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Douglas L. Brutlag - Publications

Affiliations: 
Stanford University, Palo Alto, CA 
Area:
Bioinformatics
Website:
http://cmgm.stanford.edu/~brutlag/index.html
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69 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, 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
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  0.742
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  0.36
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  0.755
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  0.766
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  0.61
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  0.747
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  0.345
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  0.721
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  0.338
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  0.783
2004 Shapiro J, Brutlag D. FoldMiner and LOCK 2: Protein structure comparison and motif discovery on the web Nucleic Acids Research. 32: W536-W541. PMID 15215444 DOI: 10.1093/Nar/Gkh389  0.347
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  0.592
2004 Shapiro J, Brutlag D. FoldMiner: Structural motif discovery using an improved superposition algorithm Protein Science. 13: 278-294. PMID 14691242 DOI: 10.1110/Ps.03239404  0.376
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  0.704
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  0.746
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  0.414
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  0.347
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  0.759
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  0.727
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  0.428
2001 Huang JY, Brutlag DL. The EMOTIF database. Nucleic Acids Research. 29: 202-4. PMID 11125091 DOI: 10.1093/Nar/29.1.202  0.396
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.  0.699
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  0.735
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 DOI: 10.1093/Bioinformatics/16.3.233  0.745
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 DOI: 10.1089/Cmb.1999.6.219  0.733
1998 Brutlag DL. Genomics and computational molecular biology. Current Opinion in Microbiology. 1: 340-5. PMID 10066490 DOI: 10.1016/S1369-5274(98)80039-8  0.339
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 DOI: 10.1089/Cmb.1998.5.585  0.722
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  0.703
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  0.777
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  0.77
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  0.31
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 DOI: 10.1089/Cmb.1994.1.349  0.313
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  0.388
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  0.323
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 DOI: 10.1093/Bioinformatics/7.1.9  0.314
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 DOI: 10.1093/Bioinformatics/6.3.237  0.395
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 DOI: 10.1073/Pnas.86.1.42  0.335
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  0.709
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  0.704
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 DOI: 10.1073/Pnas.83.3.696  0.726
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 DOI: 10.1093/Nar/12.1Part1.263  0.35
1984 Gilson E, Clément JM, Brutlag D, Hofnung M. A family of dispersed repetitive extragenic palindromic DNA sequences in E. coli Embo Journal. 3: 1417-1421. PMID 6378622 DOI: 10.1002/J.1460-2075.1984.Tb01986.X  0.397
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  0.487
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  0.491
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  0.398
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  0.351
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  0.383
1980 Hsieh TS, Brutlag D. ATP-dependent DNA topoisomerase from D. melanogaster reversibly catenates duplex DNA rings Cell. 21: 115-125. PMID 6250707 DOI: 10.1016/0092-8674(80)90119-1  0.329
1979 Carlson M, Brutlag D. Different regions of a complex satellite DNA vary in size and sequence of the repeating unit Journal of Molecular Biology. 135: 483-500. PMID 231677 DOI: 10.1016/0022-2836(79)90448-0  0.358
1979 Hsieh TS, Brutlag D. Sequence and sequence variation within the 1.688 g/cm3 satellite DNA of Drosophila melanogaster Journal of Molecular Biology. 135: 465-481. PMID 231676 DOI: 10.1016/0022-2836(79)90447-9  0.419
1979 Germond JE, Rouviere-Yaniv J, Yaniv M, Brutlag D. Nicking-closing enzyme assembles nucleosome-like structures in vitro Proceedings of the National Academy of Sciences of the United States of America. 76: 3779-3783. PMID 226980 DOI: 10.1073/Pnas.76.8.3779  0.313
1979 Fry K, Brutlag D. Detection and resolution of closely related satellite DNA sequences by molecular cloning Journal of Molecular Biology. 135: 581-593. PMID 119872 DOI: 10.1016/0022-2836(79)90165-7  0.346
1979 Nelson T, Hsieh TS, Brutlag D. Extracts of Drosophila embryos mediate chromatin assembly in vitro Proceedings of the National Academy of Sciences of the United States of America. 76: 5510-5514. PMID 118449 DOI: 10.1073/Pnas.76.11.5510  0.315
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 DOI: 10.1073/Pnas.76.2.726  0.378
1979 Nelson T, Brutlag D. [3] Addition of homopolymers to the 3′-ends of duplex DNA with terminal transferase Methods in Enzymology. 68: 41-50. DOI: 10.1016/0076-6879(79)68005-9  0.33
1978 Carlson M, Brutlag D. A gene adjacent to satellite DNA in Drosophila melanogaster Proceedings of the National Academy of Sciences of the United States of America. 75: 5898-5902. PMID 104294 DOI: 10.1073/Pnas.75.12.5898  0.352
1978 Carlson M, Brutlag D. One of the copia genes is adjacent to satellite DNA in Drosophila melanogaster Cell. 15: 733-742. PMID 103627 DOI: 10.1016/0092-8674(78)90259-3  0.368
1977 Carlson M, Brutlag D. Cloning and characterization of a complex satellite DNA from drosophila melanogaster Cell. 11: 371-381. PMID 408008 DOI: 10.1016/0092-8674(77)90054-X  0.36
1977 Brutlag D, Appels R, Dennis ES, Peacock WJ. Highly repeated DNA in Drosophila melanogaster Journal of Molecular Biology. 112: 31-47. PMID 407366 DOI: 10.1016/S0022-2836(77)80154-X  0.316
1977 Brutlag D, Fry K, Nelson T, Hung P. Synthesis of hybrid bacterial plasmids containing highly repeated satellite DNA Cell. 10: 509-519. PMID 403010 DOI: 10.1016/0092-8674(77)90038-1  0.347
1977 Brutlag D, Carlson M, Fry K, Hsieh TS. DNA sequence organization in Drosophila heterochromatin Cold Spring Harbor Symposia On Quantitative Biology. 42: 1137-1146. PMID 98265 DOI: 10.1101/Sqb.1978.042.01.114  0.354
1974 Peacock WJ, Brutlag D, Goldring E, Appels R, Hinton CW, Lindsley DL. The organization of highly repeated DNA sequences in Drosophila melanogaster chromosomes. Cold Spring Harbor Symposia On Quantitative Biology. 38: 405-16. PMID 4133985 DOI: 10.1101/Sqb.1974.038.01.043  0.333
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 DOI: 10.1073/Pnas.69.9.2691  0.687
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 DOI: 10.1073/Pnas.69.4.965  0.682
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  0.541
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 DOI: 10.1073/Pnas.68.11.2826  0.614
1969 Brutlag D, Atkinson MR, Setlow P, Kornberg A. An active fragment of DNA polymerase produced by proteolytic cleavage. Biochemical and Biophysical Research Communications. 37: 982-9. PMID 4982877 DOI: 10.1016/0006-291X(69)90228-9  0.563
1969 Brutlag D, Atkinson MR, Setlow P, Kornberg A. An active fragment of DNA polymerase produced by proteolytic cleavage. Biochemical and Biophysical Research Communications. 37: 982-9. PMID 4982877 DOI: 10.1016/0006-291X(69)90228-9  0.563
1969 Brutlag D, Atkinson MR, Setlow P, Kornberg A. An active fragment of DNA polymerase produced by proteolytic cleavage. Biochemical and Biophysical Research Communications. 37: 982-9. PMID 4982877 DOI: 10.1016/0006-291X(69)90228-9  0.563
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