Academic lineage
Video highlight
CyuR is a Dual Regulator for L-Cysteine Dependent Antimicrobial Resistance in Escherichia coli
- Irina A Rodionova, Hyun Gyu Lim, Dmitry A Rodionov, …, Ye Gao, Jonathan Monk, Bernhard O Palsson
- None, 10.1101/2023.05.16.541025
Systems biology of competency in Vibrio natriegens is revealed by applying novel data analytics to the transcriptome
- Jongoh Shin, Kevin Rychel, Bernhard O Palsson
- Cell Rep, 10.1016/j.celrep.2023.112619
Metabolic homeostasis and growth in abiotic cells
- Amir Akbari, Bernhard O Palsson, Amir Akbari, …, Bernhard O Palsson, Amir Akbari, Bernhard O Palsson
- Proc Natl Acad Sci U S A, 10.1073/pnas.2300687120
The Escherichia coli Fur pan-regulon has few conserved but many unique regulatory targets
- Ye Gao, Ina Bang, Yara Seif, …, Yara Seif, Donghyuk Kim, Bernhard O Palsson
- Nucleic Acids Res, 10.1093/nar/gkad253
Whole-genome sequences from wild-type and laboratory-evolved strains define the alleleome and establish its hallmarks
- Edward Alexander Catoiu, Patrick Phaneuf, Jonathan Monk, …, Patrick Phaneuf, Jonathan Monk, Bernhard O Palsson
- Proc Natl Acad Sci U S A, 10.1073/pnas.2218835120
Comprehensive whole genome sequencing with hybrid assembly of multi-drug resistant Candida albicans isolate causing cerebral abscess
- Monika Kumaraswamy, Alison Coady, Richard Szubin, …, Bernhard Palsson, Victor Nizet, Jonathan M Monk
- None, 10.1016/j.crmicr.2023.100180
High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917
- Max van ‘t Hof, Omkar S Mohite, Jonathan M Monk, …, Tilmann Weber, Bernhard O Palsson, Morten O A Sommer
- BMC Bioinformatics, 10.1186/s12859-022-05108-9
An unexpected role for leucyl aminopeptidase in UV tolerance revealed by a genome-wide fitness assessment in a model cyanobacterium
- Elliot L Weiss, Mingxu Fang, Arnaud Taton, …, Bernhard Ø Palsson, B Greg Mitchell, Susan S Golden
- Proc Natl Acad Sci U S A, 10.1073/pnas.2211789119
Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of Pseudomonas aeruginosa
- Akanksha Rajput, Hannah Tsunemoto, Anand V Sastry, …, Siddharth M Chauhan, Joe Pogliano, Bernhard O Palsson
- Nucleic Acids Res, 10.1093/nar/gkac743
Positively charged mineral surfaces promoted the accumulation of organic intermediates at the origin of metabolism
- Amir Akbari, Bernhard O Palsson
- PLoS Comput Biol, 10.1371/journal.pcbi.1010377
Adaptive laboratory evolution and independent component analysis disentangle complex vancomycin adaptation trajectories
- Anaëlle Fait, Yara Seif, Kasper Mikkelsen, …, Jerry M Wells, Bernhard O Palsson, Hanne Ingmer
- Proc Natl Acad Sci U S A, 10.1073/pnas.2118262119
Pangenome analysis of Enterobacteria reveals richness of secondary metabolite gene clusters and their associated gene sets
- Omkar S Mohite, Colton J Lloyd, Jonathan M Monk, Tilmann Weber, Bernhard O Palsson
- None, 10.1016/j.synbio.2022.04.011
Genome-scale analysis of genetic regulatory elements in Streptomyces avermitilis MA-4680 using transcript boundary information
- Yongjae Lee, Namil Lee, Soonkyu Hwang, …, Suhyung Cho, Bernhard O Palsson, Byung-Kwan Cho
- BMC Genomics, 10.1186/s12864-022-08314-0
Re-classification of Streptomyces venezuelae strains and mining secondary metabolite biosynthetic gene clusters
- Namil Lee, Mira Choi, Woori Kim, …, Bernhard Palsson, Kyoung-Soon Jang, Byung-Kwan Cho
- None, 10.1016/j.isci.2021.103410
Discovery of novel secondary metabolites encoded in actinomycete genomes through coculture
- Ji Hun Kim, Namil Lee, Soonkyu Hwang, …, Suhyung Cho, Bernhard O Palsson, Byung-Kwan Cho
- J Ind Microbiol Biotechnol, 10.1093/jimb/kuaa001
Author Correction: Transcriptome and translatome profiles of Streptomyces species in different growth phases
- Woori Kim, Soonkyu Hwang, Namil Lee, …, Suhyung Cho, Bernhard Palsson, Byung-Kwan Cho
- Sci Data, 10.1038/s41597-021-00858-2
Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types
- Ke Chen, Amitesh Anand, Connor Olson, …, Ye Gao, Nathan Mih, Bernhard O Palsson
- PLoS Comput Biol, 10.1371/journal.pcbi.1008596
Systems and synthetic biology to elucidate secondary metabolite biosynthetic gene clusters encoded in Streptomyces genomes
- Namil Lee, Soonkyu Hwang, Woori Kim, …, Min-Kyu Oh, Bernhard O Palsson, Byung-Kwan Cho
- Nat Prod Rep, 10.1039/d0np00071j
Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome
- Kevin Rychel, Anand V Sastry, Bernhard O Palsson
- Nat Commun, 10.1038/s41467-020-20153-9
Genome-Scale Metabolic Model of Xanthomonas phaseoli pv. manihotis : An Approach to Elucidate Pathogenicity at the Metabolic Level
- David Botero, Jonathan Monk, María Juliana Rodríguez Cubillos, …, Bernhard Ø Palsson, Silvia Restrepo, Adriana Bernal
- None, 10.3389/fgene.2020.00837
System-level understanding of gene expression and regulation for engineering secondary metabolite production in Streptomyces
- Yongjae Lee, Namil Lee, Soonkyu Hwang, …, Suhyung Cho, Bernhard O Palsson, Byung-Kwan Cho
- J Ind Microbiol Biotechnol, 10.1007/s10295-020-02298-0
Redefining fundamental concepts of transcription initiation in bacteria
- Citlalli Mejía-Almonte, Stephen J W Busby, Joseph T Wade, …, Bernhard O Palsson, James E Galagan, Julio Collado-Vides
- Nat Rev Genet, 10.1038/s41576-020-0254-8
Impact of insertion sequences on convergent evolution of Shigella species
- Jane Hawkey, Jonathan M Monk, Helen Billman-Jacobe, Bernhard Palsson, Kathryn E Holt
- PLoS Genet, 10.1371/journal.pgen.1008931
Mini review: Genome mining approaches for the identification of secondary metabolite biosynthetic gene clusters in Streptomyces
- Namil Lee, Soonkyu Hwang, Jihun Kim, Suhyung Cho, Bernhard Palsson, Byung-Kwan Cho
- None, 10.1016/j.csbj.2020.06.024
Comparative Genomics Determines Strain-Dependent Secondary Metabolite Production in Streptomyces venezuelae Strains
- Woori Kim, Namil Lee, Soonkyu Hwang, …, Suhyung Cho, Bernhard Palsson, Byung-Kwan Cho
- Biomolecules, 10.3390/biom10060864
Genome Sequence Comparison of Staphylococcus aureus TX0117 and a Beta-Lactamase-Cured Derivative Shows Increased Cationic Peptide Resistance Accompanying Mutations in relA and mnaA
- Mia Jade Sales, George Sakoulas, Richard Szubin, …, Kavindra V Singh, Barbara E Murray, Jonathan M Monk
- None, 10.1128/mra.01515-19
Directed Metabolic Pathway Evolution Enables Functional Pterin-Dependent Aromatic-Amino-Acid Hydroxylation in Escherichia coli
- Hao Luo, Lei Yang, Se Hyeuk Kim, …, Adam M Feist, Markus Herrgard, Bernhard Ø Palsson
- ACS Synth Biol, 10.1021/acssynbio.9b00488
Thirty complete Streptomyces genome sequences for mining novel secondary metabolite biosynthetic gene clusters
- Namil Lee, Woori Kim, Soonkyu Hwang, …, Suhyung Cho, Bernhard Palsson, Byung-Kwan Cho
- Sci Data, 10.1038/s41597-020-0395-9
Iron competition triggers antibiotic biosynthesis in Streptomyces coelicolor during coculture with Myxococcus xanthus
- Namil Lee, Woori Kim, Jinkyoo Chung, …, Sun Chang Kim, Bernhard Palsson, Byung-Kwan Cho
- ISME J, 10.1038/s41396-020-0594-6
STATR: A simple analysis pipeline of Ribo-Seq in bacteria
- Donghui Choe, Bernhard Palsson, Byung-Kwan Cho
- J Microbiol, 10.1007/s12275-020-9536-2
Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion
- Jahir M Gutierrez, Amir Feizi, Shangzhong Li, …, Bernhard O Palsson, Jens Nielsen, Nathan E Lewis
- Nat Commun, 10.1038/s41467-019-13867-y
Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection
- Jinyuan Yan, Henri Estanbouli, Chen Liao, …, Bernhard O Palsson, Weigang Qiu, Joao B Xavier
- PLoS Comput Biol, 10.1371/journal.pcbi.1007562
Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media
- Akanksha Rajput, Saugat Poudel, Hannah Tsunemoto, …, Bernhard O Palsson, Adam M Feist, Joe Pogliano
- Sci Data, 10.1038/s41597-019-0331-z
Strain-Specific Metabolic Requirements Revealed by a Defined Minimal Medium for Systems Analyses of Staphylococcus aureus
- Henrique Machado, Liam L Weng, Nicholas Dillon, …, Victor Nizet, Bernhard O Palsson, Adam M Feist
- Appl Environ Microbiol, 10.1128/aem.01773-19
Metabolic Systems Analysis of Shock-Induced Endotheliopathy (SHINE) in Trauma: A New Research Paradigm
- Hanne H Henriksen, Sarah McGarrity, Rósa S SigurÐardóttir, …, Charles E Wade, Óttar Rolfsson, Pär I Johansson
- Ann Surg, 10.1097/sla.0000000000003307
Flow cytometric characterization of perfused human bone marrow cultures: identification of the major cell lineages and correlation with the CFU-GM assay
- D A Brott, R J Maher, C R Parrish, R J Richardson, A K Smith
- Cytometry A, 10.1002/cyto.a.10034