| Publication Title | Authors | Publication Year Sort ascending |
|---|---|---|
| Reframing gene essentiality in terms of adaptive flexibility. | G.I. Guzman; C.A. Olson; Y. Hefner; P.V. Phaneuf; E. Catoiu; L.B. Crepaldi; L.Goldschmid Micas; B.O. Palsson; A.M. Feist |
2018 |
| Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits. | Y. Seif; E. Kavvas; J.C. Lachance; J.T. Yurkovich; S.P. Nuccio; X. Fang; E. Catoiu; M. Raffatellu; B.O. Palsson; J.M. Monk |
2018 |
| Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae. | T. Strucko; K. Zirngibl; F. Pereira; E. Kafkia; E.T. Mohamed; M. Rettel; F. Stein; A.M. Feist; P. Jouhten; K.Raosaheb Patil; J. Forster |
2018 |
| ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation. | P.V. Phaneuf; D. Gosting; B.O. Palsson; A.M. Feist |
2018 |
| Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism. | D. McCloskey; S. Xu; T.E. Sandberg; E. Brunk; Y. Hefner; R. Szubin; A.M. Feist; B.O. Palsson |
2018 |
| Systems biology as an emerging paradigm in transfusion medicine. | J.T. Yurkovich; A. Bordbar; O.E. Sigurjónsson; B.O. Palsson |
2018 |
| Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates | D. Heckmann; D.C. Zielinski; B.O. Palsson |
2018 |
| Multiple optimal phenotypes overcome redox and glycolytic intermediate metabolite imbalances in knockout evolutions. | D. McCloskey; S. Xu; T.E. Sandberg; E. Brunk; Y. Hefner; R. Szubin; A.M. Feist; B.O. Palsson |
2018 |
| Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions. | E.S. Kavvas; Y. Seif; J.T. Yurkovich; C. Norsigian; S. Poudel; W.W. Greenwald; S. Ghatak; B.O. Palsson; J.M. Monk |
2018 |
| Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models | D. Heckmann; C.J. Lloyd; N. Mih; Y. Ha; D.C. Zielinski; Z.B. Haiman; A.Amer Desouki; M.J. Lercher; B.O. Palsson |
2018 |
| Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655. | Y. Gao; J.T. Yurkovich; S.Woo Seo; I. Kabimoldayev; A. Dräger; K. Chen; A.V. Sastry; X. Fang; N. Mih; L. Yang; J. Eichner; B.K. Cho; D. Kim; B.O. Palsson |
2018 |
| Recon3D enables a three-dimensional view of gene variation in human metabolism. | E. Brunk; S. Sahoo; D.C. Zielinski; A. Altunkaya; A. Dräger; N. Mih; F. Gatto; A. Nilsson; G.Andres Pre Gonzalez; M.Kathrin Aurich; A. Prlić; A. Sastry; A.D. Danielsdottir; A. Heinken; A. Noronha; P.W. Rose; S.K. Burley; R.M.T. Fleming; J. Nielsen; I. Thiele; B.O. Palsson |
2018 |
| Gapless, Unambiguous Genome Sequence for Escherichia coli C, a Workhorse of Industrial Biology | J.E. Pekar; P. Phaneuf; R. Szubin; B. Palsson; A. Feist; J.M. Monk |
2018 |
| Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials. | J.T. Yurkovich; M.A. Alcantar; Z.B. Haiman; B.O. Palsson |
2018 |
| ssbio: A Python Framework for Structural Systems Biology | N. Mih; E. Brunk; K. Chen; E. Catoiu; A. Sastry; E. Kavvas; J.M. Monk; Z. Zhang; B.O. Palsson |
2018 |
| Predicting the metabolic capabilities of Synechococcus elongatus PCC 7942 adapted to different light regimes. | J.T. Broddrick; D.G. Welkie; D. Jallet; S.S. Golden; G. Peers; B.O. Palsson |
2018 |
| A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0 | A. Santos-Zavaleta; M. Sánchez-Pérez; H. Salgado; D.A. Vázquez-Ramírez; S. Gama-Castro; V.H. Tierrafría; S.J.W. Busby; P. Aquino; X. Fang; B.O. Palsson; J.E. Galagan; J. Collado-Vides |
2018 |
| Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP. | D. Kim; S.Woo Seo; Y. Gao; H. Nam; G.I. Guzman; B.K. Cho; B.O. Palsson |
2018 |
| Mannose and fructose metabolism in red blood cells during cold storage in SAGM. | O. Rolfsson; F. Johannsson; M. Magnúsdóttir; G. Paglia; O.E. Sigurjónsson; A. Bordbar; S. Palsson; S. Brynjólfsson; S. Guðmundsson; B. Palsson |
2017 |
| Whole-Genome Sequencing of Invasion-Resistant Cells Identifies Laminin α2 as a Host Factor for Bacterial Invasion. | X.M. van Wijk; S. Döhrmann; B.M. Hallström; S. Li; B.G. Voldborg; B.X. Meng; K.K. McKee; T.H. van Kuppevelt; P.D. Yurchenco; B.O. Palsson; N.E. Lewis; V. Nizet; J.D. Esko |
2017 |
| COBRAme: A Computational Framework for Building and Manipulating Models of Metabolism and Gene Expression | C.J. Lloyd; A. Ebrahim; L. Yang; Z.A. King; E. Catoiu; E.J. O'Brien; J.K. Liu; B.O. Palsson |
2017 |
| Metabolic Models of Protein Allocation Call for the Kinetome. | A. Nilsson; J. Nielsen; B.O. Palsson |
2017 |
| Topological and Kinetic Determinants of the Modal Matrices of Dynamic Models of Metabolism | B. Du; D.C. Zielinski; B.O. Palsson |
2017 |
| Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli. | C.P. Long; J.E. Gonzalez; A.M. Feist; B.O. Palsson; M.R. Antoniewicz |
2017 |
| Expanding The Computable Reactome In Pseudomonas putida Reveals Metabolic Cycles Providing Robustness | J. Nogales; S. Gudmundsson; E. Duque; J.Lewis Ramos; B.O. Palsson |
2017 |
| Antibiotic-Induced Changes to the Host Metabolic Environment Inhibit Drug Efficacy and Alter Immune Function. | J.H. Yang; P. Bhargava; D. McCloskey; N. Mao; B.O. Palsson; J.J. Collins |
2017 |
| Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655. | S.Woo Seo; Y. Gao; D. Kim; R. Szubin; J. Yang; B.K. Cho; B.O. Palsson |
2017 |
| Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution. | E.T. Mohamed; S. Wang; R.M. Lennen; M.J. Herrgard; B.A. Simmons; S.W. Singer; A.M. Feist |
2017 |
| Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies. | T.E. Sandberg; C.J. Lloyd; B.O. Palsson; A.M. Feist |
2017 |
| Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks. | J.T. Yurkovich; D.C. Zielinski; L. Yang; G. Paglia; O. Rolfsson; O.E. Sigurjónsson; J.T. Broddrick; A. Bordbar; K. Wichuk; S. Brynjólfsson; S. Palsson; S. Gudmundsson; B.O. Palsson |
2017 |