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Author Details

Marcin P Joachimiak
E O Lawrence Berkeley National Laboratory, UCSF Medical Center, University of California, Berkeley, University of Chicago
0000-0001-8175-045X
1997
39
22
PMIDPaper TitleJournal TitlePublished Year
38078749A bacterial sensor taxonomy across earth ecosystems for machine learning applications.mSystems2024
36933632Developing a Knowledge Graph for Pharmacokinetic Natural Product-Drug Interactions.J Biomed Inform2023
37389415KG-Hub-building and exchanging biological knowledge graphs.Bioinformatics2023
35431364Why was this cited? Explainable machine learning applied to COVID-19 research literature.Scientometrics2022
33395417Zinc against COVID-19? Symptom surveillance and deficiency risk groups.PLoS Negl Trop Dis2021
33622857Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities.mSystems2021
33947809Correction for Vangay et al., "Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities".mSystems2021
33196056KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response.Patterns (N Y)2021
32839776KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response.bioRxiv2020
32020066How many rare diseases are there?Nat Rev Drug Discov2020
29979655KBase: The United States Department of Energy Systems Biology Knowledgebase.Nat Biotechnol2018
23575373Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution.ISME J2013
23871664Effects of genetic variation on the E. coli host-circuit interface.Cell Rep2013
22156435Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough.Appl Environ Microbiol2012
22739494Functional responses of methanogenic archaea to syntrophic growth.ISME J2012
22904289Deletion of the Desulfovibrio vulgaris carbon monoxide sensor invokes global changes in transcription.J Bacteriol2012
22507456Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state.BMC Genomics2012
22253435Mutual information analysis reveals coevolving residues in Tat that compensate for two distinct functions in HIV-1 gene expression.J Biol Chem2012
22217654Application of phenotypic microarrays to environmental microbiology.Curr Opin Biotechnol2012
21071404An SF1 affinity model to identify branch point sequences in human introns.Nucleic Acids Res2011
21602393Shewanella oneidensis MR-1 sensory box protein involved in aerobic and anoxic growth.Appl Environ Microbiol2011
21738675Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough.PLoS One2011
20038696Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation.Appl Environ Microbiol2010
20482586Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough.Environ Microbiol2010
20445634Impact of elevated nitrate on sulfate-reducing bacteria: a comparative study of Desulfovibrio vulgaris.ISME J2010
19906701MicrobesOnline: an integrated portal for comparative and functional genomics.Nucleic Acids Res2010
19321007Snapshot of iron response in Shewanella oneidensis by gene network reconstruction.BMC Genomics2009
19293273Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation.Nucleic Acids Res2009
17355171The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families.PLoS Biol2007
17921288Response of Desulfovibrio vulgaris to alkaline stress.J Bacteriol2007
17545284Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough.J Bacteriol2007
16640789JColorGrid: software for the visualization of biological measurements.BMC Bioinformatics2006
12620119Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray.Genome Biol2003
12537566JEvTrace: refinement and variations of the evolutionary trace in JAVA.Genome Biol2002
11713369The impact of whole genome sequence data on drug discovery--a malaria case study.Mol Med2001
10860738Co-evolution of proteins with their interaction partners.J Mol Biol2000
9920734Evolutionary, mechanistic, and predictive analyses of the hydroxymethyldihydropterin pyrophosphokinase family of proteins.Biochem Biophys Res Commun1999
9790926Structure prediction in a post-genomic environment: a secondary and tertiary structural model for the initiation factor 5A family.Biochem Biophys Res Commun1998
11038571Wheat cytosolic acetyl-CoA carboxylase complements an ACC1 null mutation in yeast.Proc Natl Acad Sci U S A1997
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Collaborators

Adam P Arkin
Lawrence Berkeley National Laboratory
Co-authored papers 18
Jizhong Zhou
Institute for Environmental Genomics, University of Oklahoma
Co-authored papers 11
Terry C Hazen
University of Tennessee
Co-authored papers 10
Judy D Wall
University of Missouri
Co-authored papers 10
Jay D Keasling
University of California berkeley
Co-authored papers 9
Zhili He
Environmental Microbiomics Research Center, Sun Yat-Sen University
Co-authored papers 9
David A Stahl
University of Washington
Co-authored papers 7
Aindrila Mukhopadhyay
Joint BioEnergy Institute
Co-authored papers 7
Matthew W Fields
Center for Biofilm Engineering (CBE), Montana State University
Co-authored papers 7
Fred E Cohen
University of California san francisco
Co-authored papers 6
Christopher J Mungall
International Society for Biocuration, Lawrence Berkeley National Laboratory, University of Edinburgh, University of Edinburgh School of Biological Sciences
Co-authored papers 6
Qiang He
University of Tennessee
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Alyssa M Redding
Lawrence Berkeley National Laboratory, Joint BioEnergy Institute
Co-authored papers 6
Dominique C Joyner
University of Tennessee
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John-Marc Chandonia
Lawrence Berkeley National Laboratory
Co-authored papers 5
Paramvir S Dehal
Lawrence Berkeley National Laboratory
Co-authored papers 5
Nomi L Harris
Lawrence Berkely National Laboratory, Massachusetts Institute of Technology, Princeton University
Co-authored papers 5
Aifen Zhou
University of Oklahoma
Co-authored papers 5
Deepak R Unni
Lawrence Berkeley National Laboratory
Co-authored papers 4
Peter N Robinson
William Harvey Research Institute, Queen Mary University of London
Co-authored papers 4
Jason K Baumohl
E.O. Lawrence Berkeley National Laboratory
Co-authored papers 4
Zamin K Yang
Oak Ridge National Laboratory
Co-authored papers 4
Christopher L Hemme
University of Rhode Island
Co-authored papers 4
Tiffany J Callahan
Columbia University
Co-authored papers 4
Sharon Borglin
Lawrence Berkeley National Laboratory
Co-authored papers 3
Vida Ravanmehr
MD Anderson Cancer Center
Co-authored papers 3
Grant M Zane
University of Missouri
Co-authored papers 3
Eric J Alm
Massachusetts Institute of Technology 21 Ames St. Cambridge
Co-authored papers 3
Melissa A Haendel
American Medical Informatics Association, Oregon Health and Science University, Oregon State University, University of Colorado Anschutz Medical Campus, University of North Carolina at Chapel Hill, University of Wisconsin-Madison
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Monica C Munoz-Torres
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Release 1.2