Douglas L. Brutlag - Publications

Affiliations: 
Stanford University, Palo Alto, CA 
Area:
Bioinformatics
Website:
http://cmgm.stanford.edu/~brutlag/index.html

72 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2008 Brutlag DL. Inferring Protein Function from Sequence Bioinformatics-From Genomes to Therapies. 3: 1087-1119. DOI: 10.1002/9783527619368.ch30  0.64
2007 Chiang TH, Apaydin MS, Brutlag DL, Hsu D, Latombe JC. Using stochastic roadmap simulation to predict experimental quantities in protein folding kinetics: folding rates and phi-values. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 14: 578-93. PMID 17683262 DOI: 10.1089/cmb.2007.R004  0.64
2007 Huang X, Brutlag DL. Dynamic use of multiple parameter sets in sequence alignment. Nucleic Acids Research. 35: 678-86. PMID 17182633 DOI: 10.1093/nar/gkl1063  0.64
2006 Rhee SY, Taylor J, Wadhera G, Ben-Hur A, Brutlag DL, Shafer RW. Genotypic predictors of human immunodeficiency virus type 1 drug resistance. Proceedings of the National Academy of Sciences of the United States of America. 103: 17355-60. PMID 17065321 DOI: 10.1073/pnas.0607274103  0.64
2006 Naughton BT, Fratkin E, Batzoglou S, Brutlag DL. A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites. Nucleic Acids Research. 34: 5730-9. PMID 17041233 DOI: 10.1093/nar/gkl585  0.64
2006 Fratkin E, Naughton BT, Brutlag DL, Batzoglou S. MotifCut: regulatory motifs finding with maximum density subgraphs. Bioinformatics (Oxford, England). 22: e150-7. PMID 16873465 DOI: 10.1093/bioinformatics/btl243  0.64
2006 Ebert J, Brutlag D. Development and validation of a consistency based multiple structure alignment algorithm. Bioinformatics (Oxford, England). 22: 1080-7. PMID 16473868 DOI: 10.1093/bioinformatics/btl046  0.52
2006 Saxonov S, Berg P, Brutlag DL. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proceedings of the National Academy of Sciences of the United States of America. 103: 1412-7. PMID 16432200 DOI: 10.1073/pnas.0510310103  0.64
2006 Tellez AB, Crowder S, Spagnolo JF, Thompson AA, Peersen OB, Brutlag DL, Kirkegaard K. Nucleotide channel of RNA-dependent RNA polymerase used for intermolecular uridylylation of protein primer. Journal of Molecular Biology. 357: 665-75. PMID 16427083 DOI: 10.1016/j.jmb.2005.12.044  0.64
2006 Chiang TH, Apaydin MS, Brutlag DL, Hsu D, Latombe JC. Predicting experimental quantities in protein folding kinetics using stochastic roadmap simulation Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3909: 410-424. DOI: 10.1007/11732990_34  0.64
2005 Bertaccini EJ, Shapiro J, Brutlag DL, Trudell JR. Homology modeling of a human glycine alpha 1 receptor reveals a plausible anesthetic binding site. Journal of Chemical Information and Modeling. 45: 128-35. PMID 15667138 DOI: 10.1021/ci0497399  0.64
2005 Su QJ, Lu L, Saxonov S, Brutlag DL. eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity. Nucleic Acids Research. 33: D178-82. PMID 15608172 DOI: 10.1093/nar/gki060  0.64
2005 Wang H, Segal E, Ben-Hur A, Koller D, Brutlag DL. Identifying protein-protein interaction sites on a genome-wide scale Advances in Neural Information Processing Systems 0.64
2004 Liu Y, Wei L, Batzoglou S, Brutlag DL, Liu JS, Liu XS. A suite of web-based programs to search for transcriptional regulatory motifs. Nucleic Acids Research. 32: W204-7. PMID 15215381 DOI: 10.1093/nar/gkh461  0.64
2004 Liang MP, Troyanskaya OG, Laederach A, Brutlag DL, Altman RB. Computational functional genomics Ieee Signal Processing Magazine. 21: 62-69. DOI: 10.1109/MSP.2004.1359143  0.64
2004 Apaydin MS, Brutlag DL, Guestrin C, Hsu D, Latombe JC. Stochastic conformational roadmaps for computing ensemble properties of molecular motion Springer Tracts in Advanced Robotics. 7: 131-147. DOI: 10.1007/978-3-540-45058-0_9  0.64
2003 Apaydin MS, Brutlag DL, Guestrin C, Hsu D, Latombe JC, Varma C. Stochastic roadmap simulation: an efficient representation and algorithm for analyzing molecular motion. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 10: 257-81. PMID 12935328 DOI: 10.1089/10665270360688011  0.64
2003 Bennett SP, Lu L, Brutlag DL. 3MATRIX and 3MOTIF: a protein structure visualization system for conserved sequence motifs. Nucleic Acids Research. 31: 3328-32. PMID 12824319 DOI: 10.1093/nar/gkg564  0.64
2003 Liang MP, Banatao DR, Klein TE, Brutlag DL, Altman RB. WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures. Nucleic Acids Research. 31: 3324-7. PMID 12824318 DOI: 10.1093/nar/gkg553  0.64
2003 Bennett SP, Nevill-Manning CG, Brutlag DL. 3MOTIF: visualizing conserved protein sequence motifs in the protein structure database. Bioinformatics (Oxford, England). 19: 541-2. PMID 12611811 DOI: 10.1093/bioinformatics/btf862  0.64
2003 Liang MP, Brutlag DL, Altman RB. Automated construction of structural motifs for predicting functional sites on protein structures. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 204-15. PMID 12603029  0.64
2002 Apaydin MS, Guestrin CE, Varma C, Brutlag DL, Latombe JC. Stochastic roadmap simulation for the study of ligand-protein interactions. Bioinformatics (Oxford, England). 18: S18-26. PMID 12385979  0.64
2002 Liu XS, Brutlag DL, Liu JS. An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nature Biotechnology. 20: 835-9. PMID 12101404 DOI: 10.1038/nbt717  0.64
2001 Liu X, Brutlag DL, Liu JS. BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 127-38. PMID 11262934  0.64
2001 Huang JY, Brutlag DL. The EMOTIF database. Nucleic Acids Research. 29: 202-4. PMID 11125091  0.64
2001 Apaydin MS, Singh AP, Brutlag DL, Latombe JC. Capturing molecular energy landscapes with probabilistic conformational roadmaps Proceedings - Ieee International Conference On Robotics and Automation. 1: 932-939.  0.64
2000 Schmidler SC, Liu JS, Brutlag DL. Bayesian segmentation of protein secondary structure. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 7: 233-48. PMID 10890399 DOI: 10.1089/10665270050081496  0.64
2000 Wu TD, Nevill-Manning CG, Brutlag DL. Fast probabilistic analysis of sequence function using scoring matrices. Bioinformatics (Oxford, England). 16: 233-44. PMID 10869016  0.64
1999 Singh AP, Latombe JC, Brutlag DL. A motion planning approach to flexible ligand binding. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 252-61. PMID 10786308  0.64
1999 Wu TD, Nevill-Manning CG, Brutlag DL. Minimal-risk scoring matrices for sequence analysis. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 6: 219-35. PMID 10421524  0.64
1998 Brutlag DL. Genomics and computational molecular biology. Current Opinion in Microbiology. 1: 340-5. PMID 10066490  0.64
1998 Wu TD, Schmidler SC, Hastie T, Brutlag DL. Regression analysis of multiple protein structures. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 5: 585-95. PMID 9773352  0.64
1998 Rindfleisch TC, Brutlag DL. Directions for clinical research and genomic research into the next decade: implications for informatics. Journal of the American Medical Informatics Association : Jamia. 5: 404-11. PMID 9760387  0.64
1998 Wu TD, Schmidler SC, Hastie T, Brutlag DL. Modeling and superposition of multiple protein structures using affine transformations: analysis of the globins. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 509-20. PMID 9697208  0.64
1998 Nevill-Manning CG, Wu TD, Brutlag DL. Highly specific protein sequence motifs for genome analysis. Proceedings of the National Academy of Sciences of the United States of America. 95: 5865-71. PMID 9600885 DOI: 10.1073/pnas.95.11.5865  0.64
1997 Singh AP, Brutlag DL. Hierarchical protein structure superposition using both secondary structure and atomic representations. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 5: 284-93. PMID 9322051  0.64
1997 Nevill-Manning CG, Sethi KS, Wu TD, Brutlag DL. Enumerating and ranking discrete motifs. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 5: 202-9. PMID 9322037  0.64
1996 Tomita M, Shimizu N, Brutlag DL. Introns and reading frames: correlation between splicing sites and their codon positions. Molecular Biology and Evolution. 13: 1219-23. PMID 8896374  0.64
1996 Wu TD, Brutlag DL. Discovering empirically conserved amino acid substitution groups in databases of protein families. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 4: 230-40. PMID 8877523  0.64
1996 Brutlag DL, Sternberg MJ. Sequences and topology challenges for algorithms and experts. Current Opinion in Structural Biology. 6: 343-5. PMID 8804838 DOI: 10.1016/S0959-440X(96)80053-4  0.64
1995 Wu TD, Brutlag DL. Identification of protein motifs using conserved amino acid properties and partitioning techniques. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 3: 402-10. PMID 7584465  0.64
1994 Naor D, Brutlag DL. On near-optimal alignments of biological sequences. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 1: 349-66. PMID 8790476  0.64
1994 Klingler TM, Brutlag DL. Discovering structural correlations in alpha-helices. Protein Science : a Publication of the Protein Society. 3: 1847-57. PMID 7849600 DOI: 10.1002/pro.5560031024  0.64
1994 Klingler TM, Brutlag DL. Discovering side-chain correlation in alpha-helices. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 2: 236-43. PMID 7584396  0.64
1993 Klingler TM, Brutlag DL. Detection of correlations in tRNA sequences with structural implications. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 1: 225-33. PMID 7584340  0.64
1993 Brutlag DL, Dautricourt JP, Diaz R, Fier J, Moxon B, Stamm R. BLAZE™: An implementation of the Smith-Waterman sequence comparison algorithm on a massively parallel computer Computers and Chemistry. 17: 203-207. DOI: 10.1016/0097-8485(93)85011-Z  0.64
1991 Brutlag DL, Galper AR, Millis DH. Knowledge-based simulation of DNA metabolism: prediction of enzyme action. Computer Applications in the Biosciences : Cabios. 7: 9-19. PMID 2004281  0.64
1991 Barsalou T, Brutlag DL. Searching gene and protein sequence databases. M.D. Computing : Computers in Medical Practice. 8: 144-9. PMID 1857191  0.64
1990 Brutlag DL, Dautricourt JP, Maulik S, Relph J. Improved sensitivity of biological sequence database searches. Computer Applications in the Biosciences : Cabios. 6: 237-45. PMID 2207748  0.64
1989 Goldstein A, Brutlag DL. Is there a relationship between DNA sequences encoding peptide ligands and their receptors? Proceedings of the National Academy of Sciences of the United States of America. 86: 42-5. PMID 2536158  0.64
1989 Hipeau-Jacquotte R, Brutlag DL, Brégégère F. Conversion and reciprocal exchange between tandem repeats in Drosophila melanogaster. Molecular & General Genetics : Mgg. 220: 140-6. PMID 2514345 DOI: 10.1007/BF00260868  0.64
1988 Fairman R, Brutlag DL. Expression of the Drosophila type II topoisomerase is developmentally regulated. Biochemistry. 27: 560-5. PMID 2831969  0.64
1987 Lohe AR, Brutlag DL. Adjacent satellite DNA segments in Drosophila structure of junctions. Journal of Molecular Biology. 194: 171-9. PMID 3112414 DOI: 10.1016/0022-2836(87)90366-4  0.64
1987 Lohe AR, Brutlag DL. Identical satellite DNA sequences in sibling species of Drosophila. Journal of Molecular Biology. 194: 161-70. PMID 3112413 DOI: 10.1016/0022-2836(87)90365-2  0.64
1986 Lohe AR, Brutlag DL. Multiplicity of satellite DNA sequences in Drosophila melanogaster. Proceedings of the National Academy of Sciences of the United States of America. 83: 696-700. PMID 3080746  0.64
1986 Heller RA, Shelton ER, Dietrich V, Elgin SC, Brutlag DL. Multiple forms and cellular localization of Drosophila DNA topoisomerase II. The Journal of Biological Chemistry. 261: 8063-9. PMID 3011806  0.64
1984 Dahmus GK, Glover CV, Brutlag DL, Dahmus ME. Similarities in structure and function of calf thymus and Drosophila casein kinase II. The Journal of Biological Chemistry. 259: 9001-6. PMID 6589223  0.64
1984 Abarbanel RM, Wieneke PR, Mansfield E, Jaffe DA, Brutlag DL. Rapid searches for complex patterns in biological molecules. Nucleic Acids Research. 12: 263-80. PMID 6546419  0.64
1983 Osheroff N, Shelton ER, Brutlag DL. DNA topoisomerase II from Drosophila melanogaster. Relaxation of supercoiled DNA. The Journal of Biological Chemistry. 258: 9536-43. PMID 6308011  0.64
1983 Shelton ER, Osheroff N, Brutlag DL. DNA topoisomerase II from Drosophila melanogaster. Purification and physical characterization. The Journal of Biological Chemistry. 258: 9530-5. PMID 6308010  0.64
1983 Glover CV, Shelton ER, Brutlag DL. Purification and characterization of a type II casein kinase from Drosophila melanogaster. The Journal of Biological Chemistry. 258: 3258-65. PMID 6298230  0.64
1982 Brutlag DL, Clayton J, Friedland P, Kedes LH. SEQ: a nucleotide sequence analysis and recombination system. Nucleic Acids Research. 10: 279-94. PMID 7063402 DOI: 10.1093/nar/10.1.279  0.64
1982 Bach R, Friedland P, Brutlag DL, Kedes L. MAXAMIZE. A DNA sequencing strategy advisor. Nucleic Acids Research. 10: 295-304. PMID 6278407 DOI: 10.1093/nar/10.1.295  0.64
1981 Wiegand RC, Brutlag DL. Histone acetylase from Drosophila melanogaster specific for H4. The Journal of Biological Chemistry. 256: 4578-83. PMID 6783663  0.64
1980 Brutlag DL. Molecular arrangement and evolution of heterochromatic DNA. Annual Review of Genetics. 14: 121-44. PMID 6260016 DOI: 10.1146/annurev.ge.14.120180.001005  0.64
1979 Hsieh T, Brutlag DL. A protein that preferentially binds Drosophila satellite DNA. Proceedings of the National Academy of Sciences of the United States of America. 76: 726-30. PMID 106393  0.64
1973 Westergaard O, Brutlag D, Kornberg A. Initiation of deoxyribonucleic acid synthesis. IV. Incorporation of the ribonucleic acid primer into the phage replicative form Journal of Biological Chemistry. 248: 1361-1364. PMID 4568814  0.64
1972 Schekman R, Wickner W, Westergaard O, Brutlag D, Geider K, Bertsch LL, Kornberg A. Initiation of DNA synthesis: synthesis of phiX174 replicative form requires RNA synthesis resistant to rifampicin. Proceedings of the National Academy of Sciences of the United States of America. 69: 2691-5. PMID 4560696  0.64
1972 Wickner W, Brutlag D, Schekman R, Kornberg A. RNA synthesis initiates in vitro conversion of M13 DNA to its replicative form. Proceedings of the National Academy of Sciences of the United States of America. 69: 965-9. PMID 4554537  0.64
1972 Setlow P, Brutlag D, Kornberg A. Deoxyribonucleic acid polymerase: two distinct enzymes in one polypeptide. I. A proteolytic fragment containing the polymerase and 3' leads to 5' exonuclease functions. The Journal of Biological Chemistry. 247: 224-31. PMID 4552924  0.64
1972 Brutlag D, Kornberg A. Enzymatic synthesis of deoxyribonucleic acid. 36. A proofreading function for the 3' leads to 5' exonuclease activity in deoxyribonucleic acid polymerases Journal of Biological Chemistry. 247: 241-248. PMID 4336040  0.64
1971 Brutlag D, Schekman R, Kornberg A. A possible role for RNA polymerase in the initiation of M13 DNA synthesis Proceedings of the National Academy of Sciences of the United States of America. 68: 2826-2829. PMID 4941987  0.64
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