Publications

2024

• Lan, W., H. Liao, Q. Chen, Y. Chen, Z. Zhang and J. Wang MULGONET: an interpretable neural network framework to integrate multi-omics data for cancer recurrence prediction and biomarker discovery " Under Review
  
  
• Wang, Y., X. Chen, Z. Zheng, L. Huang, W. Xie, F. Wang, Z. Zhang and K. Wong "scGREAT: Transformer-Based Deep Language Model for Gene Regulatory Network Inference from Single-Cell Transcriptomics." Under Review
  
  
• Yang, Y., G. Li, K. Pang, W. Cao, X. Li and Z. Zhang "Deciphering 3’ UTR mediated gene regulation using interpretable deep representation learning." Under Review
  
  
• Zhang, K., J. Zhu, D. Kong and Z. Zhang "Modeling Single Cell Trajectory Using Forward-Backward Stochastic Differential Equations." In Revision
  
  

2023

• Kim, K. H., T. Kim, I. Novitzky-Basso, H. Lee, Y. Yoo, J. S. Ahn, I. Pasic, A. Law, W. Lam, F. V. Michelis, A. Gerbitz, A. Viswabandya, J. Lipton, R. Kumar, J. Mattsson, Z. Zhang, N. Kaushansky, Y. Brilon, N. Chapal-Ilani, T. Biezuner, L. I. Shlush and D. D. H. Kim "Clonal hematopoiesis in the donor does not adversely affect long-term outcomes following allogeneic hematopoietic stem cell transplantation: result from a 13-year follow-up." Haematologica (2023) 108(7): 1817-1826.
  
  
• Nabeel-Shah, S., J. Garg, K. Ashraf, R. Jeyapala, H. Lee, A. Petrova, J. D. Burns, S. Pu, Z. Zhang, J. F. Greenblatt, R. E. Pearlman, J. P. Lambert and J. Fillingham "Multilevel interrogation of H3.3 reveals a primordial role in transcription regulation." " Epigenetics Chromatin (2023) 16(1): 10.
  
  
• Segal, D., S. Maier, G. J. Mastromarco, W. W. Qian, S. Nabeel-Shah, H. Lee, G. Moore, J. Lacoste, B. Larsen, Z. Y. Lin, A. Selvabaskaran, K. Liu, C. Smibert, Z. Zhang, J. Greenblatt, J. Peng, H. O. Lee, A. C. Gingras and M. Taipale "A central chaperone-like role for 14-3-3 proteins in human cells." Mol Cell (2023) 83(6): 974-993 e915.
  
  
• Ying, S., T. Heung, B. Thiruvahindrapuram, W. Engchuan, Y. Yin, C. Blagojevic, Z. Zhang, R. A. Hegele, R. K. C. Yuen and A. S. Bassett "Polygenic risk for triglyceride levels in the presence of a high impact rare variant." BMC Med Genomics (2023) 16(1): 281.
  
  

2022

• Jiang P, Gao F, Liu S, Zhang S, Zhang X, Xia Z, Zhang W, Jiang T, Zhu J, Zhang Z, Shu Q, Snyder M, Li J "Longitudinally tracking personal physiomes for precision management of childhood epilepsy" PLOS Digital Health, 2022
  
  
• Deng Z, Gu R, Bi H, Wang X, Ma H, Zhang Z, Wen H "Predicting Ligand – RNA Binding Using E3-Equivariant Network and Pretraining." NeurIPS 2022 Machine Learning in Structure Biology (MLSB) Workshop
  
  
• Ying, S., Heung, T., Zhang, Z., Yuen, R. and Bassett, A. "Schizophrenia risk and microRNA targets overlapped by rare copy number variants in 22q11.2 deletion syndrome. " Front Genet. 2022;13
  
  
• Liao, S., M. Bokhari, P. Chakraborty, A. Suszko, G. Jones, D. Spears, M. Gollob, Z. Zhang, B. Wang and V. S. Chauhan "Use of Wearable Technology and Deep Learning to Improve the Diagnosis of Brugada Syndrome." JACC Clin Electrophysiol 8(8): 1010-1020.
  
  
• Jiao, L., J. Song, H. Chen, D. Gu, S. Liao, J. Zhou, T. Wu, J. Zhang, X. Hu, H. Bai, Q. Wu, M. Lyu, Z. Meng, Z. Zhao, T. Liu, H. Zhong, L. Wu, W. Zhou, B. Zhang, Z. Zhang, X. Lu and B. Ying "Genetic architecture of tuberculosis susceptibility: A comprehensive research synopsis, meta-analyses, and epidemiological evidence." Infect Genet Evol 104: 105352.
  
  
• Sun, S., Yang, J. and Zhang, Z. "RNALigands: a database and web server for RNA - ligand interactions " RNA. 2022;28(2):115-22. Server
  
  
• Song, J., Syed, N., Pu, S., Lee, H., Braunschweig, U., Ni, Z., Ahmed, N., Marcon, E., Zhong, G., Ray, D. et al. "Regulation of alternative polyadenylation by the C2H2-zinc finger protein Sp1" Mol Cell. 2022;82(17):3135-50 e9
  
  
• Song GY, Kim T, Ahn SY, Jung SH, Kim M, Yang DH, et al. "Allogeneic hematopoietic cell transplantation can overcome the adverse prognosis indicated by secondary-type mutations in de novo acute myeloid leukemia" Bone Marrow Transplant. 2022.
  
  
• Nabeel-Shah S, Lee H, Ahmed N, Burke G, Farhangmehr S, Ashraf K, Pu S, Braunschweig U, Zhong G, Wei H, Tang H, Yang J, Marcon E, Blencowe B, Zhang Z, Greenblatt JF "SARS-CoV-2 Nucleocapsid protein attenuates stress granule formation and interacts directly with mRNAs to impair host stress response " iScience. 2022;25(1):103562.
  
  
• Ma, H., Wen, H., Xue, Z., Li, G. and Zhang, Z. "RNANetMotif: identifying sequence-structure RNA network motifs in RNA-protein binding sites " PLoS Comput Biol. 2022;18(7):e1010293. Server
  
  
• Liu, Y., Li, R., Luo, J. and Z, Zhang "Inferring RNA-binding protein target preferences using adversarial domain adaptation" PLoS Comput Biol. 2022;18(2):e1009863.
  
  
• Kim, T., Lee, H., Capo-Chichi, J., Chang, M., Yoo, Y., Basi, G., Ketela, T., Smith, A., Tierens, A., Minden, M. et al "Single-cell proteogenomic sequencing allows early detection of relapse clone with CN-LOH at FLT3-ITD locus from initial diagnosis in AML" EJHaem. 2022;3(2):426-33.
  
  
• Kim T, Ahn JS, Son MH, Novitzky-Basso I, Yi SY, Ahn SY, et al. "Genetic changes during leukemic transformation to secondary acute myeloid leukemia from myeloproliferative neoplasms." Leuk Res. 2022;118:106858.
  
  
• Hou H, Chan C, Yuki KE, Sokolowski D, Roy A, Qu R, et al. "Postnatal developmental trajectory of sex-biased gene expression in the mouse pituitary gland." Biol Sex Differ 2022 Oct 11:(13)
  
  
• Gabra MM, Chow JT, Kim T, Son MH, Arruda A, Woolley JF, et al. "A 5-microRNA signature derived from core binding factor-AML is predictive in adult and childhood AML." Leuk Res. 2022;123:106968.
  
  
• Ahn JS, Kim T, Jung SH, Ahn SY, Song GY, Kim M, et al. Next-generation sequencing-based analysis to assess the pattern of relapse in patients with Philadelphia-positive acute lymphoblastic leukemia. EJHaem. 2022;3(4):1145-53.
  
  

2021

• Nabeel-Shah, S., Garg, J., Saettone, A., Ashraf, K., Lee, H., Wahab, S., Ahmed, N., Fine, J., Derynck, J., Pu, S. et al. "Functional characterization of RebL1 highlights the evolutionary conservation of oncogenic activities of the RBBP4/7 orthologue in Tetrahymena thermophila." Nucleic Acids Res, 49, 6196-6212.
  
  
• Liu, S., Zhang, Y., Shang, X. and Zhang, Z. "ProTICS reveals prognostic impact of tumor infiltrating immune cells in different molecular subtypes.ProTICS reveals prognostic impact of tumor infiltrating immune cells in different molecular subtypes." Briefing in Bioinfo 2021
  
  
• Liao, S., Ragot, D., Nayyar, S., Suszko, A., Zhang, Z., Wang, B. and Chauhan, V.S. "Deep Learning Classification of Unipolar Electrograms in Human Atrial Fibrillation: Application in Focal Source Mapping. " Front Physiol, 12, 704122.
  
  
• Liao, S., Kiros, J., Chen, J., Zhang, Z. and Chen, T. "Improving domain adaptation in de-identification of electronic health records through self-training" J Am Med Inform Assoc, 28, 2093-2100.
  
  
• Dong, N., Bandura, J., Zhang, Z., Wang, Y., Labadie, K., Noel, B., Davison, A., Koene, J.M., Sun, H.S., Coutellec, M.A. et al "Ion channel profiling of the Lymnaea stagnalis ganglia via transcriptome analysis." BMC Genomics, 22, 18.
  
  
• Daher-Reyes, G., Kim, T., Novitzky-Basso, I., Kim, K.H., Smith, A., Stockley, T., Capochichi, J.M., Al-Shaibani, Z., Pasic, I., Law, A. et al. "Prognostic impact of the adverse molecular-genetic profile on long-term outcomes following allogeneic hematopoietic stem cell transplantation in acute myeloid leukemia. " Bone Marrow Transplant.
  
  
• Ahn, J.S., Kim, T., Jung, S.H., Ahn, S.Y., Jung, S.Y., Song, G.Y., Kim, M., Yang, D.H., Lee, J.J., Choi, S. et al. "Allogeneic transplant can abrogate the risk of relapse in the patients of first remission acute myeloid leukemia with detectable measurable residual disease by next-generation sequencing." Bone Marrow Transplant, 56, 1159-1170
  
  

2020

• Liu Y, Pan C, Kong D, Luo J*, Zhang Z* "A survey of regulatory interactions among RNA binding proteins and microRNAs in cancer" Frontiers in Genetics 2020
  
  
• Hu X, Liao S, Bai H, Gupta S, Zhou Y, Zhou J, Jiao L, Wu L, Wang M, Chen X, Zhou Y, Lu X, Hu TY, Zhang Z*, Ying B.* "Long Noncoding RNA and Predictive Model To Improve Diagnosis of Clinically Diagnosed Pulmonary Tuberculosis" J of Clinical Microbiology 2020 June
  
  
• Lin J, Zhang Z, Zhang S, Chen J, Wong K "CRISPR‐Net: A Recurrent Convolutional Network Quantifies CRISPR Off‐Target Activities with Mismatches and Indels" Advanced Science 2020
  
  
• Jianguo Chen, Kenli Li, Zhaolei Zhang, Keqin Li, Philip S. Yu "A Survey on Applications of Artificial Intelligence in Fighting Against COVID-19" arXiv 2020
  
  

2019

• Lee H, Zhang Z, Krause HM "Long Noncoding RNAs and Repetitive Elements: Junk or Intimate Evolutionary Partners?" Trends in Genetics 2019
  
  
• Hu X(e), Liao S(e), Bai H(e), 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 2019 Feb
  
  
• 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 2019 Mar
  
  

2018

• Kim T, Moon JH, Ahn J, Kim Y, Lee S, Ahn S, Jung S, Yang D, Lee J, Choi SH, Lee S, Tyndel MS, Shin M, Lee YJ, Sohn SK, Park SK, Zhang Z*, Kim H*, Kim DD* "Next-generation sequencing based post-transplant monitoring of acute myeloid leukemia" Blood 2018 Oct 11 132 (15)
  GenomeWeb the Pathologist UofT News EurekAlert Bild
  
  
• 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 Neurosci. 2018 Feb;21(2):195-206
  
  
• Ahn J, Kim HJ, Kim YK, Lee SS, Ahn SY,Jung SH, Yang DH, Lee JJ, Park HJ, Choi SH, Jung CW, Jang JH, Kim HJ, Moon JH, Sohn SK, Lee YJ, Won JH, Kim SH, Zhang Z, Kim Tm and Kim DD "Assessment of a new genomic classification system in acute myeloid leukemia with a normal karyotype" OncoTarget 2018 9:4961-4968
  
  

2017

• 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 2017 Sep;31(9):1928-1935.
  
  
• 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 2017 Jan 5;7(1):95-108
  
  
• 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 2017 Jan 5;129(1):38-47.
  
  

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, 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
  
  
• 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.
  
  
• 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
  
  
• 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
  
  
• 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
  
  
• 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
  
  
• 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
  
  

2015

• 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) PMID:
  
  
• 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
  
  
• 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 (In Press) PMID: 26362319
  
  
• 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) PMID: 26113155
  
  
• 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. PMID: 26092943
  
  
• Li Y, and Zhang Z "Computational Biology in microRNA" Wiley Interdisciplinary Reviews (WIREs) RNA 2015 Jul-Aug;6(4):435-52. PMID: 25914300
  
  
• 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. PMID: 25788622
  
  
• 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 PMID: 25546499
  
  
• 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
  
  
• 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
  
  

2014

• 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
  
  
• Li Y, and Zhang Z "Potential microRNA-mediated oncogenic intercellular communication revealed by pan-cancer analysis" Scientific Reports 2014 Nov 18;4:7097. PMID: 25403569
  
  
• 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 Oct 15;6(10):2897-917. PMID: 25323955
  
  
• Li Y, Liang M and Zhang Z "Regression Analysis of Combinatorial Gene Expression Regulation in Acute Myeloid Leukemia" PLOS Computational Biology, 2014 Oct 23;10(10):e1003908, PMID: 25340776
  
  
• Li Y, Liang C, Easterbrook S, Luo J, Zhang Z "Investigating functional implication of reinforcing feedback loop in transcriptional regulatory network" Molecular Biosystems,2014 Dec;10(12):3238-48, PMID: 25286350
  
  
• Li Y, Liang C, Wong KC, Luo J and Zhang Z "Mirsynergy: detecting synergistic miRNA regulatory modules by overlapping neighbourhood expansion" Bioinformatics 2014 Sep 15;30(18):2627-35., PMID: 24894504
  
  
• 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 May;42(9):e76. PMID: 24609385
  
  
• 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 May;24(5):775-85, PMID: 24663241
  
  
• Wong KC and Zhang Z "SNPdryad: Predicting Deleterious Non-synonymous Human SNPs Using Only Orthologous Protein Sequences" Bioinformatics 2014, 30 (8): 1112-1119, PMID: 24389653
  
  
• 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 Feb;16(2):191-8, PMID: 24394384
  
  

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 2014 Mar 1;30(5):621-8, PMID: 24135265
  
  
• 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
  
  
• 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 Oct;163(1):62-7, PMID: 24159609
  
  
• Wong KC, Chan TM, Peng C., Li Y., and Zhang Z. "DNA Motif Elucidation using belief propagation" Nucleic Acids Research. 2013 Sep;41(16):e153, PMID: 23814189
  
  
• 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 Sep;9(9):565-72. PMID: 23831759
  
  
• 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 Apr;41(8):e94, PMID: 23455476 RIPSeeker on Bioconductor
  
  
• Li J. and Zhang Z. "microRNA Regulatory Variation in Human Evolution" Trends in Genetics 2013 Feb;29(2):116-24 PMID: 23128010
  
  

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, PMID: 23281599
  
  
• 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, PMID: 22457636
  
  
• 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" 2012 Jan;40(Database issue):D687-94, PMID: 22009677 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;787:189-203, PMID: 21898237
  
  
• 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 Apr;29(4):361-7. PMID: 21441928
  
  
• 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) PMID: 22399467
  
  
• 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) PMID: 21877287
  
  
• 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. PMID: 21075748
  
  
• 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. PMID: 20876685
  
  
• 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. PMID: 20865155
  
  

2010

• Li J, Yuan Z., Zhang Z., "The Cellular Robustness by Genetic Redundancy in Budding Yeast" PLOS Genetics, 2010 Nov 4;6(11):e1001187. PMID: 21079672
  
  
• 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 PMID: 20935054
  
  
• 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). PMID: 20865155
  
  
• 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 PMID: 20489180
  
  
• 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 PMID: 20455264
  
  
• 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] PMID: 20139146
  
  
• 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 PMID: 20065090
  
  
• 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 PMID: 20010809
  
  
• 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 PMID: 19933172
  
  
• 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.] PMID: 19995808
  
  

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 PMID: 19775440
  
  
• 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) PMID: 20014473
  
  
• Guo X., Zhang Z., Gerstein M., and Zheng D. "Small RNAs Originated From Pseudogenes, cis- or trans-Acting? " PLOS Computational Biology (2009) PMID: 19649160
  
  
• 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) PMID: 20333195
  
  
• 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) PMID: 19536198
  
  
• 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) PMID: 19254184
  
  
• 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 PMID: 19521829
  
  
• 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) PMID: 18727826
  
  
• 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) PMID: 18616827
  
  
• 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) PMID: 18463300
  
  
• 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 PMID: 19348634
  
  
• 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) PMID: 18218112

• Gunewardena S., Zhang Z., "A Hybrid Model for Robust Detection of Transcription Factor Binding Sites" Bioinformatics (2008) 24(4):484-491 PMID: 18184687

• 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 PMID: 17925355
  
  
• 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 PMID: 17925354
  
  
• 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) PMID: 17630806
  
  
• 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) PMID: 17612295
  
  
• 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 PMID: 17428571
  
  
• *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. PMID: 17288572
  
  
• 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) PMID: 17099229
  
  

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)
  
  PMID: 16574694
• 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]