diff --git a/content/pubs/PM26537759.md b/content/pubs/PM26537759.md new file mode 100644 index 0000000..5428ad1 --- /dev/null +++ b/content/pubs/PM26537759.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM30053414.md b/content/pubs/PM30053414.md new file mode 100644 index 0000000..72436d6 --- /dev/null +++ b/content/pubs/PM30053414.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM33247119.md b/content/pubs/PM33247119.md index b6840cc..8f4ec3e 100644 --- a/content/pubs/PM33247119.md +++ b/content/pubs/PM33247119.md @@ -1,5 +1,5 @@ +++ -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" diff --git a/content/pubs/PM35050136.md b/content/pubs/PM35050136.md new file mode 100644 index 0000000..1e216b6 --- /dev/null +++ b/content/pubs/PM35050136.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM35063075.md b/content/pubs/PM35063075.md new file mode 100644 index 0000000..39b7f9f --- /dev/null +++ b/content/pubs/PM35063075.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM35590448.md b/content/pubs/PM35590448.md new file mode 100644 index 0000000..b7bb714 --- /dev/null +++ b/content/pubs/PM35590448.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM35603544.md b/content/pubs/PM35603544.md new file mode 100644 index 0000000..e1046c3 --- /dev/null +++ b/content/pubs/PM35603544.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM35924931.md b/content/pubs/PM35924931.md new file mode 100644 index 0000000..48001cc --- /dev/null +++ b/content/pubs/PM35924931.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM35975326.md b/content/pubs/PM35975326.md new file mode 100644 index 0000000..952dbc3 --- /dev/null +++ b/content/pubs/PM35975326.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM36053127.md b/content/pubs/PM36053127.md new file mode 100644 index 0000000..563ec14 --- /dev/null +++ b/content/pubs/PM36053127.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM36054839.md b/content/pubs/PM36054839.md new file mode 100644 index 0000000..61c79be --- /dev/null +++ b/content/pubs/PM36054839.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM36081364.md b/content/pubs/PM36081364.md new file mode 100644 index 0000000..d29610c --- /dev/null +++ b/content/pubs/PM36081364.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM36111857.md b/content/pubs/PM36111857.md new file mode 100644 index 0000000..877ff78 --- /dev/null +++ b/content/pubs/PM36111857.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM36144212.md b/content/pubs/PM36144212.md new file mode 100644 index 0000000..fd1d301 --- /dev/null +++ b/content/pubs/PM36144212.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM36154140.md b/content/pubs/PM36154140.md new file mode 100644 index 0000000..fc4b59c --- /dev/null +++ b/content/pubs/PM36154140.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM36187917.md b/content/pubs/PM36187917.md new file mode 100644 index 0000000..f4398aa --- /dev/null +++ b/content/pubs/PM36187917.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM36198709.md b/content/pubs/PM36198709.md new file mode 100644 index 0000000..2f6c2fe --- /dev/null +++ b/content/pubs/PM36198709.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM36215728.md b/content/pubs/PM36215728.md new file mode 100644 index 0000000..8ab2f87 --- /dev/null +++ b/content/pubs/PM36215728.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM36227553.md b/content/pubs/PM36227553.md new file mode 100644 index 0000000..ac445c0 --- /dev/null +++ b/content/pubs/PM36227553.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM36284276.md b/content/pubs/PM36284276.md new file mode 100644 index 0000000..be3fa1b --- /dev/null +++ b/content/pubs/PM36284276.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM36304309.md b/content/pubs/PM36304309.md new file mode 100644 index 0000000..0fb3ad4 --- /dev/null +++ b/content/pubs/PM36304309.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM36307414.md b/content/pubs/PM36307414.md new file mode 100644 index 0000000..701793f --- /dev/null +++ b/content/pubs/PM36307414.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM36314754.md b/content/pubs/PM36314754.md new file mode 100644 index 0000000..d3e7e99 --- /dev/null +++ b/content/pubs/PM36314754.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM36316339.md b/content/pubs/PM36316339.md new file mode 100644 index 0000000..bcc7ad6 --- /dev/null +++ b/content/pubs/PM36316339.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM36321827.md b/content/pubs/PM36321827.md new file mode 100644 index 0000000..acc6103 --- /dev/null +++ b/content/pubs/PM36321827.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM36340344.md b/content/pubs/PM36340344.md new file mode 100644 index 0000000..03e41d5 --- /dev/null +++ b/content/pubs/PM36340344.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM36350610.md b/content/pubs/PM36350610.md new file mode 100644 index 0000000..c7ddef7 --- /dev/null +++ b/content/pubs/PM36350610.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM36409069.md b/content/pubs/PM36409069.md new file mode 100644 index 0000000..737dd0b --- /dev/null +++ b/content/pubs/PM36409069.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM36446790.md b/content/pubs/PM36446790.md new file mode 100644 index 0000000..9b51d5a --- /dev/null +++ b/content/pubs/PM36446790.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM36451100.md b/content/pubs/PM36451100.md new file mode 100644 index 0000000..07f68d8 --- /dev/null +++ b/content/pubs/PM36451100.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM36504784.md b/content/pubs/PM36504784.md new file mode 100644 index 0000000..0d8423e --- /dev/null +++ b/content/pubs/PM36504784.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM36508473.md b/content/pubs/PM36508473.md new file mode 100644 index 0000000..c14a51c --- /dev/null +++ b/content/pubs/PM36508473.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM36511689.md b/content/pubs/PM36511689.md new file mode 100644 index 0000000..4e73868 --- /dev/null +++ b/content/pubs/PM36511689.md @@ -0,0 +1,11 @@ ++++ +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 = [] ++++ + diff --git a/content/pubs/PM36536290.md b/content/pubs/PM36536290.md new file mode 100644 index 0000000..4d542a6 --- /dev/null +++ b/content/pubs/PM36536290.md @@ -0,0 +1,11 @@ ++++ +authors = ["Kenefake D", "Armingol E", "Lewis NE", "Pistikopoulos EN."] +title = "An improved algorithm for flux variability analysis" +journal = "BMC Bioinformatics" +what = "article" +doi = "10.1186/s12859-022-05089-9" +pubmed = "36536290" +date = "2022-12-19" +keywords = [] ++++ + diff --git a/content/pubs/PM36575180.md b/content/pubs/PM36575180.md new file mode 100644 index 0000000..520bbcf --- /dev/null +++ b/content/pubs/PM36575180.md @@ -0,0 +1,11 @@ ++++ +authors = ["Tibocha-Bonilla JD", "Zuñiga C", "Lekbua A", "Lloyd C", "Rychel K", "Short K", "Zengler K."] +title = "Predicting stress response and improved protein overproduction in Bacillus subtilis" +journal = "NPJ Syst Biol Appl" +what = "article" +doi = "10.1038/s41540-022-00259-0" +pubmed = "36575180" +date = "2022-12-27" +keywords = [] ++++ + diff --git a/content/pubs/PM36585633.md b/content/pubs/PM36585633.md new file mode 100644 index 0000000..2b15173 --- /dev/null +++ b/content/pubs/PM36585633.md @@ -0,0 +1,11 @@ ++++ +authors = ["van 't Hof M", "Mohite OS", "Monk JM", "Weber T", "Palsson BO", "Sommer MOA."] +title = "High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917" +journal = "BMC Bioinformatics" +what = "article" +doi = "10.1186/s12859-022-05108-9" +pubmed = "36585633" +date = "2022-12-30" +keywords = [] ++++ + diff --git a/content/pubs/PM36604447.md b/content/pubs/PM36604447.md new file mode 100644 index 0000000..a37afbb --- /dev/null +++ b/content/pubs/PM36604447.md @@ -0,0 +1,11 @@ ++++ +authors = ["Fernandes P", "Sharma Y", "Zulqarnain F", "McGrew B", "Shrivastava A", "Ehsan L", "Payne D", "Dillard L", "Powers D", "Aldridge I", "Matthews J", "Kugathasan S", "Fernández FM", "Gaul D", "Papin JA", "Syed S."] +title = "Identifying metabolic shifts in Crohn's disease using' omics-driven contextualized computational metabolic network models" +journal = "Sci Rep" +what = "article" +doi = "10.1038/s41598-022-26816-5" +pubmed = "36604447" +date = "2023-01-05" +keywords = [] ++++ + diff --git a/content/pubs/PM36607958.md b/content/pubs/PM36607958.md new file mode 100644 index 0000000..5211f39 --- /dev/null +++ b/content/pubs/PM36607958.md @@ -0,0 +1,11 @@ ++++ +authors = ["Karlsen E", "Gylseth M", "Schulz C", "Almaas E."] +title = "A study of a diauxic growth experiment using an expanded dynamic flux balance framework" +journal = "PLoS One" +what = "article" +doi = "10.1371/journal.pone.0280077" +pubmed = "36607958" +date = "2023-01-06" +keywords = [] ++++ + diff --git a/content/pubs/PM36620068.md b/content/pubs/PM36620068.md new file mode 100644 index 0000000..abba321 --- /dev/null +++ b/content/pubs/PM36620068.md @@ -0,0 +1,11 @@ ++++ +authors = ["Benito-Vaquerizo S", "Nouse N", "Schaap PJ", "Hugenholtz J", "Brul S", "López-Contreras AM", "Martins Dos Santos VAP", "Suarez-Diez M."] +title = "Model-driven approach for the production of butyrate from CO(2)/H(2) by a novel co-culture of C. autoethanogenum and C. beijerinckii" +journal = "Front Microbiol" +what = "article" +doi = "10.3389/fmicb.2022.1064013" +pubmed = "36620068" +date = "2023-01-09" +keywords = [] ++++ + diff --git a/content/pubs/PM36631881.md b/content/pubs/PM36631881.md new file mode 100644 index 0000000..7a1d7d1 --- /dev/null +++ b/content/pubs/PM36631881.md @@ -0,0 +1,11 @@ ++++ +authors = ["Devika NT", "Katneni VK", "Jangam AK", "Suganya PN", "Shekhar MS", "Jithendran KP."] +title = "In silico prediction of potential indigenous microbial biomarkers in Penaeus vannamei identified through meta-analysis and genome-scale metabolic modelling" +journal = "Environ Microbiome" +what = "article" +doi = "10.1186/s40793-022-00458-6" +pubmed = "36631881" +date = "2023-01-11" +keywords = [] ++++ + diff --git a/content/pubs/PM36677051.md b/content/pubs/PM36677051.md new file mode 100644 index 0000000..794e346 --- /dev/null +++ b/content/pubs/PM36677051.md @@ -0,0 +1,11 @@ ++++ +authors = ["Moškon M", "Režen T."] +title = "Context-Specific Genome-Scale Metabolic Modelling and Its Application to the Analysis of COVID-19 Metabolic Signatures" +journal = "Metabolites" +what = "article" +doi = "10.3390/metabo13010126" +pubmed = "36677051" +date = "2023-01-21" +keywords = [] ++++ + diff --git a/content/pubs/PM36677469.md b/content/pubs/PM36677469.md new file mode 100644 index 0000000..fe05d03 --- /dev/null +++ b/content/pubs/PM36677469.md @@ -0,0 +1,11 @@ ++++ +authors = ["Wu K", "Mao Z", "Mao Y", "Niu J", "Cai J", "Yuan Q", "Yun L", "Liao X", "Wang Z", "Ma H."] +title = "ecBSU1: A Genome-Scale Enzyme-Constrained Model of Bacillus subtilis Based on the ECMpy Workflow" +journal = "Microorganisms" +what = "article" +doi = "10.3390/microorganisms11010178" +pubmed = "36677469" +date = "2023-01-21" +keywords = [] ++++ + diff --git a/content/pubs/PM36685725.md b/content/pubs/PM36685725.md new file mode 100644 index 0000000..e3d48b1 --- /dev/null +++ b/content/pubs/PM36685725.md @@ -0,0 +1,11 @@ ++++ +authors = ["Park JY", "Lee SM", "Ebrahim A", "Scott-Nevros ZK", "Kim J", "Yang L", "Sastry A", "Seo SW", "Palsson BO", "Kim D."] +title = "Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli" +journal = "NAR Genom Bioinform" +what = "article" +doi = "10.1093/nargab/lqad006" +pubmed = "36685725" +date = "2023-01-23" +keywords = [] ++++ + diff --git a/content/pubs/PM36692133.md b/content/pubs/PM36692133.md new file mode 100644 index 0000000..8188838 --- /dev/null +++ b/content/pubs/PM36692133.md @@ -0,0 +1,11 @@ ++++ +authors = ["Oarga A", "Bannerman BP", "Júlvez J."] +title = "CONTRABASS: exploiting flux constraints in genome-scale models for the detection of vulnerabilities" +journal = "Bioinformatics" +what = "article" +doi = "10.1093/bioinformatics/btad053" +pubmed = "36692133" +date = "2023-01-24" +keywords = [] ++++ + diff --git a/content/pubs/PM36726720.md b/content/pubs/PM36726720.md new file mode 100644 index 0000000..9e63dee --- /dev/null +++ b/content/pubs/PM36726720.md @@ -0,0 +1,11 @@ ++++ +authors = ["V K P", "Sinha S."] +title = "A systems level approach to study metabolic networks in prokaryotes with the aromatic amino acid biosynthesis pathway" +journal = "Front Genet" +what = "article" +doi = "10.3389/fgene.2022.1084727" +pubmed = "36726720" +date = "2023-02-02" +keywords = [] ++++ + diff --git a/content/pubs/PM36748558.md b/content/pubs/PM36748558.md new file mode 100644 index 0000000..668cb33 --- /dev/null +++ b/content/pubs/PM36748558.md @@ -0,0 +1,11 @@ ++++ +authors = ["Cummins EA", "Hall RJ", "Connor C", "McInerney JO", "McNally A."] +title = "Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types" +journal = "Microb Genom" +what = "article" +doi = "10.1099/mgen.0.000903" +pubmed = "36748558" +date = "2023-02-07" +keywords = [] ++++ + diff --git a/content/pubs/PM36765199.md b/content/pubs/PM36765199.md new file mode 100644 index 0000000..1e8f85a --- /dev/null +++ b/content/pubs/PM36765199.md @@ -0,0 +1,11 @@ ++++ +authors = ["Dahal S", "Renz A", "Dräger A", "Yang L."] +title = "Genome-scale model of Pseudomonas aeruginosa metabolism unveils virulence and drug potentiation" +journal = "Commun Biol" +what = "article" +doi = "10.1038/s42003-023-04540-8" +pubmed = "36765199" +date = "2023-02-10" +keywords = [] ++++ + diff --git a/content/pubs/PM36814842.md b/content/pubs/PM36814842.md new file mode 100644 index 0000000..7c28604 --- /dev/null +++ b/content/pubs/PM36814842.md @@ -0,0 +1,11 @@ ++++ +authors = ["Zampieri G", "Campanaro S", "Angione C", "Treu L."] +title = "Metatranscriptomics-guided genome-scale metabolic modeling of microbial communities" +journal = "Cell Rep Methods" +what = "article" +doi = "10.1016/j.crmeth.2022.100383" +pubmed = "36814842" +date = "2023-02-23" +keywords = [] ++++ + diff --git a/content/pubs/PM36847213.md b/content/pubs/PM36847213.md new file mode 100644 index 0000000..e702c29 --- /dev/null +++ b/content/pubs/PM36847213.md @@ -0,0 +1,11 @@ ++++ +authors = ["Coppens L", "Tschirhart T", "Leary DH", "Colston SM", "Compton JR", "Hervey WJ 4th", "Dana KL", "Vora GJ", "Bordel S", "Ledesma-Amaro R."] +title = "Vibrio natriegens genome-scale modeling reveals insights into halophilic adaptations and resource allocation" +journal = "Mol Syst Biol" +what = "article" +doi = "10.15252/msb.202110523" +pubmed = "36847213" +date = "2023-02-27" +keywords = [] ++++ + diff --git a/content/pubs/PM36866411.md b/content/pubs/PM36866411.md new file mode 100644 index 0000000..9562bbd --- /dev/null +++ b/content/pubs/PM36866411.md @@ -0,0 +1,11 @@ ++++ +authors = ["Strain B", "Morrissey J", "Antonakoudis A", "Kontoravdi C."] +title = "How reliable are Chinese hamster ovary (CHO) cell genome-scale metabolic models?" +journal = "Biotechnol Bioeng" +what = "article" +doi = "10.1002/bit.28366" +pubmed = "36866411" +date = "2023-03-03" +keywords = [] ++++ + diff --git a/content/pubs/PM36894723.md b/content/pubs/PM36894723.md new file mode 100644 index 0000000..3c043a4 --- /dev/null +++ b/content/pubs/PM36894723.md @@ -0,0 +1,11 @@ ++++ +authors = ["Pavao A", "Girinathan B", "Peltier J", "Altamirano Silva P", "Dupuy B", "Muti IH", "Malloy C", "Cheng LL", "Bry L."] +title = "Elucidating dynamic anaerobe metabolism with HRMAS (13)C NMR and genome-scale modeling" +journal = "Nat Chem Biol" +what = "article" +doi = "10.1038/s41589-023-01275-9" +pubmed = "36894723" +date = "2023-03-09" +keywords = [] ++++ + diff --git a/content/pubs/PM36913519.md b/content/pubs/PM36913519.md new file mode 100644 index 0000000..08919b6 --- /dev/null +++ b/content/pubs/PM36913519.md @@ -0,0 +1,11 @@ ++++ +authors = ["Hunt H", "Brueggen N", "Galle A", "Vanderauwera S", "Frohberg C", "Fernie AR", "Sonnewald U", "Sweetlove LJ."] +title = "Analysis of companion cell and phloem metabolism using a transcriptome-guided model of Arabidopsis metabolism" +journal = "Plant Physiol" +what = "article" +doi = "10.1093/plphys/kiad154" +pubmed = "36913519" +date = "2023-03-13" +keywords = [] ++++ + diff --git a/content/pubs/PM36915687.md b/content/pubs/PM36915687.md new file mode 100644 index 0000000..b131b57 --- /dev/null +++ b/content/pubs/PM36915687.md @@ -0,0 +1,11 @@ ++++ +authors = ["González-Arrué N", "Inostroza I", "Conejeros R", "Rivas-Astroza M."] +title = "Phenotype-specific estimation of metabolic fluxes using gene expression data" +journal = "iScience" +what = "article" +doi = "10.1016/j.isci.2023.106201" +pubmed = "36915687" +date = "2023-03-14" +keywords = [] ++++ + diff --git a/content/pubs/PM36926613.md b/content/pubs/PM36926613.md new file mode 100644 index 0000000..e1b2ad7 --- /dev/null +++ b/content/pubs/PM36926613.md @@ -0,0 +1,11 @@ ++++ +authors = ["Kim S", "Nam Y", "Kim MJ", "Kwon SH", "Jeon J", "Shin SJ", "Park S", "Chang S", "Kim HU", "Lee YY", "Kim HS", "Moon M."] +title = "Proteomic analysis for the effects of non-saponin fraction with rich polysaccharide from Korean Red Ginseng on Alzheimer's disease in a mouse model" +journal = "J Ginseng Res" +what = "article" +doi = "10.1016/j.jgr.2022.09.008" +pubmed = "36926613" +date = "2023-03-17" +keywords = [] ++++ + diff --git a/content/pubs/PM36947103.md b/content/pubs/PM36947103.md new file mode 100644 index 0000000..e0063a5 --- /dev/null +++ b/content/pubs/PM36947103.md @@ -0,0 +1,11 @@ ++++ +authors = ["Abrusán G", "Foguet C."] +title = "An Assessment of Quaternary Structure Functionality in Homomer Protein Complexes" +journal = "Mol Biol Evol" +what = "article" +doi = "10.1093/molbev/msad070" +pubmed = "36947103" +date = "2023-03-22" +keywords = [] ++++ + diff --git a/content/pubs/PM36952396.md b/content/pubs/PM36952396.md new file mode 100644 index 0000000..b02cf8a --- /dev/null +++ b/content/pubs/PM36952396.md @@ -0,0 +1,11 @@ ++++ +authors = ["Leonidou N", "Renz A", "Mostolizadeh R", "Dräger A."] +title = "New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells" +journal = "PLoS Comput Biol" +what = "article" +doi = "10.1371/journal.pcbi.1010903" +pubmed = "36952396" +date = "2023-03-23" +keywords = [] ++++ + diff --git a/content/pubs/PM36979028.md b/content/pubs/PM36979028.md new file mode 100644 index 0000000..a4324a4 --- /dev/null +++ b/content/pubs/PM36979028.md @@ -0,0 +1,11 @@ ++++ +authors = ["Jamshidi N", "Nigam KB", "Nigam SK."] +title = "Loss of the Kidney Urate Transporter, Urat1, Leads to Disrupted Redox Homeostasis in Mice" +journal = "Antioxidants (Basel)" +what = "article" +doi = "10.3390/antiox12030780" +pubmed = "36979028" +date = "2023-03-29" +keywords = [] ++++ + diff --git a/content/pubs/PM36979435.md b/content/pubs/PM36979435.md new file mode 100644 index 0000000..17c3cad --- /dev/null +++ b/content/pubs/PM36979435.md @@ -0,0 +1,11 @@ ++++ +authors = ["Sorokin A", "Goryanin I."] +title = "FBA-PRCC. Partial Rank Correlation Coefficient (PRCC) Global Sensitivity Analysis (GSA) in Application to Constraint-Based Models" +journal = "Biomolecules" +what = "article" +doi = "10.3390/biom13030500" +pubmed = "36979435" +date = "2023-03-29" +keywords = [] ++++ + diff --git a/content/pubs/PM36994165.md b/content/pubs/PM36994165.md new file mode 100644 index 0000000..1e95e84 --- /dev/null +++ b/content/pubs/PM36994165.md @@ -0,0 +1,11 @@ ++++ +authors = ["Kaste JAM", "Shachar-Hill Y."] +title = "Model Validation and Selection in Metabolic Flux Analysis and Flux Balance Analysis" +journal = "ArXiv" +what = "article" +doi = "nan" +pubmed = "36994165" +date = "2023-03-30" +keywords = [] ++++ + diff --git a/content/pubs/PM36998399.md b/content/pubs/PM36998399.md new file mode 100644 index 0000000..41883da --- /dev/null +++ b/content/pubs/PM36998399.md @@ -0,0 +1,11 @@ ++++ +authors = ["Santos-Merino M", "Gargantilla-Becerra Á", "de la Cruz F", "Nogales J."] +title = "Highlighting the potential of Synechococcus elongatus PCC 7942 as platform to produce α-linolenic acid through an updated genome-scale metabolic modeling" +journal = "Front Microbiol" +what = "article" +doi = "10.3389/fmicb.2023.1126030" +pubmed = "36998399" +date = "2023-03-31" +keywords = [] ++++ + diff --git a/content/pubs/PM37055413.md b/content/pubs/PM37055413.md new file mode 100644 index 0000000..1ac179a --- /dev/null +++ b/content/pubs/PM37055413.md @@ -0,0 +1,11 @@ ++++ +authors = ["Pettersen JP", "Almaas E."] +title = "Parameter inference for enzyme and temperature constrained genome-scale models" +journal = "Sci Rep" +what = "article" +doi = "10.1038/s41598-023-32982-x" +pubmed = "37055413" +date = "2023-04-13" +keywords = [] ++++ + diff --git a/content/pubs/PM37106602.md b/content/pubs/PM37106602.md new file mode 100644 index 0000000..2ba4485 --- /dev/null +++ b/content/pubs/PM37106602.md @@ -0,0 +1,11 @@ ++++ +authors = ["Wang J", "Chen Z", "Deng X", "Yuan Q", "Ma H."] +title = "Engineering Escherichia coli for Poly-β-hydroxybutyrate Production from Methanol" +journal = "Bioengineering (Basel)" +what = "article" +doi = "10.3390/bioengineering10040415" +pubmed = "37106602" +date = "2023-04-28" +keywords = [] ++++ + diff --git a/content/pubs/PM37117207.md b/content/pubs/PM37117207.md new file mode 100644 index 0000000..8771928 --- /dev/null +++ b/content/pubs/PM37117207.md @@ -0,0 +1,11 @@ ++++ +authors = ["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", "Burnum-Johnson KE."] +title = "PeakDecoder enables machine learning-based metabolite annotation and accurate profiling in multidimensional mass spectrometry measurements" +journal = "Nat Commun" +what = "article" +doi = "10.1038/s41467-023-37031-9" +pubmed = "37117207" +date = "2023-04-28" +keywords = [] ++++ + diff --git a/content/pubs/PM37128079.md b/content/pubs/PM37128079.md new file mode 100644 index 0000000..2d035b9 --- /dev/null +++ b/content/pubs/PM37128079.md @@ -0,0 +1,11 @@ ++++ +authors = ["Walsh AM", "Macori G", "Kilcawley KN", "Cotter PD."] +title = "Meta-analysis of cheese microbiomes highlights contributions to multiple aspects of quality" +journal = "Nat Food" +what = "article" +doi = "10.1038/s43016-020-0129-3" +pubmed = "37128079" +date = "2023-05-02" +keywords = [] ++++ + diff --git a/content/pubs/PM37147292.md b/content/pubs/PM37147292.md new file mode 100644 index 0000000..a961fda --- /dev/null +++ b/content/pubs/PM37147292.md @@ -0,0 +1,11 @@ ++++ +authors = ["Sahin A", "Weilandt DR", "Hatzimanikatis V."] +title = "Optimal enzyme utilization suggests that concentrations and thermodynamics determine binding mechanisms and enzyme saturations" +journal = "Nat Commun" +what = "article" +doi = "10.1038/s41467-023-38159-4" +pubmed = "37147292" +date = "2023-05-05" +keywords = [] ++++ + diff --git a/content/pubs/PM37153490.md b/content/pubs/PM37153490.md new file mode 100644 index 0000000..6e5320b --- /dev/null +++ b/content/pubs/PM37153490.md @@ -0,0 +1,11 @@ ++++ +authors = ["Bannerman BP", "Oarga A", "Júlvez J."] +title = "Mycobacterial metabolic model development for drug target identification" +journal = "GigaByte" +what = "article" +doi = "10.46471/gigabyte.80" +pubmed = "37153490" +date = "2023-05-08" +keywords = [] ++++ + diff --git a/content/pubs/PM37158271.md b/content/pubs/PM37158271.md new file mode 100644 index 0000000..8b88106 --- /dev/null +++ b/content/pubs/PM37158271.md @@ -0,0 +1,11 @@ ++++ +authors = ["Mao Z", "Yuan Q", "Li H", "Zhang Y", "Huang Y", "Yang C", "Wang R", "Yang Y", "Wu Y", "Yang S", "Liao X", "Ma H."] +title = "CAVE: a cloud-based platform for analysis and visualization of metabolic pathways" +journal = "Nucleic Acids Res" +what = "article" +doi = "10.1093/nar/gkad360" +pubmed = "37158271" +date = "2023-05-09" +keywords = [] ++++ + diff --git a/content/pubs/PM37160875.md b/content/pubs/PM37160875.md new file mode 100644 index 0000000..54098b9 --- /dev/null +++ b/content/pubs/PM37160875.md @@ -0,0 +1,11 @@ ++++ +authors = ["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", "Erb TJ."] +title = "Engineering a new-to-nature cascade for phosphate-dependent formate to formaldehyde conversion in vitro and in vivo" +journal = "Nat Commun" +what = "article" +doi = "10.1038/s41467-023-38072-w" +pubmed = "37160875" +date = "2023-05-10" +keywords = [] ++++ + diff --git a/content/pubs/PM37162365.md b/content/pubs/PM37162365.md new file mode 100644 index 0000000..078bd22 --- /dev/null +++ b/content/pubs/PM37162365.md @@ -0,0 +1,11 @@ ++++ +authors = ["Lipscomb GL", "Crowley AT", "Nguyen DMN", "Keller MW", "O'Quinn HC", "Tanwee TNN", "Vailionis JL", "Zhang K", "Zhang Y", "Kelly RM", "Adams MWW."] +title = "Manipulating Fermentation Pathways in the Hyperthermophilic Archaeon Pyrococcus furiosus for Ethanol Production up to 95°C Driven by Carbon Monoxide Oxidation" +journal = "Appl Environ Microbiol" +what = "article" +doi = "10.1128/aem.00012-23" +pubmed = "37162365" +date = "2023-05-10" +keywords = [] ++++ + diff --git a/content/pubs/PM37183600.md b/content/pubs/PM37183600.md new file mode 100644 index 0000000..8b85591 --- /dev/null +++ b/content/pubs/PM37183600.md @@ -0,0 +1,11 @@ ++++ +authors = ["Ha MH", "Kim MS", "An HJ", "Sung MJ", "Lee YH", "Yang DH", "Jung SH", "Baek J", "Choi Y", "Taylor DM", "Zhang Y", "Lee SY", "Jeong HY."] +title = "PTEN-induced kinase 1 is associated with renal aging, via the cGAS-STING pathway" +journal = "Aging Cell" +what = "article" +doi = "10.1111/acel.13865" +pubmed = "37183600" +date = "2023-05-15" +keywords = [] ++++ + diff --git a/content/pubs/PM37244928.md b/content/pubs/PM37244928.md new file mode 100644 index 0000000..0218e6a --- /dev/null +++ b/content/pubs/PM37244928.md @@ -0,0 +1,11 @@ ++++ +authors = ["Molversmyr H", "Øyås O", "Rotnes F", "Vik JO."] +title = "Extracting functionally accurate context-specific models of Atlantic salmon metabolism" +journal = "NPJ Syst Biol Appl" +what = "article" +doi = "10.1038/s41540-023-00280-x" +pubmed = "37244928" +date = "2023-05-27" +keywords = [] ++++ + diff --git a/content/pubs/PM37252834.md b/content/pubs/PM37252834.md new file mode 100644 index 0000000..2676731 --- /dev/null +++ b/content/pubs/PM37252834.md @@ -0,0 +1,11 @@ ++++ +authors = ["Guil F", "Hidalgo JF", "García JM."] +title = "On the representativeness and stability of a set of EFMs" +journal = "Bioinformatics" +what = "article" +doi = "10.1093/bioinformatics/btad356" +pubmed = "37252834" +date = "2023-05-30" +keywords = [] ++++ + diff --git a/content/pubs/PM37279743.md b/content/pubs/PM37279743.md new file mode 100644 index 0000000..347014c --- /dev/null +++ b/content/pubs/PM37279743.md @@ -0,0 +1,11 @@ ++++ +authors = ["Jenior ML", "Glass EM", "Papin JA."] +title = "Reconstructor: a COBRApy compatible tool for automated genome-scale metabolic network reconstruction with parsimonious flux-based gap-filling" +journal = "Bioinformatics" +what = "article" +doi = "10.1093/bioinformatics/btad367" +pubmed = "37279743" +date = "2023-06-06" +keywords = [] ++++ + diff --git a/content/pubs/PM37286882.md b/content/pubs/PM37286882.md new file mode 100644 index 0000000..48ac555 --- /dev/null +++ b/content/pubs/PM37286882.md @@ -0,0 +1,11 @@ ++++ +authors = ["Karlsen ST", "Rau MH", "Sánchez BJ", "Jensen K", "Zeidan AA."] +title = "From genotype to phenotype: computational approaches for inferring microbial traits relevant to the food industry" +journal = "FEMS Microbiol Rev" +what = "article" +doi = "10.1093/femsre/fuad030" +pubmed = "37286882" +date = "2023-06-07" +keywords = [] ++++ + diff --git a/content/pubs/PM37288452.md b/content/pubs/PM37288452.md new file mode 100644 index 0000000..9951c4b --- /dev/null +++ b/content/pubs/PM37288452.md @@ -0,0 +1,11 @@ ++++ +authors = ["Boto ST", "Bardl B", "Harnisch F", "Rosenbaum MA."] +title = "Microbial electrosynthesis with Clostridium ljungdahlii benefits from hydrogen electron mediation and permits a greater variety of products" +journal = "Green Chem" +what = "article" +doi = "10.1039/d3gc00471f" +pubmed = "37288452" +date = "2023-06-08" +keywords = [] ++++ + diff --git a/content/pubs/PM37289026.md b/content/pubs/PM37289026.md new file mode 100644 index 0000000..abc9ead --- /dev/null +++ b/content/pubs/PM37289026.md @@ -0,0 +1,11 @@ ++++ +authors = ["Fakih I", "Got J", "Robles-Rodriguez CE", "Siegel A", "Forano E", "Muñoz-Tamayo R."] +title = "Dynamic genome-based metabolic modeling of the predominant cellulolytic rumen bacterium Fibrobacter succinogenes S85" +journal = "mSystems" +what = "article" +doi = "10.1128/msystems.01027-22" +pubmed = "37289026" +date = "2023-06-08" +keywords = [] ++++ + diff --git a/content/pubs/PM37289085.md b/content/pubs/PM37289085.md new file mode 100644 index 0000000..12833d0 --- /dev/null +++ b/content/pubs/PM37289085.md @@ -0,0 +1,11 @@ ++++ +authors = ["Vailionis JL", "Zhao W", "Zhang K", "Rodionov DA", "Lipscomb GL", "Tanwee TNN", "O'Quinn HC", "Bing RG", "Kelly RM", "Adams MWW", "Zhang Y."] +title = "Optimizing Strategies for Bio-Based Ethanol Production Using Genome-Scale Metabolic Modeling of the Hyperthermophilic Archaeon, Pyrococcus furiosus" +journal = "Appl Environ Microbiol" +what = "article" +doi = "10.1128/aem.00563-23" +pubmed = "37289085" +date = "2023-06-08" +keywords = [] ++++ + diff --git a/content/pubs/PM37324717.md b/content/pubs/PM37324717.md new file mode 100644 index 0000000..55b45ca --- /dev/null +++ b/content/pubs/PM37324717.md @@ -0,0 +1,11 @@ ++++ +authors = ["Germann AT", "Nakielski A", "Dietsch M", "Petzel T", "Moser D", "Triesch S", "Westhoff P", "Axmann IM."] +title = "A systematic overexpression approach reveals native targets to increase squalene production in Synechocystis sp. PCC 6803" +journal = "Front Plant Sci" +what = "article" +doi = "10.3389/fpls.2023.1024981" +pubmed = "37324717" +date = "2023-06-16" +keywords = [] ++++ + diff --git a/content/pubs/PM37370567.md b/content/pubs/PM37370567.md new file mode 100644 index 0000000..ac53b8f --- /dev/null +++ b/content/pubs/PM37370567.md @@ -0,0 +1,11 @@ ++++ +authors = ["Kuriya Y", "Murata M", "Yamamoto M", "Watanabe N", "Araki M."] +title = "Prediction of Metabolic Flux Distribution by Flux Sampling: As a Case Study, Acetate Production from Glucose in Escherichia coli" +journal = "Bioengineering (Basel)" +what = "article" +doi = "10.3390/bioengineering10060636" +pubmed = "37370567" +date = "2023-06-28" +keywords = [] ++++ + diff --git a/content/pubs/PM37387581.md b/content/pubs/PM37387581.md new file mode 100644 index 0000000..4e1a1f4 --- /dev/null +++ b/content/pubs/PM37387581.md @@ -0,0 +1,11 @@ ++++ +authors = ["Potter AD", "Baiocco CM", "Papin JA", "Criss AK."] +title = "Transcriptome-guided metabolic network analysis reveals rearrangements of carbon flux distribution in Neisseria gonorrhoeae during neutrophil co-culture" +journal = "mSystems" +what = "article" +doi = "10.1128/msystems.01265-22" +pubmed = "37387581" +date = "2023-06-30" +keywords = [] ++++ + diff --git a/content/pubs/PM37438349.md b/content/pubs/PM37438349.md new file mode 100644 index 0000000..0142386 --- /dev/null +++ b/content/pubs/PM37438349.md @@ -0,0 +1,11 @@ ++++ +authors = ["Kroll A", "Rousset Y", "Hu XP", "Liebrand NA", "Lercher MJ."] +title = "Turnover number predictions for kinetically uncharacterized enzymes using machine and deep learning" +journal = "Nat Commun" +what = "article" +doi = "10.1038/s41467-023-39840-4" +pubmed = "37438349" +date = "2023-07-12" +keywords = [] ++++ + diff --git a/content/pubs/PM37446331.md b/content/pubs/PM37446331.md new file mode 100644 index 0000000..ba3c4d5 --- /dev/null +++ b/content/pubs/PM37446331.md @@ -0,0 +1,11 @@ ++++ +authors = ["Fernández-García M", "Ares-Arroyo M", "Wedel E", "Montero N", "Barbas C", "Rey-Stolle MF", "González-Zorn B", "García A."] +title = "Multiplatform Metabolomics Characterization Reveals Novel Metabolites and Phospholipid Compositional Rules of Haemophilus influenzae Rd KW20" +journal = "Int J Mol Sci" +what = "article" +doi = "10.3390/ijms241311150" +pubmed = "37446331" +date = "2023-07-14" +keywords = [] ++++ + diff --git a/content/pubs/PM37455283.md b/content/pubs/PM37455283.md new file mode 100644 index 0000000..e95cbf6 --- /dev/null +++ b/content/pubs/PM37455283.md @@ -0,0 +1,11 @@ ++++ +authors = ["Qin Y", "Li Q", "Fan L", "Ning X", "Wei X", "You C."] +title = "Biomanufacturing by In Vitro Biotransformation (ivBT) Using Purified Cascade Multi-enzymes" +journal = "Adv Biochem Eng Biotechnol" +what = "article" +doi = "10.1007/10_2023_231" +pubmed = "37455283" +date = "2023-07-16" +keywords = [] ++++ + diff --git a/content/pubs/PM37474497.md b/content/pubs/PM37474497.md new file mode 100644 index 0000000..99cc637 --- /dev/null +++ b/content/pubs/PM37474497.md @@ -0,0 +1,11 @@ ++++ +authors = ["Mirhakkak MH", "Chen X", "Ni Y", "Heinekamp T", "Sae-Ong T", "Xu LL", "Kurzai O", "Barber AE", "Brakhage AA", "Boutin S", "Schäuble S", "Panagiotou G."] +title = "Genome-scale metabolic modeling of Aspergillus fumigatus strains reveals growth dependencies on the lung microbiome" +journal = "Nat Commun" +what = "article" +doi = "10.1038/s41467-023-39982-5" +pubmed = "37474497" +date = "2023-07-20" +keywords = [] ++++ + diff --git a/content/pubs/PM37487080.md b/content/pubs/PM37487080.md new file mode 100644 index 0000000..b7a1815 --- /dev/null +++ b/content/pubs/PM37487080.md @@ -0,0 +1,11 @@ ++++ +authors = ["Gellner G", "McCann K", "Hastings A."] +title = "Stable diverse food webs become more common when interactions are more biologically constrained" +journal = "Proc Natl Acad Sci U S A" +what = "article" +doi = "10.1073/pnas.2212061120" +pubmed = "37487080" +date = "2023-07-24" +keywords = [] ++++ + diff --git a/content/pubs/PM37526524.md b/content/pubs/PM37526524.md new file mode 100644 index 0000000..6a55198 --- /dev/null +++ b/content/pubs/PM37526524.md @@ -0,0 +1,11 @@ ++++ +authors = ["Mathur D", "Liao C", "Lin W", "La Ferlita A", "Alaimo S", "Taylor S", "Zhong Y", "Iacobuzio-Donahue C", "Ferro A", "Xavier JB."] +title = "The Ratio of Key Metabolic Transcripts Is a Predictive Biomarker of Breast Cancer Metastasis to the Lung" +journal = "Cancer Res" +what = "article" +doi = "10.1158/0008-5472.CAN-23-0153" +pubmed = "37526524" +date = "2023-08-01" +keywords = [] ++++ + diff --git a/content/pubs/PM37537166.md b/content/pubs/PM37537166.md new file mode 100644 index 0000000..be9ca04 --- /dev/null +++ b/content/pubs/PM37537166.md @@ -0,0 +1,11 @@ ++++ +authors = ["Bekiaris PS", "Klamt S."] +title = "Network-wide thermodynamic constraints shape NAD(P)H cofactor specificity of biochemical reactions" +journal = "Nat Commun" +what = "article" +doi = "10.1038/s41467-023-40297-8" +pubmed = "37537166" +date = "2023-08-03" +keywords = [] ++++ + diff --git a/content/pubs/PM37537192.md b/content/pubs/PM37537192.md new file mode 100644 index 0000000..3a30573 --- /dev/null +++ b/content/pubs/PM37537192.md @@ -0,0 +1,11 @@ ++++ +authors = ["Faure L", "Mollet B", "Liebermeister W", "Faulon JL."] +title = "A neural-mechanistic hybrid approach improving the predictive power of genome-scale metabolic models" +journal = "Nat Commun" +what = "article" +doi = "10.1038/s41467-023-40380-0" +pubmed = "37537192" +date = "2023-08-03" +keywords = [] ++++ + diff --git a/content/pubs/PM37554249.md b/content/pubs/PM37554249.md new file mode 100644 index 0000000..aa7fb2a --- /dev/null +++ b/content/pubs/PM37554249.md @@ -0,0 +1,11 @@ ++++ +authors = ["Wu Y", "Yuan Q", "Yang Y", "Liu D", "Yang S", "Ma H."] +title = "Construction and application of high-quality genome-scale metabolic model of Zymomonas mobilis to guide rational design of microbial cell factories" +journal = "Synth Syst Biotechnol" +what = "article" +doi = "10.1016/j.synbio.2023.07.001" +pubmed = "37554249" +date = "2023-08-09" +keywords = [] ++++ + diff --git a/content/pubs/PM37561998.md b/content/pubs/PM37561998.md new file mode 100644 index 0000000..ed48e98 --- /dev/null +++ b/content/pubs/PM37561998.md @@ -0,0 +1,11 @@ ++++ +authors = ["Wu C", "Guarnieri M", "Xiong W."] +title = "FreeFlux: A Python Package for Time-Efficient Isotopically Nonstationary Metabolic Flux Analysis" +journal = "ACS Synth Biol" +what = "article" +doi = "10.1021/acssynbio.3c00265" +pubmed = "37561998" +date = "2023-08-10" +keywords = [] ++++ + diff --git a/content/pubs/PM37578975.md b/content/pubs/PM37578975.md new file mode 100644 index 0000000..6b68b60 --- /dev/null +++ b/content/pubs/PM37578975.md @@ -0,0 +1,11 @@ ++++ +authors = ["Scott WT Jr", "Benito-Vaquerizo S", "Zimmermann J", "Bajić D", "Heinken A", "Suarez-Diez M", "Schaap PJ."] +title = "A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia" +journal = "PLoS Comput Biol" +what = "article" +doi = "10.1371/journal.pcbi.1011363" +pubmed = "37578975" +date = "2023-08-14" +keywords = [] ++++ + diff --git a/content/pubs/PM37603746.md b/content/pubs/PM37603746.md new file mode 100644 index 0000000..838e974 --- /dev/null +++ b/content/pubs/PM37603746.md @@ -0,0 +1,11 @@ ++++ +authors = ["He L", "Groom JD", "Wilson EH", "Fernandez J", "Konopka MC", "Beck DAC", "Lidstrom ME."] +title = "A methanotrophic bacterium to enable methane removal for climate mitigation" +journal = "Proc Natl Acad Sci U S A" +what = "article" +doi = "10.1073/pnas.2310046120" +pubmed = "37603746" +date = "2023-08-21" +keywords = [] ++++ + diff --git a/content/pubs/PM37616156.md b/content/pubs/PM37616156.md new file mode 100644 index 0000000..cfd903a --- /dev/null +++ b/content/pubs/PM37616156.md @@ -0,0 +1,11 @@ ++++ +authors = ["van Lent P", "Schmitz J", "Abeel T."] +title = "Simulated Design-Build-Test-Learn Cycles for Consistent Comparison of Machine Learning Methods in Metabolic Engineering" +journal = "ACS Synth Biol" +what = "article" +doi = "10.1021/acssynbio.3c00186" +pubmed = "37616156" +date = "2023-08-24" +keywords = [] ++++ + diff --git a/content/pubs/PM37619982.md b/content/pubs/PM37619982.md new file mode 100644 index 0000000..0fe8bef --- /dev/null +++ b/content/pubs/PM37619982.md @@ -0,0 +1,11 @@ ++++ +authors = ["Takano S", "Vila JCC", "Miyazaki R", "Sánchez Á", "Bajić D."] +title = "The Architecture of Metabolic Networks Constrains the Evolution of Microbial Resource Hierarchies" +journal = "Mol Biol Evol" +what = "article" +doi = "10.1093/molbev/msad187" +pubmed = "37619982" +date = "2023-08-24" +keywords = [] ++++ + diff --git a/content/pubs/PM37645048.md b/content/pubs/PM37645048.md new file mode 100644 index 0000000..00799fc --- /dev/null +++ b/content/pubs/PM37645048.md @@ -0,0 +1,11 @@ ++++ +authors = ["Xu J", "Geng G", "Nguyen ND", "Perena-Cortes C", "Samuels C", "Sauro HM."] +title = "SBcoyote: An Extensible Python-Based Reaction Editor and Viewer" +journal = "ArXiv" +what = "article" +doi = "nan" +pubmed = "37645048" +date = "2023-08-30" +keywords = [] ++++ + diff --git a/content/pubs/PM37652926.md b/content/pubs/PM37652926.md new file mode 100644 index 0000000..448b1ec --- /dev/null +++ b/content/pubs/PM37652926.md @@ -0,0 +1,11 @@ ++++ +authors = ["Liu L", "Li J", "Gai Y", "Tian Z", "Wang Y", "Wang T", "Liu P", "Yuan Q", "Ma H", "Lee SY", "Zhang D."] +title = "Protein engineering and iterative multimodule optimization for vitamin B(6) production in Escherichia coli" +journal = "Nat Commun" +what = "article" +doi = "10.1038/s41467-023-40928-0" +pubmed = "37652926" +date = "2023-08-31" +keywords = [] ++++ + diff --git a/content/pubs/PM37653010.md b/content/pubs/PM37653010.md new file mode 100644 index 0000000..9e78c9c --- /dev/null +++ b/content/pubs/PM37653010.md @@ -0,0 +1,11 @@ ++++ +authors = ["Gralka M", "Pollak S", "Cordero OX."] +title = "Genome content predicts the carbon catabolic preferences of heterotrophic bacteria" +journal = "Nat Microbiol" +what = "article" +doi = "10.1038/s41564-023-01458-z" +pubmed = "37653010" +date = "2023-08-31" +keywords = [] ++++ + diff --git a/content/pubs/PM37675104.md b/content/pubs/PM37675104.md new file mode 100644 index 0000000..87608e9 --- /dev/null +++ b/content/pubs/PM37675104.md @@ -0,0 +1,11 @@ ++++ +authors = ["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", "Boscá L."] +title = "Immunometabolic actions of trabectedin and lurbinectedin on human macrophages: relevance for their anti-tumor activity" +journal = "Front Immunol" +what = "article" +doi = "10.3389/fimmu.2023.1211068" +pubmed = "37675104" +date = "2023-09-07" +keywords = [] ++++ + diff --git a/content/pubs/PM37704397.md b/content/pubs/PM37704397.md new file mode 100644 index 0000000..cb99576 --- /dev/null +++ b/content/pubs/PM37704397.md @@ -0,0 +1,11 @@ ++++ +authors = ["Ziegler AL", "Grütering C", "Poduschnick L", "Mitsos A", "Blank LM."] +title = "Co-feeding enhances the yield of methyl ketones" +journal = "J Ind Microbiol Biotechnol" +what = "article" +doi = "10.1093/jimb/kuad029" +pubmed = "37704397" +date = "2023-09-13" +keywords = [] ++++ + diff --git a/content/pubs/PM37705596.md b/content/pubs/PM37705596.md new file mode 100644 index 0000000..48beb62 --- /dev/null +++ b/content/pubs/PM37705596.md @@ -0,0 +1,11 @@ ++++ +authors = ["Aghakhani S", "Silva-Saffar SE", "Soliman S", "Niarakis A."] +title = "Hybrid computational modeling highlights reverse warburg effect in breast cancer-associated fibroblasts" +journal = "Comput Struct Biotechnol J" +what = "article" +doi = "10.1016/j.csbj.2023.08.015" +pubmed = "37705596" +date = "2023-09-14" +keywords = [] ++++ + diff --git a/content/pubs/PM37726433.md b/content/pubs/PM37726433.md new file mode 100644 index 0000000..83a3407 --- /dev/null +++ b/content/pubs/PM37726433.md @@ -0,0 +1,11 @@ ++++ +authors = ["Arif M", "Matyas C", "Mukhopadhyay P", "Yokus B", "Trojnar E", "Paloczi J", "Paes-Leme B", "Zhao S", "Lohoff FW", "Haskó G", "Pacher P."] +title = "Data-driven transcriptomics analysis identifies PCSK9 as a novel key regulator in liver aging" +journal = "Geroscience" +what = "article" +doi = "10.1007/s11357-023-00928-w" +pubmed = "37726433" +date = "2023-09-19" +keywords = [] ++++ + diff --git a/content/pubs/PM37729340.md b/content/pubs/PM37729340.md new file mode 100644 index 0000000..10a7d8b --- /dev/null +++ b/content/pubs/PM37729340.md @@ -0,0 +1,11 @@ ++++ +authors = ["Cunha E", "Silva M", "Chaves I", "Demirci H", "Lagoa DR", "Lima D", "Rocha M", "Rocha I", "Dias O."] +title = "The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber" +journal = "PLoS Comput Biol" +what = "article" +doi = "10.1371/journal.pcbi.1011499" +pubmed = "37729340" +date = "2023-09-20" +keywords = [] ++++ + diff --git a/content/pubs/PM37737281.md b/content/pubs/PM37737281.md new file mode 100644 index 0000000..40210e1 --- /dev/null +++ b/content/pubs/PM37737281.md @@ -0,0 +1,11 @@ ++++ +authors = ["Moore RA", "Azua-Bustos A", "González-Silva C", "Carr CE."] +title = "Unveiling metabolic pathways involved in the extreme desiccation tolerance of an Atacama cyanobacterium" +journal = "Sci Rep" +what = "article" +doi = "10.1038/s41598-023-41879-8" +pubmed = "37737281" +date = "2023-09-22" +keywords = [] ++++ + diff --git a/content/pubs/PM37739963.md b/content/pubs/PM37739963.md new file mode 100644 index 0000000..793b827 --- /dev/null +++ b/content/pubs/PM37739963.md @@ -0,0 +1,11 @@ ++++ +authors = ["Kugler A", "Stensjö K."] +title = "Optimal energy and redox metabolism in the cyanobacterium Synechocystis sp. PCC 6803" +journal = "NPJ Syst Biol Appl" +what = "article" +doi = "10.1038/s41540-023-00307-3" +pubmed = "37739963" +date = "2023-09-22" +keywords = [] ++++ + diff --git a/content/pubs/PM37790242.md b/content/pubs/PM37790242.md new file mode 100644 index 0000000..888948d --- /dev/null +++ b/content/pubs/PM37790242.md @@ -0,0 +1,11 @@ ++++ +authors = ["Caivano A", "van Winden W", "Dragone G", "Mussatto SI."] +title = "Enzyme-constrained metabolic model and in silico metabolic engineering of Clostridium ljungdahlii for the development of sustainable production processes" +journal = "Comput Struct Biotechnol J" +what = "article" +doi = "10.1016/j.csbj.2023.09.015" +pubmed = "37790242" +date = "2023-10-04" +keywords = [] ++++ + diff --git a/content/pubs/PM37815531.md b/content/pubs/PM37815531.md new file mode 100644 index 0000000..545144d --- /dev/null +++ b/content/pubs/PM37815531.md @@ -0,0 +1,11 @@ ++++ +authors = ["Vezina B", "Watts SC", "Hawkey J", "Cooper HB", "Judd LM", "Jenney AWJ", "Monk JM", "Holt KE", "Wyres KL."] +title = "Bactabolize is a tool for high-throughput generation of bacterial strain-specific metabolic models" +journal = "Elife" +what = "article" +doi = "10.7554/eLife.87406" +pubmed = "37815531" +date = "2023-10-10" +keywords = [] ++++ + diff --git a/content/pubs/PM37838667.md b/content/pubs/PM37838667.md new file mode 100644 index 0000000..609e07b --- /dev/null +++ b/content/pubs/PM37838667.md @@ -0,0 +1,11 @@ ++++ +authors = ["Gu B", "Kim DG", "Kim DK", "Kim M", "Kim HU", "Oh MK."] +title = "Heterologous overproduction of oviedomycin by refactoring biosynthetic gene cluster and metabolic engineering of host strain Streptomyces coelicolor" +journal = "Microb Cell Fact" +what = "article" +doi = "10.1186/s12934-023-02218-8" +pubmed = "37838667" +date = "2023-10-14" +keywords = [] ++++ + diff --git a/content/pubs/PM37854702.md b/content/pubs/PM37854702.md new file mode 100644 index 0000000..d09d5fd --- /dev/null +++ b/content/pubs/PM37854702.md @@ -0,0 +1,11 @@ ++++ +authors = ["Casini I", "McCubbin T", "Esquivel-Elizondo S", "Luque GG", "Evseeva D", "Fink C", "Beblawy S", "Youngblut ND", "Aristilde L", "Huson DH", "Dräger A", "Ley RE", "Marcellin E", "Angenent LT", "Molitor B."] +title = "An integrated systems biology approach reveals differences in formate metabolism in the genus Methanothermobacter" +journal = "iScience" +what = "article" +doi = "10.1016/j.isci.2023.108016" +pubmed = "37854702" +date = "2023-10-19" +keywords = [] ++++ + diff --git a/content/pubs/PM37876626.md b/content/pubs/PM37876626.md new file mode 100644 index 0000000..347b421 --- /dev/null +++ b/content/pubs/PM37876626.md @@ -0,0 +1,11 @@ ++++ +authors = ["Gonçalves DM", "Henriques R", "Costa RS."] +title = "Predicting metabolic fluxes from omics data via machine learning: Moving from knowledge-driven towards data-driven approaches" +journal = "Comput Struct Biotechnol J" +what = "article" +doi = "10.1016/j.csbj.2023.10.002" +pubmed = "37876626" +date = "2023-10-25" +keywords = [] ++++ + diff --git a/content/pubs/PM37880541.md b/content/pubs/PM37880541.md new file mode 100644 index 0000000..4720127 --- /dev/null +++ b/content/pubs/PM37880541.md @@ -0,0 +1,11 @@ ++++ +authors = ["McDaniel EA", "Scarborough M", "Mulat DG", "Lin X", "Sampara PS", "Olson HM", "Young RP", "Eder EK", "Attah IK", "Markillie LM", "Hoyt DW", "Lipton MS", "Hallam SJ", "Ziels RM."] +title = "Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium" +journal = "ISME J" +what = "article" +doi = "10.1038/s41396-023-01542-6" +pubmed = "37880541" +date = "2023-10-25" +keywords = [] ++++ + diff --git a/content/pubs/PM37885608.md b/content/pubs/PM37885608.md new file mode 100644 index 0000000..c0441d1 --- /dev/null +++ b/content/pubs/PM37885608.md @@ -0,0 +1,11 @@ ++++ +authors = ["Meydan Y", "Baldini F", "Korem T."] +title = "pymgpipe: microbiome metabolic modeling in Python" +journal = "J Open Source Softw" +what = "article" +doi = "10.21105/joss.05545" +pubmed = "37885608" +date = "2023-10-27" +keywords = [] ++++ + diff --git a/content/pubs/PM37888487.md b/content/pubs/PM37888487.md new file mode 100644 index 0000000..50ac22f --- /dev/null +++ b/content/pubs/PM37888487.md @@ -0,0 +1,11 @@ ++++ +authors = ["Bernstein DB", "Akkas B", "Price MN", "Arkin AP."] +title = "Evaluating E. coli genome-scale metabolic model accuracy with high-throughput mutant fitness data" +journal = "Mol Syst Biol" +what = "article" +doi = "10.15252/msb.202311566" +pubmed = "37888487" +date = "2023-10-27" +keywords = [] ++++ + diff --git a/content/pubs/PM37898597.md b/content/pubs/PM37898597.md new file mode 100644 index 0000000..4f46c50 --- /dev/null +++ b/content/pubs/PM37898597.md @@ -0,0 +1,11 @@ ++++ +authors = ["Liu Y", "Westerhoff HV."] +title = "'Social' versus 'asocial' cells-dynamic competition flux balance analysis" +journal = "NPJ Syst Biol Appl" +what = "article" +doi = "10.1038/s41540-023-00313-5" +pubmed = "37898597" +date = "2023-10-29" +keywords = [] ++++ + diff --git a/content/pubs/PM37907472.md b/content/pubs/PM37907472.md new file mode 100644 index 0000000..31e7931 --- /dev/null +++ b/content/pubs/PM37907472.md @@ -0,0 +1,11 @@ ++++ +authors = ["Bay ÖF", "Hayes KS", "Schwartz JM", "Grencis RK", "Roberts IS."] +title = "A genome-scale metabolic model of parasitic whipworm" +journal = "Nat Commun" +what = "article" +doi = "10.1038/s41467-023-42552-4" +pubmed = "37907472" +date = "2023-11-01" +keywords = [] ++++ + diff --git a/content/pubs/PM37930022.md b/content/pubs/PM37930022.md new file mode 100644 index 0000000..a43fd38 --- /dev/null +++ b/content/pubs/PM37930022.md @@ -0,0 +1,11 @@ ++++ +authors = ["Bessell B", "Loecker J", "Zhao Z", "Aghamiri SS", "Mohanty S", "Amin R", "Helikar T", "Puniya BL."] +title = "COMO: a pipeline for multi-omics data integration in metabolic modeling and drug discovery" +journal = "Brief Bioinform" +what = "article" +doi = "10.1093/bib/bbad387" +pubmed = "37930022" +date = "2023-11-06" +keywords = [] ++++ + diff --git a/content/pubs/PM37931133.md b/content/pubs/PM37931133.md new file mode 100644 index 0000000..3df97aa --- /dev/null +++ b/content/pubs/PM37931133.md @@ -0,0 +1,11 @@ ++++ +authors = ["Carrasco Muriel J", "Long C", "Sonnenschein N."] +title = "Simultaneous application of enzyme and thermodynamic constraints to metabolic models using an updated Python implementation of GECKO" +journal = "Microbiol Spectr" +what = "article" +doi = "10.1128/spectrum.01705-23" +pubmed = "37931133" +date = "2023-11-06" +keywords = [] ++++ + diff --git a/content/pubs/PM37936955.md b/content/pubs/PM37936955.md new file mode 100644 index 0000000..cfbd343 --- /dev/null +++ b/content/pubs/PM37936955.md @@ -0,0 +1,11 @@ ++++ +authors = ["Bäuerle F", "Döbel GO", "Camus L", "Heilbronner S", "Dräger A."] +title = "Genome-scale metabolic models consistently predict in vitro characteristics of Corynebacterium striatum" +journal = "Front Bioinform" +what = "article" +doi = "10.3389/fbinf.2023.1214074" +pubmed = "37936955" +date = "2023-11-08" +keywords = [] ++++ + diff --git a/content/pubs/PM37943960.md b/content/pubs/PM37943960.md new file mode 100644 index 0000000..e80a733 --- /dev/null +++ b/content/pubs/PM37943960.md @@ -0,0 +1,11 @@ ++++ +authors = ["Ghini V", "Vieri W", "Celli T", "Pecchioli V", "Boccia N", "Alonso-Vásquez T", "Pelagatti L", "Fondi M", "Luchinat C", "Bertini L", "Vannucchi V", "Landini G", "Turano P."] +title = "COVID-19: A complex disease with a unique metabolic signature" +journal = "PLoS Pathog" +what = "article" +doi = "10.1371/journal.ppat.1011787" +pubmed = "37943960" +date = "2023-11-09" +keywords = [] ++++ + diff --git a/content/pubs/PM37948450.md b/content/pubs/PM37948450.md new file mode 100644 index 0000000..1c69008 --- /dev/null +++ b/content/pubs/PM37948450.md @@ -0,0 +1,11 @@ ++++ +authors = ["Backman TWH", "Schenk C", "Radivojevic T", "Ando D", "Singh J", "Czajka JJ", "Costello Z", "Keasling JD", "Tang Y", "Akhmatskaya E", "Garcia Martin H."] +title = "BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale" +journal = "PLoS Comput Biol" +what = "article" +doi = "10.1371/journal.pcbi.1011111" +pubmed = "37948450" +date = "2023-11-10" +keywords = [] ++++ + diff --git a/content/pubs/PM37948461.md b/content/pubs/PM37948461.md new file mode 100644 index 0000000..2b6b4d6 --- /dev/null +++ b/content/pubs/PM37948461.md @@ -0,0 +1,11 @@ ++++ +authors = ["Yubero P", "Lavin AA", "Poyatos JF."] +title = "The limitations of phenotype prediction in metabolism" +journal = "PLoS Comput Biol" +what = "article" +doi = "10.1371/journal.pcbi.1011631" +pubmed = "37948461" +date = "2023-11-10" +keywords = [] ++++ + diff --git a/content/pubs/PM37956203.md b/content/pubs/PM37956203.md new file mode 100644 index 0000000..c6c50ea --- /dev/null +++ b/content/pubs/PM37956203.md @@ -0,0 +1,11 @@ ++++ +authors = ["Brunner JD", "Gallegos-Graves LA", "Kroeger ME."] +title = "Inferring microbial interactions with their environment from genomic and metagenomic data" +journal = "PLoS Comput Biol" +what = "article" +doi = "10.1371/journal.pcbi.1011661" +pubmed = "37956203" +date = "2023-11-13" +keywords = [] ++++ + diff --git a/content/pubs/PM37961608.md b/content/pubs/PM37961608.md new file mode 100644 index 0000000..bdbddc0 --- /dev/null +++ b/content/pubs/PM37961608.md @@ -0,0 +1,11 @@ ++++ +authors = ["Vila JCC", "Goldford J", "Estrela S", "Bajic D", "Sanchez-Gorostiaga A", "Damian-Serrano A", "Lu N", "Marsland R 3rd", "Rebolleda-Gomez M", "Mehta P", "Sanchez A."] +title = "Metabolic similarity and the predictability of microbial community assembly" +journal = "bioRxiv" +what = "article" +doi = "10.1101/2023.10.25.564019" +pubmed = "37961608" +date = "2023-11-14" +keywords = [] ++++ + diff --git a/content/pubs/PM37990145.md b/content/pubs/PM37990145.md new file mode 100644 index 0000000..c3bd929 --- /dev/null +++ b/content/pubs/PM37990145.md @@ -0,0 +1,11 @@ ++++ +authors = ["Pettersen JP", "Castillo S", "Jouhten P", "Almaas E."] +title = "Genome-scale metabolic models reveal determinants of phenotypic differences in non-Saccharomyces yeasts" +journal = "BMC Bioinformatics" +what = "article" +doi = "10.1186/s12859-023-05506-7" +pubmed = "37990145" +date = "2023-11-22" +keywords = [] ++++ + diff --git a/content/pubs/PM37997613.md b/content/pubs/PM37997613.md new file mode 100644 index 0000000..b38108f --- /dev/null +++ b/content/pubs/PM37997613.md @@ -0,0 +1,11 @@ ++++ +authors = ["Kaste JAM", "Shachar-Hill Y."] +title = "Model validation and selection in metabolic flux analysis and flux balance analysis" +journal = "Biotechnol Prog" +what = "article" +doi = "10.1002/btpr.3413" +pubmed = "37997613" +date = "2023-11-24" +keywords = [] ++++ + diff --git a/content/pubs/PM38017439.md b/content/pubs/PM38017439.md new file mode 100644 index 0000000..6c6dfad --- /dev/null +++ b/content/pubs/PM38017439.md @@ -0,0 +1,11 @@ ++++ +authors = ["Gotsmy M", "Strobl F", "Weiß F", "Gruber P", "Kraus B", "Mairhofer J", "Zanghellini J."] +title = "Sulfate limitation increases specific plasmid DNA yield and productivity in E. coli fed-batch processes" +journal = "Microb Cell Fact" +what = "article" +doi = "10.1186/s12934-023-02248-2" +pubmed = "38017439" +date = "2023-11-29" +keywords = [] ++++ + diff --git a/content/pubs/PM38019129.md b/content/pubs/PM38019129.md new file mode 100644 index 0000000..202f9db --- /dev/null +++ b/content/pubs/PM38019129.md @@ -0,0 +1,11 @@ ++++ +authors = ["Dhamija B", "Marathe S", "Sawant V", "Basu M", "Attrish D", "Mukherjee D", "Kumar S", "Pai MGJ", "Wad S", "Sawant A", "Nayak C", "Venkatesh KV", "Srivastava S", "Barthel SR", "Purwar R."] +title = "IL-17A Orchestrates Reactive Oxygen Species/HIF1α-Mediated Metabolic Reprogramming in Psoriasis" +journal = "J Immunol" +what = "article" +doi = "10.4049/jimmunol.2300319" +pubmed = "38019129" +date = "2023-11-29" +keywords = [] ++++ + diff --git a/content/pubs/PM38024155.md b/content/pubs/PM38024155.md new file mode 100644 index 0000000..1aa71de --- /dev/null +++ b/content/pubs/PM38024155.md @@ -0,0 +1,11 @@ ++++ +authors = ["Wilson AN", "St John PC", "Marin DH", "Hoyt CB", "Rognerud EG", "Nimlos MR", "Cywar RM", "Rorrer NA", "Shebek KM", "Broadbelt LJ", "Beckham GT", "Crowley MF."] +title = "PolyID: Artificial Intelligence for Discovering Performance-Advantaged and Sustainable Polymers" +journal = "Macromolecules" +what = "article" +doi = "10.1021/acs.macromol.3c00994" +pubmed = "38024155" +date = "2023-11-29" +keywords = [] ++++ + diff --git a/content/pubs/PM38053556.md b/content/pubs/PM38053556.md new file mode 100644 index 0000000..f4a5fd2 --- /dev/null +++ b/content/pubs/PM38053556.md @@ -0,0 +1,11 @@ ++++ +authors = ["Wu P", "Yuan Q", "Cheng T", "Han Y", "Zhao W", "Liao X", "Wang L", "Cai J", "He Q", "Guo Y", "Zhang X", "Lu F", "Wang J", "Ma H", "Huang Z."] +title = "Genome sequencing and metabolic network reconstruction of a novel sulfur-oxidizing bacterium Acidithiobacillus Ameehan" +journal = "Front Microbiol" +what = "article" +doi = "10.3389/fmicb.2023.1277847" +pubmed = "38053556" +date = "2023-12-06" +keywords = [] ++++ + diff --git a/content/pubs/PM38059748.md b/content/pubs/PM38059748.md new file mode 100644 index 0000000..d1c6d83 --- /dev/null +++ b/content/pubs/PM38059748.md @@ -0,0 +1,11 @@ ++++ +authors = ["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", "Baines JF."] +title = "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" +journal = "Gut Microbes" +what = "article" +doi = "10.1080/19490976.2023.2286675" +pubmed = "38059748" +date = "2023-12-07" +keywords = [] ++++ + diff --git a/content/pubs/PM38075858.md b/content/pubs/PM38075858.md new file mode 100644 index 0000000..547df82 --- /dev/null +++ b/content/pubs/PM38075858.md @@ -0,0 +1,11 @@ ++++ +authors = ["Marcos-Zambrano LJ", "López-Molina VM", "Bakir-Gungor B", "Frohme M", "Karaduzovic-Hadziabdic K", "Klammsteiner T", "Ibrahimi E", "Lahti L", "Loncar-Turukalo T", "Dhamo X", "Simeon A", "Nechyporenko A", "Pio G", "Przymus P", "Sampri A", "Trajkovik V", "Lacruz-Pleguezuelos B", "Aasmets O", "Araujo R", "Anagnostopoulos I", "Aydemir Ö", "Berland M", "Calle ML", "Ceci M", "Duman H", "Gündoğdu A", "Havulinna AS", "Kaka Bra KHN", "Kalluci E", "Karav S", "Lode D", "Lopes MB", "May P", "Nap B", "Nedyalkova M", "Paciência I", "Pasic L", "Pujolassos M", "Shigdel R", "Susín A", "Thiele I", "Truică CO", "Wilmes P", "Yilmaz E", "Yousef M", "Claesson MJ", "Truu J", "Carrillo de Santa Pau E."] +title = "A toolbox of machine learning software to support microbiome analysis" +journal = "Front Microbiol" +what = "article" +doi = "10.3389/fmicb.2023.1250806" +pubmed = "38075858" +date = "2023-12-11" +keywords = [] ++++ + diff --git a/content/pubs/PM38093511.md b/content/pubs/PM38093511.md new file mode 100644 index 0000000..2bf10e9 --- /dev/null +++ b/content/pubs/PM38093511.md @@ -0,0 +1,11 @@ ++++ +authors = ["Xue B", "Liu Y", "Yang C", "Liu H", "Yuan Q", "Wang S", "Su H."] +title = "Co-Cultivated Enzyme Constraint Metabolic Network Model for Rational Guidance in Constructing Synthetic Consortia to Achieve Optimal Pathway Allocation Prediction" +journal = "Adv Sci (Weinh)" +what = "article" +doi = "10.1002/advs.202306662" +pubmed = "38093511" +date = "2023-12-14" +keywords = [] ++++ + diff --git a/content/pubs/PM38113208.md b/content/pubs/PM38113208.md new file mode 100644 index 0000000..9ee2e5d --- /dev/null +++ b/content/pubs/PM38113208.md @@ -0,0 +1,11 @@ ++++ +authors = ["Li Z", "Selim A", "Kuehn S."] +title = "Statistical prediction of microbial metabolic traits from genomes" +journal = "PLoS Comput Biol" +what = "article" +doi = "10.1371/journal.pcbi.1011705" +pubmed = "38113208" +date = "2023-12-19" +keywords = [] ++++ + diff --git a/content/pubs/PM38129392.md b/content/pubs/PM38129392.md new file mode 100644 index 0000000..00647f1 --- /dev/null +++ b/content/pubs/PM38129392.md @@ -0,0 +1,11 @@ ++++ +authors = ["Melkonian C", "Zorrilla F", "Kjærbølling I", "Blasche S", "Machado D", "Junge M", "Sørensen KI", "Andersen LT", "Patil KR", "Zeidan AA."] +title = "Microbial interactions shape cheese flavour formation" +journal = "Nat Commun" +what = "article" +doi = "10.1038/s41467-023-41059-2" +pubmed = "38129392" +date = "2023-12-21" +keywords = [] ++++ + diff --git a/content/pubs/PM38131671.md b/content/pubs/PM38131671.md new file mode 100644 index 0000000..8575fa4 --- /dev/null +++ b/content/pubs/PM38131671.md @@ -0,0 +1,11 @@ ++++ +authors = ["Tanwee TNN", "Lipscomb GL", "Vailionis JL", "Zhang K", "Bing RG", "O'Quinn HC", "Poole FL", "Zhang Y", "Kelly RM", "Adams MWW."] +title = "Metabolic engineering of Caldicellulosiruptor bescii for 2,3-butanediol production from unpretreated lignocellulosic biomass and metabolic strategies for improving yields and titers" +journal = "Appl Environ Microbiol" +what = "article" +doi = "10.1128/aem.01951-23" +pubmed = "38131671" +date = "2023-12-22" +keywords = [] ++++ + diff --git a/content/pubs/PM38138131.md b/content/pubs/PM38138131.md new file mode 100644 index 0000000..d971574 --- /dev/null +++ b/content/pubs/PM38138131.md @@ -0,0 +1,11 @@ ++++ +authors = ["Kulyashov MA", "Kolmykov SK", "Khlebodarova TM", "Akberdin IR."] +title = "State-of the-Art Constraint-Based Modeling of Microbial Metabolism: From Basics to Context-Specific Models with a Focus on Methanotrophs" +journal = "Microorganisms" +what = "article" +doi = "10.3390/microorganisms11122987" +pubmed = "38138131" +date = "2023-12-23" +keywords = [] ++++ + diff --git a/content/pubs/PM38145946.md b/content/pubs/PM38145946.md new file mode 100644 index 0000000..971f9ee --- /dev/null +++ b/content/pubs/PM38145946.md @@ -0,0 +1,11 @@ ++++ +authors = ["Chen X", "Deng M", "Wang Z", "Huang C."] +title = "MMP3C: an in-silico framework to depict cancer metabolic plasticity using gene expression profiles" +journal = "Brief Bioinform" +what = "article" +doi = "10.1093/bib/bbad471" +pubmed = "38145946" +date = "2023-12-25" +keywords = [] ++++ + diff --git a/content/pubs/PM38150474.md b/content/pubs/PM38150474.md new file mode 100644 index 0000000..d32121f --- /dev/null +++ b/content/pubs/PM38150474.md @@ -0,0 +1,11 @@ ++++ +authors = ["Tubergen PJ", "Medlock G", "Moore A", "Zhang X", "Papin JA", "Danna CH."] +title = "A computational model of Pseudomonas syringae metabolism unveils a role for branched-chain amino acids in Arabidopsis leaf colonization" +journal = "PLoS Comput Biol" +what = "article" +doi = "10.1371/journal.pcbi.1011651" +pubmed = "38150474" +date = "2023-12-27" +keywords = [] ++++ + diff --git a/content/pubs/PM38172830.md b/content/pubs/PM38172830.md new file mode 100644 index 0000000..9ce744e --- /dev/null +++ b/content/pubs/PM38172830.md @@ -0,0 +1,11 @@ ++++ +authors = ["Wefelmeier K", "Schmitz S", "Kösters BJ", "Liebal UW", "Blank LM."] +title = "Methanol bioconversion into C3, C4, and C5 platform chemicals by the yeast Ogataea polymorpha" +journal = "Microb Cell Fact" +what = "article" +doi = "10.1186/s12934-023-02283-z" +pubmed = "38172830" +date = "2024-01-03" +keywords = [] ++++ + diff --git a/content/pubs/PM38179456.md b/content/pubs/PM38179456.md new file mode 100644 index 0000000..1de56e3 --- /dev/null +++ b/content/pubs/PM38179456.md @@ -0,0 +1,11 @@ ++++ +authors = ["Medina-Chávez NO", "Torres-Cerda A", "Chacón JM", "Harcombe WR", "De la Torre-Zavala S", "Travisano M."] +title = "Disentangling a metabolic cross-feeding in a halophilic archaea-bacteria consortium" +journal = "Front Microbiol" +what = "article" +doi = "10.3389/fmicb.2023.1276438" +pubmed = "38179456" +date = "2024-01-05" +keywords = [] ++++ + diff --git a/content/pubs/PM38180324.md b/content/pubs/PM38180324.md new file mode 100644 index 0000000..07c11cf --- /dev/null +++ b/content/pubs/PM38180324.md @@ -0,0 +1,11 @@ ++++ +authors = ["Bordel S", "Martín-González D", "Börner T", "Muñoz R", "Santos-Beneit F."] +title = "Genome-scale metabolic model of the versatile bacterium Paracoccus denitrificans Pd1222" +journal = "mSystems" +what = "article" +doi = "10.1128/msystems.01077-23" +pubmed = "38180324" +date = "2024-01-05" +keywords = [] ++++ + diff --git a/content/pubs/PM38182559.md b/content/pubs/PM38182559.md new file mode 100644 index 0000000..93879f1 --- /dev/null +++ b/content/pubs/PM38182559.md @@ -0,0 +1,11 @@ ++++ +authors = ["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", "Dottorini T."] +title = "Convergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken farms in China" +journal = "Nat Commun" +what = "article" +doi = "10.1038/s41467-023-44272-1" +pubmed = "38182559" +date = "2024-01-05" +keywords = [] ++++ + diff --git a/content/pubs/PM38189538.md b/content/pubs/PM38189538.md new file mode 100644 index 0000000..6a77482 --- /dev/null +++ b/content/pubs/PM38189538.md @@ -0,0 +1,11 @@ ++++ +authors = ["Qiu S", "Zhao S", "Yang A."] +title = "DLTKcat: deep learning-based prediction of temperature-dependent enzyme turnover rates" +journal = "Brief Bioinform" +what = "article" +doi = "10.1093/bib/bbad506" +pubmed = "38189538" +date = "2024-01-08" +keywords = [] ++++ + diff --git a/content/pubs/PM38229031.md b/content/pubs/PM38229031.md new file mode 100644 index 0000000..392de99 --- /dev/null +++ b/content/pubs/PM38229031.md @@ -0,0 +1,11 @@ ++++ +authors = ["Han S", "Kim D", "Kim Y", "Yoon SH."] +title = "Genome-scale metabolic network model and phenome of solvent-tolerant Pseudomonas putida S12" +journal = "BMC Genomics" +what = "article" +doi = "10.1186/s12864-023-09940-y" +pubmed = "38229031" +date = "2024-01-16" +keywords = [] ++++ + diff --git a/content/pubs/PM38287320.md b/content/pubs/PM38287320.md new file mode 100644 index 0000000..1d794af --- /dev/null +++ b/content/pubs/PM38287320.md @@ -0,0 +1,11 @@ ++++ +authors = ["Hassani L", "Moosavi MR", "Setoodeh P", "Zare H."] +title = "FastKnock: an efficient next-generation approach to identify all knockout strategies for strain optimization" +journal = "Microb Cell Fact" +what = "article" +doi = "10.1186/s12934-023-02277-x" +pubmed = "38287320" +date = "2024-01-29" +keywords = [] ++++ + diff --git a/content/pubs/PM38291231.md b/content/pubs/PM38291231.md new file mode 100644 index 0000000..06af802 --- /dev/null +++ b/content/pubs/PM38291231.md @@ -0,0 +1,11 @@ ++++ +authors = ["Woo H", "Kim Y", "Kim D", "Yoon SH."] +title = "Machine learning identifies key 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"Koellensperger G", "Mattanovich D", "Gasser B."] +title = "Protein production dynamics and physiological adaptation of recombinant Komagataella phaffii at near-zero growth rates" +journal = "Microb Cell Fact" +what = "article" +doi = "10.1186/s12934-024-02314-3" +pubmed = "38331812" +date = "2024-02-08" +keywords = [] ++++ + diff --git a/content/pubs/PM38370212.md b/content/pubs/PM38370212.md new file mode 100644 index 0000000..ad1f120 --- /dev/null +++ b/content/pubs/PM38370212.md @@ -0,0 +1,11 @@ ++++ +authors = ["Taherkhani H", "KavianFar A", "Aminnezhad S", "Lanjanian H", "Ahmadi A", "Azimzadeh S", "Masoudi-Nejad A."] +title = "Deciphering the impact of microbial interactions on COPD exacerbation: An in-depth analysis of the lung microbiome" +journal = "Heliyon" +what = "article" +doi = "10.1016/j.heliyon.2024.e24775" +pubmed = "38370212" +date = "2024-02-19" +keywords = [] ++++ + diff --git a/content/pubs/PM38376382.md b/content/pubs/PM38376382.md new file mode 100644 index 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"38386685" +date = "2024-02-22" +keywords = [] ++++ + diff --git a/content/pubs/PM38391229.md b/content/pubs/PM38391229.md new file mode 100644 index 0000000..a3cec88 --- /dev/null +++ b/content/pubs/PM38391229.md @@ -0,0 +1,11 @@ ++++ +authors = ["Jiang F", "Ruan Y", "Chen X-H", "Yu H-L", "Cheng T", "Duan X-Y", "Liu Y-G", "Zhang H-Y", "Zhang Q-Y."] +title = "Metabolites of pathogenic microorganisms database (MPMdb) and its seed metabolite applications" +journal = "Microbiol Spectr" +what = "article" +doi = "10.1128/spectrum.02342-23" +pubmed = "38391229" +date = "2024-02-23" +keywords = [] ++++ + diff --git a/content/pubs/PM38437212.md b/content/pubs/PM38437212.md new file mode 100644 index 0000000..af13d31 --- /dev/null +++ b/content/pubs/PM38437212.md @@ -0,0 +1,11 @@ ++++ +authors = ["Nayyara P", "Permana D", "Ermawar RA", "Fahayana R."] +title = "Computational analysis into the potential of azo dyes as a feedstock for actinorhodin biosynthesis in Pseudomonas putida" +journal = "PLoS One" +what = "article" +doi = "10.1371/journal.pone.0299128" +pubmed = "38437212" +date = "2024-03-04" +keywords = [] ++++ + diff --git a/content/pubs/PM38448436.md b/content/pubs/PM38448436.md new file mode 100644 index 0000000..c48c24a --- /dev/null +++ b/content/pubs/PM38448436.md @@ -0,0 +1,11 @@ ++++ +authors = ["Hasibi R", "Michoel T", "Oyarzún DA."] +title = "Integration of graph neural networks and genome-scale metabolic models for predicting gene essentiality" +journal = "NPJ Syst Biol Appl" +what = "article" +doi = "10.1038/s41540-024-00348-2" +pubmed = "38448436" +date = "2024-03-06" +keywords = [] ++++ + diff --git a/content/pubs/PM38452346.md b/content/pubs/PM38452346.md new file mode 100644 index 0000000..5c153b6 --- /dev/null +++ b/content/pubs/PM38452346.md @@ -0,0 +1,11 @@ ++++ +authors = ["Carrasco Muriel J", "Cowie N", "Taylor Parkins S", "Mansouvar M", "Groves T", "Nielsen LK."] +title = "Shu: visualization of high-dimensional biological pathways" +journal = "Bioinformatics" +what = "article" +doi = "10.1093/bioinformatics/btae140" +pubmed = "38452346" +date = "2024-03-07" +keywords = [] ++++ + diff --git a/content/pubs/PM38468344.md b/content/pubs/PM38468344.md new file mode 100644 index 0000000..7da2d8c --- /dev/null +++ b/content/pubs/PM38468344.md @@ -0,0 +1,11 @@ ++++ +authors = ["Lee G", "Lee SM", "Lee S", "Jeong CW", "Song H", "Lee SY", "Yun H", "Koh Y", "Kim HU."] +title = "Prediction of metabolites associated with somatic mutations in cancers by using genome-scale metabolic models and mutation data" +journal = "Genome Biol" +what = "article" +doi = "10.1186/s13059-024-03208-8" +pubmed = "38468344" +date = "2024-03-12" +keywords = [] ++++ + diff --git a/content/pubs/PM38532295.md b/content/pubs/PM38532295.md new file mode 100644 index 0000000..17149df --- /dev/null +++ b/content/pubs/PM38532295.md @@ -0,0 +1,11 @@ ++++ +authors = ["Predl M", "Mießkes M", "Rattei T", "Zanghellini J."] +title = "PyCoMo: a python package for community metabolic model creation and analysis" +journal = "Bioinformatics" +what = "article" +doi = "10.1093/bioinformatics/btae153" +pubmed = "38532295" +date = "2024-03-27" +keywords = [] ++++ + diff --git a/content/pubs/PM38565568.md b/content/pubs/PM38565568.md new file mode 100644 index 0000000..338a877 --- /dev/null +++ b/content/pubs/PM38565568.md @@ -0,0 +1,11 @@ ++++ +authors = ["Mahout M", "Carlson RP", "Simon L", "Peres S."] +title = "Logic programming-based Minimal Cut Sets reveal consortium-level therapeutic targets for chronic wound infections" +journal = "NPJ Syst Biol Appl" +what = "article" +doi = "10.1038/s41540-024-00360-6" +pubmed = "38565568" +date = "2024-04-02" +keywords = [] ++++ + diff --git a/content/pubs/PM38565581.md b/content/pubs/PM38565581.md new file mode 100644 index 0000000..98f5cf8 --- /dev/null +++ b/content/pubs/PM38565581.md @@ -0,0 +1,11 @@ ++++ +authors = ["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", "Berthelot L."] +title = "Investigating the metabolite signature of an altered oral microbiota as a discriminant factor for multiple sclerosis: a pilot study" +journal = "Sci Rep" +what = "article" +doi = "10.1038/s41598-024-57949-4" +pubmed = "38565581" +date = "2024-04-02" +keywords = [] ++++ + diff --git a/content/pubs/PM38590605.md b/content/pubs/PM38590605.md new file mode 100644 index 0000000..0ca844d --- /dev/null +++ b/content/pubs/PM38590605.md @@ -0,0 +1,11 @@ ++++ +authors = ["Ye A", "Shen JN", "Li Y", "Lian X", "Ma BG", "Guo FB."] +title = "Reconstruction of the genome-scale metabolic network model of Sinorhizobium fredii CCBAU45436 for free-living and symbiotic states" +journal = "Front Bioeng Biotechnol" +what = "article" +doi = "10.3389/fbioe.2024.1377334" +pubmed = "38590605" +date = "2024-04-09" +keywords = [] ++++ + diff --git 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and genomic sequencing of the oleaginous clade Lipomyces" +journal = "Front Bioeng Biotechnol" +what = "article" +doi = "10.3389/fbioe.2024.1356551" +pubmed = "38638323" +date = "2024-04-19" +keywords = [] ++++ + diff --git a/content/pubs/PM38651096.md b/content/pubs/PM38651096.md new file mode 100644 index 0000000..c04e40b --- /dev/null +++ b/content/pubs/PM38651096.md @@ -0,0 +1,11 @@ ++++ +authors = ["Mao Z", "Niu J", "Zhao J", "Huang Y", "Wu K", "Yun L", "Guan J", "Yuan Q", "Liao X", "Wang Z", "Ma H."] +title = "ECMpy 2.0: A Python package for automated construction and analysis of enzyme-constrained models" +journal = "Synth Syst Biotechnol" +what = "article" +doi = "10.1016/j.synbio.2024.04.005" +pubmed = "38651096" +date = "2024-04-23" +keywords = [] ++++ + diff --git a/content/pubs/PM38652457.md b/content/pubs/PM38652457.md new file mode 100644 index 0000000..c7bca6c --- /dev/null +++ b/content/pubs/PM38652457.md @@ -0,0 +1,11 @@ ++++ +authors = ["Leonidou N", "Ostyn L", "Coenye T", "Crabbé A", "Dräger A."] +title = "Genome-scale model of Rothia mucilaginosa predicts gene essentialities and reveals metabolic capabilities" +journal = "Microbiol Spectr" +what = "article" +doi = "10.1128/spectrum.04006-23" +pubmed = "38652457" +date = "2024-04-23" +keywords = [] ++++ + diff --git a/content/pubs/PM38669236.md b/content/pubs/PM38669236.md new file mode 100644 index 0000000..08f50eb --- /dev/null +++ b/content/pubs/PM38669236.md @@ -0,0 +1,11 @@ ++++ +authors = ["Kuper TJ", "Islam MM", "Peirce-Cottler SM", "Papin JA", "Ford RM."] +title = "Spatial transcriptome-guided multi-scale framework connects P. aeruginosa metabolic states to oxidative stress biofilm microenvironment" +journal = "PLoS Comput Biol" +what = "article" +doi = "10.1371/journal.pcbi.1012031" +pubmed = "38669236" +date = "2024-04-26" +keywords = [] ++++ + diff --git a/content/pubs/PM38671332.md b/content/pubs/PM38671332.md new file mode 100644 index 0000000..aef11d6 --- /dev/null +++ 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"10.1126/sciadv.ado2623" +pubmed = "39018398" +date = "2024-07-17" +keywords = [] ++++ + diff --git a/content/pubs/PM39057688.md b/content/pubs/PM39057688.md new file mode 100644 index 0000000..bdf7750 --- /dev/null +++ b/content/pubs/PM39057688.md @@ -0,0 +1,11 @@ ++++ +authors = ["Schroeder WL", "Suthers PF", "Willis TC", "Mooney EJ", "Maranas CD."] +title = "Current State, Challenges, and Opportunities in Genome-Scale Resource Allocation Models: A Mathematical Perspective" +journal = "Metabolites" +what = "article" +doi = "10.3390/metabo14070365" +pubmed = "39057688" +date = "2024-07-26" +keywords = [] ++++ + diff --git a/content/pubs/PM39060274.md b/content/pubs/PM39060274.md new file mode 100644 index 0000000..5b55d6d --- /dev/null +++ b/content/pubs/PM39060274.md @@ -0,0 +1,11 @@ ++++ +authors = ["Beura S", "Kundu P", "Das AK", "Ghosh A."] +title = "Genome-scale community modelling elucidates the metabolic interaction in Indian type-2 diabetic gut microbiota" +journal = "Sci Rep" 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+

+ Tags: {{ range $i, $e := $p.Params.tags }} + {{ if $i }}, {{ end }}{{ partial "tag_link.html" $e }} + {{ end }} +


{{ $p.Content }} diff --git a/layouts/taxonomy/tag.html b/layouts/taxonomy/tag.html index 4be1bd7..0ea61f2 100644 --- a/layouts/taxonomy/tag.html +++ b/layouts/taxonomy/tag.html @@ -28,7 +28,11 @@

{{ .Title }}

{{ end }} -

Tags: {{ delimit (apply .Params.tags "partial" "tag_link" ".") ", "}}

+

+ Tags: {{ range $i, $e := .Params.tags }} + {{ if $i }}, {{ end }}{{ partial "tag_link.html" $e }} +{{ end }} +


{{ .Summary }}

diff --git a/layouts/taxonomy/tag.terms.html b/layouts/taxonomy/tag.terms.html index 24cdad9..006d023 100644 --- a/layouts/taxonomy/tag.terms.html +++ b/layouts/taxonomy/tag.terms.html @@ -28,7 +28,11 @@

{{ .Title }}

{{ end }} -

Tags: {{ delimit (apply .Params.tags "partial" "tag_link" ".") ", "}}

+

+ Tags: {{ range $i, $e := .Params.tags }} + {{ if $i }}, {{ end }}{{ partial "tag_link.html" $e }} +{{ end }} +


{{ .Summary }}

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