Douglas L. Brutlag

2007
46	EE	Tsung-Han Chiang, Mehmet Serkan Apaydin, Douglas L. Brutlag, David Hsu, Jean-Claude Latombe: Using Stochastic Roadmap Simulation to Predict Experimental Quantities in Protein Folding Kinetics: Folding Rates and Phi-Values. Journal of Computational Biology 14(5): 578-593 (2007)
2006
45	EE	Eugene Fratkin, Brian T. Naughton, Douglas L. Brutlag, Serafim Batzoglou: MotifCut: regulatory motifs finding with maximum density subgraphs. ISMB (Supplement of Bioinformatics) 2006: 156-157
44	EE	Tsung-Han Chiang, Mehmet Serkan Apaydin, Douglas L. Brutlag, David Hsu, Jean-Claude Latombe: Predicting Experimental Quantities in Protein Folding Kinetics Using Stochastic Roadmap Simulation. RECOMB 2006: 410-424
43	EE	Jessica Ebert, Douglas L. Brutlag: Development and validation of a consistency based multiple structure alignment algorithm. Bioinformatics 22(9): 1080-1087 (2006)
2005
42	EE	Edward J. Bertaccini, Jessica Shapiro, Douglas L. Brutlag, James R. Trudell: Homology Modeling of a Human Glycine Alpha 1 Receptor Reveals a Plausible Anesthetic Binding Site. Journal of Chemical Information and Modeling 45(1): 128-135 (2005)
41	EE	Qiaojuan Jane Su, Lin Lu, Serge Saxonov, Douglas L. Brutlag: eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity. Nucleic Acids Research 33(Database-Issue): 178-182 (2005)
2004
40	EE	Haidong Wang, Eran Segal, Asa Ben-Hur, Daphne Koller, Douglas L. Brutlag: Identifying Protein-Protein Interaction Sites on a Genome-Wide Scale. NIPS 2004
39		Yueyi Liu, Liping Wei, Serafim Batzoglou, Douglas L. Brutlag, Jun S. Liu, X. Shirley Liu: A suite of web-based programs to search for transcriptional regulatory motifs. Nucleic Acids Research 32(Web-Server-Issue): 204-207 (2004)
38		Jessica Shapiro, Douglas L. Brutlag: FoldMiner and LOCK 2: protein structure comparison and motif discovery on the web. Nucleic Acids Research 32(Web-Server-Issue): 536-541 (2004)
2003
37	EE	Mike P. Liang, Douglas L. Brutlag, Russ B. Altman: Automatic Construction of 3D Structural Motifs for Protein Function Prediction. CSB 2003: 613-614
36	EE	Asa Ben-Hur, Douglas L. Brutlag: Remote homology detection: a motif based approach. ISMB (Supplement of Bioinformatics) 2003: 26-33
35	EE	Mike P. Liang, Douglas L. Brutlag, Russ B. Altman: Automated Construction of Structural Motifs for Predicting Functional Sites on Protein Structures. Pacific Symposium on Biocomputing 2003: 204-215
34		Steven P. Bennett, Craig G. Nevill-Manning, Douglas L. Brutlag: 3MOTIF: visualizing conserved protein sequence motifs in the protein structure database. Bioinformatics 19(4): 541-542 (2003)
33	EE	Mehmet Serkan Apaydin, Douglas L. Brutlag, Carlos Guestrin, David Hsu, Jean-Claude Latombe, Chris Varma: Stochastic Roadmap Simulation: An Efficient Representation and Algorithm for Analyzing Molecular Motion. Journal of Computational Biology 10(3/4): 257-281 (2003)
32		Mike P. Liang, D. Rey Banatao, Teri E. Klein, Douglas L. Brutlag, Russ B. Altman: WebFEATURE: an interactive web tool for identifying and visualizing functional sites on macromolecular structures. Nucleic Acids Research 31(13): 3324-3327 (2003)
31		Steven P. Bennett, Lin Lu, Douglas L. Brutlag: 3MATRIX and 3MOTIF: a protein structure visualization system for conserved sequence motifs. Nucleic Acids Research 31(13): 3328-3332 (2003)
2002
30		Mehmet Serkan Apaydin, Carlos Guestrin, Chris Varma, Douglas L. Brutlag, Jean-Claude Latombe: Stochastic roadmap simulation for the study of ligand-protein interactions. ECCB 2002: 18-26
29		Douglas L. Brutlag, Mehmet Serkan Apaydin, Carlos Guestrin, David Hsu, Chris Varma, Amit Pal Singh, Jean-Claude Latombe: Using robotics to fold proteins and dock ligands. ECCB 2002: 74-74
28	EE	Mehmet Serkan Apaydin, Douglas L. Brutlag, Carlos Guestrin, David Hsu, Jean-Claude Latombe: Stochastic roadmap simulation: an efficient representation and algorithm for analyzing molecular motion. RECOMB 2002: 12-21
2001
27		Mehmet Serkan Apaydin, Amit Pal Singh, Douglas L. Brutlag, Jean-Claude Latombe: Capturing Molecular Energy Landscapes with Probabilistic Conformational Roadmaps. ICRA 2001: 932-939
26	EE	X. Liu, Douglas L. Brutlag, Jun S. Liu: BioProspector: Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes. Pacific Symposium on Biocomputing 2001: 127-138
25		Jimmy Y. Huang, Douglas L. Brutlag: The EMOTIF database. Nucleic Acids Research 29(1): 202-204 (2001)
2000
24		Thomas D. Wu, Craig G. Nevill-Manning, Douglas L. Brutlag: Fast probabilistic analysis of sequence function using scoring matrices. Bioinformatics 16(3): 233-244 (2000)
23		Scott C. Schmidler, Jun S. Liu, Douglas L. Brutlag: Bayesian Segmentation of Protein Secondary Structure. Journal of Computational Biology 7(1-2): 233-248 (2000)
1999
22		Thomas Lengauer, Reinhard Schneider, Peer Bork, Douglas L. Brutlag, Janice I. Glasgow, Hans-Werner Mewes, Ralf Zimmer: Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, August 6-10, 1999, Heidelberg, Germany AAAI 1999
21		Amit Pal Singh, Jean-Claude Latombe, Douglas L. Brutlag: A Motion Planning Approach to Flexible Ligand Binding. ISMB 1999: 252-261
20		Thomas D. Wu, Craig G. Nevill-Manning, Douglas L. Brutlag: Minimal-Risk Scoring Matrices for Sequence Analysis. Journal of Computational Biology 6(2): 219-236 (1999)
1998
19	EE	Thomas D. Wu, Trevor Hastie, Scott C. Schmidler, Douglas L. Brutlag: Regression analysis of multiple protein structures. RECOMB 1998: 276-284
18		Thomas D. Wu, Scott C. Schmidler, Trevor Hastie, Douglas L. Brutlag: Regression Analysis of Multiple Protein Structures. Journal of Computational Biology 5(3): 585-596 (1998)
1997
17		Craig G. Nevill-Manning, Komal S. Sethi, Thomas D. Wu, Douglas L. Brutlag: Enumerating and Ranking Discrete Motifs. ISMB 1997: 202-209
16		Amit Pal Singh, Douglas L. Brutlag: Hierarchical Protein Structure Superposition Using Both Secondary Structure and Atomic Representations. ISMB 1997: 284-293
1996
15		Thomas D. Wu, Douglas L. Brutlag: Discovering Empirically Conserved Amino Acid Substitution Groups in Databases of Protein Families. ISMB 1996: 230-240
1995
14		Thomas D. Wu, Douglas L. Brutlag: Identification of Protein Motifs Using Conserved Amino Acid Properties and Partitioning Techniques. ISMB 1995: 402-410
1994
13		Russ B. Altman, Douglas L. Brutlag, Peter D. Karp, Richard H. Lathrop, David B. Searls: Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, August 14-17, 1994, Stanford University, Stanford, California, USA AAAI 1994
12		Tod M. Klingler, Douglas L. Brutlag: Discovering Side-Chain Correlations In alpha-Helices. ISMB 1994: 236-243
11		Dalit Naor, Douglas L. Brutlag: On Near-Optimal Alignments of Biological Sequences. Journal of Computational Biology 1(4): 349- (1994)
1993
10		Dalit Naor, Douglas L. Brutlag: On Suboptimal Alignments of Biological Sequences. CPM 1993: 179-196
9		Tod M. Klingler, Douglas L. Brutlag: Detection of Correlations in tRNA Sequences with Structural Implications. ISMB 1993: 225-233
8	EE	Douglas L. Brutlag, Jean-Pierre Dautricourt, Ron Diaz, Jeff Fier, Bruce Moxon, Richard Stamm: BLAZETM: An Implementation of the Smith-Waterman Sequence Comparison Algorithm on a Massively Parallel Computer. Computers & Chemistry 17(2): 203-207 (1993)
1991
7		Douglas L. Brutlag, A. R. Galper, D. H. Millis: Knowledge-based simulation of DNA metabolism: prediction of enzyme action. Computer Applications in the Biosciences 7(1): 9-19 (1991)
1990
6		Douglas L. Brutlag, Jean-Pierre Dautricourt, S. Maulik, J. Relph: Improved sensitivity of biological sequence database searches. Computer Applications in the Biosciences 6(3): 237-245 (1990)
1986
5		Dennis H. Smith, Douglas L. Brutlag, Peter Friedland, Laurence H. Kedes: BIONET: national computer resource for molecular biology. Nucleic Acids Research 14(1): 17-20 (1986)
1984
4		R. M. Abarbanel, Paul R. Wieneke, E. Mansfield, David A. Jaffe, Douglas L. Brutlag: Rapid searches for complex patterns in biological molecules. Nucleic Acids Research 12(1): 263-280 (1984)
1982
3		Douglas L. Brutlag, J. Clayton, Peter Friedland, Laurence H. Kedes: SEQ: a nucleotide sequence analysis and recombination system. Nucleic Acids Research 10(1): 279-294 (1982)
2		R. Bach, Peter Friedland, Douglas L. Brutlag, Laurence H. Kedes: MAXAMIZE. A DNA sequencing strategy advisor. Nucleic Acids Research 10(1): 295-304 (1982)
1		Peter Friedland, Laurence H. Kedes, Douglas L. Brutlag, Yumi Iwasaki, R. Bach: GENESIS, a knowledge-based genetic engineering simulation system for representation of genetic data and experiment planning. Nucleic Acids Research 10(1): 323-340 (1982)

Coauthor Index

1	R. M. Abarbanel	[4]
2	Russ B. Altman	[13] [32] [35] [37]
3	Mehmet Serkan Apaydin	[27] [28] [29] [30] [33] [44] [46]
4	R. Bach	[1] [2]
5	D. Rey Banatao	[32]
6	Serafim Batzoglou	[39] [45]
7	Asa Ben-Hur	[36] [40]
8	Steven P. Bennett	[31] [34]
9	Edward J. Bertaccini	[42]
10	Peer Bork	[22]
11	Tsung-Han Chiang	[44] [46]
12	J. Clayton	[3]
13	Jean-Pierre Dautricourt	[6] [8]
14	Ron Diaz	[8]
15	Jessica Ebert	[43]
16	Jeff Fier	[8]
17	Eugene Fratkin	[45]
18	Peter Friedland	[1] [2] [3] [5]
19	A. R. Galper	[7]
20	Janice I. Glasgow	[22]
21	Carlos Guestrin	[28] [29] [30] [33]
22	Trevor Hastie	[18] [19]
23	David Hsu	[28] [29] [33] [44] [46]
24	Jimmy Y. Huang	[25]
25	Yumi Iwasaki	[1]
26	David A. Jaffe	[4]
27	Peter D. Karp	[13]
28	Laurence H. Kedes	[1] [2] [3] [5]
29	Teri E. Klein	[32]
30	Tod M. Klingler	[9] [12]
31	Daphne Koller	[40]
32	Richard H. Lathrop	[13]
33	Jean-Claude Latombe	[21] [27] [28] [29] [30] [33] [44] [46]
34	Thomas Lengauer	[22]
35	Mike P. Liang	[32] [35] [37]
36	Jun S. Liu	[23] [26] [39]
37	X. Liu	[26]
38	X. Shirley Liu	[39]
39	Yueyi Liu	[39]
40	Lin Lu	[31] [41]
41	E. Mansfield	[4]
42	S. Maulik	[6]
43	Hans-Werner Mewes	[22]
44	D. H. Millis	[7]
45	Bruce Moxon	[8]
46	Dalit Naor	[10] [11]
47	Brian T. Naughton	[45]
48	Craig G. Nevill-Manning	[17] [20] [24] [34]
49	J. Relph	[6]
50	Serge Saxonov	[41]
51	Scott C. Schmidler	[18] [19] [23]
52	Reinhard Schneider	[22]
53	David B. Searls	[13]
54	Eran Segal	[40]
55	Komal S. Sethi	[17]
56	Jessica Shapiro	[38] [42]
57	Amit Pal Singh	[16] [21] [27] [29]
58	Dennis H. Smith	[5]
59	Richard Stamm	[8]
60	Qiaojuan Jane Su	[41]
61	James R. Trudell	[42]
62	Chris Varma	[29] [30] [33]
63	Haidong Wang	[40]
64	Liping Wei	[39]
65	Paul R. Wieneke	[4]
66	Thomas D. Wu	[14] [15] [17] [18] [19] [20] [24]
67	Ralf Zimmer	[22]

Colors in the list of coauthors