Papers of the Computational Biology Group

Published Papers

D. Greenberg, S. Istrail, The chimeric mapping problem: algorithmic strategies and performance evaluation on synthetic genomic data, Computers and Chemistry , Vol. 18. No.3 pp. 207-220, 1994
D. Greenberg, S. Istrail, Physical mapping by STS hybridization and the challenge of software evaluation, Journal of Computational Biology , August (1995) 70 pp
W. E. Hart, S. Istrail, Fast protein folding in the hydrophobic-hydrophilic model within 3/8 of optimal, 34th ACM Annual Symposium on the Theory of Computing, Las Vegas, Nevada, May 1995, p. 157-168 (Final version submitted to Journal of Computational Biology (77 pp)

D. Greenberg, C. Philips, Ambiguity in fragment-clone matrices, (Extended Abstract)
J. Atkins, The 2-consecutive ones problems remains NP-complete for sparse genomic matrices, 15pp
W. E. Hart, S. Istrail, Crystallographical universal approximability: A complexity theory of protein folding algorithms on crystal lattices, (Extended Abstract), 16 pp
W. E. Hart, S. Istrail, The side chain packing conformation problem, 18 pp
W.E. Hart, S. Istrail, Combinatorial problems in protein folding models: hardness and approximability (Extended Abstract), 10 pp

K. Dill (UC San Francisco), W.E. Hart, S. Istrail, "New protein folding algorithms with near-optimal performance"
W. E. Hart, S. Istrail, J. King (MIT), R. Ravi (Carnegie Mellon), The protein misfolding problem: reaching the native state through pathways of self-avoidance
S. Istrail, R. Ravi (Carnegie Mellon), Are there fair multiple sequence alignments ? Coping with intrinsic biases in scoring schemes
S. Istrail, Where do the local search neghborhoods come from ? Cycle-basis algorithms in matroids and applications
S. Istrail, The repeated probes problem in physical mapping