Zemin Zhang, Ph. D
Download 89.57 Kb.
|
- Navigate this page:
- Professional Experiences
- Professional Activities Journal Editorial Services
- Professional Memberships
- Invited Talks (selected)
- Selected Achievements at Genentech
| Zemin Zhang, Ph.D.
Principal Scientist Genentech, Inc. 1 DNA Way South San Francisco, CA 94080 +1 (650) 225-4293 (office), +1 (650) 580-0284 (cell) Email: zeminz@yahoo.com, zemin@gene.com Profile and Research InterestsExecutive Profile: Proven scientific thought leader with strong organizational and communication skills, academic reputation, and track record in target discovery and drug development. Research Interests: Innovative therapeutics and diagnostics development through cancer genomics Genomics-driven diagnostic biomarker and target discovery for cancer therapeutics Understanding genetic basis of cancer by applying innovative technologies such as next generation sequencing to cancer genome studies Virus-human genome and transcriptome interaction in cancers Identification of epigenetic regulators as targets and biomarkers for cancer treatment Education and Training1995-1998 Postdoctoral Fellow, University of California, San Francisco, CA Howard Hughes Medical Institute (Laboratory of Yuet Wai Kan)
Pennsylvania State University, University Park, PA (Laboratory of Andrew R. Buchman) 1988-1989 CUSBEA (China-US Biochemistry Exchange Program) training program B.S. in Genetics, Nankai University, Tianjin, China 1997-2001 Part time training in information technology at UC Berkeley extension Professional Experiences1/1998-present: Genentech Inc., South San Francisco, CA 11/2010-present: Principal Scientist, Department of Bioinformatics and Computational Biology Systematic identification of hepatitis B virus integration in the human genome Characterization of the impact viral integration on the human genome by RNA-Seq and whole genome sequencing of liver cancer samples Application of next-generation sequencing technologies, including RNA-Seq, Exome Sequencing and whole genome sequencing, to discover novel genomic features important for tumorigenesis and target discovery; Identification of novel biomarkers/features associated with lung cancer drug response based on combined RNA-Seq and whole genome sequencing Serve as the Chair of the Bioinformatics Steering Committee that oversees many key aspects of scientific operation and directions within the department Serve as the Bioinformatics lead to review and approve all next generation sequencing projects within Genentech Research Member of the Cancer Epigenetics leadership team to provide strategic and technical guidance on epigenomics-based target discovery initiative Continue to lead an expanded cancer informatics group to provide genomics support for and collaborate with cancer biologists Serve as a member of the Computational Biologist Appointment and Promotion Committee that oversees the hiring and promotion process of the Computational Biologist job family 3/2008-9/2009: Acting Director, Department of Bioinformatics Providing leadership and strategic planning for Department of Bioinformatics (~50 people); Supervising all bioinformatics and bio-computing groups to ensure proper alignment between group efforts and departmental goals, and to stimulate maximal productivity from each group; To ensure smooth business operations, assume financial responsibilities, and actively balance the achievement/reward equilibrium; Identifying internal and external collaboration opportunities; identifying and recruiting talents for long-term success of the department; 5/2004-11/2010: Senior Scientist, Department of Bioinformatics Managing a research and programming group to provide bioinformatics/genomics support for multiple oncology-related departments in Research; Leading the informatics and scientific efforts for DNA copy number analysis using CGH and SNP array platforms; Leading the effort to identify causal mutations in cancer using computational approaches; Leading the informatics effort to study the connection between microRNAs and cancer; Leading the functional variant association program using the cell-line system; 1/2000-4/2004: Bioinformatics Scientist, with joint appointment in Molecular Oncology Development of methods for detecting and analyzing cancer-associated gene variants; Providing Bioinformatics support as a liaison for Department of Molecular Oncology; Integration of external and internal microarray data for expression analysis and target discovery; Development of techniques for analyzing genomic instability in cancer; Development of novel methods for analyzing protein sequences and functional classification; Lead a team of programmers in developing of GeneHub as solution for biological data integration; Large-scale gene annotation and functional classification for microarray analysis; 12/1998-12/1999: Associate Bioinformatics Scientist, Department of Bioinformatics Development of EST-based expression profiling technology and application of expression informatics in searching for cancer targets; Method development for signal peptide prediction using hidden Markov models; Application of the signal peptide methods to gene discovery using both EST and human genomics data; Supervision of postdoctoral trainees in the gene discovery program 4/1998-12/1998: Programmer Analyst II, Research Bioinformatics group in Dept. Molecular Biology Development of sequence analysis pipeline; Process automation for data mining, such as automated feature extraction database loading for EST clone and EST library information; Integrated analyses based on sequence homology and signal peptide prediction; 1/1998-4/1998: Senior Research Associate, Research Bioinformatics group in Dept. Molecular Biology Large-scale identification of genes for novel secreted proteins by reviewing protein/DNA sequences identified by computational algorithms; Full-length gene assembly by in silico EST sequence extension and clone ordering; Sequence database curation and quality control; 7/1995-1/1998: Postdoctoral Research Fellow, UCSF, San Francisco, CA Long range genetic engineering using yeast artificial chromosome (YAC); Understanding roles of cis-acting elements in the beta globin locus during mouse embryonic development; YAC transgenic mice generation and genetic characterization; 8/1989-56/1995: Graduate Assistant, Penn State University, State College, PA Establishment of multiple genetic screens, including two-hybrid screens and DNA dosage-based expression systems, to identify genetic elements involved in transcriptional silencing in yeast; Using Sanger method to sequence >100 clones of yeast DNA with genetic role in transcriptional regulation, and perform computational analysis on these cis- and trans-acting elements; Perform genetic and biochemical characterization of RIS1 gene through various gene knockout and in vitro protein-protein and protein-DNA binding studies; Establishing specific interaction between RIS1 and multiple other proteins by yeast two hybrid studies Professional ActivitiesJournal Editorial Services:Cancer Informatics (2011-present, Associate Editor in Chief) The Open Systems Biology Journal (2009-present, Editorial Advisory Board Member) I. J. Functional Informatics and Personalized Medicine (2009-present, Editorial Board Member) Professional MembershipsAmerican Association for Cancer Research (AACR) International Society for Computational Biology (ISCB) American Society of Human Genetics (ASHG) Academic ServicesSan Jose State University Bioinformatics Industry Advisory Board member (since 2011) Lecturer of the international Summer School on NGS and GWAS for Complex and Monogenic Disorders (9/5-9/2011, Sardinia, Italy) NCI (National Cancer Institute) grant review and discussion panel IACR (Italian Association for Cancer Research) grant review A-STAR (Agency for Science, Technology and Research, Singapore) grant review GIS (Genome Institute of Singapore) SAB (Scientific Advisory Board) ad hoc member 2010 ISMB meeting proceeding review Journal Article Referee
Award and Honors1989 CUSBEA Scholar (China-US Biochemistry Exchange and Application Program) Featured scientist in the 2005 Genentech Annual Report, and 2012 Genentech Billboard (with theme “To us, science is personal”) Publication featured by major media including MSN, Business Week, Reuters, US World News Co-PI of a UCSF Discovery Grant that was funded Genentech Key Contributor Awards (multiple times) Granted PatentsRepresentative patents from a total of 57 granted US patents and numerous European patents: United States Patent 7,803,915, Cairns et al., “Antibody compositions for the diagnosis and treatment of tumor”, Issue date: September 28, 2010 United States Patent 7,585,953, Chen et al., “Antibodies specific for TAT285-1”, Issue date: September 8, 2009 United States Patent 7,514,538, Goddard et al., “Compositions and methods for the diagnosis and treatment of tumor”, Issue date: April 7, 2009 United States Patent 7,390,879, Ashkenazi et al., “Secreted and transmembrane polypeptides and nucleic acids encoding the same”, Issue date: June 24, 2008 United States Patent 7,307,153, Fong et al., “Antibodies that bind PRO9912”, Issue date: December 11, 2007 Other issued US patent numbers: 7,056,736, 7,070,955, 7,109,305, 7,125,962, 7,189,813, 7,189,817, 7,192,587, 7,247,446, 7,250,490, 7,276,578, 7,279,552, 7,285,644, 7,291,704, 7,291,705, 7,291,718, 7,294,335, 7,294,693, 7,294,695, 7,294,696, 7,297,769, 7,297,770, 7,297,769, 7,304,126, 7,309,771, 7,309,778, 7,312,303, 7,317,092, 7,335,730, 7,344,880, 7,365,157, 7,368,250, 7,378,487, 7,385,031, 7,390,882, 7,408,042, 7,432,345, 7,452,975, 7,497,797, 7,534,856, 7,547,768, 7,563,867, 7,576,185, 7,642,242, 7,696,319, 7,700,736, 7,718,770, 7,749,504, 7,767,403, 7,803,915, 7,939,268, 7,951,546, 8,084,200 Invited Talks (selected)“Human-Viral Genome Interactions: lessons learned from the hepatocellular carcinoma genomes and transcriptomes”, The 10th International Conference on Pathways, Networks, and Systems, Rhodes, Greece, June 10-15, 2012 “Genome and Transcriptome Analyses of Cancer Samples”, Roche Molecular Diagnostics. Pleasanton, CA, April 9, 2012 “Combined Whole Genome and Transcriptome Analysis of Lung and Liver Cancers”, US-Japan Cancer Genomics Workshop. Kyoto, Japan, October 22-24, 2011 “Impact of Hepatitis B Virus on Liver Cancer”, (Keynote Speaker), IEEE International Conference on Systems Biology. Zhuhai, China, September 2-4, 2011 “Personal Genome and Transcriptome: lessons learned from lung and liver tumors”, Tsinghua University, Beijing, China, August 15, 2011 “Combined Analyses of Cancer Genomes and Transcriptomes”, Beyond Sequencing 2011: Managing Resources and Maintaining NGS Platforms for Peak Performance. (Session Chair for all Keynote Speakers) San Francisco, CA. June 21-22, 2011 “Understanding Human Cancers by Whole Genome Sequencing”, The 12th Annual Advances in Genome Biology and Technology (AGBT, Complete Genomics Track). Marco Island, FL. February 2-5, 2011 “Whole Genome Sequencing of Lung Cancer Samples”, Genome Institute of Singapore, Singapore, November 16, 2010 “Understanding Cancer by Genomics Technologies -- an ‘industry’ bioinformatics journey” (Keynote Speech at the Biomedical Computation at Stanford conference), Stanford University, Palo Alto, CA, November 6, 2010 “Whole Genome Sequencing of Cancer Samples” University of California, Berkeley, CA, October 28, 2010 “Biomarker Discovery and Whole Genome Sequencing”, The AACR conference of Molecular Diagnostics in Cancer Therapeutic Development, Denver, CO, September 27-30, 2010 “Whole Genome Sequencing of Lung Cancer Samples”, The Personal Genomes. Cold Spring Harbor, NY, September 12-14, 2010 “Lung Cancer Mutation Landscape Revealed by Full Genome Sequencing”, Next Generation Sequencing & Genomic Medicine Applications Summit, Burlingame, CA. August 2-4, 2010 “Whole Genome Analysis of Lung Cancer Samples”, Nanjing University Medical School, Nanjing, China, June 22, 2010 “Whole Genome Analysis of Lung Cancer Samples”, BGI (Beijing Genomics), Shenzhen, China, June 18, 2010 “Primary Lung Tumor Somatic Mutation Spectrum Revealed by Paired Genome Sequencing”, The 11th Annual Advances in Genome Biology and Technology (AGBT). Marco Island, FL. February 24-27, 2010 “The Mutation Spectrum Revealed by Paired Genome Sequences from a Lung Cancer Patient”, The 2nd Advances in Bioinformatics and Genomics Symposium. Menlo Park/Stanford University, CA. February 19, 2010 “Mutational Landscape of a Fully Sequenced Lung Tumor”, Roche, Nutley, NJ, November 13, 2009 “Target Selection from DNA Copy Number and Expression Analyses of Breast and Ovarian Tumors” , Molecular Medicine Tri-Conference, San Francisco, CA, February, 2009 “Causal Gene Discovery from the Cancer Genome” (short talk), University of California, Berkeley, CA, October, 2007 “Computational Approaches to Distinguishing Deviants from Variants in the Cancer Genome”, University of Southern California (USC), Los Angeles, CA, September, 2007 “Bioinformatics Analysis of Missense Mutations”, AACR (American Association for Cancer Research) Annual Meeting 2007, Los Angeles, CA, April, 2007 “Somatic Mutations in Cancers”, San Francisco State University, San Francisco, CA, 2006 “Cancer Gene Identification Based on DNA Copy Number Analysis”, University of California, San Francisco, CA, 2005 “The Application of Oncogenomics Technologies in Cancer Target Discovery and Molecular Diagnostics”, Bay Area Bioinformatics Discussion Group, Stanford University, Palo Alto, CA, 2005 “The Application of Oncogenomics Technologies in Cancer Target Discovery and Molecular Diagnostics”, Roche Molecular Systems, Alameda, CA, 2005 “Cancer Target Discovery from Multiple Heterogeneous Data Sources”, 13th Annual Bioinformatics and Genome Research. San Francisco, CA, 2004 “Bioinformatics and Cancer Target Discovery”, The 8th Chinese and Oversea Forum on Discovery of New Drugs in Post-Genomic Era. Beijing, China, 2004 “From Computational Data to Cancer Genetics”, Nankai University, Tianjin, China, 2004 “Application of Bioinformatics in Cancer Target Discovery”, Macau University of Science and Technology, Macau, 2004 “Cancer Target Discovery from Multiple Heterogeneous Data Sources”, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, 2004 “From expressed sequence tags to cancer therapeutic targets”, Gordon Research Conference, Bioinformatics: From Prediction to Inference. Oxford University, Oxford, UK, 2003 “Identification of tumor antigens from EST data”, The Drug Discovery Technology World Congress. Boston, NY, 2003 “Bioinformatics searching and genomic organization of cancer-specific genes”, University of The Sciences In Philadelphia, PA, 2003 “Biological data integration using a data warehousing approach”, The Drug Discovery & Development Information Integration Congress, Miami, FL, 2003 “Large-scale data mining and career opportunities in bioinformatics”, University of California, San Francisco, CA, 1999 Publications(Correspondence-author articles have name underlined) Z. Jiang*, S. Jhunihunwala*, J. Liu, P. Haverty, K. Pant, M. I. Kennemer, P. Carnevali, Y. Guan, J. Stinson, P. Dijkgraaf, J. Rae, S. Johnson, C. Watanabe, J. Diao, S. Kapadia, F. de Sauvage, R. Gentleman, H. Stern, S. Seshagiri, Z. Modrusan, D. Ballinger, Z. Zhang (2012) The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients. Genome Research, 22:593-601 (cover article) J. Liu, W. Lee, Z. Chen, Z. Jiang, S. Jhunjhunwala, P. M Haverty, F. Gnad, Y. Guan, H. Gilbert, J. Stinson, C. Klijn, J. Guillory, D. Bhatt, S. Vartanian, K. Walter, J. Chan, P. Dijkgraaf, S. Johnson, J. Koeman, J. Minna, A. Gazdar, H. M. Stern, K. P. Hoeflich, T. D. Wu, F. J. de Sauvage, R. C. Gentleman, R. M. Neve, D. Stokoe, Z. Modrusan, S. Seshagiri, D. S. Shames, Z. Zhang (2012) Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events. (under review by Genome Research) Y. Wu, H. Grabsch, T. Ivanova, I. B. Tan, J. Murray, C. H. Ooi, A. Wright, J. Wu, M. Lee, J. Lee, J. H. Koo, K. G. Yeoh, N. van Grieken, B. Ylstra, S. Y. Rha, Z. Zhang, J. A. Ajani, T. D. Wu, J. H. Cheong, S. H. Noh, A. Boussioutas, J-S Lee, P. Tan (2012) Genomic Meta-analysis Reveals Histopathological Phenotypes for Refining Gastric Cancer Prognosis Prediction. J. Clin. Invest. (under revision) S. Seshagiri, E. Stawiski, S. Durinck, Z. Modrusan, E. Storm, S. Chaudhuri, Y. Guan, V. Janakiraman, J. Guillory, C. Parikh, C. Ha, P. Dijkgraaf, J. Stinson, F. Gnad, M. Huntley, J. Degenhardt, P. M. Haverty, W. Wang, H. Koeppan, R. Gentleman, Z. Zhang, T. D. Wu and F. J. de Sauvage (2012) Comprehensive analysis of colon cancer genomes identifies recurrent mutations and R-spondin fusions. (revised for Nature) W. Yuan, E. Stawiski, V. Janakiraman, E. Chan, S. Durinck, K. Edgar, N. M. Kljavin, C. S. Rivers, F. Gnad, M. Roose-Girma, P. M. Haverty, G. Fedorowicz, S. Heldens, R.H. Soriano, Z. Zhang, J. Wallin, L. Johnson, M. Merchant, Z. Modrusan, H. Stern and S. Seshagiri (2012) Conditional activation of PIK3CA H1047R in a knock-in mouse promotes mammary tumorigenesis and emergence of mutations. Oncogene (advance online publication doi: 10.1038/onc.2012.53) Z. Kan, B. S. Jaiswal, J. Stinson, V. Janakiraman, D. Bhatt, H. M. Stern, P. Yue, P. M. Haverty, R. Bourgon, J. Zheng, M. Moorhead, S. Chaudhuri, L. P. Tomsho, B. A. Peters, K. Pujara, S. Cordes, D. P. Davis, V. E. Carlton, W. Yuan, L. Li, W. Wang, C. Eigenbrot, J. S. Kaminker, D. A. Eberhard, P. Waring, S. C. Schuster, Z. Modrusan, Z. Zhang, D. Stokoe, F. J. de Sauvage, M. Faham and S. Seshagiri. (2010) Diverse somatic mutation patterns and pathway alterations in human cancers. Nature, 466: 869-873 W. Lee, Z. Jiang, J. Liu, P. M. Haverty, Y. Guan, J. Stinson, P. Yue, Y. Zhang, K. P. Pant, D. Bhatt, C. Ha, S. Johnson., M. I. Kennemer, S. Mohan, I. Nazarenko, C. Watanabe, A. B. Sparks, D. S. Shames, R. Gentleman, F. J. de Sauvage, H. Stern, A. Pandita, D. G. Ballinger, R. Drmanac, Z. Modrusan, S. Seshagiri, and Z. Zhang (2010) The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature, 465:473-477 P. Yue, J. S. Kaminker, W. F. Forrest, S. Lohr, Z. Zhang and G. Cavet (2010) Inferring the functional effects of mutation through clusters of mutations in homologous proteins. Human Mutation, 31 (3): 264-271 W. Lee, Y. Zhang, K. Mukhyala, R. Lazarus and Z. Zhang. (2009) Bi-directional SIFT predicts a subset of activating mutations. PLoS ONE, 4 (12): e8311. doi:10.1371/journal.pone.0008311 W. Lee, P. Yue, and Z. Zhang. (2009) Analytical methods for inferring functional effects of single base-pair substitutions in human cancers. Human Genetics, 126:481-498 L. S. Hon, Y. Zhang, J. S. Kaminker, and Z. Zhang. (2009) Computational prediction of the functional effects of amino acid substitutions in signal peptides using a model-based approach. Human Mutation, 30 (1): 99-106 P. M. Haverty, L. S. Hon, J. S. Kaminker, J. Chant*, and Z. Zhang*. (2009) High-resolution analysis of copy number alterations and associated expression changes in ovarian tumors. BMC Medical Genomics, 2:21 (* co-correspondence authors) H. Jin, R. Yang, Z. Zheng, M. Romero, J. Ross, H. Bou-Reslan, R. A. D. Carano, I. Kasman, E. Mai, J. Young, J. Zha, Z. Zhang, S. Ross, R. Schwall, G. Colbern, and M. Merchant. (2008) MetMAb, the one-armed 5D5 anti-c-Met antibody, inhibits orthotopic pancreatic tumor growth and improves survival. Cancer Res., 68 (11): 4360-4368 J. Liu, Y. Zhang, X. Lei, and Z. Zhang. (2008) Natural selection of protein structural and functional properties: a SNP perspective. Genome Biol., 9(4): R69 P. M. Haverty, J. Fridlyand, L. Li, G. Getz, R. Beroukhim, S. Lohr, T. D. Wu, G. Cavet, Z. Zhang*, and J. Chant*. (2008) High-resolution genomic and expression analyses of copy number alterations in breast tumors. Genes, Chromosomes and Cancer, 47: 530-542 (* co-correspondence authors) L. S. Hon, J. S. Kaminker, and Z. Zhang. (2008) Computational approaches for predicting causal missense mutations in cancer genome projects. Current Bioinformatics, 3 (1): 46-55 N. Kayagaki, Q. Phung, S. Chan, R. Chaudhari, C. Quan, K. M. O'Rourke, M. Eby, E. Pietras, G. Cheng, J. F. Bazan, Z. Zhang, D. Arnott, and V. M. Dixit. (2007) DUBA: a deubiquitinase that regulates type I interferon production. Science, 318: 1628-1632 L. D. Wood, D. W. Parsons, S. Jones, J. Lin, T. Sjöblom, R. J. Leary, D. Shen, S. M. Boca, T. Barber, J. Ptak, N. Silliman, S. Szabo, Z. Dezso, V. Ustyanksky, T. Nikolskaya, Y. Nikolsky, R. Karchin, P. A. Wilson, J. S. Kaminker, Z. Zhang, R. Croshaw, J. Willis, D. Dawson, M. Shipitsin, J. K. V. Willson, S. Sukumar, K. Polyak, B. H. Park, C. L. Pethiyagoda, P. V. K. Pant, D. G. Ballinger, A. B. Sparks, J. Hartigan, D. R. Smith, E. Suh, N. Papadopoulos, P. Buckhaults, S. D. Markowitz, G. Parmigiani, K. W. Kinzler, V. E. Velculescu, and B. Vogelstein. (2007) The genomic landscapes of human breast and colorectal cancers. Science, 318: 1108-1113 L. S. Hon and Z. Zhang. (2007) The roles of binding site arrangement and combinatorial targeting in microRNA repression of gene expression. Genome Biol., 8 (8): R166 J. S. Kaminker, Y. Zhang, C. Watanabe, and Z. Zhang. (2007) CanPredict: A computational tool for predicting missense cancer-associated mutations. Nucleic Acid Res., 35: W595-598 Y. Zhang, S-M Luoh, L. S. Hon, R. Baertsch, W. I. Wood and Z. Zhang. (2007) GeneHub-GEPIS: Digital expression profiling for normal and cancer tissues based on an integrated gene database. Nucleic Acid Res., 35: W152-158 J. S. Kaminker, Y. Zhang, A. Waugh, P. Haverty, J. Stinson, B. Peters, D. Sebisanovic, W. F. Forrest, J. F. Bazan, S. Seshagiri, and Z. Zhang. (2007) Distinguishing cancer associated missense mutations from common polymorphisms. Cancer Res., 67: 465-473 X-D. Wang, B. Wang, R. Soriano, J. Zha, Z. Zhang, Z. Modrusan, G.R. Cunha, and W-Q Gao. (2007) Expression profiling of the mouse prostate after castration and hormone replacement: implication of H-cadherin in prostate tumorigenesis. Differentiation, 75: 219-234 D. Gray, A. M. Jubb, D. Hogue, P. Dowd, N. Kljavin, S. Yi, G. Frantz, W. Bai, Z. Zhang, H. Koeppen, F. de Sauvage, and D. Davis. (2005) Maternal Embryonic Leucine Zipper Kinase/Murine Protein Serine-Threonine Kinase 38 is a promising therapeutic target for multiple cancers. Cancer Res., 65: 97511-9761 Z. Zhang and W. J. Henzel. (2004) Signal peptide prediction based on analysis of experimentally verified cleavage sites. Protein Science, 13: 2819-2824 Y. Zhang, D. Eberhard, G. D. Frantz, P. Dowd, T. D. Wu, C. Watanabe, Y. Zhou, P. Polakis, K. J. Hillan, W. I. Wood, and Z. Zhang. (2004) GEPIS – Quantitative gene expression profiling in normal and cancer tissues. Bioinformatics, 20: 2390-2398 B. Desany and Z. Zhang. (2004) Bioinformatics and cancer target discovery. Drug Discov. Today, 9: 795-802 I. E. Wertz, K. M. O’Rourke, Z. Zhang, D. Dornan, D. Arnott, R. J. Deshaies, and V. M. Dixit. (2004) Human De-etiolated-1 regulates c-Jun by assembling a CUL4A ubiquitin ligase. Science, 303: 1371-1374 Z. Zhang. (2004) Bioinformatics and cancer target discovery. (Book chapter) New Drug Target Discovery in the Post-Genomic Era. 63-72 Y. Zhou, S-M. Luoh, Y. Zhang, C. Watanabe, T. D. Wu, M. Ostland, W. I. Wood, and Z. Zhang. (2003) Genome-wide identification of chromosome regions of increased tumor expression by transcriptome analysis. Cancer Res., 63: 5781-5784 K. M. L. Gaensler, Z. Zhang, C. Lin, S. Yang, K. Hardt, and L. Flebbe-Rehwaldt. (2003) Sequences in the A- intergenic regions are not required for stage-specific regulation of the human -globin gene locus. Proc. Natl. Acad. Sci. USA, 100 (6): 3374-3379 Z. Zhang and W. I. Wood. (2003) A profile hidden Markov model for signal peptides generated by HMMER. Bioinformatics, 19 (2): 307-308 H. F. Clark, A. L. Gurney, E. Abaya, K. Baker, D. Baldwin, J. Brush, J. Chen, B. Chow, C. Chui, C. Crowley, B. Currell, B. Deuel, P. Dowd, D. Eaton, J. Foster, C. Grimaldi, Q. Gu, P. E. Hass, S. Heldens, A. Huang, H. S. Kim, L. Klimowski, Y. Jin, S. Johnson, J. Lee, L. Lewis, D. Liao, M. Mark, E. Robbie, C. Sanchez, J. Schoenfeld, S. Seshagiri, L. Simmons, J. Singh, V. Smith, J. Stinson, A. Vagts, R. Vandlen, C. Watanabe, D. Wieand, K. Woods, M-H. Xie, D.Yansura, S. Yi, G. Yu, J. Yuan, M. Zhang, Z. Zhang, A. Goddard, W. I. Wood, and P. Godowski. (2003) The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. Genome Res., 13: 2265-2270 J. LeCouter, R. Lin, G. Frantz, Z. Zhang, K. J. Hillan, and N. Ferrara. (2003) Mouse endocrine gland-derived vascular endothelial growth factor: a distinct expression pattern from its human ortholog suggests different roles as a regulator of organ-specific angiogenesis. Endocrinology, 144 (6): 2606-2616 M. Yan, Z. Zhang, J. R. Brady, S. Schilbach, W. J. Fairbrother, and V. M. Dixit. (2002) Identification of a novel death domain-containing adaptor molecule for Ectodysplasin-A receptor that is mutated in crinkled Mice. Cur. Biol., 12: 409-413 J. LeCouter, J. Kowalski, J. Foster, P. Hass, Z. Zhang, L. Dillard-Telm, G. Frantz, L. Rangell, L. DeGuzman, G-A. Keller, F. Peale, A. Gurney, K. J. Hillan, and N. Ferrara. (2001) Identification of an angiogenic mitogen selective for endocrine gland endothelium. Nature, 412: 877-884 A. Kishiyama, Z. Zhang, and W. J. Henzel. (2000) Cleavage and identification of proteins, a modified Aspartyl-Prolyl Cleavage. Anal. Chem. 72 (21): 5431-5436 M-H. Xie, S. Aggarwal, W-H. Ho, J. Foster, Z. Zhang, J. Stinson, W. Wood, A. Goddard, and A. Gurney. (2000) Identification of IL-22, a novel human cytokine that signals through the interferon receptor-related proteins CRF2-4 and IL-22R. J. Biol. Chem. 275 (40): 31335-31339 Z. Zhang and A. R. Buchman. (1997) Identification of a member of a DNA-dependent ATPase family that causes interference with silencing. Mol. Cell. Biol. 17 (9):5461-5472 S. Porcu, M. Kitamura, E. Witkowska, Z. Zhang, A. Mutero, C. Lin, J. Chang, and K. L. M. Gaensler. (1997) The human globin locus introduced by YAC transfer exhibit a specific and reproducible pattern of developmental regulation in transgenic mice. Blood, 90 (11): 4602-4609 Selected Achievements at GenentechResponsible for the identification of >400 novel secreted proteins for the SPDI project, including such important genes as EG-VEGF, p19 (IL23), and IL22; Identified key components in the TNF signaling pathway Key contributor in the Tumor Antigen Project target mining program, and directly contributed to the initial identification of a large fraction of the current targets for antibody therapy Founding members of several inter-departmental target mining programs, including Secreted Tumor Over-expressed Proteins, Tumor Antigen for Hematology/Oncology, Tumor Associated Kinases, and contributed to the initial identification of many important targets Developed an essential and widely used system GeneHub, which serves as an integrated gene information database and provide gene and probe annotations for microarray for >9 years Developed or led the development of many novel bioinformatics analysis tools at Genentech, including a signal peptide prediction method, GEPIS for in silico expression profiling, an expression-based Amplicon prediction method, OCTOPUS for integrating external microarray data, CGH for array CGH analysis, and multiple methods for predicting and functional effect of mutations Actively promoted Genentech Bioinformatics reputation by publishing independent research (including 20 lead author publications), collaborating with external groups, and hosting high-profile seminar speakers Actively involved in team building: hired many key members, promoted star contributors, and developed some of the current principal investigators Established the Bioinformatics Tech Steering Committeee to provide technical guidance to the entire department, and organized many departmental activities such as the Bioinformatics Open House, the Professional Development Forum, the department offsites, the Cancer Informatics offsite, and the Next Generation Sequencing Journal Club Coordinated numerous cross functional activities, including bioinformatics/biostatistics project coordination, the early stage secretome project, IP filing and Legal consultation, and CIT/GI coordination Carried out successful projects with external collaborators, including Bert Vogelstein / Victor Velculescu from Johns Hopkins (leading to a publication in Science) and the Complete Genomics team (leading to a publication in Nature) Directory: upload upload -> 587 Return function, r i(X) r i(0) r i(1) r i(2) r i(3) 1 0 2 4 6 Thermal Station, I 2 0 1 5 6 3 0 3 5 6 10 upload -> Department of science and humanities department of mathematics part-a questions and answers upload -> The Case Against the nypd’s Quota-Driven ‘Broken Windows’ Policing What Is It? upload -> For want of a nail upload -> Traditional British values upload -> Tv shows, Made for tv movies, Mini Series & Internet Programs Shot at Paramount Ranch upload -> Ownership Models There are two different types of ownership models upload -> Police Militarization upload -> City of rising star regular meting thursday, july 14, 2016 upload -> Township of winfield Download 89.57 Kb. Share with your friends:
|