Academic lineage
- Bernhard Ø Palsson - Ph.D. student
Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes
- Nathan Mih, Jonathan M Monk, Xin Fang, …, David Heckmann, Laurence Yang, Bernhard O Palsson
- BMC Bioinformatics, 10.1186/s12859-020-3505-y
Structure of galactarate dehydratase, a new fold in an enolase involved in bacterial fitness after antibiotic treatment
- Monica Rosas-Lemus, George Minasov, Ludmilla Shuvalova, …, Bernhard Palsson, Adam Godzik, Karla J F Satchell
- Protein Sci, 10.1002/pro.3796
Cellular responses to reactive oxygen species are predicted from molecular mechanisms
- Laurence Yang, Nathan Mih, Amitesh Anand, …, Ying Hefner, Adam M Feist, Bernhard O Palsson
- Proc Natl Acad Sci U S A, 10.1073/pnas.1905039116
A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types
- Yara Seif, Jonathan M Monk, Nathan Mih, …, Jared Broddrick, Karsten Zengler, Bernhard O Palsson
- PLoS Comput Biol, 10.1371/journal.pcbi.1006644
Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant
- Victoria A Feher, Jamie M Schiffer, Daniel J Mermelstein, …, Levi C T Pierce, J Andrew McCammon, Rommie E Amaro
- Biophys J, 10.1016/j.bpj.2018.09.035
Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models
- David Heckmann, Colton J Lloyd, Nathan Mih, …, Abdelmoneim Amer Desouki, Martin J Lercher, Bernhard O Palsson
- Nat Commun, 10.1038/s41467-018-07652-6
Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance
- Erol S Kavvas, Edward Catoiu, Nathan Mih, …, Victor Nizet, Jonathan M Monk, Bernhard O Palsson
- Nat Commun, 10.1038/s41467-018-06634-y
Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655
- Ye Gao, James T Yurkovich, Sang Woo Seo, …, Byung-Kwan Cho, Donghyuk Kim, Bernhard O Palsson
- Nucleic Acids Res, 10.1093/nar/gky752
Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa
- Xin Fang, Jonathan M Monk, Nathan Mih, …, Yara Seif, Larry Smarr, Bernhard O Palsson
- None, 10.1186/s12918-018-0587-5
The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures
- Kumari S Choudhary, Nathan Mih, Jonathan Monk, …, James T Yurkovich, George Sakoulas, Bernhard O Palsson
- None, 10.3389/fmicb.2018.01082
Recon3D enables a three-dimensional view of gene variation in human metabolism
- Elizabeth Brunk, Swagatika Sahoo, Daniel C Zielinski, …, Jens Nielsen, Ines Thiele, Bernhard O Palsson
- Nat Biotechnol, 10.1038/nbt.4072
ssbio: a Python framework for structural systems biology
- Nathan Mih, Elizabeth Brunk, Ke Chen, …, Jonathan M Monk, Zhen Zhang, Bernhard O Palsson
- Bioinformatics, 10.1093/bioinformatics/bty077