Zhaolei Zhang, Ph.D.
Curriculum Vitae
ADDRESS
160 College Street, Room 608
Donnelly Centre for Cellular & Biomolecular Research (CCBR)
University of Toronto
Toronto, ON M5S 3E1, Canada
Tel: (416) 946-0924
Email: Zhaolei - dot - Zhang -AT- utoronto.ca
Web: http://sites.utoronto.ca/zhanglab/
EMPLOYMENT HISTORY
Professor - July 2014 to present
Associate Professor (with tenure) - July 2009 to June 2014
Assistant Professor (Tenure-stream) - Nov. 2004 to June 2009
Banting & Best Department of Medical Research (BBDMR) and
Department of Molecular Genetics
University of Toronto, Faculty of Medicine, Toronto, Ontario, Canada
Other affiliations: Donnelly Centre for Cellular and Biomolecular Research (CCBR);
Collaborative Graduate Program in Genome Biology & Bioinformatics
Department of Computer Science (Cross-appointed)
Post-doctoral Associate - Mar. 2001 - Oct. 2004
Yale University, New Haven, Connecticut, USA
Department of Molecular Biophysics and Biochemistry (MB&B)
Supervisor: Professor Mark Gerstein
Graduate Student Research Assistant - Oct. 1995 – Feb. 2001
University of California at Berkeley, Department of Chemistry and
Lawrence Berkeley National Laboratory (LBNL), Physical Bioscience Division, Berkeley, CA, USA
Supervisor: Dr. Ed Berry and Professor Sung-Hou Kim
EDUCATION
University of California at Berkeley, Berkeley, CA, USA
Ph.D., Biophysics, December 2000,
Advisor: Professor Sung-Hou Kim
Thesis: Crystal Structural Studies of Avian Mitochondrial Cytochrome bc1 Complex
RESEARCH INTERESTS
- Comparative genomics, discovery and analysis of novel functional transcripts in the mammalian genome
- Developing novel and efficient tools for characterization and discovery of transcription factor binding sites
- Analysis of protein-protein interaction networks in yeast, evolution of duplicated genes.
HONOURS AND AWARDS
- CIHR New Investigator Award, 2008 - 2014
- One of 30 "Rising young investigators" named by Genome Technology magazine, 2008
- Early Researcher Award, by Ontario Ministry of Research and Innovation, 2006
- Finalist, Maud Menten New Principal Investigator Prize, CIHR-Institute of Genetics, 2006
ACTIVITIES & SERVICES
- Professional Membership: International Society for Computational Biology (ISCB)
- Area Co-Chair, ISMB Annual Conference, 2006-2009
- Associate Editor, BMC Systems Biology
- Ad hoc reviewer for following journals: Bioinformatics, BMC
Bioinformatics, BMC Evolutionary Biology, Cytogenetic and Genome
Research, Genome Biology, Genome Research, Journal of Medical Genetics,
Journal of Molecular Biology, Journal of Molecular Evolution, Nature
Biotechnology, Nucleic Acids Research, Pacific Symposium on
Biocomputing, Protein Science, Proteins
GRANT SURPORT
- CIHR Operating Grant: "Epigenomics of major depressive disorder: dissecting environmental, heritable, and stochastic contributions", 2014-2019 (PI: A Petronis)
- Canadian Cancer Society Innovation Grant: "Investigating regulatory roles of pseudogenes and other non-coding RNAs in cancer", 2013-2015
- CIHR Operating Grant: "Evolution and genetic variation of microRNA regulatory network in humans", 2011-2016 (PI)
- Ontario Research Fund (ORF) - GL2: "Protein Complexes in the Epigenetics of Human Disease and Stem Cell Fate",
2010-2014 (PI: Jack Greenblatt)
- CIHR Catalyst Grant: "Bioinformatics Approaches to Cancer Research", 2009-2010 (PI:ZZ, with four other investigators)
- NSERC Discovery Grant: "Computational Modeing of Gene Regulation", 2009-2014
- CIHR Operating Grant: "Global Exploration of Cellular Networks and Pathways using Yeast Phenomics", 2009-2012,
(Co-PI; PI: Charlie Boone, Brenda Andrews)
- CIHR Operating Grant: "Mapping the reference genetic network of a eukaryotic cell with automated yeast genetic analysis",
2010-2015 (Co-PI, PI: Charlie Boone, Brenda Andrews)
- CIHR Team Grant: "Model Organism Interactomes and Human Diseases",
2007-2012, (Co-PI, PI: Shoshana Wodak)
- CIHR Operating Grant: Bioinformatics Detection and Experimental
Validation of Functional Transcripts in Mammalian Genome,
2006-2011, (PI)
- Genome Canada: "Integrative Biology", 2006-2009, (co-PI)
- Early Researcher Award (Ontario Ministry of Research and Innovation), 2006-2011
- University of Toronto Connaught New Staff Matching Grant: 2007 (Sole PI)
- University of Toronto Faculty of Medicine Dean’s Fund: 2005-2006, (Sole PI)
- University of Toronto Connaught Committee Start-up Award: 2005-2006 (Sole PI)
PUBLICATIONS
[113] Kim T, Tyndel MS, Kim HJ, Ahn J, Choi SH, Park HJ, Kim Y, Yang D, Lee J, Jung S, Kim SY, Min YH, Cheong J, Sohn SK, Moon JH, Choi M, Lee M, Zhang Z, Kim DD "The clonal origins of leukemic progression of myelodysplasia" Leukemia (To Appear)
[112] Leach MD, Kim T, DiGregorio S, Collins C, Zhang Z, Duennwald ML, and Cowen LE "Candida albicans is Resistant to Polyglutamine 1 Aggregation and Toxicity" G3:Genes Genomes Genetics 2016
[111] Kim T, Tyndel Ms, Kim HJ, Ahn J, Choi SH, Park H, Kim Y, Kim SY, Lipton JH, Zhang Z*, Kim DD* "Spectrum of somatic mutation dynamics in chronic myeloid leukemia following tyrosine kinase inhibitor therapy" Blood 2016
[110] Styles EB, Founk KJ, Zamparo LA, Sing TL, Altintas D, Ribeyre C, Ribaud V, Rougemont J, Mayhew D, Costanzo M, Usaj M, Verster AJ, Koch EN, Novarina D, Graf M, Luke B, Muzi-Falconi M, Myers CL, Mitra RD, Shore D, Brown GW, Zhang Z, Boone C, Andrews BJ. "Exploring Quantitative Yeast Phenomics with Single-Cell Analysis of DNA Damage Foci" Cell Systems 2016 Sep 28;3(3):264-277 PMID: 27617677
[109] Olsen JB, Wong L, Deimling S, Miles A, Guo H, Li Y, Zhang Z, Greenblatt JF, Emili A, Tropepe V. "G9a and ZNF644 Physically Associate to Suppress Progenitor Gene Expression during Neurogenesis" Stem Cell Reports 2016 Sep 13;7(3):454-70.
[108] Paul JM, Toosi B, Vizeacoumar FS, Bhanumathy KK, Li Y, Gerger C, El Zawily A, Freywald T, Anderson DH, Mousseau D, Kanthan R, Zhang Z, Vizeacoumar FJ, Freywald A. "Targeting synthetic lethality between the SRC kinase and the EPHB6 receptor may benefit cancer treatment." Oncotarget 2016 Jul 13. doi: 10.18632/oncotarget.10569
[107] Dibitetto D, Ferrari M, Rawal CC, Balint A, Kim T, Zhang Z, Smolka MB, Brown GW, Marini F, Pellicioli A. "Slx4 and Rtt107 control checkpoint signalling and DNA resection at double-strand breaks" Nucleic Acids Research 2016 Jan 29;44(2) PMID: 26490958
[106] Yimit A, Kim T, Anand RP, Meister S, Ou J, Haber JE, Zhang Z, Brown GW. "MTE1 Functions with MPH1 in Double-Strand Break Repair." Genetics 2016 May 203(1) PMID: 26920759
[105] Gu Z, Jin K, Crabbe MJ, Zhang Y, Liu X, Huang Y, Hua M, Nan P, Zhang Z, Zhong Y. "Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome." Protein Cell 2016 April; 7(4) PMID: 26861146
[104] Kim T, Yoshida K, Kim YK, Tyndel MS, Park HJ, Choi S, Ahn J, Jung S, Yang D, Lee J, Kim HJ, Kong G, Ogawa S, Zhang Z, Kim HJ and Kim D "Clonal dynamics in a single AML case tracked for 9 years reveals the complexity of leukemia progression" Leukemia 2016 Feb;30(2) PMID: 26424407
[103] Li, J., Ma, Z., Shi, M., Malty, R.H., Aoki, H.A., Jin, K., Phanse, S., Minic, Z., Wall, D.P., Zhang, Z., Urban, A.E., Hallmayer, J., Babu, M., and Snyder, M. "Identification of Human Neuronal Protein Complexes Reveals Biochemical Activities and Convergent Mechanisms of Action in Autism Spectrum Disorders" Cell Systems 2015 Vol 1 (5)
[102] Wong KC*, Li Y, Peng C, Moses AM, Zhang Z* "Computational Learning on Specificity-Determining Residue-Nucleotide Interactions" Nucleic Acids Research 2015 Nov 2 (Advanced Access) PMID: 26527718
[101] Jablonowski CM, Cussiol JR, Oberly S, Yimit A, Balint A, Kim T, Zhang Z, Brown GW and Smolka MB "Termination of Replication Stress Signaling via Concerted Action of the Slx4-Rtt107 Scaffolds" Genetics 2015 2015 Nov;201(3)
[100] Balint A, Kim T, Gallo D, J.R. C, Bastos de Oliveira FM, Yimit A, Ou J, Nakato R, Gurevich A, Shirahige K, Smolka MB, Zhang Z, Brown WG. "Assembly of Slx4 Signaling Complexes Behind DNA Replication Forks." EMBO Journal, 2015 Aug 13;34(16)
[99] Li Y, Wang Y, Zhang Z, Zamudio AV and JC Zhao "Genome-wide detection of high abundance N6-methyladenosine sites by microarray" RNA 2015 Aug;21(8):1511-8.
[98] Li Y, and Zhang Z "Computational Biology in microRNA" Wiley Interdiscip Rev RNA. 2015 Jul-Aug;6(4):435-52
[97] Liang C, Li Y, Luo J and Zhang Z "A novel motif-discovery algorithm to identify co-regulatory motifs in large transcription factor and microRNA co-regulatory networks in human " Bioinformatics. 2015 Jul 15;31(14):2348-55.
[96] Jin K, Musso G, Vlasblom J, Jessulat M, Deineko V, Negroni J, Mosca R, Malty R, Nguyen-Tran DH, Aoki H, Minic Z, Freywald T, Phanse S, Xiang Q, Freywald A, Aloy P, Zhang Z*, Babu M.* "Yeast mitochondrial protein-protein interactions reveal diverse complexes and disease-relevant functional relationships." Journal of Proteome Research 2015 Feb 6;14(2):1220-37
[95] Malty R, Jessulat M, Jin K, Musso G, Vlasblom J, Phanse S, Zhang Z, and Babu M "Mitochondrial Targets for Pharmacological Intervention in Human Diseases" Journal of Proteome Research 2015 Jan 2;14(1):5-21 , PMID: 25367773
[94] Wong KC, Li Y, Peng C and Zhang Z "SignalSpider: Probabilistic Pattern Discovery on Multiple Normalized ChIP-Seq Signal Profiles" Bioinformatics 2015 Jan 1;31(1):17-24, PMID: 25192742
[93] Yang L, Wang Y, Zhang Z, He S "Comprehensive transcriptome analysis reveals accelerated genic evolution in a Tibet fish, Gymnodiptychus pachycheilus." Genome Biology and Evolution, 2014 Dec 26. [Epub ahead of print], PMID: 25543049
[92] Li Y, and Zhang Z "Potential microRNA-mediated oncogenic intercellular communication revealed by pan-cancer analysis" Scientific Reports 2014 (In Press )
[91] Cromar, G., Wong, K-C., Loughran, N.B., On, T., Song, H., Xiong, X., Zhang, Z. and Parkinson, J. "New tricks for ‘old’ domains: How novel architectures and promiscuous hubs contributed to the organization and evolution of the ECM" Genome Biology and Evolution 2014 (In Press)
[90] Li Y, Liang M and Zhang Z "Regression Analysis of Combinatorial Gene Expression Regulation in Acute Myeloid Leukemia" PLOS Computational Biology, 2014 October
[89] Li Y, Liang C, Easterbrook S, Luo J, Zhang Z "Investigating functional implication of reinforcing feedback loop in transcriptional regulatory network" Molecular Biosystems, 2014
[88] Li Y, Liang C, Wong KC, Luo J and Zhang Z "Mirsynergy: detecting synergistic miRNA regulatory modules by overlapping neighbourhood expansion" Bioinformatics 2014
[87] Li Y, Liang C, Wong KC, Jin K, and Zhang Z "Inferring probabilistic miRNA-mRNA interaction signatures in cancers: a role-switch approach" Nucleic Acids Research 2014
[86] Li J, Kim T, Nutiu R, Ray D, Hughes TR and Zhang Z "Identifying mRNA Sequence Elements for Target Recognition by Human Argonaute Proteins" Genome Research 2014
[85] Wong KC and Zhang Z "SNPdryad: Predicting Deleterious Non-synonymous Human SNPs Using Only Orthologous Protein Sequences" Bioinformatics 2014
[84] Wang Y, Li Y, Toth JI, Petroski MD, Zhang Z, and Zhao J. "N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells" Nature Cell Biology 2014 (
[83] Zheng D. and Zhang Z "Pseudogene Evolution in the Human Genome" eLS 2013, John Wiley & Sons Ltd: Chicheste [DOI: 10.1002/9780470015902.a0020836.pub2]
[82] Li Y, Goldenberg A, Wong KC, and Zhang Z. "A probabilistic approach to explore human miRNA targetome by integrating miRNA-overexpression data and sequence information" Bioinformatics. Advanced Online October 2013
[81] Zhao D.Y., Li Y., Greenblatt J.F., ang Zhang Z., "ncRNA–Protein Interactions in Development and Diseases from the Perspective of High-Throughput Studies", book chapter in "Systems Analysis of Chromatin-Related Protein Complexes in Cancer", Springer, (In Press)
[80] Choi H*, Jung C*, Sohn S.*3, Kim S., Kim H., Kim Y., Kim T., Zhang Z., Shin E., Lee J., Moon J., Kim S., Kim K., Mun Y., Kim H., Park J., Kim J. and Kim D., "Genome-wide genotype-based risk model for survival in acute myeloid leukemia patients with normal karyotype" British Journal of Haematology 2013 (in press)
[79] Wong KC, Chan TM, Peng C., Li Y., and Zhang Z. "DNA Motif Elucidation using belief propagation" Nucleic Acids Research 2013
[78]Snider J., Hanif A., Lee M.E., Jin K., Yu A.R., Chuk M., Damajanovic D., Graham C., Wierzbicka M., Tang P., Balderes D., Wong V., San Luis B., Shevelev I., Sturley S.L., Boone C., Greenblatt J.F., Babu M., Zhang Z., Paumi C.M., Park H., Michaelis S., and Stagljar I. "Mapping the functional yeast ABC transporter interactome." Nature Chemical Biology 2013 (in press)
[77] Li Y., Zhao D.Y., Greenblatt J., and Zhang Z. "RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments" Nucleic Acids Research, 2013
[76] Li J. and Zhang Z. "microRNA Regulatory Variation in Human Evolution" Trends in Genetics Volume 29, Issue 2, February 2013, Pages 116–124
[75] Yang Z., Dong D., Zhang Z., Crabbe M J C, Wang L and Yang Zhong "Preferential regulation of stably expressed genes in the human genome suggests a widespread expression buffering role of microRNAs" BMC Genomics 2012, 13(Suppl 7):S14
[74] Li J.(e)., Liu Y.(e), Xin X., Kim T., Cabeza, EA, Ren J., Nielsen R., Wrana JL*, Zhang Z* "Evidence for positive selection on a number of microRNA regulatory interactions during recent human evolution" PLoS Genet. 2012 Mar;8(3):e1002578
[73] Jin K., Li J., Vizeacoumar FS., Li Z., Min R., Zamparo L., Vizeacoumar FJ, Datti A., Andrews B.*, Boone C.*, Zhang Z.* "PhenoM: a database of morphological phenotypes caused by mutation of essential genes in Saccharomyces cerevisiae" Nucleic Acids Research, Database Issue (2012)
[72] Li Z., Vizeacoumar FJ, Bahr S., Li J., Warringer J., Vizeacoumar FS, Min R., VanderSluis B., Bellay J., Devit M., Fleming JA, Stephens A., Hasse J., Lin Z., Baryshnikova A., Lu H.m Yan Z., Jin K., Barker S., Datti A.m Giaever G., Nislow C., Bulawa C., Myers CL, Costanzo M., Gingas A., Zhang Z., Blomberg A., Bloom K., Andrews B*., Boone C.* “Systematic Exploration of Essential Yeast Gene Function with Temperature sensitive
Mutants” Nature Biotechnology 2011
[71] Li J., Yuan Z., and Zhang Z. "The cellular robustness by genetic redundancy in budding yeast" PLOS Genetics (2010, November 04)
[70] Dong D., Shao X., Deng N. and Zhang Z. "Differential effects of chromatin regulators and transcription factors on gene regulation: A nucleosomal perspective" Bioinformatics (2010, November)
[69] Turinsky AL, Turner B., Borja R., James Gleeson J. Heath M., Pu S., Switzer T., Dong D., Gong Y., On T., Xiong X., Emili E., Greenblatt J., Parkinson J., Zhang Z., Shoshana WJ "DAnCER: Disease-Annotated Chromatin Epigenetics Resource" Nucleic Acids Research (2011 Database issue)
[68] Dong D., Yuan Z., and Zhang Z. "Evidences and mechanisms for the increased expression variation of duplicate genes in budding yeast: from cis- to trans- regulation effects"
Nucleic Acids Research (2010, October)
[67] Dong D., Shao X., Deng N. and Zhang Z. "Gene expression variations are predictive for stochastic noise" Nucleic Acids Research (2010, September)
[66] Li J., Liu Y., Kim T., Min R., and Zhang Z. "Gene expression variability within and between human populations and implications toward disease susceptibility" PLOS Computational Biology (2010, August)
[65] Li J., Min R., Vizeacoumar FJ, Jin K., Xin X., Zhang Z. "Exploiting the determinants of stochastic gene expression in S. cerevisiae for genome-wide prediction of expression noise" PNAS (2010, May 20)
[64] Min R., van der Maaten L., Yuan Z., Bonner A., Zhang Z. "Deep Supervised T-Distributed Embedding" 27th International Conference on Machine Learning (ICML 2010)
[63] On, T., Xiong, X., Pu, S., Turinsky, A., Gong, Y., Emili, A., Zhang, Z., Greenblatt, J., Wodak, SJ. and Parkinson, J. "The evolutionary landscape of the chromatin modification machinery" Proteins 2010 Jul;78(9):2075-89
[62] Li J., Yuan Z., Zhang Z. "Revisiting the contribution of cis elements to expression divergence between duplicated genes: the role of chromatin structure" Molecular Biology and Evolution (2010, Feb. 5)
[61] Vizeacoumar FJ., van Dyk N., Vizeacoumar FS., Cheung V., Li J., Sydorskyy Y., Case N., Li Z., Datti A., Nislow C., Raught B., Zhang Z., Frey B., Bloom K., Boone C.# and Andrews B.J.# "Integrating High-throughput Genetic Interaction Mapping and High-content Screening to Explore Yeast Spindle Morphogenesis" Journal of Cell Biology, 2010 Jan 11;188(1):69-8
[60] Li R., Fan W., ... Zhang Z., ... Dong D., Cook K., ... Yang H., Wang J., Wang J., (total co-123 authors) "The sequence and de novo assembly of the giant panda genome" Nature 2010 Jan 21;463(7279):311-7. Epub 2009 Dec 1
[59] Li J., Liu Y., Dong D., Zhang Z. "Evolution of an X-linked primate-specific microRNA cluster" Molecular Biology and Evolution 2009 Nov 19. [Epub ahead of print]
[58] Ren J., Jiang C., Gao X., Liu Z., Yuan Z., Jin C., Wen L., Zhang Z.*, Xue Y.*, Yao X.* "PhosSNP:systematic analysis of genetic polymorphisms that influence protein phosphorylation" Molecular & Cell Proteomics, 2009 Dec 8. [Epub ahead of print]
[57] Feng, Z.-P., Zhang, Z., van Kesteren, R.E., Straub, V.A., van Nierop, P., Jin, K., Nejatbakhsh, N., Goldberg, J.I., Spencer, G.E., Yeoman, M.S., Wildering, W., Coorssen, J.R., Croll, R.P., Buck, L., Syed, N.I., Smit, A.B., "Transcriptome analysis of the central nervous system of the mollusc Lymnaea stagnalis" BMC Genomics ( 2009)
[56] Min R., Stanley D.A., Yuan Z., Bonner A., and Zhang Z., "A Deep Non-Linear Feature Mapping for Large-Margin kNN Classification" IEEE International Conference on Data Mining (ICDM 2009)
[55] Li J.*, Min R.*, Bonner A., and Zhang Z., "A Probabilistic Framework to Improve microRNA Target Prediction by Incorporating Proteomics Data" Jounral of Bioinformatics and Computational Biology (2009)
[54] Guo X., Zhang Z., Gerstein M., and Zheng D. "Small RNAs Originated From Pseudogenes, cis- or trans-Acting? " PLOS Computational Biology (2009)
[53] Dong D., He G., Zhang S, and Zhang Z. "Evolution of olfactory receptor genes in primates dominated by birth-and-death process"" Genome Biology and Evolution (2009)
[52] Gong Y., Kakihara Y., Krogan N., Greenblatt J., Emili A., Zhang Z., Houry W. "An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: Implications to protein folding pathways in the cell " Molecular Systems Biology (2009)
[51] Kittanakom S, Chuk M, Wong V, Snyder J, Edmonds D, Lydakis A, Zhang Z, Auerbach D, Stagljar I. "Analysis of membrane protein complexes using the split-ubiquitin membrane yeast two-hybrid system." Methods in Molecular Biology (2009) 548:247-71
[50] Min R., Kuang R., Bonner A., and Zhang Z. "Learning Random-Walk Kernels for Protein Remote Homology Identification and Motif Discovery" SIAM International Conference on Data Mining (SDM09) (2009)
[49] Min R., Bonner A., Li J., and Zhang Z. "Learned Random-Walk Kernels and Empirical-Map Kernels for Protein Sequence Classification" Journal of Computational Biology (2009)
[48] Li J., Musso G., and Zhang Z. "Preferential regulation of duplicated genes by microRNAs in mammals" Genome Biology (2008)
[47] Borozan I., Chen L., Heathcote E.J., Edwards A., Katze M., Zhang Z. and I. McGilvray "MAID : An effect size based model for microarray data integration across laboratories and platforms" BMC Bioinformatcs (2008)
[46] Musso G., Costanzo M., Huangfu M., Smith A.M., Paw J., San Luis B., Boone C., Giaever G., Nislow C., Emili A.*, Zhang Z.*
"The extensive and condition-dependent nature of epistasis among whole-genome-duplicates in yeast"
Genome Research (2008)
[45] Gong Y., Zhang Z.
"Global robustness and identifiability of random, scale-free and small-world networks. " Annals of the New York Academy of Sciences (2008)
[44] Davids W., Zhang Z.,
"The impact of horizontal gene transfer in shaping operons and protein interaction networks in E. coli - direct evidence of preferential attachment"
BMC Evolutionary Biology (2008 )
[43] Gunewardena S., Zhang Z.,
"A Hybrid Model for Robust Detection of Transcription Factor Binding Sites"
Bioinformatics (2008)
[42] Zheng D., Zhang Z.,
"Pseudogene Evolution In the Human Genome"
Chapter in Handbook of Human Molecular Evolution, (John Wiley & Sons)
[41]Min R., Bonner A., and Zhang Z.,
"Modifying Kernels Using Label Information Improves SVM Classification Performance"
International Conference on Machine Learning and Applications (ICMLA 2007)
[40] Gong Y., Zhang Z.
"Alternative pathway approach for automating analysis and validation of cell perturbation networks and design of perturbation experiments"
Annals of the New York Academy of Sciences (2007)
[39] Gong Y., Zhang Z.
"CellFrame: a data structure for abstraction of cell biology experiments and construction of perturbation network"
Annals of the New York Academy of Sciences (2007)
[38] Musso G., Zhang Z., and Emili A.,
"Experimental and Computational Procedures for the Assessment of Protein Complexes on a Genome-wide Scale "
Chemical Reviews (2007)
[37] Mockli N., Deplazes A., Hassa P.O., Zhang Z., Peter M., Hottiger M.O., Stagljar I., Auerbach
"A yeast split-ubiquitin based cytosolic screening system (cytoY2H) to detect interactions between transcriptionally active proteins. "
Biotechniques (2007)
[36] Musso G., Zhang Z.*, and Emili A.*,
"Retention of protein-protein interactions by ancient duplicated gene products in budding yeast"
Trends in Genetics (2007)
[35] Karro J., Yan Y., Zheng D., Zhang Z., Cariero N., Harrison P., and
Gerstein M. “Pseudogene.org: A comprehensive database and
comparison platform for pseudogene annotation” Nucleic Acids
Research (2007, database issue)
[34] Zhang Z.*, Pang A., Gerstein M. "Comparative analysis of genome
tiling array data reveals many novel primatespecificfunctional RNAs in
human. " BMC Evolutionary Biology (2007)
[33] Zhang Z., Carriero N., Zheng D., Karro J., Harrison P.M., Gerstein
M., “PseudoPipe: an automated pseudogene identification
pipeline” Bioinformatics (2006) 15;22(12):1437-9
[32] Gunewardena S.S.A, Jeavons, P. and Zhang, Z., "Finding
transcription factor binding sites in DNA sequences: a template based
approach" Journal of Computational Biology (2006) Vol. 13, No. 4:
929-945
[31] Gunewardena S.S.A and Zhang, Z., “Accounting For Physical
properties And Nucleotide Polymorphisms in the Quantitative Prediction
of DNA-protein Interactions” Pacific Symposium of Biocomputing
2006
[30] Gong Y. and Zhang Z., “Alternative signaling pathways: when,
where and why?” FEBS Letters (2005) 579(24) 5265:5274
[29] Gunewardena S.S.A and Zhang, Z., “Finding Transcription
Factor Binding Sites in DNA Sequences: A Template Based
Approach.” Proceedings of the 13th IEEE Workshop on Statistical
Signal Processing (SSP'05), Bordeaux, France, July 2005.
-- At Yale --
[28] Harrison, P., Zheng, D., Zhang, Z., Gerstein, M., "Transcribed
processed pseudogenes in the human genome: An intermediate form of
expressed retrosequence lacking protein-coding ability." Nucleic Acids
Research (2005) 33(8):2374-83
[27] Zheng, D., Zhang, Z., Harrison, P.M., Karro, J., Carriero, N., and
Gerstein M., "Integrated Pseudogene Annotation for Human Chromosome 22:
Evidence for Transcription." Journal of Molecular Biology (2005)
349(1):27-45
[26] Zhang, Z. and Gerstein, M., “Large-scale Analysis of
Pseudogenes in the Human Genome.” Current Opinion in Genetics
& Development (2004) 14(4):328-35
[25] Lehnert, U., Xia, Y., Royce T., Goh, C., Liu, Y., Senes, A., Yu,
H., Zhang, Z., Engelman, D.M., and Gerstein, M., “Computational
analysis of membrane proteins: genomic occurrence, structure prediction
and helix interactions.” Quarterly Reviews of Biophysics(2004)
[24] Zhang, Z. and Gerstein, M., “Comparative analysis of
processed pseudogenes in the mouse and human genomes.” Trends in
Genetics(2004) 20:2 62-65
[23] Zhang, Z., Harrison, P., and Gerstein, M., “Millions of
years of evolution preserved: a comprehensive catalogue of over 8000
pseudogenes in the human genome.” Genome Research (2003)
13:2541-2558
[22] Zhang, Z. and Gerstein, M. “Reconstructing Genetic Networks
in Yeast.” Nature Biotechnology(2003) 21(11): 1295-97
[21] Zhang, Z. and Gerstein, M., “Patterns of nucleotide
substitutions, insertions and deletions in the human genome as inferred
from human pseudogenes.” Nucleic Acids Research (2003) 31 (18):
5338-48.
[20] Zhang, Z. and Gerstein, M., “Of mice and men: Phylogenetic
footprinting Aids Regulatory Elements Discovery.” Journal of
Biology(2003) 2:11
[19] Zhang, Z. and Gerstein, M., “The human genome has 49
cytochrome cpseudogenes, including a relic of a primordial gene that
still functions in mouse.” Gene(2003) 312:61-72
[18] Harrison, P., Zhang Z., Milburn, D. and Gerstein, M.,
“Identification of pseudogenes in the Drosophila
melanogastergenome.” Nucleic Acids Research(2003) 31:1033-37
[17] Zhang, Z. and Gerstein, M., “Mapping and characterization of
over 100 mitochondrial ribosomal protein pseudogenes in the human
genome.” Genomics(2003) 81:468-80
[16] Zhang, Z., Harrison, P. and Gerstein, M., “Identification
and analysis of over 2000 ribosomal protein pseudogenes in the human
genome and implications for retrotransposition.” Genome
Research(2002) 12: 1466-82
[15] Zhang, Z., Harrison, P., and Gerstein, M., “Digging Deep for
Ancient Relics: A Survey of Protein Motifs in the Intergenic Sequences
of Four Eukaryotic Genomes.” Journal of Molecular Biology(2002)
323: 811-22.
[14] Liu, Y., Luscombe, N., Alexandrov, V., Bertone, P., Harrison, P.,
Zhang, Z., and Gerstein, M., “Structure genomics: a new era for
pharmaceutical research.” Genome Biology(2002) 3(2)
[13] Luscombe, N.M., Qian, J., Zhang, Z., Johnson, T., and Gerstein,
M., “Power-law behavior applies to a wide variety of genomic
properties.” Genome Biology(2002) 25; 3 (8).
[12] Echols, N., Harrison, P., Balasubramanian, S., Bertone, P.,
Johnson, T., Luscombe, N., Zhang, Z., and Gerstein, M.,
“Comprehensive analysis of amino acid and nucleotide composition
in eukaryotic genomes, comparing genes and pseudogenes.” Nucleic
Acids Research (2002) 30:10
[11] Balasubramanian, S., Harrison, P., Hegyi, H., Bertone, P.,
Luscombe, N., Echols, N., McGarvey, P., Zhang, Z., and Gerstein, M.,
“SNPs on human chromosome 21 and 22 – analysis in terms of
protein features and pseudogenes.” Pharmacogenomics(2002)
3(3).
-- At Berkeley --
[10] Zhang, Z. “Crystal structural studies of avian mitochondrial
cytochrome bc1 complex.” Ph.D. Dissertation, UC Berkeley, 2000
[9] Berry, E., Zhang, Z., Bellamy, H., and Huang, L.,
“Crystallographic location of two Zn (2+)-binding sites in the
avian cytochrome bc (1) complex.” Biochim Biophys Acta(2000) 1459
(2-3): 440-48.
[8] Zhang, Z., Berry, E., Huang, L., and Kim, S. -H.,
“Mitochondrial cytochrome bc1 complex.” Book chapter in
Subcellular Biochemistry, volume 36. Plenum (2000) U.K.
[7] Chi, Y, Huang, L., Zhang, Z., Fernandez-Velasco, J., and Berry, E.,
“High resolution structure of a truncated form of cytochrome
from Chlamydomonas reinhardtii.” Biochemistry (2000) 4; 39(26):
7689-701.
[6] Berry, E., Huang, L., Zhang, Z., and Kim S. -H., “Structure
of the avian mitochondrial cytochrome bc1 complex.” J. Bioenerg.
Biomembr. (1999) 3:177-90
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