Bioinformatics Services for Data-Driven Design of Cell Factories and Communities

Informations projet

DD-DeCaF

N° de convention de subvention: 686070

DOI

10.3030/686070

Projet clôturé

Date de signature de la CE 25 Février 2016

Date de début 1 Mars 2016

Date de fin 29 Février 2020

Financé au titre de

• INDUSTRIAL LEADERSHIP - Leadership in enabling and industrial technologies – Biotechnology

Coût total

€ 7 091 021,25

Contribution de l’UE

€ 6 250 636,25

Coordonné par

DANMARKS TEKNISKE UNIVERSITET
Denmark

CORDIS fournit des liens vers les livrables publics et les publications des projets HORIZON.

Les liens vers les livrables et les publications des projets du 7e PC, ainsi que les liens vers certains types de résultats spécifiques tels que les jeux de données et les logiciels, sont récupérés dynamiquement sur OpenAIRE .

Livrables

Other (34)

Bi-directional connectivity of the visualization components with APIs and data sources
Novel enzyme and pathway candidates publicly available
Metabolic interaction simulation software publically available
First version of the database providing novel functional and enzyme annotations
Genomic/metagenomic gene catalog database

Multiple genomic and metagenomic resources will be mined to produce a normalized gene catalog database EMBL inhouse STRING and eggNOG databases currently providing proteinprotein interactions and orthology information for more than 3600 qualityfiltered genomes will be used to obtain data from fully sequenced organisms Additionally 2000 human gut samples and 240 ocean samples will be exploited to extract gene pools from unculturable organisms The expected size of the final database is estimated to be over 50M sequences Given the amount and heterogeneity of the source data optimal database design and administration will be critical Therefore this task will be carried out with the technical support of biobyte Solutions P9

Algorithms for optimization using model with protein synthesis and secretion
Large-scale kinetic models of relevant production hosts
Cloud hosting solution for web-services on CSC compute infrastructure
Models for quantitative simulation of protein secretion
Results of optimization for selected case-studies
Interactive pathway visualization components are available on the DeCaF platform
A toolbox for integration of metabolomics data into thermodynamically-curated GEMs

A toolbox for integration of metabolomics data into thermodynamicallycurated GEMs

Community design software publically available
Integration of gene and pathway mining components from WP2
Models for quantitative simulation of protein secretion by fungi
Models for quantitative simulation of protein secretion by bacterial hosts
Community model reconstruction pipeline publically available
Thermodynamically-curated GEMs with integrated metabolomics data
Software for designing synthetic microbial communities
Identifier translation service for metabolite, enzyme, gene, protein and reaction identifiers
Software for simulating metabolic interactions in microbial communities
General metaheuristics-based optimization framework
Functional annotation of gene catalog
Upload and access control system for processed omics data
Web-based cell factory and community design platform (DeCaF) hosted on CSC infrastructure
Algorithms for optimization using community models
Consortium-wide repository of methods, algorithms, software, and web-services that can be deployed as docker containers
Large-scale kinetic models of one fungal organism with integrated enzyme biosynthesis module
Models for yeast, E. coli and two other microorganisms that accounts for protein content
Large-scale kinetic models of one bacterial organism with integrated enzyme biosynthesis module
Algorithms for optimization using large-scale kinetic models
Integration of the visualization components with public data sources is implemented
Functional annotation pipeline established
Bioinformatics pipeline for building community metabolic models

Websites, patent fillings, videos etc. (7)

2nd annual DeCaF workshop

Annual workshop

Periodic newsletters

Annual newsletters distributed every 12 months

Technology Transfer Activities, including training to SMEs
1st annual DeCaF workshop

Annual workshops

3rd annual DeCaF workshop

Annual workshop

Project website: the report will provide a functional description of the project website, its main sections and how the access to the private area is implemented.

Project website: the report will provide a functional description of the project website, its main sections and how the access to the private area is implemented

Press release about the launching of the project

Open Research Data Pilot (1)

Data Management Plan

First version of data management plan as required by Open Research Data Pilot

Publications

Peer reviewed articles (47)

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies

Auteurs: Melanie Tramontano, Sergej Andrejev, Mihaela Pruteanu, Martina Klünemann, Michael Kuhn, Marco Galardini, Paula Jouhten, Aleksej Zelezniak, Georg Zeller, Peer Bork, Athanasios Typas, Kiran Raosaheb Patil
Publié dans: Nature Microbiology, Numéro 3/4, 2018, Page(s) 514-522, ISSN 2058-5276
Éditeur: Nature Publishing Group
DOI: 10.1038/s41564-018-0123-9

CRISPR/Cpf1 enables fast and simple genome editing of Saccharomyces cerevisiae

Auteurs: René Verwaal, Nathalie Buiting-Wiessenhaan, Sacha Dalhuijsen, Johannes A. Roubos
Publié dans: Yeast, Numéro 35/2, 2018, Page(s) 201-211, ISSN 0749-503X
Éditeur: John Wiley & Sons Inc.
DOI: 10.1002/yea.3278

Similarity of the dog and human gut microbiomes in gene content and response to diet

Auteurs: Luis Pedro Coelho, Jens Roat Kultima, Paul Igor Costea, Coralie Fournier, Yuanlong Pan, Gail Czarnecki-Maulden, Matthew Robert Hayward, Sofia K. Forslund, Thomas Sebastian Benedikt Schmidt, Patrick Descombes, Janet R. Jackson, Qinghong Li, Peer Bork
Publié dans: Microbiome, Numéro 6/1, 2018, ISSN 2049-2618
Éditeur: Springer Nature
DOI: 10.1186/s40168-018-0450-3

Stoichiometric Representation of Gene–Protein–Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction

Auteurs: Machado, Daniel; Herrgard, Markus; Rocha, Isabel
Publié dans: PLoS Computational Biology, Numéro 1, 2016, ISSN 1553-7358
Éditeur: Public Library of Science
DOI: 10.1371/journal.pcbi.1005140

SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework

Auteurs: Benjamín J. Sánchez, Feiran Li, Eduard J. Kerkhoven, Jens Nielsen
Publié dans: BMC Systems Biology, Numéro 13/1, 2019, ISSN 1752-0509
Éditeur: BioMed Central
DOI: 10.1186/s12918-018-0673-8

pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis

Auteurs: Pierre Salvy, Georgios Fengos, Meric Ataman, Thomas Pathier, Keng C Soh, Vassily Hatzimanikatis
Publié dans: Bioinformatics, 2018, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/bty499

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

Auteurs: Daniel Machado, Sergej Andrejev, Melanie Tramontano, Kiran Raosaheb Patil
Publié dans: Nucleic Acids Research, Numéro 46/15, 2018, Page(s) 7542-7553, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gky537

Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production strains

Auteurs: Ilaria Massaiu, Lorenzo Pasotti, Nikolaus Sonnenschein, Erlinda Rama, Matteo Cavaletti, Paolo Magni, Cinzia Calvio, Markus J. Herrgård
Publié dans: Microbial Cell Factories, Numéro 18/1, 2019, ISSN 1475-2859
Éditeur: BioMed Central
DOI: 10.1186/s12934-018-1052-2

Microbial cell factories for the sustainable manufacturing of B vitamins

Auteurs: Carlos G Acevedo-Rocha, Luisa S Gronenberg, Matthias Mack, Fabian M Commichau, Hans J Genee
Publié dans: Current Opinion in Biotechnology, Numéro 56, 2019, Page(s) 18-29, ISSN 0958-1669
Éditeur: Elsevier BV
DOI: 10.1016/j.copbio.2018.07.006

RapidRIP quantifies the intracellular metabolome of 7 industrial strains of E. coli

Auteurs: Douglas McCloskey, Julia Xu, Lars Schrübbers, Hanne B. Christensen, Markus J. Herrgård
Publié dans: Metabolic Engineering, Numéro 47, 2018, Page(s) 383-392, ISSN 1096-7176
Éditeur: Academic Press
DOI: 10.1016/j.ymben.2018.04.009

Structure and function of the global topsoil microbiome

Auteurs: Mohammad Bahram, Falk Hildebrand, Sofia K. Forslund, Jennifer L. Anderson, Nadejda A. Soudzilovskaia, Peter M. Bodegom, Johan Bengtsson-Palme, Sten Anslan, Luis Pedro Coelho, Helery Harend, Jaime Huerta-Cepas, Marnix H. Medema, Mia R. Maltz, Sunil Mundra, Pål Axel Olsson, Mari Pent, Sergei Põlme, Shinichi Sunagawa, Martin Ryberg, Leho Tedersoo, Peer Bork
Publié dans: Nature, Numéro 560/7717, 2018, Page(s) 233-237, ISSN 0028-0836
Éditeur: Nature Publishing Group
DOI: 10.1038/s41586-018-0386-6

Integration of Biomass Formulations of Genome-Scale Metabolic Models with Experimental Data Reveals Universally Essential Cofactors in Prokaryotes

Auteurs: Xavier, Joana C.; Patil, Kiran Raosaheb; Rocha, Isabel
Publié dans: Metabolic Engineering, 2017, ISSN 1096-7176
Éditeur: Academic Press
DOI: 10.1016/j.ymben.2016.12.002

Optlang: An algebraic modeling language for mathematical optimization

Auteurs: Kristian Jensen, Joao G.R. Cardoso, Nikolaus Sonnenschein
Publié dans: The Journal of Open Source Software, Numéro 2/9, 2017, ISSN 2475-9066
Éditeur: The Journal of Open Source Software
DOI: 10.21105/joss.00139

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes

Auteurs: Daniel R. Mende, Ivica Letunic, Jaime Huerta-Cepas, Simone S. Li, Kristoffer Forslund, Shinichi Sunagawa, Peer Bork
Publié dans: Nucleic Acids Research, Numéro 45/D1, 2017, Page(s) D529-D534, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkw989

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

Auteurs: Jaime Huerta-Cepas, Kristoffer Forslund, Luis Pedro Coelho, Damian Szklarczyk, Lars Juhl Jensen, Christian von Mering, Peer Bork
Publié dans: Molecular Biology and Evolution, 2017, ISSN 0737-4038
Éditeur: Oxford University Press
DOI: 10.1093/molbev/msx148

Metabolic anchor reactions for robust biorefining

Auteurs: Paula Jouhten, Jaime Huerta-Cepas, Peer Bork, Kiran Raosaheb Patil
Publié dans: Metabolic Engineering, Numéro 40, 2017, Page(s) 1-4, ISSN 1096-7176
Éditeur: Academic Press
DOI: 10.1016/j.ymben.2017.02.010

Systems biology solutions for biochemical production challenges

Auteurs: Anne Sofie L?rke Hansen, Rebecca M. Lennen, Nikolaus Sonnenschein, Markus J Herrg?rd
Publié dans: Current Opinion in Biotechnology, Numéro 45, 2017, Page(s) 85-91, ISSN 0958-1669
Éditeur: Elsevier BV
DOI: 10.1016/j.copbio.2016.11.018

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

Auteurs: Joana C. Xavier, Kiran Raosaheb Patil, Isabel Rocha
Publié dans: PLOS Computational Biology, Numéro 14/11, 2018, Page(s) e1006556, ISSN 1553-7358
Éditeur: PLOS Computational Biology
DOI: 10.1371/journal.pcbi.1006556

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

Auteurs: Guillem Salazar, Lucas Paoli, Adriana Alberti, Jaime Huerta-Cepas, Hans-Joachim Ruscheweyh, Miguelangel Cuenca, Christopher M. Field, Luis Pedro Coelho, Corinne Cruaud, Stefan Engelen, Ann C. Gregory, Karine Labadie, Claudie Marec, Eric Pelletier, Marta Royo-Llonch, Simon Roux, Pablo Sánchez, Hideya Uehara, Ahmed A. Zayed, Georg Zeller, Margaux Carmichael, Céline Dimier, Joannie Ferland, Stefani
Publié dans: Cell, Numéro 179/5, 2019, Page(s) 1068-1083.e21, ISSN 0092-8674
Éditeur: Cell Press
DOI: 10.1016/j.cell.2019.10.014

MARSI: metabolite analogues for rational strain improvement

Auteurs: João G R Cardoso, Ahmad A Zeidan, Kristian Jensen, Nikolaus Sonnenschein, Ana Rute Neves, Markus J Herrgård
Publié dans: Bioinformatics, Numéro 34/13, 2018, Page(s) 2319-2321, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/bty108

Selecting the Best: Evolutionary Engineering of Chemical Production in Microbes

Auteurs: Denis Shepelin, Anne Hansen, Rebecca Lennen, Hao Luo, Markus Herrgård
Publié dans: Genes, Numéro 9/5, 2018, Page(s) 249, ISSN 2073-4425
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/genes9050249

A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory

Auteurs: Thordis Kristjansdottir, Elleke F. Bosma, Filipe Branco dos Santos, Emre Özdemir, Markus J. Herrgård, Lucas França, Bruno Ferreira, Alex T. Nielsen, Steinn Gudmundsson
Publié dans: Microbial Cell Factories, Numéro 18/1, 2019, ISSN 1475-2859
Éditeur: BioMed Central
DOI: 10.1186/s12934-019-1229-3

Comparison of pathway analysis and constraint-based methods for cell factory design

Auteurs: Vítor Vieira, Paulo Maia, Miguel Rocha, Isabel Rocha
Publié dans: BMC Bioinformatics, Numéro 20/1, 2019, ISSN 1471-2105
Éditeur: BioMed Central
DOI: 10.1186/s12859-019-2934-y

A Review of Dynamic Modeling Approaches and Their Application in Computational Strain Optimization for Metabolic Engineering

Auteurs: Osvaldo D. Kim, Miguel Rocha, Paulo Maia
Publié dans: Frontiers in Microbiology, Numéro 9, 2018, ISSN 1664-302X
Éditeur: Frontiers Media
DOI: 10.3389/fmicb.2018.01690

Cameo: A Python Library for Computer Aided Metabolic Engineering and Optimization of Cell Factories

Auteurs: João G. R. Cardoso, Kristian Jensen, Christian Lieven, Anne Sofie Lærke Hansen, Svetlana Galkina, Moritz Beber, Emre Özdemir, Markus J. Herrgård, Henning Redestig, Nikolaus Sonnenschein
Publié dans: ACS Synthetic Biology, Numéro 7/4, 2018, Page(s) 1163-1166, ISSN 2161-5063
Éditeur: American Chemical Society
DOI: 10.1021/acssynbio.7b00423

Antibiotics-induced monodominance of a novel gut bacterial order

Auteurs: Falk Hildebrand, Lucas Moitinho-Silva, Sonja Blasche, Martin T Jahn, Toni Ingolf Gossmann, Jaime Huerta-Cepas, Rajna Hercog, Mechthild Luetge, Mohammad Bahram, Anna Pryszlak, Renato J Alves, Sebastian M Waszak, Ana Zhu, Lumeng Ye, Paul Igor Costea, Steven Aalvink, Clara Belzer, Sofia K Forslund, Shinichi Sunagawa, Ute Hentschel, Christoph Merten, Kiran Raosaheb Patil, Vladimir Benes, Peer Bork
Publié dans: Gut, Numéro 68/10, 2019, Page(s) 1781-1790, ISSN 0017-5749
Éditeur: BMJ Publishing Group
DOI: 10.1136/gutjnl-2018-317715

Discovery and implementation of a novel pathway for n-butanol production via 2-oxoglutarate

Auteurs: Sofia Ferreira, Rui Pereira, Filipe Liu, Paulo Vilaça, Isabel Rocha
Publié dans: Biotechnology for Biofuels, Numéro 12/1, 2019, ISSN 1754-6834
Éditeur: Biotechnology and Biofuels
DOI: 10.1186/s13068-019-1565-x

SamPler – a novel method for selecting parameters for gene functional annotation routines

Auteurs: Fernando Cruz, Davide Lagoa, João Mendes, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha, Oscar Dias
Publié dans: BMC Bioinformatics, Numéro 20/1, 2019, ISSN 1471-2105
Éditeur: BioMed Central
DOI: 10.1186/s12859-019-3038-4

Genome-wide sequencing and metabolic annotation of Pythium irregulare CBS 494.86: understanding Eicosapentaenoic acid production

Auteurs: Bruna S. Fernandes, Oscar Dias, Gisela Costa, Antonio A. Kaupert Neto, Tiago F. C. Resende, Juliana V. C. Oliveira, Diego M. Riaño-Pachón, Marcelo Zaiat, José G. C. Pradella, Isabel Rocha
Publié dans: BMC Biotechnology, Numéro 19/1, 2019, ISSN 1472-6750
Éditeur: BioMed Central
DOI: 10.1186/s12896-019-0529-3

iDS372, a Phenotypically Reconciled Model for the Metabolism of Streptococcus pneumoniae Strain R6

Auteurs: Oscar Dias, João Saraiva, Cristiana Faria, Mario Ramirez, Francisco Pinto, Isabel Rocha
Publié dans: Frontiers in Microbiology, Numéro 10, 2019, ISSN 1664-302X
Éditeur: Frontiers Media
DOI: 10.3389/fmicb.2019.01283

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity

Auteurs: Oleksandr M. Maistrenko, Daniel R. Mende, Mechthild Luetge, Falk Hildebrand, Thomas S. B. Schmidt, Simone S. Li, João F. Matias Rodrigues, Christian von Mering, Luis Pedro Coelho, Jaime Huerta-Cepas, Shinichi Sunagawa, Peer Bork
Publié dans: The ISME Journal, Numéro 14/5, 2020, Page(s) 1247-1259, ISSN 1751-7362
Éditeur: Nature Publishing Group
DOI: 10.1038/s41396-020-0600-z

CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models

Auteurs: Vítor Vieira, Miguel Rocha
Publié dans: Bioinformatics, Numéro 35/24, 2019, Page(s) 5361-5362, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btz598

OptCouple: Joint simulation of gene knockouts, insertions and medium modifications for prediction of growth-coupled strain designs

Auteurs: Kristian Jensen, Valentijn Broeken, Anne Sofie Lærke Hansen, Nikolaus Sonnenschein, Markus J. Herrgård
Publié dans: Metabolic Engineering Communications, Numéro 8, 2019, Page(s) e00087, ISSN 2214-0301
Éditeur: Elsevier BV
DOI: 10.1016/j.mec.2019.e00087

Wiring cell growth to product formation

Auteurs: Josi Buerger, Luisa S. Gronenberg, Hans Jasper Genee, Morten O.A. Sommer
Publié dans: Current Opinion in Biotechnology, Numéro 59, 2019, Page(s) 85-92, ISSN 0958-1669
Éditeur: Elsevier BV
DOI: 10.1016/j.copbio.2019.02.014

NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language

Auteurs: Luis Pedro Coelho, Renato Alves, Paulo Monteiro, Jaime Huerta-Cepas, Ana Teresa Freitas, Peer Bork
Publié dans: Microbiome, Numéro 7/1, 2019, ISSN 2049-2618
Éditeur: Microbiome
DOI: 10.1186/s40168-019-0684-8

Particle-Based Simulation Reveals Macromolecular Crowding Effects on the Michaelis-Menten Mechanism

Auteurs: Daniel R. Weilandt, Vassily Hatzimanikatis
Publié dans: Biophysical Journal, Numéro 117/2, 2019, Page(s) 355-368, ISSN 0006-3495
Éditeur: Biophysical Society
DOI: 10.1016/j.bpj.2019.06.017

The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models

Auteurs: Pierre Salvy, Vassily Hatzimanikatis
Publié dans: Nature Communications, Numéro 11/1, 2020, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-019-13818-7

A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

Auteurs: Hongzhong Lu, Feiran Li, Benjamín J. Sánchez, Zhengming Zhu, Gang Li, Iván Domenzain, Simonas Marcišauskas, Petre Mihail Anton, Dimitra Lappa, Christian Lieven, Moritz Emanuel Beber, Nikolaus Sonnenschein, Eduard J. Kerkhoven, Jens Nielsen
Publié dans: Nature Communications, Numéro 10/1, 2019, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-019-11581-3

Model-Assisted Fine-Tuning of Central Carbon Metabolism in Yeast through dCas9-Based Regulation

Auteurs: Raphael Ferreira, Christos Skrekas, Alex Hedin, Benjamín J. Sánchez, Verena Siewers, Jens Nielsen, Florian David
Publié dans: ACS Synthetic Biology, Numéro 8/11, 2019, Page(s) 2457-2463, ISSN 2161-5063
Éditeur: American Chemical Society
DOI: 10.1021/acssynbio.9b00258

CRISPR/Cas12a Multiplex Genome Editing of <em>Saccharomyces cerevisiae</em> and the Creation of Yeast Pixel Art

Auteurs: Klaudia Ciurkot, Brenda Vonk, Thomas E. Gorochowski, Johannes A. Roubos, René Verwaal
Publié dans: Journal of Visualized Experiments, Numéro 147, 2019, ISSN 1940-087X
Éditeur: MYJoVE Corporation
DOI: 10.3791/59350

Improved biotin, thiamine, and lipoic acid biosynthesis by engineering the global regulator IscR

Auteurs: Anne P. Bali, David Lennox-Hvenekilde, Nils Myling-Petersen, Josi Buerger, Bo Salomonsen, Luisa S. Gronenberg, Morten O.A. Sommer, Hans J. Genee
Publié dans: Metabolic Engineering, Numéro 60, 2020, Page(s) 97-109, ISSN 1096-7176
Éditeur: Academic Press
DOI: 10.1016/j.ymben.2020.03.005

Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations

Auteurs: Tuure Hameri, Georgios Fengos, Meric Ataman, Ljubisa Miskovic, Vassily Hatzimanikatis
Publié dans: Metabolic Engineering, Numéro 52, 2019, Page(s) 29-41, ISSN 1096-7176
Éditeur: Academic Press
DOI: 10.1016/j.ymben.2018.10.005

Energy metabolism controls phenotypes by protein efficiency and allocation

Auteurs: Yu Chen, Jens Nielsen
Publié dans: Proceedings of the National Academy of Sciences, Numéro 116/35, 2019, Page(s) 17592-17597, ISSN 0027-8424
Éditeur: National Academy of Sciences
DOI: 10.1073/pnas.1906569116

redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models

Auteurs: Meric Ataman, Daniel F. Hernandez Gardiol, Georgios Fengos, Vassily Hatzimanikatis
Publié dans: PLOS Computational Biology, Numéro 13/7, 2017, Page(s) e1005444, ISSN 1553-7358
Éditeur: Public Library of Science
DOI: 10.1371/journal.pcbi.1005444

lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites

Auteurs: Meric Ataman, Vassily Hatzimanikatis
Publié dans: PLOS Computational Biology, Numéro 13/7, 2017, Page(s) e1005513, ISSN 1553-7358
Éditeur: Public Library of Science
DOI: 10.1371/journal.pcbi.1005513

Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints

Auteurs: Benjamín J Sánchez, Cheng Zhang, Avlant Nilsson, Petri‐Jaan Lahtvee, Eduard J Kerkhoven, Jens Nielsen
Publié dans: Molecular Systems Biology, Numéro 13/8, 2017, Page(s) 935, ISSN 1744-4292
Éditeur: Nature Publishing Group
DOI: 10.15252/msb.20167411

Yeast Creates a Niche for Symbiotic Lactic Acid Bacteria through Nitrogen Overflow

Auteurs: Olga Ponomarova, Natalia Gabrielli, Daniel C. Sévin, Michael Mülleder, Katharina Zirngibl, Katsiaryna Bulyha, Sergej Andrejev, Eleni Kafkia, Athanasios Typas, Uwe Sauer, Markus Ralser, Kiran Raosaheb Patil
Publié dans: Cell Systems, 2017, ISSN 2405-4712
Éditeur: Elsevier Inc
DOI: 10.1016/j.cels.2017.09.002

Conference proceedings (1)

Identification of robust strain designs via tandem pFBA/LMOMA phenotype prediction

Auteurs: Paulo Maia, Isabel Rocha, Miguel Rocha
Publié dans: Proceedings of the Genetic and Evolutionary Computation Conference Companion on - GECCO '17, 2017, Page(s) 1661-1668, ISBN 9781-450349390
Éditeur: ACM Press
DOI: 10.1145/3067695.3082542