CD36-dependent
Regulation of Muscle FoxO1 and PDK4 in the PPARgamma/beta-mediated
Adaptation to Metabolic Stress. J. Biol. Chem. In press. PDF
Barrera
LO, Li Z, Smith AD, Arden KC,
Cavenee WK, Zhang MQ, Green RD,
Ren B (2008) Genome-wide mapping
and analysis of active promoters in mouse embryonic stem cells and adult
organs. Genome Res. 18:46-59.
PDF
Wang Z, Rosenfeld J, Schones DE,
Zang C, Barski A, Cuddapah S, Cui K, Roh T-Y, Peng W, Zhang MQ, Zhao K (2008) Genome-wide
correlation analysis of histone acetylation and methylation in human T
cells. Nat. Genet. (equal contributing first author), Nat Genet, 40:897-903.
Wu X, Jiang R, Zhang MQ, Li S
(2008) Large-scale network-based prediction of human disease genes.
Mol. Sys. Biol. 4:189.
PDF.
Wang X, Gu J, Zhang MQ, Li Y
(2008) Identification of phylogenetically conserved microRNA cis-regulatory
elements across 12 Drosophila species. Bioinformatics, 24:165-71.
Fan S, Fang F, Zhang X, Zhang MQ (2007) Putative Zinc Finger Protein Binding Sites Are
Over-represented in the Boundaries of Methylation-resistant CpG Islands in
the Human Genome. PLoS ONE, 2007; 2(11): e1184. PDF
Zhang
MQ (2007) Computational
analyses of eukaryotic promoters. Review proceeding of Otto Warburg
International Summer School and Workshop on Networks and Regulation, Peter
F Arndt & Martine Vingron eds. BMC Bioinformatics, 8(Suppl 6):S2.
Wang X, Bandyopadhya S, Xuan Z, Zhao X, Zhang MQ, Zhang X (2007) PREDICTION OF TRANSCRIPTION START SITES
BASED ON FEATURE SELECTION USING AMOSA. Proc. Comp. Sys. Bioinf.
Conference. San Diego,
Aug. 2007. World Scientific. eProceedings.
PDF
Zhang C, Krainer AR,
Zhang MQ. (2007) Evolutionary
impact of limited splicing fidelity in mammalian genes. Trends in Genetics.
23:484-8. PDF
Zhang C, Hastings
ML Krainer AR, Zhang
MQ. (2007) Dual-specificity splice sites function alternatively as 5'
and 3' splice sites. Proc. Natl.
Acad. Sci. USA 104, 15028-15033 PDF
Zhang C, Zhang MQ. (2007) Biomedical literature mining. Chap 10. in Introduction
to Bioinformatics: A workbook approach. Mathura V ed. Elsevier. In press.
Zhao
X, Leotta A, Kustanovich V, Lajonchere C, Geschwind DH, Law K, Law P,
Qiu S, Lord C, Sebat J, Ye K, Wigler M. (2007) A unified genetic theory for
sporadic and inherited autism. Proc Natl Acad Sci U S A. 104:12831-6.
Jiang
B, Zhang MQ and Zhang X. (2007)
OSCAR: One-class SVM for Accurate Recognition of Cis-elements.
Bioinformatics, PDF 23:2823-8.
He L, He X, Lim LP,
de Stanchina E, Xuan Z, Liang
Y, Xue W, Zender L, Magnus J, Ridzon D, Jackson AL, Linsley PS, Chen C,
Lowe SW, Cleary MA, Hannon GJ (2007) A microRNA component of the p53 tumour
suppressor network. Nature. 447, 1130-4.
Yang Z, Jiang H, Zhao F, Shankar DB, Sakamoto KM, Zhang MQ, Lin S (2007) A highly
conserved distal regulatory element controls hematopoietic expression of
GATA-2. BMC Developmental Biology, 7:97.
Chen G, Li W, Zhang Q-S,
Regulski M, Sinha N, Barditch J, Tully T, Krainer AR, Zhang MQ*, Dubnau J* (2008) Identification of synaptic targets
of Drosophila Pumilio. PLoS Comp Biol. (joint corresponding authors). 4(2):e1000026.
Eguchi J, Yan Q-W, Schones DE,
Kamal M, Hsu C-H, Zhang MQ,
Crawford GE, Rosen ED (2008) Identification of interferon-regulatory
factors (IRFs) as regulators of adipocyte gene expression by mapping Dnase
hypersensitive sites during adipogenesis. Cell Metabolism. 7:86-94.
Cuddapah S, Chen X, Xuan Z,
Roh T-Y, Cui K, Smith AD, Byun
JS, Zhang MQ, Fuller MT, Zhao K (2007) Identification of potential human
polycomb response elements in T cells. Submitted.
Bernard D, Prasanth KV, Nakamura T, Xuan
Z, Zhang MQ, Sedel F,
Triller A, Spector DL, Bessis A (2007) A nuclear retained non-coding RNA
regulates synaptogenesis. Submitted.
Kim TH, Abdullaev Z, Smith AD,
Ching KA, Loukinow D, Green RD, Zhang
MQ, Lobanenkov V, Ren B (2007) Analysis of the vertebrate insulator
protein CTCF binding sites in the human genome. Cell 128(6):1231-45. PDF
Murchison EP, Stein P, Xuan Z,
Pan H, Zhang MQ, Schultz RM,
Hannon GJ (2007) Critical roles for Dicer in the female germline. Gene
& Dev. 21:682-93.
Mignone JL, Roig-Lopez JL, Fedtsova N, Schones DE, Manganas LN, Maletic-Savatic M, Keyes WM, Mills AA,
Gleiberman A, Zhang MQ,
Enikolopov G. (2007) Neural Potential of a Stem Cell Population in the Hair
Follicle. Cell Cycle 6:2161-70. (cover
image!)
D. Das and M.Q. Zhang. (2007) Predictive
Models of Gene Regulation: Application of Regression Methods to Microarray
Data. Methods in Molecular Biology, ed. M. Korenberg. 377:95.
Zhang J, Jiang B, Li M, Tromp J, Zhang X and Zhang MQ (2007) Computing exact p-values for DNA motifs (Part
I). Bioinformatics. 23:531-7. PDF
Schones DE, Smith AD and Zhang MQ
(2007) Statistical significance of cis-regulatory modules. BMC
Bioinformatics 8:19 PDF
Jiang C, Xuan Z, Zhao F, Zhang MQ (2007) TRED: A
Transcriptional Regulatory Element Database, new entries and other
development. Nucleic Acid Res 35: D137-D140 PDF
Zhang C, Zhao X, Zhang MQ (2007) Functional in silico analysis of gene
regulatory polymorphism - Chapter 12 in: Bioinformatics for
Geneticists: A Bioinformatics Primer for the Analysis of Genetic Data, 2nd
edition
(M.R. Barnes, ed.) Pp281-310 Wiley-VCH
PDF
Zhao
X, Xuan Z, Zhang MQ (2007) Boosting with stumps for predicting
transcription start sites. Genome Biology 8:R17 PDF
Martinez MJ, Smith AD, Li B, Zhang MQ,
Harrod KS. (2007) Computational prediction of
novel components of lung transcriptional networks. Bioinformatics.
23:21-29. PDF
Smith AD, Sumazin P and Zhang MQ
(2007) Tissue-specific regulatory elements in mammalian promoters. Mol Sys Biol. 3:73 PDF
Zhang C, Zhang X, Zhang MQ, Li Y (2007) Neighbor
number, valley seeking and clustering. Pattern Recognition Letters.
28:173-180. PDF
Zhang
MQ (2007) Inferring Gene Regulatory
Networks - Chapter 21 in: Bioinformatics - From Genomes to Therapies
(T. Lengauer, ed.) Wiley-VCH. p807-828.
Kim YC, Jung Y-C, Xuan Z,
Tong H, Zhang MQ, Wang SM (2006)
Pan-genome isolation of low abundant transcripts through SAGE. FEBS Lett
580:6721-6729 PDF (equal contributing first author)
Schaffer JD, Dimitrova N, Zhang
MQ (2006) Bioinformatics. Chap. 26 in Advances in Healthcare
Technology: Shaping the Future of Medical Care. Spekowius G & Wendler T
eds. Pp421-438. Springer. PDF
Smith PJ, Zhang C, Wang J,
Chew SL, Zhang MQ, Krainer AR
(2006) An increased specificity score matrix for the prediction of
SF2/ASF-specific exonix splicing enhancers. Hum Mol Genet 15(16):2490-2508.
PDF
Li J, Zhang MQ and Zhang X
(2006) A new method for detecting human recombination hotspots and its
applications to the HapMap ENCODE data. Am. J. Hum. Genet. 79:628-639. PDF
Das R, Dimitrova N, Xuan Z, Rollins RA, Haghighi F, Edwards JR, Ju J,
Bestor TH, Zhang MQ (2006)
Computational prediction of methylation status in human genomic sequences. Proc
Natl Acad Sci U S A. 2006 Jul 3; 103:10713-6. PDF
Fang F, Fan SC, Zhang X and Zhang MQ
(2006) Predicting Methylation Status of CpG Islands in the Human Brain.
Bioinformatics, 22:2204-2209. PDF
Benita Y, Oosting RS, Xuan Z, Wise MJ, Zhang MQ, Humphery-Smith I (2006).
Challenges in the prediction of small genes in the human genome. Review.
Suzuki H, Zuo Y, Wang J, Zhang MQ,
Malhotra A, Mayeda A (2006) Characterization of RNase R-digested DNA source
that consists of lariat and circular RNAs derived from pre-mRNA splicing.
Nucleic Acids Res 34(8):e63 HTML
PDF
Zhang C, Xuan Z, Mandel G, Zhang MQ (2006) A Clustering
Property of Highly-degenerate Transcription Factor Binding Sites in the
Mammalian Genome. Nucleic Acid Res 34(8):2238-2246 HTML
PDF
Smith
AD, Sumazin P, Xuan Z, Zhang MQ (2006)
DNA motifs in human and mouse proximal promoters predict tissue-specific
expression. Proc Natl Acad Sci USA 103(16):6275-6280 PDF, Supplemental Data
Das D, Nahle Z, Zhang
MQ (2006) Adaptively Inferring Human Transcriptional Subnetworks. Mol Sys
Biol. 2:2006.0029. Epub 2006 Jun 6. PDF
Commentary1
Commentary2
Grosse I, Zhang MQ, Herzel H
(2006) On the dynamic origin of large-scale GC variations in warmblooded
vertebrate genomes. Submitted.
Chaolin Zhang,
Hai-Ri Li, Jian-Bing Fan, Jessica Wang-Rodriguez, Tracy Downs, Xiang-Dong
Fu, Michael Q Zhang (2006)
Profiling alternatively spliced mRNA isoforms for prostate cancer
classification BMC Bioinformatics 2006 Apr;7:202 PDF
Rollins RA, Haghighi FG, Edwards JR, Das R, Zhang MQ, Ju J, Bester TH
(2006) Large-scale structure of genomic methylation patterns.Genome Res.
2006 Feb;16(2):157-63 PDF
Zhang MQ (2005) Using Core Promoters to Find
Human Core Promoter Regions - Chapter 2 in Current Protocols in Bioinformatics (AD Baxevanis & DB Davison, eds.) pp.2.9.1-2.9.10
John Wiley & Sons, Inc. PDF
Zhang MQ (2005) Computational Molecular
Biology of Genome Expression and Regulation. PReMI05 Lecture Notes in
Computer Science, pp31-38, Springer-Verlag GMbH. PDF
Prasanth KV, Prasanth SG, Xuan ZY, Sachidandam
R, Hearn S, Frier SM, Bennett CF, Zhang MQ and Spector DL (2005) Regulating
Gene Expression Through RNA Nuclear Retention - Cell.
2005 Oct 21;123(2):249-63 PDF
Wang J, Smith PH, Krainer AR, Zhang MQ (2005)
Distribution of SR Protein Exonic Splicing Enhancer Motifs in Human
Protein-Coding Genes - Nucleic
Acids Research 2005 33(16):5053-5062 HTML
PDF
Xuan Z, Zhao
F, Wang J, Chen G, Zhang MQ (2005) Genome-Wide Promoter Extraction and
Analysis in Human, Mouse and Rat - Genome
Biol 6(8):R72 HTML PDF
Smith AD, Sumazin P, Das D, Zhang MQ (2005)
Mining ChIP-chip Data for Transcription Factor and CoFactor Binding Sites -
Bioinformatics
21:Suppl 1:i403-i412 PDF
Zhao F, Xuan Z, Liu L, Zhang MQ (2005) TRED: A
Transcription Regulatory Element Database and a Platform for in silico
Gene Regulation Studies - Nucl Acid
Res 33:D103-107 HTML
PDF
Xuan Z, Zhang MQ
(2005) From Worm to Human: Bioinformatics
Approaches to Identify FOXO Target Genes - Mech Ageing
Dev 126(1):209-215 HTML PDF
Sumazin P, Chen G, Hata N, Smith AD, Zhang T,
Zhang MQ (2005) DWE: Discriminating Word Enumerator - Bioinformatics
21(1):31-38 HTML
PDF
Smith AD, Sumazin P, Zhang MQ (2005)
Identifying Tissue-Specific Transcription Factor Binding Sites in
Vertebrate Promoters - Proc Natl Acad
Sci USA - 102(5):1560-1565 HTML
PDF, DME License.
Schones DE, Sumazin P, Zhang MQ (2005) Similarity of Position
Frequency Matrices for Transcription Factor Binding Sites - Bioinformatics
21(3):307-313 HTML
PDF, MatCompare License.
Wang JH, Hata N, Fu XD, Zhang MQ (2005)
Searching for Tissue Specific Splicing cis-Elements in Human Alternatively
Spliced Genes - Unpublished
Banerjee N and Zhang MQ (2005) Transcription
Regulatory Networks in Yeast Cell Cycle - Chapter in: Microarray
Expression Profiling and Transcriptional Regulatory Networks (F
Shannon and S Rao, eds.) In
Press. PDF
Guigo R, Zhang MQ (2005) Gene Predictions and
Annotations - Chapter 17 in Mammalian Genomics (A Ruvinsky and JA
Marshall Graves, eds.) pp429 Wallingford:CAB International PDF
Zhang J, Li F, Li J, Zhang MQ, Zhang X (2004)
Evidence and Characteristics of Putative Human alpha Recombination Hotspots
- Hum Mol
Genet 13(22):2823-2828 HTML
PDF
Long F, Liu H, Hahn C, Sumazin P, Zhang MQ,
Zilberstein A (2004) Genome-Wide Prediction and Analysis of
Function-Specific Transcription Factor Binding Sites - In Silico Biology,
4(3):0033 HTML
Das D, Banerjee N, Zhang MQ (2004) Interacting
Models of Cooperative Gene Regulation - Proc Natl
Acad Sci USA 101(46):16234-16239 HTML
PDF, MARSMotif License.
Chen J, Lee S, Sun M, Xu ZY, Zhou G, Zhang RS,
Rowley JD, Zhang MQ, Wang SM (2004) Exhaustive Identification of Novel
Transcription Units in the Human Genome Using Novel SAGE Tags - Unpublished
Dike S, Balija VS, Gnoj L, Xuan Z, Ou J,
Zutavern T, Palmer LE, Hannon G, Zhang MQ, McCombie WR (2004) The Mouse
Genome: Experimental Examination of Gene Predictions and Transcriptional
Start Sites - Genome Res
14(12):2424-2429 HTML
PDF
Chen G, Hata N, Zhang MQ (2004) Transcription
Factor Binding Element Detection Using Functional Clustering of Mutant
Expression Data - Nucl Acid
Res 32(8):2362-2371 HTML
PDF
Kato M, Hata N, Banerjee N, Futcher B, Zhang
MQ (2004) Identifying Combinatorial Regulation of Transcription Factors and
Binding Motifs - Genome Biol
5(8):R56 HTML
PDF
Wang JH, Xuan ZY, Fu XD and Zhang MQ (2004)
Cross-Species Comparison of Alternative Splicing and Cross-Species
Comparison Between Human and Mouse - Unpublished
Davuluri R, Gross I, Zhang MQ (2004)
Annotation of Promoters and First Exons in the Human Genome - Unpublished
Zhang MQ (2003) Prediction, Annotation and
Analysis of Human Promoters - CSHL Quantitative Biology Symposium 68.
pp217-225 Cold Spring
Harb Symp Quant Biol 2003;68:217-225 PDF
Banerjee N, Zhang MQ (2003) Identifying
Cooperativity Among Transcription Factors Controlling the Cell Cycle in
Yeast - Nucl Acid
Res 31(23):7024-7031 HTML
PDF
Davuluri R, Zhang MQ (2003) Computer Software to
Find Genes in Plant Genomic DNA - Chapter 6, Methods Mol
Biol 236:87-108, Plant Functional Genomics Methods and Protocols
HTML
PDF
Li Z, Van Calcar S, Qu C, Cavenee WK, Zhang
MQ, Ren B (2003) A Global Transcriptional Regulatory Role for c-Myc in
Burkitt’s Lymphoma Cells - Proc Natl
Acad Sci USA 100(14):8164-8169 HTML
PDF
Cartegni L, Wang J, Zhu A, Zhang MQ, Krainer
AR (2003) ESEfinder: A Web Resource to Identify Exonic Enhancers - Nucl Acid
Res 31(13)3568-3571 HTML
PDF
Xuan Z, Wang J, Zhang MQ (2003) Computational
Comparison of Two Mouse Draft Genomes and the Human Golden Path - Genome Biol
4(1):R1 HTML
PDF
Zhang MQ (2003) Using MZEF to Find Internal
Coding Exons - Current Protocols in Bioinformatics (AD
Baxevanis & DB Davison, eds.) John Wiley & Sons, Inc.
1,4.2.1-18 PDF
Carmell M, Xuan Z, Zhang MQ, Hannon GJ (2002)
The Argonaute Family: Tentacles that Reach into RNAi, Developmental
Control, Stem Cell Maintenance, and Tumorigenesis - Genes Dev
16(21):2733-2742 HTML
PDF
Zhang MQ (2002) Extracting Functional Information
from Microarrays: A Challenge for Functional Genomics - Proc Natl
Acad Sci USA 99(20):12509-12511 HTML
PDF
Nahle Z, Polakoff J, Davuluri RV, McCurrach
ME, Jacobson MD, Narita M, Zhang MQ, Lazebnik Y, Bar-Sagi D and Lowe SW
(2002) Direct Coupling of the Cell Cycle and Cell Death Machinery by E2F - Nat Cell
Biol 4(11):859-864 HTML
PDF
Zhang MQ (2002) Computational Prediction of
Eukaryotic Protein-Coding Genes - Nat Rev
Genet 3(9):698-709 HTML
PDF
Zhang MQ (2002) Predicting Full-Length
Transcripts (discussion) - Trends
Biotechnol 20(7):273-275, discussion 275 HTML
PDF
Banerjee N, Zhang MQ (2002) Functional
Genomics as Applied to Mapping Transcription Regulatory Networks - Curr Opin
Microbiol 5(3):313-317 HTML
PDF
Herzel H, Grosse I, Zhang MQ (2002) On the
Dynamic Origin of Isochores - (Presented at the CSHL Genome Meeting, May
2001) Unpublished
Xuan Z, McCombie WR, Zhang MQ (2002) GFScan: A
Gene Family Search Tool at Genomic DNA Level - Genome Res
12(7):1142-1149 HTML
PDF
Zhang MQ (2002) Computational Methods for
Promoter Recognition - Chapter 10, Current
Topics in Computational Molecular Biology (Jiang T, Xu Y
& Zhang MQ, eds.) pp249-268 MIT Press,
Cambridge, Massachusetts PDF
Jaradat SA, Tanaka TS, O'Neill L, Chen G,
Banerjee N, Becker KG, Zhang MQ, Boheler KR, Ko MSH (2002) Dynamic Genetic
Reprogramming of Pluripotent Embryonic Stem Cells During Differentiation -
Unpublished
Zhang Y, Mei P, Lou R, Zhang MQ, Wu G, Qiang
B, Zhang Z, Shen Y (2002) Gene Expression Profiling in Developing Human
Hippocampus - J Neurosci
Res 70(2):200-208 HTML
PDF
Chen G, Jaradat SA, Banerjee N, Tanaka TS, Ko
MSH, Zhang MQ (2002) Cluster Analysis of Microarray Gene Expression Data:
Application to and Evaluation with NIA Mouse 15K Array on ES Cell
Differentiation - Statistica Sinica 12:241-262 PDF
Weinmann AS, Bartley SM, Zhang T, Zhang MQ,
Farnham PJ (2001) Use of Chromatin Immunoprecipitation to Clone Novel E2F
Target Promoters - Mol Cell
Biol 21(20):6820-6832 HTML
PDF
Davuluri RV, Grosse I, Zhang MQ (2001)
Computational Identification of Promoters and First Exons in the Human
Genome - Nat Genet
29(4):412-417 HTML
PDF
Zhang T, Zhang M (2001) Promoter Extraction
from GenBank (PEG): Automatic Extraction of Eukaryotic Promoter Sequences
in Large Sets of Genes - Bioinformatics
17(12):1232-1233 HTML
PDF
Kel AE, Kel-Margoulis OV, Farnham PJ, Bartley
SM, Wingender E, Zhang MQ (2001) Computer-Assisted Identification of Cell
Cycle-Related Genes: New Targets for E2F Transcription Factors - J Mol Biol
309(1):99-120 HTML PDF
Wu Q, Zhang T, Cheng JF, Kim Y, Grimwood J,
Schmutz J, Dickson M, Noonan JP, Zhang MQ, Myers RM, Maniatis T (2001)
Comparative DNA Sequence Analysis of Mouse and Human Protocadherin Gene
Clusters - Genome Res
11(3):389-404 HTML
PDF
Tabaska JE, Davuluri RV, Zhang MQ (2001)
Identifying the 3'-Terminal in Human DNA (Presented at CSHL Computational
Biology Workshop, Sept. 1999) - Bioinformatics
17(7):602-607 HTML
PDF
Liu HX, Cartegni L, Zhang MQ, Krainer AR
(2001) A Mechanism of Exon Skipping Caused by Nonsense or Missense
Mutations in the BRCA1 and other Genes - Nat Genet
27(1):55-58 HTML
PDF
Ando S, Sarlis NJ, Krishnan J, Feng X,
Refetoff S, Zhang MQ, Oldfield EH, Yen PM (2001) Aberrant Alternative
Splicing of Thyroid Hormone Receptor in a TSH-Secreting Pituitary Tumor is
a Mechanism for Hormone Resistance - Mol
Endocrinol 15(9):1529-1538 HTML
PDF
Zhang MQ (2000) Discriminant Analysis and its
Application in DNA Sequence Motif Recognition (Based on a lecture given at
EBI Symposium: Genome Based Gene Structure Determination; Jun 1-2, 2000, Cambridge, UK) - Brief
Bioinform 1(4):331-342 PDF
Stamm S, Zhu J, Nakai K, Stoilov P, Stoss O,
Zhang MQ (2000) An Alternative-Exon Database and its Statistical Analysis -
DNA Cell
Biol 19(12):739-756
Davuluri RV, Suzuki Y, Sugano S, Zhang MQ
(2000) CART Classification of Human 5'UTR Sequences - Genome Res
10(11):1807-1816 HTML
PDF
Ioshikhes IP, Zhang MQ (2000) Large-Scale
Human Promoter Mapping Using CpG
Islands - Nat Genet
26(1):61-63 HTML
PDF
Getz G, Levine E, Domany E, Zhang MQ (2000)
Super-Paramagnetic Clustering of Yeast Gene Expression Profiles - Physica A
279:457-464 PDF
Clusters
Liu, HX, Chew SL, Cartegni L, Zhang MQ,
Krainer AR (2000) Exonic Splicing Enhancer Motif Recognized by Human SC35
Under Splicing Conditions - Mol Cell
Biol 20(3):1063-1071 HTML
PDF
Machida M, Yamazaki S, Kunihiro S, Tanaka T,
Kushida N, Jinnno K, Haikawa Y, Yamazaki J, Yamamoto S, Sekine M, Ogudhi A,
Nagai Y, Sakai M, Aoki K, Ogura K, Kudoh Y, Kikuchi H, Zhang MQ, Yanagida M
(2000) - A 38 kb Segment Containing 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 - Yeast
16(1):71-80 HTML
PDF
Zhu J, Zhang MQ (1999) Cluster, Function and
Promoter: Analysis of Yeast Expression Array - Proceedings of Pacific Symposium
on Biocomputing 2000 (RB Altman, et al, eds.)
5:476-487 PDF
Mayeda A, Badolato J, Kobayashi R, Zhang MQ,
Gardiner EM, Krainer AR (1999) Purification and Characterization of Human
RNPS1: A General Activator of Pre-mRNA Splicing - EMBO J
18(16):4560-4570 HTML
PDF
Zhang MQ (1999) Large Scale Gene Expression
Data Analysis: A New Challenge to Computational Biologists - Genome Res
9(8):681-688 HTML
PDF
Tabaska JE, Zhang MQ (1999) Detection of
Polyadenylation Signals in Human DNA Sequences - Gene
231(1-2):77-86 PDF
Ioshikhes I, Trifonov EN, Zhang MQ (1999)
Periodical Distribution of Transcription Factor Sites in Promoter Regions
and Connection with Chromatin Structure - Proc Natl
Acad Sci USA 96(6):2891-2895 HTML
PDF
Zhang MQ (1999) Promoter Analysis of
Co-Regulated Genes in the Yeast Genome - Comput Chem
23(3-4):233-250 PDF
Zhu J and Zhang MQ (1999) SCPD: A Promoter
Database of Yeast Saccharomyces cerevisiae - Bioinformatics
15:607-611 HTML
PDF
Spellman PT, Sherlock G, Zhang MQ, Iyer VR,
Anders K, Eisen MB, Brown PO, Botstein D, Futcher B (1998) Comprehensive
Identification of Cell Cycle-Regulated Genes of the Yeast Saccharomyces
cerevisiae by Microarray Hybridization - Mol Biol
Cell 9(12):3273-3297 HTML
PDF
Liu HX, Zhang MQ and Krainer AR (1998) Identification
of Functional Exonic Splicing Enhancer Motifs Recognized by Individual SR
Proteins - Gene Dev
12(13):1998-2012 HTML
PDF
Zhang MQ (1998) Identification of Protein
Coding Regions in Arabidopsis thaliana Genome Based on Quadratic
Discriminant Analysis - Mol Plant
Biol 37(5):803-806 HTML
PDF
Zhang MQ (1998) Identification of Human Gene
Core Promoters in Silico - Genome Res
8(1):319-326 HTML
PDF
Zhang MQ (1998) Statistical Features of Human
Exons and Their Flanking Regions - Hum Mol
Genet 7(5):919-932 HTML
PDF
Zhang MQ (1998) A Discrimination Study of
Human Core Promoters - Proceedings of Pacific Symposium on Biocomputing
(RB Altman, et al, eds.) Pac Symp
Biocomput 1998;:240-51 PDF
Chen T and Zhang MQ (1998) POMBE: A Fission
Yeast Gene-Finding and Exon-Intron Structure Prediction System for Fission
Yeast- Yeast
14(8):701-710 HTML
PDF
Zhang MQ (1997) Identification of Protein
Coding Regions in the Human Genome by Quadratic Discriminant Analysis - Proc Natl
Acad Sci USA 94(2):565-568 HTML
PDF
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