The lab has a fun group of very talented students and postdocs working on a variety of projects from a variety of perspectives. You can see some short descriptions of our current research themes, and read some of our papers. We also enjoy the quality of life in the area; e.g., here's a photo of one of our lab hikes up nearby Mt. Cardigan.
Prospective Students and Postdocs
If you are a Dartmouth undergraduate or graduate student with a potential interest in computational biology (particularly in studies of protein structure and function, including protein engineering), then let's talk! Computational types: it's fine if you don't (yet) know the biology; you can learn in the context of a project. (I also offer relevant classes fairly routinely, as do others; ask me.)
If you are interested in pursuing graduate studies in computational biology at Dartmouth, then you should apply for admission to the CS department (PhD or MS admissions) or the Quantitative Biomedical Sciences program (application). While I'm glad for you to contact me to express your interest, you're not really applying for a position with me, but rather to join the department / program, and a committee decides admissions.
Current Lab Members
Postdocs
- Natalia Syzochenko
Graduate students
- Bowen Dai (PhD candidate)
- Daniel Mattox (PhD candidate)
- Andrew O'Laughlin (PhD candidate)
- Srivamship Pittala (PhD candidate)
Undergraduate students
- Arij Elfaki (WISP intern, 2018)
- Ellen Smalley (sophomore science scholar, 2016-2017; Neukom fellow W18; UGAR fellow S18)
- Neerja Thakkar (sophomore science scholar, 2017)
Alumni
Postdocs
- Ickwon Choi (2012-13)
Machine learning methods for analyzing antibody feature-function relationships - Yoonjoo Choi (2012-17)
Therapeutic protein deimmunization; antibody engineering - Karen Dowell (2013-15)
Analysis and modeling of the antibody response to infection and vaccination - Deeptak Verma (2013-17)
Protein library design; therapeutic protein engineering - Jason Vertrees (2008-9)
Sequence- & structure-based prediction of protein function
PhD students
- Himanshu Chandola (2013)
Thesis: "Geometrical and probabilistic methods for determining association models and structures of protein complexes". - Lu He (2014)
Thesis: "Computational Methods for the Discovery and Application of Protein Sequence-Structure-Function Relationships". - Andrew Scott Parker (2012)
Thesis: "Combinatorial optimization methods for the design of deimmunized protein therapeutics". - Shobha Potluri (2007)
Thesis: "Complete Configuration Space Analysis for Structure Determination of Symmetric Homo-oligomers by NMR". - John Thomas (2009)
Thesis: "Graphical Models of Sequence Constraints on Protein Families". - Olga Vitek (Purdue statistics 2005)
Thesis: "An inferential approach to protein backbone nuclear magnetic resonance assignment". - Fei Xiong (2010)
Thesis: "Graph algorithms for NMR resonance assignment and cross-link experiment planning". - Xiaoduan Ye (2007)
Thesis: "Experiment planning for protein structure elucidation and site-directed protein recombination". - Wei Zheng (2010)
Thesis: "Optimization algorithms for site-directed protein recombination experiment planning".
MS students
- David Callender
Data mining for pandemic preparedness - Sheetal Chainraj (Purdue 2004)
Random graph algorithms for automated assignment in NMR. - Jairav Desai
Robotic assembly of chimaeric libraries - Bornika Ghosh (2011)
Graphical models of proteins and protein-protein interactions. - Li Jiang (2015)
Thesis: Improving MHC-peptide binding prediction from sparse data with a multi-allele graphical model and active learning - Hetu Kamisetty (Purdue 2005)
Graph algorithms and pattern recognition in NMR. - Jiangtian Li (Purdue industrial engineering 2004) Computation, analysis, and optimization of free energies of association for serine proteinase inhibitors.
- Jae Woo Lee (2015)
Graphical models of protein-protein interactions - Tuobin Wang (2012)
Data mining in proteomics and immunoinformatics
Undergraduate students
- Ryan Amos (senior honors thesis student, 2015-2016)
Computationally-guided redesign of interacting proteins - Jessie Anderson (Sophomore Science Fellow, fall 2015-winter 2016)
Lectin family analysis - Amelia Antrim (senior honors thesis, 2014)
Discontinuous B-cell epitope prediction from peptide binding data - Noah Benson (Purdue 2005; Hughes bioinformatics fellow)
Graph analysis and algorithms for NOESY-based NMR automated assignment. - Megan Crapster (WISP intern, spring/summer 2006)
Target identification for protein complex determination. - Elena Doty (WISP intern, 2017)
Antibody profile visualization - Mark Henle (Presidential Scholar, 2005)
Algorithms in protein engineering by recombination. - Betty Huang (WISP intern, winter/spring 2011)
Proteomic analysis of antibody effector function. - Aly Azeem Khan (Purdue 2004; Hughes bioinformatics fellow)
Computational modeling of protein structure, flexibility, and complexes for model discrimination via cross-linking and mass spectrometry. - Kyle Krull (Purdue 2003)
Computational modeling of protein-protein interactions for design of enzyme inhibitors. - Rebecca Lau (WISP intern, winter/spring 2010)
Planning gene shuffling experiments. - Melissa Lokensgard (WISP intern, winter/summer 2007)
Solution scattering for protein complexes - Liane Makatura (WISP intern, winter/spring 2014)
Visualizing influenza vaccine data with hierarchical clustering - Jeff Milloy (honors thesis, 2009)
Accelerating mass spectrometry proteomics studies - Grace Nauman (WISP intern, winter/summer 2009)
Correlated mutations in HIV-1 protease. - Karlam Ng (Purdue 2003)
Algorithms for classification of amino acid type from NMR data. - Chris Park (senior thesis student, 2017)
Thesis: "“An Iterative Approach to Computational Epitope Localization by Integrating Epitope Binning Data and Antigen Mutagenesis Analysis” - Liz Saftalov (Purdue 2005; Ruzicka fellow)
Algorithms in protein engineering by recombination. - Chetak Sirsat (Purdue 2004; Hughes bioinformatics fellow)
Algorithms for interpretation of mass spectral data under intra- and inter-molecular cross-linking. - Mike Stoppelman (Purdue 2004)
Bridging the molecular-cellular modeling divide. - Michelle Vaccaro (WISP intern, winter-spring 2015)
Interactive analysis of HIV antibody data - Shelley Weaver (WISP intern, winter/spring 2006)
Robotic combinatorial construction of chimaeric genes. - Yifei Wang (WISP intern, winter/spring 2010)
Graphical models of protein-protein interactions. - Jeremy Warburg (Dartmouth 2008)
Visualization of residue coupling motifs - Tim Williamson (Purdue 2005; Hughes fellow)
Solution scattering for protein structure discrimination. - Isaura Zelaya (Dartmouth 2008; WISP intern)
Protein-protein interactions. - Nan Zheng (Presidential Scholar, fall 2009/winter 2010; WISP intern, winter/spring 2008)
Interactive visualization and querying of graphical models of proteins. - Jean Zhou (Sophomore Science Fellow, fall 2015; WISP intern, winter-spring2015)
Interactive analysis of HIV antibody data
Collaborators
Our research is highly collaborative, and we're very lucky to be working with great researchers at Dartmouth and other universities.
- Margie Ackerman (engineering, Dartmouth)
- Galit Alter (Ragon Institute
- Bruce Craig (statistics, Purdue)
- Annie De Groot and the Institute for Immunology and Informatics
- Bruce Donald (computer science and biochemistry, Duke)
- Alan Friedman (biology, Purdue)
- Scott Gerber (genetics, Dartmouth)
- Karl Griswold (engineering, Dartmouth)
- Chris Langmead (computer science, CMU)
- Gopal Pandurangan (computer science, NTU Singapore)
- Naren Ramakrishnan (computer science, Virginia Tech)