Dmitry Ravcheev

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Ines ThieleNational University of Ireland, GalwayVerified email at nuigalway.ie
Almut HeinkenNational University of Ireland, GalwayVerified email at nuigalway.ie
Alexey KazakovLawrence Berkeley National LaboratoryVerified email at lbl.gov
Ronan M.T. FlemingSenior Lecturer, National University of Ireland, Galway, & Asst. Professor, Leiden UniversityVerified email at lacdr.leidenuniv.nl
Stefania MagnusdottirPhD Student, University of LuxembourgVerified email at uni.lu
Semen LeynSanford Burnham Prebys Medical Discovery InstituteVerified email at sbpdiscovery.org
Marat KazanovInstitute for Information Transmission Problems, RAS, Moscow, RussiaVerified email at iitp.ru
Anna Gerasimova,PhDStaff Scientist, Bioinformatics and Computational BiologyVerified email at questdiagnostics.com
Inna DubchakSenior Scientist, Lawrence Berkeley National Laboratory, USAVerified email at lbl.gov
Adam Paul ArkinDepartment of Bioengineering, University of California, Berkeley, Physical Biosciences Division, E.OVerified email at lbl.gov
Karsten ZenglerUniversity of California, San DiegoVerified email at eng.ucsd.edu
Eugen BauerJohannes Gutenberg-Universität Mainz, Institute of Zoology, GermanyVerified email at uni-mainz.de
Alberto NoronhaResearch Associate, Luxembourg Centre for Systems Biomedicine (LCSB)Verified email at uni.lu
Paul WilmesProfessorVerified email at uni.lu
Christian JägerLCSB - University of LuxembourgVerified email at uni.lu
Valerie de Crecy-LagardMicrobiology and Cell Science, University of FloridaVerified email at ufl.edu
Roman A. SutorminSoftware Engineer, GoogleVerified email at google.com
Adam GodzikProfessor, University of California Riverside School of MedicineVerified email at medsch.ucr.edu
Aaron BestHarrison C. and Mary L. Visscher Professor of Genetics, Hope CollegeVerified email at hope.edu
Vsevolod MakeevVavilov Institute of General Genetics, Department of computational systems biologyVerified email at vigg.ru

Dmitry Ravcheev

National University of Ireland Galway

Verified email at nuigalway.ie - Homepage

Bioinformatics Comparative genomics Metabolic reconstruction Transcription regulation Molecular evolution


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Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota S Magnúsdóttir, A Heinken, L Kutt, DA Ravcheev, E Bauer, A Noronha, ... Nature biotechnology 35 (1), 81-89, 2017	358	2017
Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes S Magnúsdóttir, D Ravcheev, V de Crécy-Lagard, I Thiele Frontiers in genetics 6, 148, 2015	305	2015
RegPrecise 3.0–a resource for genome-scale exploration of transcriptional regulation in bacteria PS Novichkov, AE Kazakov, DA Ravcheev, SA Leyn, GY Kovaleva, ... BMC genomics 14 (1), 1-12, 2013	250	2013
A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length AV Favorov, MS Gelfand, AV Gerasimova, DA Ravcheev, AA Mironov, ... Bioinformatics 21 (10), 2240-2245, 2005	147	2005
Transcriptional regulation of central carbon and energy metabolism in bacteria by redox-responsive repressor Rex DA Ravcheev, X Li, H Latif, K Zengler, SA Leyn, YD Korostelev, ... Journal of bacteriology 194 (5), 1145-1157, 2012	124	2012
The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease A Noronha, J Modamio, Y Jarosz, E Guerard, N Sompairac, G Preciat, ... Nucleic acids research 47 (D1), D614-D624, 2019	108	2019
Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks DA Ravcheev, A Godzik, AL Osterman, DA Rodionov BMC genomics 14 (1), 1-17, 2013	98	2013
Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease A Heinken, DA Ravcheev, F Baldini, L Heirendt, RMT Fleming, I Thiele Microbiome 7 (1), 1-18, 2019	86*	2019
Visualization of individual DNA loops and a map of loop domains in the human dystrophin gene OV Iarovaia, A Bystritskiy, D Ravcheev, R Hancock, SV Razin Nucleic acids research 32 (7), 2079-2086, 2004	86	2004
Comparative genomics of ethanolamine utilization O Tsoy, D Ravcheev, A Mushegian Journal of bacteriology 191 (23), 7157-7164, 2009	81	2009
Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus DA Rodionov, PS Novichkov, ED Stavrovskaya, IA Rodionova, X Li, ... BMC genomics 12 (1), 1-17, 2011	63	2011
Redox-responsive repressor Rex modulates alcohol production and oxidative stress tolerance in Clostridium acetobutylicum L Zhang, X Nie, DA Ravcheev, DA Rodionov, J Sheng, Y Gu, S Yang, ... Journal of bacteriology 196 (22), 3949-3963, 2014	53	2014
Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae) DA Ravcheev, AV Gerasimova, AA Mironov, MS Gelfand BMC genomics 8 (1), 1-17, 2007	52	2007
Comparative genomics and evolution of regulons of the LacI-family transcription factors DA Ravcheev, MS Khoroshkin, ON Laikova, OV Tsoy, NV Sernova, ... Frontiers in microbiology 5, 294, 2014	46	2014
Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima DA Rodionov, IA Rodionova, X Li, DA Ravcheev, Y Tarasova, VA Portnoy, ... Frontiers in microbiology 4, 244, 2013	45	2013
Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics-based evidence DA Ravcheev, AA Best, N Tintle, M DeJongh, AL Osterman, PS Novichkov, ... Journal of bacteriology 193 (13), 3228-3240, 2011	45	2011
Nitrogen fixation and molecular oxygen: comparative genomic reconstruction of transcription regulation in Alphaproteobacteria OV Tsoy, DA Ravcheev, J Čuklina, MS Gelfand Frontiers in microbiology 7, 1343, 2016	39	2016
Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria DA Ravcheev, AA Best, NV Sernova, MD Kazanov, PS Novichkov, ... BMC genomics 14 (1), 1-14, 2013	39	2013
Genomic analysis of the human gut microbiome suggests novel enzymes involved in quinone biosynthesis DA Ravcheev, I Thiele Frontiers in microbiology 7, 128, 2016	35	2016
Regulation and evolution of malonate and propionate catabolism in proteobacteria IA Suvorova, DA Ravcheev, MS Gelfand Journal of bacteriology 194 (12), 3234-3240, 2012	35	2012

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