| Year |
Citation |
Score |
| 2024 |
Cooper HB, Vezina B, Hawkey J, Passet V, López-Fernández S, Monk JM, Brisse S, Holt KE, Wyres KL. A validated pangenome-scale metabolic model for the species complex. Microbial Genomics. 10. PMID 38376382 DOI: 10.1099/mgen.0.001206 |
0.378 |
|
| 2023 |
Hyun JC, Monk JM, Szubin R, Hefner Y, Palsson BO. Global pathogenomic analysis identifies known and candidate genetic antimicrobial resistance determinants in twelve species. Nature Communications. 14: 7690. PMID 38001096 DOI: 10.1038/s41467-023-43549-9 |
0.469 |
|
| 2023 |
Vezina B, Watts SC, Hawkey J, Cooper HB, Judd LM, Jenney AWJ, Monk JM, Holt KE, Wyres KL. Bactabolize is a tool for high-throughput generation of bacterial strain-specific metabolic models. Elife. 12. PMID 37815531 DOI: 10.7554/eLife.87406 |
0.448 |
|
| 2023 |
Rodionova IA, Lim HG, Rodionov DA, Hutchison Y, Dalldorf C, Gao Y, Monk J, Palsson BO. CyuR is a Dual Regulator for L-Cysteine Dependent Antimicrobial Resistance in . Biorxiv : the Preprint Server For Biology. PMID 37292663 DOI: 10.1101/2023.05.16.541025 |
0.637 |
|
| 2023 |
Catoiu EA, Phaneuf P, Monk J, Palsson BO. Whole-genome sequences from wild-type and laboratory-evolved strains define the alleleome and establish its hallmarks. Proceedings of the National Academy of Sciences of the United States of America. 120: e2218835120. PMID 37011218 DOI: 10.1073/pnas.2218835120 |
0.809 |
|
| 2023 |
Kumaraswamy M, Coady A, Szubin R, Martin TC, Palsson B, Nizet V, Monk JM. Comprehensive whole genome sequencing with hybrid assembly of multi-drug resistant isolate causing cerebral abscess. Current Research in Microbial Sciences. 4: 100180. PMID 36685102 DOI: 10.1016/j.crmicr.2023.100180 |
0.476 |
|
| 2022 |
van 't Hof M, Mohite OS, Monk JM, Weber T, Palsson BO, Sommer MOA. High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917. Bmc Bioinformatics. 23: 566. PMID 36585633 DOI: 10.1186/s12859-022-05108-9 |
0.505 |
|
| 2022 |
Kavvas ES, Long CP, Sastry A, Poudel S, Antoniewicz MR, Ding Y, Mohamed ET, Szubin R, Monk JM, Feist AM, Palsson BO. Experimental Evolution Reveals Unifying Systems-Level Adaptations but Diversity in Driving Genotypes. Msystems. e0016522. PMID 36226969 DOI: 10.1128/msystems.00165-22 |
0.805 |
|
| 2022 |
Monk JM. Genome-scale metabolic network reconstructions of diverse strains reveal strain-specific adaptations. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 377: 20210236. PMID 35989599 DOI: 10.1098/rstb.2021.0236 |
0.413 |
|
| 2022 |
Mohite OS, Lloyd CJ, Monk JM, Weber T, Palsson BO. Pangenome analysis of Enterobacteria reveals richness of secondary metabolite gene clusters and their associated gene sets. Synthetic and Systems Biotechnology. 7: 900-910. PMID 35647330 DOI: 10.1016/j.synbio.2022.04.011 |
0.795 |
|
| 2022 |
Vezina B, Judd LM, McDougall FK, Boardman WSJ, Power ML, Hawkey J, Brisse S, Monk JM, Holt KE, Wyres KL. Transmission of Klebsiella strains and plasmids within and between grey-headed flying fox colonies. Environmental Microbiology. PMID 35590448 DOI: 10.1111/1462-2920.16047 |
0.328 |
|
| 2022 |
Rodionova IA, Gao Y, Monk J, Hefner Y, Wong N, Szubin R, Lim HG, Rodionov DA, Zhang Z, Saier MH, Palsson BO. A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli. Scientific Reports. 12: 7274. PMID 35508583 DOI: 10.1038/s41598-022-11134-7 |
0.813 |
|
| 2022 |
Norsigian CJ, Danhof HA, Brand CK, Midani FS, Broddrick JT, Savidge TC, Britton RA, Palsson BO, Spinler JK, Monk JM. Systems biology approach to functionally assess the pangenome reveals genetic diversity with discriminatory power. Proceedings of the National Academy of Sciences of the United States of America. 119: e2119396119. PMID 35476524 DOI: 10.1073/pnas.2119396119 |
0.805 |
|
| 2022 |
Xavier JB, Monk JM, Poudel S, Norsigian CJ, Sastry AV, Liao C, Bento J, Suchard MA, Arrieta-Ortiz ML, Peterson EJR, Baliga NS, Stoeger T, Ruffin F, Richardson RAK, Gao CA, et al. Mathematical models to study the biology of pathogens and the infectious diseases they cause. Iscience. 25: 104079. PMID 35359802 DOI: 10.1016/j.isci.2022.104079 |
0.781 |
|
| 2022 |
Hawkey J, Vezina B, Monk JM, Judd LM, Harshegyi T, Lopez-Fernandez S, Rodrigues C, Brisse S, Holt K, Wyres KL. A curated collection of metabolic models reveals variable substrate usage and gene essentiality. Genome Research. PMID 35277433 DOI: 10.1101/gr.276289.121 |
0.395 |
|
| 2022 |
Hyun JC, Monk JM, Palsson BO. Comparative pangenomics: analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity. Bmc Genomics. 23: 7. PMID 34983386 DOI: 10.1186/s12864-021-08223-8 |
0.467 |
|
| 2021 |
Lachance JC, Matteau D, Brodeur J, Lloyd CJ, Mih N, King ZA, Knight TF, Feist AM, Monk JM, Palsson BO, Jacques PÉ, Rodrigue S. Genome-scale metabolic modeling reveals key features of a minimal gene set. Molecular Systems Biology. 17: e10099. PMID 34288418 DOI: 10.15252/msb.202010099 |
0.83 |
|
| 2021 |
Lloyd CJ, Monk J, Yang L, Ebrahim A, Palsson BO. Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth. Plos Computational Biology. 17: e1007817. PMID 34161321 DOI: 10.1371/journal.pcbi.1007817 |
0.823 |
|
| 2021 |
Wilken SE, Monk JM, Leggieri PA, Lawson CE, Lankiewicz TS, Seppälä S, Daum CG, Jenkins J, Lipzen AM, Mondo SJ, Barry KW, Grigoriev IV, Henske JK, Theodorou MK, Palsson BO, et al. Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus. Msystems. 6. PMID 33594000 DOI: 10.1128/mSystems.00002-21 |
0.565 |
|
| 2021 |
Rajput A, Seif Y, Choudhary KS, Dalldorf C, Poudel S, Monk JM, Palsson BO. Pangenome Analytics Reveal Two-Component Systems as Conserved Targets in ESKAPEE Pathogens. Msystems. 6. PMID 33500331 DOI: 10.1128/mSystems.00981-20 |
0.793 |
|
| 2021 |
Rajput A, Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Seif Y, Lamsa A, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Knight R, et al. Identifying the effect of vancomycin on health care-associated methicillin-resistant Staphylococcus aureus strains using bacteriological and physiological media. Gigascience. 10. PMID 33420779 DOI: 10.1093/gigascience/giaa156 |
0.777 |
|
| 2020 |
Broddrick JT, Szubin R, Norsigian CJ, Monk JM, Palsson BO, Parenteau MN. High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies. Frontiers in Microbiology. 11: 596626. PMID 33281796 DOI: 10.3389/fmicb.2020.596626 |
0.822 |
|
| 2020 |
Norsigian CJ, Danhof HA, Brand CK, Oezguen N, Midani FS, Palsson BO, Savidge TC, Britton RA, Spinler JK, Monk JM. Systems biology analysis of the Clostridioides difficile core-genome contextualizes microenvironmental evolutionary pressures leading to genotypic and phenotypic divergence. Npj Systems Biology and Applications. 6: 31. PMID 33082337 DOI: 10.1038/s41540-020-00151-9 |
0.843 |
|
| 2020 |
Botero D, Monk J, Rodríguez Cubillos MJ, Rodríguez Cubillos A, Restrepo M, Bernal-Galeano V, Reyes A, González Barrios A, Palsson BØ, Restrepo S, Bernal A. Genome-Scale Metabolic Model of pv. : An Approach to Elucidate Pathogenicity at the Metabolic Level. Frontiers in Genetics. 11: 837. PMID 32849823 DOI: 10.3389/Fgene.2020.00837 |
0.587 |
|
| 2020 |
Hawkey J, Monk JM, Billman-Jacobe H, Palsson B, Holt KE. Impact of insertion sequences on convergent evolution of Shigella species. Plos Genetics. 16: e1008931. PMID 32644999 DOI: 10.1371/Journal.Pgen.1008931 |
0.519 |
|
| 2020 |
Kavvas ES, Yang L, Monk JM, Heckmann D, Palsson BO. A biochemically-interpretable machine learning classifier for microbial GWAS. Nature Communications. 11: 2580. PMID 32444610 DOI: 10.1038/S41467-020-16310-9 |
0.775 |
|
| 2020 |
Sales MJ, Sakoulas G, Szubin R, Palsson B, Arias C, Singh KV, Murray BE, Monk JM. Genome Sequence Comparison of Staphylococcus aureus TX0117 and a Beta-Lactamase-Cured Derivative Shows Increased Cationic Peptide Resistance Accompanying Mutations in and . Microbiology Resource Announcements. 9. PMID 32354985 DOI: 10.1128/MRA.01515-19 |
0.438 |
|
| 2020 |
Mih N, Monk JM, Fang X, Catoiu E, Heckmann D, Yang L, Palsson BO. Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes. Bmc Bioinformatics. 21: 162. PMID 32349661 DOI: 10.1186/S12859-020-3505-Y |
0.817 |
|
| 2020 |
Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, ... ... Monk JM, et al. Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology. 38: 504. PMID 32265554 DOI: 10.1038/S41587-020-0477-4 |
0.799 |
|
| 2020 |
Jensen CS, Norsigian CJ, Fang X, Nielsen XC, Christensen JJ, Palsson BO, Monk JM. Reconstruction and Validation of a Genome-Scale Metabolic Model of (iCJ415), a Human Commensal and Opportunistic Pathogen. Frontiers in Genetics. 11: 116. PMID 32194617 DOI: 10.3389/Fgene.2020.00116 |
0.825 |
|
| 2020 |
Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, ... ... Monk JM, et al. MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology. PMID 32123384 DOI: 10.1038/S41587-020-0446-Y |
0.805 |
|
| 2020 |
Hyun JC, Kavvas ES, Monk JM, Palsson BO. Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens. Plos Computational Biology. 16: e1007608. PMID 32119670 DOI: 10.1371/Journal.Pcbi.1007608 |
0.518 |
|
| 2019 |
Norsigian CJ, Fang X, Seif Y, Monk JM, Palsson BO. A workflow for generating multi-strain genome-scale metabolic models of prokaryotes. Nature Protocols. PMID 31863076 DOI: 10.1038/S41596-019-0254-3 |
0.816 |
|
| 2019 |
Yan J, Estanbouli H, Liao C, Kim W, Monk JM, Rahman R, Kamboj M, Palsson BO, Qiu W, Xavier JB. Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection. Plos Computational Biology. 15: e1007562. PMID 31860667 DOI: 10.1371/Journal.Pcbi.1007562 |
0.444 |
|
| 2019 |
Rajput A, Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Lamsa A, Seif Y, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Knight R, et al. Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media. Scientific Data. 6: 322. PMID 31848353 DOI: 10.1038/S41597-019-0331-Z |
0.791 |
|
| 2019 |
Nogales J, Mueller J, Gudmundsson S, Canalejo FJ, Duque E, Monk J, Feist AM, Ramos JL, Niu W, Palsson BO. High-quality genome-scale metabolic modeling of Pseudomonas putida highlights its broad metabolic capabilities. Environmental Microbiology. PMID 31657101 DOI: 10.1111/1462-2920.14843 |
0.826 |
|
| 2019 |
Machado H, Weng LL, Dillon N, Seif Y, Holland M, Pekar JE, Monk JM, Nizet V, Palsson BO, Feist AM. A defined minimal medium for systems analyses of reveals strain-specific metabolic requirements. Applied and Environmental Microbiology. PMID 31471305 DOI: 10.1128/Aem.01773-19 |
0.826 |
|
| 2019 |
Seif Y, Monk JM, Machado H, Kavvas E, Palsson BO. Systems Biology and Pangenome of O-Antigens. Mbio. 10. PMID 31455646 DOI: 10.1128/Mbio.01247-19 |
0.785 |
|
| 2019 |
Yang L, Mih N, Anand A, Park JH, Tan J, Yurkovich JT, Monk JM, Lloyd CJ, Sandberg TE, Seo SW, Kim D, Sastry AV, Phaneuf P, Gao Y, Broddrick JT, et al. Cellular responses to reactive oxygen species are predicted from molecular mechanisms. Proceedings of the National Academy of Sciences of the United States of America. PMID 31270234 DOI: 10.1073/Pnas.1905039116 |
0.721 |
|
| 2019 |
Norsigian CJ, Attia H, Szubin R, Yassin AS, Palsson BØ, Aziz RK, Monk JM. Comparative Genome-Scale Metabolic Modeling of Metallo-Beta-Lactamase-Producing Multidrug-Resistant Clinical Isolates. Frontiers in Cellular and Infection Microbiology. 9: 161. PMID 31179245 DOI: 10.3389/fcimb.2019.00161 |
0.825 |
|
| 2019 |
Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Lamsa A, Seif Y, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Pogliano J, Knight R, et al. Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media. Scientific Data. 6: 43. PMID 31028276 DOI: 10.1038/S41597-019-0051-4 |
0.779 |
|
| 2019 |
Lachance JC, Lloyd CJ, Monk JM, Yang L, Sastry AV, Seif Y, Palsson BO, Rodrigue S, Feist AM, King ZA, Jacques PÉ. BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data. Plos Computational Biology. 15: e1006971. PMID 31009451 DOI: 10.1371/Journal.Pcbi.1006971 |
0.811 |
|
| 2019 |
Attia H, Szubin R, Yassin AS, Monk JM, Aziz RK. Draft Genome Sequences of Four Metallo-Beta-Lactamase-Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates, Including Two Colistin-Resistant Strains, from Cairo, Egypt. Microbiology Resource Announcements. 8. PMID 30801061 DOI: 10.1128/MRA.01418-18 |
0.306 |
|
| 2019 |
Seif Y, Monk JM, Mih N, Tsunemoto H, Poudel S, Zuniga C, Broddrick J, Zengler K, Palsson BO. A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types. Plos Computational Biology. 15: e1006644. PMID 30625152 DOI: 10.1371/Journal.Pcbi.1006644 |
0.806 |
|
| 2018 |
Pekar JE, Phaneuf P, Szubin R, Palsson B, Feist A, Monk JM. Gapless, Unambiguous Genome Sequence for Escherichia coli C, a Workhorse of Industrial Biology. Microbiology Resource Announcements. 7. PMID 30533692 DOI: 10.1128/MRA.00890-18 |
0.808 |
|
| 2018 |
Monk JM. Predicting Antimicrobial Resistance and Associated Genomic Features from Whole Genome Sequencing. Journal of Clinical Microbiology. PMID 30463894 DOI: 10.1128/JCM.01610-18 |
0.358 |
|
| 2018 |
Fang X, Monk JM, Nurk S, Akseshina M, Zhu Q, Gemmell C, Gianetto-Hill C, Leung N, Szubin R, Sanders J, Beck PL, Li W, Sandborn WJ, Gray-Owen SD, Knight R, et al. Metagenomics-Based, Strain-Level Analysis of From a Time-Series of Microbiome Samples From a Crohn's Disease Patient. Frontiers in Microbiology. 9: 2559. PMID 30425690 DOI: 10.3389/Fmicb.2018.02559 |
0.59 |
|
| 2018 |
Kavvas ES, Catoiu E, Mih N, Yurkovich JT, Seif Y, Dillon N, Heckmann D, Anand A, Yang L, Nizet V, Monk JM, Palsson BO. Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance. Nature Communications. 9: 4306. PMID 30333483 DOI: 10.1038/S41467-018-06634-Y |
0.794 |
|
| 2018 |
Du B, Zielinski DC, Monk JM, Palsson BO. Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice. Proceedings of the National Academy of Sciences of the United States of America. PMID 30309961 DOI: 10.1073/Pnas.1805367115 |
0.699 |
|
| 2018 |
Seif Y, Kavvas E, Lachance JC, Yurkovich JT, Nuccio SP, Fang X, Catoiu E, Raffatellu M, Palsson BO, Monk JM. Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits. Nature Communications. 9: 3771. PMID 30218022 DOI: 10.1038/S41467-018-06112-5 |
0.833 |
|
| 2018 |
Fang X, Monk JM, Mih N, Du B, Sastry AV, Kavvas E, Seif Y, Smarr L, Palsson BO. Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa. Bmc Systems Biology. 12: 66. PMID 29890970 DOI: 10.1186/S12918-018-0587-5 |
0.792 |
|
| 2018 |
Choudhary KS, Mih N, Monk J, Kavvas E, Yurkovich JT, Sakoulas G, Palsson BO. The Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures. Frontiers in Microbiology. 9: 1082. PMID 29887846 DOI: 10.3389/Fmicb.2018.01082 |
0.813 |
|
| 2018 |
Norsigian CJ, Kavvas E, Seif Y, Palsson BO, Monk JM. iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of AYE. Frontiers in Genetics. 9: 121. PMID 29692801 DOI: 10.3389/Fgene.2018.00121 |
0.831 |
|
| 2018 |
Kavvas ES, Seif Y, Yurkovich JT, Norsigian C, Poudel S, Greenwald WW, Ghatak S, Palsson BO, Monk JM. Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions. Bmc Systems Biology. 12: 25. PMID 29499714 DOI: 10.1186/S12918-018-0557-Y |
0.773 |
|
| 2018 |
Mih N, Brunk E, Chen K, Catoiu E, Sastry A, Kavvas E, Monk JM, Zhang Z, Palsson BO, Valencia A. ssbio: A Python Framework for Structural Systems Biology. Bioinformatics (Oxford, England). PMID 29444205 DOI: 10.1093/Bioinformatics/Bty077 |
0.792 |
|
| 2018 |
Monk J, Bosi E. Integration of Comparative Genomics with Genome-Scale Metabolic Modeling to Investigate Strain-Specific Phenotypical Differences. Methods in Molecular Biology (Clifton, N.J.). 1716: 151-175. PMID 29222753 DOI: 10.1007/978-1-4939-7528-0_7 |
0.536 |
|
| 2017 |
Monk JM, Lloyd CJ, Brunk E, Mih N, Sastry A, King Z, Takeuchi R, Nomura W, Zhang Z, Mori H, Feist AM, Palsson BO. iML1515, a knowledgebase that computes Escherichia coli traits. Nature Biotechnology. 35: 904-908. PMID 29020004 DOI: 10.1038/Nbt.3956 |
0.76 |
|
| 2017 |
Sastry A, Monk J, Tegel H, Uhlén M, Palsson BO, Rockberg J, Brunk E. Machine Learning in Computational Biology to Accelerate High-Throughput Protein Expression. Bioinformatics (Oxford, England). PMID 28398465 DOI: 10.1093/Bioinformatics/Btx207 |
0.779 |
|
| 2017 |
Aziz RK, Monk JM, Andrews KA, Nhan J, Khaw VL, Wong H, Palsson BO, Charusanti P. The aldehyde dehydrogenase, AldA, is essential for L-1,2-propanediol utilization in laboratory-evolved Escherichia coli. Microbiological Research. 194: 47-52. PMID 27938862 DOI: 10.1016/J.Micres.2016.10.006 |
0.469 |
|
| 2016 |
Monk JM, Koza A, Campodonico MA, Machado D, Seoane JM, Palsson BO, Herrgård MJ, Feist AM. Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes. Cell Systems. PMID 27667363 DOI: 10.1016/J.Cels.2016.08.013 |
0.796 |
|
| 2016 |
Bosi E, Monk JM, Aziz RK, Fondi M, Nizet V, Palsson BØ. Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity. Proceedings of the National Academy of Sciences of the United States of America. PMID 27286824 DOI: 10.1073/Pnas.1523199113 |
0.588 |
|
| 2016 |
Brunk E, George KW, Alonso-Gutierrez J, Thompson M, Baidoo E, Wang G, Petzold CJ, McCloskey D, Monk J, Yang L, O'Brien EJ, Batth TS, Martin HG, Feist A, Adams PD, et al. Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow. Cell Systems. PMID 27211860 DOI: 10.1016/J.Cels.2016.04.004 |
0.81 |
|
| 2016 |
Brunk E, Mih N, Monk J, Zhang Z, O'Brien EJ, Bliven SE, Chen K, Chang RL, Bourne PE, Palsson BO. Systems biology of the structural proteome. Bmc Systems Biology. 10: 26. PMID 26969117 DOI: 10.1186/S12918-016-0271-6 |
0.807 |
|
| 2016 |
Fouts DE, Matthias MA, Adhikarla H, Adler B, Amorim-Santos L, Berg DE, Bulach D, Buschiazzo A, Chang YF, Galloway RL, Haake DA, Haft DH, Hartskeerl R, Ko AI, Levett PN, ... ... Monk JM, et al. What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira. Plos Neglected Tropical Diseases. 10: e0004403. PMID 26890609 DOI: 10.1371/Journal.Pntd.0004403 |
0.515 |
|
| 2015 |
Aziz RK, Monk JM, Lewis RM, In Loh S, Mishra A, Abhay Nagle A, Satyanarayana C, Dhakshinamoorthy S, Luche M, Kitchen DB, Andrews KA, Fong NL, Li HJ, Palsson BO, Charusanti P. Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations. Scientific Reports. 5: 16025. PMID 26531810 DOI: 10.1038/Srep16025 |
0.504 |
|
| 2015 |
Aziz RK, Khaw VL, Monk JM, Brunk E, Lewis R, Loh SI, Mishra A, Nagle AA, Satyanarayana C, Dhakshinamoorthy S, Luche M, Kitchen DB, Andrews KA, Palsson BØ, Charusanti P. Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC. Frontiers in Microbiology. 6: 958. PMID 26441892 DOI: 10.3389/Fmicb.2015.00958 |
0.77 |
|
| 2015 |
Yang L, Tan J, O'Brien EJ, Monk JM, Kim D, Li HJ, Charusanti P, Ebrahim A, Lloyd CJ, Yurkovich JT, Du B, Dräger A, Thomas A, Sun Y, Saunders MA, et al. Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data. Proceedings of the National Academy of Sciences of the United States of America. PMID 26261351 DOI: 10.1073/Pnas.1501384112 |
0.801 |
|
| 2015 |
O'Brien EJ, Monk JM, Palsson BO. Using Genome-scale Models to Predict Biological Capabilities. Cell. 161: 971-987. PMID 26000478 DOI: 10.1016/J.Cell.2015.05.019 |
0.764 |
|
| 2015 |
Guzmán GI, Utrilla J, Nurk S, Brunk E, Monk JM, Ebrahim A, Palsson BO, Feist AM. Model-driven discovery of underground metabolic functions in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America. 112: 929-34. PMID 25564669 DOI: 10.1073/Pnas.1414218112 |
0.828 |
|
| 2014 |
Monk J, Palsson BO. Genetics. Predicting microbial growth. Science (New York, N.Y.). 344: 1448-9. PMID 24970063 DOI: 10.1126/Science.1253388 |
0.573 |
|
| 2014 |
Monk J, Nogales J, Palsson BO. Optimizing genome-scale network reconstructions. Nature Biotechnology. 32: 447-52. PMID 24811519 DOI: 10.1038/Nbt.2870 |
0.734 |
|
| 2014 |
Bordbar A, Monk JM, King ZA, Palsson BO. Constraint-based models predict metabolic and associated cellular functions. Nature Reviews. Genetics. 15: 107-20. PMID 24430943 DOI: 10.1038/Nrg3643 |
0.678 |
|
| 2013 |
Monk JM, Charusanti P, Aziz RK, Lerman JA, Premyodhin N, Orth JD, Feist AM, Palsson BØ. Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments. Proceedings of the National Academy of Sciences of the United States of America. 110: 20338-43. PMID 24277855 DOI: 10.1073/Pnas.1307797110 |
0.831 |
|
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