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Zhaolei Zhang

Research Profile

Occupations

Computational Biology

Genes & Molecular Sequences

Concepts & Ideas

Procedures

Living Beings

Phenomena

Evolution, Molecular

Chemicals & Drugs

Activities & Behaviors

Software

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Publications

TOP 3
Yue Li; Jack F Greenblatt; Dorothy Yanling Zhao; Zhaolei Zhang
RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments.
Jingjing Li; Zhaolei Zhang
miRNA regulatory variation in human evolution.
Zhen Yang; Zhaolei Zhang; M James C Crabbe; Dong Dong; Li Wang; Yang Zhong
Preferential regulation of stably expressed genes in the human genome suggests a widespread expression buffering role of microRNAs.

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All Publications

2013: Yue Li; Jack F Greenblatt; Dorothy Yanling Zhao; Zhaolei Zhang
RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments.
Nucleic acids research 2013;41(8):e94.
2013: Jingjing Li; Zhaolei Zhang
miRNA regulatory variation in human evolution.
Trends in genetics : TIG 2013;29(2):116-24.
2012: Zhen Yang; Zhaolei Zhang; M James C Crabbe; Dong Dong; Li Wang; 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.
2012: Jingjing Li; Yu Liu; Rasmus Nielsen; Jie Ren; Jeffrey L Wrana; Xiaofeng Xin; Eduardo Aguiar Cabeza; Taehyung Simon Kim; Zhaolei Zhang
Evidence for positive selection on a number of MicroRNA regulatory interactions during recent human evolution.
PLoS genetics 2012;8(3):e1002578.
2012: Gabriel Musso; Andrew Emili; Zhaolei Zhang
Characterization and evolutionary analysis of protein-protein interaction networks.
Methods in molecular biology (Clifton, N.J.) 2012;856():363-80.
2012: Ke Jin; Jingjing Li; Zhijian Li; Renqiang Min; Frederick S Vizeacoumar; Franco Vizeacoumar; Lee Zamparo; Brenda Andrews; Charles Boone; Alessandro Datti; Zhaolei Zhang
PhenoM: a database of morphological phenotypes caused by mutation of essential genes in Saccharomyces cerevisiae.
Nucleic acids research 2012;40(Database issue):D687-94.
2011: Zhaolei Zhang; Elaine Lanza; A Catharine Ross; Paul S Albert; N H Colburn; Michael J Rovine; D Bagshaw; Jan S Ulbrecht; Terryl J Hartman
A high-legume low-glycemic index diet reduces fasting plasma leptin in middle-aged insulin-resistant and -sensitive men.
European journal of clinical nutrition 2011;65(3):415-8.
2011: Dong Dong; Zineng Yuan; Zhaolei Zhang
Evidences for increased expression variation of duplicate genes in budding yeast: from cis- to trans-regulation effects.
Nucleic acids research 2011;39(3):837-47.
2011: Dong Dong; Xiaojian Shao; Zhaolei Zhang
Differential effects of chromatin regulators and transcription factors on gene regulation: a nucleosomal perspective.
Bioinformatics (Oxford, England) 2011;27(2):147-52.
2011: Yunchen Gong; Zhaolei Zhang; Walid A Houry
Bioinformatic approach to identify chaperone pathway relationship from large-scale interaction networks.
Methods in molecular biology (Clifton, N.J.) 2011;787():189-203.
2011: Gabriel Musso; Andrew Emili; Zhaolei Zhang
Filtering and interpreting large-scale experimental protein-protein interaction data.
Methods in molecular biology (Clifton, N.J.) 2011;781():295-309.
2011: Andrei L Turinsky; Brian Turner; Rosanne C Borja; James A Gleeson; Michael Heath; Shuye Pu; Thomas Switzer; Dong Dong; Yunchen Gong; Tuan On; Xuejian Xiong; Andrew Emili; Jack Greenblatt; John Parkinson; Zhaolei Zhang; Shoshana J Wodak
DAnCER: disease-annotated chromatin epigenetics resource.
Nucleic acids research 2011;39(Database issue):D889-94.
2011: Dong Dong; Xiaojian Shao; Naiyang Deng; Zhaolei Zhang
Gene expression variations are predictive for stochastic noise.
Nucleic acids research 2011;39(2):403-13.
2010: Alexie M Kolpak; F J Walker; J W Reiner; Y Segal; D Su; M S Sawicki; C C Broadbridge; Zhaolei Zhang; Y Zhu; C H Ahn; Sohrab Ismail-Beigi
Interface-induced polarization and inhibition of ferroelectricity in epitaxial SrTiO₃/Si.
Physical review letters 2010;105(21):217601.
2010: Jingjing Li; Zineng Yuan; Zhaolei Zhang
The cellular robustness by genetic redundancy in budding yeast.
PLoS genetics 2010;6(11):e1001187.
2010: Tuan On; Xuejian Xiong; Shuye Pu; Andrei Turinsky; Yunchen Gong; Andrew Emili; Zhaolei Zhang; Jack Greenblatt; Shoshana J Wodak; John Parkinson
The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses.
Proteins 2010;78(9):2075-89.
2010: Jingjing Li; Zineng Yuan; Zhaolei Zhang
Revisiting the contribution of cis-elements to expression divergence between duplicated genes: the role of chromatin structure.
Molecular biology and evolution 2010;27(7):1461-6.
2010: Jingjing Li; Renqiang Min; Franco Vizeacoumar; Ke Jin; Xiaofeng Xin; Zhaolei Zhang
Exploiting the determinants of stochastic gene expression in Saccharomyces cerevisiae for genome-wide prediction of expression noise.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(23):10472-7.
2010: Jian Ren; Chunhui Jiang; Xinjiao Gao; Zexian Liu; Zineng Yuan; Changjiang Jin; Longping Wen; Zhaolei Zhang; Yu Xue; Xuebiao Yao
PhosSNP for systematic analysis of genetic polymorphisms that influence protein phosphorylation.
Molecular & cellular proteomics : MCP 2010;9(4):623-34.
2010: C A F Vaz; J Hoffman; Y Segal; J W Reiner; R D Grober; Zhaolei Zhang; C H Ahn; F J Walker
Origin of the magnetoelectric coupling effect in Pb(Zr0.2Ti0.8)O{3}/La{0.8}Sr{0.2}MnO{3} Multiferroic heterostructures.
Physical review letters 2010;104(12):127202.
2010: Jingjing Li; Yu Liu; Dong Dong; Zhaolei Zhang
Evolution of an X-linked primate-specific micro RNA cluster.
Molecular biology and evolution 2010;27(3):671-83.
2010: Franco Vizeacoumar; Nydia van Dyk; Frederick S Vizeacoumar; Vincent Cheung; Jingjing Li; Yaroslav Sydorskyy; Nicolle Case; Zhijian Li; Alessandro Datti; Corey Nislow; Brian Raught; Zhaolei Zhang; Brendan Frey; Kerry Bloom; Charles Boone; Brenda J Andrews
Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis.
The Journal of cell biology 2010;188(1):69-81.
2010: Shuye Pu; Andrei L Turinsky; James Vlasblom; Tuan On; Xuejian Xiong; Andrew Emili; Zhaolei Zhang; Jack Greenblatt; John Parkinson; Shoshana J Wodak
Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human.
PloS one 2010;5(11):e14122.
2010: Jingjing Li; Yu Liu; Taehyung Kim; Renqiang Min; Zhaolei Zhang
Gene expression variability within and between human populations and implications toward disease susceptibility.
PLoS computational biology 2010;6(8):.
2010: Jian Ren; Zexian Liu; Xinjiao Gao; Changjiang Jin; Mingliang Ye; Hanfa Zou; Longping Wen; Zhaolei Zhang; Yu Xue; Xuebiao Yao
MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore.
Nucleic acids research 2010;38(Database issue):D155-60.
2009: Jingjing Li; Renqiang Min; Anthony Bonner; Zhaolei Zhang
A probabilistic framework to improve microrna target prediction by incorporating proteomics data.
Journal of bioinformatics and computational biology 2009;7(6):955-72.
2009: Xingyi Guo; Zhaolei Zhang; Mark B Gerstein; Deyou Zheng
Small RNAs originated from pseudogenes: cis- or trans-acting?
PLoS computational biology 2009;5(7):e1000449.
2009: Y Segal; J W Reiner; A M Kolpak; Zhaolei Zhang; Sohrab Ismail-Beigi; C H Ahn; F J Walker
Atomic structure of the epitaxial BaO/Si(001) interface.
Physical review letters 2009;102(11):116101.
2009: Yunchen Gong; Zhaolei Zhang
Global robustness and identifiability of random, scale-free, and small-world networks.
Annals of the New York Academy of Sciences 2009;1158():82-92.
2009: Renqiang Min; Anthony Bonner; Jingjing Li; Zhaolei Zhang
Learned random-walk kernels and empirical-map kernels for protein sequence classification.
Journal of computational biology : a journal of computational molecular cell biology 2009;16(3):457-74.
2009: Dong Dong; Guimei He; Shuyi Zhang; Zhaolei Zhang
Evolution of olfactory receptor genes in primates dominated by birth-and-death process.
Genome biology and evolution 2009;1():258-64.
2009: Zhong-Ping Feng; Zhaolei Zhang; R E van Kesteren; V A Straub; P van Nierop; K Jin; N Nejatbakhsh; J I Goldberg; G E Spencer; M S Yeoman; W Wildering; J R Coorssen; R P Croll; Leslie Thomas Buck; N I Syed; A B Smit
Transcriptome analysis of the central nervous system of the mollusc Lymnaea stagnalis.
BMC genomics 2009;10():451.
2009: Yunchen Gong; Yoshito Kakihara; Nevan J Krogan; Jack Greenblatt; Andrew Emili; Zhaolei Zhang; Walid A Houry
An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell.
Molecular systems biology 2009;5():275.
2009: Saranya Kittanakom; Matthew Chuk; Victoria Wong; Jamie Snyder; Dawn Edmonds; Apostolos Lydakis; Zhaolei Zhang; Daniel Auerbach; Igor Stagljar
Analysis of membrane protein complexes using the split-ubiquitin membrane yeast two-hybrid (MYTH) system.
Methods in molecular biology (Clifton, N.J.) 2009;548():247-71.
2008: Gabriel Musso; Michael Costanzo; Manqin Huangfu; Andrew M Smith; Jadine Paw; Bryan-Joseph San Luis; Charles Boone; Guri Giaever; Corey Nislow; Andrew Emili; Zhaolei Zhang
The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast.
Genome research 2008;18(7):1092-9.
2008: Sumedha Gunewardena; Zhaolei Zhang
A hybrid model for robust detection of transcription factor binding sites.
Bioinformatics (Oxford, England) 2008;24(4):484-91.
2008: Jingjing Li; Gabriel Musso; Zhaolei Zhang
Preferential regulation of duplicated genes by microRNAs in mammals.
Genome biology 2008;9(8):R132.
2008: Ivan Borozan; limin chen; Bryan Paeper; Jenny Heathcote; Aled M Edwards; Michael Katze; Zhaolei Zhang; Ian D McGilvray
MAID : an effect size based model for microarray data integration across laboratories and platforms.
BMC bioinformatics 2008;9():305.
2008: Wagied Davids; Zhaolei Zhang
The impact of horizontal gene transfer in shaping operons and protein interaction networks--direct evidence of preferential attachment.
BMC evolutionary biology 2008;8():23.
2007: Yunchen Gong; Zhaolei Zhang
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;1115():267-85.
2007: Yunchen Gong; Zhaolei Zhang
CellFrame: a data structure for abstraction of cell biology experiments and construction of perturbation networks.
Annals of the New York Academy of Sciences 2007;1115():249-66.
2007: Gabriel A Musso; Zhaolei Zhang; Andrew Emili
Experimental and computational procedures for the assessment of protein complexes on a genome-wide scale.
Chemical reviews 2007;107(8):3585-600.
2007: Natalie Möckli; Anna Deplazes; Paul O Hassa; Zhaolei Zhang; Matthias Peter; Michael Hottiger; Igor Stagljar; Stephan Keller
Yeast split-ubiquitin-based cytosolic screening system to detect interactions between transcriptionally active proteins.
BioTechniques 2007;42(6):725-30.
2007: Gabriel Musso; Zhaolei Zhang; Andrew Emili
Retention of protein complex membership by ancient duplicated gene products in budding yeast.
Trends in genetics : TIG 2007;23(6):266-9.
2007: Zhaolei Zhang; Andy Wing Chun Pang; Mark Gerstein
Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human.
BMC evolutionary biology 2007;7 Suppl 1():S14.
2007: John Karro; Yangpan Yan; Deyou Zheng; Zhaolei Zhang; Nicholas Carriero; Philip Cayting; Paul Harrrison; Mark Gerstein
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation.
Nucleic acids research 2007;35(Database issue):D55-60.
2006: Zhaolei Zhang; Nicholas Carriero; Deyou Zheng; John Karro; Paul M Harrison; Mark Gerstein
PseudoPipe: an automated pseudogene identification pipeline.
Bioinformatics (Oxford, England) 2006;22(12):1437-9.
2006: Sumedha Gunewardena; Peter Jeavons; Zhaolei Zhang
Enhancing the prediction of transcription factor binding sites by incorporating structural properties and nucleotide covariations.
Journal of computational biology : a journal of computational molecular cell biology 2006;13(4):929-45.
2006: Sumedha Gunewardena; Zhaolei Zhang
Accounting for structural properties and nucleotide co-variations in the quantitative prediction of binding affinities of protein-DNA interactions.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2006;():379-90.
2005: Yunchen Gong; Zhaolei Zhang
Alternative signaling pathways: when, where and why?
FEBS letters 2005;579(24):5265-74.
2005: Deyou Zheng; Zhaolei Zhang; Paul M Harrison; John Karro; Nicholas Carriero; Mark Gerstein
Integrated pseudogene annotation for human chromosome 22: evidence for transcription.
Journal of molecular biology 2005;349(1):27-45.
2005: Paul M Harrison; Deyou Zheng; Zhaolei Zhang; Nicholas Carriero; Mark Gerstein
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.
2004: Zhaolei Zhang; Mark Gerstein
Large-scale analysis of pseudogenes in the human genome.
Current opinion in genetics & development 2004;14(4):328-35.
2004: Zhaolei Zhang; Nicholas Carriero; Mark Gerstein
Comparative analysis of processed pseudogenes in the mouse and human genomes.
Trends in genetics : TIG 2004;20(2):62-7.
2003: Zhaolei Zhang; Paul M Harrison; Yin Liu; Mark Gerstein
Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome.
Genome research 2003;13(12):2541-58.
2003: Zhaolei Zhang; Mark Gerstein
Reconstructing genetic networks in yeast.
Nature biotechnology 2003;21(11):1295-7.
2003: Zhaolei Zhang; Mark Gerstein
Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes.
Nucleic acids research 2003;31(18):5338-48.
2003: Zhaolei Zhang; Mark Gerstein
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.
2003: Zhaolei Zhang; Mark Gerstein
Identification and characterization of over 100 mitochondrial ribosomal protein pseudogenes in the human genome.
Genomics 2003;81(5):468-80.
2003: Paul M Harrison; Duncan Milburn; Zhaolei Zhang; Paul Bertone; Mark Gerstein
Identification of pseudogenes in the Drosophila melanogaster genome.
Nucleic acids research 2003;31(3):1033-7.
2003: Zhaolei Zhang; Mark Gerstein
Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements.
Journal of biology 2003;2(2):11.
2002: Zhaolei Zhang; Paul Harrison; Mark Gerstein
Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome.
Genome research 2002;12(10):1466-82.
2002: Nicholas M Luscombe; Jiang Qian; Zhaolei Zhang; Ted Johnson; Mark Gerstein
The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties.
Genome biology 2002;3(8):RESEARCH0040.
2002: Nathaniel Echols; Paul Harrison; Suganthi Balasubramanian; Nicholas M Luscombe; Paul Bertone; Zhaolei Zhang; Mark Gerstein
Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes.
Nucleic acids research 2002;30(11):2515-23.
2002: Suganthi Balasubramanian; Paul Harrison; Hedi Hegyi; Paul Bertone; Nicholas M Luscombe; Nathaniel Echols; Patrick McGarvey; Zhaolei Zhang; Mark Gerstein
SNPs on human chromosomes 21 and 22 -- analysis in terms of protein features and pseudogenes.
Pharmacogenomics 2002;3(3):393-402.
2002: Yang Liu; Nicholas M Luscombe; Vadim Alexandrov; Paul Bertone; Paul Harrison; Zhaolei Zhang; Mark Gerstein
Structural genomics: a new era for pharmaceutical research.
Genome biology 2002;3(2):REPORTS4004.
2000: Liliana Florea; Cathy Riemer; Scott Schwartz; Zhaolei Zhang; Nikola Stojanovic; Webb Miller; Michael McClelland
Web-based visualization tools for bacterial genome alignments.
Nucleic acids research 2000;28(18):3486-96.
2000: Scott Schwartz; Zhaolei Zhang; K A Frazer; Arian Smit; Cathy Riemer; John Bouck; Richard Gibbs; Ross C Hardison; Webb Miller
PipMaker--a web server for aligning two genomic DNA sequences.
Genome research 2000;10(4):577-86.
2000: Piotr Berman; Zhaolei Zhang; Y I Wolf; Eugene V Koonin; Webb Miller
Winnowing sequences from a database search.
Journal of computational biology : a journal of computational molecular cell biology 2000;7(1-2):293-302.
2000: Zhaolei Zhang; S Schwartz; L Wagner; Webb Miller
A greedy algorithm for aligning DNA sequences.
Journal of computational biology : a journal of computational molecular cell biology 2000;7(1-2):203-14.
1999: Zhaolei Zhang; P Berman; T Wiehe; W Miller
Post-processing long pairwise alignments.
Bioinformatics (Oxford, England) 1999;15(12):1012-9.
1999: Zhaolei Zhang; Kathryn D Curtin; YA Sun; Robert J Wyman
Nested transcripts of gap junction gene have distinct expression patterns.
Journal of neurobiology 1999;40(3):288-301.
1999: Kathryn D Curtin; Zhaolei Zhang; Robert J Wyman
Drosophila has several genes for gap junction proteins.
Gene 1999;232(2):191-201.
1998: Liliana Florea; G Hartzell; Zhaolei Zhang; G M Rubin; Webb Miller
A computer program for aligning a cDNA sequence with a genomic DNA sequence.
Genome research 1998;8(9):967-74.
1998: Zhaolei Zhang; Alejandro A Schäffer; Webb Miller; Thomas L Madden; David Lipman; Eugene V Koonin; Stephen F Altschul
Protein sequence similarity searches using patterns as seeds.
Nucleic acids research 1998;26(17):3986-90.
1998: Zhaolei Zhang; Piotr Berman; Webb Miller
Alignments without low-scoring regions.
Journal of computational biology : a journal of computational molecular cell biology 1998;5(2):197-210.
1997: Stephen F Altschul; Thomas L Madden; Alejandro A Schäffer; J Zhang; Zhaolei Zhang; Webb Miller; David Lipman
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Nucleic acids research 1997;25(17):3389-402.
1997: Zhaolei Zhang; W R Pearson; Webb Miller
Aligning a DNA sequence with a protein sequence.
Journal of computational biology : a journal of computational molecular cell biology 1997;4(3):339-49.
1994: Zhaolei Zhang
An exponential example for a partial digest mapping algorithm.
Journal of computational biology : a journal of computational molecular cell biology 1994;1(3):235-9.
1994: Zhaolei Zhang; B Raghavachari; Ross C Hardison; Webb Miller
Chaining multiple-alignment blocks.
Journal of computational biology : a journal of computational molecular cell biology 1994;1(3):217-26.
1994: Webb Miller; M Boguski; B Raghavachari; Zhaolei Zhang; Ross C Hardison
Constructing aligned sequence blocks.
Journal of computational biology : a journal of computational molecular cell biology 1994;1(1):51-64.