Shuly Avraham
shuly@cshl.edu
Bioinformatics Consultant
Born Israel
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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. |
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Jer-Ming Chia
chia@cshl.edu
Scientific Informatics Analyst
Born Singapore
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Jer-Ming joined the lab in August 2008 after finishing with graduate school in Singapore. He has a background in population genetics and has 8 years of experience as a bioinformaticist in industry and academia. He currently works on the various diversity projects including the grape and maize variation discovery projects using massively parallel sequencing. When not in front of his computer, Jer-Ming can usually be found on the tennis courts at Central Park. |
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Aaron Chuah
achuah@cshl.edu
Scientific Informatics Analyst II
Born Kuala Lumpur, Malaysia
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Aaron came to CSHL in April 2009 after tinkering in
bioinfo, telco and pharma industries for 11 years. Always keen on the
many flavors of Unix (and Mac ever since OSX), he's been known to be
obsessed by code/length optimizations, and holds some rusty
patent/chrome trophies for such. Aaron presently enjoys working on
Next Gen Diversity analyses and vis(ualizat)ions. He has a BE in
electrical engineering from the National University of Singapore and
is relieved to be moving along with his wife to Manhattan after
enduring half a year on the pretty/remote summit of Sea Cliff. During
weekends, they may be spotted cuisine-hopping or trundling through
museums, exhibitions and parks, God forbid, with their two
leashed/uncooperative cats in tow. |
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Nicholas DiPaola
nicholasdipaola@yahoo.com
URP
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Nicholas DiPaola joined the lab in November of 2008. He is a student at Huntington High School and is graduating in June of 2009. He has always been around the labs, taking all the CSH Learning Center summer courses and strived through four years in the science research program at Huntington High School. Nicholas is currently assisting LiFang Zhang and Zhijie Liu with Yeast-1 Hybrid screening, small RNA library construction and organizing large amounts of data. When he is not at the labs, he is playing soccer, working out, spending hours at the beach, and hanging out with friends. |
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Andrea Eveland
eveland@cshl.edu
Postdoctoral Fellow
Born Long Island, NY
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Andrea came to CSHL in October of 2008 as an NSF postdoctoral fellow in Biological Informatics. Her interdisciplinary research combines maize genetics and computational biology to study developmental networks modulating maize inflorescence architecture and is jointly sponsored by David Jackson and Doreen Ware. Andrea's background in plant biology extends back to numerous jobs in horticulture throughout high school and college. She received her BS in Botany from SUNY Binghamton, NY in 2000 and during her time as a research assistant at TMRI (Syngenta), San Diego, CA, her interests shifted to molecular-based crop biology. Andrea received her Ph.D. in Plant Molecular Biology from the University of Florida, Gainesville, in May 2008, where her research focused on maize floral physiology and high-throughput sequencing applications for genome-wide expression profiling. Andrea currently lives in Astoria, NY, and in her spare time enjoys yoga, biking, wine tasting, and spending time with her adorable pup, Cody. |
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Bonnie Hurwitz
hurwitz@cshl.edu
Bioinformatics Consultant
Born San Diego, CA
(Past member)
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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. |
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Sunita Kumari
kumari@cshl.edu
Scientific Informatics Analyst III
Born India
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Sunita joined Ware Lab at CSHL in January 2009. Primarily,
she works on computational prediction & functional analysis of miRNA
targets and cis-regulatory elements to develop gene regulatory
networks. Earlier, she worked as post-doc at bioinformatics &
computational biology, GMU, VA. She did her PhD from IARI, New Delhi;
MS in bioinformatics from GMU; additional expertise in molecular
biology & bioinformatics from JHU; and computational skills from
IUPUI. In India, she worked as a research scientist at IARI for 7
years and received the national young scientist award from ISPP. Also
worked as a visiting scientist at CSIRO, Perth on CLIMA fellowship.
She enjoys hiking in her free time with her family. |
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Tzitziki Lemus
lemus@cshl.edu
URP
Born Colima, Mexico
(Past member)
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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. |
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Michael Levy
Michael_J_Levy@brown.edu
URP
Born Manhasset, NY
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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. |
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Chengzhi Liang
liang@cshl.edu
Scientific Informatics Manager I
Born Shandong, China
(Past member)
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Chengzhi's main interest is to apply computational systems to biological data. He is 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). |
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Zhijie Liu
liuz@cshl.edu
Graduate student
Born Wuhan, HuBei, China
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Zhijie is a visiting graduate student from Huazhong Agricultural University. He now is working with LiFang on the Yeast one hybrid screening and Small RNA library construction. His major research field in China is one the maize under submergence stress. |
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Jerry Lu
luj@cshl.edu
Scientific Informatics Developer
Born Shanghai, China
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Jerry joined CSHL in 2007 to work on the Hapmap project.
Prior to that, he worked in Monsanto's swine genomics group as a
Bioinformaticist for 3 years. He is currently working on iPlant project
from St. Louis, MO. Jerry holds an MS in both Biochemistry and
Computer Science. In his spare time, he likes to hang out with his
friends. |
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Linda McMahan
mcmahan@cshl.edu
Bioinformatics Consultant
Born Da Nang, Vietnam
(Past member)
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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. |
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Apurva Narechania
apurva@cshl.edu
Scientific Informatics Developer I
Born Manchester, CT
(Past member)
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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. |
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Andrew Olson
olson@cshl.edu
Scientific Informatics Analyst II
Born New Jersey, USA
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Andrew joined the Ware lab in May of 2009 after working as a bioinformatician for Dart Neuroscience LLC in San Diego and the Dart NeuroGenomics Alliance at CSHL. Prior to CSHL he spent 4 years at Compugen. He is now working on coding and non-coding gene annotation pipelines. He is also interested in identifying new technologies and developing bioinformatics tools that utilize them. Andrew holds a M.S. degree in Computer Science from Rutgers University. |
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Shiran Pasternak
shiran@cshl.edu
Scientific Informatics Manager II
Born Rishon Le'Zion, Israel
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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. |
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Liya Ren
ren@cshl.edu
Scientific Informatics Developer II
Born Anyang, Henan, China
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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. |
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William Spooner
whs@ebi.ac.uk
Bioinformatics Consultant
Born London, UK
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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. |
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Joshua Stein
steinj@cshl.edu
Manager, Scientific Informatics III
Born New York City, NY
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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. |
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Jim Thomason
thomason@cshl.edu
Scientific Informatics Developer III
Born Brooklyn, NY
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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. |
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Doreen Ware
ware@cshl.edu
Adjunct Assistant Professor, USDA-ARS
Born New Jersey, USA
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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. |
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Sharon Wei
weix@cshl.edu
Scientific Informatics Developer II
Born Jingzhou, Hubei, China
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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. |
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Ken Youens-Clark
kclark@cshl.edu
Scientific Informatics Manager I
Born Jackson, Mississippi
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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 is the project manager for the Gramene website, and has 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. |
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Lifang Zhang
zhangl@cshl.edu
Lab Technician III
Born Luoyang, Henan, China
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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. |
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Yuan Zhang
zhangy@cshl.edu
Intern
Born China
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Yuan is a college intern for the summer of 2008. She is a rising sophomore of College of Life Science at Peking University in China. During the summer, she worked with Lifang learning and doing experiments. She likes the company of her friends, music and movies. |
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Wei Zhao
zhaow@cshl.edu
Scientific Informatics Analyst I
Born China
(Past member)
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Wei is interested in the comparative genomics of the cereals, especially that of maize and rice. She joined CSHL in 2001. Currently Wei is focusing on the study of synteny between rice, maize, and sorghum, and has identified the syntenic regions between maize and rice and between sorghum and rice. She is also working on the "Molecular and Functional Diversity in the Maize Genome" project. Wei had also worked on Gramene and her past responsibilities include building comparative rice and maize maps, providing data for rice-maize synteny-view, and developing and maintaining the protein and literature modules. Wei received her M.S. in physics from University of Connecticut and her M.S. in Computer Science from Rensselaer Polytechnic Institute. |
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