Literature DB >> 17636889

Comparative genomic reconstruction of transcriptional regulatory networks in bacteria.

Dmitry A Rodionov1.   

Abstract

Mesh：

Year:  2007        PMID： 17636889      PMCID： PMC2643304          DOI： 10.1021/cr068309+

Source DB:  PubMed          Journal:  Chem Rev        ISSN： 0009-2665            Impact factor:   60.622


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  275 in total

Review 1.  DNA binding sites: representation and discovery.

Authors:  G D Stormo
Journal:  Bioinformatics       Date:  2000-01       Impact factor: 6.937

2.  A biophysical approach to transcription factor binding site discovery.

Authors:  Marko Djordjevic; Anirvan M Sengupta; Boris I Shraiman
Journal:  Genome Res       Date:  2003-11       Impact factor: 9.043

3.  Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea.

Authors:  Ernesto Pérez-Rueda; Julio Collado-Vides; Lorenzo Segovia
Journal:  Comput Biol Chem       Date:  2004-12       Impact factor: 2.877

4.  Evolution of sensory complexity recorded in a myxobacterial genome.

Authors:  B S Goldman; W C Nierman; D Kaiser; S C Slater; A S Durkin; J A Eisen; J Eisen; C M Ronning; W B Barbazuk; M Blanchard; C Field; C Halling; G Hinkle; O Iartchuk; H S Kim; C Mackenzie; R Madupu; N Miller; A Shvartsbeyn; S A Sullivan; M Vaudin; R Wiegand; H B Kaplan
Journal:  Proc Natl Acad Sci U S A       Date:  2006-10-02       Impact factor: 11.205

5.  Methods for calculating the probabilities of finding patterns in sequences.

Authors:  R Staden
Journal:  Comput Appl Biosci       Date:  1989-04

6.  Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes.

Authors:  Dmitry A Rodionov; Alexey G Vitreschak; Andrey A Mironov; Mikhail S Gelfand
Journal:  J Biol Chem       Date:  2003-07-17       Impact factor: 5.157

7.  The cobZ gene of Methanosarcina mazei Go1 encodes the nonorthologous replacement of the alpha-ribazole-5'-phosphate phosphatase (CobC) enzyme of Salmonella enterica.

Authors:  Carmen L Zayas; Jesse D Woodson; Jorge C Escalante-Semerena
Journal:  J Bacteriol       Date:  2006-04       Impact factor: 3.490

8.  Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes.

Authors:  Ali Nahvi; Jeffrey E Barrick; Ronald R Breaker
Journal:  Nucleic Acids Res       Date:  2004-01-02       Impact factor: 16.971

9.  From genomics to chemical genomics: new developments in KEGG.

Authors:  Minoru Kanehisa; Susumu Goto; Masahiro Hattori; Kiyoko F Aoki-Kinoshita; Masumi Itoh; Shuichi Kawashima; Toshiaki Katayama; Michihiro Araki; Mika Hirakawa
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

10.  Transcription factor distribution in Escherichia coli: studies with FNR protein.

Authors:  David C Grainger; Hirofumi Aiba; Douglas Hurd; Douglas F Browning; Stephen J W Busby
Journal:  Nucleic Acids Res       Date:  2006-12-12       Impact factor: 16.971
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  121 in total

1.  Premature terminator analysis sheds light on a hidden world of bacterial transcriptional attenuation.

Authors:  Magali Naville; Daniel Gautheret
Journal:  Genome Biol       Date:  2010-09-29       Impact factor: 13.583

2.  Transcriptional repression mediated by a TetR family protein, PfmR, from Thermus thermophilus HB8.

Authors:  Yoshihiro Agari; Keiko Sakamoto; Seiki Kuramitsu; Akeo Shinkai
Journal:  J Bacteriol       Date:  2012-06-29       Impact factor: 3.490

3.  Evolution of prokaryotic genes by shift of stop codons.

Authors:  Anna A Vakhrusheva; Marat D Kazanov; Andrey A Mironov; Georgii A Bazykin
Journal:  J Mol Evol       Date:  2010-11-17       Impact factor: 2.395

4.  Comparative genomics and functional analysis of the NiaP family uncover nicotinate transporters from bacteria, plants, and mammals.

Authors:  Linda Jeanguenin; Aurora Lara-Núñez; Dmitry A Rodionov; Andrei L Osterman; Nataliya Y Komarova; Doris Rentsch; Jesse F Gregory; Andrew D Hanson
Journal:  Funct Integr Genomics       Date:  2011-09-28       Impact factor: 3.410

Review 5.  Network inference and network response identification: moving genome-scale data to the next level of biological discovery.

Authors:  Diogo F T Veiga; Bhaskar Dutta; Gábor Balázsi
Journal:  Mol Biosyst       Date:  2009-12-11

6.  A novel class of modular transporters for vitamins in prokaryotes.

Authors:  Dmitry A Rodionov; Peter Hebbeln; Aymerick Eudes; Josy ter Beek; Irina A Rodionova; Guus B Erkens; Dirk J Slotboom; Mikhail S Gelfand; Andrei L Osterman; Andrew D Hanson; Thomas Eitinger
Journal:  J Bacteriol       Date:  2008-10-17       Impact factor: 3.490

7.  The nitrogen-regulated response regulator NrrA controls cyanophycin synthesis and glycogen catabolism in the cyanobacterium Synechocystis sp. PCC 6803.

Authors:  Deng Liu; Chen Yang
Journal:  J Biol Chem       Date:  2013-12-11       Impact factor: 5.157

8.  Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children.

Authors:  Laura V Blanton; Mark R Charbonneau; Tarek Salih; Michael J Barratt; Siddarth Venkatesh; Olga Ilkaveya; Sathish Subramanian; Mark J Manary; Indi Trehan; Josh M Jorgensen; Yue-Mei Fan; Bernard Henrissat; Semen A Leyn; Dmitry A Rodionov; Andrei L Osterman; Kenneth M Maleta; Christopher B Newgard; Per Ashorn; Kathryn G Dewey; Jeffrey I Gordon
Journal:  Science       Date:  2016-02-19       Impact factor: 47.728

9.  The effects of micronutrient deficiencies on bacterial species from the human gut microbiota.

Authors:  Matthew C Hibberd; Meng Wu; Dmitry A Rodionov; Xiaoqing Li; Jiye Cheng; Nicholas W Griffin; Michael J Barratt; Richard J Giannone; Robert L Hettich; Andrei L Osterman; Jeffrey I Gordon
Journal:  Sci Transl Med       Date:  2017-05-17       Impact factor: 17.956

10.  Comparative Analysis of the IclR-Family of Bacterial Transcription Factors and Their DNA-Binding Motifs: Structure, Positioning, Co-Evolution, Regulon Content.

Authors:  Inna A Suvorova; Mikhail S Gelfand
Journal:  Front Microbiol       Date:  2021-06-10       Impact factor: 5.640
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