Curriculum Vitae

Yan Zhang, PhD

(Last updated Aug. 2020)

• Genome structural variation

  • Functional impact of structural variations in both normal and abnormal genomes

  • Retroduplication discovery, and functional and evolutionary analysis

  • Association and eQTL analysis

• Cancer genomics

  • Cancer signature, subtype, and subclone identification

• Integrative analysis of proteomic and genomic data

  • Structural variation, fusion genes, splice isoforms

• Deep learning in functional genomics

• Comparative genomics

Academic Positions

• Tenure-track Assistant Professor, Department of Biomedical Informatics, The Ohio State University, 2016-2020.

• Faculty Member, Biomedical Sciences Graduate Program, The Ohio State University, 2016-2020.

• Faculty Member, Center for Pharmacogenomics, The Ohio State University, 2016-2020.

• Faculty Member, Cancer Biology Research Program (previous Molecular Biology and Cancer Genetics Research Program), OSUCCC – James, 2016-2020.

• Faculty Member, OSUCCC Biomedical Informatics Shared Resource (BISR), The Ohio State University, 2018-2020.

• Affiliated Faculty, Translational Data Analytics Institute (TDAI), The Ohio State University, 2019-2020.

Training

• Postdoctoral Associate, Genomics and Proteomics (Advisor: Mark Gerstein), Program in Computational Biology and Bioinformatics; Department of Molecular Biophysics and Biochemistry, Yale University, Oct 2012-Jan 2016.

Education

• Ph.D. in Computational Medicine & Bioinformatics, University of Michigan - Ann Arbor, 2012.

• M.A. in Statistics, University of Michigan - Ann Arbor, 2011.

• M.S. in Biology (Bioinformatics), Tsinghua University, Beijing, China, 2007.

• B.E. in Automation (Control Science and Engineering), Tsinghua University, Beijing, China, 2005.

        * co-first author    # corresponding author    ¶ trainee   

[C] conference papers   [J] journal papers   [A] abstracts [B] invited book chapters

     Peer-Reviewed Papers

• [J26] T.S. Johnson¶, C.Y. Yu, Z. Huang, S. Xu, T. Wang, C. Dong, W. Shao, M.A. Zaid, Y. Wang, C. Bartlett, Y. Zhang, Y. Liu, J. Zhang, K. Huang (2020). Diagnostic Evidence GAuge of Single cells (DEGAS): A Transfer Learning Framework to Infer Impressions of Cellular and Patient Phenotypes between Patients and Single Cells. Submitted.

• [B1] Y. Zhang and D. Zheng (2020). Pseudogene Profiling for Cancer Subtype Classification. Submitted.

• [J25] X. Li, S. Kumar, A. Harmanci, S. Li, R. Kitchen, Y. Zhang, V.B. Wali, S. Krishnamurthy, S. Reddy, W. Woodward, J. Reuben, C. Hatzis, N.T. Ueno,  S. Krishnamurthy, L. Pusztai, M. Gerstein (2020). Genomic Landscape of Inflammatory Breast Cancer by Whole-Genome Sequencing. Submitted.

• [J24] Z. Xu, H. Li, E. Li, W. Dong, Y. Zhang, Y. Guan (2019). LightNuclei: Simultaneous Nuclei Counting and Segmentation by a Light-weighted Deep Learning Model. Submitted.

• [J23] E.M. Mokrzan, C.P. Ahearn, J.R. Buzzo, L.A. Novotny, Y. Zhang, S.D. Goodman, L.O. Bakaletz (2020). Nontypeable Haemophilus influenzae Newly Released (NRel) from Biofilms by Antibody-Mediated Dispersal Versus Antibody-Mediated Disruption Are Phenotypically Distinct. Biofilm. Accepted.

• [J22] T.S. Johnson¶, S. Xiang, B.R. Helm, Z.B. Abrams, P. Neidecker, R. Machiraju, Y. Zhang, K. Huang, J. Zhang (2020). Spatial Cell Type Composition in Normal and Alzheimers Human Brains is Revealed Using Integrated Mouse and Human Single Cell RNA Sequencing. Scientific Reports 10, Article number: 18014. [IF: 4.576]

• [J21] K. Fan¶, Y. Zhang# (2020). Pseudo2GO: A Graph-Based Deep Learning Method for Pseudogene Function Prediction by Borrowing Information from Coding Genes. Frontiers in Genetics. 18 August 2020. [IF: 3.360] Code & Tool - Pseudo2GO

• [J20] K. Fan¶, Y. Guan#, Y. Zhang# (2020). Graph2GO: A Multi-Modal Attributed Network Embedding Method for Inferring Protein Functions. GigaScience 9(8). Graph2GO Search Supporting Data [IF: 6.950]

• [J19] S. Kumar, J. Warrell, S. Li, P. McGillivray, W. Meyerson, L. Salichos, A. Harmanci, A. Martinez-Fundichely, C.W.Y. Chan, M. Nielsen, L. Lochovsky, Y. Zhang, X. Li, S. Lou, J.S. Pedersen, C. Herrmann, G. Getz, E. Khurana, M. Gerstein (2020). Passenger Mutations in 2500 Cancer Genomes: Overall Molecular Functional Impact and Consequences. Cell 180(5):915-927. [IF: 36.216]

• [J18] The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, including Y. Zhang (2020). Pan-Cancer Analysis of Whole Genomes. Nature 578(7793):82-93. Featured in Nature. Highlight in Nature, Science and Wellcome Sanger Institute News. [IF: 43.070]

• [J17] E. Liu, G.H. Kinnebrew, J. Li, P. Zhang, Y. Zhang, L. Cheng, L. Li (2019). A Fast and Furious Bayesian Network (FFBN) and Its Application of Identifying Colon Cancer to Liver Metastasis Gene Regulatory Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2019 Oct 1. doi: 10.1109/TCBB.2019.2944826. [IF: 2.428]

• [J16/C] A. Awasthi*¶, S. Tan*¶, T.S. Johnson¶, X.-M. Mo, K. Fan¶, Y. Zhang# (2019). PgenePapers: A Novel Database and Search Tools of Reported Regulatory Pseudogenes. International Journal of Computational Biology and Drug Design. In press. (Accepted at ICIBM 2019)

• [J15/C] T. Eicher​*¶, A. Patt*¶​, E. Kautto¶​, R. Machiraju#, E. Mathé#, Y. Zhang# (2019). ​Challenges in Proteogenomics: A Comparison of Analysis Methods with the Case Study of the DREAM Proteogenomics Sub-Challenge. BMC Bioinformatics 20(Suppl 24):669. (Oral presentation at ICIBM 2019) [IF: 2.970] 

• [J14/C]  S. Smerekanych*¶, T.S. Johnson*¶, K. Huang, Y. Zhang# (2019). Pseudogene-Gene Functional Networks Are Prognostic of Patient Survival in Breast Cancer. BMC Medical Genomics 13(Suppl 5):51. (Oral presentation at ICIBM 2019) [IF: 3.062]

• [J13] T.S. Johnson¶, T. Wang, Z. Huang, C.Y. Yu, Y. Wu, Y. Han, Y. Zhang, K. Huang, J. Zhang (2019). LAmbDA: Label Ambiguous Domain Adaptation Dataset Integration Reduces Batch Effects and Improves Subtype Detection. Bioinformatics 35(22):4696-4706. [IF: 4.531]

• [J12] T.S. Johnson¶, S. Li¶, E. Franz, Z. Huang, S.D. Li, M.J. Campbell, K. Huang, Y. Zhang# (2019). PseudoFuN: Deriving Functional Potentials of Pseudogenes from Integrative Relationships with Genes and miRNAs across 32 Cancers. GigaScience 8(5). PseudoFuN DB Search Supporting Data [IF: 7.267]

• [J11] A. Frankish, M. Diekhans, A.-M. Ferreira, R. Johnson, I. Jungreis, J. Loveland, J.M. Mudge, C. Sisu, J. Wright, J. Armstrong, I. Barnes, A. Berry, A. Bignell, S.C. Sala, J. Chrast, F. Cunningham, T.D. Domenico, S. Donaldson, I.T. Fiddes, C.G. Girón, J.M. Gonzalez, T. Grego, M. Hardy, T. Hourlier, T. Hunt, O.G. Izuogu, J. Lagarde, F.J. Martin, L. Martínez, S. Mohanan, P. Muir, F.C.P. Navarro, A. Parker, B. Pei, F. Pozo, M. Ruffier, B.M. Schmitt, E. Stapleton, M.-M. Suner, I. Sycheva, B. Uszczynska-Ratajczak, J. Xu, A. Yates, D. Zerbino, Y. Zhang, B. Aken, J.S. Choudhary, M. Gerstein, R. Guigó, T.J.P. Hubbard, M. Kellis, B. Paten, A. Reymond, M.L. Tress, P. Flicek (2018). GENCODE Reference Annotation for the Human and Mouse Genomes. Nucleic Acids Research 47(D1):D766-D773. [IF: 11.561]

• [C3] T.S. Johnson¶, S. Li¶, J.R. Kho, K. Huang, Y. Zhang# (2018). Network Analysis of Pseudogene-Gene Relationships: From Pseudogene Evolution to Their Functional Potentials. Pacific Symposium on Biocomputing 23:536-547. [IF: 2.82] (Selected for oral presentation, PSB 2018 Travel Award to trainee)

• [J10] T. Johnson¶, Z. Abrams, X. Mo, Y. Zhang, K. Huang (2017). Lack of Human Cytomegalovirus Expression in Single Cells from Glioblastoma Tumors and Cell Lines. Journal of NeuroVirology 23(5):671-678. [IF: 3.206]

• [J9] Y. Zhang*, S. Li*, A. Abyzov, M.B. Gerstein (2017). Landscape and Variation of Novel Retroduplications in 26 Human Populations. PLoS Computational Biology 13(6): e1005567. [IF: 4.587] Code & Tool - Retrodup

• [C2] T. Johnson¶, Z. Abrams, Y. Zhang, K. Huang (2017). Mapping Neuronal Cell Types Using Integrative Multi-Species Modeling of Human and Mouse Single Cell RNA Sequencing. Pacific Symposium on Biocomputing 22:599-610. [IF: 2.82]

• [J8] P.H. Sudmant*, T. Rausch*, E.J. Gardner*, R.E. Handsaker*, A. Abyzov*, J. Huddleston*, Y. Zhang*, K. Ye*, G. Jun, M.H.Y. Fritz, M.K. Konkel, A. Malhotra, A.M. Stütz, X. Shi, F.P. Casale, J. Chen, F. Hormozdiari, G. Dayama, K. Chen, M. Malig, M.J.P. Chaisson, K. Walter, S. Meiers, S. Kashin, E. Garrison, A. Auton, H.Y.K. Lam, X.J. Mu, C. Alkan, D. Antaki, T. Bae, E. Cerveira, P. Chines, Z. Chong, L. Clarke, E. Dal, L. Ding, S. Emery, X. Fan, M. Gujral, F. Kahveci, J.M. Kidd, Y. Kong, E.W. Lameijer, S. McCarthy, P. Flicek, R.A. Gibbs, G. Marth, C.E. Mason, A. Menelaou, D.M. Muzny, B.J. Nelson, A. Noor, N.F. Parrish, M. Pendleton, A. Quitadamo, B. Raeder, E.E. Schadt, M. Romanovitch, A. Schlattl, R. Sebra, A.A. Shabalin, A. Untergasser, J.A. Walker, M. Wang, F. Yu, C. Zhang, J. Zhang, X. Zheng-Bradley, W. Zhou, T. Zichner, J. Sebat, M.A. Batzer, S.A. McCarroll, The 1000 Genomes Project Consortium, R.E. Mills, M.B. Gerstein, A. Bashir, O. Stegle, S.E. Devine, C. Lee, E.E. Eichler, J.O. Korbel (2015). An Integrated Map of Structural Variation in 2,504 Human Genomes. Nature 526(7571), 75–81. Featured in Nature. Highlight in YaleNews, Nature, NIH News Release, and EMBL Press Release. [IF: 38.138]

• [J7] The 1000 Genomes Project Consortium, including Y. Zhang (2015). A Global Reference for Human Genetic Variation. Nature 526(7571), 68–74. Featured in Nature. Highlight in YaleNews, Nature, NIH News Release, and EMBL Press Release. [IF: 38.138]

• [J6] C. Sisu*, B. Pei*, J. Leng*, A. Frankish*, Y. Zhang*, S. Balasubramanian, R. Harte, D. Wang, M. Rutenberg-Schoenberg, W. Clark, M. Diekhans, J. Rozowsky, T. Hubbard, J. Harrow, M.B. Gerstein (2014). Comparative Analysis of Pseudogenes across Three Phyla. PNAS 111(37):13361-6. Highlight in YaleNews and ScienceDaily [IF: 9.674]

• [J5] M.B. Gerstein, J. Rozowsky, K. Yan, D. Wang, C. Cheng, J.B. Brown, C.A. Davis, L. Hillier, C. Sisu, J.J. Li, B. Pei, A.O. Harmanci, M.O. Duff, S. Djebali, R.P. Alexander, B.H. Alver, R. Auerbach, K. Bell, P.J. Bickel, M.E. Boeck, N.P. Boley, B.W. Booth, L. Cherbas, P. Cherbas, C. Di, A. Dobin, J. Drenkow, B. Ewing, G. Fang, M. Fastuca, E.A. Feingold, A. Frankish, G. Gao, P.J. Good, R. Guigó, A. Hammonds, J. Harrow, R.A. Hoskins, C. Howald, L. Hu, H. Huang, T.J.P. Hubbard, C. Huynh, S. Jha, D. Kasper, M. Kato, T.C. Kaufman, R.R. Kitchen, E. Ladewig, J. Lagarde, E. Lai, J. Leng, Z. Lu, M. MacCoss, G. May, R. McWhirter, G. Merrihew, D.M. Miller, A. Mortazavi, R. Murad, B. Oliver, S. Olson, P.J. Park, M.J. Pazin, N. Perrimon, D. Pervouchine, V. Reinke, A. Reymond, G. Robinson, A. Samsonova, G.I. Saunders, F. Schlesinger, A. Sethi, F.J. Slack, W.C. Spencer, M.H. Stoiber, P. Strasbourger, A. Tanzer, O.A. Thompson, K.H. Wan, G. Wang, H. Wang, K.L. Watkins, J. Wen, K. Wen, C. Xue, L. Yang, K. Yip, C. Zaleski, Y. Zhang, H. Zheng, S.E. Brenner, B.R. Graveley, S.E. Celniker, T.R. Gingeras, R. Waterston (2014). Comparative Analysis of the Transcriptome across Distant Species. Nature 512(7515), 445-8. Highlight in YaleNews and ScienceDaily. [IF: 41.456]

• [J4] Y. Zhang, H.K. Kweon, C. Shively, A. Kumar, P.C. Andrews (2013). Towards Systematic Discovery of Signaling Networks in Budding Yeast Filamentous Growth Stress Response Using Interventional Phosphorylation Data. PLoS Computational Biology 9(6): e1003077. [IF: 4.839]

• [J3] R. Menon, Q. Zhang, Y. Zhang, D. Fermin, N. Bardeesy, R.A. DePinho, C. Lu, S.M. Hanash, G.S. Omenn, D.J. States (2009). Identification of Novel Alternative Splice Isoforms of Circulating Proteins in a Mouse Model of Human Pancreatic Cancer. Cancer Research 69(1):300-9. [IF: 7.543]

• [J2] C. Song, Q. Liu, Y. Zhang, B. Jiang, Z. Xu, Y. Xia, X. Liu (2008). A Novel Method of Literature Data Mining and Visualization. Beijing Biomedical Engineering 27(2):156-160. [IF: 0.399]

• [C1] Y. Zhang, Q. Liu, Y. Guo, C. Song, J. Wang, X. Zhang, Y. Xia, Y. Cai, X. Liu (2007). eMIS: Protein Modification Database and Flow Processing System of Chinese Human Liver Proteome Project. ICBBE 2007, IEEE Conference Publications, pages 162–167. 

• [J1] Y. Zhang (2005). A Method of Science Research Informatization. Chinese Journal of Medical Science Research Management 18(6): 355-358, 347. [IF: 0.361]

     Peer-Reviewed Conference Abstracts

• [A5] K. Fan¶, Y. Zhang# (2019). PseudoNet: A Graph Representation Learning Method For Inferring Pseudogene Functions by Borrowing Information From Coding Genes. Presented as poster presentation at the 69th Annual Meeting of The American Society of Human Genetics, Oct 16, 2019, Houston, TX. (PgmNr 1512/W, Main Session: Bioinformatics and Computational Approaches.)

• [A4] Y. Zhang#, S. Tan¶, X.-M. Mo (2018). Reconstruct Pseudogene Regulatory Networks Using Natural Language Processing For Novel Drug Target Prediction. Presented as poster presentation at the 68th Annual Meeting of The American Society of Human Genetics, Oct 19, 2018, San Diego, CA. (PgmNr 836/F, Main Session: Cancer Genetics.)

• [A3] S. Kumar, J. Warrel, P. Mcgillivray, W. Meyerson, S. Li, L. Salichos, A. Harmanci, A. Fundichely, C. Chan, C. Herrmann, M. Nielsen, L. Lochovsky, Y. Zhang, X. Li, E. Khurana, G. Getz, M. Gerstein (2018). Passenger Mutation Landscape in Cancer Genomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1279.

• [A2] Y. Zhang#, T. Johnson¶, S. Yu, K. Huang (2017). Evaluating Relationships between Pseudogenes and Genes: From Pseudogene Evolution to Their Functional Potentials. Presented as poster presentation at the 67th Annual Meeting of The American Society of Human Genetics, Oct 20, 2017, Orlando, FL. (PgmNr 735/F, Main Session: Cancer Genetics.)

• [A1] M. Gerstein, S. Kumar, P. McGillivray, W. Myerson, L. Salichos, S. Li, A. Harmanci, J. Warrell, E. Khurana, A. Fundichely, C. Chan, C. Herrmann, M. Nielsen, X. Li, Y. Zhang (2017). Passenger Mutations in 2500 Cancer Genomes: Overall Molecular Functional Impact and Consequences. Presented as platform presentation at the 67th Annual Meeting of The American Society of Human Genetics, Oct 18, 2017, Orlando, FL. (PgmNr 53, Main Session: Landscape of Cancer: Bioinformatic Analyses.)

         * co-first author    # corresponding author    ¶ trainee    ^ trainee as presenter

• [CT14] E. Becker¶^, Y. Zhang# (2020). COVID-19 Predictive Model. The Ohio State University Comprehensive Cancer Center & Kenyon College Pelotonia Partnership Undergraduate Research Symposium, online, Jul 23, 2020.

• [CT13] Y. Zhang (2019). Probing Pseudogene Functional Impact from Multiple Omics and Multiple Angles. Cancer Systems Biology Retreat, The Ohio State University, Columbus, OH, Jun 28, 2019.

• [CT12] T. Eicher*​¶, A. Patt*¶^​, E. Kautto¶​, R. Machiraju#, E. Mathé#, Y. Zhang# (2019). ​Challenges in Proteogenomics: A Comparison of Analysis Methods with the Case Study of the DREAM Proteogenomics Sub-Challenge. International Conference on Intelligent Biology and Medicine (ICIBM 2019), Columbus, OH, Jun 11, 2019.

• [CT11]  S. Smerekanych*¶, T.S. Johnson*¶^, K. Huang, Y. Zhang# (2019). Pseudogene-Gene Functional Networks Are Prognostic of Patient Survival in Breast Cancer. International Conference on Intelligent Biology and Medicine (ICIBM 2019), Columbus, OH, Jun 10, 2019.

• [CT10] Y. Zhang (2019). Functional Annotation of Coding and Non-coding Genomic Regions. Cancer Systems Biology Meeting, The Ohio State University, Columbus, OH, Apr 25, 2019.

• [CT9] K. Fan¶^, Y. Zhang# (2019). Use Deep Learning to Study the Potential Functions of Coding Regions. OSU Comprehensive Cancer Center (OSUCCC - James) Molecular Biology and Cancer Genetics Program 2019 Retreat, Grange Insurance Audubon Center, Columbus, OH, Feb 9, 2019.

• [CT8] Y. Zhang (2018). Pseudogene Discovery and Function Study. Cancer Systems Biology Meeting, The Ohio State University, Columbus, OH, Nov 28, 2018.

• [CT7] S. Smerekanych¶^, Y. Zhang# (2018). Interpretable Model Integrating Molecular and Clinical Information For Patient Survival Prediction in Breast Cancer. The Ohio State University Comprehensive Cancer Center & Kenyon College Pelotonia Partnership Undergraduate Research Symposium, The Ohio State University, Columbus, OH, Jul 27, 2018.

• [CT6] Y. Zhang (2018). Genome Structural Variation and Disease Propensity. Cancer Systems Biology Meeting, The Ohio State University, Columbus, OH, Feb 7, 2018.

• [CT5] T.S. Johnson¶^, S. Li¶, J.R. Kho, K. Huang, Y. Zhang# (2018). Network Analysis of Pseudogene-Gene Relationships: From Pseudogene Evolution to Their Functional Potentials. PSB (Pacific Symposium on Biocomputing) 2018, Hawai'i, HI, Jan 7, 2018. (Podium presentation with accepted paper)

• [CT4] Y. Zhang (2017). An NBT Practice: Search For the Functional Elements in Gene Deserts. No-Boundary Thinking (NBT) Workshop, Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, Dec 1, 2017.

• [CT3] Y. Zhang (2017). Duplication, Retroduplication and Fusion Genes. Work-In-Progress in High Dimensional Biological Data Analysis, Department of Biomedical Informatics, The Ohio State University, Columbus, OH, Oct 30, 2017.

• [CT2] Y. Zhang (2017). Functional Analysis of Genome Structural Variations. CALIBRE Meeting, Department of Biomedical Informatics, The Ohio State University, Columbus, OH, Mar 24, 2017.

• [CT1] Y. Zhang, M.B. Gerstein, A. Abyzov (2016). Functional Analysis: Relate SVs to Molecular Mechanisms, Population Divergence and Disease Propensity. HGSVC (Human Genome Structural Variation Consortium) Meeting at ASHG 2016, Vancouver, BC, Canada, Oct 18, 2016.

         * co-first author    # corresponding author    ¶ trainee

• [P34] A. Cloud¶, W. Tarver, Y. Zhang, B. Bernardo, T. Adeyanju, E.D. Paskett (2020). A Systematic Review of COVID-19 across the Cancer Care Continuum. OSUCCC Center for Cancer Health Equity, 2020 Undergraduate Summer Research Internship Program Symposium, online, Aug 7, 2020. 

• [P33] K. Fan¶, Y. Zhang# (2019). Pseudo2GO: Inferring Pseudogene Functions by Borrowing Information from Coding Genes Using Graph Neural Networks. CCTS Annual Scientific Meeting, The Ohio State University, Dec 3, 2019. (Category: AI and data analytics. First Place Winner poster.)

• [P32] L. Wang¶, T.S. Johnson¶, C. Song, M.J. Campbell, J. Parvin, Y. Zhang# (2019). Identification of Prognostic Pseudogene-Gene Interactions and microRNA-Gene Interactions in Prostate Cancer. CCTS Annual Scientific Meeting, The Ohio State University, Dec 3, 2019. (Category: AI and data analytics.)

• [P31] K. Fan¶, Y. Zhang# (2019). Pseudo2GO: Inferring Pseudogene Functions by Borrowing Information from Coding Genes. 69th Annual Meeting of The American Society of Human Genetics, Houston, TX, Oct 16, 2019.

• [P30] L. Wang¶, T.S. Johnson¶, C. Song, M.J. Campbell, Y. Zhang# (2019). Interaction Networks of mRNA, Pseudogene, and microRNA in Prostate Cancer Prognosis. BMI Summer Internship Program Poster Session, Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, Jul 25, 2019.

• [P29] S. Li¶, A. Awasthi¶, Y. Zhang# (2019). Modeling Pseudogenes’ Activity in Human Genome: Exploring the Features That Determine Pseudogenes’ Functionality in Different Cancer Types. BMI Summer Internship Program Poster Session, Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, Jul 25, 2019.

• [P28] E. Encarnacion¶, S. Li¶, Y. Zhang# (2019). Characterization of Coding and Non-coding Genes in the Human Genome.  Cancer Research Experience for the Advancement and Training of Emerging Scientists (CREATES) High School Poster Session, OSUCCC - James, Columbus, OH, Jul 25, 2019.

• [P27] A. Awasthi*¶, S. Tan*¶, X.-M. Mo, K. Fan¶, Yan Zhang# (2019). PgenePapers: A Novel Database and Search Tools of Reported Regulatory Pseudogenes. International Conference on Intelligent Biology and Medicine (ICIBM 2019), Columbus, OH, USA, Jun 9, 2019.

• [P26] T.S. Johnson¶, S. Smerekanych¶, K. Huang, Y. Zhang# (2019). Fossil Molecules of Evolution and Their Living Relatives: A Prognostic Tool. OSU Comprehensive Cancer Center (OSUCCC - James) 20th Annual Scientific Meeting, The Ohio State University, Columbus, OH, May 8, 2019.

• [P25] T. Johnson¶, Z. Abrams, B. Helm, P. Neidecker, R. Machiraju, Y. Zhang, K. Huang, J. Zhang (2019). Integration of Mouse and Human Single-cell RNA Sequencing Infers Spatial Cell-type Composition in Human Brains. Late Breaking Posters, RECOMB 2019 (23rd Annual International Conference on Research in Computational Molecular Biology), The George Washington University, Washington, DC, May 5-8, 2019.

• [P24] K. Fan¶, Y. Guan, Y. Zhang# (2019). Graph2GO: A Network Embedding Method for Protein Function Prediction Using Multiple Sources of Information. 2019 OSUWMC Trainee Research Day, Columbus, OH, April 11, 2019.

• [P23] A. Awasthi¶, S. Tan¶, X.-M. Mo, K. Fan¶, Y. Zhang# (2019). PgenePapers: A Novel Pseudogene Database - Reconstruct Pseudogene Regulatory Networks Using NLP. 2019 OSUWMC Trainee Research Day, Columbus, OH, April 11, 2019.

• [P22] S. Li¶, R. Li¶, Y. Zhang# (2019). The Comparison of Different Fusion Transcript Detection Methods. 2019 OSUWMC Trainee Research Day, Columbus, OH, April 11, 2019.

• [P21] S. Tan¶, A. Awasthi¶, X.-M. Mo, Y. Zhang# (2018). Reconstruct Pseudogene Regulatory Networks Using Natural Language Processing For Novel Drug Target Prediction. 68th Annual Meeting of The American Society of Human Genetics, San Diego, CA, Oct 2018.

• [P20] S. Li¶, R. Li¶, Y. Zhang# (2018). Setting Up A Pipeline For Whole Genome Sequencing Variant Calling. BMI Summer Internship Program Poster Session, Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, Aug 9, 2018.

• [P19] S. Tan¶, X.-M. Mo, Y. Zhang# (2018). Reconstruct Pseudogene Regulatory Networks Using Natural Language Processing for Novel Drug Target Prediction. OSU Comprehensive Cancer Center (OSUCCC - James) 19th Annual Scientific Meeting, The Ohio State University, Columbus, OH, Apr 27, 2018.

• [P18] S. Kumar, J. Warrel, P. Mcgillivray, W. Meyerson, S. Li, L. Salichos, A. Harmanci, A. Fundichely, C. Chan, C. Herrmann, M. Nielsen, L. Lochovsky, Y. Zhang, X. Li, E. Khurana, G. Getz, M. Gerstein (2018). Passenger Mutation Landscape in Cancer Genomes. American Association for Cancer Research (AACR) Annual Meeting 2018, Chicago, IL, Apr 16, 2018.

• [P17] T.S. Johnson¶, S. Li¶, J.R. Kho, K. Huang, Y. Zhang# (2018). Network Analysis of Pseudogene-Gene Relationships: From Pseudogene Evolution to Their Functional Potentials. PSB (Pacific Symposium on Biocomputing) 2018, Hawai'i, HI, Jan 2018. (Accompanying poster with podium presentation and accepted paper)

• [P16] Y. Zhang#, T. Johnson¶, S. Yu, K. Huang (2017). Evaluating Relationships between Pseudogenes and Genes: From Pseudogene Evolution to Their Functional Potentials. 67th Annual Meeting of The American Society of Human Genetics, Orlando, FL, Oct 2017.

• [P15] T. Johnson¶, S. Yu, K. Huang, Y. Zhang# (2017). Building a Pseudogene-Gene Network Database Linking Homologous and Phylogenetic Relationships to Potential Functions of ‘Activated’ Pseudogenes in Cancer. NLM 2017 Informatics Training Conference, University of California San Diego, La Jolla, CA, Jun 2017.

• [P14] T. Johnson¶, S. Yu, K. Huang, Y. Zhang# (2017). Building a Pseudogene-Gene Network Database Linking Homologous and Phylogenetic Relationships to Potential Functions of ‘Activated’ Pseudogenes in Cancer. OSU Comprehensive Cancer Center (OSUCCC - James) 18th Annual Scientific Meeting, The Ohio State University, Columbus, OH, Apr 28, 2017.

• [P13] T.S. Johnson¶, Z.B. Abrams, P. Neidecker, R. Machiraju, Y. Zhang, K. Huang (2017). Exploring Spatial Cell-type Expression Across the Entire Human Allen Brain Atlas Using Mouse and Human Single-cell Sequencing. 2017 OSUWMC Trainee Research Day, Columbus, OH, April 13, 2017. 

• [P12] T. Johnson¶, Z. Abrams, Y. Zhang, K. Huang (2017). Mapping Neuronal Cell Types Using Integrative Multi-Species Modeling of Human and Mouse Single Cell RNA Sequencing. PSB (Pacific Symposium on Biocomputing) 2017, Hawai'i, HI, Jan 2017. (Poster with accepted paper)  

• [P11] Y. Zhang*, T. Johnson*¶, R. Aldana, G. Feng, K. Huang (2016). Comparing Variant Concordance in DNA-seq and RNA-seq from Matched Samples. ISMB (Intelligent Systems for Molecular Biology) 2016, Orlando, FL, Jul 2016.

• [P10] T. Johnson¶, J. Kho, Ü.V. Çatalyürek, K. Huang, Y. Zhang# (2016). Identification of Key Mutation Signatures from Conservation Analysis of Gene-pseudogene Families in Human. ISMB (Intelligent Systems for Molecular Biology) 2016, Orlando, FL, Jul 2016.

• [P9] Y. Zhang, N. Downing, E. Bucholz, S. Balasubramanian, S.X. Li, T. Liptak, H. Krumholz, M. Gerstein (2014). Applying Novel Tree-based Frameworks to Big Data for Classification of Heart Failure Patients and Prediction of Clinical Responses. Yale Day of Data 2014, Yale University, New Haven, CT, Sep 2014.

• [P8] B. Pei, C. Sisu, Y. Zhang, A. Frankish, C. Howald, L. Habegger, X.J. Mu, R. Harte, S. Balasubramanian, A. Tanzer, M. Diekhans, A. Reymond, T.J. Hubbard, J. Harrow, M.B. Gerstein (2013). ENCODE Pseudogenes: Human, Worm, and Fly – a Comparative Study. ENCODE 2013 Consortium Meeting, Stanford University, Palo Alto, CA, May 2013.

• [P7] M.B. Gerstein, et al. including Y. Zhang (2013). Principles of Transcription Revealed from Transcriptome Comparison of Divergent Metazoans: Statistical Models of Transcription. ENCODE 2013 Consortium Meeting, Stanford University, Palo Alto, CA, May 2013.

• [P6] Y. Zhang, H.K. Kweon, C. Shively, A. Kumar, P.C. Andrews (2011). Quantitative Phosphoproteomic Analysis to Elucidate Signaling Networks of Yeast Filamentous Growth. 59th ASMS Conference on Mass Spectrometry and Allied Topics, Denver, CO, Jun 2011.

• [P5] C.A. Shively, H.K. Kweon, T. Xu, Y. Zhang, C. Dobry, Q. Song, C. Johnson, P.C. Andrews, A. Kumar. Quantitative Phosphoproteomics Identifies Relationships between Stress Responses in Saccharomyces cerevisiae. CMB (Cellular & Molecular Biology) Symposium, University of Michigan, Ann Arbor, MI, Fall 2011.

• [P4] Y. Zhang, H.K. Kweon, P.C. Andrews (2010). Tandem Mass Spectrometry Data Analysis to Map Signaling Pathways and Protein Interaction Network. JSM (Joint Statistical Meetings) 2010, Vancouver, BC, Canada, Jul 31-Aug 5, 2010.

• [P3] Quantitative Phosphoproteomic Analysis to Elucidate Signaling Networks of Yeast Filamentous Growth. (with H.K. Kweon, C.A. Shively, A. Kumar and P.C. Andrews) Michigan Mass Spectrometry Discussion Group, Ann Arbor, MI, Dec 2010.

• [P2] Modeling Based Interpretation of Protein Isoforms in IPAS. (with R. Menon, D.J. States and G.S. Omenn) Additional Biological Applications of the NCIBI All Hand Meeting, Ann Arbor, MI, Apr 2008.

• [P1] An Approach to Identify Cell Line Contamination (HeLa) in Microarray Data. (with Z.S. Qin and D.J. States) Additional Biological Applications of the NCIBI All Hand Meeting, Ann Arbor, MI, Apr 2008.

• Statistical computing: R, MatLab/Octave, SPSS.

• Programming and database development: C/C++, Shell, Python, Perl, SQL, Java.

• Parallel computing: PBS, LSF, Slurm.

• Others: LaTeX, XML.