  | Heinken, A. K., Ravcheev, D., Baldini, F., Heirendt, L., Fleming, R. M., & Thiele, I. (2019). Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease. Microbiome. doi:10.1186/s40168-019-0689-3  Peer Reviewed verified by ORBi |
 | Noronha, A., Modamio Chamarro, J., Jarosz, Y., Guerard, E., Sompairac, N., Preciat Gonzalez, G. A., Danielsdottir, A. D., Krecke, M., Merten, D., Haraldsdottir, H., Heinken, A. K., Heirendt, L., Magnusdottir, S., Ravcheev, D., Sahoo, S., Gawron, P., Friscioni, L., Garcia Santa Cruz, B., Prendergast, M., ... Thiele, I. (2018). The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Research. doi:10.1093/nar/gky992 Peer Reviewed verified by ORBi |
 | Ravcheev, D., & Thiele, I. (29 August 2017). 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. Frontiers in Genetics, 8, 111. doi:10.3389/fgene.2017.00111 Peer Reviewed verified by ORBi |
  | Magnusdottir, S., Heinken, A. K., Kutt, L., Ravcheev, D., Bauer, E., Noronha, A., Greenhalgh, K., Jäger, C., Baginska, J., Wilmes, P., Fleming, R. M., & Thiele, I. (2016). Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota. Nature Biotechnology. doi:10.1038/nbt.3703 Peer Reviewed verified by ORBi |
Heinken, A. K., Ravcheev, D., & Thiele, I. (2016). Systems biology of bacteria-host interactions. In L. Nibali & B. Henderson (Eds.), The Human Microbiota and Chronic Disease: Dysbiosis as a Cause of Human Pathology. Hoboken, New Jersey, United States: John Wiley & Sons, i nc. doi:10.1002/9781118982907.ch7 Peer reviewed |
 | Leyn, S., Suvorova, I., Kazakov, A., Ravcheev, D., Stepanova, V., Novichkov, P., & Rodionov, D. (2016). Comparative genomics and evolution of transcriptional regulons in Proteobacteria. Microbial Genomics. doi:10.1099/mgen.0.000061 Peer reviewed |
 | Ravcheev, D., & Thiele, I. (25 January 2016). Genomic analysis of the human gut microbiome suggests novel enzymes involved in quinone biosynthesis. Frontiers in Microbiology, 7 (128). doi:10.3389/fmicb.2016.00128 Peer Reviewed verified by ORBi |
 | Magnusdottir, S., Ravcheev, D., de Crecy-Lagard, V., & Thiele, I. (April 2015). Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes. Frontiers in Genetics, 6, 148. doi:10.3389/fgene.2015.00148 Peer Reviewed verified by ORBi |
 | Zhang, H., Ravcheev, D., Hu, D., Zhang, F., Gong, X., Hao, L., Cao, M., Rodionov, D. A., Wang, C., & Feng, Y. (2015). Two novel regulators of N-acetyl-galactosamine utilization pathway and distinct roles in bacterial infections. MicrobiologyOpen, 4 (6), 983-1000. doi:10.1002/mbo3.307 Peer Reviewed verified by ORBi |
 | Feng, Y., Kumar, R., Ravcheev, D., & Zhang, H. (2015). Paracoccus denitrificans possesses two BioR homologs having a role in regulation of biotin metabolism. MicrobiologyOpen, 4, 644–659. doi:10.1002/mbo3.270 Peer Reviewed verified by ORBi |
 | Ravcheev, D., & Thiele, I. (2014). Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota. Frontiers in Microbiology. doi:10.3389/fmicb.2014.00674 Peer Reviewed verified by ORBi |
 | Ravcheev, D., Khoroshkin, M. S., Laikova, O. N., Tsoy, O. V., Semova, N. V., Petrova, S. A., Rakhmaninova, A. B., Novichkov, P. S., Gelfand, M. S., & Rodionov, D. A. (June 2014). Comparative genomics and evolution of regulons of the LacI-family transcription factors. Frontiers in Microbiology, 5, 1-16. doi:10.3389/fmicb.2014.00294 Peer Reviewed verified by ORBi |
 | Zhang, L., Nie, X., Ravcheev, D., Rodionov, D. A., Sheng, J., Gu, Y., Yang, S., Jiang, W., & Yang, C. (2014). Redox-responsive repressor Rex modulates alcohol production and oxidative stress tolerance in Clostridium acetobutylicum. Journal of Bacteriology, 196 (22), 3949-3963. doi:10.1128/JB.02037-14 Peer Reviewed verified by ORBi |
 | Rodionov, D. A., Rodionova, I. A., Li, Ravcheev, D., Tarasova, Z., Portnoy, V. A., Zengler, K., & Osterman, A. L. (August 2013). Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima. Frontiers in Microbiology, 4 (244), 1-14. doi:10.3389/fmicb.2013.00244 Peer Reviewed verified by ORBi |
 | Novichkov, P. S., Kazakov, A. E., Ravcheev, D., Leyn, S. A., Kovaleva, G. Y., Sutormin, R. A., Kazanov, M. D., Riehl, W., Arkin, A. P., Dubchak, I., & Rodionov, D. A. (2013). RegPrecise 3.0 - a resource for genome-scale exploration of transcriptional regulation in Bacteria. BMC Genomics, 14 (745), 1-12. doi:10.1186/1471-2164-14-745 Peer Reviewed verified by ORBi |
 | Ravcheev, D., Godzik, A., Osterman, A., & Rodionov, D. (2013). Polysaccharide utilization in Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks. BMC Genomics, 14 (873), 1-17. doi:10.1186/1471-2164-14-873 Peer Reviewed verified by ORBi |
 | Ravcheev, D., Best, A. A., Sernova, N. V., Kazanov, M. D., Novichkov, P. S., & Rodionov, D. A. (2013). Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria. BMC Genomics, 14 (94), 1-14. doi:10.1186/1471-2164-14-94 Peer Reviewed verified by ORBi |
 | Pavlova, O., Lavysh, D., Klimuk, E., Djordjevic, M., Ravcheev, D., Gelfand, M. S., Severinov, K., & Akulenko, N. (2012). Temporal regulation of gene expression of the Escherichia coli bacteriophage phiEco32. Journal of Molecular Biology, 416, 389-399. doi:10.1016/j.jmb.2012.01.002 Peer Reviewed verified by ORBi |
 | Suvorova, I. A., Ravcheev, D., & Gelfand, M. S. (2012). Regulation and evolution of malonate and propionate catabolism in proteobacteria. Journal of Bacteriology, 194 (12), 3234-3240. doi:10.1128/JB.00163-12 Peer Reviewed verified by ORBi |
 | Ravcheev, D., Li, X., Latif, H., Zengler, K., Leyn, S. A., Korostelev, Y. D., Kazakov, A. E., Novichkov, P. S., Osterman, A. L., & Rodionov, D. A. (2012). Transcriptional regulation of central carbon and energy metabolism in bacteria by redox responsive repressor Rex. Journal of Bacteriology, 194 (5), 1145-1157. doi:10.1128/JB.06412-11 Peer Reviewed verified by ORBi |
 | Suvorova, I. A., Tutukina, M. N., Ravcheev, D., Rodionov, D. A., Ozoline, O. N., & Gelfand, M. S. (2011). Comparative genomic analysis of the hexuronate metabolism genes and their regulation in gamma-proteobacteria. Journal of Bacteriology, 193 (15), 3956-3963. doi:10.1128/JB.00277-11 Peer Reviewed verified by ORBi |
 | Ravcheev, D., Best, A. A., Tintle, N., DeJongh, M., Osterman, A. L., Novichkov, P. S., & Rodionov, D. A. (2011). Inference of the Transcriptional Regulatory Network in Staphylococcus aureus by Integration of Experimental and Genomics-Based Evidence. Journal of Bacteriology, 193 (12), 3228-3240. doi:10.1128/JB.00350-11 Peer Reviewed verified by ORBi |
 | Rodionov, D. A., Novichkov, P. S., Stavrovskaya, E. D., Rodionova, I. A., Li, X., Kazanov, M. D., Ravcheev, D., Gerasimova, A. V., Kazakov, A. E., Kovaleva, G. Y., Permina, E. A., Laikova, O. N., Overbeek, R., Romine, M. F., Fredrickson, J. K., Arkin, A. P., Dubchak, I., Osterman, A. L., & Gelfand, M. S. (2011). Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. BMC Genomics, 12 (Suppl 1) (S3), 1-17. doi:10.1186/1471-2164-12-S1-S3 Peer Reviewed verified by ORBi |
 | Tsoy, O., Ravcheev, D., & Mushegian, A. (2009). Comparative genomics of ethanolamine utilization. Journal of Bacteriology, 191 (23), 7157-7164. doi:10.1128/JB.00838-09 Peer Reviewed verified by ORBi |
 | Tsyganova, M. O., Gelfand, M. S., & Ravcheev, D. (2007). Regulation of Bacterial Respiration: Comparison of Microarray and Comparative Genomics Data. Molecular Biology, 41 (3), 497-512. doi:10.1134/S0026893307030168 Peer Reviewed verified by ORBi |
 | Ravcheev, D., Gerasimova, A. V., Mironov, A. A., & Gelfand, M. S. (2007). Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae). BMC Genomics, 8 (54), 1-17. doi:10.1186/1471-2164-8-54 Peer Reviewed verified by ORBi |
 | Ravcheev, D., Rakhmaninova, A. B., Mironov, A. A., & Gelfand, M. S. (2005). Regulation of nitrate and nitrite respiration in γ-proteobacteria: a comparative genomics study. Molecular Biology, 39 (5), 727-740. doi:10.1007/s11008-005-0088-7 Peer Reviewed verified by ORBi |
 | Favorov, A. A., Gelfand, M. S., Gerasimova, A. V., Ravcheev, D., Mironov, A. A., & Makeev, V. J. (2005). A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length. Bioinformatics, 21 (10), 2240-2245. doi:10.1093/bioinformatics/bti336 Peer reviewed |
 | Iarovaia, O. V., Bystritskiy, A., Ravcheev, D., Hancock, R., & Razin, S. V. (2004). Visualization of individual DNA loops and a map of loop domains in the human dystrophin gene. Nucleic Acids Research, 32 (7), 2079-2086. doi:10.1093/nar/gkh532 Peer Reviewed verified by ORBi |
 | Ravcheev, D., Gelfand, M. S., Mironov, A. A., & Rakhmaninova, A. B. (2002). Purine regulon of gamma-proteobacteria: a detailed description. Russian Journal of Genetics, 38 (9), 1015-1025. doi:10.1023/A:1020231513079 Peer Reviewed verified by ORBi |