Reconstructor: a COBRApy compatible tool for automated genome-scale metabolic network reconstruction with parsimonious flux-based gap-filling

por Jenior, Matthew L, Glass, Emma M, Papin, Jason A
Publicado 2023

Genome-scale metabolic modeling reveals increased reliance on valine catabolism in clinical isolates of Klebsiella pneumoniae

por Jenior, Matthew L., Dickenson, Mary E., Papin, Jason A.
Publicado 2022

Network analysis of toxin production in Clostridioides difficile identifies key metabolic dependencies

por Powers, Deborah A., Jenior, Matthew L., Kolling, Glynis L., Papin, Jason A.
Publicado 2023

Clostridium difficile Colonizes Alternative Nutrient Niches during Infection across Distinct Murine Gut Microbiomes

por Jenior, Matthew L., Leslie, Jhansi L., Young, Vincent B., Schloss, Patrick D.
Publicado 2017

Clostridium difficile Alters the Structure and Metabolism of Distinct Cecal Microbiomes during Initial Infection To Promote Sustained Colonization

por Jenior, Matthew L., Leslie, Jhansi L., Young, Vincent B., Schloss, Patrick D.
Publicado 2018

The Gut Microbiota Is Associated with Clearance of Clostridium difficile Infection Independent of Adaptive Immunity

por Leslie, Jhansi L., Vendrov, Kimberly C., Jenior, Matthew L., Young, Vincent B.
Publicado 2019

Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments

por Jenior, Matthew L., Moutinho, Thomas J., Dougherty, Bonnie V., Papin, Jason A.
Publicado 2020

Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions

por Moutinho, Thomas J., Neubert, Benjamin C., Jenior, Matthew L., Papin, Jason A.
Publicado 2022

Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system

por Schloss, Patrick D., Jenior, Matthew L., Koumpouras, Charles C., Westcott, Sarah L., Highlander, Sarah K.
Publicado 2016

Multidimensional Clinical Surveillance of Pseudomonas aeruginosa Reveals Complex Relationships between Isolate Source, Morphology, and Antimicrobial Resistance

por Dunphy, Laura J., Kolling, Glynis L., Jenior, Matthew L., Carroll, Joanne, Attai, April E., Farnoud, Farzad, Mathers, Amy J., Hughes, Molly A., Papin, Jason A.
Publicado 2021

Novel Drivers of Virulence in Clostridioides difficile Identified via Context-Specific Metabolic Network Analysis

por Jenior, Matthew L., Leslie, Jhansi L., Powers, Deborah A., Garrett, Elizabeth M., Walker, Kimberly A., Dickenson, Mary E., Petri, William A., Tamayo, Rita, Papin, Jason A.
Publicado 2021

Protection from Lethal Clostridioides difficile Infection via Intraspecies Competition for Cogerminant

por Leslie, Jhansi L., Jenior, Matthew L., Vendrov, Kimberly C., Standke, Alexandra K., Barron, Madeline R., O’Brien, Tricia J., Unverdorben, Lavinia, Thaprawat, Pariyamon, Bergin, Ingrid L., Schloss, Patrick D., Young, Vincent B.
Publicado 2021

Lewis Blood-group Antigens Are Associated With Altered Susceptibility to Shigellosis

por Leslie, Jhansi L, Weddle, Erin, Yum, Lauren K, Lin, Ye, Jenior, Matthew L, Lee, Benjamin, Ma, Jennie Z, Kirkpatrick, Beth D, Nayak, Uma, Platts-Mills, James A, Agaisse, Herve F, Haque, Rashidul, Petri, William A
Publicado 2020

Ten simple rules to increase computational skills among biologists with Code Clubs

por Hagan, Ada K., Lesniak, Nicholas A., Balunas, Marcy J., Bishop, Lucas, Close, William L., Doherty, Matthew D., Elmore, Amanda G., Flynn, Kaitlin J., Hannigan, Geoffrey D., Koumpouras, Charlie C., Jenior, Matthew L., Kozik, Ariangela J., McBride, Kathryn, Rifkin, Samara B., Stough, Joshua M. A., Sovacool, Kelly L., Sze, Marc A., Tomkovich, Sarah, Topcuoglu, Begum D., Schloss, Patrick D.
Publicado 2020