ZhaoLei Zhang, Ph.D. - Publications

Affiliations: 
2000 University of California, Berkeley, Berkeley, CA 
Area:
Structural biology

102 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Ahn JS, Kim T, Kim YK, Cho YC, Cho S, Jung SH, Ahn SY, Jung SY, Yang DH, Lee JJ, Choi S, Lee JY, Shin MG, Yoshida K, Ogawa S, ... ... Zhang Z, et al. Remission clone in acute myeloid leukemia shows growth advantage after chemotherapy but is distinct from leukemic clone. Experimental Hematology. PMID 31199945 DOI: 10.1016/j.exphem.2019.06.001  0.88
2019 Hu X, Liao S, Bai H, Wu L, Wang M, Wu Q, Zhou J, Jiao L, Chen X, Zhou Y, Lu X, Ying B, Zhang Z, Li W. Integrating exosomal microRNAs and electronic health data improved tuberculosis diagnosis. Ebiomedicine. PMID 30745169 DOI: 10.1016/j.ebiom.2019.01.023  0.72
2019 Gallo D, Kim T, Szakal B, Saayman X, Narula A, Park Y, Branzei D, Zhang Z, Brown GW. Rad5 Recruits Error-Prone DNA Polymerases for Mutagenic Repair of ssDNA Gaps on Undamaged Templates. Molecular Cell. PMID 30733119 DOI: 10.1016/j.molcel.2019.01.001  0.4
2018 Kim T, Moon JH, Ahn JS, Kim YK, Lee SS, Ahn SY, Jung SH, Yang DH, Lee JJ, Choi SH, Lee JY, Tyndel MS, Shin MG, Lee YJ, Sohn SK, ... ... Zhang Z, et al. Next-generation sequencing based post-transplant monitoring of acute myeloid leukemia. Blood. PMID 30108064 DOI: 10.1182/blood-2018-04-848028  0.88
2018 Wang Y, Li Y, Yue M, Wang J, Kumar S, Wechsler-Reya RJ, Zhang Z, Ogawa Y, Kellis M, Duester G, Zhao JC. Publisher Correction: N-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications. Nature Neuroscience. PMID 29880878 DOI: 10.1038/s41593-018-0169-2  1
2018 Ahn JS, Kim HJ, Kim YK, Lee SS, Ahn SY, Jung SH, Yang DH, Lee JJ, Park HJ, Lee JY, Choi SH, Jung CW, Jang JH, Kim HJ, Moon JH, ... ... Zhang Z, et al. Assessment of a new genomic classification system in acute myeloid leukemia with a normal karyotype. Oncotarget. 9: 4961-4968. PMID 29435155 DOI: 10.18632/oncotarget.23575  0.88
2018 Schneider R, McKeever P, Kim T, Graff C, van Swieten JC, Karydas A, Boxer A, Rosen H, Miller BL, Laforce R, Galimberti D, Masellis M, Borroni B, Zhang Z, Zinman L, et al. Downregulation of exosomal miR-204-5p and miR-632 as a biomarker for FTD: a GENFI study. Journal of Neurology, Neurosurgery, and Psychiatry. PMID 29434051 DOI: 10.1136/jnnp-2017-317492  0.4
2018 Wang Y, Li Y, Yue M, Wang J, Kumar S, Wechsler-Reya RJ, Zhang Z, Ogawa Y, Kellis M, Duester G, Zhao JC. N6-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications. Nature Neuroscience. PMID 29335608 DOI: 10.1038/s41593-017-0057-1  1
2017 Kim T, Tyndel MS, Zhang Z, Ahn J, Choi S, Szardenings M, Lipton JH, Kim HJ, Kim Dong Hwan D. Exome sequencing reveals DNMT3A and ASXL1 variants associate with progression of chronic myeloid leukemia after tyrosine kinase inhibitor therapy. Leukemia Research. 59: 142-148. PMID 28667884 DOI: 10.1016/j.leukres.2017.06.009  0.88
2017 McKeever PM, Kim T, Hesketh AR, MacNair L, Miletic D, Favrin G, Oliver SG, Zhang Z, St George-Hyslop P, Robertson J. Cholinergic neuron gene expression differences captured by translational profiling in a mouse model of Alzheimer's disease. Neurobiology of Aging. 57: 104-119. PMID 28628896 DOI: 10.1016/j.neurobiolaging.2017.05.014  0.4
2016 Leach MD, Kim T, DiGregorio S, Collins C, Zhang Z, Duennwald ML, Cowen LE. Candida albicans Is Resistant to Polyglutamine Aggregation and Toxicity. G3 (Bethesda, Md.). PMID 27807047 DOI: 10.1534/g3.116.035675  0.4
2016 Yang L, Zhang Z, He S. Both male-biased and female-biased genes evolve faster in fish genomes. Genome Biology and Evolution. PMID 27742722 DOI: 10.1093/gbe/evw239  0.76
2016 Kim T, Tyndel MS, Kim HJ, Ahn JS, Choi SH, Park HJ, Kim YK, Kim SY, Lipton JH, Zhang Z, Kim DD. Spectrum of somatic mutation dynamics in chronic myeloid leukemia following tyrosine kinase inhibitor therapy. Blood. PMID 27733357 DOI: 10.1182/blood-2016-04-708560  0.88
2016 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, ... ... Zhang Z, et al. Exploring Quantitative Yeast Phenomics with Single-Cell Analysis of DNA Damage Foci. Cell Systems. PMID 27617677 DOI: 10.1016/j.cels.2016.08.008  0.96
2016 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. PMID 27546533 DOI: 10.1016/j.stemcr.2016.06.012  0.96
2016 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. PMID 27418135 DOI: 10.18632/oncotarget.10569  1
2016 Yimit A, Kim T, Anand R, Meister S, Ou J, Haber JE, Zhang Z, Brown GW. MTE1 Functions with MPH1 in Double-Strand Break Repair. Genetics. PMID 26920759 DOI: 10.1534/genetics.115.185454  0.96
2016 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. PMID 26861146 DOI: 10.1007/s13238-015-0240-7  0.96
2015 Li J, Ma Z, Shi M, Malty RH, Aoki H, Minic Z, Phanse S, Jin K, Wall DP, Zhang Z, Urban AE, Hallmayer J, Babu M, Snyder M. Identification of Human Neuronal Protein Complexes Reveals Biochemical Activities and Convergent Mechanisms of Action in Autism Spectrum Disorders. Cell Systems. 1: 361-374. PMID 26949739 DOI: 10.1016/j.cels.2015.11.002  1
2015 Wong KC, Li Y, Peng C, Moses AM, Zhang Z. Computational learning on specificity-determining residue-nucleotide interactions. Nucleic Acids Research. PMID 26527718 DOI: 10.1093/nar/gkv1134  1
2015 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. PMID 26490958 DOI: 10.1093/nar/gkv1080  0.96
2015 Jablonowski CM, Cussiol JR, Oberly S, Yimit A, Balint A, Kim T, Zhang Z, Brown GW, Smolka MB. Termination of Replication Stress Signaling via Concerted Action of the Slx4 Scaffold and the PP4 Phosphatase. Genetics. PMID 26362319 DOI: 10.1534/genetics.115.181479  0.4
2015 Zhang Z, Zhou L, Zhou Y, Liu J, Xing X, Zhong J, Xu G, Kang Z, Liu J. Mitophagy induced by nanoparticle-peptide conjugates enabling an alternative intracellular trafficking route. Biomaterials. 65: 56-65. PMID 26142776 DOI: 10.1016/j.biomaterials.2015.06.029  0.72
2015 Balint A, Kim T, Gallo D, Cussiol JR, Bastos de Oliveira FM, Yimit A, Ou J, Nakato R, Gurevich A, Shirahige K, Smolka MB, Zhang Z, Brown GW. Assembly of Slx4 signaling complexes behind DNA replication forks. The Embo Journal. PMID 26113155 DOI: 10.15252/embj.201591190  0.4
2015 Li Y, Wang Y, Zhang Z, Zamudio AV, Zhao JC. Genome-wide detection of high abundance N6-methyladenosine sites by microarray. Rna (New York, N.Y.). 21: 1511-8. PMID 26092943 DOI: 10.1261/rna.051474.115  1
2015 Jessulat M, Malty RH, Nguyen-Tran DH, Deineko V, Aoki H, Vlasblom J, Omidi K, Jin K, Minic Z, Hooshyar M, Burnside D, Samanfar B, Phanse S, Freywald T, Prasad B, ... Zhang Z, et al. Spindle Checkpoint Factors Bub1 and Bub2 Promote DNA Double-Strand Break Repair by Nonhomologous End Joining. Molecular and Cellular Biology. 35: 2448-63. PMID 25963654 DOI: 10.1128/MCB.00007-15  0.96
2015 Yang L, Zhang Z, He S. Bichir microRNA repertoire suggests a ray-finned fish affinity of Polypteriforme. Gene. 566: 242-7. PMID 25917619 DOI: 10.1016/j.gene.2015.04.058  0.96
2015 Li Y, Zhang Z. Computational Biology in microRNA. Wiley Interdisciplinary Reviews. Rna. 6: 435-52. PMID 25914300 DOI: 10.1002/wrna.1286  1
2015 Liang C, Li Y, Luo J, Zhang Z. A novel motif-discovery algorithm to identify co-regulatory motifs in large transcription factor and microRNA co-regulatory networks in human. Bioinformatics (Oxford, England). 31: 2348-55. PMID 25788622 DOI: 10.1093/bioinformatics/btv159  1
2015 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, ... ... Zhang Z, et al. Yeast mitochondrial protein-protein interactions reveal diverse complexes and disease-relevant functional relationships. Journal of Proteome Research. 14: 1220-37. PMID 25546499 DOI: 10.1021/pr501148q  0.96
2015 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. 7: 251-61. PMID 25543049 DOI: 10.1093/gbe/evu279  0.96
2015 Malty RH, Jessulat M, Jin K, Musso G, Vlasblom J, Phanse S, Zhang Z, Babu M. Mitochondrial targets for pharmacological intervention in human disease. Journal of Proteome Research. 14: 5-21. PMID 25367773 DOI: 10.1021/pr500813f  1
2015 Wong KC, Li Y, Peng C, Zhang Z. SignalSpider: probabilistic pattern discovery on multiple normalized ChIP-Seq signal profiles. Bioinformatics (Oxford, England). 31: 17-24. PMID 25192742 DOI: 10.1093/bioinformatics/btu604  1
2014 Li Y, Zhang Z. Potential microRNA-mediated oncogenic intercellular communication revealed by pan-cancer analysis. Scientific Reports. 4: 7097. PMID 25403569 DOI: 10.1038/srep07097  1
2014 Li Y, Liang M, Zhang Z. Regression analysis of combined gene expression regulation in acute myeloid leukemia. Plos Computational Biology. 10: e1003908. PMID 25340776 DOI: 10.1371/journal.pcbi.1003908  1
2014 Cromar G, Wong KC, Loughran N, On T, Song H, Xiong X, Zhang Z, 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. 6: 2897-917. PMID 25323955 DOI: 10.1093/gbe/evu228  0.96
2014 Li Y, Liang C, Easterbrook S, Luo J, Zhang Z. Investigating the functional implications of reinforcing feedback loops in transcriptional regulatory networks. Molecular Biosystems. 10: 3238-48. PMID 25286350 DOI: 10.1039/c4mb00526k  0.96
2014 Li Y, Liang C, Wong KC, Luo J, Zhang Z. Mirsynergy: detecting synergistic miRNA regulatory modules by overlapping neighbourhood expansion. Bioinformatics (Oxford, England). 30: 2627-35. PMID 24894504 DOI: 10.1093/bioinformatics/btu373  1
2014 Li J, Kim T, Nutiu R, Ray D, Hughes TR, Zhang Z. Identifying mRNA sequence elements for target recognition by human Argonaute proteins. Genome Research. 24: 775-85. PMID 24663241 DOI: 10.1101/gr.162230.113  0.96
2014 Li Y, Liang C, Wong KC, Jin K, Zhang Z. Inferring probabilistic miRNA-mRNA interaction signatures in cancers: a role-switch approach. Nucleic Acids Research. 42: e76. PMID 24609385 DOI: 10.1093/nar/gku182  1
2014 Wang Y, Li Y, Toth JI, Petroski MD, Zhang Z, Zhao JC. N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells. Nature Cell Biology. 16: 191-8. PMID 24394384 DOI: 10.1038/ncb2902  1
2014 Wong KC, Zhang Z. SNPdryad: predicting deleterious non-synonymous human SNPs using only orthologous protein sequences. Bioinformatics (Oxford, England). PMID 24389653 DOI: 10.1093/bioinformatics/btt769  0.96
2014 Li Y, Goldenberg A, Wong KC, Zhang Z. A probabilistic approach to explore human miRNA targetome by integrating miRNA-overexpression data and sequence information. Bioinformatics (Oxford, England). 30: 621-8. PMID 24135265 DOI: 10.1093/bioinformatics/btt599  1
2013 Choi H, Jung C, Sohn SK, Kim S, Kim HJ, Kim YK, Kim T, Zhang Z, Shin ES, Lee JE, Moon JH, Kim SH, Kim KH, Mun YC, Kim H, et al. Genome-wide genotype-based risk model for survival in acute myeloid leukaemia patients with normal karyotype. British Journal of Haematology. 163: 62-71. PMID 24159609 DOI: 10.1111/bjh.12492  0.96
2013 Snider J, Hanif A, Lee ME, Jin K, Yu AR, Graham C, Chuk M, Damjanovic D, Wierzbicka M, Tang P, Balderes D, Wong V, Jessulat M, Darowski KD, San Luis BJ, ... ... Zhang Z, et al. Mapping the functional yeast ABC transporter interactome. Nature Chemical Biology. 9: 565-72. PMID 23831759 DOI: 10.1038/nchembio.1293  0.96
2013 Wong KC, Chan TM, Peng C, Li Y, Zhang Z. DNA motif elucidation using belief propagation. Nucleic Acids Research. 41: e153. PMID 23814189 DOI: 10.1093/nar/gkt574  1
2013 Li Y, Zhao DY, Greenblatt JF, Zhang Z. RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments. Nucleic Acids Research. 41: e94. PMID 23455476 DOI: 10.1093/nar/gkt142  0.96
2013 Li J, Zhang Z. miRNA regulatory variation in human evolution. Trends in Genetics : Tig. 29: 116-24. PMID 23128010 DOI: 10.1016/j.tig.2012.10.008  1
2012 Yang Z, Dong D, Zhang Z, Crabbe MJ, Wang L, Zhong Y. Preferential regulation of stably expressed genes in the human genome suggests a widespread expression buffering role of microRNAs. Bmc Genomics. 13: S14. PMID 23281599 DOI: 10.1186/1471-2164-13-S7-S14  0.76
2012 Li J, Liu Y, Xin X, Kim TS, 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 Genetics. 8: e1002578. PMID 22457636 DOI: 10.1371/journal.pgen.1002578  0.96
2012 Musso G, Emili A, Zhang Z. Characterization and evolutionary analysis of protein-protein interaction networks. Methods in Molecular Biology (Clifton, N.J.). 856: 363-80. PMID 22399467 DOI: 10.1007/978-1-61779-585-5_15  1
2012 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. 40: D687-94. PMID 22009677 DOI: 10.1093/nar/gkr827  0.96
2011 Gong Y, Zhang Z, Houry WA. Bioinformatic approach to identify chaperone pathway relationship from large-scale interaction networks. Methods in Molecular Biology (Clifton, N.J.). 787: 189-203. PMID 21898237 DOI: 10.1007/978-1-61779-295-3_15  0.96
2011 Musso G, Emili A, Zhang Z. Filtering and interpreting large-scale experimental protein-protein interaction data. Methods in Molecular Biology (Clifton, N.J.). 781: 295-309. PMID 21877287 DOI: 10.1007/978-1-61779-276-2_14  1
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, Haase J, Lin ZY, Baryshnikova A, ... ... Zhang Z, et al. Systematic exploration of essential yeast gene function with temperature-sensitive mutants. Nature Biotechnology. 29: 361-7. PMID 21441928 DOI: 10.1038/nbt.1832  0.96
2011 Dong D, Shao X, Zhang Z. Differential effects of chromatin regulators and transcription factors on gene regulation: a nucleosomal perspective. Bioinformatics (Oxford, England). 27: 147-52. PMID 21075748 DOI: 10.1093/bioinformatics/btq637  0.76
2011 Dong D, Yuan Z, Zhang Z. Evidences for increased expression variation of duplicate genes in budding yeast: from cis- to trans-regulation effects. Nucleic Acids Research. 39: 837-47. PMID 20935054 DOI: 10.1093/nar/gkq874  0.84
2011 Turinsky AL, Turner B, Borja RC, Gleeson JA, Heath M, Pu S, Switzer T, Dong D, Gong Y, On T, Xiong X, Emili A, Greenblatt J, Parkinson J, Zhang Z, et al. DAnCER: disease-annotated chromatin epigenetics resource. Nucleic Acids Research. 39: D889-94. PMID 20876685 DOI: 10.1093/nar/gkq857  0.96
2011 Dong D, Shao X, Deng N, Zhang Z. Gene expression variations are predictive for stochastic noise. Nucleic Acids Research. 39: 403-13. PMID 20860999 DOI: 10.1093/nar/gkq844  0.76
2010 Pu S, Turinsky AL, Vlasblom J, On T, Xiong X, Emili A, Zhang Z, Greenblatt J, Parkinson J, Wodak SJ. Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human. Plos One. 5: e14122. PMID 21124763 DOI: 10.1371/journal.pone.0014122  0.96
2010 Li J, Yuan Z, Zhang Z. The cellular robustness by genetic redundancy in budding yeast. Plos Genetics. 6: e1001187. PMID 21079672 DOI: 10.1371/journal.pgen.1001187  1
2010 Li J, Liu Y, Kim T, Min R, Zhang Z. Gene expression variability within and between human populations and implications toward disease susceptibility. Plos Computational Biology. 6. PMID 20865155 DOI: 10.1371/journal.pcbi.1000910  0.96
2010 Li J, Min R, Vizeacoumar FJ, Jin K, Xin X, Zhang Z. 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. 107: 10472-7. PMID 20489180 DOI: 10.1073/pnas.0914302107  1
2010 On T, Xiong X, Pu S, Turinsky A, Gong Y, Emili A, Zhang Z, Greenblatt J, Wodak SJ, Parkinson J. The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses. Proteins. 78: 2075-89. PMID 20455264 DOI: 10.1002/prot.22723  0.96
2010 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. 27: 1461-6. PMID 20139146 DOI: 10.1093/molbev/msq041  1
2010 Vizeacoumar FJ, van Dyk N, S Vizeacoumar F, Cheung V, Li J, Sydorskyy Y, Case N, Li Z, Datti A, Nislow C, Raught B, Zhang Z, Frey B, Bloom K, Boone C, et al. Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis. The Journal of Cell Biology. 188: 69-81. PMID 20065090 DOI: 10.1083/jcb.200909013  0.96
2010 Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z, Zhang Y, Wang W, Li J, Wei F, ... ... Zhang Z, et al. The sequence and de novo assembly of the giant panda genome. Nature. 463: 311-7. PMID 20010809 DOI: 10.1038/nature08696  1
2010 Ren J, Jiang C, Gao X, Liu Z, Yuan Z, Jin C, Wen L, Zhang Z, Xue Y, Yao X. PhosSNP for systematic analysis of genetic polymorphisms that influence protein phosphorylation. Molecular & Cellular Proteomics : McP. 9: 623-34. PMID 19995808 DOI: 10.1074/mcp.M900273-MCP200  0.84
2010 Li J, Liu Y, Dong D, Zhang Z. Evolution of an X-linked primate-specific micro RNA cluster. Molecular Biology and Evolution. 27: 671-83. PMID 19933172 DOI: 10.1093/molbev/msp284  1
2010 Ren J, Liu Z, Gao X, Jin C, Ye M, Zou H, Wen L, Zhang Z, Xue Y, Yao X. MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore. Nucleic Acids Research. 38: D155-60. PMID 19783819 DOI: 10.1093/nar/gkp784  0.76
2009 Dong D, He G, Zhang S, Zhang Z. Evolution of olfactory receptor genes in primates dominated by birth-and-death process. Genome Biology and Evolution. 1: 258-64. PMID 20333195 DOI: 10.1093/gbe/evp026  0.76
2009 Li J, Min R, Bonner A, Zhang Z. A probabilistic framework to improve microrna target prediction by incorporating proteomics data. Journal of Bioinformatics and Computational Biology. 7: 955-72. PMID 20014473  1
2009 Guo X, Zhang Z, Gerstein MB, Zheng D. Small RNAs originated from pseudogenes: cis- or trans-acting? Plos Computational Biology. 5: e1000449. PMID 19649160 DOI: 10.1371/journal.pcbi.1000449  0.96
2009 Gong Y, Kakihara Y, Krogan N, Greenblatt J, Emili A, Zhang Z, Houry WA. An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell. Molecular Systems Biology. 5: 275. PMID 19536198 DOI: 10.1038/msb.2009.26  0.96
2009 Gong Y, Zhang Z. Global robustness and identifiability of random, scale-free, and small-world networks. Annals of the New York Academy of Sciences. 1158: 82-92. PMID 19348634 DOI: 10.1111/j.1749-6632.2008.03752.x  0.76
2009 Min R, Bonner A, Li J, Zhang Z. Learned random-walk kernels and empirical-map kernels for protein sequence classification. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 457-74. PMID 19254184 DOI: 10.1089/cmb.2008.0031  0.96
2008 Li J, Musso G, Zhang Z. Preferential regulation of duplicated genes by microRNAs in mammals. Genome Biology. 9: R132. PMID 18727826 DOI: 10.1186/gb-2008-9-8-r132  1
2008 Musso G, Costanzo M, Huangfu M, Smith AM, Paw J, San Luis BJ, 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. 18: 1092-9. PMID 18463300 DOI: 10.1101/gr.076174.108  0.96
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. 1115: 267-85. PMID 17925355 DOI: 10.1196/annals.1407.011  0.76
2007 Gong Y, Zhang Z. CellFrame: a data structure for abstraction of cell biology experiments and construction of perturbation networks. Annals of the New York Academy of Sciences. 1115: 249-66. PMID 17925354 DOI: 10.1196/annals.1407.010  0.76
2007 Musso GA, Zhang Z, Emili A. Experimental and computational procedures for the assessment of protein complexes on a genome-wide scale. Chemical Reviews. 107: 3585-600. PMID 17630806 DOI: 10.1021/cr0682857  0.72
2007 Musso G, Zhang Z, Emili A. Retention of protein complex membership by ancient duplicated gene products in budding yeast. Trends in Genetics : Tig. 23: 266-9. PMID 17428571 DOI: 10.1016/j.tig.2007.03.012  1
2007 Zhang Z, Pang AW, Gerstein M. Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human. Bmc Evolutionary Biology. 7: S14. PMID 17288572 DOI: 10.1186/1471-2148-7-S1-S14  0.64
2007 Karro JE, Yan Y, Zheng D, Zhang Z, Carriero N, Cayting P, Harrrison P, Gerstein M. Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Research. 35: D55-60. PMID 17099229 DOI: 10.1093/nar/gkl851  0.96
2006 Zhang Z, Carriero N, Zheng D, Karro J, Harrison PM, Gerstein M. PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics (Oxford, England). 22: 1437-9. PMID 16574694 DOI: 10.1093/bioinformatics/btl116  0.64
2005 Gong Y, Zhang Z. Alternative signaling pathways: when, where and why? Febs Letters. 579: 5265-74. PMID 16194539 DOI: 10.1016/j.febslet.2005.08.062  0.76
2005 Zheng D, Zhang Z, Harrison PM, Karro J, Carriero N, Gerstein M. Integrated pseudogene annotation for human chromosome 22: evidence for transcription. Journal of Molecular Biology. 349: 27-45. PMID 15876366 DOI: 10.1016/j.jmb.2005.02.072  0.64
2005 Harrison PM, Zheng D, Zhang Z, Carriero N, Gerstein M. Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. Nucleic Acids Research. 33: 2374-83. PMID 15860774 DOI: 10.1093/nar/gki531  0.64
2004 Zhang Z, Gerstein M. Large-scale analysis of pseudogenes in the human genome. Current Opinion in Genetics & Development. 14: 328-35. PMID 15261647 DOI: 10.1016/j.gde.2004.06.003  0.64
2004 Zhang Z, Carriero N, Gerstein M. Comparative analysis of processed pseudogenes in the mouse and human genomes. Trends in Genetics : Tig. 20: 62-7. PMID 14746985 DOI: 10.1016/j.tig.2003.12.005  0.64
2003 Zhang Z, Harrison PM, Liu Y, Gerstein M. Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Research. 13: 2541-58. PMID 14656962 DOI: 10.1101/gr.1429003  0.8
2003 Zhang Z, Gerstein M. Reconstructing genetic networks in yeast. Nature Biotechnology. 21: 1295-7. PMID 14595359 DOI: 10.1038/nbt1103-1295  0.64
2003 Zhang Z, Gerstein M. Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucleic Acids Research. 31: 5338-48. PMID 12954770  0.64
2003 Zhang Z, Gerstein M. The human genome has 49 cytochrome c pseudogenes, including a relic of a primordial gene that still functions in mouse. Gene. 312: 61-72. PMID 12909341  0.64
2003 Zhang Z, Gerstein M. Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements. Journal of Biology. 2: 11. PMID 12814519 DOI: 10.1186/1475-4924-2-11  0.64
2003 Zhang Z, Gerstein M. Identification and characterization of over 100 mitochondrial ribosomal protein pseudogenes in the human genome. Genomics. 81: 468-80. PMID 12706105  0.64
2003 Harrison PM, Milburn D, Zhang Z, Bertone P, Gerstein M. Identification of pseudogenes in the Drosophila melanogaster genome. Nucleic Acids Research. 31: 1033-7. PMID 12560500 DOI: 10.1093/nar/gkg169  0.96
2002 Zhang Z, Harrison P, Gerstein M. Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. Genome Research. 12: 1466-82. PMID 12368239 DOI: 10.1101/gr.331902  0.64
2002 Luscombe NM, Qian J, Zhang Z, Johnson T, Gerstein M. The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties. Genome Biology. 3: RESEARCH0040. PMID 12186647  0.96
2002 Balasubramanian S, Harrison P, Hegyi H, Bertone P, Luscombe N, Echols N, McGarvey P, Zhang Z, Gerstein M. SNPs on human chromosomes 21 and 22 -- analysis in terms of protein features and pseudogenes. Pharmacogenomics. 3: 393-402. PMID 12052146 DOI: 10.1517/14622416.3.3.393  0.96
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