Large-scale genetic characterization of the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough
- Valentine V Trotter, Maxim Shatsky, Morgan N Price, …, Adam M Deutschbauer, John-Marc Chandonia, Gareth P Butland
- None, 10.3389/fmicb.2023.1095191
iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology
- Benjamin Bolduc, Olivier Zablocki, Jiarong Guo, …, Simon Roux, Matthew Vaughn, Matthew B Sullivan
- None, 10.1038/s43705-021-00083-3
Quantifying the local adaptive landscape of a nascent bacterial community
- Joao A Ascensao, Kelly M Wetmore, Benjamin H Good, …, Benjamin H Good, Adam P Arkin, Oskar Hallatschek
- Nat Commun, 10.1038/s41467-022-35677-5
Publisher Correction: Metagenome-assembled genome extraction and analysis from microbiomes using KBase
- Sean P Jungbluth, Paramvir S Dehal, Elisha M Wood-Charlson, …, Robert W Cottingham, Chris S Henry, Adam P Arkin
- Nat Protoc, 10.1038/s41596-022-00794-4
Interactive Analysis of Functional Residues in Protein Families
- Morgan N Price, Adam P Arkin, Morgan N Price, …, Adam P Arkin, Morgan N Price, Adam P Arkin
- mSystems, 10.1128/msystems.00705-22
CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis
- Pavel S Novichkov, John-Marc Chandonia, Adam P Arkin, …, Pavel S Novichkov, John-Marc Chandonia, Adam P Arkin
- Gigascience, 10.1093/gigascience/giac089
Ten simple rules for getting and giving credit for data
- Elisha M Wood-Charlson, Zachary Crockett, Chris Erdmann, Adam P Arkin, Carly B Robinson
- PLoS Comput Biol, 10.1371/journal.pcbi.1010476
Ecophysiological and genomic analyses of a representative isolate of highly abundant Bacillus cereus strains in contaminated subsurface sediments
- Jennifer L Goff, Elizabeth G Szink, Michael P Thorgersen, …, Jizhong Zhou, Adam P Arkin, Michael W W Adams
- Environ Microbiol, 10.1111/1462-2920.16173
Genomics analysis of Drosophila sechellia response to Morinda citrifolia fruit diet
- Zachary Drum, Stephen Lanno, Sara M Gregory, …, Acadia Thielking, Phie Towle, Joseph Coolon
- G3 (Bethesda), 10.1093/g3journal/jkac153
Development of a Markerless Deletion Mutagenesis System in Nitrate-Reducing Bacterium Rhodanobacter denitrificans
- Xuanyu Tao, Aifen Zhou, Megan L Kempher, …, Adam M Deutschbauer, Adam P Arkin, Jizhong Zhou
- Appl Environ Microbiol, 10.1128/aem.00401-22
Biofilm Interaction Mapping and Analysis (BIMA) of Interspecific Interactions in Pseudomonas Co-culture Biofilms
- Suzanne M Kosina, Peter Rademacher, Kelly M Wetmore, …, Adam P Arkin, Adam M Deutschbauer, Trent R Northen
- None, 10.3389/fmicb.2021.757856
Deciphering Microbial Metal Toxicity Responses via Random Bar Code Transposon Site Sequencing and Activity-Based Metabolomics
- Michael P Thorgersen, Jingchuan Xue, Erica L W Majumder, …, Adam M Deutschbauer, Gary Siuzdak, Michael W W Adams
- Appl Environ Microbiol, 10.1128/aem.01037-21
Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance
- Ankita Kothari, Simon Roux, Hanqiao Zhang, …, Eric J Alm, Romy Chakraborty, Aindrila Mukhopadhyay
- mSystems, 10.1128/msystems.00537-21
Deletion Mutants, Archived Transposon Library, and Tagged Protein Constructs of the Model Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough
- Judy D Wall, Grant M Zane, Thomas R Juba, …, Gareth Butland, Adam P Arkin, Adam M Deutschbauer
- None, 10.1128/mra.00072-21
Molecular pharming to support human life on the moon, mars, and beyond
- Matthew J McNulty, Yongao Mary Xiong, Kevin Yates, …, Nancy E Lane, Somen Nandi, Karen A McDonald
- Crit Rev Biotechnol, 10.1080/07388551.2021.1888070
Diverse Bacterial Genes Modulate Plant Root Association by Beneficial Bacteria
- Fernanda Plucani do Amaral, Thalita Regina Tuleski, Vania Carla Silva Pankievicz, …, Adam Deutschbauer, Rose Adele Monteiro, Gary Stacey
- mBio, 10.1128/mbio.03078-20
Characterization of a Metal-Resistant Bacillus Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation
- Xiaoxuan Ge, Michael P Thorgersen, Farris L Poole, …, Adam P Arkin, Terry C Hazen, Michael W W Adams
- None, 10.3389/fmicb.2020.587127
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes
- Samuel M D Seaver, Filipe Liu, Qizhi Zhang, …, Robert W Cottingham, Adam P Arkin, Christopher S Henry
- Nucleic Acids Res, 10.1093/nar/gkaa1143
Draft Genome Sequence of Bacillus sp. Strain EB106-08-02-XG196, Isolated from High-Nitrate-Contaminated Sediment
- Xiaoxuan Ge, Michael P Thorgersen, Farris L Poole, …, Adam P Arkin, Terry C Hazen, Michael W W Adams
- None, 10.1128/mra.01149-20
Effects of Genetic and Physiological Divergence on the Evolution of a Sulfate-Reducing Bacterium under Conditions of Elevated Temperature
- Megan L Kempher, Xuanyu Tao, Rong Song, …, Adam P Arkin, Aifen Zhou, Jizhong Zhou
- mBio, 10.1128/mbio.00569-20
Redefining fundamental concepts of transcription initiation in bacteria
- Citlalli MejÃa-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
GapMind: Automated Annotation of Amino Acid Biosynthesis
- Morgan N Price, Adam M Deutschbauer, Adam P Arkin
- mSystems, 10.1128/msystems.00291-20
Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer
- Ji-Won Moon, Charles J Paradis, Dominique C Joyner, …, David A Stahl, Dwayne A Elias, Terry C Hazen
- Chemosphere, 10.1016/j.chemosphere.2020.126951
Selective carbon sources influence the end products of microbial nitrate respiration
- Hans K Carlson, Lauren M Lui, Morgan N Price, …, Torben Nielsen, Adam P Arkin, Adam M Deutschbauer
- ISME J, 10.1038/s41396-020-0666-7
Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity
- Renmao Tian, Daliang Ning, Zhili He, …, David A Stahl, Eric J Alm, Jizhong Zhou
- Microbiome, 10.1186/s40168-020-00825-w
High spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquifer
- Anna J Zelaya, Albert E Parker, Kathryn L Bailey, …, Terry C Hazen, Adam P Arkin, Matthew W Fields
- Water Res, 10.1016/j.watres.2019.114917
Nitrate-Utilizing Microorganisms Resistant to Multiple Metals from the Heavily Contaminated Oak Ridge Reservation
- Michael P Thorgersen, Xiaoxuan Ge, Farris L Poole, Morgan N Price, Adam P Arkin, Michael W W Adams
- Appl Environ Microbiol, 10.1128/aem.00896-19
Early-Career Scientists Shaping the World
- Ileana M Cristea, Pieter C Dorrestein, Jonathan A Eisen, …, Pamela A Silver, Nicole S Webster, Jian Xu
- mSystems, 10.1128/msystems.00196-19
Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Pseudomonas putida Lysine Metabolism
- Mitchell G Thompson, Jacquelyn M Blake-Hedges, Pablo Cruz-Morales, …, Adam P Arkin, Adam M Deutschbauer, Jay D Keasling
- mBio, 10.1128/mbio.02577-18
Curated BLAST for Genomes
- Morgan N Price, Adam P Arkin
- mSystems, 10.1128/msystems.00072-19
A versatile platform strain for high-fidelity multiplex genome editing
- Robert G Egbert, Harneet S Rishi, Benjamin A Adler, …, Esteban Toro, Ryan T Gill, Adam P Arkin
- Nucleic Acids Res, 10.1093/nar/gkz085
Older Blood Is Associated With Increased Mortality and Adverse Events in Massively Transfused Trauma Patients: Secondary Analysis of the PROPPR Trial
- Allison R Jones, Rakesh P Patel, Marisa B Marques, …, Stacia M DeSantis, John R Hess, Henry E Wang
- Ann Emerg Med, 10.1016/j.annemergmed.2018.09.033
