Literature DB >> 29020004

iML1515, a knowledgebase that computes Escherichia coli traits.

Jonathan M Monk1, Colton J Lloyd1, Elizabeth Brunk1, Nathan Mih1, Anand Sastry1, Zachary King1, Rikiya Takeuchi2, Wataru Nomura2, Zhen Zhang1, Hirotada Mori2, Adam M Feist1,3, Bernhard O Palsson1,3.   

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Year:  2017        PMID： 29020004      PMCID： PMC6521705          DOI： 10.1038/nbt.3956

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


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  30 in total

Review 1.  Using Genome-scale Models to Predict Biological Capabilities.

Authors:  Edward J O'Brien; Jonathan M Monk; Bernhard O Palsson
Journal:  Cell       Date:  2015-05-21       Impact factor: 41.582

2.  Optimizing genome-scale network reconstructions.

Authors:  Jonathan Monk; Juan Nogales; Bernhard O Palsson
Journal:  Nat Biotechnol       Date:  2014-05       Impact factor: 54.908

3.  Discovery of the curcumin metabolic pathway involving a unique enzyme in an intestinal microorganism.

Authors:  Azam Hassaninasab; Yoshiteru Hashimoto; Kaori Tomita-Yokotani; Michihiko Kobayashi
Journal:  Proc Natl Acad Sci U S A       Date:  2011-04-05       Impact factor: 11.205

4.  Update on the Keio collection of Escherichia coli single-gene deletion mutants.

Authors:  Natsuko Yamamoto; Kenji Nakahigashi; Tomoko Nakamichi; Mihoko Yoshino; Yuki Takai; Yae Touda; Akemi Furubayashi; Satoko Kinjyo; Hitomi Dose; Miki Hasegawa; Kirill A Datsenko; Toru Nakayashiki; Masaru Tomita; Barry L Wanner; Hirotada Mori
Journal:  Mol Syst Biol       Date:  2009-12-22       Impact factor: 11.429

5.  The Escherichia coli K-12 "wild types" W3110 and MG1655 have an rph frameshift mutation that leads to pyrimidine starvation due to low pyrE expression levels.

Authors:  K F Jensen
Journal:  J Bacteriol       Date:  1993-06       Impact factor: 3.490

6.  Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution.

Authors:  Astrid von Mentzer; Thomas R Connor; Lothar H Wieler; Torsten Semmler; Atsushi Iguchi; Nicholas R Thomson; David A Rasko; Enrique Joffre; Jukka Corander; Derek Pickard; Gudrun Wiklund; Ann-Mari Svennerholm; Åsa Sjöling; Gordon Dougan
Journal:  Nat Genet       Date:  2014-11-10       Impact factor: 38.330

7.  Potentiating antibacterial activity by predictably enhancing endogenous microbial ROS production.

Authors:  Mark P Brynildsen; Jonathan A Winkler; Catherine S Spina; I Cody MacDonald; James J Collins
Journal:  Nat Biotechnol       Date:  2013-01-06       Impact factor: 54.908

8.  A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011.

Authors:  Jeffrey D Orth; Tom M Conrad; Jessica Na; Joshua A Lerman; Hojung Nam; Adam M Feist; Bernhard Ø Palsson
Journal:  Mol Syst Biol       Date:  2011-10-11       Impact factor: 11.429

9.  RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.

Authors:  Socorro Gama-Castro; Verónica Jiménez-Jacinto; Martín Peralta-Gil; Alberto Santos-Zavaleta; Mónica I Peñaloza-Spinola; Bruno Contreras-Moreira; Juan Segura-Salazar; Luis Muñiz-Rascado; Irma Martínez-Flores; Heladia Salgado; César Bonavides-Martínez; Cei Abreu-Goodger; Carlos Rodríguez-Penagos; Juan Miranda-Ríos; Enrique Morett; Enrique Merino; Araceli M Huerta; Luis Treviño-Quintanilla; Julio Collado-Vides
Journal:  Nucleic Acids Res       Date:  2007-12-23       Impact factor: 16.971

10.  An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR).

Authors:  Jennifer L Reed; Thuy D Vo; Christophe H Schilling; Bernhard O Palsson
Journal:  Genome Biol       Date:  2003-08-28       Impact factor: 13.583
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  111 in total

Review 1.  The EcoCyc Database.

Authors:  Peter D Karp; Wai Kit Ong; Suzanne Paley; Richard Billington; Ron Caspi; Carol Fulcher; Anamika Kothari; Markus Krummenacker; Mario Latendresse; Peter E Midford; Pallavi Subhraveti; Socorro Gama-Castro; Luis Muñiz-Rascado; César Bonavides-Martinez; Alberto Santos-Zavaleta; Amanda Mackie; Julio Collado-Vides; Ingrid M Keseler; Ian Paulsen
Journal:  EcoSal Plus       Date:  2018-11

2.  A quantitative method for proteome reallocation using minimal regulatory interventions.

Authors:  Gustavo Lastiri-Pancardo; Jonathan S Mercado-Hernández; Juhyun Kim; José I Jiménez; José Utrilla
Journal:  Nat Chem Biol       Date:  2020-07-13       Impact factor: 15.040

3.  Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice.

Authors:  Bin Du; Daniel C Zielinski; Jonathan M Monk; Bernhard O Palsson
Journal:  Proc Natl Acad Sci U S A       Date:  2018-10-11       Impact factor: 11.205

4.  Fast automated reconstruction of genome-scale metabolic models for microbial species and communities.

Authors:  Daniel Machado; Sergej Andrejev; Melanie Tramontano; Kiran Raosaheb Patil
Journal:  Nucleic Acids Res       Date:  2018-09-06       Impact factor: 16.971

5.  BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks.

Authors:  Paul F Lang; Yassmine Chebaro; Xiaoyue Zheng; John A P Sekar; Bilal Shaikh; Darren A Natale; Jonathan R Karr
Journal:  Genome Biol       Date:  2020-05-18       Impact factor: 13.583

6.  Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models.

Authors:  Noushin Hadadi; Vikash Pandey; Anush Chiappino-Pepe; Marian Morales; Hector Gallart-Ayala; Florence Mehl; Julijana Ivanisevic; Vladimir Sentchilo; Jan R van der Meer
Journal:  NPJ Syst Biol Appl       Date:  2020-01-07

Review 7.  Network reduction methods for genome-scale metabolic models.

Authors:  Dipali Singh; Martin J Lercher
Journal:  Cell Mol Life Sci       Date:  2019-11-20       Impact factor: 9.261

8.  Integrated Experimental and Computational Analyses Reveal Differential Metabolic Functionality in Antibiotic-Resistant Pseudomonas aeruginosa.

Authors:  Laura J Dunphy; Phillip Yen; Jason A Papin
Journal:  Cell Syst       Date:  2019-01-02       Impact factor: 10.304

9.  Genome-Scale Identification of Essential Metabolic Processes for Targeting the Plasmodium Liver Stage.

Authors:  Rebecca R Stanway; Ellen Bushell; Anush Chiappino-Pepe; Magali Roques; Theo Sanderson; Blandine Franke-Fayard; Reto Caldelari; Murielle Golomingi; Mary Nyonda; Vikash Pandey; Frank Schwach; Séverine Chevalley; Jai Ramesar; Tom Metcalf; Colin Herd; Paul-Christian Burda; Julian C Rayner; Dominique Soldati-Favre; Chris J Janse; Vassily Hatzimanikatis; Oliver Billker; Volker T Heussler
Journal:  Cell       Date:  2019-11-14       Impact factor: 41.582

10.  A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action.

Authors:  Jason H Yang; Sarah N Wright; Meagan Hamblin; Douglas McCloskey; Miguel A Alcantar; Lars Schrübbers; Allison J Lopatkin; Sangeeta Satish; Amir Nili; Bernhard O Palsson; Graham C Walker; James J Collins
Journal:  Cell       Date:  2019-05-09       Impact factor: 41.582
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