Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways.

by Zachary A King, Andreas Dräger, Ali Ebrahim, Nikolaus Sonnenschein, Nathan E Lewis, Bernhard O Palsson
Published 2015-08-01

Matrix formalism to describe functional states of transcriptional regulatory systems.

by Erwin P Gianchandani, Jason A Papin, Nathan D Price, Andrew R Joyce, Bernhard O Palsson
Published 2006-08-01

Integrated Regulatory and Metabolic Networks of the Marine Diatom Phaeodactylum tricornutum Predict the Response to Rising CO2 Levels

by Jennifer Levering, Christopher L. Dupont, Andrew E. Allen, Bernhard O. Palsson, Karsten Zengler, Xiaoxia Lin
Published 2017-02-01

High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies

by Jared T. Broddrick, Richard Szubin, Charles J. Norsigian, Jonathan M. Monk, Bernhard O. Palsson, Mary N. Parenteau
Published 2020-11-01

Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes

by Nathan Mih, Jonathan M. Monk, Xin Fang, Edward Catoiu, David Heckmann, Laurence Yang, Bernhard O. Palsson
Published 2020-04-01

Dataset on economic analysis of mass production of algae in LED-based photobioreactors

by Weiqi Fu, Steinn Gudmundsson, Kristine Wichuk, Sirus Palsson, Bernhard O. Palsson, Kourosh Salehi-Ashtiani, Sigurður Brynjólfsson
Published 2019-02-01

Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types.

by Ke Chen, Amitesh Anand, Connor Olson, Troy E Sandberg, Ye Gao, Nathan Mih, Bernhard O Palsson
Published 2021-01-01

Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655

by Sang Woo Seo, Ye Gao, Donghyuk Kim, Richard Szubin, Jina Yang, Byung-Kwan Cho, Bernhard O. Palsson
Published 2017-05-01

ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions.

by Haythem Latif, Stephen Federowicz, Ali Ebrahim, Janna Tarasova, Richard Szubin, Jose Utrilla, Karsten Zengler, Bernhard O Palsson
Published 2018-01-01

A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks.

by Hojung Nam, Miguel Campodonico, Aarash Bordbar, Daniel R Hyduke, Sangwoo Kim, Daniel C Zielinski, Bernhard O Palsson
Published 2014-09-01

Pangenome Analytics Reveal Two-Component Systems as Conserved Targets in ESKAPEE Pathogens

by Akanksha Rajput, Yara Seif, Kumari Sonal Choudhary, Christopher Dalldorf, Saugat Poudel, Jonathan M. Monk, Bernhard O. Palsson
Published 2021-02-01

Genome-scale metabolic models highlight stage-specific differences in essential metabolic pathways in Trypanosoma cruzi.

by Isabel S Shiratsubaki, Xin Fang, Rodolpho O O Souza, Bernhard O Palsson, Ariel M Silber, Jair L Siqueira-Neto
Published 2020-10-01

Genome-scale determination of 5´ and 3´ boundaries of RNA transcripts in Streptomyces genomes

by Yongjae Lee, Namil Lee, Soonkyu Hwang, Woori Kim, Yujin Jeong, Suhyung Cho, Bernhard O. Palsson, Byung-Kwan Cho
Published 2020-12-01

Evolution of E. coli on [U-13C]Glucose Reveals a Negligible Isotopic Influence on Metabolism and Physiology.

by Troy E Sandberg, Christopher P Long, Jacqueline E Gonzalez, Adam M Feist, Maciek R Antoniewicz, Bernhard O Palsson
Published 2016-01-01

Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism

by Douglas McCloskey, Sibei Xu, Troy E. Sandberg, Elizabeth Brunk, Ying Hefner, Richard Szubin, Adam M. Feist, Bernhard O. Palsson
Published 2018-09-01

A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types.

by Yara Seif, Jonathan M Monk, Nathan Mih, Hannah Tsunemoto, Saugat Poudel, Cristal Zuniga, Jared Broddrick, Karsten Zengler, Bernhard O Palsson
Published 2019-01-01

Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting.

by Alyaa M Abdel-Haleem, Hooman Hefzi, Katsuhiko Mineta, Xin Gao, Takashi Gojobori, Bernhard O Palsson, Nathan E Lewis, Neema Jamshidi
Published 2018-01-01

Biochemical characterization of human gluconokinase and the proposed metabolic impact of gluconic acid as determined by constraint based metabolic network analysis.

by Neha Rohatgi, Tine Kragh Nielsen, Sara Petersen Bjørn, Ivar Axelsson, Giuseppe Paglia, Bjørn Gunnar Voldborg, Bernhard O Palsson, Óttar Rolfsson
Published 2014-01-01

Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene.

by Pep Charusanti, Tom M Conrad, Eric M Knight, Karthik Venkataraman, Nicole L Fong, Bin Xie, Yuan Gao, Bernhard Ø Palsson
Published 2010-11-01

Elucidating the Regulatory Elements for Transcription Termination and Posttranscriptional Processing in the Streptomyces clavuligerus Genome

by Soonkyu Hwang, Namil Lee, Donghui Choe, Yongjae Lee, Woori Kim, Yujin Jeong, Suhyung Cho, Bernhard O. Palsson, Byung-Kwan Cho
Published 2021-06-01