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ArticlesPeer ReviewedFull Text
Bioactivity assessment of natural compounds using machine learning models trained on target similarity between drugs
Author / Creator:Periwal, Vinita ; Bassler, Stefan ; Andrejev, Sergej ; Gabrielli, Natalia ; Patil, Kaustubh Raosaheb ; Typas, Athanasios ; Patil, Kiran Raosaheb
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2022-04, Vol.18 (4), p.e1010029-e1010029
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Molecular biology for green recovery—A call for action
Author / Creator:Rodríguez-Martínez, Marta ; Nielsen, Jens ; Dupont, Sam ; Vamathevan, Jessica ; Glover, Beverley J. ; Crosswell, Lindsey C. ; Rouse, Brendan ; Luisi, Ben F. ; Bowler, Chris ; Gasser, Susan M. ; Arendt, Detlev ; Erb, Tobias J. ; de Lorenzo, Victor ; Heard, Edith ; Patil, Kiran Raosaheb
Publisher:United States: Public Library of Science
Journal title:PLoS biology, 2022-04, Vol.20 (4), p.e3001623
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Extensive impact of non-antibiotic drugs on human gut bacteria
Author / Creator:Maier, Lisa ; Pruteanu, Mihaela ; Kuhn, Michael ; Zeller, Georg ; Telzerow, Anja ; Anderson, Exene Erin ; Brochado, Ana Rita ; Fernandez, Keith Conrad ; Dose, Hitomi ; Mori, Hirotada ; Patil, Kiran Raosaheb ; Bork, Peer ; Typas, Athanasios
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2018-03, Vol.555 (7698), p.623-628
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Towards a mechanistic understanding of reciprocal drug–microbiome interactions
Author / Creator:Zimmermann, Michael ; Patil, Kiran Raosaheb ; Typas, Athanasios ; Maier, Lisa
Publisher:London: Nature Publishing Group UK
Journal title:Molecular systems biology, 2021-03, Vol.17 (3), p.e10116-n/a
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Metabolic dependencies drive species co-occurrence in diverse microbial communities
Author / Creator:Zelezniak, Aleksej ; Andrejev, Sergej ; Ponomarova, Olga ; Mende, Daniel R. ; Bork, Peer ; Patil, Kiran Raosaheb
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2015-05, Vol.112 (20), p.6449-6454
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Contribution of Network Connectivity in Determining the Relationship between Gene Expression and Metabolite Concentration Changes
Author / Creator:Zelezniak, Aleksej ; Sheridan, Steven ; Patil, Kiran Raosaheb
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2014-04, Vol.10 (4), p.e1003572-e1003572
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Uncovering Transcriptional Regulation of Metabolism by Using Metabolic Network Topology
Author / Creator:Patil, Kiran Raosaheb ; Nielsen, Jens ; Green, Philip P.
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2005-02, Vol.102 (8), p.2685-2689
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Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community
Author / Creator:Blasche, Sonja ; Kim, Yongkyu ; Mars, Ruben A. T. ; Machado, Daniel ; Maansson, Maria ; Kafkia, Eleni ; Milanese, Alessio ; Zeller, Georg ; Teusink, Bas ; Nielsen, Jens ; Benes, Vladimir ; Neves, Rute ; Sauer, Uwe ; Patil, Kiran Raosaheb
Publisher:London: Nature Publishing Group UK
Journal title:Nature microbiology, 2021-02, Vol.6 (2), p.196-208
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Unravelling metabolic cross‐feeding in a yeast–bacteria community using 13C‐based proteomics
Author / Creator:Gabrielli, Natalia ; Maga‐Nteve, Christoniki ; Kafkia, Eleni ; Rettel, Mandy ; Loeffler, Jakob ; Kamrad, Stephan ; Typas, Athanasios ; Patil, Kiran Raosaheb
Publisher:London: Nature Publishing Group UK
Journal title:Molecular systems biology, 2023-04, Vol.19 (4), p.1-n/a
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Adaptive laboratory evolution of microbial co‐cultures for improved metabolite secretion
Author / Creator:Konstantinidis, Dimitrios ; Pereira, Filipa ; Geissen, Eva‐Maria ; Grkovska, Kristina ; Kafkia, Eleni ; Jouhten, Paula ; Kim, Yongkyu ; Devendran, Saravanan ; Zimmermann, Michael ; Patil, Kiran Raosaheb
Publisher:London: Nature Publishing Group UK
Journal title:Molecular systems biology, 2021-08, Vol.17 (8), p.e10189-n/a
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ArticlesPeer ReviewedFull Text
Proteomic characterization of extracellular vesicles produced by several wine yeast species
Author / Creator:Mencher, Ana ; Morales, Pilar ; Valero, Eva ; Tronchoni, Jordi ; Patil, Kiran Raosaheb ; Gonzalez, Ramon
Publisher:United States: John Wiley & Sons, Inc
Journal title:Microbial biotechnology, 2020-09, Vol.13 (5), p.1581-1596
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ArticlesPeer ReviewedFull Text
Co-translational assembly orchestrates competing biogenesis pathways
Author / Creator:Seidel, Maximilian ; Becker, Anja ; Pereira, Filipa ; Landry, Jonathan J. M. ; de Azevedo, Nayara Trevisan Doimo ; Fusco, Claudia M. ; Kaindl, Eva ; Romanov, Natalie ; Baumbach, Janina ; Langer, Julian D. ; Schuman, Erin M. ; Patil, Kiran Raosaheb ; Hummer, Gerhard ; Benes, Vladimir ; Beck, Martin
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2022-03, Vol.13 (1), p.1224-15, Article 1224
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Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes
Author / Creator:Xavier, Joana C. ; Patil, Kiran Raosaheb ; Rocha, I.
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2018-11, Vol.14 (11), p.1-23
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ArticlesPeer ReviewedFull Text
Evolutionary programming as a platform for in silico metabolic engineering
Author / Creator:Patil, Kiran Raosaheb ; Rocha, Isabel ; Förster, Jochen ; Nielsen, Jens
Publisher:England: BioMed Central Ltd
Journal title:BMC bioinformatics, 2005-12, Vol.6 (1), p.308-308, Article 308
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ArticlesPeer ReviewedFull Text
Improved vanillin production in baker's yeast through in silico design
Author / Creator:Brochado, Ana Rita ; Matos, Claudia ; Møller, Birger L ; Hansen, Jørgen ; Mortensen, Uffe H ; Patil, Kiran Raosaheb
Publisher:England: BioMed Central Ltd
Journal title:Microbial cell factories, 2010-11, Vol.9 (1), p.84-84, Article 84
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ArticlesPeer ReviewedFull Text
Metabolic Network Topology Reveals Transcriptional Regulatory Signatures of Type 2 Diabetes
Author / Creator:Zelezniak, Aleksej ; Pers, Tune H. ; Soares, Simão ; Patti, Mary Elizabeth ; Patil, Kiran Raosaheb
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2010-04, Vol.6 (4), p.e1000729-e1000729
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ArticlesPeer ReviewedFull Text
Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium
Author / Creator:Montagud, Arnau ; Navarro, Emilio ; Fernández de Córdoba, Pedro ; Urchueguía, Javier F ; Patil, Kiran Raosaheb
Publisher:England: BioMed Central Ltd
Journal title:BMC systems biology, 2010-11, Vol.4 (1), p.156-156, Article 156
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The metabolic background is a global player in Saccharomyces gene expression epistasis
Author / Creator:Alam, Mohammad Tauqeer ; Zelezniak, Aleksej ; Mülleder, Michael ; Shliaha, Pavel ; Schwarz, Roland ; Capuano, Floriana ; Vowinckel, Jakob ; Radmaneshfar, Elahe ; Krüger, Antje ; Calvani, Enrica ; Michel, Steve ; Börno, Stefan ; Christen, Stefan ; Patil, Kiran Raosaheb ; Timmermann, Bernd ; Lilley, Kathryn S. ; Ralser, Markus
Publisher:London: Nature Publishing Group UK
Journal title:Nature microbiology, 2016-02, Vol.1 (3), p.15030-15030, Article 15030
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The Role of High-throughput Transcriptome Analysis in Metabolic Engineering
Author / Creator:Jewett, Michael C ; Oliveira, Ana Paula ; Patil, Kiran Raosaheb ; Nielsen, Jens
Publisher:한국생물공학회
Journal title:Biotechnology and Bioprocess Engineering, 2005, 10(5), , pp.385-399
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Unravelling the collateral damage of antibiotics on gut bacteria
Author / Creator:Maier, Lisa ; Goemans, Camille V. ; Wirbel, Jakob ; Kuhn, Michael ; Eberl, Claudia ; Pruteanu, Mihaela ; Müller, Patrick ; Garcia-Santamarina, Sarela ; Cacace, Elisabetta ; Zhang, Boyao ; Gekeler, Cordula ; Banerjee, Tisya ; Anderson, Exene Erin ; Milanese, Alessio ; Löber, Ulrike ; Forslund, Sofia K. ; Patil, Kiran Raosaheb ; Zimmermann, Michael ; Stecher, Bärbel ; Zeller, Georg ; Bork, Peer ; Typas, Athanasios
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2021-11, Vol.599 (7883), p.120-124
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Bioactivity assessment of natural compounds using machine learning models trained on target similarity between drugs

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Molecular biology for green recovery—A call for action

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Extensive impact of non-antibiotic drugs on human gut bacteria

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Towards a mechanistic understanding of reciprocal drug–microbiome interactions

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Metabolic dependencies drive species co-occurrence in diverse microbial communities

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Contribution of Network Connectivity in Determining the Relationship between Gene Expression and Metabolite Concentration Changes

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Uncovering Transcriptional Regulation of Metabolism by Using Metabolic Network Topology

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Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community

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Unravelling metabolic cross‐feeding in a yeast–bacteria community using 13C‐based proteomics

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Adaptive laboratory evolution of microbial co‐cultures for improved metabolite secretion

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Proteomic characterization of extracellular vesicles produced by several wine yeast species

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Co-translational assembly orchestrates competing biogenesis pathways

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Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes

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Evolutionary programming as a platform for in silico metabolic engineering

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Improved vanillin production in baker's yeast through in silico design

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Metabolic Network Topology Reveals Transcriptional Regulatory Signatures of Type 2 Diabetes

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Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium

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The metabolic background is a global player in Saccharomyces gene expression epistasis

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The Role of High-throughput Transcriptome Analysis in Metabolic Engineering

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Unravelling the collateral damage of antibiotics on gut bacteria

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