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Bernhard O. Palsson, PhD

Affiliations: 
1984-1995 Chemical Engineering University of Michigan, Ann Arbor, Ann Arbor, MI 
 1995- Bioengineering University of California, San Diego, La Jolla, CA 
Website:
http://systemsbiology.ucsd.edu/Researchers/Palsson
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"Bernhard Palsson"
Bio:

Department of Bioengineering, University of California, San Diego La Jolla, CA 92093-0412, USA

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Parents

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Edwin N. Lightfoot grad student UW Madison

Children

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Abhay Joshi grad student 1988 University of Michigan
Gyun Min Lee grad student 1990 University of Michigan
Sadettin Ozturk grad student 1990 University of Michigan
Craig Halberstadt grad student 1991 University of Michigan
Minoo Javanmardian grad student 1991 University of Michigan
Jay D. Keasling grad student 1991 University of Michigan (Chemistry Tree)
Joanne Savinell grad student 1991 University of Michigan
Richard M. Schwartz grad student 1991 University of Michigan
Amit Varma grad student 1993 University of Michigan
Choul Gyun Lee grad student 1994 University of Michigan
Ramkumar Mandalam grad student 1994 University of Michigan
Alice Chuck grad student 1995 University of Michigan
Ching An Peng grad student 1995 University of Michigan
Stylianos Andreadis grad student 1996 University of Michigan
Jeremy S. Edwards grad student 1999 UCSD
Karl Francis grad student 1999 UCSD
Christophe Schilling grad student 2000 UCSD
Markus Willard Covert grad student 2003 UCSD
Jochen Förster grad student 2003 (Chemistry Tree)
Sharon Jane Wiback grad student 2003 UCSD
Iman Famili grad student 2004 UCSD
Stephen Sailoong Fong grad student 2004 UCSD
Markus Juhana Herrgard grad student 2004 UCSD
Jason A. Papin grad student 2004 UCSD
Timothy Eric Allen grad student 2005 UCSD
Nathan Daniel Price grad student 2005 UCSD
Jennifer Leanne Reed grad student 2005 UCSD
Natalie Christine Hurlen grad student 2006 UCSD
Thuy D. Vo grad student 2006 UCSD
Scott Anthony Becker grad student 2007 UCSD
Andrew Robert Joyce grad student 2007 UCSD
Adam Michael Feist grad student 2008 UCSD
Neema Jamshidi grad student 2009 UCSD
Monica L. Mo grad student 2009 UCSD
Ines Thiele grad student 2009 UCSD
Margaret Kenyon Applebee grad student 2010 UCSD
Thomas Conrad grad student 2010 UCSD
Vasiliy A. Portnoy grad student 2010 UCSD
Jan Schellenberger grad student 2010 UCSD
Roger Larken Chang grad student 2012 UCSD
Nathan Enoch Lewis grad student 2012 UCSD
Harish Nagarajan grad student 2012 UCSD
Jeffrey David Orth grad student 2012 UCSD
Aarash Bordbar grad student 2014 UCSD
Mallory Embree grad student 2014 UCSD
Stephen Federowicz grad student 2014 UCSD
Donghyuk Kim grad student 2014 UCSD
Haythem Latif grad student 2014 UCSD
Joshua Adam Lerman grad student 2014 UCSD
Jonathan Monk grad student 2015 UCSD
Edward J. O'Brien grad student 2015 UCSD
Daniel Zielinski grad student 2015 UCSD
Ali Ebrahim grad student 2016 UCSD
Ryan LaCroix grad student 2016 UCSD
Douglas McCloskey grad student 2011-2016 UCSD
Jared Broddrick grad student 2013-2018 UCSD
Nathan Mih grad student 2013-2018 UCSD
James Yurkovich grad student 2013-2018 UCSD
Bin Du grad student 2019 UCSD
Colton Lloyd grad student 2019 UCSD
Justin Tan grad student 2019 UCSD
Xin Fang grad student 2020 UCSD
Ye Gao grad student 2020 UCSD
Erol Kavvas grad student 2020 UCSD
Anand Sastry grad student 2020 UCSD
Yara Seif grad student 2020 UCSD
Charles Norsigian grad student 2021 UCSD
Patrick Phaneuf grad student 2021 UCSD
Saugat Poudel grad student 2017-2022 (Microtree)
Juan Nogales post-doc 2010-2012 UCSD (Microtree)
Nikolaus Sonnenschein post-doc 2011-2013 UCSD
Sang Woo Seo post-doc 2013-2015 UCSD
Elizabeth Brunk post-doc 2014-2017
David Heckmann post-doc 2019 UCSD
Julia Kleinmanns post-doc 2019 UCSD
Sonal Choudhary post-doc 2020 UCSD
Henrique Machado post-doc 2020 UCSD
Amitesh Anand post-doc 2021 UCSD
Hyun Gyu Lim post-doc 2018-2023 UCSD
Laurence Yang research scientist 2019 UCSD (Chemistry Tree)

Collaborators

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Jason H. Yang collaborator 2015-2017 UCSD
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Publications

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Josephs-Spaulding J, Rajput A, Hefner Y, et al. (2024) Reconstructing the transcriptional regulatory network of probiotic is enabled by transcriptomics and machine learning. Msystems. e0125723
Zhao J, Chen K, Palsson BO, et al. (2024) StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses. Plos Computational Biology. 20: e1011865
Qiu S, Wan X, Liang Y, et al. (2024) Inferred regulons are consistent with regulator binding sequences in E. coli. Plos Computational Biology. 20: e1011824
Lee SM, Le HT, Taizhanova A, et al. (2024) Experimental promoter identification of a foodborne pathogen subsp. serovar Typhimurium with near single base-pair resolution. Frontiers in Microbiology. 14: 1271121
Menon ND, Poudel S, Sastry AV, et al. (2024) Independent component analysis reveals 49 independently modulated gene sets within the global transcriptional regulatory architecture of multidrug-resistant . Msystems. e0060623
Hyun JC, Monk JM, Szubin R, et al. (2023) Global pathogenomic analysis identifies known and candidate genetic antimicrobial resistance determinants in twelve species. Nature Communications. 14: 7690
Mattei G, Gan Z, Ramazzotti M, et al. (2023) Differential Expression Analysis Utilizing Condition-Specific Metabolic Pathways. Metabolites. 13
Miano A, Rychel K, Lezia A, et al. (2023) High-resolution temporal profiling of E. coli transcriptional response. Nature Communications. 14: 7606
Kim GB, Kim JY, Lee JA, et al. (2023) Functional annotation of enzyme-encoding genes using deep learning with transformer layers. Nature Communications. 14: 7370
Lamoureux CR, Decker KT, Sastry AV, et al. (2023) A multi-scale expression and regulation knowledge base for Escherichia coli. Nucleic Acids Research
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