Timothy S. Gardner - Publications

Affiliations: 
2000 Boston University, Boston, MA, United States 

26 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
2018 Juergens H, Niemeijer M, Jennings-Antipov LD, Mans R, Morel J, van Maris AJA, Pronk JT, Gardner TS. Evaluation of a novel cloud-based software platform for structured experiment design and linked data analytics. Scientific Data. 5: 180195. PMID 30280721 DOI: 10.1038/Sdata.2018.195  0.355
2013 Gardner TS. Synthetic biology: from hype to impact. Trends in Biotechnology. 31: 123-5. PMID 23419209 DOI: 10.1016/J.Tibtech.2013.01.018  0.351
2012 Bansal M, Della Gatta G, Wierzbowski J, Gardner T, di Bernardo D. Discovering drug mode of action using reverse-engineered gene networks. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2005: 4739-42. PMID 17281300 DOI: 10.1109/IEMBS.2005.1615530  0.332
2010 Cosgrove EJ, Gardner TS, Kolaczyk ED. On the choice and number of microarrays for transcriptional regulatory network inference. Bmc Bioinformatics. 11: 454. PMID 20825684 DOI: 10.1186/1471-2105-11-454  0.776
2010 Thaden JT, Lory S, Gardner TS. Quorum-sensing regulation of a copper toxicity system in Pseudomonas aeruginosa. Journal of Bacteriology. 192: 2557-68. PMID 20233934 DOI: 10.1128/Jb.01528-09  0.666
2008 Cosgrove EJ, Zhou Y, Gardner TS, Kolaczyk ED. Predicting gene targets of perturbations via network-based filtering of mRNA expression compendia. Bioinformatics (Oxford, England). 24: 2482-90. PMID 18779235 DOI: 10.1093/Bioinformatics/Btn476  0.766
2008 Fredrickson JK, Romine MF, Beliaev AS, Auchtung JM, Driscoll ME, Gardner TS, Nealson KH, Osterman AL, Pinchuk G, Reed JL, Rodionov DA, Rodrigues JL, Saffarini DA, Serres MH, Spormann AM, et al. Towards environmental systems biology of Shewanella. Nature Reviews. Microbiology. 6: 592-603. PMID 18604222 DOI: 10.1038/Nrmicro1947  0.734
2008 Song W, Juhn FS, Naiman DQ, Konstantinidis KT, Gardner TS, Ward MJ. Predicting sigma28 promoters in eleven Shewanella genomes. Fems Microbiology Letters. 283: 223-30. PMID 18430000 DOI: 10.1111/J.1574-6968.2008.01175.X  0.377
2008 Faith JJ, Driscoll ME, Fusaro VA, Cosgrove EJ, Hayete B, Juhn FS, Schneider SJ, Gardner TS. Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. Nucleic Acids Research. 36: D866-70. PMID 17932051 DOI: 10.1093/Nar/Gkm815  0.634
2007 Driscoll ME, Romine MF, Juhn FS, Serres MH, McCue LA, Beliaev AS, Fredrickson JK, Gardner TS. Identification of diverse carbon utilization pathways in Shewanella oneidensis MR-1 via expression profiling. Genome Informatics. International Conference On Genome Informatics. 18: 287-98. PMID 18546496 DOI: 10.11234/Gi1990.18.287  0.743
2007 Faith JJ, Olson AJ, Gardner TS, Sachidanandam R. Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context. Bmc Bioinformatics. 8: 344. PMID 17877794 DOI: 10.1186/1471-2105-8-344  0.588
2007 Hayete B, Gardner TS, Collins JJ. Size matters: network inference tackles the genome scale. Molecular Systems Biology. 3: 77. PMID 17299414 DOI: 10.1038/Msb4100118  0.774
2007 Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. Plos Biology. 5: e8. PMID 17214507 DOI: 10.1371/Journal.Pbio.0050008  0.736
2007 Zhong Q, Boscolo R, Gardner TS, Roychowdhury VP. Inferring regulatory interactions between transcriptional factors and genes by propagating known regulatory links 2007 Ieee Symposium On Computational Intelligence and Bioinformatics and Computational Biology, Cibcb 2007. 205-211.  0.368
2006 Xing H, Gardner TS. The mode-of-action by network identification (MNI) algorithm: a network biology approach for molecular target identification. Nature Protocols. 1: 2551-4. PMID 17406508 DOI: 10.1038/Nprot.2006.300  0.482
2006 Driscoll ME, Gardner TS. Identification and control of gene networks in living organisms via supervised and unsupervised learning Journal of Process Control. 16: 303-311. DOI: 10.1016/J.Jprocont.2005.06.010  0.769
2005 Gardner TS, Faith JJ. Reverse-engineering transcription control networks. Physics of Life Reviews. 2: 65-88. PMID 20416858 DOI: 10.1016/J.Plrev.2005.01.001  0.637
2005 di Bernardo D, Thompson MJ, Gardner TS, Chobot SE, Eastwood EL, Wojtovich AP, Elliott SJ, Schaus SE, Collins JJ. Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nature Biotechnology. 23: 377-83. PMID 15765094 DOI: 10.1038/Nbt1075  0.543
2005 Bansal M, Della Gatta G, Wierzbowski J, Gardner T, Di Bernardo D. Discovering drug mode of action using reverse-engineered gene networks Annual International Conference of the Ieee Engineering in Medicine and Biology - Proceedings. 7: 4739-4742.  0.332
2004 Kobayashi H, Kaern M, Araki M, Chung K, Gardner TS, Cantor CR, Collins JJ. Programmable cells: interfacing natural and engineered gene networks. Proceedings of the National Academy of Sciences of the United States of America. 101: 8414-9. PMID 15159530 DOI: 10.1073/Pnas.0402940101  0.473
2004 Di Bernardo D, Gardner TS, Collins JJ. Robust identification of large genetic networks. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 486-97. PMID 14992527  0.527
2003 Gardner TS, di Bernardo D, Lorenz D, Collins JJ. Inferring genetic networks and identifying compound mode of action via expression profiling. Science (New York, N.Y.). 301: 102-5. PMID 12843395 DOI: 10.1126/Science.1081900  0.753
2000 Gardner TS, Collins JJ. Neutralizing noise in gene networks. Nature. 405: 520-1. PMID 10850696 DOI: 10.1038/35014708  0.484
2000 Gardner TS, Cantor CR, Collins JJ. Construction of a genetic toggle switch in Escherichia coli. Nature. 403: 339-42. PMID 10659857 DOI: 10.1038/35002131  0.52
1999 Dolnik M, Gardner TS, Epstein IR, Collins JJ. Frequency Control of an Oscillatory Reaction by Reversible Binding of an Autocatalyst Physical Review Letters. 82: 1582-1585. DOI: 10.1103/Physrevlett.82.1582  0.39
1998 Gardner TS, Dolnik M, Collins JJ. A theory for controlling cell cycle dynamics using a reversibly binding inhibitor. Proceedings of the National Academy of Sciences of the United States of America. 95: 14190-5. PMID 9826676 DOI: 10.1073/Pnas.95.24.14190  0.433
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