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Istrail Lab Members

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Istrail Lab Alumni (see Current Members)

Gabriel Negara visited Brown University from University of Iasi, Romania in 2006.

Angel Murakami worked as Sorin Istrail's executive assistant from 2010-2012.

Erin Klopfenstein worked as Sorin Istrail's executive assistant from 2005-2009.

Fumei Lam was a Postdoctoral Fellow in the Istrail Lab working on Computational Methods in Disease Associations, Human Genetics, and Protein Folding. Her involvement in the Istrail Laboratory can be seen in the ProFolding and Computational Models of SNPs and Haplotypes projects.

Eric Koskinen was a CS graduate student working with Sorin on the project "CMPL – Cellarium Meta Programming Language" in May 2007. He is now a graduate student in computer science at Oxford University.

Linag Wu, PhD student in Department of Physics at Brown. Research project: "Shannon Channel Capacity Theorem, Statistical mechancics, and Molecular Biology" (2006).

Yongxing Guo was Sorin's MS student when he completed his MS Project entitled "A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotype phase" in December 2007.

Joanne Joo was an MS student under the direction of Sorin Istrail completing her MS Thesis "Haplotype Phasing Algorithms and Comparison" on May 2007. She is now a PhD student at Korea Institute of Science and Technology/Functional Proteomics Center and was accepted as PhD student in Human Genetics/Computer Science at UCLA.

Michael Gaiman was an MS student under the direction of Sorin Istrail completing his MS Thesis entitled "Cellarium – a Computational Biology Workflowing Environment". He is currentlty employed by Google.

Chris Maloney was Sorin's MS student when he completed his MS Project entitled "Protein Folding Editor". He is currentlty employed by Microsoft.

Zack Schubert was an MS student completing his project entitled "Cellarium: An Ajax-based Map of the Genome" in May 2007.

John Aras

Kyle Schutter was the senior annotator and undergraduate team leader for the Cyrene project.

David Moskowitz is a senior concentrating in Computational Biology under the Computational Genomics track. David, who received the Karen T. Romer Undergraduate Teaching and Research Award in 2008, is currently involved in the haplotype phasing analysis of Multiple Sclerosis GWAS data. For his undergraduate honors thesis, David is creating 3D visualization software in CELLARIUM which will provide an interactive environment for the visualization and manipulation of cellular processes. David has also participated in a number of other Istrail Laboratory projects including:

  • Analyzed tumor biopsy images to formalize algorithms and produce software for computational support of diagnosis of cancer malignancy
  • Collaborated with the Eric Davidson Laboratory at the California Institute of Technology to create software to coordinate their data with NCBI databases
  • Developed library of Mathematica programs with biological applications designed to be accessible to biologists
  • Wrote literature extraction software to help automate and assist in further building of the regulatory database

He completed his senior research project "Virtual Sea Urchin: A 4-Dimonsional Map of the Sea Urchin Embryo" in May 2009.

Allan Stewart is interested in algorithms for biomolecular modeling and genomic regulation. He has spent the most recent summer researching binding of various transcription factors (Oct4, Sox2) along the genome. Allan's work involves the use of structural prediction tools, including RNA secondary structure and protein folding algorithms. He is developing a new protein folding algorithm that optimizes hydrophobic packing in the FCC lattice. Allan's work is a part of Istrail Lab's ongoing Profolding project.

Lian Garton's senior thesis titled "An investigation of Population Subdivision methods in disease associations with a focus on Markov Chain Monte Carlo" was accepted May 2008. She also won the S.C. Lamport Award and is currently employed by Amazon.

Jeff Erickson completed his senior project "Mathematica Simulator of Short Reads Assembly by High Throughput Technologies" in May 2009 and is now a bioinformatician at Harvard Medical School.

William Haynes Heaton was an Undergraduate member of the Istrail Lab. His senior project was entitled "Clonning Dr. Resnick – Computational Support for Cancer Pathology Diagnosis" and he is now a medical student at Brown Medical School.

Sanjay Trehan was a founding member of the Cyrene Project and a Generation II Annotators Trainer.

Rohan Maddamsetti was a founding member of the Cyrene Project and a Generation II Annotators Trainer. Rohan, Sanjay Trehan, and Ryan Tarpine made an annotation ontology for the cis-Regulatory Gene Regulatory Network Browser and Database, which is a genomic map of developmental regulatory circuitry in the sea urchin (S. purpuratus) genome. Since his time at the Istrail Lab, he has joined Rich Lenski's lab at Michigan State.

Eric Lim worked on the early stages of the CYRENE project.

Shrivaths R. Iyengar was an MS student under the direction of Sorin Istrail and is now employed by Microsoft.

Srividya Kalyanaraman worked with Sorin on the research project "Viral Genomes: An Insight into the past and the future".

Kim Burchett was an MS student completing her project entitled "Protein Folding and Voting Theory" in May 2006.

Kenneth Estrellas worked as a professional annotator on the CYRENE project.

Mei Cao worked as a professional annotator on the CYRENE project.

Nicole Noronha worked as a professional annotator on the CYRENE project.

Jean Ye-Qiong worked as a professional annotator on the CYRENE project.

Daniel Yang worked as a professional annotator on the CYRENE project.

After working with Sorin, Alejandro Hasfura continued his studies at MIT.