UNC Bioinformatics and Computational Biology

FIRST YEAR.........................................................................................................

Damien Croteau-Chonka
Home Department: Curriculum in Genetics and Molecular Biology
Prior Institution: Boston College

Ozgun Erdogan
Home Department: Biochemistry
Prior Institution: Sabanci University

Ning Jin
Home Department: Computer Science
Prior Institution: Peking University

Amie Rodgers
Home Department: Toxicology
Prior Institution: University of California at Berkeley

Arti Singh
Home Department: School of Information and Library Science
Prior Institution: Purdue University

Jeran Stratford
Home Department: Pharmacology
Prior Institution: Utah State University

Alison Wise
Home Department: Biostatistics
Prior Institution: Pomona College

SECOND YEAR
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Matt Berginski
Home Department: Biomedical Engineering
Advisor: Shawn Gomez
Prior Institution: Georgia Tech University

Thomas Clarke
Home Department: Curriculum in Genetics and Molecular Biology
Advisor: Todd Vision
Prior Institution: Princeton University

Emily Colby
Home Department: Biostatistics
Advisor: Fred Wright
Prior Institution: Virginia Commonwealth University

Daniel Gatti
Home Department: Environmental Science and Engineering
Advisor: Ivan Rusyn
Prior Institution: Georgia Tech University

Yi Gong
Home Department: Biostatistics
Advisor: Fei Zou
Prior Institution: Bowling Green State University

Matthew Martin
Home Department: Environmental Science and Engineering
Advisor: Ivan Rusyn
Prior Institution: James Madison University

Daniel Samarov
Home Department: Statistics and Operations Research
Advisor: Alex Tropsha
Prior Institution: Rutgers University

Shantanu Sharma
Home Department: Biochemistry and Biophysics
Advisor: Nikolay Dokholyan
Prior Institution: Indian Institute of Technology

Theo Walker
Home Department: Computer Science
Advisor: Brian Kuhlman
Prior Institution: Rensselaer Polytechnic Institute

THIRD YEAR
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Kwangbom Choi
Home Department: Computer Science
Advisor: Shawn Gomez
Current Research Project: Protein co-evolutionary analysis, Multiple Sequence Alignment
Prior Institution: North Carolina State University

Ron Jacak
Home Department: Biochemistry & Biophysics
Advisor: Brian Kuhlman
Current Research Project: Redesigning protein-protein interfaces, specifically the interface between the G-protein Ral and it's effectors; Designing proteins for stability and solubility
Prior Institution: Boston University

Jennifer Staab
Home Department: Computer Science
Advisor: Shawn Gomez
Current Research Project: Improving analysis techniques of temporal metabolomic data
Prior Institution: North Carolina State University

Suzy Vasa
Home Department: Biomedical Engineering
Advisor: Morgan Giddings
Current Research Project: RNA Structure
Prior Institution: Iowa State University

Xeuyi Wang
Home Department: Computer Science
Advisor: Jack Snoeyink
Current Research Project: TBA
Prior Institution: Zhejiang University

Yuying Xie
Home Department: Curriculum in Genetics & Molecular Biology
Advisor: David Threadgill
Current Research Project: Computational haplotype analysis to find cancer susceptibility gene candidates
Prior Institution: Fudan University

THIRD YEAR
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Kyle Gaulton
Home Department: Curriculum in Genetics and Molecular Biology
Advisor: Karen Mohlke
Current Research Project: Identification of the genetic variation influencing susceptibility to type 2 diabetes and other complex traits in humans
Prior Institution: University of Pennsylvania

Paul Giresi
Home Department: Biology
Advisor: Jason Lieb
Current Research Project: Using biochemical techniques along with DNA microarrays to resolve nucleosome organization genome wide
Prior Institution: Loyola College

Stuart Jefferys
Home Department: Curriculum in Genetics and Molecular Biology
Advisor: Morgan Giddings
Current Research Project: Post translational modifications & MS data, predicting host-parasite interaction via protein structure analogs
Prior Institution: North Carolina State University

Jameson Miller
Home Department: Computer Science
Advisor: Morgan Giddings
Current Research Project: Computational methods applied to analysis of mass spectrometry
Prior Institution: University of North Carolina at Chapel Hill

Scott Vu
Home Department: Biomedical Engineering
Advisor: David Lalush
Current Research Project: Effects of Codon Usage on free energy based model and translational
Prior Institution: North Carolina State University

Jennifer Young
Home Department: Mathematics
Current Research Project: Biomechanics of the cell membrane
Advisor: Sorin Mitran
Prior Institution: University of Delaware

SENIOR STUDENTS
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Nancy Cole Baker
Home Department: Information and Library Science
Advisor: Brad Hemminger
Current Research Project: Text-mining in biomedical information.
Prior Institution: University of the South and University of North Carolina at Chapel Hill

Kristen K. Dang
Home Department: Biomedical Engineering
Website: http://www.unc.edu/~kamerath
Advisors: Christina Burch and Ronald Swanstrom
Current Research Project: Mechanistic constraints on evolution-robustness, conditional neutrality, and RNA secondary structure-with applications to RNA viruses and lentiviruses
Prior Institution: University of Utah

Barry Kesner
Home Department: Cell & Developmental Biology
Advisor: Sharon Milgram
Current Research Project: CFTR Interacting Proteins
Prior Institution: New York University

Deanne Sammond
Home Department: Biochemistry and Biophysics
Advisor: Brian Kuhlman
Current Research Project: Computation Protein Interface Design.
Prior Institution: University of Colorado, Boulder

Victor Weigman
Home Department: Biology
Website: http://www.unc.edu/~weigman/
Advisor: Chuck Perou
Current Research Project: Use of gene expression, pathway and other data to predict breast cancer patient outcome.
Prior Institution: University of North Carolina at Chapel Hill

ALUMNI
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Jun (Luke) Huan
Home Department: Computer Science
Advisor: Wei Wang
Current Position: Assistant Professor; Department of Electrical Engineering and Computer Science at University of Kansas

Andrew Leaver-Fay
Home Department: Computer Science
Advisor: Jack Snoeyink
Current Position: Post Doctoral Fellow, Brian Kuhlman Laboratory at UNC-Chapel Hill

Xiao Wang
Home Department: Statistics & Operations Research
Advisor: Timothy C. Elston
Current Position: Post Doctoral Fellow, Jim Collin Laboratory at UNC-Chapel Hill

SELECTED RECENT STUDENT PUBLICATIONS
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Azevedo RBR, Lohaus R, Srinivasan S, Dang KK, Burch CL. 2006 "Sexual reproduction selects for robustness and negative epistasis in artifical gene networks." Nature. 440: 87-90.

Gaulton KJ, Mohlke KL, Vision TJ. "A computational system to select candidate genes for complex human traits." Bioinformatics. 2007 May 1;23(9):1132-40. Epub 2007 Jan 19.

Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD, "FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin." Genome Res. 2007 Jun;17(6):877-85. Epub 2006 Dec 19.

Ercan S, Giresi PG, Whittle CM, Zhang X, Green RD, Lieb JD. "X chromosome repression by localization of the C. elegans dosage compensation machinery to sites of transcription initiation." Nat Genet. 2007 Mar;39(3):403-8. Epub 2007 Feb 11.

Giresi PG, Lieb JD. "How to find an opening (or lots of them)." Nat Methods. 2006 Jul;3(7):501-2.

Giresi PG, Gupta M, Lieb JD. "Regulation of nucleosome stability as a mediator of chromatin function." Curr. Opin Genet. Dev. 2006 Apr;16(2):171-6. Epub 2006 Feb 28.

Martin MT, Brennan RJ, Hu W, Ayanoglu E, Lau C, Ren H, Wood CR, Corton JC, Kavlock RJ, Dix DJ. "Toxicogenomic study of triazole fungicides and perfluoroalkyl acids in rat livers predicts toxicity and categorizes chemicals based on mechanisms of toxicity." Toxicol Sci. 2007 Jun;97(2):595-613. Epub 2007 Mar 22. Herschkowitz, JI, Simin K,

Sammond DW, Eletr ZM, Purbeck, C, Kimple RJ, Siderovski DP, Kuhlman B. "Structure-based Protocol for Identifying Mutations that Enhance Protein-Protein Binding Affinities." J Mo Biol.l 2007 Jun 8.

Weigman VJ, Mikaelian I, Usary J, Hu Z, Rasmussen KE, Jones LP, Assefnia S, Chandrasekharan S, Backlund MG, Yin Y, Khramtsov AI, Bastein R, Quackenbush J, Glazer RI, Brown PH, Green JE, Kopelovich L, Furth PA, Palazzo JP, Olopade OI, Bernard PS, Churchill GA, Van Dyke T, Perou CM. "Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors." Genome Biol. 2007 May 10;8(5):R76