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Genomic distribution of B-vitamin auxotrophy and uptake transporters in environmental bacteria from the C hloroflexi phylum.
Published in:
Environmental Microbiology Reports, 2015, v. 7, n. 2, p. 204, doi. 10.1111/1758-2229.12227
By:
- Rodionova, Irina A.;
- Li, Xiaoqing;
- Plymale, Andrew E.;
- Motamedchaboki, Khatereh;
- Konopka, Allan E.;
- Romine, Margaret F.;
- Fredrickson, James K.;
- Osterman, Andrei L.;
- Rodionov, Dmitry A.
Publication type:
Article
A deimmunized and pharmacologically optimized Toll-like receptor 5 agonist for therapeutic applications.
Published in:
Communications Biology, 2021, v. 4, n. 1, p. 1, doi. 10.1038/s42003-021-01978-6
By:
- Mett, Vadim;
- V. Kurnasov, Oleg;
- A. Bespalov, Ivan;
- Molodtsov, Ivan;
- M. Brackett, Craig;
- G. Burdelya, Lyudmila;
- A. Purmal, Andrei;
- S. Gleiberman, Anatoli;
- A. Toshkov, Ilia;
- A. Burkhart, Catherine;
- N. Kogan, Yakov;
- L. Andrianova, Ekaterina;
- V. Gudkov, Andrei;
- L. Osterman, Andrei
Publication type:
Article
Prediction of enzymatic pathways by integrative pathway mapping.
Published in:
eLife, 2018, p. 1, doi. 10.7554/eLife.31097
By:
- Calhoun, Sara;
- Korczynska, Magdalena;
- Wichelecki, Daniel J.;
- Francisco, Brian San;
- Suwen Zhao;
- Rodionov, Dmitry A.;
- Vetting, Matthew W.;
- Al-Obaidi, Nawar F.;
- Lin, Henry;
- O'Meara, Matthew J.;
- Scott, David A.;
- Morris, John H.;
- Russel, Daniel;
- Almo, Steven C.;
- Osterman, Andrei L.;
- Gerlt, John A.;
- Jacobson, Matthew P.;
- Shoichet, Brian K.;
- Sali, Andrej
Publication type:
Article
A novel bifunctional transcriptional regulator of riboflavin metabolism in Archaea.
Published in:
Nucleic Acids Research, 2017, v. 45, n. 7, p. 3725, doi. 10.1093/nar/gkw1331
By:
- Rodionova, Irina A.;
- Vetting, Matthew W.;
- Xiaoqing Li;
- Almo, Steven C.;
- Osterman, Andrei L.;
- Rodionov, Dmitry A.
Publication type:
Article
Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum.
Published in:
Nucleic Acids Research, 2013, v. 41, n. 2, p. 790, doi. 10.1093/nar/gks1184
By:
- Kazanov, Marat D.;
- Li, Xiaoqing;
- Gelfand, Mikhail S.;
- Osterman, Andrei L.;
- Rodionov, Dmitry A.
Publication type:
Article
PMAP: databases for analyzing proteolytic events and pathways.
Published in:
Nucleic Acids Research, 2009, v. 37, n. suppl_1, p. D611, doi. 10.1093/nar/gkn683
By:
- Igarashi, Yoshinobu;
- Heureux, Emily;
- Doctor, Kutbuddin S.;
- Talwar, Priti;
- Gramatikova, Svetlana;
- Gramatikoff, Kosi;
- Zhang, Ying;
- Blinov, Michael;
- Ibragimova, Salmaz S.;
- Boyd, Sarah;
- Ratnikov, Boris;
- Cieplak, Piotr;
- Godzik, Adam;
- Smith, Jeffrey W.;
- Osterman, Andrei L.;
- Eroshkin, Alexey M.
Publication type:
Article
Transcriptional regulation of NAD metabolism in bacteria: NrtR family of Nudix-related regulators.
Published in:
Nucleic Acids Research, 2008, v. 36, n. 6, p. 2047, doi. 10.1093/nar/gkn047
By:
- Rodionov, Dmitry A.;
- De Ingeniis, Jessica;
- Mancini, Chiara;
- Cimadamore, Flavio;
- Zhang, Hong;
- Osterman, Andrei L.;
- Raffaelli, Nadia
Publication type:
Article
Transcriptional regulation of NAD metabolism in bacteria: genomic reconstruction of NiaR (YrxA) regulon.
Published in:
Nucleic Acids Research, 2008, v. 36, n. 6, p. 2032, doi. 10.1093/nar/gkn046
By:
- Rodionov, Dmitry A.;
- Li, Xiaoqing;
- Rodionova, Irina A.;
- Yang, Chen;
- Sorci, Leonardo;
- Dervyn, Etienne;
- Martynowski, Dariusz;
- Zhang, Hong;
- Gelfand, Mikhail S.;
- Osterman, Andrei L.
Publication type:
Article
CutDB: a proteolytic event database.
Published in:
Nucleic Acids Research, 2007, v. 35, p. d546, doi. 10.1093/nar/gkl813
By:
- Igarashi, Yoshinobu;
- Eroshkin, Alexey;
- Gramatikova, Svetlana;
- Gramatikoff, Kosi;
- Zhang, Ying;
- Smith, Jeffrey W.;
- Osterman, Andrei L.;
- Godzik, Adam
Publication type:
Article
Genomics-Guided Analysis of NAD Recycling Yields Functional Elucidation of COG1058 as a New Family of Pyrophosphatases.
Published in:
PLoS ONE, 2013, v. 8, n. 6, p. 1, doi. 10.1371/journal.pone.0065595
By:
- Cialabrini, Lucia;
- Ruggieri, Silverio;
- Kazanov, Marat D.;
- Sorci, Leonardo;
- Mazzola, Francesca;
- Orsomando, Giuseppe;
- Osterman, Andrei L.;
- Raffaelli, Nadia
Publication type:
Article
Functional Specialization in Proline Biosynthesis of Melanoma.
Published in:
PLoS ONE, 2012, v. 7, n. 9, p. 1, doi. 10.1371/journal.pone.0045190
By:
- De Ingeniis, Jessica;
- Ratnikov, Boris;
- Richardson, Adam D.;
- Scott, David A.;
- Aza-Blanc, Pedro;
- De, Surya K.;
- Kazanov, Marat;
- Pellecchia, Maurizio;
- Ronai, Ze'ev;
- Osterman, Andrei L.;
- Smith, Jeffrey W.;
- Parker, Emily
Publication type:
Article
Glutamine versus Ammonia Utilization in the NAD Synthetase Family.
Published in:
PLoS ONE, 2012, v. 7, n. 6, p. 1, doi. 10.1371/journal.pone.0039115
By:
- De Ingeniis, Jessica;
- Kazanov, Marat D.;
- Shatalin, Konstantin;
- Gelfand, Mikhail S.;
- Osterman, Andrei L.;
- Sorci, Leonardo
Publication type:
Article
Sequence-derived structural features driving proteolytic processing.
Published in:
Proteomics, 2014, v. 14, n. 1, p. 42, doi. 10.1002/pmic.201300416
By:
- Belushkin, Alexander A.;
- Vinogradov, Dmitry V.;
- Gelfand, Mikhail S.;
- Osterman, Andrei L.;
- Cieplak, Piotr;
- Kazanov, Marat D.
Publication type:
Article
Targeting the Warburg effect via LDHA inhibition engages ATF4 signaling for cancer cell survival.
Published in:
EMBO Journal, 2018, v. 37, n. 20, p. N.PAG, doi. 10.15252/embj.201899735
By:
- Pathria, Gaurav;
- Scott, David A;
- Feng, Yongmei;
- Sang Lee, Joo;
- Fujita, Yu;
- Zhang, Gao;
- Sahu, Avinash D;
- Ruppin, Eytan;
- Herlyn, Meenhard;
- Osterman, Andrei L;
- Ronai, Ze'ev A
Publication type:
Article
The RAST Server: Rapid Annotations using Subsystems Technology.
Published in:
BMC Genomics, 2008, v. 9, p. 1, doi. 10.1186/1471-2164-9-75
By:
- Aziz, Ramy K.;
- Bartels, Daniela;
- Best, Aaron A.;
- DeJongh, Matthew;
- Disz, Terrence;
- Edwards, Robert A.;
- Formsma, Kevin;
- Gerdes, Svetlana;
- Glass, Elizabeth M.;
- Kuba, Michael;
- Meyer, Folker;
- Olsen, Gary J.;
- Olson, Robert;
- Osterman, Andrei L.;
- Overbeek, Ross A.;
- McNeil, Leslie K.;
- Paarmann, Daniel;
- Paczian, Tobias;
- Parrello, Bruce;
- Pusch, Gordon D.
Publication type:
Article
Crystallization and preliminary X-ray studies of ornithine decarboxylase from Trypanosoma brucei.
Published in:
Proteins, 1996, v. 24, n. 2, p. 272, doi. 10.1002/(SICI)1097-0134(199602)24:2<272::AID-PROT17>3.0.CO;2-K
By:
- Grishin, Nick V.;
- Osterman, Andrei L.;
- Goldsmith, Elizabeth J.;
- Phillips, Margaret A.
Publication type:
Article
Novel inositol catabolic pathway in Thermotoga maritima.
Published in:
Environmental Microbiology, 2013, v. 15, n. 8, p. 2254, doi. 10.1111/1462-2920.12096
By:
- Rodionova, Irina A.;
- Leyn, Semen A.;
- Burkart, Michael D.;
- Boucher, Nathalie;
- Noll, Kenneth M.;
- Osterman, Andrei L.;
- Rodionov, Dmitry A.
Publication type:
Article
Tagaturonate-fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network in Thermotoga maritima.
Published in:
Environmental Microbiology, 2012, v. 14, n. 11, p. 2920, doi. 10.1111/j.1462-2920.2012.02856.x
By:
- Rodionova, Irina A.;
- Scott, David A.;
- Grishin, Nick V.;
- Osterman, Andrei L.;
- Rodionov, Dmitry A.
Publication type:
Article
Arginylation regulates purine nucleotide biosynthesis by enhancing the activity of phosphoribosyl pyrophosphate synthase.
Published in:
Nature Communications, 2015, v. 6, n. 7, p. 7517, doi. 10.1038/ncomms8517
By:
- Zhang, Fangliang;
- Patel, Devang M.;
- Colavita, Kristen;
- Rodionova, Irina;
- Buckley, Brian;
- Scott, David A.;
- Kumar, Akhilesh;
- Shabalina, Svetlana A.;
- Saha, Sougata;
- Chernov, Mikhail;
- Osterman, Andrei L.;
- Kashina, Anna
Publication type:
Article
The effects of micronutrient deficiencies on bacterial species from the human gut microbiota.
Published in:
Science Translational Medicine, 2017, v. 9, n. 390, p. 1, doi. 10.1126/scitranslmed.aal4069
By:
- Hibberd, Matthew C.;
- Meng Wu;
- Rodionov, Dmitry A.;
- Xiaoqing Li;
- Jiye Cheng;
- Griffin, Nicholas W.;
- Barratt, Michael J.;
- Giannone, Richard J.;
- Hettich, Robert L.;
- Osterman, Andrei L.;
- Gordon, Jeffrey I.
Publication type:
Article
Towards environmental systems biology of Shewanella.
Published in:
Nature Reviews Microbiology, 2008, v. 6, n. 8, p. 592, doi. 10.1038/nrmicro1947
By:
- Fredrickson, James K.;
- Romine, Margaret F.;
- Beliaev, Alexander S.;
- Auchtung, Jennifer M.;
- Driscoll, Michael E.;
- Gardner, Timothy S.;
- Nealson, Kenneth H.;
- Osterman, Andrei L.;
- Pinchuk, Grigoriy;
- Reed, Jennifer L.;
- Rodionov, Dmitry A.;
- Rodrigues, Jorge L. M.;
- Saffarini, Daad A.;
- Serres, Margrethe H.;
- Spormann, Alfred M.;
- Zhulin, Igor B.;
- Tiedje, James M.
Publication type:
Article
Binary Metabolic Phenotypes and Phenotype Diversity Metrics for the Functional Characterization of Microbial Communities.
Published in:
Frontiers in Microbiology, 2021, v. 12, p. 1, doi. 10.3389/fmicb.2021.653314
By:
- Iablokov, Stanislav N.;
- Novichkov, Pavel S.;
- Osterman, Andrei L.;
- Rodionov, Dmitry A.
Publication type:
Article
Reduced AIBP expression in bronchial epithelial cells of asthmatic patients: Potential therapeutic target.
Published in:
Clinical & Experimental Allergy, 2022, v. 52, n. 8, p. 979, doi. 10.1111/cea.14150
By:
- Miller, Marina;
- Pham, Alexa K.;
- Gonen, Ayelet;
- Navia-Pelaez, Juliana M.;
- Xia, Katherine;
- Sungwoo Park;
- Osterman, Andrei L.;
- Bacon, Kevin;
- Beaton, Graham;
- Kurten, Richard C.;
- Broide, David H.;
- Miller, Yury I.
Publication type:
Article
Modeling of interaction between cytochrome c and the WD domains of Apaf-1: bifurcated salt bridges underlying apoptosome assembly.
Published in:
Biology Direct, 2015, v. 10, n. 1, p. 1, doi. 10.1186/s13062-015-0059-4
By:
- Shalaeva, Daria N.;
- Dibrova, Daria V.;
- Galperin, Michael Y.;
- Mulkidjanian, Armen Y.;
- Osterman, Andrei L.;
- Srinivasan, Narayanaswamy;
- Berezovsky, Igor N.;
- Vriend, Gerrit
Publication type:
Article
A microbiome-directed therapeutic food for children recovering from severe acute malnutrition.
Published in:
Science Translational Medicine, 2024, v. 16, n. 767, p. 1, doi. 10.1126/scitranslmed.adn2366
By:
- Hartman, Steven J.;
- Hibberd, Matthew C.;
- Mostafa, Ishita;
- Naila, Nurun N.;
- Islam, Md. Munirul;
- Zaman, Mahabub Uz;
- Huq, Sayeeda;
- Mahfuz, Mustafa;
- Islam, Md. Tazul;
- Mukherji, Kallol;
- Moghaddam, Vaha Akbary;
- Chen, Robert Y.;
- Province, Michael A.;
- Webber, Daniel M.;
- Henrissat, Suzanne;
- Henrissat, Bernard;
- Terrapon, Nicolas;
- Rodionov, Dmitry A.;
- Osterman, Andrei L.;
- Barratt, Michael J.
Publication type:
Article
Glutamine-fueled mitochondrial metabolism is decoupled from glycolysis in melanoma.
Published in:
Pigment Cell & Melanoma Research, 2012, v. 25, n. 6, p. 732, doi. 10.1111/pcmr.12000
By:
- Filipp, Fabian V.;
- Ratnikov, Boris;
- De Ingeniis, Jessica;
- Smith, Jeffrey W.;
- Osterman, Andrei L.;
- Scott, David A.
Publication type:
Article
Reverse TCA cycle flux through isocitrate dehydrogenases 1 and 2 is required for lipogenesis in hypoxic melanoma cells.
Published in:
Pigment Cell & Melanoma Research, 2012, v. 25, n. 3, p. 375, doi. 10.1111/j.1755-148X.2012.00989.x
By:
- Filipp, Fabian V.;
- Scott, David A.;
- Ronai, Ze'ev A.;
- Osterman, Andrei L.;
- Smith, Jeffrey W.
Publication type:
Article
Genomic variations on a CoA biosynthetic theme.
Published in:
Nature Chemical Biology, 2009, v. 5, n. 12, p. 871, doi. 10.1038/nchembio.267
By:
- Osterman, Andrei L.
Publication type:
Article
Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks.
Published in:
BMC Genomics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2164-14-873
By:
- Ravcheev, Dmitry A.;
- Godzik, Adam;
- Osterman, Andrei L;
- Rodionov, Dmitry A.
Publication type:
Article
Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus.
Published in:
BMC Genomics, 2011, v. 12, p. 1, doi. 10.1186/1471-2164-12-S1-S3
By:
- Rodionov, Dmitry A.;
- Novichkov, Pavel S.;
- Stavrovskaya, Elena D.;
- Rodionova, Irina A.;
- Xiaoqing Li;
- Kazanov, Marat D.;
- Ravcheev, Dmitry A.;
- Gerasimova, Anna V.;
- Kazakov, Alexey E.;
- Yu Kovaleva, Galina;
- 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.
Publication type:
Article
Genomic encyclopedia of sugar utilization pathways in the Shewanella genus.
Published in:
BMC Genomics, 2010, v. 11, p. 494, doi. 10.1186/1471-2164-11-494
By:
- Rodionov, Dmitry A.;
- Chen Yang;
- Xiaoqing Li;
- Rodionova, Irina A.;
- Yanbing Wang;
- Obraztsova, Anna Y.;
- Zagnitko, Olga P.;
- Overbeek, Ross;
- Romine, Margaret F.;
- Reed, Samantha;
- Fredrickson, James K.;
- Nealson, Kenneth H.;
- Osterman, Andrei L.;
- osterman@burnham.org
Publication type:
Article
B-Vitamin Sharing Promotes Stability of Gut Microbial Communities.
Published in:
Frontiers in Microbiology, 2019, p. 1, doi. 10.3389/fmicb.2019.01485
By:
- Sharma, Vandana;
- Rodionov, Dmitry A.;
- Leyn, Semen A.;
- Tran, David;
- Iablokov, Stanislav N.;
- Ding, Hua;
- Peterson, Daniel A.;
- Osterman, Andrei L.;
- Peterson, Scott N.
Publication type:
Article
Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome.
Published in:
Frontiers in Microbiology, 2019, p. N.PAG, doi. 10.3389/fmicb.2019.01316
By:
- Rodionov, Dmitry A.;
- Arzamasov, Aleksandr A.;
- Khoroshkin, Matvei S.;
- Iablokov, Stanislav N.;
- Leyn, Semen A.;
- Peterson, Scott N.;
- Novichkov, Pavel S.;
- Osterman, Andrei L.
Publication type:
Article
B Vitamins and Their Role in Immune Regulation and Cancer.
Published in:
Nutrients, 2020, v. 12, n. 11, p. 3380, doi. 10.3390/nu12113380
By:
- Peterson, Christine Tara;
- Rodionov, Dmitry A.;
- Osterman, Andrei L.;
- Peterson, Scott N.
Publication type:
Article

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