Lab photo, 3/07. Left-to-right:
John, Wei, Shobha, Bornika, Chris, Xiaoduan, Himanshu, Fei

I moved from Purdue to Dartmouth in the summer of 2004, and collaborate with folks at both places (as well as others). The lab has a fun group of very talented students working on a variety of projects from a variety of perspectives. Here are some pictures from a "typical" group meeting (Xiaoduan leading a discussion of a paper, on top of nearby Mt. Cardigan): image 1; image 2; image 3. Students interested in working with us should refer to the prosective student information page. Following are a few sound bites, in relation to the main research themes of the lab.

Current Students

• David Callender (MS candidate)
  Data mining for pandemic preparedness.
   
  
• Himanshu Chandola (PhD student)
   
  
• Bornika Ghosh (PhD student)
   
  
• John Thomas (PhD candidate)
  Graphical models of residue coupling in protein families.
   
  
• Fei Xiong (PhD candidate)
  Graph algorithms for structure-based assignment.
   
  
• Wei Zheng (PhD candidate)
  Computational-experimental inference of protein family constraints.

• Jeremy Warburg
  Visualization of residue coupling motifs
   
  
• Melissa Lokensgard (WISP intern, winter/summer 2007)
  Solution scattering for protein complexes
   
  
• Nan Zheng (WISP intern, winter/spring 2008)

Alumni

Students who worked in the lab for multiple semesters.

• Shobha Potluri (2007)
  Thesis: "Complete Configuration Space Analysis for Structure Determination of Symmetric Homo-oligomers by NMR".
  On to a postdoc at Pfizer Global Research.
   
  
• Olga Vitek (Purdue statistics 2005)
  Thesis: "An inferential approach to protein backbone nuclear magnetic resonance assignment".
  On to a postdoc with Dr. Ruedi Aebersold, and then a faculty position in Statistics and CS at Purdue.
   
  
• Xiaoduan Ye (2007)
  Thesis: "Experiment planning for protein structure elucidation and site-directed protein recombination"

• Sheetal Chainraj (Purdue 2004)
  NMR: Random graph algorithms for automated assignment in NMR.
  On to employment at Bloomberg.
   
  
• Jairav Desai
  Robotic assembly of chimaeric libraries
   
  
• Hetu Kamisetty (Purdue 2005)
  NMR: Graph algorithms and pattern recognition in NMR.
  On to the PhD program at CMU.
   
  
• Jiangtian Li (Purdue industrial engineering 2004)
  Computation, analysis, and optimization of free energies of association for serine proteinase inhibitors.
  On to the PhD program at NCSU.
   
  

• Noah Benson (Purdue 2005; Hughes bioinformatics fellow)
  Graph analysis and algorithms for NOESY-based NMR automated assignment.
  On to graduate studies in computational biology at the University of Washington.
   
  
• Megan Crapster (WISP intern, spring/summer 2006)
  Target identification for protein complex determination.
   
  
• Mark Henle (Presidential Scholar, 2005)
  Algorithms in protein engineering by recombination.
   
  
• 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.
  On to graduate studies in computational biology at CMU.
   
  
• Kyle Krull (Purdue 2003)
  Computational modeling of protein-protein interactions for design of enzyme inhibitors.
  On to graduate studies in biochemistry / molecular biology at Purdue.
   
  
• Karlam Ng (Purdue 2003)
  Algorithms for classification of amino acid type from NMR data.
  On to graduate studies in CS at Stanford.
   
  
• Liz Saftalov (Purdue 2005; Ruzicka fellow)
  Algorithms in protein engineering by recombination.
  On to graduate studies in psychology at Purdue.
   
  
• Chetak Sirsat (Purdue 2004; Hughes bioinformatics fellow)
  Algorithms for interpretation of mass spectral data under intra- and inter-molecular cross-linking.
  On to graduate studies in computational biology at Purdue.
   
  
• Mike Stoppelman (Purdue 2004)
  Bridging the molecular-cellular modeling divide.
  On to employment at Google.
   
  
• Shelley Weaver (WISP intern, winter/spring 2006)
  Robotic combinatorial construction of chimaeric genes.
   
  
• Tim Williamson (Purdue 2005; Hughes fellow)
  Solution scattering for protein structure discrimination.
  On to the MS program in Computational Life Sciences at Purdue.
   
  
• Isaura Zelaya (Dartmouth 2008; WISP intern)
  Protein-protein interactions.
   
  

Collaborators

Our research is highly collaborative, and we're very lucky to be working with great researchers.

• Janusz Bujnicki (IIMCB bioinformatics)
• Bruce Craig (statistics, Purdue)
• Bruce Donald (computer science and biochemistry, Duke)
• Alan Friedman (biology, Purdue)
• Carol Post (biology and MCMP, Purdue)
• Naren Ramakrishnan (computer science, Virginia Tech)

Lab News

• 5/5/08: Congratulations to Xiaoduan, whose paper "Optimizing Bayes Error for Protein Structure Model Selection by Stability Mutagenesis" was accepted to CSB.
• 4/3/08: Our Stability + diversity in recombination paper is out (Proc. RECOMB / LNCS).
• 3/20/08: Congraulations to Fei, whose paper "Contact Replacement for NMR Resonance Assignment" was accepted to ISMB.
• 1/22/08: Our SVD for solution scattering paper has hit the press (epub) at Biophys. J.
• 12/12/07: Our Robomix paper has hit the press (epub) at J. Comb. Chem.
• 12/10/07: Congratulations to Wei, whose paper "Algorithms for joint optimization of stability and diversity in planning combinatorial libraries of chimeric proteins" was accepted to RECOMB.
• 10/29/07: We welcome Nan Zheng, who will be joining us this winter as a WISP intern.
• 10/28/07: Congratulations to Jairav and Shelley, whose paper "Robotic hierarchical mixing for the production of combinatorial libraries of proteins and small molecules" has been accepted for publication in Journal of Combinatorial Chemistry.
• 10/2/07: Congratulations to Tim, whose paper "Analysis of self-associating proteins by singular value decomposition of solution scattering data" has been accepted for publication in Biophysical Journal.
• 9/22/07: John is giving a talk, and most students are giving posters, at the Dartmouth Computer Science Research Symposium.
• 7/30/07: Congratulations to Fei, whose paper "A hierarchical grow-and-match algorithm for backbone resonance assignment given 3D structure" has been accepted to IEEE BIBE.
• 7/1/07: Xiaoduan's paper on minimizing perturbation in site-directed recombination has hit the press in JCB.
• 6/10/07: Graduation for Shobha and Xiaoduan! A few pictures (Chris obviously needs a floppy hat):
  
• 5/22/07: Congratulations to Dr. Xiaoduan Ye, who successfully defended his thesis "Experiment Planning for Protein Structure Elucidation and Site-Directed Protein Recombination"! Xiaoduan will be moving from biology to finance, joining Bloomberg after he graduates.
• 5/10/07: Chris has been promoted to Associate Professor (with tenure). Thanks to all lab members, collaborators, and students for the great work that has made this possible!
• 4/30/07: Congratulation to Wei and Xiaoduan, whose paper "Algorithms for selecting breakpoint locations to optimize diversity in protein engineering by site-directed protein recombination" has been accepted to CSB.
• 4/3/07: Congratulations to John, whose paper "Graphical Models of Residue Coupling in Protein Families" has been accepted for publication in IEEE/ACM Transactions on Computational Biology and Bioinformatics.
• 3/21/07: Congratulations to Dr. Shobha Potluri, who successfully defended her thesis "Complete Configuration Space Analysis for Structure Determination of Symmetric Homo-oligomers by NMR"! Shobha will soon be starting a postdoc at Pfizer Global Research.
• 1/07: Shobha's NOE assignment + structure determination paper has been published in Protein Science.
• 11/6/06: We are organizing a SIAM-DM 2007 Workshop on Data Mining for Pandemic Preparedness. The draft call-for-papers is up.
• 10/30/06: We welcome Melissa Lokensgard, who will be joining us this winter as a WISP intern.
• 10/23/06: The extended version of Xiaoduan's RECOMB paper on hypergraphs for recombination has been accepted for publication in J. Comp. Biol.
• 10/5/06: Shobha and Tony's paper "A complete algorithm to resolve ambiguity for inter-subunit NOE assignment in structure determination of symmetric homo-oligomers" has been accepted for publication in Protein Science.
• Fall 2006: Welcome to new graduate students in computational biology: Himanshu Chandola, Jairav Desai, and Bornika Ghosh. Looking forward to great things!
• 9/22/06: Dartmouth CS research symposium! Shobha is giving a talk and other members of the lab are presenting posters (and Chris will give the 10-minute glimpse of what's going on in the lab).
• 8/8/06: Shobha and Tony's homo-oligomer structure determination paper is up (early view) at Proteins.
• 7/20/06: Olga's sparse inferential assignment paper is up (early view) at J. Biomol. NMR.
• 6/16/06: Liz's SPLISO paper (Specific PLanned LIgation of Short Overhangs) is up (early view) at Proteins.
• 6/2/06: QR-06 web proceedings are up. The workshop will be held July 10-12 at Dartmouth; registration is due June 22. In addition to paper presentations, we'll have keynotes by Hidde de Jong (QR for gene regulatory networks) and Ken Forbus (QR for cognitive science).
• 5/18/06: The call-for-papers for BioKDD 06 is up.
• 5/15/06: Shobha and Tony's paper "Structure Determination of Symmetric Homo-oligomers by a Complete Search of Symmetry Configuration Space Using NMR Restraints and van der Waals Packing" has been accepted to Proteins.
  They will also be giving an oral presentation on the work at WAFR (the Workshop on Algorithmic Foundations of Robotics).
• 5/8/06: Olga's paper "Inferential backbone assignment for sparse data" has been accepted to J. Biomolecular NMR.
• 4/20/06: SIAM-DM 2006 Spatial Data Mining Workshop papers are up.
• 4/13/06: Shobha and Tony are giving a poster "Structure determination of symmetric homo-oligomers by a complete search using NMR restraints and vdW packing" at the Fifth NIH Protein Structure Initiative Bottlenecks Workshop.
• 3/30/06: Xiaoduan's RECOMB-06 paper on hypergraphs for recombination is up.
• 2/14/06: Liz's paper "Site-Directed Combinatorial Construction of Chimaeric Genes: General Method for Optimizing Assembly of Gene Fragments" has been accepted to Proteins.
• 2/8/06: Check out the AI@50 celebration that will be held at Dartmouth this summer -- great retrospective and prospective look at the field.
• 2/3/06: Our paper on functional evolution in protein superfamilies is up (early view) at Proteins.
• 1/15/06: Hetu's paper on contact-based NMR assignment has already hit the press at Bioinformatics.
• 1/06: We welcome Wei Zheng to the lab. Wei has done a bunch of great work on data mining and pattern recognition (e.g., in analyzing MRI data to detect cancer). He will be pursuing his dissertation research in the general area of computational-experimental inference of protein family constraints.
• Old news, fun for nostalgia.