Multi-omic data integration and exploiting metabolic models using systems biology approach increase precision in subtyping and early diagnosis of cancer
Spatiotemporal 4D Whole-cell Modeling of a Minimal Autotroph Reveals Central Carbon Metabolism Regulated Locally by Protein Megacomplexes via Post-translational ModiBications under Light Disturbance
BioRxiv 2026
Johnson CGM, Chan A, Rozum J, George A, Parvate AD, Kim DN, Feng S, Bohutskyi P, Johnson Z, Sadler N, Garcia M, Li X, Trejo J, Wu R, Sineath W, Anderson LN, Evans JE, Mehta AP, Qian WJ, Luthey-Schulten Z and Cheung MS.
Metabolic flux analysis revealed key roles of ArcB in ADI pathway and IlvC in BCAA biosynthesis during Streptococcus suis anaerobic growth and infection
Virulence 2025
Tang H, Zhang Q, Yang J, Ruan Y, Zhang X, Pang S, Qiao Z, Huang J, Langford PR, Zhou R, Zhang H, Zhang Q and Li L.
Integrated genomic and transcriptomic Insights into methanol tolerance mechanisms in Methylobacterium extorquens AM1, identifying key targets for strain engineering
Production of hydrogen from crude glycerol via an integrated process of L-malate biosynthesis by Escherichia coli and photofermentation by Rhodobacter capsulatus
Microb Cell Fact 2025
Marcos JL, Cabrera G, Hernandez DF, Luque B, Valle A and Bolivar J.
RB-TnSeq elucidates dicarboxylic-acid-specific catabolism in β-proteobacteria for improved plastic monomer upcycling
Appl Environ Microbiol 2025
Pearson AN, Lynch JM, Ho CN, Hudson GA, Roberts JB, Menasalvas J, Vilchez AA, Incha MR, Schmidt M, Mukhopadhyay A, Deutschbauer AM, Thompson MG, Shih PM and Keasling JD.
Investigating Lipid and Energy Dyshomeostasis Induced by Per- and Polyfluoroalkyl Substances (PFAS) Congeners in Mouse Model Using Systems Biology Approaches
Genome-scale flux balance analysis reveals redox trade-offs in the metabolism of the thermoacidophile Methylacidiphilum fumariolicum under auto-, hetero-and methanotrophic conditions
Glutaminase as a metabolic target of choice to counter acquired resistance to Palbociclib by colorectal cancer cells
Oncogene 2025
Tarrado-Castellarnau M, Foguet C, Tarragó-Celada J, Palobart M, Hernández-Carro C, Perarnau J, Zodda E, Polat IH, Marin S, Suarez-Bonnet A, Lozano JJ, Yuneva M, Thomson TM and Cascante M.
Atlas-scale metabolic activities inferred from single-cell and spatial transcriptomics
BioRxiv 2025
Armingol E, Ashcroft J, Mareckova M, Prete M, Lorenzi V, Icoresi Mazzeo C, Lee JTH, Moullet M, Bayraktar OA, Becker C, Zondervan K, Garcia-Alonso L, Lewis NE and Vento-Tormo R.
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ISME J 2025
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Determination of the genome-scale metabolic network of Bartonella quintana str. Toulouse to optimize growth for its use as chassis for synthetic biology
Design and implementation of aerobic and ambient CO(2)-reduction as an entry-point for enhanced carbon fixation
Nat Commun 2025
Satanowski A, Marchal DG, Perret A, Petit JL, Bouzon M, Döring V, Dubois I, He H, Smith EN, Pellouin V, Petri HM, Rainaldi V, Nattermann M, Burgener S, Paczia N, Zarzycki J, Heinemann M, Bar-Even A and Erb TJ.
Computation-aided designs enable developing auxotrophic metabolic sensors for wide-range glyoxylate and glycolate detection
Nat Commun 2025
Orsi E, Schulz-Mirbach H, Cotton CAR, Satanowski A, Petri HM, Arnold SL, Grabarczyk N, Verbakel R, Jensen KS, Donati S, Paczia N, Glatter T, Küffner AM, Chotel T, Schillmüller F, De Maria A, He H, Lindner SN, Noor E, Bar-Even A, Erb TJ and Nikel PI.
Immunometabolic Effect of Nitric Oxide on Human Macrophages Challenged With the SARS-CoV2-Induced Cytokine Storm. A Fluxomic Approach
Adv Healthc Mater 2024
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Core and accessory genomic traits of Vibrio cholerae O1 drive lineage transmission and disease severity
Nat Commun 2024
Maciel-Guerra A, Babaarslan K, Baker M, Rahman A, Hossain M, Sadique A, Alam J, Uzzaman S, Ferdous Rahman Sarker M, Sultana N, Islam Khan A, Ara Begum Y, Hassan Afrad M, Senin N, Hossain Habib Z, Shirin T, Qadri F and Dottorini T.
Kumar M, Tibocha-Bonilla JD, Füssy Z, Lieng C, Schwenck SM, Levesque AV, Al-Bassam MM, Passi A, Neal M, Zuniga C, Kaiyom F, Espinoza JL, Lim H, Polson SW, Allen LZ and Zengler K.
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IScience 2024
Zulqarnain F, Zhao X, Setchell KDR, Sharma Y, Fernandes P, Srivastava S, Shrivastava A, Ehsan L, Jain V, Raghavan S, Moskaluk C, Haberman Y, Denson LA, Mehta K, Iqbal NT, Rahman N, Sadiq K, Ahmad Z, Idress R, Iqbal J, Ahmed S, Hotwani A, Umrani F, Amadi B, Kelly P, Brown DE, Moore SR, Ali SA and Syed S.
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Front Bioeng Biotechnol 2024
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Investigating the metabolite signature of an altered oral microbiota as a discriminant factor for multiple sclerosis: a pilot study
Sci Rep 2024
Boussamet L, Montassier E, Mathé C, Garcia A, Morille J, Shah S, Dugast E, Wiertlewski S, Gourdel M, Bang C, Stürner KH, Masson D, Nicot AB, Vince N, Laplaud DA, Feinstein DL and Berthelot L.
Convergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken farms in China
Nat Commun 2024
Baker M, Zhang X, Maciel-Guerra A, Babaarslan K, Dong Y, Wang W, Hu Y, Renney D, Liu L, Li H, Hossain M, Heeb S, Tong Z, Pearcy N, Zhang M, Geng Y, Zhao L, Hao Z, Senin N, Chen J, Peng Z, Li F and Dottorini T.
Metabolic engineering of Caldicellulosiruptor bescii for 2,3-butanediol production from unpretreated lignocellulosic biomass and metabolic strategies for improving yields and titers
Appl Environ Microbiol 2023
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Co-Cultivated Enzyme Constraint Metabolic Network Model for Rational Guidance in Constructing Synthetic Consortia to Achieve Optimal Pathway Allocation Prediction
Adv Sci (Weinh) 2023
Xue B, Liu Y, Yang C, Liu H, Yuan Q, Wang S and Su H.
A toolbox of machine learning software to support microbiome analysis
Front Microbiol 2023
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Evolution of E. coli in a mouse model of inflammatory bowel disease leads to a disease-specific bacterial genotype and trade-offs with clinical relevance
Gut Microbes 2023
Unni R, Andreani NA, Vallier M, Heinzmann SS, Taubenheim J, Guggeis MA, Tran F, Vogler O, Künzel S, Hövener JB, Rosenstiel P, Kaleta C, Dempfle A, Unterweger D and Baines JF.
Enzyme-constrained metabolic model and in silico metabolic engineering of Clostridium ljungdahlii for the development of sustainable production processes
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Immunometabolic actions of trabectedin and lurbinectedin on human macrophages: relevance for their anti-tumor activity
Front Immunol 2023
Povo-Retana A, Fariñas M, Landauro-Vera R, Mojena M, Alvarez-Lucena C, Fernández-Moreno MA, Castrillo A, de la Rosa Medina JV, Sánchez-García S, Foguet C, Mas F, Marin S, Cascante M and Boscá L.
Transcriptome-guided metabolic network analysis reveals rearrangements of carbon flux distribution in Neisseria gonorrhoeae during neutrophil co-culture
Karp PD, Paley S, Caspi R, Kothari A, Krummenacker M, Midford PE, Moore LR, Subhraveti P, Gama-Castro S, Tierrafria VH, Lara P, Muñiz-Rascado L, Bonavides-Martinez C, Santos-Zavaleta A, Mackie A, Sun G, Ahn-Horst TA, Choi H, Covert MW, Collado-Vides J and Paulsen I.
Manipulating Fermentation Pathways in the Hyperthermophilic Archaeon Pyrococcus furiosus for Ethanol Production up to 95°C Driven by Carbon Monoxide Oxidation
Appl Environ Microbiol 2023
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Engineering a new-to-nature cascade for phosphate-dependent formate to formaldehyde conversion in vitro and in vivo
Nat Commun 2023
Nattermann M, Wenk S, Pfister P, He H, Lee SH, Szymanski W, Guntermann N, Zhu F, Nickel L, Wallner C, Zarzycki J, Paczia N, Gaißert N, Franciò G, Leitner W, Gonzalez R and Erb TJ.
PeakDecoder enables machine learning-based metabolite annotation and accurate profiling in multidimensional mass spectrometry measurements
Nat Commun 2023
Bilbao A, Munoz N, Kim J, Orton DJ, Gao Y, Poorey K, Pomraning KR, Weitz K, Burnet M, Nicora CD, Wilton R, Deng S, Dai Z, Oksen E, Gee A, Fasani RA, Tsalenko A, Tanjore D, Gardner J, Smith RD, Michener JK, Gladden JM, Baker ES, Petzold CJ, Kim YM, Apffel A, Magnuson JK and Burnum-Johnson KE.
Highlighting the potential of Synechococcus elongatus PCC 7942 as platform to produce α-linolenic acid through an updated genome-scale metabolic modeling
Front Microbiol 2023
Santos-Merino M, Gargantilla-Becerra Á, de la Cruz F and Nogales J.
In silico prediction of potential indigenous microbial biomarkers in Penaeus vannamei identified through meta-analysis and genome-scale metabolic modelling
Environ Microbiome 2023
Devika NT, Katneni VK, Jangam AK, Suganya PN, Shekhar MS and Jithendran KP.
Application of comparative genomics of Acetobacter species facilitates genome-scale metabolic reconstruction of the Acetobacter ghanensis LMG 23848(T) and Acetobacter senegalensis 108B cocoa strains
Genetically personalised organ-specific metabolic models in health and disease
Nat Commun 2022
Foguet C, Xu Y, Ritchie SC, Lambert SA, Persyn E, Nath AP, Davenport EE, Roberts DJ, Paul DS, Di Angelantonio E, Danesh J, Butterworth AS, Yau C and Inouye M.
YEASTRACT+: a portal for the exploitation of global transcription regulation and metabolic model data in yeast biotechnology and pathogenesis
Nucleic Acids Res 2022
Teixeira MC, Viana R, Palma M, Oliveira J, Galocha M, Mota MN, Couceiro D, Pereira MG, Antunes M, Costa IV, Pais P, Parada C, Chaouiya C, Sá-Correia I and Monteiro PT.
Drug transporters OAT1 and OAT3 have specific effects on multiple organs and gut microbiome as revealed by contextualized metabolic network reconstructions
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.
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 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.
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.
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.
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.
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.
Fundamental behaviors emerge from simulations of a living minimal cell
Cell 2022
Thornburg ZR, Bianchi DM, Brier TA, Gilbert BR, Earnest EE, Melo MCR, Safronova N, Sáenz JP, Cook AT, Wise KS, Hutchison CA 3rd, Smith HO, Glass JI and Luthey-Schulten Z.
Structural systems pharmacology: A framework for integrating metabolic network and structure-based virtual screening for drug discovery against bacteria
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.
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.
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.
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
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.
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.
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.
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.
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.
Genome-Scale Metabolic Model of Xanthomonas phaseoli pv. manihotis: An Approach to Elucidate Pathogenicity at the Metabolic Level
Front Genet 2020
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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.
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.
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.
Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom
Nat Commun 2019
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PLoS Biol 2019
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Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0
Nat Protoc 2019
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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.
Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient
Front Microbiol 2018
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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
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Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa
BMC Syst Biol 2018
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Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models
PLoS Comput Biol 2018
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Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions
BMC Syst Biol 2018
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Plasma and urinary metabolomic profiles of Down syndrome correlate with alteration of mitochondrial metabolism
Sci Rep 2018
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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.
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
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What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira
PLoS Negl Trop Dis 2016
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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
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Front Microbiol 2015
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