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Group: TNT - library [158 articles]

Recent papers posted by members of the TNT group
  • Inferring Pairwise Regulatory Relationships from Multiple Time Series Datasets.
    Bioinformatics (19 January 2007)
    by Yanxin Shi, Tom Mitchell, Ziv Bar-Joseph
    posted to regulation network modelling by icases to the group TNT on 2007-02-11 14:49:41 as *****
  • Transcriptional regulation of protein complexes within and across species
    PNAS, Vol. 104, No. 4. (23 January 2007), pp. 1283-1288.
    by Kai Tan, Tomer Shlomi, Hoda Feizi, Trey Ideker, Roded Sharan
    posted to transcription regulation network evolution by icases to the group TNT on 2007-01-25 19:33:03 as ***** along with 4 people and 1 group nickluscombe zwang dylan77 carlk EBI-regulation
  • Assessing computational tools for the discovery of transcription factor binding sites
    Nature Biotechnology, Vol. 23, No. 1. (06 January 2005), pp. 137-144.
    by Martin Tompa, Nan Li, Timothy L Bailey, George M Church, Bart D De Moor, Eleazar Eskin, Alexander V Favorov, Martin C Frith, Yutao Fu, James J Kent, Vsevolod J Makeev, Andrei A Mironov, William S Noble, Giulio Pavesi, Graziano Pesole, Mireille Régnier, Nicolas Simonis, Saurabh Sinha, Gert Thijs, Jacques v van Helden, Mathias Vandenbogaert, Zhiping Weng, Christopher Workman, Chun Ye, Zhou Zhu
    posted to prediction promoter transcription by icases to the group TNT on 2006-12-20 16:27:03 as ***** along with 26 people and 5 groups emptyhb bryankr ana barry aalibes aprasad jfr tuck chad_davis lyongu tabu dquest neveaire ranb johncumbers noano xiaobeizhao olympos GustavoLacerda nklee mdimon dandaman vietanh0 ep161302 nuin Stew structural_bioinformatics Biostatistics Computational-Genomics Bioinformatics Neuroscience
  • Applied bioinformatics for the identification of regulatory elements.
    Nat Rev Genet, Vol. 5, No. 4. (April 2004), pp. 276-287.
    by WW Wasserman, A Sandelin
    posted to prediction promoter regulation transcription by icases to the group TNT on 2006-12-20 15:21:04 as ***** along with 16 people and 7 groups ana chad_davis moborg gpalidwor dchughes nickluscombe johncumbers giovanni xiaobeizhao bertelsen Stew nklee jdiezperezj ArtemPankin mariakmejia isimpson structural_bioinformatics Bioinformatics EisenLab G4ID EBI-regulation GeschwindLab Genetics-of-Gambling
  • Genomic analysis of regulatory network dynamics reveals large topological changes.
    Nature, Vol. 431, No. 7006. (16 September 2004), pp. 308-312.
    by NM Luscombe, MM Babu, H Yu, M Snyder, SA Teichmann, M Gerstein
    posted to dynamics metabolism network simulation yeast by icases to the group TNT on 2005-02-08 14:56:06 as ***** along with 21 people and 6 groups vertikalist camster snuppepuppan hununu lna lfriedl alexg nirfriedman dgront nickluscombe kairita comb kengg gespim koller timflutre fishtank cjeans rebeccamancy faion carlk BTS-PT-AS-CS dbk-lab kdl EBI-regulation ColDyn Plantandetc
  • Analysis of catRABC operon for catechol degradation from phenol-degrading Rhodococcus erythropolis.
    Applied microbiology and biotechnology, Vol. 76, No. 1. (August 2007), pp. 159-168.
    by M Veselý, M Knoppová, J Nesvera, M Pátek
    posted to biodegradation catr for-the-review iclr regulation transcription by gcarbajosa to the group TNT on 2008-07-21 18:13:45 as ****
  • The MarR-type repressor MhqR (YkvE) regulates multiple dioxygenases/glyoxalases and an azoreductase which confer resistance to 2-methylhydroquinone and catechol in Bacillus subtilis.
    Molecular microbiology, Vol. 66, No. 1. (October 2007), pp. 40-54.
    by S Töwe, M Leelakriangsak, K Kobayashi, N Van Duy, M Hecker, P Zuber, H Antelmann
    posted to biodegradation for-the-review marr regulation transcription by gcarbajosa to the group TNT on 2008-07-21 17:52:33 as ****
  • Oligomerization of BenM, a LysR-type transcriptional regulator: structural basis for the aggregation of proteins in this family
    Acta Crystallographica Section F: Structural Biology and Crystallization Communications, Vol. 63, No. 5. (May 2007), pp. 361-368.
    by Ezezika, , Haddad, , Neidle, , Momany,
    posted to biodegradation for-the-review regulation structure transcription by gcarbajosa to the group TNT on 2008-07-16 21:35:09 as ****
  • BzdR, a repressor that controls the anaerobic catabolism of benzoate in Azoarcus sp. CIB, is the first member of a new subfamily of transcriptional regulators.
    The Journal of biological chemistry, Vol. 280, No. 11. (18 March 2005), pp. 10683-10694.
    by MJ Barragán, B Blázquez, MT Zamarro, JM Mancheño, JL García, E Díaz, M Carmona
    posted to biodegradation for-the-review new-family regulation transcription by gcarbajosa to the group TNT on 2008-07-16 20:41:24 as ****
  • Promoters in the environment: transcriptional regulation in its natural context
    Nature Reviews Microbiology, Vol. 3, No. 2. (01 February 2005), pp. 105-118.
    by Ildefonso Cases, Victor de Lorenzo
    posted to biodegradation for-the-review integration regulation review transcription by gcarbajosa to the group TNT on 2008-07-11 15:24:31 as ****
  • Integrated Response to Inducers by Communication between a Catabolic Pathway and Its Regulatory System
    J. Bacteriol., Vol. 189, No. 10. (15 May 2007), pp. 3768-3775.
    by Olga Martinez-Perez, Aroa Lopez-Sanchez, Francisca Reyes-Ramirez, Belen Floriano, Eduardo Santero
    posted to biodegradation for-the-review integration metabolism regulation transcription by gcarbajosa to the group TNT on 2008-07-10 16:20:05 as ****
  • Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae.
    Nat Biotechnol, Vol. 22, No. 1. (January 2004), pp. 86-92.
    by J Ihmels, R Levy, N Barkai
    posted to yeast transcription regulation pathways evolution eukariot by icases to the group TNT on 2007-02-05 18:54:16 as **** along with 7 people and 3 groups adepace nickluscombe koller arne shung hryk siebert EisenLab EBI-regulation dIEMoSIRIS
  • Modeling the Evolution of Protein Domain Architectures Using Maximum Parsimony
    Journal of Molecular Biology, Vol. 366, No. 1. (9 February 2007), pp. 307-315.
    by Jessica H Fong, Lewis Y Geer, Anna R Panchenko, Stephen H Bryant
    posted to metabolism evolution bacteria by icases to the group TNT on 2007-01-26 17:34:18 as **** along with 5 people and 2 groups marcius tny choonpeng redelings zwang BioinfoCIPF SGU-CIPF
  • Dynamic usage of transcription start sites within core promoters
    Genome Biology, Vol. 7 (12 December 2006), R118.
    by Hideya Kawaji, Martin C Frith, Shintaro Katayama, Albin Sandelin, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki
    posted to eukariot promoter transcription by icases to the group TNT on 2006-12-14 10:08:56 as **** along with 2 people gjuggler xiaobeizhao
  • The individual and common repertoire of DNA-binding transcriptional regulators of Corynebacterium glutamicum, Corynebacterium efficiens, Corynebacterium diphtheriae and Corynebacterium jeikeium deduced from the complete genome sequences.
    BMC genomics, Vol. 6, No. 1. (2005)
    by I Brune, K Brinkrolf, J Kalinowski, A Pühler, A Tauch
    posted to biodegradation corynebacterium for-the-review regulation transcription by gcarbajosa to the group TNT on 2008-07-28 14:03:47 as ***
  • BLASTing small molecules--statistics and extreme statistics of chemical similarity scores
    Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. i357-365.
    by Pierre Baldi, Ryan W Benz
    posted to chemical-distance score statistics tanimoto by gcarbajosa to the group TNT on 2008-07-28 10:31:42 as *** along with 4 people chad_davis Yoyek dullhunk girschick
  • TouR-mediated effector-independent growth phase-dependent activation of the sigma54 Ptou promoter of Pseudomonas stutzeri OX1.
    Journal of bacteriology, Vol. 186, No. 21. (November 2004), pp. 7353-7363.
    by D Solera, FL Arenghi, T Woelk, E Galli, P Barbieri
    posted to biodegradation for-the-review ntrc regulation sigma54 tour transcription by gcarbajosa to the group TNT on 2008-07-24 10:47:13 as ***
  • Characterizing the regulation of the Pu promoter in Acinetobacter baylyi ADP1
    Environmental Microbiology, Vol. 10, No. 7. (July 2008), pp. 1668-1680.
    by Huang, E Wei, Singer, C Andrew, Spiers, J Andrew, Preston, M Gail, Whiteley, S Andrew
    posted to biodegradation for-the-review regulation transcription xylr by gcarbajosa to the group TNT on 2008-07-24 10:27:34 as ***
  • Identification of anthranilate and benzoate metabolic operons of Pseudomonas fluorescens and functional characterization of their promoter regions.
    Microbial cell factories, Vol. 5 (2006)
    by DM Retallack, TC Thomas, Y Shao, KL Haney, SM Resnick, VD Lee, CH Squires
    posted to arac biodegradation for-the-review regulation transcription by gcarbajosa to the group TNT on 2008-07-23 20:43:29 as ***
  • Transcriptional activation of quinoline degradation operons of Pseudomonas putida 86 by the AraC/XylS-type regulator OxoS and cross-regulation of the PqorM promoter by XylS.
    Applied and environmental microbiology, Vol. 71, No. 12. (December 2005), pp. 8618-8626.
    by B Carl, S Fetzner
    posted to biodegradation for-the-review quinoline regulation transcription xyls by gcarbajosa to the group TNT on 2008-07-23 20:13:17 as ***
  • Roles of effectors in XylS-dependent transcription activation: intramolecular domain derepression and DNA binding.
    Journal of bacteriology, Vol. 190, No. 9. (May 2008), pp. 3118-3128.
    by P Domínguez-Cuevas, P Marín, S Busby, JL Ramos, S Marqués
    posted to biodegradation for-the-review regulation transcription xyls by gcarbajosa to the group TNT on 2008-07-23 19:51:59 as ***
  • Distinct effector-binding sites enable synergistic transcriptional activation by BenM, a LysR-type regulator.
    Journal of molecular biology, Vol. 367, No. 3. (30 March 2007), pp. 616-629.
    by OC Ezezika, S Haddad, TJ Clark, EL Neidle, C Momany
    posted to benm biodegradation catm cross-regulation for-the-review regulation synergystic transcription by gcarbajosa to the group TNT on 2008-07-23 17:57:00 as ***
  • The homogentisate pathway: a central catabolic pathway involved in the degradation of L-phenylalanine, L-tyrosine, and 3-hydroxyphenylacetate in Pseudomonas putida.
    Journal of bacteriology, Vol. 186, No. 15. (August 2004), pp. 5062-5077.
    by E Arias-Barrau, ER Olivera, JM Luengo, C Fernández, B Galán, JL García, E Díaz, B Miñambres
    posted to biodegradation for-the-review hmgr homogentisate regulation transcription by gcarbajosa to the group TNT on 2008-07-23 17:23:25 as *** along with 1 person min013
  • NahR: effects of replacements at Asn 169 and Arg 248 on promoter binding and inducer recognition
    Archives of Biochemistry and Biophysics, Vol. 434, No. 1. (1 February 2005), pp. 67-74.
    by Hoo H Park, Hae Y Lee, Woon K Lim, Hae J Shin
    posted to binding for-the-review inducer lysr regulation transcription by gcarbajosa to the group TNT on 2008-07-23 16:16:19 as ***
  • The organization of the microbial biodegradation network from a systems-biology perspective.
    EMBO Rep, Vol. 4, No. 10. (October 2003), pp. 994-999.
    by F Pazos, A Valencia, V De Lorenzo
    posted to biodegradation for-the-review network regulation by gcarbajosa to the group TNT on 2008-07-22 16:55:45 as *** along with 1 person icases
  • Regulation of quinone detoxification by the thiol stress sensing DUF24/MarR-like repressor, YodB in Bacillus subtilis.
    Molecular microbiology, Vol. 67, No. 5. (March 2008), pp. 1108-1124.
    by M Leelakriangsak, NT Huyen, S Töwe, N van Duy, D Becher, M Hecker, H Antelmann, P Zuber
    posted to biodegradation for-the-review marr regulation transcription by gcarbajosa to the group TNT on 2008-07-22 16:36:01 as ***
  • Growth phase-dependent expression of the Pseudomonas putida KT2440 transcriptional machinery analysed with a genome-wide DNA microarray
    Environmental Microbiology, Vol. 8, No. 1. (January 2006), pp. 165-177.
    by Luis Yuste, Ana B Hervas, Ines Canosa, Raquel Tobes, Jose I Jimenez, Juan Nogales, Manuel M Perez-Perez, Eduardo Santero, Eduardo Diaz, Juan-Luis Ramos, Victor de Lorenzo, Fernando Rojo
    posted to biodegradation cell-cycle for-the-review integration regulation transcription by gcarbajosa to the group TNT on 2008-07-21 18:15:33 as ***
  • The m-xylene biodegradation capacity of Pseudomonas putida mt-2 is submitted to adaptation to abiotic stresses: evidence from expression profiling of xyl genes
    Environmental Microbiology, Vol. 8, No. 4. (April 2006), pp. 591-602.
    by Francisco Velazquez, Victor de Lorenzo, Marc Valls
    posted to adaptation biodegradation for-the-review in-situ integration regulation transcription by gcarbajosa to the group TNT on 2008-07-21 18:12:10 as ***
  • The coordinate regulation of multiple terminal oxidases by the Pseudomonas putida ANR global regulator
    Environmental Microbiology, Vol. 10, No. 7. (July 2008), pp. 1690-1702.
    by Ugidos, Ana, Morales, Gracia, Rial, Eduardo, Williams, D Huw, Rojo, Fernando
    posted to anr biodegradation for-the-review integration regulation transcription by gcarbajosa to the group TNT on 2008-07-21 18:09:46 as ***
  • Transcriptional regulatory networks in bacteria: from input signals to output responses.
    Curr Opin Microbiol, Vol. 9, No. 5. (October 2006), pp. 511-519.
    by AS Seshasayee, P Bertone, GM Fraser, NM Luscombe
    posted to for-the-review integration regulation signals transcription by gcarbajosa to the group TNT on 2008-07-21 17:50:25 as *** along with 1 person and 1 group nickluscombe EBI-regulation
  • Reduction of polynitroaromatic compounds: the bacterial nitroreductases.
    FEMS microbiology reviews, Vol. 32, No. 3. (May 2008), pp. 474-500.
    by MD Roldán, E Pérez-Reinado, F Castillo, C Moreno-Vivián
    posted to biodegradation for-the-review marra regulation review soxrs tcst transcription by gcarbajosa to the group TNT on 2008-07-21 17:48:06 as ***
  • Regulation and Characterization of Two Nitroreductase Genes, nprA and nprB, of Rhodobacter capsulatus
    Appl. Environ. Microbiol., Vol. 71, No. 12. (1 December 2005), pp. 7643-7649.
    by Eva Perez-Reinado, Rafael Blasco, Francisco Castillo, Conrado Moreno-Vivian, Dolores M Roldan
    posted to biodegradation for-the-review regulation tcst transcription by gcarbajosa to the group TNT on 2008-07-21 17:45:21 as ***
  • Degradation of o-Xylene by Pseudomonas stutzeri OX1 (Pseudomonas sp. OX1)
    Pseudomonas (2007), pp. 89-105.
    by Paola Barbieri, Dafne Solera, Enrica Galli, Faustino Vidal-Aroca, Giovanni Bertoni
    posted to biodegradation for-the-review regulation tour transcription by gcarbajosa to the group TNT on 2008-07-21 17:42:41 as ***
  • Functional genomics of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1.
    Applied microbiology and biotechnology, Vol. 68, No. 5. (September 2005), pp. 580-587.
    by R Rabus
    posted to anaerobic biodegradation for-the-review regulation tcst transcription by gcarbajosa to the group TNT on 2008-07-21 17:39:25 as ***
  • Members of the IclR family of bacterial transcriptional regulators function as activators and/or repressors.
    FEMS microbiology reviews, Vol. 30, No. 2. (March 2006), pp. 157-186.
    by AJ Molina-Henares, T Krell, M Eugenia Guazzaroni, A Segura, JL Ramos
    posted to biodegradation for-the-review iclr regulation transcription by gcarbajosa to the group TNT on 2008-07-21 17:38:12 as ***
  • Anaerobic biodegradation of natural gas condensate can be stimulated by the addition of gasoline
    Biodegradation, Vol. 18, No. 4. (August 2007), pp. 515-523.
    by Prince, Roger, Suflita, Joseph
    posted to anaerobic biodegradation for-the-review in-situ by gcarbajosa to the group TNT on 2008-07-21 17:33:47 as ***
  • The Pseudomonas putida Crc global regulator is an RNA binding protein that inhibits translation of the AlkS transcriptional regulator
    Molecular Microbiology, Vol. 64, No. 3. (May 2007), pp. 665-675.
    by Moreno, Renata, Ruiz-Manzano, Ana, Yuste, Luis, Rojo, Fernando
    posted to alks biodegradation crc for-the-review integration regulation transcription translation by gcarbajosa to the group TNT on 2008-07-21 17:31:51 as ***
  • Surveying biotransformations with a la carte genetic traps: translating dehydrochlorination of lindane (gamma-hexachlorocyclohexane) into lacZ-based phenotypes
    Environmental Microbiology, Vol. 8, No. 3. (March 2006), pp. 546-555.
    by William W Mohn, Junkal Garmendia, Teca C Galvao, Victor de Lorenzo
    posted to biodegradation for-the-review regulation synthetic-biology transcription by gcarbajosa to the group TNT on 2008-07-21 17:28:42 as ***
  • Mechanism controlling the extended lag period associated with vinyl chloride starvation in Nocardioides sp. strain JS614
    Archives of Microbiology, Vol. 187, No. 3. (March 2007), pp. 217-226.
    by Mattes, Timothy, Coleman, Nicholas, Chuang, Adina, Rogers, Andrea, Spain, Jim, Gossett, James
    posted to biodegradation for-the-review inducers integration regulation transcription by gcarbajosa to the group TNT on 2008-07-21 17:24:47 as ***
  • Styrene, an Unpalatable Substrate with Complex Regulatory Networks
    Pseudomonas (2007), pp. 59-87.
    by Livia Leoni, Giordano Rampioni, Elisabetta Zennaro
    posted to biodegradation for-the-review integration model regulation tcst transcription by gcarbajosa to the group TNT on 2008-07-21 17:21:57 as ***
  • Microbial remediation of nitro-aromatic compounds: an overview.
    Journal of environmental management, Vol. 85, No. 2. (October 2007), pp. 496-512.
    by M Kulkarni, A Chaudhari
    posted to biodegradation for-the-review review by gcarbajosa to the group TNT on 2008-07-21 17:20:40 as ***
  • The IclR family of transcriptional activators and repressors can be defined by a single profile
    Protein Sci, Vol. 15, No. 5. (1 May 2006), pp. 1207-1213.
    by Tino Krell, Antonio J Molina-Henares, Juan L Ramos
    posted to biodegradation family for-the-review iclr profile regulation transcription by gcarbajosa to the group TNT on 2008-07-21 17:05:42 as ***
  • Relevance of nucleotides of the PcaU binding site from Acinetobacter baylyi
    Microbiology, Vol. 154, No. 3. (1 March 2008), pp. 756-766.
    by Bettina Jerg, Ulrike Gerischer
    posted to binding biodegradation for-the-review regulation transcription by gcarbajosa to the group TNT on 2008-07-21 17:03:44 as ***
  • Emergence of novel functions in transcriptional regulators by regression to <i>stem</i> protein types
    Molecular Microbiology, Vol. 65, No. 4. (2007), pp. 907-919.
    by Teca C Galvão, Mario Mencía, Víctor de Lorenzo
    posted to biodegradation evolution for-the-review regulation transcription xylr by gcarbajosa to the group TNT on 2008-07-21 16:59:04 as ***
  • Selection of biocatalysts for chemical synthesis.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 103, No. 6. (7 February 2006), pp. 1693-1698.
    by S van Sint Fiet, JB van Beilen, B Witholt
    posted to biodegradation biosensors for-the-review regulation transcription by gcarbajosa to the group TNT on 2008-07-21 16:56:36 as ***
  • New insights into the BzdR-mediated transcriptional regulation of the anaerobic catabolism of benzoate in Azoarcus sp. CIB
    Microbiology, Vol. 154, No. 1. (1 January 2008), pp. 306-316.
    by Gonzalo Durante-Rodriguez, Teresa M Zamarro, Jose L Garcia, Eduardo Diaz, Manuel Carmona
    posted to benzoate biodegradation bzdr for-the-review new-family regulation transcription by gcarbajosa to the group TNT on 2008-07-21 16:54:49 as ***
  • Differential regulation and xenobiotic induction of tandem P450 monooxygenase genes pc-1 (CYP63A1) and pc-2 (CYP63A2) in the white-rot fungus Phanerochaete chrysosporium
    Applied Microbiology and Biotechnology, Vol. 65, No. 5. (1 October 2004), pp. 559-565.
    by Harshavardhan Doddapaneni, Jagjit S Yadav
    posted to biodegradation for-the-review fungi regulation transcription by gcarbajosa to the group TNT on 2008-07-21 16:53:40 as ***
  • Identification and analysis of a glutaryl-CoA dehydrogenase-encoding gene and its cognate transcriptional regulator from Azoarcus sp. CIB
    Environmental Microbiology, Vol. 10, No. 2. (February 2008), pp. 474-482.
    by Blazquez, Blas, Carmona, Manuel, Garcia, Jose Luis, Diaz, Eduardo
    posted to biodegradation for-the-review lysr regulation transcription by gcarbajosa to the group TNT on 2008-07-21 16:52:28 as ***
  • Characterization of two alkane hydroxylase genes from the marine hydrocarbonoclastic bacterium Alcanivorax borkumensis.
    Environmental microbiology, Vol. 6, No. 3. (March 2004), pp. 264-273.
    by JB van Beilen, MM Marín, TH Smits, M Röthlisberger, AG Franchini, B Witholt, F Rojo
    posted to alkane alks biodegradation for-the-review regulation transcription by gcarbajosa to the group TNT on 2008-07-21 16:51:11 as ***
  • Dual Role of Response Regulator StyR in Styrene Catabolism Regulation
    Appl. Environ. Microbiol., Vol. 71, No. 9. (1 September 2005), pp. 5411-5419.
    by Livia Leoni, Giordano Rampioni, Valeria Di Stefano, Elisabetta Zennaro
    posted to binding biodegradation for-the-review regulation styrene transcription by gcarbajosa to the group TNT on 2008-07-17 05:47:41 as ***
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