Academic lineage
A functional microbiome catalog crowdsourced from North American rivers
- Mikayla A Borton, Bridget B McGivern, Kathryn R Willi, …, Byron C Crump, James C Stegen, Kelly C Wrighton
- None, 10.1101/2023.07.22.550117
Engineering of increased L-Threonine production in bacteria by combinatorial cloning and machine learning
- Paul Hanke, Bruce Parrello, Olga Vasieva, …, Dionysios Antonopoulos, Rick Stevens, Michael Fonstein
- Metab Eng, 10.1016/j.mec.2023.e00225
kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase
- Michael Shaffer, Mikayla A Borton, Ben Bolduc, …, Matthew B Sullivan, Christopher S Henry, Kelly C Wrighton
- Bioinformatics, 10.1093/bioinformatics/btad110
Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine
- Almut Heinken, Johannes Hertel, Geeta Acharya, …, Christopher S Henry, Ronan M T Fleming, Ines Thiele
- Nat Biotechnol, 10.1038/s41587-022-01628-0
Functional characterization of prokaryotic dark matter: the road so far and what lies ahead
- Pedro Escudeiro, Christopher S Henry, Ricardo P M Dias, Pedro Escudeiro, Christopher S Henry, Ricardo P M Dias
- None, 10.1016/j.crmicr.2022.100159
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
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/s41596-022-00747-x
Respiratory energy demands and scope for demand expansion and destruction
- Ulschan Bathe, Bryan J Leong, Kristen Van Gelder, …, Christopher S Henry, Jeffrey S Amthor, Andrew D Hanson
- Plant Physiol, 10.1093/plphys/kiac493
Interaction Networks Are Driven by Community-Responsive Phenotypes in a Chitin-Degrading Consortium of Soil Microbes
- Ryan McClure, Yuliya Farris, Robert Danczak, …, Christopher Henry, Janet K Jansson, Kirsten S Hofmockel
- mSystems, 10.1128/msystems.00372-22
A roadmap for the functional annotation of protein families: a community perspective
- Valérie de Crécy-Lagard, Rocio Amorin de Hegedus, Cecilia Arighi, …, Valerie Wood, Elisha M Wood-Charlson, Jin Xu
- Database (Oxford), 10.1093/database/baac062
Metabolite Damage and Damage Control in a Minimal Genome
- Drago Haas, Antje M Thamm, Jiayi Sun, …, Andrew D Hanson, Christopher S Henry, Valérie de Crécy-Lagard
- mBio, 10.1128/mbio.01630-22
Genome-scale modeling of the primary-specialized metabolism interface
- Kathleen Beilsmith, Christopher S Henry, Samuel M D Seaver
- Curr Opin Plant Biol, 10.1016/j.pbi.2022.102244
Chemical-damage MINE: A database of curated and predicted spontaneous metabolic reactions
- James G Jeffryes, Claudia Lerma-Ortiz, Filipe Liu, …, Andrew D Hanson, Keith Ej Tyo, Christopher S Henry
- Metab Eng, 10.1016/j.ymben.2021.11.009
ORT: a workflow linking genome-scale metabolic models with reactive transport codes
- Rebecca L Rubinstein, Mikayla A Borton, Haiyan Zhou, …, Christopher S Henry, Kelly C Wrighton, Roelof Versteeg
- Bioinformatics, 10.1093/bioinformatics/btab753
Application of the Metabolic Modeling Pipeline in KBase to Categorize Reactions, Predict Essential Genes, and Predict Pathways in an Isolate Genome
- Benjamin H Allen, Nidhi Gupta, Janaka N Edirisinghe, José P Faria, Christopher S Henry
- Methods Mol Biol, 10.1007/978-1-0716-1585-0_13