The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering

Nat Commun 2022

Hérisson J, Duigou T, du Lac M, Bazi-Kabbaj K, Sabeti Azad M, Buldum G, Telle O, El Moubayed Y, Carbonell P, Swainston N, Zulkower V, Kushwaha M, Baldwin GS and Faulon JL.

Type 2 diabetes, gut microbiome, and systems biology: A novel perspective for a new era

Gut Microbes 2022

Martínez-López YE, Esquivel-Hernández DA, Sánchez-Castañeda JP, Neri-Rosario D, Guardado-Mendoza R and Resendis-Antonio O.

Muconic acid production from glucose and xylose in Pseudomonas putida via evolution and metabolic engineering

Nat Commun 2022

Ling C, Peabody GL, Salvachúa D, Kim YM, Kneucker CM, Calvey CH, Monninger MA, Munoz NM, Poirier BC, Ramirez KJ, St John PC, Woodworth SP, Magnuson JK, Burnum-Johnson KE, Guss AM, Johnson CW and Beckham GT.

In silico genome-scale metabolic modeling and in vitro static time-kill studies of exogenous metabolites alone and with polymyxin B against Klebsiella pneumoniae

Front Pharmacol 2022

Chung WY, Abdul Rahim N, Mahamad Maifiah MH, Hawala Shivashekaregowda NK, Zhu Y and Wong EH.

Genome-scale metabolic network reconstructions of diverse Escherichia strains reveal strain-specific adaptations

Philos Trans R Soc Lond B Biol Sci 2022

Monk JM.

Spatial resolution of an integrated C(4)+CAM photosynthetic metabolism

Sci Adv 2022

Moreno-Villena JJ, Zhou H, Gilman IS, Tausta SL, Cheung CYM and Edwards EJ.

A compendium of predicted growths and derived symbiotic relationships between 803 gut microbes in 13 different diets

Curr Res Microb Sci 2022

Singh R, Dutta A, Bose T and Mande SS.

Multi-Objective Optimization of Microalgae Metabolism: An Evolutive Algorithm Based on FBA

Metabolites 2022

Briones-Baez MF, Aguilera-Vazquez L, Rangel-Valdez N, Martinez-Salazar AL and Zuñiga C.

Constraint-Based Reconstruction and Analyses of Metabolic Models: Open-Source Python Tools and Applications to Cancer

Front Oncol 2022

Ng RH, Lee JW, Baloni P, Diener C, Heath JR and Su Y.

Metabolic modeling of the International Space Station microbiome reveals key microbial interactions

Microbiome 2022

Kumar RK, Singh NK, Balakrishnan S, Parker CW, Raman K and Venkateswaran K.

Machine learning-guided evaluation of extraction and simulation methods for cancer patient-specific metabolic models

Comput Struct Biotechnol J 2022

Lee SM, Lee G and Kim HU.

Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0

Nat Commun 2022

Domenzain I, Sánchez B, Anton M, Kerkhoven EJ, Millán-Oropeza A, Henry C, Siewers V, Morrissey JP, Sonnenschein N and Nielsen J.

A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale

PLoS Comput Biol 2022

Vieira V, Ferreira J and Rocha M.

Comparative genomic analysis of Streptomyces rapamycinicus NRRL 5491 and its mutant overproducing rapamycin

Sci Rep 2022

Jo HG, Adidjaja JJ, Kim DK, Park BS, Lee N, Cho BK, Kim HU and Oh MK.

Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum

Microb Cell Fact 2022

Benito-Vaquerizo S, Parera Olm I, de Vroet T, Schaap PJ, Sousa DZ, Martins Dos Santos VAP and Suarez-Diez M.

SALARECON connects the Atlantic salmon genome to growth and feed efficiency

PLoS Comput Biol 2022

Zakhartsev M, Rotnes F, Gulla M, Øyås O, van Dam JCJ, Suarez-Diez M, Grammes F, Hafþórsson RA, van Helvoirt W, Koehorst JJ, Schaap PJ, Jin Y, Mydland LT, Gjuvsland AB, Sandve SR, Martins Dos Santos VAP and Vik JO.

Lactobacillus rhamnosus colonisation antagonizes Candida albicans by forcing metabolic adaptations that compromise pathogenicity

Nat Commun 2022

Alonso-Roman R, Last A, Mirhakkak MH, Sprague JL, Möller L, Großmann P, Graf K, Gratz R, Mogavero S, Vylkova S, Panagiotou G, Schäuble S, Hube B and Gresnigt MS.

Dissecting carbon metabolism of Yarrowia lipolytica type strain W29 using genome-scale metabolic modelling

Comput Struct Biotechnol J 2022

Guo Y, Su L, Liu Q, Zhu Y, Dai Z and Wang Q.

Reconstruction of a Genome-Scale Metabolic Network for Shewanella oneidensis MR-1 and Analysis of its Metabolic Potential for Bioelectrochemical Systems

Front Bioeng Biotechnol 2022

Luo J, Yuan Q, Mao Y, Wei F, Zhao J, Yu W, Kong S, Guo Y, Cai J, Liao X, Wang Z and Ma H.

Engineering nonphotosynthetic carbon fixation for production of bioplastics by methanogenic archaea

Proc Natl Acad Sci U S A 2022

Thevasundaram K, Gallagher JJ, Cherng F and Chang MCY.

A genome-scale metabolic model of Cupriavidus necator H16 integrated with TraDIS and transcriptomic data reveals metabolic insights for biotechnological applications

PLoS Comput Biol 2022

Pearcy N, Garavaglia M, Millat T, Gilbert JP, Song Y, Hartman H, Woods C, Tomi-Andrino C, Reddy Bommareddy R, Cho BK, Fell DA, Poolman M, King JR, Winzer K, Twycross J and Minton NP.

BioUML-towards a universal research platform

Nucleic Acids Res 2022

Kolpakov F, Akberdin I, Kiselev I, Kolmykov S, Kondrakhin Y, Kulyashov M, Kutumova E, Pintus S, Ryabova A, Sharipov R, Yevshin I, Zhatchenko S and Kel A.

BioSimulators: a central registry of simulation engines and services for recommending specific tools

Nucleic Acids Res 2022

Shaikh B, Smith LP, Vasilescu D, Marupilla G, Wilson M, Agmon E, Agnew H, Andrews SS, Anwar A, Beber ME, Bergmann FT, Brooks D, Brusch L, Calzone L, Choi K, Cooper J, Detloff J, Drawert B, Dumontier M, Ermentrout GB, Faeder JR, Freiburger AP, Fröhlich F, Funahashi A, Garny A, Gennari JH, Gleeson P, Goelzer A, Haiman Z, Hasenauer J, Hellerstein JL, Hermjakob H, Hoops S, Ison JC, Jahn D, Jakubowski HV, Jordan R, Kalaš M, König M, Liebermeister W, Sheriff RSM, Mandal S, McDougal R, Medley JK, Mendes P, Müller R, Myers CJ, Naldi A, Nguyen TVN, Nickerson DP, Olivier BG, Patoliya D, Paulevé L, Petzold LR, Priya A, Rampadarath AK, Rohwer JM, Saglam AS, Singh D, Sinha A, Snoep J, Sorby H, Spangler R, Starruß J, Thomas PJ, van Niekerk D, Weindl D, Zhang F, Zhukova A, Goldberg AP, Schaff JC, Blinov ML, Sauro HM, Moraru II and Karr JR.

Fermentative Indole Production via Bacterial Tryptophan Synthase Alpha Subunit and Plant Indole-3-Glycerol Phosphate Lyase Enzymes

J Agric Food Chem 2022

Ferrer L, Mindt M, Suarez-Diez M, Jilg T, Zagorščak M, Lee JH, Gruden K, Wendisch VF and Cankar K.

Network Reconstruction and Modelling Made Reproducible with moped

Metabolites 2022

Saadat NP, van Aalst M and Ebenhöh O.

iNovo479: Metabolic Modeling Provides a Roadmap to Optimize Bioproduct Yield from Deconstructed Lignin Aromatics by Novosphingobium aromaticivorans

Metabolites 2022

Linz AM, Ma Y, Scholz S, Noguera DR and Donohue TJ.

Underground metabolism as a rich reservoir for pathway engineering

Bioinformatics 2022

Kovács SC, Szappanos B, Tengölics R, Notebaart RA and Papp B.

PyMiner: A method for metabolic pathway design based on the uniform similarity of substrate-product pairs and conditional search

PLoS One 2022

Song X, Dong M and Liu M.

Systems Biology on Acetogenic Bacteria for Utilizing C1 Feedstocks

Adv Biochem Eng Biotechnol 2022

Song Y, Bae J, Shin J, Jin S, Kang S, Lee H, Cho S and Cho BK.

A genetic toolkit and gene switches to limit Mycoplasma growth for biosafety applications

Nat Commun 2022

Broto A, Gaspari E, Miravet-Verde S, Dos Santos VAPM and Isalan M.

Production of indole by Corynebacterium glutamicum microbial cell factories for flavor and fragrance applications

Microb Cell Fact 2022

Mindt M, Beyraghdar Kashkooli A, Suarez-Diez M, Ferrer L, Jilg T, Bosch D, Martins Dos Santos V, Wendisch VF and Cankar K.

In Silico Exploration of Mycobacterium tuberculosis Metabolic Networks Shows Host-Associated Convergent Fluxomic Phenotypes

Biomolecules 2022

Santamaria G, Ruiz-Rodriguez P, Renau-Mínguez C, Pinto FR and Coscollá M.

A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality

Genome Res 2022

Hawkey J, Vezina B, Monk JM, Judd LM, Harshegyi T, López-Fernández S, Rodrigues C, Brisse S, Holt KE and Wyres KL.

Integrative Genome-Scale Metabolic Modeling Reveals Versatile Metabolic Strategies for Methane Utilization in Methylomicrobium album BG8

MSystems 2022

Villada JC, Duran MF, Lim CK, Stein LY and Lee PKH.

Computational Models for Clinical Applications in Personalized Medicine-Guidelines and Recommendations for Data Integration and Model Validation

J Pers Med 2022

Collin CB, Gebhardt T, Golebiewski M, Karaderi T, Hillemanns M, Khan FM, Salehzadeh-Yazdi A, Kirschner M, Krobitsch S, Eu-Stands Pm Consortium and Kuepfer L.

CobraMod: A pathway-centric curation tool for constraint-based metabolic models

Bioinformatics 2022

Camborda S, Weder JN and Töpfer N.

Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models

PLoS Comput Biol 2022

Carey MA, Medlock GL, Stolarczyk M, Petri WA Jr, Guler JL and Papin JA.

Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale

Nat Biotechnol 2022

Liew FE, Nogle R, Abdalla T, Rasor BJ, Canter C, Jensen RO, Wang L, Strutz J, Chirania P, De Tissera S, Mueller AP, Ruan Z, Gao A, Tran L, Engle NL, Bromley JC, Daniell J, Conrado R, Tschaplinski TJ, Giannone RJ, Hettich RL, Karim AS, Simpson SD, Brown SD, Leang C, Jewett MC and Köpke M.

CRISPR-assisted rational flux-tuning and arrayed CRISPRi screening of an L-proline exporter for L-proline hyperproduction

Nat Commun 2022

Liu J, Liu M, Shi T, Sun G, Gao N, Zhao X, Guo X, Ni X, Yuan Q, Feng J, Liu Z, Guo Y, Chen J, Wang Y, Zheng P and Sun J.

Global pleiotropic effects in adaptively evolved Escherichia coli lacking CRP reveal molecular mechanisms that define the growth physiology

Open Biol 2022

Pal A, Iyer MS, Srinivasan S, Narain Seshasayee AS and Venkatesh KV.

Vivarium: an interface and engine for integrative multiscale modeling in computational biology

Bioinformatics 2022

Agmon E, Spangler RK, Skalnik CJ, Poole W, Peirce SM, Morrison JH and Covert MW.

INTEGRATE: Model-based multi-omics data integration to characterize multi-level metabolic regulation

PLoS Comput Biol 2022

Di Filippo M, Pescini D, Galuzzi BG, Bonanomi M, Gaglio D, Mangano E, Consolandi C, Alberghina L, Vanoni M and Damiani C.

ECMpy, a Simplified Workflow for Constructing Enzymatic Constrained Metabolic Network Model

Biomolecules 2022

Mao Z, Zhao X, Yang X, Zhang P, Du J, Yuan Q and Ma H.

Enzyme-constrained models predict the dynamics of Saccharomyces cerevisiae growth in continuous, batch and fed-batch bioreactors

Microb Biotechnol 2022

Moreno-Paz S, Schmitz J, Martins Dos Santos VAP and Suarez-Diez M.

Total of 44 publications. 😄

Structural systems pharmacology: A framework for integrating metabolic network and structure-based virtual screening for drug discovery against bacteria

PLoS One 2021

Nazarshodeh E, Marashi SA and Gharaghani S.

CNApy: a CellNetAnalyzer GUI in Python for Analyzing and Designing Metabolic Networks

Bioinformatics 2021

Thiele S, von Kamp A, Bekiaris PS, Schneider P and Klamt S.

High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032

Front Microbiol 2021

Feierabend M, Renz A, Zelle E, Nöh K, Wiechert W and Dräger A.

A Standardized Brain Molecular Atlas: A Resource for Systems Modeling and Simulation

Front Mol Neurosci 2021

Shichkova P, Coggan JS, Markram H and Keller D.

eQuilibrator 3.0: a database solution for thermodynamic constant estimation

Nucleic Acids Res 2021

Beber ME, Gollub MG, Mozaffari D, Shebek KM, Flamholz AI, Milo R and Noor E.

Genome-Scale Reconstruction of Microbial Dynamic Phenotype: Successes and Challenges

Microorganisms 2021

Panikov NS.

Agent Clustering Strategy Based on Metabolic Flux Distribution and Transcriptome Expression for Novel Drug Development

Biomedicines 2021

Ruan Y, Chen XH, Jiang F, Liu YG, Liang XL, Lv BM, Zhang HY and Zhang QY.

COBREXA.jl: constraint-based reconstruction and exascale analysis

Bioinformatics 2021

Kratochvíl M, Heirendt L, Wilken SE, Pusa T, Arreckx S, Noronha A, van Aalst M, Satagopam VP, Ebenhöh O, Schneider R, Trefois C and Gu W.

Protein allocation and utilization in the versatile chemolithoautotroph Cupriavidus necator

Elife 2021

Jahn M, Crang N, Janasch M, Hober A, Forsström B, Kimler K, Mattausch A, Chen Q, Asplund-Samuelsson J and Hudson EP.

Global connectivity in genome-scale metabolic networks revealed by comprehensive FBA-based pathway analysis

BMC Microbiol 2021

Gao Y, Yuan Q, Mao Z, Liu H and Ma H.

MPA_Pathway_Tool: User-Friendly, Automatic Assignment of Microbial Community Data on Metabolic Pathways

Int J Mol Sci 2021

Walke D, Schallert K, Ramesh P, Benndorf D, Lange E, Reichl U and Heyer R.

Simulating Metabolic Flexibility in Low Energy Expenditure Conditions Using Genome-Scale Metabolic Models

Metabolites 2021

Cabbia A, Hilbers PAJ and van Riel NAW.

Intelligent host engineering for metabolic flux optimisation in biotechnology

Biochem J 2021

Munro LJ and Kell DB.

Novel Symbiotic Genome-Scale Model Reveals Wolbachia's Arboviral Pathogen Blocking Mechanism in Aedes aegypti

MBio 2021

Jiménez NE, Gerdtzen ZP, Olivera-Nappa Á, Salgado JC and Conca C.

A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)

Nat Protoc 2021

Dukovski I, Bajić D, Chacón JM, Quintin M, Vila JCC, Sulheim S, Pacheco AR, Bernstein DB, Riehl WJ, Korolev KS, Sanchez A, Harcombe WR and Segrè D.

Novel Drivers of Virulence in Clostridioides difficile Identified via Context-Specific Metabolic Network Analysis

MSystems 2021

Jenior ML, Leslie JL, Powers DA, Garrett EM, Walker KA, Dickenson ME, Petri WA Jr, Tamayo R and Papin JA.

Genome Scale Modeling to Study the Metabolic Competition between Cells in the Tumor Microenvironment

Cancers (Basel) 2021

Frades I, Foguet C, Cascante M and Araúzo-Bravo MJ.

In vivo, in vitro and in silico: an open space for the development of microbe-based applications of synthetic biology

Microb Biotechnol 2021

Danchin A.

Path to improving the life cycle and quality of genome-scale models of metabolism

Cell Syst 2021

Seif Y and Palsson BØ.

Programmatic modeling for biological systems

Curr Opin Syst Biol 2021

Lubbock ALR and Lopez CF.

Diversity begets diversity during community assembly until ecological limits impose a diversity ceiling

Mol Ecol 2021

San Roman M and Wagner A.

Enabling rational gut microbiome manipulations by understanding gut ecology through experimentally-evidenced in silico models

Gut Microbes 2021

Molina Ortiz JP, McClure DD, Shanahan ER, Dehghani F, Holmes AJ and Read MN.

Thermodynamic Genome-Scale Metabolic Modeling of Metallodrug Resistance in Colorectal Cancer

Cancers (Basel) 2021

Herrmann HA, Rusz M, Baier D, Jakupec MA, Keppler BK, Berger W, Koellensperger G and Zanghellini J.

Modular dynamic biomolecular modelling with bond graphs: the unification of stoichiometry, thermodynamics, kinetics and data

J R Soc Interface 2021

Gawthrop PJ, Pan M and Crampin EJ.

Investigating the Chemolithoautotrophic and Formate Metabolism of Nitrospira moscoviensis by Constraint-Based Metabolic Modeling and (13)C-Tracer Analysis

MSystems 2021

Lawson CE, Mundinger AB, Koch H, Jacobson TB, Weathersby CA, Jetten MSM, Pabst M, Amador-Noguez D, Noguera DR, McMahon K and Lücker S.

Metabolome and proteome analyses reveal transcriptional misregulation in glycolysis of engineered E. coli

Nat Commun 2021

Wang CY, Lempp M, Farke N, Donati S, Glatter T and Link H.

Thermodynamic and Kinetic Modeling of Co-utilization of Glucose and Xylose for 2,3-BDO Production by Zymomonas mobilis

Front Bioeng Biotechnol 2021

Wu C, Spiller R, Dowe N, Bomble YJ and St John PC.

Genome-scale integration of transcriptome and metabolome unveils squalene synthase and dihydrofolate reductase as targets against AML cells resistant to chemotherapy

Comput Struct Biotechnol J 2021

Karakitsou E, Foguet C, Contreras Mostazo MG, Kurrle N, Schnütgen F, Michaelis M, Cinatl J, Marin S and Cascante M.

A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

Nat Commun 2021

Oftadeh O, Salvy P, Masid M, Curvat M, Miskovic L and Hatzimanikatis V.

Imaging and modelling of poly(3-hydroxybutyrate) synthesis in Paracoccus denitrificans

AMB Express 2021

Bordel S, van Spanning RJM and Santos-Beneit F.

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

Mol Syst Biol 2021

Konstantinidis D, Pereira F, Geissen EM, Grkovska K, Kafkia E, Jouhten P, Kim Y, Devendran S, Zimmermann M and Patil KR.

Transcriptomic and Metabolic Network Analysis of Metabolic Reprogramming and IGF-1 Modulation in SCA3 Transgenic Mice

Int J Mol Sci 2021

Lin YT, Lin YS, Cheng WL, Chang JC, Chao YC, Liu CS and Wei AC.

Integrated human/SARS-CoV-2 metabolic models present novel treatment strategies against COVID-19

Life Sci Alliance 2021

Bannerman BP, Júlvez J, Oarga A, Blundell TL, Moreno P and Floto RA.

Genome-Scale Metabolic Models and Machine Learning Reveal Genetic Determinants of Antibiotic Resistance in Escherichia coli and Unravel the Underlying Metabolic Adaptation Mechanisms

MSystems 2021

Pearcy N, Hu Y, Baker M, Maciel-Guerra A, Xue N, Wang W, Kaler J, Peng Z, Li F and Dottorini T.

Potential inhibitors of the main protease of SARS-CoV-2 and modulators of arachidonic acid pathway: Non-steroidal anti-inflammatory drugs against COVID-19

Comput Biol Med 2021

Sisakht M, Solhjoo A, Mahmoodzadeh A, Fathalipour M, Kabiri M and Sakhteman A.

PolyRound: Polytope rounding for random sampling in metabolic networks

Bioinformatics 2021

Theorell A, Jadebeck JF, Nöh K and Stelling J.

Public good exploitation in natural bacterioplankton communities

Sci Adv 2021

Pollak S, Gralka M, Sato Y, Schwartzman J, Lu L and Cordero OX.

Genome-scale metabolic modeling reveals key features of a minimal gene set

Mol Syst Biol 2021

Lachance JC, Matteau D, Brodeur J, Lloyd CJ, Mih N, King ZA, Knight TF, Feist AM, Monk JM, Palsson BO, Jacques PÉ and Rodrigue S.

Stoichiometric Modeling of Artificial String Chemistries Reveals Constraints on Metabolic Network Structure

J Mol Evol 2021

Moyer D, Pacheco AR, Bernstein DB and Segrè D.

Enhancing Sesquiterpenoid Production from Methane via Synergy of the Methylerythritol Phosphate Pathway and a Short-Cut Route to 1-Deoxy-D-xylulose 5-Phosphate in Methanotrophic Bacteria

Microorganisms 2021

Nguyen AD, Pham DN, Chau THT and Lee EY.

Synthetic Formatotrophs for One-Carbon Biorefinery

Adv Sci (Weinh) 2021

Bang J, Ahn JH, Lee JA, Hwang CH, Kim GB, Lee J and Lee SY.

Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus

NPJ Syst Biol Appl 2021

Renz A and Dräger A.

Dissecting the Fitness Costs of Complex Mutations

Mol Biol Evol 2021

Yubero P and Poyatos JF.

Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth

PLoS Comput Biol 2021

Lloyd CJ, Monk J, Yang L, Ebrahim A and Palsson BO.

Multi-omics Study of Planobispora rosea, Producer of the Thiopeptide Antibiotic GE2270A

MSystems 2021

Del Carratore F, Iorio M, Pérez-Bonilla M, Schmidt K, Pérez-Redondo R, Sosio M, Macdonald SJ, Gyulev IS, Tsigkinopoulou A, Thomas GH, Genilloud O, Rodríguez-García A, Donadio S, Breitling R and Takano E.

The LASER database: Formalizing design rules for metabolic engineering

Metab Eng Commun 2021

Winkler JD, Halweg-Edwards AL and Gill RT.

Non-natural Aldol Reactions Enable the Design and Construction of Novel One-Carbon Assimilation Pathways in vitro

Front Microbiol 2021

Mao Y, Yuan Q, Yang X, Liu P, Cheng Y, Luo J, Liu H, Yao Y, Sun H, Cai T and Ma H.

Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals

PLoS Comput Biol 2021

Bekiaris PS and Klamt S.

Inclusion of maintenance energy improves the intracellular flux predictions of CHO

PLoS Comput Biol 2021

Széliová D, Štor J, Thiel I, Weinguny M, Hanscho M, Lhota G, Borth N, Zanghellini J, Ruckerbauer DE and Rocha I.

RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats

Nucleic Acids Res 2021

Shaikh B, Marupilla G, Wilson M, Blinov ML, Moraru II and Karr JR.

First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies

Metabolites 2021

Renz A, Widerspick L and Dräger A.

An integrative drug repositioning framework discovered a potential therapeutic agent targeting COVID-19

Signal Transduct Target Ther 2021

Ge Y, Tian T, Huang S, Wan F, Li J, Li S, Wang X, Yang H, Hong L, Wu N, Yuan E, Luo Y, Cheng L, Hu C, Lei Y, Shu H, Feng X, Jiang Z, Wu Y, Chi Y, Guo X, Cui L, Xiao L, Li Z, Yang C, Miao Z, Chen L, Li H, Zeng H, Zhao D, Zhu F, Shen X and Zeng J.

Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments

Elife 2021

Estrela S, Sanchez-Gorostiaga A, Vila JC and Sanchez A.

Analysis of metabolic network disruption in engineered microbial hosts due to enzyme promiscuity

Metab Eng Commun 2021

Porokhin V, Amin SA, Nicks TB, Gopinarayanan VE, Nair NU and Hassoun S.

Simultaneous Integration of Gene Expression and Nutrient Availability for Studying the Metabolism of Hepatocellular Carcinoma Cell Lines

Biomolecules 2021

Weglarz-Tomczak E, Mondeel TDGA, Piebes DGE and Westerhoff HV.

Genome-scale metabolic model of the diatom Thalassiosira pseudonana highlights the importance of nitrogen and sulfur metabolism in redox balance

PLoS One 2021

van Tol HM and Armbrust EV.

Probabilistic Thermodynamic Analysis of Metabolic Networks

Bioinformatics 2021

Gollub MG, Kaltenbach HM and Stelling J.

Complex yeast-bacteria interactions affect the yield of industrial ethanol fermentation

Nat Commun 2021

Senne de Oliveira Lino F, Bajic D, Vila JCC, Sánchez A and Sommer MOA.

multiTFA: a python package for multi-variate thermodynamics-based flux analysis

Bioinformatics 2021

Mahamkali V, McCubbin T, Beber ME, Noor E, Ma E, Marcellin LK and Nielsen LK.

The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases

Metabolites 2021

Koblitz J, Will SE, Riemer SA, Ulas T, Neumann-Schaal M and Schomburg D.

Development of a Genome-Scale Metabolic Model and Phenome Analysis of the Probiotic Escherichia coli Strain Nissle 1917

Int J Mol Sci 2021

Kim D, Kim Y and Yoon SH.

Multiomics Data Collection, Visualization, and Utilization for Guiding Metabolic Engineering

Front Bioeng Biotechnol 2021

Roy S, Radivojevic T, Forrer M, Marti JM, Jonnalagadda V, Backman T, Morrell W, Plahar H, Kim J, Hillson N and Garcia Martin H.

Dynamic Allocation of Carbon Storage and Nutrient-Dependent Exudation in a Revised Genome-Scale Model of Prochlorococcus

Front Genet 2021

Ofaim S, Sulheim S, Almaas E, Sher D and Segrè D.

Automatic reconstruction of metabolic pathways from identified biosynthetic gene clusters

BMC Bioinformatics 2021

Sulheim S, Fossheim FA, Wentzel A and Almaas E.

Emergence of diauxie as an optimal growth strategy under resource allocation constraints in cellular metabolism

Proc Natl Acad Sci U S A 2021

Salvy P and Hatzimanikatis V.

Addressing uncertainty in genome-scale metabolic model reconstruction and analysis

Genome Biol 2021

Bernstein DB, Sulheim S, Almaas E and Segrè D.

Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus

MSystems 2021

Wilken SE, Monk JM, Leggieri PA, Lawson CE, Lankiewicz TS, Seppälä S, Daum CG, Jenkins J, Lipzen AM, Mondo SJ, Barry KW, Grigoriev IV, Henske JK, Theodorou MK, Palsson BO, Petzold LR and O'Malley MA.

Multi-Omics Driven Metabolic Network Reconstruction and Analysis of Lignocellulosic Carbon Utilization in Rhodosporidium toruloides

Front Bioeng Biotechnol 2021

Kim J, Coradetti ST, Kim YM, Gao Y, Yaegashi J, Zucker JD, Munoz N, Zink EM, Burnum-Johnson KE, Baker SE, Simmons BA, Skerker JM, Gladden JM and Magnuson JK.

Metabolic Modeling of the C(3)-CAM Continuum Revealed the Establishment of a Starch/Sugar-Malate Cycle in CAM Evolution

Front Plant Sci 2021

Tay IYY, Odang KB and Cheung CYM.

Phenotype and multi-omics comparison of Staphylococcus and Streptococcus uncovers pathogenic traits and predicts zoonotic potential

BMC Genomics 2021

Zondervan NA, Martins Dos Santos VAP, Suarez-Diez M and Saccenti E.

GEM-Based Metabolic Profiling for Human Bone Osteosarcoma under Different Glucose and Glutamine Availability

Int J Mol Sci 2021

Weglarz-Tomczak E, Rijlaarsdam DJ, Tomczak JM and Brul S.

PhenoMapping: a protocol to map cellular phenotypes to metabolic bottlenecks, identify conditional essentiality, and curate metabolic models

STAR Protoc 2021

Chiappino-Pepe A and Hatzimanikatis V.

M2R: a Python add-on to cobrapy for modifying human genome-scale metabolic reconstruction using the gut microbiota models

Bioinformatics 2021

Weglarz-Tomczak E, Tomczak JM and Brul S.

MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics

PLoS Comput Biol 2021

Haiman ZB, Zielinski DC, Koike Y, Yurkovich JT and Palsson BO.

MEWpy: A Computational Strain Optimization Workbench in Python

Bioinformatics 2021

Pereira V, Cruz F and Rocha M.

Evaluating accessibility, usability and interoperability of genome-scale metabolic models for diverse yeasts species

FEMS Yeast Res 2021

Domenzain I, Li F, Kerkhoven EJ and Siewers V.

Total of 76 publications. 😄

FBA reveals guanylate kinase as a potential target for antiviral therapies against SARS-CoV-2

Bioinformatics 2020

Renz A, Widerspick L and Dräger A.

The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale

Microorganisms 2020

Zielinski DC, Patel A and Palsson BO.

A Multi-Scale Approach to Modeling E. coli Chemotaxis

Entropy (Basel) 2020

Agmon E and Spangler RK.

High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies

Front Microbiol 2020

Broddrick JT, Szubin R, Norsigian CJ, Monk JM, Palsson BO and Parenteau MN.

Metabolic flux configuration determination using information entropy

PLoS One 2020

Rivas-Astroza M and Conejeros R.

Acetate and glycerol are not uniquely suited for the evolution of cross-feeding in E. coli

PLoS Comput Biol 2020

San Roman M and Wagner A.

Environmental flexibility does not explain metabolic robustness

NPJ Syst Biol Appl 2020

Libiseller-Egger J, Coltman B, Gerstl MP and Zanghellini J.

Modeling a co-culture of Clostridium autoethanogenum and Clostridium kluyveri to increase syngas conversion to medium-chain fatty-acids

Comput Struct Biotechnol J 2020

Benito-Vaquerizo S, Diender M, Parera Olm I, Martins Dos Santos VAP, Schaap PJ, Sousa DZ and Suarez-Diez M.

Comprehensive Multi-omics Analysis Reveals Mitochondrial Stress as a Central Biological Hub for Spaceflight Impact

Cell 2020

da Silveira WA, Fazelinia H, Rosenthal SB, Laiakis EC, Kim MS, Meydan C, Kidane Y, Rathi KS, Smith SM, Stear B, Ying Y, Zhang Y, Foox J, Zanello S, Crucian B, Wang D, Nugent A, Costa HA, Zwart SR, Schrepfer S, Elworth RAL, Sapoval N, Treangen T, MacKay M, Gokhale NS, Horner SM, Singh LN, Wallace DC, Willey JS, Schisler JC, Meller R, McDonald JT, Fisch KM, Hardiman G, Taylor D, Mason CE, Costes SV and Beheshti A.

The Entner-Doudoroff Pathway Is an Essential Metabolic Route for Methylotuvimicrobium buryatense 5GB1C

Appl Environ Microbiol 2020

He L, Groom JD and Lidstrom ME.

A Distance-Based Framework for the Characterization of Metabolic Heterogeneity in Large Sets of Genome-Scale Metabolic Models

Patterns (N Y) 2020

Cabbia A, Hilbers PAJ and van Riel NAW.

Awakening a latent carbon fixation cycle in Escherichia coli

Nat Commun 2020

Satanowski A, Dronsella B, Noor E, Vögeli B, He H, Wichmann P, Erb TJ, Lindner SN and Bar-Even A.

Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production

Metab Eng Commun 2020

Suthers PF, Dinh HV, Fatma Z, Shen Y, Chan SHJ, Rabinowitz JD, Zhao H and Maranas CD.

Model-driven design allows growth of Mycoplasma pneumoniae on serum-free media

NPJ Syst Biol Appl 2020

Gaspari E, Malachowski A, Garcia-Morales L, Burgos R, Serrano L, Martins Dos Santos VAP and Suarez-Diez M.

Functional reconstitution of a bacterial CO(2) concentrating mechanism in Escherichia coli

Elife 2020

Flamholz AI, Dugan E, Blikstad C, Gleizer S, Ben-Nissan R, Amram S, Antonovsky N, Ravishankar S, Noor E, Bar-Even A, Milo R and Savage DF.

Genome-scale metabolic models highlight stage-specific differences in essential metabolic pathways in Trypanosoma cruzi

PLoS Negl Trop Dis 2020

Shiratsubaki IS, Fang X, Souza ROO, Palsson BO, Silber AM and Siqueira-Neto JL.

Reconstruction and analysis of genome-scale metabolic model of weak Crabtree positive yeast Lachancea kluyveri

Sci Rep 2020

Nanda P, Patra P, Das M and Ghosh A.

Diagnosing and Predicting Mixed-Culture Fermentations with Unicellular and Guild-Based Metabolic Models

MSystems 2020

Scarborough MJ, Hamilton JJ, Erb EA, Donohue TJ and Noguera DR.

Development of a Genome-Scale Metabolic Model of Clostridium thermocellum and Its Applications for Integration of Multi-Omics Datasets and Computational Strain Design

Front Bioeng Biotechnol 2020

Garcia S, Thompson RA, Giannone RJ, Dash S, Maranas CD and Trinh CT.

Reconstructing organisms in silico: genome-scale models and their emerging applications

Nat Rev Microbiol 2020

Fang X, Lloyd CJ and Palsson BO.

Genome-Scale Metabolic Model of Xanthomonas phaseoli pv. manihotis: An Approach to Elucidate Pathogenicity at the Metabolic Level

Front Genet 2020

Botero D, Monk J, Rodríguez Cubillos MJ, Rodríguez Cubillos A, Restrepo M, Bernal-Galeano V, Reyes A, González Barrios A, Palsson BØ, Restrepo S and Bernal A.

Best Practices for Making Reproducible Biochemical Models

Cell Syst 2020

Porubsky VL, Goldberg AP, Rampadarath AK, Nickerson DP, Karr JR and Sauro HM.

Community standards to facilitate development and address challenges in metabolic modeling

Mol Syst Biol 2020

Carey MA, Dräger A, Beber ME, Papin JA and Yurkovich JT.

A steady-state model of microbial acclimation to substrate limitation

PLoS Comput Biol 2020

Casey JR and Follows MJ.

Defining the nutritional input for genome-scale metabolic models: A roadmap

PLoS One 2020

Marinos G, Kaleta C and Waschina S.

Publishing reproducible dynamic kinetic models

Brief Bioinform 2020

Porubsky V, Smith L and Sauro HM.

Modeling the metabolic interplay between a parasitic worm and its bacterial endosymbiont allows the identification of novel drug targets

Elife 2020

Curran DM, Grote A, Nursimulu N, Geber A, Voronin D, Jones DR, Ghedin E and Parkinson J.

In silico co-factor balance estimation using constraint-based modelling informs metabolic engineering in Escherichia coli

PLoS Comput Biol 2020

de Arroyo Garcia L and Jones PR.

A quantitative method for proteome reallocation using minimal regulatory interventions

Nat Chem Biol 2020

Lastiri-Pancardo G, Mercado-Hernández JS, Kim J, Jiménez JI and Utrilla J.

A Genome-Scale Metabolic Model of 2,3-Butanediol Production by Thermophilic Bacteria Geobacillus icigianus

Microorganisms 2020

Kulyashov M, Peltek SE and Akberdin IR.

Revealing 29 sets of independently modulated genes in Staphylococcus aureus, their regulators, and role in key physiological response

Proc Natl Acad Sci U S A 2020

Poudel S, Tsunemoto H, Seif Y, Sastry AV, Szubin R, Xu S, Machado H, Olson CA, Anand A, Pogliano J, Nizet V and Palsson BO.

A comparison of Monte Carlo sampling methods for metabolic network models

PLoS One 2020

Fallahi S, Skaug HJ and Alendal G.

Plasma metabolome and cognitive skills in Down syndrome

Sci Rep 2020

Antonaros F, Ghini V, Pulina F, Ramacieri G, Cicchini E, Mannini E, Martelli A, Feliciello A, Lanfranchi S, Onnivello S, Vianello R, Locatelli C, Cocchi G, Pelleri MC, Vitale L, Strippoli P, Luchinat C, Turano P, Piovesan A and Caracausi M.

Synthesizing Systems Biology Knowledge from Omics Using Genome-Scale Models

Proteomics 2020

Dahal S, Yurkovich JT, Xu H, Palsson BO and Yang L.

Metabolic role of pyrophosphate-linked phosphofructokinase pfk for C1 assimilation in Methylotuvimicrobium alcaliphilum 20Z

Microb Cell Fact 2020

Nguyen AD, Nam G, Kim D and Lee EY.

Simulating the evolutionary trajectories of metabolic pathways for insect symbionts in the genus Sodalis

Microb Genom 2020

Hall RJ, Thorpe S, Thomas GH and Wood AJ.

A biochemically-interpretable machine learning classifier for microbial GWAS

Nat Commun 2020

Kavvas ES, Yang L, Monk JM, Heckmann D and Palsson BO.

Fluxer: a web application to compute, analyze and visualize genome-scale metabolic flux networks

Nucleic Acids Res 2020

Hari A and Lobo D.

Distinct actions of the fermented beverage kefir on host behaviour, immunity and microbiome gut-brain modules in the mouse

Microbiome 2020

van de Wouw M, Walsh AM, Crispie F, van Leuven L, Lyte JM, Boehme M, Clarke G, Dinan TG, Cotter PD and Cryan JF.

Adaptive laboratory evolution enhances methanol tolerance and conversion in engineered Corynebacterium glutamicum

Commun Biol 2020

Wang Y, Fan L, Tuyishime P, Liu J, Zhang K, Gao N, Zhang Z, Ni X, Feng J, Yuan Q, Ma H, Zheng P, Sun J and Ma Y.

Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions

PLoS Comput Biol 2020

Medlock GL, Moutinho TJ and Papin JA.

Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis

Cell Rep 2020

Peterson EJR, Abidi AA, Arrieta-Ortiz ML, Aguilar B, Yurkovich JT, Kaur A, Pan M, Srinivas V, Shmulevich I and Baliga NS.

Enhanced succinic acid production by Mannheimia employing optimal malate dehydrogenase

Nat Commun 2020

Ahn JH, Seo H, Park W, Seok J, Lee JA, Kim WJ, Kim GB, Kim KJ and Lee SY.

Flux-based hierarchical organization of Escherichia coli's metabolic network

PLoS Comput Biol 2020

Robaina-Estévez S and Nikoloski Z.

Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments

PLoS Comput Biol 2020

Jenior ML, Moutinho TJ Jr, Dougherty BV and Papin JA.

Genome sequence of the potential probiotic eukaryote Saccharomyces cerevisiae KCCM 51299

3 Biotech 2020

Hwang J, Bang I, Kim D, Shin SC, Chin YW, Kim TW and Kim HJ.

Genome-Scale Metabolic Model Reconstruction and in Silico Investigations of Methane Metabolism in Methylosinus trichosporium OB3b

Microorganisms 2020

Naizabekov S and Lee EY.

Model-based integration of genomics and metabolomics reveals SNP functionality in Mycobacterium tuberculosis

Proc Natl Acad Sci U S A 2020

Øyås O, Borrell S, Trauner A, Zimmermann M, Feldmann J, Liphardt T, Gagneux S, Stelling J, Sauer U and Zampieri M.

Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen

Front Genet 2020

Jensen CS, Norsigian CJ, Fang X, Nielsen XC, Christensen JJ, Palsson BO and Monk JM.

MEMOTE for standardized genome-scale metabolic model testing

Nat Biotechnol 2020

Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, Feist AM, Fengos G, Fleming RMT, García-Jiménez B, Hatzimanikatis V, van Helvoirt W, Henry CS, Hermjakob H, Herrgård MJ, Kaafarani A, Kim HU, King Z, Klamt S, Klipp E, Koehorst JJ, König M, Lakshmanan M, Lee DY, Lee SY, Lee S, Lewis NE, Liu F, Ma H, Machado D, Mahadevan R, Maia P, Mardinoglu A, Medlock GL, Monk JM, Nielsen J, Nielsen LK, Nogales J, Nookaew I, Palsson BO, Papin JA, Patil KR, Poolman M, Price ND, Resendis-Antonio O, Richelle A, Rocha I, Sánchez BJ, Schaap PJ, Malik Sheriff RS, Shoaie S, Sonnenschein N, Teusink B, Vilaça P, Vik JO, Wodke JAH, Xavier JC, Yuan Q, Zakhartsev M and Zhang C.

LK-DFBA: a linear programming-based modeling strategy for capturing dynamics and metabolite-dependent regulation in metabolism

BMC Bioinformatics 2020

Dromms RA, Lee JY and Styczynski MP.

Setup of a scientific computing environment for computational biology: Simulation of a genome-scale metabolic model of Escherichia coli as an example

J Microbiol 2020

Jeon J and Kim HU.

FastMM: an efficient toolbox for personalized constraint-based metabolic modeling

BMC Bioinformatics 2020

Li GH, Dai S, Han F, Li W, Huang J and Xiao W.

Metabolic Analyses of Nitrogen Fixation in the Soybean Microsymbiont Sinorhizobium fredii Using Constraint-Based Modeling

MSystems 2020

Contador CA, Lo SK, Chan SHJ and Lam HM.

In Vivo Rate of Formaldehyde Condensation with Tetrahydrofolate

Metabolites 2020

He H, Noor E, Ramos-Parra PA, García-Valencia LE, Patterson JA, Díaz de la Garza RI, Hanson AD and Bar-Even A.

MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota

MSystems 2020

Diener C, Gibbons SM and Resendis-Antonio O.

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

Nat Commun 2020

Salvy P and Hatzimanikatis V.

Automatic construction of metabolic models with enzyme constraints

BMC Bioinformatics 2020

Bekiaris PS and Klamt S.

Guiding the Refinement of Biochemical Knowledgebases with Ensembles of Metabolic Networks and Machine Learning

Cell Syst 2020

Medlock GL and Papin JA.

Genome-Scale Metabolic Reconstruction of Acetobacter pasteurianus 386B, a Candidate Functional Starter Culture for Cocoa Bean Fermentation

Front Microbiol 2020

Pelicaen R, Gonze D, Teusink B, De Vuyst L and Weckx S.

Gapsplit: efficient random sampling for non-convex constraint-based models

Bioinformatics 2020

Keaty TC and Jensen PA.

Total of 61 publications. 😄

A workflow for generating multi-strain genome-scale metabolic models of prokaryotes

Nat Protoc 2019

Norsigian CJ, Fang X, Seif Y, Monk JM and Palsson BO.

Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection

PLoS Comput Biol 2019

Yan J, Estanbouli H, Liao C, Kim W, Monk JM, Rahman R, Kamboj M, Palsson BO, Qiu W and Xavier JB.

SAMMI: a semi-automated tool for the visualization of metabolic networks

Bioinformatics 2019

Schultz A and Akbani R.

Harnessing the intracellular triacylglycerols for titer improvement of polyketides in Streptomyces

Nat Biotechnol 2019

Wang W, Li S, Li Z, Zhang J, Fan K, Tan G, Ai G, Lam SM, Shui G, Yang Z, Lu H, Jin P, Li Y, Chen X, Xia X, Liu X, Dannelly HK, Yang C, Yang Y, Zhang S, Alterovitz G, Xiang W and Zhang L.

Conversion of Escherichia coli to Generate All Biomass Carbon from CO(2)

Cell 2019

Gleizer S, Ben-Nissan R, Bar-On YM, Antonovsky N, Noor E, Zohar Y, Jona G, Krieger E, Shamshoum M, Bar-Even A and Milo R.

Genome-Scale Metabolic Networks Shed Light on the Carotenoid Biosynthesis Pathway in the Brown Algae Saccharina japonica and Cladosiphon okamuranus

Antioxidants (Basel) 2019

Nègre D, Aite M, Belcour A, Frioux C, Brillet-Guéguen L, Liu X, Bordron P, Godfroy O, Lipinska AP, Leblanc C, Siegel A, Dittami SM, Corre E and Markov GV.

Application of a genome-scale model in tandem with enzyme assays for identification of metabolic signatures of high and low CHO cell producers

Metab Eng Commun 2019

Calmels C, Arnoult S, Ben Yahia B, Malphettes L and Andersen MR.

A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data

Metab Eng Commun 2019

Dinh HV, Suthers PF, Chan SHJ, Shen Y, Xiao T, Deewan A, Jagtap SS, Zhao H, Rao CV, Rabinowitz JD and Maranas CD.

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

Microb Cell Fact 2019

Kristjansdottir T, Bosma EF, Branco Dos Santos F, Özdemir E, Herrgård MJ, França L, Ferreira B, Nielsen AT and Gudmundsson S.

Metabolite-mediated modelling of microbial community dynamics captures emergent behaviour more effectively than species-species modelling

J R Soc Interface 2019

Brunner JD and Chia N.

In silico-guided engineering of Pseudomonas putida towards growth under micro-oxic conditions

Microb Cell Fact 2019

Kampers LFC, van Heck RGA, Donati S, Saccenti E, Volkers RJM, Schaap PJ, Suarez-Diez M, Nikel PI and Martins Dos Santos VAP.

Effects of MCHM on yeast metabolism

PLoS One 2019

Pupo A, Ku KM and Gallagher JEG.

Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom

Nat Commun 2019

Smith SR, Dupont CL, McCarthy JK, Broddrick JT, Oborník M, Horák A, Füssy Z, Cihlář J, Kleessen S, Zheng H, McCrow JP, Hixson KK, Araújo WL, Nunes-Nesi A, Fernie A, Nikoloski Z, Palsson BO and Allen AE.

RetSynth: determining all optimal and sub-optimal synthetic pathways that facilitate synthesis of target compounds in chassis organisms

BMC Bioinformatics 2019

Whitmore LS, Nguyen B, Pinar A, George A and Hudson CM.

p13CMFA: Parsimonious 13C metabolic flux analysis

PLoS Comput Biol 2019

Foguet C, Jayaraman A, Marin S, Selivanov VA, Moreno P, Messeguer R, de Atauri P and Cascante M.

Gene connectivity and enzyme evolution in the human metabolic network

Biol Direct 2019

Dobon B, Montanucci L, Peretó J, Bertranpetit J and Laayouni H.

Flux sampling is a powerful tool to study metabolism under changing environmental conditions

NPJ Syst Biol Appl 2019

Herrmann HA, Dyson BC, Vass L, Johnson GN and Schwartz JM.

A systems biology approach for studying Wolbachia metabolism reveals points of interaction with its host in the context of arboviral infection

PLoS Negl Trop Dis 2019

Jiménez NE, Gerdtzen ZP, Olivera-Nappa Á, Salgado JC and Conca C.

Systems Biology and Pangenome of Salmonella O-Antigens

MBio 2019

Seif Y, Monk JM, Machado H, Kavvas E and Palsson BO.

Simulation of heterosis in a genome-scale metabolic network provides mechanistic explanations for increased biomass production rates in hybrid plants

NPJ Syst Biol Appl 2019

Vacher M and Small I.

FindTargetsWEB: A User-Friendly Tool for Identification of Potential Therapeutic Targets in Metabolic Networks of Bacteria

Front Genet 2019

Merigueti TC, Carneiro MW, Carvalho-Assef APD, Silva-Jr FP and da Silva FAB.

Human Systems Biology and Metabolic Modelling: A Review-From Disease Metabolism to Precision Medicine

Biomed Res Int 2019

Angione C.

Closing the gap between formats for storing layout information in systems biology

Brief Bioinform 2019

Hoksza D, Gawron P, Ostaszewski M, Hasenauer J and Schneider R.

A mass and charge balanced metabolic model of Setaria viridis revealed mechanisms of proton balancing in C4 plants

BMC Bioinformatics 2019

Shaw R and Cheung CYM.

Predicting Metabolism from Gene Expression in an Improved Whole-Genome Metabolic Network Model of Danio rerio

Zebrafish 2019

van Steijn L, Verbeek FJ, Spaink HP and Merks RMH.

Leaf Energy Balance Requires Mitochondrial Respiration and Export of Chloroplast NADPH in the Light

Plant Physiol 2019

Shameer S, Ratcliffe RG and Sweetlove LJ.

Identification of critical connectors in the directed reaction-centric graphs of microbial metabolic networks

BMC Bioinformatics 2019

Kim EY, Ashlock D and Yoon SH.

Reconstruction of a Genome Scale Metabolic Model of the polyhydroxybutyrate producing methanotroph Methylocystis parvus OBBP

Microb Cell Fact 2019

Bordel S, Rojas A and Muñoz R.

A Genome-Scale Metabolic Model of Soybean (Glycine max) Highlights Metabolic Fluxes in Seedlings

Plant Physiol 2019

Moreira TB, Shaw R, Luo X, Ganguly O, Kim HS, Coelho LGF, Cheung CYM and Rhys Williams TC.

Dataset of differential gene expression between total normal human thyroid and histologically normal thyroid adjacent to papillary thyroid carcinoma

Data Brief 2019

Vitale L, Piovesan A, Antonaros F, Strippoli P, Pelleri MC and Caracausi M.

Approaches to Computational Strain Design in the Multiomics Era

Front Microbiol 2019

St John PC and Bomble YJ.

BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data

PLoS Comput Biol 2019

Lachance JC, Lloyd CJ, Monk JM, Yang L, Sastry AV, Seif Y, Palsson BO, Rodrigue S, Feist AM, King ZA and Jacques PÉ.

Core Metabolism Shifts during Growth on Methanol versus Methane in the Methanotroph Methylomicrobium buryatense 5GB1

MBio 2019

Fu Y, He L, Reeve J, Beck DAC and Lidstrom ME.

Enzyme promiscuity shapes adaptation to novel growth substrates

Mol Syst Biol 2019

Guzmán GI, Sandberg TE, LaCroix RA, Nyerges Á, Papp H, de Raad M, King ZA, Hefner Y, Northen TR, Notebaart RA, Pál C, Palsson BO, Papp B and Feist AM.

Emergent Subpopulation Behavior Uncovered with a Community Dynamic Metabolic Model of Escherichia coli Diauxic Growth

MSystems 2019

Succurro A, Segrè D and Ebenhöh O.

Coupling S-adenosylmethionine-dependent methylation to growth: Design and uses

PLoS Biol 2019

Luo H, Hansen ASL, Yang L, Schneider K, Kristensen M, Christensen U, Christensen HB, Du B, Özdemir E, Feist AM, Keasling JD, Jensen MK, Herrgård MJ and Palsson BO.

Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen

PLoS Comput Biol 2019

Liu JK, Lloyd C, Al-Bassam MM, Ebrahim A, Kim JN, Olson C, Aksenov A, Dorrestein P and Zengler K.

The genetic basis for adaptation of model-designed syntrophic co-cultures

PLoS Comput Biol 2019

Lloyd CJ, King ZA, Sandberg TE, Hefner Y, Olson CA, Phaneuf PV, O'Brien EJ, Sanders JG, Salido RA, Sanders K, Brennan C, Humphrey G, Knight R and Feist AM.

Maximum entropy and population heterogeneity in continuous cell cultures

PLoS Comput Biol 2019

Fernandez-de-Cossio-Diaz J and Mulet R.

Multi-Omics and Genome-Scale Modeling Reveal a Metabolic Shift During C. elegans Aging

Front Mol Biosci 2019

Hastings J, Mains A, Virk B, Rodriguez N, Murdoch S, Pearce J, Bergmann S, Le Novère N and Casanueva O.

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

Nat Protoc 2019

Heirendt L, Arreckx S, Pfau T, Mendoza SN, Richelle A, Heinken A, Haraldsdóttir HS, Wachowiak J, Keating SM, Vlasov V, Magnusdóttir S, Ng CY, Preciat G, Žagare A, Chan SHJ, Aurich MK, Clancy CM, Modamio J, Sauls JT, Noronha A, Bordbar A, Cousins B, El Assal DC, Valcarcel LV, Apaolaza I, Ghaderi S, Ahookhosh M, Ben Guebila M, Kostromins A, Sompairac N, Le HM, Ma D, Sun Y, Wang L, Yurkovich JT, Oliveira MAP, Vuong PT, El Assal LP, Kuperstein I, Zinovyev A, Hinton HS, Bryant WA, Aragón Artacho FJ, Planes FJ, Stalidzans E, Maass A, Vempala S, Hucka M, Saunders MA, Maranas CD, Lewis NE, Sauter T, Palsson BØ, Thiele I and Fleming RMT.

Gsmodutils: a python based framework for test-driven genome scale metabolic model development

Bioinformatics 2019

Gilbert J, Pearcy N, Norman R, Millat T, Winzer K, King J, Hodgman C, Minton N and Twycross J.

ModelExplorer - software for visual inspection and inconsistency correction of genome-scale metabolic reconstructions

BMC Bioinformatics 2019

Martyushenko N and Almaas E.

Essential metabolism for a minimal cell

Elife 2019

Breuer M, Earnest TM, Merryman C, Wise KS, Sun L, Lynott MR, Hutchison CA, Smith HO, Lapek JD, Gonzalez DJ, de Crécy-Lagard V, Haas D, Hanson AD, Labhsetwar P, Glass JI and Luthey-Schulten Z.

Machine learning framework for assessment of microbial factory performance

PLoS One 2019

Oyetunde T, Liu D, Martin HG and Tang YJ.

Cross-compartment metabolic coupling enables flexible photoprotective mechanisms in the diatom Phaeodactylum tricornutum

New Phytol 2019

Broddrick JT, Du N, Smith SR, Tsuji Y, Jallet D, Ware MA, Peers G, Matsuda Y, Dupont CL, Mitchell BG, Palsson BO and Allen AE.

A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types

PLoS Comput Biol 2019

Seif Y, Monk JM, Mih N, Tsunemoto H, Poudel S, Zuniga C, Broddrick J, Zengler K and Palsson BO.

An interspecies malate-pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community

ISME J 2019

Wang PH, Correia K, Ho HC, Venayak N, Nemr K, Flick R, Mahadevan R and Edwards EA.

Total of 48 publications. 😄

A Genome-Scale Metabolic Model for Methylococcus capsulatus (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase

Front Microbiol 2018

Lieven C, Petersen LAH, Jørgensen SB, Gernaey KV, Herrgard MJ and Sonnenschein N.

Reframing gene essentiality in terms of adaptive flexibility

BMC Syst Biol 2018

Guzmán GI, Olson CA, Hefner Y, Phaneuf PV, Catoiu E, Crepaldi LB, Micas LG, Palsson BO and Feist AM.

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

Bioinformatics 2018

Salvy P, Fengos G, Ataman M, Pathier T, Soh KC and Hatzimanikatis V.

MoVE identifies metabolic valves to switch between phenotypic states

Nat Commun 2018

Venayak N, von Kamp A, Klamt S and Mahadevan R.

A genome-scale metabolic model of potato late blight suggests a photosynthesis suppression mechanism

BMC Genomics 2018

Botero K, Restrepo S and Pinzón A.

Predicting the metabolic capabilities of Synechococcus elongatus PCC 7942 adapted to different light regimes

Metab Eng 2018

Broddrick JT, Welkie DG, Jallet D, Golden SS, Peers G and Palsson BO.

Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient

Front Microbiol 2018

Fang X, Monk JM, Nurk S, Akseshina M, Zhu Q, Gemmell C, Gianetto-Hill C, Leung N, Szubin R, Sanders J, Beck PL, Li W, Sandborn WJ, Gray-Owen SD, Knight R, Allen-Vercoe E, Palsson BO and Smarr L.

FLYCOP: metabolic modeling-based analysis and engineering microbial communities

Bioinformatics 2018

García-Jiménez B, García JL and Nogales J.

The EcoCyc Database

EcoSal Plus 2018

Karp PD, Ong WK, Paley S, Billington R, Caspi R, Fulcher C, Kothari A, Krummenacker M, Latendresse M, Midford PE, Subhraveti P, Gama-Castro S, Muñiz-Rascado L, Bonavides-Martinez C, Santos-Zavaleta A, Mackie A, Collado-Vides J, Keseler IM and Paulsen I.

Identification of growth-coupled production strains considering protein costs and kinetic variability

Metab Eng Commun 2018

Dinh HV, King ZA, Palsson BO and Feist AM.

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

PLoS Comput Biol 2018

Wang H, Marcišauskas S, Sánchez BJ, Domenzain I, Hermansson D, Agren R, Nielsen J and Kerkhoven EJ.

A community-driven reconstruction of the Aspergillus niger metabolic network

Fungal Biol Biotechnol 2018

Brandl J, Aguilar-Pontes MV, Schäpe P, Noerregaard A, Arvas M, Ram AFJ, Meyer V, Tsang A, de Vries RP and Andersen MR.

Escher-FBA: a web application for interactive flux balance analysis

BMC Syst Biol 2018

Rowe E, Palsson BO and King ZA.

Role of phosphate limitation and pyruvate decarboxylase in rewiring of the metabolic network for increasing flux towards isoprenoid pathway in a TATA binding protein mutant of Saccharomyces cerevisiae

Microb Cell Fact 2018

Wadhwa M, Srinivasan S, Bachhawat AK and Venkatesh KV.

Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3)

PLoS One 2018

Kim H, Kim S and Yoon SH.

A Prospective Study on the Fermentation Landscape of Gaseous Substrates to Biorenewables Using Methanosarcina acetivorans Metabolic Model

Front Microbiol 2018

Nazem-Bokaee H and Maranas CD.

Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota

Cell Syst 2018

Medlock GL, Carey MA, McDuffie DG, Mundy MB, Giallourou N, Swann JR, Kolling GL and Papin JA.

An enormous potential for niche construction through bacterial cross-feeding in a homogeneous environment

PLoS Comput Biol 2018

San Roman M and Wagner A.

A Dynamic Multi-Tissue Flux Balance Model Captures Carbon and Nitrogen Metabolism and Optimal Resource Partitioning During Arabidopsis Growth

Front Plant Sci 2018

Shaw R and Cheung CYM.

Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism

BMC Genomics 2018

Amara A, Takano E and Breitling R.

COBRAme: A computational framework for genome-scale models of metabolism and gene expression

PLoS Comput Biol 2018

Lloyd CJ, Ebrahim A, Yang L, King ZA, Catoiu E, O'Brien EJ, Liu JK and Palsson BO.

DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems

BMC Syst Biol 2018

Smith RW, van Rosmalen RP, Martins Dos Santos VAP and Fleck C.

Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology

PLoS Comput Biol 2018

Medley JK, Choi K, König M, Smith L, Gu S, Hellerstein J, Sealfon SC and Sauro HM.

Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa

BMC Syst Biol 2018

Fang X, Monk JM, Mih N, Du B, Sastry AV, Kavvas E, Seif Y, Smarr L and Palsson BO.

Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models

PLoS Comput Biol 2018

Aite M, Chevallier M, Frioux C, Trottier C, Got J, Cortés MP, Mendoza SN, Carrier G, Dameron O, Guillaudeux N, Latorre M, Loira N, Markov GV, Maass A and Siegel A.

Constraint based modeling of metabolism allows finding metabolic cancer hallmarks and identifying personalized therapeutic windows

Oncotarget 2018

Bordel S.

iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE

Front Genet 2018

Norsigian CJ, Kavvas E, Seif Y, Palsson BO and Monk JM.

Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions

BMC Syst Biol 2018

Kavvas ES, Seif Y, Yurkovich JT, Norsigian C, Poudel S, Greenwald WW, Ghatak S, Palsson BO and Monk JM.

Review of Statistical Learning Methods in Integrated Omics Studies (An Integrated Information Science)

Bioinform Biol Insights 2018

Zeng ISL and Lumley T.

Quantifying complexity in metabolic engineering using the LASER database

Metab Eng Commun 2018

Winkler JD, Halweg-Edwards AL and Gill RT.

Plasma and urinary metabolomic profiles of Down syndrome correlate with alteration of mitochondrial metabolism

Sci Rep 2018

Caracausi M, Ghini V, Locatelli C, Mericio M, Piovesan A, Antonaros F, Pelleri MC, Vitale L, Vacca RA, Bedetti F, Mimmi MC, Luchinat C, Turano P, Strippoli P and Cocchi G.

ssbio: a Python framework for structural systems biology

Bioinformatics 2018

Mih N, Brunk E, Chen K, Catoiu E, Sastry A, Kavvas E, Monk JM, Zhang Z and Palsson BO.

Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP

Nucleic Acids Res 2018

Kim D, Seo SW, Gao Y, Nam H, Guzman GI, Cho BK and Palsson BO.

Prediction of reaction knockouts to maximize succinate production by Actinobacillus succinogenes

PLoS One 2018

Nag A, St John PC, Crowley MF and Bomble YJ.

Model-driven design of a minimal medium for Akkermansia muciniphila confirms mucus adaptation

Microb Biotechnol 2018

van der Ark KCH, Aalvink S, Suarez-Diez M, Schaap PJ, de Vos WM and Belzer C.

Analysis of Piscirickettsia salmonis Metabolism Using Genome-Scale Reconstruction, Modeling, and Testing

Front Microbiol 2018

Cortés MP, Mendoza SN, Travisany D, Gaete A, Siegel A, Cambiazo V and Maass A.

One-step fermentative production of aromatic polyesters from glucose by metabolically engineered Escherichia coli strains

Nat Commun 2018

Yang JE, Park SJ, Kim WJ, Kim HJ, Kim BJ, Lee H, Shin J and Lee SY.

Genome scale metabolic models as tools for drug design and personalized medicine

PLoS One 2018

Raškevičius V, Mikalayeva V, Antanavičiūtė I, Ceslevičienė I, Skeberdis VA, Kairys V and Bordel S.

Constraining Genome-Scale Models to Represent the Bow Tie Structure of Metabolism for (13)C Metabolic Flux Analysis

Metabolites 2018

Backman TWH, Ando D, Singh J, Keasling JD and García Martín H.

Total of 39 publications. 😄

In Silico Analysis of the Small Molecule Content of Outer Membrane Vesicles Produced by Bacteroides thetaiotaomicron Indicates an Extensive Metabolic Link between Microbe and Host

Front Microbiol 2017

Bryant WA, Stentz R, Le Gall G, Sternberg MJE, Carding SR and Wilhelm T.

Emerging whole-cell modeling principles and methods

Curr Opin Biotechnol 2017

Goldberg AP, Szigeti B, Chew YH, Sekar JA, Roth YD and Karr JR.

Determinism and Contingency Shape Metabolic Complementation in an Endosymbiotic Consortium

Front Microbiol 2017

Ponce-de-Leon M, Tamarit D, Calle-Espinosa J, Mori M, Latorre A, Montero F and Pereto J.

Characterizing steady states of genome-scale metabolic networks in continuous cell cultures

PLoS Comput Biol 2017

Fernandez-de-Cossio-Diaz J, Leon K and Mulet R.

Oxygen-limited metabolism in the methanotroph Methylomicrobium buryatense 5GB1C

PeerJ 2017

Gilman A, Fu Y, Hendershott M, Chu F, Puri AW, Smith AL, Pesesky M, Lieberman R, Beck DAC and Lidstrom ME.

Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks

PeerJ 2017

Laniau J, Frioux C, Nicolas J, Baroukh C, Cortes MP, Got J, Trottier C, Eveillard D and Siegel A.

Genome-wide characterization of Phytophthora infestans metabolism: a systems biology approach

Mol Plant Pathol 2017

Rodenburg SYA, Seidl MF, de Ridder D and Govers F.

Genome-Scale Architecture of Small Molecule Regulatory Networks and the Fundamental Trade-Off between Regulation and Enzymatic Activity

Cell Rep 2017

Reznik E, Christodoulou D, Goldford JE, Briars E, Sauer U, Segrè D and Noor E.

Population FBA predicts metabolic phenotypes in yeast

PLoS Comput Biol 2017

Labhsetwar P, Melo MCR, Cole JA and Luthey-Schulten Z.

Parametric studies of metabolic cooperativity in Escherichia coli colonies: Strain and geometric confinement effects

PLoS One 2017

Peterson JR, Cole JA and Luthey-Schulten Z.

Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroides

MSystems 2017

Burger BT, Imam S, Scarborough MJ, Noguera DR and Donohue TJ.

Constraint-based modeling identifies new putative targets to fight colistin-resistant A. baumannii infections

Sci Rep 2017

Presta L, Bosi E, Mansouri L, Dijkshoorn L, Fani R and Fondi M.

Metabolic modeling of energy balances in Mycoplasma hyopneumoniae shows that pyruvate addition increases growth rate

Biotechnol Bioeng 2017

Kamminga T, Slagman SJ, Bijlsma JJE, Martins Dos Santos VAP, Suarez-Diez M and Schaap PJ.

QSP Toolbox: Computational Implementation of Integrated Workflow Components for Deploying Multi-Scale Mechanistic Models

AAPS J 2017

Cheng Y, Thalhauser CJ, Smithline S, Pagidala J, Miladinov M, Vezina HE, Gupta M, Leil TA and Schmidt BJ.

DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia

Bioinformatics 2017

Heirendt L, Thiele I and Fleming RMT.

The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism

BMC Bioinformatics 2017

Birkel GW, Ghosh A, Kumar VS, Weaver D, Ando D, Backman TWH, Arkin AP, Keasling JD and Martín HG.

Mackinac: a bridge between ModelSEED and COBRApy to generate and analyze genome-scale metabolic models

Bioinformatics 2017

Mundy M, Mendes-Soares H and Chia N.

Systems approach to characterize the metabolism of liver cancer stem cells expressing CD133

Sci Rep 2017

Hur W, Ryu JY, Kim HU, Hong SW, Lee EB, Lee SY and Yoon SK.

Efficient estimation of the maximum metabolic productivity of batch systems

Biotechnol Biofuels 2017

St John PC, Crowley MF and Bomble YJ.

Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function

Archaea 2017

Thor S, Peterson JR and Luthey-Schulten Z.

Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks

PLoS Comput Biol 2017

Prigent S, Frioux C, Dittami SM, Thiele S, Larhlimi A, Collet G, Gutknecht F, Got J, Eveillard D, Bourdon J, Plewniak F, Tonon T and Siegel A.

Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression

Sci Rep 2017

Ma D, Yang L, Fleming RM, Thiele I, Palsson BO and Saunders MA.

Personalized Prediction of Proliferation Rates and Metabolic Liabilities in Cancer Biopsies

Front Physiol 2017

Diener C and Resendis-Antonio O.

Total of 23 publications. 😄

Community metabolic modeling approaches to understanding the gut microbiome: Bridging biochemistry and ecology

Free Radic Biol Med 2016

Mendes-Soares H and Chia N.

Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis

Proc Natl Acad Sci U S A 2016

Broddrick JT, Rubin BE, Welkie DG, Du N, Mih N, Diamond S, Lee JJ, Golden SS and Palsson BO.

Modelling microbial metabolic rewiring during growth in a complex medium

BMC Genomics 2016

Fondi M, Bosi E, Presta L, Natoli D and Fani R.

Multi-omic data integration enables discovery of hidden biological regularities

Nat Commun 2016

Ebrahim A, Brunk E, Tan J, O'Brien EJ, Kim D, Szubin R, Lerman JA, Lechner A, Sastry A, Bordbar A, Feist AM and Palsson BO.

Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes

Cell Syst 2016

Monk JM, Koza A, Campodonico MA, Machado D, Seoane JM, Palsson BO, Herrgård MJ and Feist AM.

solveME: fast and reliable solution of nonlinear ME models

BMC Bioinformatics 2016

Yang L, Ma D, Ebrahim A, Lloyd CJ, Saunders MA and Palsson BO.

MMinte: an application for predicting metabolic interactions among the microbial species in a community

BMC Bioinformatics 2016

Mendes-Soares H, Mundy M, Soares LM and Chia N.

From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model

Front Microbiol 2016

Cuevas DA, Edirisinghe J, Henry CS, Overbeek R, O'Connell TG and Edwards RA.

Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth Conditions

Plant Physiol 2016

Zuñiga C, Li CT, Huelsman T, Levering J, Zielinski DC, McConnell BO, Long CP, Knoshaug EP, Guarnieri MT, Antoniewicz MR, Betenbaugh MJ and Zengler K.

Integrated In Silico Analysis of Pathway Designs for Synthetic Photo-Electro-Autotrophy

PLoS One 2016

Volpers M, Claassens NJ, Noor E, van der Oost J, de Vos WM, Kengen SW and Martins Dos Santos VA.

Toward Community Standards and Software for Whole-Cell Modeling

IEEE Trans Biomed Eng 2016

Waltemath D, Karr JR, Bergmann FT, Chelliah V, Hucka M, Krantz M, Liebermeister W, Mendes P, Myers CJ, Pir P, Alaybeyoglu B, Aranganathan NK, Baghalian K, Bittig AT, Burke PE, Cantarelli M, Chew YH, Costa RS, Cursons J, Czauderna T, Goldberg AP, Gomez HF, Hahn J, Hameri T, Gardiol DF, Kazakiewicz D, Kiselev I, Knight-Schrijver V, Knupfer C, Konig M, Lee D, Lloret-Villas A, Mandrik N, Medley JK, Moreau B, Naderi-Meshkin H, Palaniappan SK, Priego-Espinosa D, Scharm M, Sharma M, Smallbone K, Stanford NJ, Song JH, Theile T, Tokic M, Tomar N, Toure V, Uhlendorf J, Varusai TM, Watanabe LH, Wendland F, Wolfien M, Yurkovich JT, Zhu Y, Zardilis A, Zhukova A and Schreiber F.

Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity

Proc Natl Acad Sci U S A 2016

Bosi E, Monk JM, Aziz RK, Fondi M, Nizet V and Palsson BØ.

Whole Cell Modeling: From Single Cells to Colonies

Isr J Chem 2016

Cole JA and Luthey-Schulten Z.

Systems biology of the structural proteome

BMC Syst Biol 2016

Brunk E, Mih N, Monk J, Zhang Z, O'Brien EJ, Bliven SE, Chen K, Chang RL, Bourne PE and Palsson BO.

Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements

Proc Natl Acad Sci U S A 2016

Davidi D, Noor E, Liebermeister W, Bar-Even A, Flamholz A, Tummler K, Barenholz U, Goldenfeld M, Shlomi T and Milo R.

What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira

PLoS Negl Trop Dis 2016

Fouts DE, Matthias MA, Adhikarla H, Adler B, Amorim-Santos L, Berg DE, Bulach D, Buschiazzo A, Chang YF, Galloway RL, Haake DA, Haft DH, Hartskeerl R, Ko AI, Levett PN, Matsunaga J, Mechaly AE, Monk JM, Nascimento AL, Nelson KE, Palsson B, Peacock SJ, Picardeau M, Ricaldi JN, Thaipandungpanit J, Wunder EA Jr, Yang XF, Zhang JJ and Vinetz JM.

PSAMM: A Portable System for the Analysis of Metabolic Models

PLoS Comput Biol 2016

Steffensen JL, Dufault-Thompson K and Zhang Y.

Total of 17 publications. 😄

FlexFlux: combining metabolic flux and regulatory network analyses

BMC Syst Biol 2015

Marmiesse L, Peyraud R and Cottret L.

Consistency Analysis of Genome-Scale Models of Bacterial Metabolism: A Metamodel Approach

PLoS One 2015

Ponce-de-Leon M, Calle-Espinosa J, Peretó J and Montero F.

Networks of energetic and metabolic interactions define dynamics in microbial communities

Proc Natl Acad Sci U S A 2015

Embree M, Liu JK, Al-Bassam MM and Zengler K.

Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations

Sci Rep 2015

Aziz RK, Monk JM, Lewis RM, In Loh S, Mishra A, Abhay Nagle A, Satyanarayana C, Dhakshinamoorthy S, Luche M, Kitchen DB, Andrews KA, Fong NL, Li HJ, Palsson BO and Charusanti P.

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

Nucleic Acids Res 2015

Caspi R, Billington R, Ferrer L, Foerster H, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS and Karp PD.

Cell scale host-pathogen modeling: another branch in the evolution of constraint-based methods

Front Microbiol 2015

Jamshidi N and Raghunathan A.

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

Nucleic Acids Res 2015

King ZA, Lu J, Dräger A, Miller P, Federowicz S, Lerman JA, Ebrahim A, Palsson BO and Lewis NE.

Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC

Front Microbiol 2015

Aziz RK, Khaw VL, Monk JM, Brunk E, Lewis R, Loh SI, Mishra A, Nagle AA, Satyanarayana C, Dhakshinamoorthy S, Luche M, Kitchen DB, Andrews KA, Palsson BØ and Charusanti P.

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

PLoS Comput Biol 2015

King ZA, Dräger A, Ebrahim A, Sonnenschein N, Lewis NE and Palsson BO.

Tools for visualization and analysis of molecular networks, pathways, and -omics data

Adv Appl Bioinform Chem 2015

Villaveces JM, Koti P and Habermann BH.

Using Genome-scale Models to Predict Biological Capabilities

Cell 2015

O'Brien EJ, Monk JM and Palsson BO.

Using bioconductor package BiGGR for metabolic flux estimation based on gene expression changes in brain

PLoS One 2015

Gavai AK, Supandi F, Hettling H, Murrell P, Leunissen JA and van Beek JH.

Integration of a constraint-based metabolic model of Brassica napus developing seeds with (13)C-metabolic flux analysis

Front Plant Sci 2015

Hay JO, Shi H, Heinzel N, Hebbelmann I, Rolletschek H and Schwender J.

Total of 13 publications. 😄

Synthetic biology outside the cell: linking computational tools to cell-free systems

Front Bioeng Biotechnol 2014

Lewis DD, Villarreal FD, Wu F and Tan C.

Improving collaboration by standardization efforts in systems biology

Front Bioeng Biotechnol 2014

Dräger A and Palsson BØ.

Current advances in systems and integrative biology

Comput Struct Biotechnol J 2014

Robinson SW, Fernandes M and Husi H.

A genome-scale metabolic flux model of Escherichia coli K-12 derived from the EcoCyc database

BMC Syst Biol 2014

Weaver DS, Keseler IM, Mackie A, Paulsen IT and Karp PD.

A data integration and visualization resource for the metabolic network of Synechocystis sp. PCC 6803

Plant Physiol 2014

Maarleveld TR, Boele J, Bruggeman FJ and Teusink B.

Total of 5 publications. 😄

Sybil--efficient constraint-based modelling in R

BMC Syst Biol 2013

Gelius-Dietrich G, Desouki AA, Fritzemeier CJ and Lercher MJ.

Path2Models: large-scale generation of computational models from biochemical pathway maps

BMC Syst Biol 2013

Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T, Keller R, Mittag F, Schubert M, Glont M, Golebiewski M, van Iersel M, Keating S, Rall M, Wybrow M, Hermjakob H, Hucka M, Kell DB, Müller W, Mendes P, Zell A, Chaouiya C, Saez-Rodriguez J, Schreiber F, Laibe C, Dräger A and Le Novère N.

Solving gap metabolites and blocked reactions in genome-scale models: application to the metabolic network of Blattabacterium cuenoti

BMC Syst Biol 2013

Ponce-de-León M, Montero F and Peretó J.

GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data

Bioinformatics 2013

Schmidt BJ, Ebrahim A, Metz TO, Adkins JN, Palsson BØ and Hyduke DR.

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

BMC Syst Biol 2013

Ebrahim A, Lerman JA, Palsson BO and Hyduke DR.

Total of 5 publications. 😄