Banerjee D, Menasalvas J, Chen Y, Gin J, Baidoo E, Petzold C
NPJ Syst Biol Appl. 2025; 11(1):8.
PMID: 39809795
PMC: 11732973.
DOI: 10.1038/s41540-024-00480-z.
Lin D, Zhang L, Zhang J, Chandrasekaran S
Cell Syst. 2025; 16(1):101164.
PMID: 39778581
PMC: 11738665.
DOI: 10.1016/j.cels.2024.12.005.
Shahreen N, Ahn J, Alsiyabi A, Chowdhury N, Shinde D, Chaudhari S
mSphere. 2025; 10(1):e0088324.
PMID: 39745366
PMC: 11774044.
DOI: 10.1128/msphere.00883-24.
Bhowmick R, Campit S, Katkam S, Keshamouni V, Chandrasekaran S
Commun Biol. 2024; 7(1):1704.
PMID: 39730911
PMC: 11681178.
DOI: 10.1038/s42003-024-07408-7.
Malla S, Sajeevan K, Acharya B, Chowdhury R, Saha R
Sci Rep. 2024; 14(1):30383.
PMID: 39638830
PMC: 11621776.
DOI: 10.1038/s41598-024-81253-w.
Metabolic Flux Analysis of Treated with Bismerthiazol Revealed Glutathione Oxidoreductase in Glutathione Metabolism Serves as an Effective Target.
Yu H, Liang X, Ge Z, Zhang Z, Ruan Y, Tang H
Int J Mol Sci. 2024; 25(22).
PMID: 39596301
PMC: 11594844.
DOI: 10.3390/ijms252212236.
Multilayer Analysis of RNA Sequencing Data in Alzheimer's Disease to Unravel Molecular Mysteries.
Uzuner D, Ilgun A, Duz E, Bozkurt F, Cakir T
Adv Neurobiol. 2024; 41:219-246.
PMID: 39589716
DOI: 10.1007/978-3-031-69188-1_9.
Catalase activity deficiency sensitizes multidrug-resistant Mycobacterium tuberculosis to the ATP synthase inhibitor bedaquiline.
Ofori-Anyinam B, Hamblin M, Coldren M, Li B, Mereddy G, Shaikh M
Nat Commun. 2024; 15(1):9792.
PMID: 39537610
PMC: 11561320.
DOI: 10.1038/s41467-024-53933-8.
Comparative Proteomics Highlights that GenX Exposure Leads to Metabolic Defects and Inflammation in Astrocytes.
Abu-Salah A, Cesur M, Anchan A, Ay M, Langley M, Shah A
Environ Sci Technol. 2024; 58(46):20525-20539.
PMID: 39499804
PMC: 11580177.
DOI: 10.1021/acs.est.4c05472.
A thermodynamic bottleneck in the TCA cycle contributes to acetate overflow in .
Shahreen N, Ahn J, Alsiyabi A, Chowdhury N, Shinde D, Chaudhari S
bioRxiv. 2024; .
PMID: 39464055
PMC: 11507952.
DOI: 10.1101/2024.10.16.618751.
A benchmark of RNA-seq data normalization methods for transcriptome mapping on human genome-scale metabolic networks.
Luleci H, Uzuner D, Cesur M, Ilgun A, Duz E, Abdik E
NPJ Syst Biol Appl. 2024; 10(1):124.
PMID: 39448682
PMC: 11502818.
DOI: 10.1038/s41540-024-00448-z.
A temperature-induced metabolic shift in the emerging human pathogen .
Carter E, Waterfield N, Constantinidou C, Alam M
mSystems. 2024; 9(11):e0097023.
PMID: 39445821
PMC: 11575385.
DOI: 10.1128/msystems.00970-23.
Deciphering Antibiotic-Targeted Metabolic Pathways in : Insights from Transcriptomics and Genome-Scale Metabolic Modeling.
Sari F, Cakir T
Life (Basel). 2024; 14(9).
PMID: 39337886
PMC: 11433532.
DOI: 10.3390/life14091102.
Genome-scale models in human metabologenomics.
Mardinoglu A, Palsson B
Nat Rev Genet. 2024; 26(2):123-140.
PMID: 39300314
DOI: 10.1038/s41576-024-00768-0.
Understanding flux switching in metabolic networks through an analysis of synthetic lethals.
Narasimha S, Malpani T, Mohite O, Nath J, Raman K
NPJ Syst Biol Appl. 2024; 10(1):104.
PMID: 39289347
PMC: 11408705.
DOI: 10.1038/s41540-024-00426-5.
Integration of proteomic data with genome-scale metabolic models: A methodological overview.
Zare F, Fleming R
Protein Sci. 2024; 33(10):e5150.
PMID: 39275997
PMC: 11400636.
DOI: 10.1002/pro.5150.
Constraint-based modelling predicts metabolic signatures of low and high-grade serous ovarian cancer.
Meeson K, Schwartz J
NPJ Syst Biol Appl. 2024; 10(1):96.
PMID: 39181893
PMC: 11344801.
DOI: 10.1038/s41540-024-00418-5.
A strategy to detect metabolic changes induced by exposure to chemicals from large sets of condition-specific metabolic models computed with enumeration techniques.
Fresnais L, Perin O, Riu A, Grall R, Ott A, Fromenty B
BMC Bioinformatics. 2024; 25(1):234.
PMID: 38992584
PMC: 11238488.
DOI: 10.1186/s12859-024-05845-z.
Metabolic model guided CRISPRi identifies a central role for phosphoglycerate mutase in persistence.
Chowdhury N, Pokorzynski N, Rucks E, Ouellette S, Carabeo R, Saha R
mSystems. 2024; 9(7):e0071724.
PMID: 38940523
PMC: 11323709.
DOI: 10.1128/msystems.00717-24.
Identification of Anticancer Enzymes and Biomarkers for Hepatocellular Carcinoma through Constraint-Based Modeling.
Wang F, Zhang H
Molecules. 2024; 29(11).
PMID: 38893469
PMC: 11173608.
DOI: 10.3390/molecules29112594.