List of works by Marcin P. Joachimiak

An SF1 affinity model to identify branch point sequences in human introns

scientific article

Application of phenotypic microarrays to environmental microbiology

scientific article published on 02 January 2012

Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough

scientific article

Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution

scientific article published on 11 April 2013

Co-evolution of proteins with their interaction partners

scientific article published on June 2000

Conservation of Modules but not Phenotype in Bacterial Response to Environmental Stress

Deletion of the Desulfovibrio vulgaris carbon monoxide sensor invokes global changes in transcription

scientific article

Evolutionary, mechanistic, and predictive analyses of the hydroxymethyldihydropterin pyrophosphokinase family of proteins

scientific article

Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation

scientific article published on 17 March 2009

Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray

scientific article

Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough

scientific article published on 9 December 2011

Functional responses of methanogenic archaea to syntrophic growth

scientific article

Genetic Adaptation to Salt Stress in Experimental Evolution of Desulfovibrio vulgaris Hildenborough

Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation

scientific article

How many rare diseases are there?

scientific article published on 01 February 2020

Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough

scientific article published in October 2010

Identification of Small RNAs in Desulfovibrio vulgaris Hildenborough

Impact of elevated nitrate on sulfate-reducing bacteria: a comparative study of Desulfovibrio vulgaris

scientific article published on 6 May 2010

JColorGrid: software for the visualization of biological measurements

scientific article

JEvTrace: refinement and variations of the evolutionary trace in JAVA

scientific article

KBase: The United States Department of Energy Systems Biology Knowledgebase

article

KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response

scientific article published on 18 August 2020

KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response

scientific article published on 9 November 2020

KG-Hub -- Building and Exchanging Biological Knowledge Graphs

preprint published in 2023

MicrobesOnline: an integrated portal for comparative and functional genomics

scientific article

Microbial community changes during sustained Cr(VI) reduction at the 100H site in Hanford, WA

Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities

scientific article published on 22 February 2021

Mutual information analysis reveals coevolving residues in Tat that compensate for two distinct functions in HIV-1 gene expression

scientific article published on 17 January 2012

Response of Desulfovibrio vulgaris to alkaline stress

scientific article

Revisiting Modes of energy generation in sulfate reducing bacteria

Semantic Integration of Clinical Laboratory Tests from Electronic Health Records for Deep Phenotyping and Biomarker Discovery: Supplementary materials

article

Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery

article

Shewanella oneidensis MR-1 sensory box protein involved in aerobic and anoxic growth

scientific article

Snapshot of iron response in Shewanella oneidensis by gene network reconstruction

scientific article

Structure prediction in a post-genomic environment: a secondary and tertiary structural model for the initiation factor 5A family

scientific article

Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning

scientific article published on 21 February 2024

Supervised learning with word embeddings derived from PubMed captures latent knowledge about protein kinases and cancer

scientific article published on 08 December 2021

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species

scientific article published on 01 January 2020

The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families

scientific article published in March 2007

The impact of whole genome sequence data on drug discovery--a malaria case study

scientific article

Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough

scientific article

Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state

scientific article

Wheat cytosolic acetyl-CoA carboxylase complements an ACC1 null mutation in yeast.

scientific article published on September 1997

Why was this cited? Explainable machine learning applied to COVID-19 research literature

scientific article published on 09 April 2022

Zinc against COVID-19? Symptom surveillance and deficiency risk groups

scientific article published on 04 January 2021

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