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Bioinformatics Shared Resources

Sanford Burnham Prebys Medical Discovery Institute

personnel

BSR PERSONNEL


Alexey Eroshkin, PhD, Bioinformatics Scientist and the Core Director



  • Microarray, Proteomics and Next-Generation sequencing (SNP, RNA-seq, DNA-seq, CHIP-seq) data analysis: from raw data to biological interpretation (e.g., finding affected pathways and networks). Network reconstruction, biomarker discovery and predictive modeling of disease status, stage etc. CRISPR screening data analysis for identification of essential genes, managing the database of broadly neutralizing HIV-1 antibodies (bNAbs) at bNAber.org, genome mining for new genes, multiple alignments and phylogenetic analysis. As a manager of the Bioinformatics Core I am also evaluating new tools, planning new projects and allocating resources.
  • Email: eroshkin@sbpdiscovery.org
  • Phone: 858-795-5336
  • Room 2406, Building 10

Andrew P. Hodges, Ph.D., Bioinformatics Specialist

 
  • Dr. Hodges implements existing and novel systems biology and machine learning approaches for target and drug discovery in cancer and other diseases. He provides pathway analysis and functional annotation, statistical simulations and synthetic network design, and heterogeneous dataset integration all applied to fundamental and translational research. Andrew incorporates advanced technologies (R/Bioconductor, Cytoscape, NextBio, GenePattern, AracNe/MI, BN+1, etc.) for validating existing and generating new hypotheses. He will be assisting researchers with database mining, network analyses, and selection of the most promising biomarkers and drug targets.​
  • Email: ahodges@sbpdiscovery.org
  • Phone: 858-646-3100 x 4332
  • Room 2405, Building 10

Vicky Guo (Xiaohui Guo). Part-time support programmer  

 
  • ​Installing, testing and adapting public domain bioinformatics tools for further use by the Core/Labs
  • Will use tested tools to analyze PI’s-generated or publicly-available data. 
  • Will modify software tools to tailor PIs needs.
  • Email: vguo@sbpdiscovery.org
  • ​Phone: 858-646-3100 x 4223
  • Room 2405, Building 10

Andrei Osterman, PhD, BSR Faculty Scientific Director


Adam Godzik, PhD, BSR Faculty Scientific Director

Rachel Berman, summer intern (currently a freshman studying Computer Science at Brown University)  

 
  • ​Developed Sample Surfer, a program designed to select samples (from a large gene expression data set) that are similar to a given gene signature
  • ​Analyzed NGS data from normal melanocytes and melanoma samples for changes in gene isoforms

Xiayu (Stacy) Huang, PhD, Biostatistician (former member)

  • Statistical data analysis, e.g., calculation of the optimum number of animals needed for the experiment
  • Microarry data analysis (GeneSpring, Bioconductor, GenePattern and related software)
  • Email: xyhuang@sbpdiscovery.org
  • Phone: 858 646-3100858 646-3100x3916
  • Room 2405, Building 10

Ally Perlina, Bioinformatics Scientist (former member)​


  • Proteomic, genomic, metabolomic, microRNA and other heterogeneous data analysis. Putting data into biological context across various disease areas to create testable hypotheses. She worked on analysis of many complex datasets from the top pharma and academic institutions 
  • Translational research
  • Drug target and biomarker discovery 
  • Email: aperlina@burnham.org
  • Phone: 858 646-3100858 646-3100x4784
  • Room 2405, Building 10

Roy Williams, PhD, Bioinformatics Specialist (former member)

  • Data analysis (microarray and proteomics) and genome annotation. You might want to ask me questions about methods for analyzing systems biology data and how to view it in a suitable biological context. I have worked with Affymetrix, GeneSpring, MatLab, Bioconductor and related software extensively over the last six years.
  • Email: royw@sbpdiscovery.org
  • Phone: 858 646-3100x3915
  • Room 2405, Building 10

Kutbuddin Doctor, PhD, Bioinformatics Specialist (former member)


  • Analysis of protein structure and function, esp. enzymes, apoptosis signaling; finding functional annotations via homology or structure; creating review articles based on families of proteins; writing bioinformatics/informatics sections of funded grants (MLSCN, caBIG); writing technical documents for bioinformatics work (caBIG); project oriented bioinformatics systems (PMAP Substrate Database, Apoptosis database, RIKEN mouse genome apoptosis functional annotation, caBIG's Cancer Molecular Pages).
  • Email: ksdo@sbpdiscovery.org
  • Phone: 858 646-3100858 646-3100 x3488
  • Room 1205, Building 10

Gerry Deckert,  Bioinformatics Specialist (former member)