Search Results - "Ravcheev, Dmitry A."

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota by Magnúsdóttir, Stefanía, Heinken, Almut, Kutt, Laura, Ravcheev, Dmitry A, Bauer, Eugen, Noronha, Alberto, Greenhalgh, Kacy, Jäger, Christian, Baginska, Joanna, Wilmes, Paul, Fleming, Ronan M T, Thiele, Ines

“…A large set of microbial metabolic models (AGORA) could be applied to better understand the functions of the human gut microbiome. Genome-scale metabolic…”
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Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine by Heinken, Almut, Hertel, Johannes, Acharya, Geeta, Ravcheev, Dmitry A., Nyga, Malgorzata, Okpala, Onyedika Emmanuel, Hogan, Marcus, Magnúsdóttir, Stefanía, Martinelli, Filippo, Nap, Bram, Preciat, German, Edirisinghe, Janaka N., Henry, Christopher S., Fleming, Ronan M. T., Thiele, Ines

“…The human microbiome influences the efficacy and safety of a wide variety of commonly prescribed drugs. Designing precision medicine approaches that…”
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Comparative Genomic Analysis of the Human Gut Microbiome Reveals a Broad Distribution of Metabolic Pathways for the Degradation of Host-Synthetized Mucin Glycans and Utilization of Mucin-Derived Monosaccharides by Ravcheev, Dmitry A, Thiele, Ines

“…The colonic mucus layer is a dynamic and complex structure formed by secreted and transmembrane mucins, which are high-molecular-weight and heavily…”
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Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease by Heinken, Almut, Ravcheev, Dmitry A, Baldini, Federico, Heirendt, Laurent, Fleming, Ronan M T, Thiele, Ines

“…The human gut microbiome performs important functions in human health and disease. A classic example for host-gut microbial co-metabolism is host biosynthesis…”
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Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis by Ravcheev, Dmitry A, Thiele, Ines

“…Ubiquinone and menaquinone are membrane lipid-soluble carriers of electrons that are essential for cellular respiration. Eukaryotic cells can synthesize…”
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Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks by Ravcheev, Dmitry A, Godzik, Adam, Osterman, Andrei L, Rodionov, Dmitry A

“…Bacteroides thetaiotaomicron, a predominant member of the human gut microbiota, is characterized by its ability to utilize a wide variety of polysaccharides…”
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Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota by Ravcheev, Dmitry A, Thiele, Ines

“…Because of the specific anatomical and physiological properties of the human intestine, a specific oxygen gradient builds up within this organ that influences…”
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Nitrogen Fixation and Molecular Oxygen: Comparative Genomic Reconstruction of Transcription Regulation in Alphaproteobacteria by Tsoy, Olga V, Ravcheev, Dmitry A, Čuklina, Jelena, Gelfand, Mikhail S

“…Biological nitrogen fixation plays a crucial role in the nitrogen cycle. An ability to fix atmospheric nitrogen, reducing it to ammonium, was described for…”
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Comparative Genomic Analysis Reveals Novel Microcompartment-Associated Metabolic Pathways in the Human Gut Microbiome by Ravcheev, Dmitry A, Moussu, Lubin, Smajic, Semra, Thiele, Ines

“…Bacterial microcompartments are self-assembling subcellular structures surrounded by a semipermeable protein shell and found only in bacteria, but not archaea…”
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Redox-Responsive Repressor Rex Modulates Alcohol Production and Oxidative Stress Tolerance in Clostridium acetobutylicum by Zhang, Lei, Nie, Xiaoqun, Ravcheev, Dmitry A, Rodionov, Dmitry A, Sheng, Jia, Gu, Yang, Yang, Sheng, Jiang, Weihong, Yang, Chen

“…Rex, a transcriptional repressor that modulates its DNA-binding activity in response to NADH/NAD+ ratio, has recently been found to play a role in the…”
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Transcriptional Regulation of Central Carbon and Energy Metabolism in Bacteria by Redox-Responsive Repressor Rex by Ravcheev, Dmitry A, Li, Xiaoqing, Latif, Haythem, Zengler, Karsten, Leyn, Semen A, Korostelev, Yuri D, Kazakov, Alexey E, Novichkov, Pavel S, Osterman, Andrei L, Rodionov, Dmitry A

“…Redox-sensing repressor Rex was previously implicated in the control of anaerobic respiration in response to the cellular NADH/NAD+ levels in Gram-positive…”
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Comparative genomics and evolution of regulons of the LacI-family transcription factors by Ravcheev, Dmitry A, Khoroshkin, Matvei S, Laikova, Olga N, Tsoy, Olga V, Sernova, Natalia V, Petrova, Svetlana A, Rakhmaninova, Aleksandra B, Novichkov, Pavel S, Gelfand, Mikhail S, Rodionov, Dmitry A

“…DNA-binding transcription factors (TFs) are essential components of transcriptional regulatory networks in bacteria. LacI-family TFs (LacI-TFs) are broadly…”
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Inference of the Transcriptional Regulatory Network in Staphylococcus aureus by Integration of Experimental and Genomics-Based Evidence by RAVCHEEV, Dmitry A, BEST, Aaron A, TINTLE, Nathan, DEJONGH, Matthew, OSTERMAN, Andrei L, NOVICHKOV, Pavel S, RODIONOV, Dmitry A

“…Article Usage Stats Services JB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
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Comparative Genomic Analysis of the Hexuronate Metabolism Genes and Their Regulation in Gammaproteobacteria by Suvorova, Inna A, Tutukina, Maria N, Ravcheev, Dmitry A, Rodionov, Dmitry A, Ozoline, Olga N, Gelfand, Mikhail S

“…Article Usage Stats Services JB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
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Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima by Rodionov, Dmitry A, Rodionova, Irina A, Li, Xiaoqing, Ravcheev, Dmitry A, Tarasova, Yekaterina, Portnoy, Vasiliy A, Zengler, Karsten, Osterman, Andrei L

“…Hyperthermophilic bacteria from the Thermotogales lineage can produce hydrogen by fermenting a wide range of carbohydrates. Previous experimental studies…”
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Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus by Rodionov, Dmitry A, Novichkov, Pavel S, Stavrovskaya, Elena D, Rodionova, Irina A, Li, Xiaoqing, Kazanov, Marat D, Ravcheev, Dmitry A, Gerasimova, Anna V, Kazakov, Alexey E, Kovaleva, Galina Yu, Permina, Elizabeth A, Laikova, Olga N, Overbeek, Ross, Romine, Margaret F, Fredrickson, James K, Arkin, Adam P, Dubchak, Inna, Osterman, Andrei L, Gelfand, Mikhail S

“…Genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in bacteria is one of the critical tasks of modern…”
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The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease by Noronha, Alberto, Modamio, Jennifer, Jarosz, Yohan, Guerard, Elisabeth, Sompairac, Nicolas, Preciat, German, Daníelsdóttir, Anna Dröfn, Krecke, Max, Merten, Diane, Haraldsdóttir, Hulda S, Heinken, Almut, Heirendt, Laurent, Magnúsdóttir, Stefanía, Ravcheev, Dmitry A, Sahoo, Swagatika, Gawron, Piotr, Friscioni, Lucia, Garcia, Beatriz, Prendergast, Mabel, Puente, Alberto, Rodrigues, Mariana, Roy, Akansha, Rouquaya, Mouss, Wiltgen, Luca, Žagare, Alise, John, Elisabeth, Krueger, Maren, Kuperstein, Inna, Zinovyev, Andrei, Schneider, Reinhard, Fleming, Ronan M T, Thiele, Ines

“…Abstract A multitude of factors contribute to complex diseases and can be measured with ‘omics’ methods. Databases facilitate data interpretation for…”
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RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria by Novichkov, Pavel S, Kazakov, Alexey E, Ravcheev, Dmitry A, Leyn, Semen A, Kovaleva, Galina Y, Sutormin, Roman A, Kazanov, Marat D, Riehl, William, Arkin, Adam P, Dubchak, Inna, Rodionov, Dmitry A

“…Genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in prokaryotes is one of the critical tasks of modern…”
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Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae) by Ravcheev, Dmitry A, Gerasimova, Anna V, Mironov, Andrey A, Gelfand, Mikhail S

“…Gamma-proteobacteria, such as Escherichia coli, can use a variety of respiratory substrates employing numerous aerobic and anaerobic respiratory systems…”
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Paracoccus denitrificans possesses two BioR homologs having a role in regulation of biotin metabolism by Feng, Youjun, Kumar, Ritesh, Ravcheev, Dmitry A., Zhang, Huimin

“…Recently, we determined that BioR, the GntR family of transcription factor, acts as a repressor for biotin metabolism exclusively distributed in certain…”
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