I was a faculty member in the Computer Science Department at Dartmouth from 2004 to 2021 (wow, time flies when you're having fun!), a tenured associate professor as of 2007 and a full professor as of 2013. I also had courtesy appointments in Chemistry and Quantitative Biomedical Sciences for some of that time. I was fortunate to be able to work with an amazing group of students, postdocs, and colleagues, pursuing a broad range of research at the intersection of computation and the life sciences. One line of research led to my starting a company with my colleague and collaborator Karl Griswold from the Dartmouth Thayer School of Engineering. Due to the success of our company in using computational methods to drive the development of next-generation biotherapeutics, I decided to take the leap and devote myself to seeing our work fully developed and applied to treating disease. I'd like to thank the department and university for supporting me throughout my time here, including my long juggling act between being a professor and doing the start-up thing. Thanks also to the students in my courses over the years, for always being engaging and keeping me on my toes, rising to the challenges I gave, and looking to get the most out of every topic. And of course huge thanks, from the bottom of my heart, to my wonderful lab members and collaborators over the years for such inspiring and memorable times working (and having fun) together.
If you're interested in our research, probably the best thing to do is browse pubmed; my name is sufficiently unique :).
Current Lab Members
- Bowen Dai (PhD candidate)
- Daniel Mattox (PhD candidate)
Lab 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 - Mahita Jarjapu (2019-20)
Computational epitope binning and characterization of determinants of specific recognition - Natalia Syzochenko (2018-19)
Computational discovery and analysis of putative bacterial autolysins - 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". - Srivamshi Pittala (2019)
Thesis: "Data-driven characterization of antibody-mediated interactions at large-scale" - 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 - Spencer Mitchell (2021)
Bioinformatic analysis of bacterial autolysins - Lisa Oh (2021)
Antibody epitope prediction - Tuobin Wang (2012)
Data mining in proteomics and immunoinformatics
Undergraduate students
- Ryan Amos (senior honors thesis, 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 - Reva Dixit (WISP intern, 2019)
Docking-based analysis of lytic enzyme function - Elena Doty (WISP intern, 2017; junior science scholar, 2019)
Machine learning models of functional glycomics data - Arij Elfaki (WISP intern, 2018; sophomore science scholar, 2018-19;
senior honors thesis, 2020)
Deimmunizing intracellular therapeutic proteins - 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 (senior 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, 2017)
Computational epitope localization - 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 - Ellen Smalley (sophomore science scholar, 2016-2017; Neukom fellow,
W18; UGAR fellow, S18; senior honors thesis, 2019)
Computational antigen design for focused immune response - Mike Stoppelman (Purdue 2004)
Bridging the molecular-cellular modeling divide - Tanli Su (WISP intern, 2019)
Docking-based analysis of lytic enzyme function - Neerja Thakkar (sophomore science scholar, 2017; junior science scholar, 2018)
Analysis of TCR repertoires - 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-spring 2015)
Interactive analysis of HIV antibody data