People

Stein/Ware Lab Retreat, May, 2007


Shuly Avraham shuly@cshl.edu Bioinformatics Consultant Born: Israel	Shuly is an application/web developer and database administrator, splitting her time between three bioinformatics projects, the Plant Ontology (structured controlled vocabulary for plants), Gramene (comparative genomics for the grasses) and the Virtual Plant Information Network (semantic web services). She joined the lab in 2002, and worked on-campus at Cold Spring Harbor Lab until 2006, when she moved back to Israel, and has been "telecommuting" since. Shuly holds a B.A. in computer science and M.S. in administrative science.

Bonnie Hurwitz hurwitz@cshl.edu Bioinformatics Consultant Born: San Diego, CA	Bonnie specializes in research computing for the life sciences and has worked for companies for such as Incyte, Accelrys and Third Wave Technologies prior to coming to CSHL. She is now working on the Oryza Map Alignment Project (OMAP), a joint project with AGI, Purdue and CSHL which focuses on evolutionary analysis in the Oryza genus between wild rice species and Oryza sativa. Her primary role in the project is data analysis and computational programming. Bonnie received her bachelor's degree from the University of California Santa Cruz in Biochemistry and Molecular Biology (1996) and certification in Bioinformatics (1999). In her spare time, Bonnie enjoys hiking and kayaking with her husband.

Michael Levy Michael_J_Levy@brown.edu URP Born: Manhasset, NY	Michael is a college intern for the summer of 2008. He is a rising sophomore at Brown University who is a Sc.B. Candidate for an Applied Mathematics Degree. He also maintains a growing interest in computational biology and bioinformatics. Before coming to the lab, Michael completed research projects throughout high school, notably at Cold Spring Harbor Labs and the Russian Academy of Sciences. Besides research, Michael enjoys the company of his friends, classic rock, poker, and baseball.

Tzitziki Lemus lemus@cshl.edu URP Born: Colima, Mexico	Tzitziki is a URP for the summer of 2008. She is a rising senior at Universidad Nacional Autonoma de Mexico who is majoring in Genomic Sciences. Tzitziki is currently taking a respite from her work on human genome dynamics in order to complete her URP project. She has previously completed work on human structural variation at Wash U. In her spare time, she like to hang out with her friends, read, draw, and exercise.

Chengzhi Liang liang@cshl.edu Scientific Informatics Manager I Born: Shandong, China	Chengzhi's main interest is to apply computational systems to biological data. He is currently the project manager for Gramene. He is also involved in building genes based on protein, cDNA, EST evidence using Ensembl pipelines. He holds a Ph.D. in Genetics, and Master's degree in Computer Science. He was trained as an experimental biologist, but went to computational field in 1999 due to his everlasting interest from as a kid. He likes playing sport games such as tennis, pingpong, badminton in spare time, and played WeiQi (GO) in the past (amateur 3d).

Linda McMahan mcmahan@cshl.edu Bioinformatics Consultant Born: Da Nang, Vietnam (naturalized U.S. citizen)	Linda is a member of the consulting team of the multi- institutional Maize and Gramene Genome Projects at CSHL. Linda received her Ph.D. in molecular biology from a biomedical Ph.D. program in medical sciences at University of Massachusetts Medical School. Her doctoral work was in the area of regulation of prokaryotic gene expression; specifically, she studied the genetics of bacteriophage P22. She was awarded the postdoctoral fellowship from Leukemia Society of America to pursue her postdoctoral work in the areas of eukaryotic genetics and molecular virology at Dana-Farber Cancer Institute, Harvard Medical School. She earned her M.S. degree in computer science from Montclair State University and her B.A. degree in mathematics and biochemistry from Mount Holyoke College. Before joining CSHL, she held computational biologist position in the Lewis-Sigler Institute for Integrative Genomics at Princeton University, bioinformatics research associate position within the New York Structural Genomics Research Consortium at Rockefeller University, and associate principal scientist position at Schering Plough Pharmaceutical Research Institute.

Apurva Narechania apurva@cshl.edu Scientific Informatics Developer I Born: Manchester, CT	Apurva joined the lab in January 2006 and is working as a member of the Maize Genome Project. He has also held positions in the protein informatics at Celera Genomics, and phylogenetics at the Albert Einstein College of Medicine. He is a graduate of the University of Illinois, Urbana and holds degrees in Biochemistry and English Literature. After completing an M.A. in journalism at New York University, he also moonlights as a freelance journalist. Recent work has appeared in The American Scholar and Orion.


Shiran Pasternak shiran@cshl.edu Scientific Informatics Analyst II Born: Rishon Le'Zion, Israel	Shiran joined CSHL in July, 2005, after spending four years as a bioinformaticist at the Human Genome Sequencing Center at Baylor College of Medicine in Houston, Texas, where he developed software applications for the Human Genome Project and the HapMap Project, and led a grassroots effort to instill software engineering best practices. He is presently project lead for the NSF-funded Maize Genome Project, collaborating with a multi-institutional consortium and working closely with Gramene to provide a system for analyzing and visualizing the maize genome sequence. Shiran is an avid road cyclist and lives with his wife in New York City. Shiran has a B.A. in Computer Science, a B.A. in Biology, and an M.S. in Computer Science, all from Johns Hopkins University in Baltimore, Maryland.

Liya Ren ren@cshl.edu Scientific Informatics Developer II Born: Anyang, Henan, China	Liya joined CSHL in December, 2002. She is responsible for maintaining and developing web interface and data loading tool for protein, gene, ontology and literature modules in Gramene. She is also working on building the metabolic pathway ricecyc database. She holds a M.A. degree in Computer and Information Science, a M.S degree in Chemistry. She has been working from Boston since January, 2006.

William Spooner whs@ebi.ac.uk Bioinformatics Consultant Born: London, UK	William is an application developer who focuses mainly on Gramene's genome browser. He previously worked for the Ensembl project at the Welcome Trust Sanger Institute. He holds a Ph.D. in Earth System Modelling, and a B.Sc. in Marine Environmental Chemistry. He works from Cambridge, UK.

Joshua Stein steinj@cshl.edu Scientist/Consultant Born: New York City, NY	Josh works remotely from his home in Massachusetts, splitting his time between the Maize Genome Project and the NSF Young Investigator Award to study the comparative genomics of rice, maize, and sorghum. Before joining CSHL in January 2005, he helped found Cantata Laboratories, a company that used metabolic profiling to develop signatures of disease and drug efficacy/safety. He has also held positions at Cereon Genomics, a subsidiary of Monsanto Company, and Novartis (now Syngenta). He earned a Ph.D. in plant molecular biology in 1994 from Cornell University. Josh enjoys family time with his wife and two sons, and playing music with friends.

Jim Thomason thomason@cshl.edu Bioinformatics Consultant Born: Brooklyn, NY	Jim is Just Another Perl Hacker who joined the lab in late 2006. He has varied industry experience, including publishing, advertising, and education - but always focusing on web development. He's a Mac guy that programs for fun in his spare time. In short, he's a computer guy. Beyond that, he's a cyclist that gets out as much as he can, loves hanging out with his two basset hounds, writes short horror fiction (sporadically) and is a really funny guy that was tempted to write up a blurb about being descended from refuge Serbian royalty but was afraid he might be taken seriously. He has a BA in computer science from Lake Forest College and works remotely from Chicago, IL.

Doreen Ware ware@cshl.edu Research Investigator Born: New Jersey, USA	Doreen is a Computational Biologist with the United States Department of Agriculture, Agriculture Research Service, with an adjunct appointment as an assistant professor at CSHL. Doreen earned Ph.D. in Plant Biology, from The Ohio State University and a B.A. in Biochemistry from University of California, San Diego. When Doreen is not working, she enjoys spending time with her family at the beach and camping.

Sharon Wei weix@cshl.edu Scientific Informatics Developer II Born: Jingzhou, Hubei, China	Sharon joined the lab in June, 2005. Before that, she was working as a Scientific Programmer at Baylor College of Medicine - Human Genome Sequencing Center. She is currently working on Gramene Project, her responsibilities include maintaining gramene biopipe and genome browser. She holds a M.S. degree in Molecular Genetics from Univeristy of Texas - M.D.Anderson Cancer Center and a M.S. degree in Computer Sciences from University of Houston.

Ken Youens-Clark kclark@cshl.edu Scientific Informatics Developer II Born: Jackson, MS	Ken came to CSHL and bioinformatics in 2001 after several years in industry. His strengths are databases and application development, especially ones written in Perl for the Internet. Ken developed the CMap comparative and genetic map application for Gramene as well as the markers, QTL, diversity, and quick search databases and interfaces. When he's not writing code, Ken enjoys making food for his wife and children and playing music. Ken has a B.A. in English Literature from the University of North Texas and works from Dallas, TX.

Lifang Zhang zhangl@cshl.edu Lab Technician III Born: Luoyang, Henan, China	Lifang joined the lab in May, 2005. She is currently focusing experiment validation of miRNAs from arabidopsis, maize, sorghum and rice. She received her Ph.D. in Biochemistry and Molecular Biology from the University of Miami, FL.; M.S. in physiology from the Institute of Zoology, Chinese Academy of Science; and B.S. in Cell Biology from Wuhan University.