Chuong (Tom) Do 353 Serra Mall Room 110, Gates Building 1A Stanford, CA 94305-9025 E-mail: chuongdo@cs.stanford.edu Phone: (972) 408-8994

Links

• CONTRA project: biosequence analysis with discriminative probabilistic models
  • CONTRAfold: RNA secondary structure prediction server
  • CONTRAlign: protein alignment server
• PROBCONS: protein alignment server
• LAGAN: genomic alignment
• PRODA: protein alignments with rearrangements and repeats

Selected publications

• Effect of genetic divergence in identifying ancestral origin using HAPAA [pdf]
  Sundquist, A., Fratkin, E., Do, C.B., Batzoglou, S. 2008. Genome Research, 18:676-682.
  (website, source code).
  
• Automatic parameter learning for multiple network alignment [pdf]
  Flannick, J., Novak, A., Do, C.B., Batzoglou, S. 2008. In Proceedings of the 12th Annual International Conference on Computational Molecular Biology (RECOMB 2008), 214-231.
  (website)
• CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction [pdf]
  Gross, S.S., Do, C.B., Sirota, M., Batzoglou, S. 2008. Genome Biology 8:R269.
  
• Efficient multiple hyperparameter learning for log-linear models [pdf]
  Do, C.B., Foo, C.-S., Ng, A.Y. 2007. In Advances in Neural Processing Systems 20.
  
• Evolution of genes and genomes on the Drosophila phylogeny [pdf]
  Drosophila 12 Genomes Consortium. 2007. Nature 450, 203-218.
• Training conditional random fields for maximum labelwise accuracy [pdf]
  Gross, S.S., Russakovsky, O., Do, C.B., Batzoglou, S. 2006. In Advances in Neural Processing Systems 19.
  (derivation of recurrences)
• CONTRAfold: RNA secondary structure prediction without physics-based models [pdf]
  Do, C.B., Woods, D.A., Batzoglou, S. 2006. Bioinformatics, 22(14):e90-e98.
  (Best Paper, ISMB 2006) (webserver, manual, recurrences, source code)
• Multiple alignment of protein sequences with repeats and rearrangements [pdf]
  Phuong, T.M., Do, C.B., Edgar, R.C., Batzoglou, S. 2006. Nucleic Acids Res, 34(20):5932-5942.
  (manual, source code)
• Evidence for intelligent (algorithm) design [pdf]
  Srinivasan, B.S., Do, C.B., Batzoglou, S. 2006. In Genome Biology, 7:322.
• CONTRAlign: Discriminative training for protein sequence alignment [pdf]
  Do, C.B., Gross, S.S., Batzoglou, S. 2006. In Proceedings of the 10th Annual International Conference on Computational Molecular Biology (RECOMB 2006), 160-174.
  (Best Poster, BCATS 2005) (webserver, source code)
• Transfer learning for text classification [pdf]
  Do, C.B., Ng, A.Y. 2006. In Advances in Neural Information Processing Systems 18, 299-306.
• PROBCONS: Probabilistic consistency-based multiple sequence alignment [pdf]
  Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. Genome Research, 15(2):330-340.
  (Best Paper, ISMB/ECCB 2004; Best Master's Thesis, Stanford Computer Science Department 2004) (webserver, source code)
• Glocal Alignment: Finding rearrangements during alignment [pdf]
  Brudno, M., Malde, S., Poliakov, A., Do, C.B., Couronne, O., Dubchak, I., and Batzoglou, S. 2003. Bioinformatics, 19S1:i54-i62.
  
• LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA [pdf]
  Brudno, M., Do, C.B., Cooper, G.M., Kim, M.F., Davydov, E., Green, E.D., Sidow, A., and Batzoglou, S; NISC Comparative Sequencing Program. 2003. Genome Research, 13(4):721-731.
  (webserver, source code)

Odds and ends

• Demosthenes: winning entry in the 2002 CS 221 Othello competition, written with Sanders Chong, Mark Tong, and Anthony Hui
• Bunny World documentation: CS 108 final project, written with Xinan Wu
• Satisfiability and peg solitaire: solving a classic puzzle with zChaff or other SAT solvers
• Dense Boggle® boards: computing dense Boggle boards with simulated annealing
• Miscellaneous tricks and tips: useful things I keep forgetting