John Parkinson

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 23

Top Topics

Machine Learning

Gene Expression

Toxoplasma Gondii

Top Venues

PLoS computational biology

Bioinformatics advances

This page only lists publications with an associated author ORCID identifier.

Publications

Lakshmipuram S Swapna, Grant C Stevens, Aline Sardinha-Silva, Lucas Zhongming Hu, Verena Brand, Daniel D Fusca, Cuihong Wan, Xuejian Xiong, Jon P Boyle, Michael E Grigg, Andrew Emili, John Parkinson
ToxoNet: A high confidence map of protein-protein interactions in Toxoplasma gondii. PLoS computational biology 20 (6) (2024)
Lakshmipuram S Swapna, Grant C Stevens, Aline Sardinha-Silva, Lucas Zhongming Hu, Verena Brand, Daniel D Fusca, Cuihong Wan, Xuejian Xiong, Jon P Boyle, Michael E Grigg, Andrew Emili, John Parkinson
ToxoNet: A high confidence map of protein-protein interactions in Toxoplasma gondii. PLoS computational biology 20 (6) (2024)
Lakshmipuram S Swapna, Grant C Stevens, Aline Sardinha-Silva, Lucas Zhongming Hu, Verena Brand, Daniel D Fusca, Cuihong Wan, Xuejian Xiong, Jon P Boyle, Michael E Grigg, Andrew Emili, John Parkinson
ToxoNet: A high confidence map of protein-protein interactions in Toxoplasma gondii. PLoS computational biology 20 (6) (2024)
Seyed Hossien Kairmi, Khaled Abdelaziz, Heidi Spahany, Jake Astill, David Trott, Blake Wang, Alice Wang, John Parkinson, Shayan Sharif
Intestinal microbiome profiles in broiler chickens raised without antibiotics exhibit altered microbiome dynamics relative to conventionally raised chickens. PloS one 19 (4) (2024)
Bhavish Verma, John Parkinson
HiTaxon: a hierarchical ensemble framework for taxonomic classification of short reads. Bioinformatics advances 4 (1) (2024)
Bhavish Verma, John Parkinson
HiTaxon: a hierarchical ensemble framework for taxonomic classification of short reads. Bioinformatics advances 4 (1) (2024)
Bhavish Verma, John Parkinson
HiTaxon: a hierarchical ensemble framework for taxonomic classification of short reads. Bioinformatics advances 4 (1) (2024)
Seyed Hossien Kairmi, Khaled Abdelaziz, Heidi Spahany, Jake Astill, David Trott, Blake Wang, Alice Wang, John Parkinson, Shayan Sharif
Intestinal microbiome profiles in broiler chickens raised without antibiotics exhibit altered microbiome dynamics relative to conventionally raised chickens. PloS one 19 (4) (2024)
Seyed Hossien Kairmi, Khaled Abdelaziz, Heidi Spahany, Jake Astill, David Trott, Blake Wang, Alice Wang, John Parkinson, Shayan Sharif
Intestinal microbiome profiles in broiler chickens raised without antibiotics exhibit altered microbiome dynamics relative to conventionally raised chickens. PloS one 19 (4) (2024)
Seyed Hossien Kairmi, Khaled Abdelaziz, Heidi Spahany, Jake Astill, David Trott, Blake Wang, Alice Wang, John Parkinson, Shayan Sharif
Intestinal microbiome profiles in broiler chickens raised without antibiotics exhibit altered microbiome dynamics relative to conventionally raised chickens. PloS one 19 (4) (2024)
Bhavish Verma, John Parkinson
HiTaxon: a hierarchical ensemble framework for taxonomic classification of short reads. Bioinformatics advances 4 (1) (2024)
Graham L Cromar, Jonathan R Epp, Ana Popovic, Yusing Gu, Violet Ha, Brandon J Walters, James St Pierre, Xuejian Xiong, John G Howland, Sheena A Josselyn, Paul W Frankland, John Parkinson
Toxoplasma infection in male mice alters dopamine-sensitive behaviors and host gene expression patterns associated with neuropsychiatric disease. PLoS neglected tropical diseases 16 (7) (2022)
Nirvana Nursimulu, Alan M Moses, John Parkinson
Architect: A tool for aiding the reconstruction of high-quality metabolic models through improved enzyme annotation. PLoS computational biology 18 (9) (2022)
Maxine Ty, Khaled Taha-Abdelaziz, Vanessa Demey, Mathieu Castex, Shayan Sharif, John Parkinson
Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry. Animal microbiome 4 (1) (2022)
Louis C Dacquay, Derek Tsang, Donny Chan, John Parkinson, Dana J Philpott, David R McMillen
E.coli Nissle increases transcription of flagella assembly and formate hydrogenlyase genes in response to colitis. Gut microbes 13 (1) (2022)
Ana Popovic, Celine Bourdon, Pauline W Wang, David S Guttman, Sajid Bashir Soofi, Zulfiqar A Bhutta, Robert H J Bandsma, John Parkinson, Lisa G Pell
Micronutrient supplements can promote disruptive protozoan and fungal communities in the developing infant gut. Nature communications 12 (1) (2021)
Gregory B Whitfield, Lindsey S Marmont, Cedoljub Bundalovic-Torma, Erum Razvi, Elyse J Roach, Cezar M Khursigara, John Parkinson, P Lynne Howell
Discovery and characterization of a Gram-positive Pel polysaccharide biosynthetic gene cluster. PLoS pathogens 16 (4) (2020)
Angela Zou, Kerry Nadeau, Pauline W Wang, Jee Yeon Lee, David S Guttman, Shayan Sharif, Doug R Korver, John H Brumell, John Parkinson
Accumulation of genetic variants associated with immunity in the selective breeding of broilers. BMC genetics 21 (1) (2020)
David M Curran, Alexandra Grote, Nirvana Nursimulu, Adam Geber, Dennis Voronin, Drew R Jones, Elodie Ghedin, John Parkinson
Modeling the metabolic interplay between a parasitic worm and its bacterial endosymbiont allows the identification of novel drug targets. eLife 9 (2020)
Cedoljub Bundalovic-Torma, Gregory B Whitfield, Lindsey S Marmont, P Lynne Howell, John Parkinson
A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries. PLoS computational biology 16 (4) (2020)
Ana Popovic, Celine Bourdon, Pauline W Wang, David S Guttman, Wieger Voskuijl, Michael E Grigg, Robert H J Bandsma, John Parkinson
Design and application of a novel two-amplicon approach for defining eukaryotic microbiota. Microbiome 6 (1) (2018)
Lakshmipuram Seshadri Swapna, Alyssa M Molinaro, Nicole Lindsay-Mosher, Bret J Pearson, John Parkinson
Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation. Genome biology 19 (1) (2018)
Xuejian Xiong, Elise S Bales, Diana Ir, Charles E Robertson, James L McManaman, Daniel N Frank, John Parkinson
Perilipin-2 modulates dietary fat-induced microbial global gene expression profiles in the mouse intestine. Microbiome 5 (1) (2017)