update webpage

content/pubs/PM26537759.md

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+authors = ["Spahn PN", "Hansen AH", "Hansen HG", "Arnsdorf J", "Kildegaard HF", "Lewis NE."]
+title = "A Markov chain model for N-linked protein glycosylation--towards a low-parameter tool for model-driven glycoengineering"
+journal = "Metab Eng"
+what = "article"
+doi = "10.1016/j.ymben.2015.10.007"
+pubmed = "26537759"
+date = "2015-11-06"
+keywords = []
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+

content/pubs/PM30053414.md

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+authors = ["Choi K", "Medley JK", "König M", "Stocking K", "Smith L", "Gu S", "Sauro HM."]
+title = "Tellurium: An extensible python-based modeling environment for systems and synthetic biology"
+journal = "Biosystems"
+what = "article"
+doi = "10.1016/j.biosystems.2018.07.006"
+pubmed = "30053414"
+date = "2018-07-28"
+keywords = []
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+

content/pubs/PM33247119.md

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-authors = ["Libiseller-Egger J", "Coltman B", "Gerstl MP", "Zanghellini J."]
+authors = ["Libiseller-Egger J", "Coltman BL", "Gerstl MP", "Zanghellini J."]
 title = "Environmental flexibility does not explain metabolic robustness"
 journal = "NPJ Syst Biol Appl"
 what = "article"

content/pubs/PM35050136.md

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+authors = ["Passi A", "Tibocha-Bonilla JD", "Kumar M", "Tec-Campos D", "Zengler K", "Zuniga C."]
+title = "Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big Data"
+journal = "Metabolites"
+what = "article"
+doi = "10.3390/metabo12010014"
+pubmed = "35050136"
+date = "2022-01-20"
+keywords = []
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+

content/pubs/PM35063075.md

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+authors = ["Thornburg ZR", "Bianchi DM", "Brier TA", "Gilbert BR", "Earnest TM", "Melo MCR", "Safronova N", "Sáenz JP", "Cook AT", "Wise KS", "Hutchison CA 3rd", "Smith HO", "Glass JI", "Luthey-Schulten Z."]
+title = "Fundamental behaviors emerge from simulations of a living minimal cell"
+journal = "Cell"
+what = "article"
+doi = "10.1016/j.cell.2021.12.025"
+pubmed = "35063075"
+date = "2022-01-22"
+keywords = []
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+

content/pubs/PM35590448.md

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+authors = ["Vezina B", "Judd LM", "McDougall FK", "Boardman WSJ", "Power ML", "Hawkey J", "Brisse S", "Monk JM", "Holt KE", "Wyres KL."]
+title = "Transmission of Klebsiella strains and plasmids within and between grey-headed flying fox colonies"
+journal = "Environ Microbiol"
+what = "article"
+doi = "10.1111/1462-2920.16047"
+pubmed = "35590448"
+date = "2022-05-20"
+keywords = []
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+

content/pubs/PM35603544.md

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+authors = ["Suthers PF", "Maranas CD."]
+title = "Examining organic acid production potential and growth-coupled strategies in Issatchenkia orientalis using constraint-based modeling"
+journal = "Biotechnol Prog"
+what = "article"
+doi = "10.1002/btpr.3276"
+pubmed = "35603544"
+date = "2022-05-23"
+keywords = []
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+

content/pubs/PM35924931.md

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+authors = ["Rau MH", "Gaspar P", "Jensen ML", "Geppel A", "Neves AR", "Zeidan AA."]
+title = "Genome-Scale Metabolic Modeling Combined with Transcriptome Profiling Provides Mechanistic Understanding of Streptococcus thermophilus CH8 Metabolism"
+journal = "Appl Environ Microbiol"
+what = "article"
+doi = "10.1128/aem.00780-22"
+pubmed = "35924931"
+date = "2022-08-04"
+keywords = []
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+

content/pubs/PM35975326.md

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+authors = ["Maddamsetti R."]
+title = "Idiosyncratic Purifying Selection on Metabolic Enzymes in the Long-Term Evolution Experiment with Escherichia coli"
+journal = "Genome Biol Evol"
+what = "article"
+doi = "10.1093/gbe/evac114"
+pubmed = "35975326"
+date = "2022-08-17"
+keywords = []
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+

content/pubs/PM36053127.md

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+authors = ["Broddrick JT", "Ware MA", "Jallet D", "Palsson BO", "Peers G."]
+title = "Integration of physiologically relevant photosynthetic energy flows into whole genome models of light-driven metabolism"
+journal = "Plant J"
+what = "article"
+doi = "10.1111/tpj.15965"
+pubmed = "36053127"
+date = "2022-09-02"
+keywords = []
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+

content/pubs/PM36054839.md

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+authors = ["Oliveira A", "Cunha E", "Cruz F", "Capela J", "Sequeira JC", "Sampaio M", "Sampaio C", "Dias O."]
+title = "Systematic assessment of template-based genome-scale metabolic models created with the BiGG Integration Tool"
+journal = "J Integr Bioinform"
+what = "article"
+doi = "10.1515/jib-2022-0014"
+pubmed = "36054839"
+date = "2022-09-02"
+keywords = []
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+

content/pubs/PM36081364.md

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+authors = ["Molina Ortiz JP", "Read MN", "McClure DD", "Holmes A", "Dehghani F", "Shanahan ER."]
+title = "High throughput genome scale modeling predicts microbial vitamin requirements contribute to gut microbiome community structure"
+journal = "Gut Microbes"
+what = "article"
+doi = "10.1080/19490976.2022.2118831"
+pubmed = "36081364"
+date = "2022-09-09"
+keywords = []
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+

content/pubs/PM36111857.md

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+authors = ["Schneider P", "Bekiaris PS", "von Kamp A", "Klamt S."]
+title = "StrainDesign: a comprehensive Python package for computational design of metabolic networks"
+journal = "Bioinformatics"
+what = "article"
+doi = "10.1093/bioinformatics/btac632"
+pubmed = "36111857"
+date = "2022-09-16"
+keywords = []
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+

content/pubs/PM36144212.md

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+authors = ["Guil F", "Sánchez-Cid G", "García JM."]
+title = "Staphylococcus epidermidis RP62A's Metabolic Network: Validation and Intervention Strategies"
+journal = "Metabolites"
+what = "article"
+doi = "10.3390/metabo12090808"
+pubmed = "36144212"
+date = "2022-09-23"
+keywords = []
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+

content/pubs/PM36154140.md

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+authors = ["McClure R", "Farris Y", "Danczak R", "Nelson W", "Song HS", "Kessell A", "Lee JY", "Couvillion S", "Henry C", "Jansson JK", "Hofmockel KS."]
+title = "Interaction Networks Are Driven by Community-Responsive Phenotypes in a Chitin-Degrading Consortium of Soil Microbes"
+journal = "mSystems"
+what = "article"
+doi = "10.1128/msystems.00372-22"
+pubmed = "36154140"
+date = "2022-09-26"
+keywords = []
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+

content/pubs/PM36187917.md

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+authors = ["Subramanian A", "Zakeri P", "Mousa M", "Alnaqbi H", "Alshamsi FY", "Bettoni L", "Damiani E", "Alsafar H", "Saeys Y", "Carmeliet P."]
+title = "Angiogenesis goes computational - The future way forward to discover new angiogenic targets?"
+journal = "Comput Struct Biotechnol J"
+what = "article"
+doi = "10.1016/j.csbj.2022.09.019"
+pubmed = "36187917"
+date = "2022-10-03"
+keywords = []
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+

content/pubs/PM36198709.md

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+authors = ["Granados JC", "Falah K", "Koo I", "Morgan EW", "Perdew GH", "Patterson AD", "Jamshidi N", "Nigam SK."]
+title = "AHR is a master regulator of diverse pathways in endogenous metabolism"
+journal = "Sci Rep"
+what = "article"
+doi = "10.1038/s41598-022-20572-2"
+pubmed = "36198709"
+date = "2022-10-05"
+keywords = []
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+

content/pubs/PM36215728.md

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+authors = ["Aichem M", "Klein K", "Czauderna T", "Garkov D", "Zhao J", "Li J", "Schreiber F."]
+title = "Towards a hybrid user interface for the visual exploration of large biomolecular networks using virtual reality"
+journal = "J Integr Bioinform"
+what = "article"
+doi = "10.1515/jib-2022-0034"
+pubmed = "36215728"
+date = "2022-10-10"
+keywords = []
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+

content/pubs/PM36227553.md

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+authors = ["Cuperlovic-Culf M", "Nguyen-Tran T", "Bennett SAL."]
+title = "Machine Learning and Hybrid Methods for Metabolic Pathway Modeling"
+journal = "Methods Mol Biol"
+what = "article"
+doi = "10.1007/978-1-0716-2617-7_18"
+pubmed = "36227553"
+date = "2022-10-13"
+keywords = []
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+

content/pubs/PM36284276.md

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+authors = ["Galuzzi BG", "Vanoni M", "Damiani C."]
+title = "Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells"
+journal = "BMC Bioinformatics"
+what = "article"
+doi = "10.1186/s12859-022-04967-6"
+pubmed = "36284276"
+date = "2022-10-26"
+keywords = []
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+

content/pubs/PM36304309.md

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+authors = ["Glöckler M", "Dräger A", "Mostolizadeh R."]
+title = "NCMW: A Python Package to Analyze Metabolic Interactions in the Nasal Microbiome"
+journal = "Front Bioinform"
+what = "article"
+doi = "10.3389/fbinf.2022.827024"
+pubmed = "36304309"
+date = "2022-10-28"
+keywords = []
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+

content/pubs/PM36307414.md

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+authors = ["Jenior ML", "Dickenson ME", "Papin JA."]
+title = "Genome-scale metabolic modeling reveals increased reliance on valine catabolism in clinical isolates of Klebsiella pneumoniae"
+journal = "NPJ Syst Biol Appl"
+what = "article"
+doi = "10.1038/s41540-022-00252-7"
+pubmed = "36307414"
+date = "2022-10-28"
+keywords = []
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+

content/pubs/PM36314754.md

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+authors = ["Enuh BM", "Nural Yaman B", "Tarzi C", "Aytar Çelik P", "Mutlu MB", "Angione C."]
+title = "Whole-genome sequencing and genome-scale metabolic modeling of Chromohalobacter canadensis 85B to explore its salt tolerance and biotechnological use"
+journal = "Microbiologyopen"
+what = "article"
+doi = "10.1002/mbo3.1328"
+pubmed = "36314754"
+date = "2022-10-31"
+keywords = []
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+

content/pubs/PM36316339.md

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+authors = ["Jamshidi N", "Nigam SK."]
+title = "Drug transporters OAT1 and OAT3 have specific effects on multiple organs and gut microbiome as revealed by contextualized metabolic network reconstructions"
+journal = "Sci Rep"
+what = "article"
+doi = "10.1038/s41598-022-21091-w"
+pubmed = "36316339"
+date = "2022-11-01"
+keywords = []
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+

content/pubs/PM36321827.md

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+authors = ["Poudel S", "Hefner Y", "Szubin R", "Sastry A", "Gao Y", "Nizet V", "Palsson BO."]
+title = "Coordination of CcpA and CodY Regulators in Staphylococcus aureus USA300 Strains"
+journal = "mSystems"
+what = "article"
+doi = "10.1128/msystems.00480-22"
+pubmed = "36321827"
+date = "2022-11-02"
+keywords = []
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+

content/pubs/PM36340344.md

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+authors = ["Ciurans C", "Guerrero JM", "Martínez-Mongue I", "Dussap CG", "Marin de Mas I", "Gòdia F."]
+title = "Enhancing control systems of higher plant culture chambers via multilevel structural mechanistic modelling"
+journal = "Front Plant Sci"
+what = "article"
+doi = "10.3389/fpls.2022.970410"
+pubmed = "36340344"
+date = "2022-11-07"
+keywords = []
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+

content/pubs/PM36350610.md

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+authors = ["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", "Monteiro PT."]
+title = "YEASTRACT+: a portal for the exploitation of global transcription regulation and metabolic model data in yeast biotechnology and pathogenesis"
+journal = "Nucleic Acids Res"
+what = "article"
+doi = "10.1093/nar/gkac1041"
+pubmed = "36350610"
+date = "2022-11-09"
+keywords = []
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+

content/pubs/PM36409069.md

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+authors = ["Santamaria G", "Liao C", "Lindberg C", "Chen Y", "Wang Z", "Rhee K", "Pinto FR", "Yan J", "Xavier JB."]
+title = "Evolution and regulation of microbial secondary metabolism"
+journal = "Elife"
+what = "article"
+doi = "10.7554/eLife.76119"
+pubmed = "36409069"
+date = "2022-11-21"
+keywords = []
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+

content/pubs/PM36446790.md

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+authors = ["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", "Inouye M."]
+title = "Genetically personalised organ-specific metabolic models in health and disease"
+journal = "Nat Commun"
+what = "article"
+doi = "10.1038/s41467-022-35017-7"
+pubmed = "36446790"
+date = "2022-11-29"
+keywords = []
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+

content/pubs/PM36451100.md

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+authors = ["Tamasco G", "Kumar M", "Zengler K", "Silva-Rocha R", "da Silva RR."]
+title = "ChiMera: an easy to use pipeline for bacterial genome based metabolic network reconstruction, evaluation and visualization"
+journal = "BMC Bioinformatics"
+what = "article"
+doi = "10.1186/s12859-022-05056-4"
+pubmed = "36451100"
+date = "2022-11-30"
+keywords = []
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+

content/pubs/PM36504784.md

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+authors = ["Pelicaen R", "Weckx S", "Gonze D", "De Vuyst L."]
+title = "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"
+journal = "Front Microbiol"
+what = "article"
+doi = "10.3389/fmicb.2022.1060160"
+pubmed = "36504784"
+date = "2022-12-12"
+keywords = []
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+

content/pubs/PM36508473.md

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+authors = ["Aghakhani S", "Soliman S", "Niarakis A."]
+title = "Metabolic reprogramming in Rheumatoid Arthritis Synovial Fibroblasts: A hybrid modeling approach"
+journal = "PLoS Comput Biol"
+what = "article"
+doi = "10.1371/journal.pcbi.1010408"
+pubmed = "36508473"
+date = "2022-12-12"
+keywords = []
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+

content/pubs/PM36511689.md

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+authors = ["Dillard LR", "Glass EM", "Lewis AL", "Thomas-White K", "Papin JA."]
+title = "Metabolic Network Models of the Gardnerella Pangenome Identify Key Interactions with the Vaginal Environment"
+journal = "mSystems"
+what = "article"
+doi = "10.1128/msystems.00689-22"
+pubmed = "36511689"
+date = "2022-12-13"
+keywords = []
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+