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David B. Gordon, Ph.D. - Publications

Affiliations: 
2000 California Institute of Technology, Pasadena, CA 
Area:
Structural Biology
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32 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
2016 Roehner N, Young E, Voigt CA, Gordon DB, Densmore D. Double Dutch: A Tool for Designing Combinatorial Libraries of Biological Systems. Acs Synthetic Biology. PMID 27110633 DOI: 10.1021/Acssynbio.5B00232  0.6
2016 Gordon D, Huddleston J, Chaisson MJ, Hill CM, Kronenberg ZN, Munson KM, Malig M, Raja A, Fiddes I, Hillier LW, Dunn C, Baker C, Armstrong J, Diekhans M, Paten B, et al. Long-read sequence assembly of the gorilla genome. Science (New York, N.Y.). 352: aae0344. PMID 27034376 DOI: 10.1126/Science.Aae0344  1
2015 Fernández-Rodríguez J, Yang L, Gorochowski TE, Gordon B, Voigt CA. Memory and combinatorial logic based on DNA inversions: dynamics and evolutionary stability. Acs Synthetic Biology. PMID 26548807 DOI: 10.1021/Acssynbio.5B00170  0.6
2014 Smanski MJ, Bhatia S, Zhao D, Park Y, B A Woodruff L, Giannoukos G, Ciulla D, Busby M, Calderon J, Nicol R, Gordon DB, Densmore D, Voigt CA. Functional optimization of gene clusters by combinatorial design and assembly. Nature Biotechnology. 32: 1241-9. PMID 25419741 DOI: 10.1038/Nbt.3063  0.6
2014 Woodruff LBA, Mikkelsen T, Smanski MJ, Gordon DB, Voigt CA, Nicol R. Scalable, accurate, and systematic engineering of synthetic pathways: Massively multiplexed DNA assembly, next-gen sequence verification, and model-guided design Systems Biology 2014 - Topical Conference At the 2014 Aiche Annual Meeting. 2.  0.6
2013 Gordon D, Green P. Consed: A graphical editor for next-generation sequencing Bioinformatics. 29: 2936-2937. PMID 23995391 DOI: 10.1093/Bioinformatics/Btt515  1
2013 Sana TR, Gordon DB, Fischer SM, Tichy SE, Kitagawa N, Lai C, Gosnell WL, Chang SP. Global mass spectrometry based metabolomics profiling of erythrocytes infected with Plasmodium falciparum. Plos One. 8: e60840. PMID 23593322 DOI: 10.1371/Journal.Pone.0060840  1
2010 Qi HH, Sarkissian M, Hu GQ, Wang Z, Bhattacharjee A, Gordon DB, Gonzales M, Lan F, Ongusaha PP, Huarte M, Yaghi NK, Lim H, Garcia BA, Brizuela L, Zhao K, et al. Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development. Nature. 466: 503-7. PMID 20622853 DOI: 10.1038/Nature09261  1
2010 Nielsen CB, Cantor M, Dubchak I, Gordon D, Wang T. Visualizing genomes: techniques and challenges. Nature Methods. 7: S5-S15. PMID 20195257 DOI: 10.1038/nmeth.1422  1
2010 Gresham D, Curry B, Ward A, Gordon DB, Brizuela L, Kruglyak L, Botstein D. Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes. Proceedings of the National Academy of Sciences of the United States of America. 107: 1482-7. PMID 20080586 DOI: 10.1073/Pnas.0913883107  1
2009 Hodges E, Rooks M, Xuan Z, Bhattacharjee A, Benjamin Gordon D, Brizuela L, Richard McCombie W, Hannon GJ. Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing. Nature Protocols. 4: 960-74. PMID 19478811 DOI: 10.1038/Nprot.2009.68  1
2009 McVicker G, Gordon D, Davis C, Green P. Widespread genomic signatures of natural selection in hominid evolution Plos Genetics. 5. PMID 19424416 DOI: 10.1371/Journal.Pgen.1000471  1
2008 Ley TJ, Mardis ER, Ding L, Fulton B, McLellan MD, Chen K, Dooling D, Dunford-Shore BH, McGrath S, Hickenbotham M, Cook L, Abbott R, Larson DE, Koboldt DC, Pohl C, ... ... Gordon D, et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature. 456: 66-72. PMID 18987736 DOI: 10.1038/Nature07485  1
2008 Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, et al. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Research. 18: 393-403. PMID 18258921 DOI: 10.1101/Gr.7080508  1
2007 Baek D, Davis C, Ewing B, Gordon D, Green P. Characterization and predictive discovery of evolutionarily conserved mammalian alternative promoters. Genome Research. 17: 145-55. PMID 17210929 DOI: 10.1101/Gr.5872707  1
2006 MacIsaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD, Fraenkel E. An improved map of conserved regulatory sites for Saccharomyces cerevisiae. Bmc Bioinformatics. 7: 113. PMID 16522208 DOI: 10.1186/1471-2105-7-113  1
2006 Macisaac KD, Gordon DB, Nekludova L, Odom DT, Schreiber J, Gifford DK, Young RA, Fraenkel E. A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data. Bioinformatics (Oxford, England). 22: 423-9. PMID 16332710 DOI: 10.1093/Bioinformatics/Bti815  1
2005 Gordon DB, Nekludova L, McCallum S, Fraenkel E. TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs. Bioinformatics (Oxford, England). 21: 3164-5. PMID 15905282 DOI: 10.1093/Bioinformatics/Bti481  1
2004 Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, et al. Transcriptional regulatory code of a eukaryotic genome. Nature. 431: 99-104. PMID 15343339 DOI: 10.1038/Nature02800  1
2004 Odom DT, Zizlsperger N, Gordon DB, Bell GW, Rinaldi NJ, Murray HL, Volkert TL, Schreiber J, Rolfe PA, Gifford DK, Fraenkel E, Bell GI, Young RA. Control of pancreas and liver gene expression by HNF transcription factors. Science (New York, N.Y.). 303: 1378-81. PMID 14988562 DOI: 10.1126/Science.1089769  1
2003 Gordon D. Viewing and editing assembled sequences using Consed Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit11.2. PMID 18428695  1
2003 Bar-Joseph Z, Gerber GK, Lee TI, Rinaldi NJ, Yoo JY, Robert F, Gordon DB, Fraenkel E, Jaakkola TS, Young RA, Gifford DK. Computational discovery of gene modules and regulatory networks. Nature Biotechnology. 21: 1337-42. PMID 14555958 DOI: 10.1038/Nbt890  1
2003 Gordon DB, Hom GK, Mayo SL, Pierce NA. Exact rotamer optimization for protein design. Journal of Computational Chemistry. 24: 232-43. PMID 12497602 DOI: 10.1002/Jcc.10121  1
2001 Zhuo D, Zhao WD, Wright FA, Yang HY, Wang JP, Sears R, Baer T, Kwon DH, Gordon D, Gibbs S, Dai D, Yang Q, Spitzner J, Krahe R, Stredney D, et al. Assembly, annotation, and integration of UNIGENE clusters into the human genome draft. Genome Research. 11: 904-18. PMID 11337484 DOI: 10.1101/Gr.Gr-1645R  1
2001 Gordon D, Desmarais C, Green P. Automated finishing with autofinish Genome Research. 11: 614-625. PMID 11282977 DOI: 10.1101/Gr.171401  1
2000 Street AG, Datta D, Gordon DB, Mayo SL. Designing protein beta-sheet surfaces by Z-score optimization. Physical Review Letters. 84: 5010-3. PMID 10990854 DOI: 10.1103/Physrevlett.84.5010  1
2000 Voigt CA, Gordon DB, Mayo SL. Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design. Journal of Molecular Biology. 299: 789-803. PMID 10835284 DOI: 10.1006/Jmbi.2000.3758  1
1999 Gordon DB, Mayo SL. Branch-and-terminate: a combinatorial optimization algorithm for protein design. Structure (London, England : 1993). 7: 1089-98. PMID 10508778 DOI: 10.1016/S0969-2126(99)80176-2  1
1999 Gordon DB, Marshall SA, Mayo SL. Energy functions for protein design. Current Opinion in Structural Biology. 9: 509-13. PMID 10449371 DOI: 10.1016/S0959-440X(99)80072-4  1
1999 Huang GM, Ng Wl, Farkas J, He L, Liang HA, Gordon D, Yu J, Hood L. Prostate cancer expression profiling by cDNA sequencing analysis Genomics. 59: 178-186. PMID 10409429 DOI: 10.1006/Geno.1999.5822  1
1998 Gordon D, Abajian C, Green P. Consed: a graphical tool for sequence finishing. Genome Research. 8: 195-202. PMID 9521923 DOI: 10.1101/Gr.8.3.195  1
1997 Dahiyat BI, Gordon DB, Mayo SL. Automated design of the surface positions of protein helices. Protein Science : a Publication of the Protein Society. 6: 1333-7. PMID 9194194 DOI: 10.1002/Pro.5560060622  1
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