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Molecular Genetics
CGPGBB
Donnelly CCBR
U of Toronto

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Publications


2014

  • 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

  • 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 (In Press)

  • Wong KC and Zhang Z "SNPdryad: Predicting Deleterious Non-synonymous Human SNPs Using Only Orthologous Protein Sequences" Bioinformatics 2014

  • 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

2013

  • Zheng D. and Zhang Z "Pseudogene Evolution in the Human Genome" eLS 2013, John Wiley & Sons Ltd: Chicheste

  • 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 October 2013 (Advanced Online)

  • 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, 2013 (in press)

  • 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)

  • Wong KC, Chan TM, Peng C., Li Y., and Zhang Z. "DNA Motif Elucidation using belief propagation" Nucleic Acids Research. Advanced Online June 2013

  • 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)

  • 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, Advanced Online February 2013 RIPSeeker on Bioconductor

  • Li J. and Zhang Z. "microRNA Regulatory Variation in Human Evolution" Trends in Genetics Volume 29, Issue 2, February 2013, Pages 116–124

2012

  • 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

  • Li Ji(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

  • 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) PhenoM Database

2011

  • Gong Y, Zhang Z, Houry WA. "Bioinformatic approach to identify chaperone pathway relationship from large-scale interaction networks." Methods in Molecular Biology, ( 2011)

  • 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., 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 Biotech (2011)

  • Musso G., Emili A., Zhang Z. "Characterization and evolutionary analysis of protein-protein interaction networks", book chapter in Evolutionary Genomics: Statistical and computational methods, (Springer-Humana, 2011)

  • Musso G., Emili A., Zhang Z. "Filtering and interpreting large-scale experimental protein-protein interaction data", book chapter in Network Biology: Methods and Protocols, (Springer-Humana, 2011)

  • Dong D., Shao X., and Zhang Z. "Differential effects of chromatin regulators and transcription factors on gene regulation: A nucleosomal perspective" Bioinformatics 2011 Jan 15;27(2):147-52. Epub 2010 Nov 11.

  • 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 Jan;39(Database issue):D889-94. Epub 2010 Sep 28.

  • Dong D., Shao X., Deng N. and Zhang Z. "Gene expression variations are predictive for stochastic noise" Nucleic Acids Research, 2011 Jan 1;39(2):403-13. Epub 2010 Sep 21.

2010

  • Li J, Yuan Z., Zhang Z., "The Cellular Robustness by Genetic Redundancy in Budding Yeast" PLOS Genetics, 2010 Nov 4;6(11):e1001187.

  • 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 Oct 8

  • 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 Aug 26;6(8).

  • 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 Jun 8;107(23):10472-7. Epub 2010 May 20

  • 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)

  • 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

  • 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. [Epub ahead of print]

  • 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

  • Li R., Fan W., ... Zhang Z., ... Dong D., Cook K., ... Yang H., Wang J., Wang J., (total 123 co-authors) "The sequence and de novo assembly of the giant panda genome" Nature 2010 Jan 21;463(7279):311-7. Epub 2009 Dec 1

  • Li J., Liu Y., Dong D., Zhang Z. "Evolution of an X-linked primate-specific microRNA cluster" Molecular Biology and Evolution 2010 27(3):671-683

  • 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, 2010, [Epub 2009 Dec 8.]

2009

  • 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) www.lymnaea.org

  • 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)

  • Li J.*, Min R.*, Bonner A., and Zhang Z., "A Probabilistic Framework to Improve microRNA Target Prediction by Incorporating Proteomics Data" Journal of Bioinformatics and Computational Biology (2009)

  • Guo X., Zhang Z., Gerstein M., and Zheng D. "Small RNAs Originated From Pseudogenes, cis- or trans-Acting? " PLOS Computational Biology (2009)

  • 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)

  • 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)

  • 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)

  • 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

  • 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) (full paper)

2008

  • Li J., Musso G., and Zhang Z. "Preferential regulation of duplicated genes by microRNAs in mammals" Genome Biology (2008)

  • 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)

  • 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)

  • 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) Proceedings of the 2nd Dialogue for Reverse Engineering Assessments and Methods Workshop (DREAM), December 7-8, 2007, New York, NY

  • 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)
  • Gunewardena S., Zhang Z., "A Hybrid Model for Robust Detection of Transcription Factor Binding Sites" Bioinformatics (2008) 24(4):484-491
  • Zheng D., Zhang Z., "Pseudogene Evolution In the Human Genome" Chapter in Handbook of Human Molecular Evolution, (John Wiley & Sons)

2007

  • 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)

  • 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) Proceedings of the 1st Dialogue for Reverse Engineering Assessments and Methods Workshop (DREAM), September 7-8, 2006, New York, NY

  • 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) Proceedings of the 1st Dialogue for Reverse Engineering Assessments and Methods Workshop (DREAM), September 7-8, 2006, New York, NY

  • 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)

  • Mockli N., Deplazes A., Hassa P.O., Zhang Z., Peter M., Hottiger M.O., Stagljar I., Auerbach D. "A yeast split-ubiquitin based cytosolic screening system (cytoY2H) to detect interactions between transcriptionally active proteins." Biotechniques (2007)

  • Musso G., Zhang Z.*, and Emili A.*, "Retention of protein-protein interactions by ancient duplicated gene products in budding yeast " Trends in Genetics (2007) 23(6):266-269

  • *Zhang Z., Pang A., Gerstein M. "Comparative analysis of genome tiling array data reveals many novel primatespecificfunctional RNAs in human. " BMC Evolutionary Biology (2007) Feb 8;7 Suppl 1:S14.

  • 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)

2006

  • 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 (Open Access)

  • Gunewardena S.S.A, Jeavons, P. and Zhang, Z., "Enhancing the Prediction of Transcription Factor Binding Sites by Incorporating Structural Properties and Nucleotide Covariations " Journal of Computational Biology (2006) Vol. 13, No. 4: 929-945 (Pubmed)

  • 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 (PSB 2006)

2005

  • Gong Y. and Zhang Z., "Alternative signaling pathways: when, where and why?" FEBS Letters (2005) 579(24)5265:5274 (Open Access)

  • Gunewardena S.S.A and Zhang, Z., " Finding Transcription Factor Binding Sites in DNA Sequences : A Template Based Approach." In Proceedings of the 13th IEEE Workshop on Statistical Signal Processing (SSP'05), Bordeaux, France, July 2005.

  • 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 [Pubmed] [PDF]

  • 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 [Pubmed] [PDF]

2004

  • Zhang, Z. and Gerstein, M., "Large-scale Analysis of Pseudogenes in the Human Genome." Current Opinion in Genetics & Development (2004) 14(4):328-35 [Pubmed][PDF]

  • 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)

  • Zhang, Z. and Gerstein, M., "Comparative analysis of processed pseudogenes in the mouse and human genomes." Trends in Genetics (2004) 20:2 62-65 [Pubmed][PDF]

2003

  • 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 [Pubmed][PDF]

  • Zhang, Z. and Gerstein, M. "Reconstructing Genetic Networks in Yeast." Nature Biotechnology (2003) 21(11): 1295-97 [Pubmed][PDF]

  • 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 [Pubmed][PDF]

  • Zhang, Z. and Gerstein, M., "Of mice and men: Phylogenetic footprinting Aids Regulatory Elements Discovery." Journal of Biology (2003) 2:11 [Pubmed][PDF]

  • Zhang, Z. and Gerstein, M., "The human genome has 49 cytochrome c pseudogenes, including a relic of a primordial gene that still functions in mouse." Gene (2003) 312:61-72 [Pubmed][PDF]

  • Harrison, P., Zhang Z., Milburn, D. and Gerstein, M., "Identification of pseudogenes in the Drosophila melanogaster genome." Nucleic Acids Research (2003) 31:1033-37 [Pubmed][PDF]

  • Zhang, Z. and Gerstein, M., "Mapping and characterization of over 100 mitochondrial ribosomal protein pseudogenes in the human genome." Genomics (2003) 81:468-80 [Pubmed][PDF]

2002

  • 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 [Pubmed][PDF]

  • 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. [Pubmed][PDF]

  • 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) [Pubmed][PDF]

  • 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) [Pubmed][PDF]

  • 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 [Pubmed][PDF]

  • 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) [Pubmed][PDF]

2000

  • Zhang, Z. "Crystal structural studies of avian mitochondrial cytochrome bc1 complex." Ph.D. Dissertation, UC Berkeley, 2000 [Abstract]

  • 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. [Pubmed][PDF]

  • 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. [Pubmed]

  • Chi, Y, Huang, L., Zhang, Z., Fernandez-Velasco, J., and Berry, E., "High resolution structure of a truncated form of cytochrome f from Chlamydomonas reinhardtii." Biochemistry (2000) 4; 39(26): 7689-701 [Pubmed][PDF]

1999

  • 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 [Pubmed][PDF]

  • Crofts, A.R., Guergova-Kuras, M., Huang, L., Kuras, R., Zhang, Z., and Berry, E., "The mechanism of ubiquinol oxidation by the bc1 complex: the role of the iron sulfur protein, and its mobility." Biochemistry (1999) 38(48): 15791-15806. [Pubmed][PDF]

  • Crofts, A., Hong, S., Zhang, Z., and Berry, E., "Physicochemical aspects of the movement of the Rieske iron sulfur protein during quinol oxidation by the bc1 complex." Biochemistry (1999) 38(48): 15827-39. [Pubmed][PDF]

  • Berry, E., Zhang, Z., Huang, L., and Kim, S. -H., "Structures of quinone-binding sites in be complexes: functional implications." Biochemical Society Transactions (1999) 27(4): 565-72. [Pubmed]

1998

  • Saribas, A.S., Valkova-Valchanova, M., Tokito, M.K., Zhang, Z., Berry, E., and Daldal, F., "Interactions between the cytochrome b, cytochrome c1, and Fe-S protein subunits at the ubihydroquinone oxidation site of the bc1 complex of Rhodobacter capsulatus." Biochemistry (1998) 37(22): 8105-14. [Pubmed] [PDF]

  • Zhang, Z., Huang, L., Shulmeister, V.M., Chi, Y., Kim, KK. Hung, L.-W., Crofts, A.R., Berry, E., and Kim, S. -H., "Electron transfer by domain movement in cytochrome bc1" Nature (1998) 392 (6677): 677-84 [Pubmed] [PDF][Summary]