Patrick S G Chain (Patrick S Chain, Patrick Sg Chain)

Loop profile ORCID

Publication Activity (10 Years)

Years Active: 2020-2024
Publications (10 Years): 26

Top Topics

Escherichia Coli

Respiratory Tract

Top Venues

Nature biotechnology

ISME communications

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

Publications

Ryan Connor, Migun Shakya, David A Yarmosh, Wolfgang Maier, Ross Martin, Rebecca Bradford, J Rodney Brister, Patrick S G Chain, Courtney A Copeland, Julia di Iulio, Bin Hu, Philip Ebert, Jonathan Gunti, Yumi Jin, Kenneth S Katz, Andrey Kochergin, Tré LaRosa, Jiani Li, Po-E Li, Chien-Chi Lo, Sujatha Rashid, Evguenia S Maiorova, Chunlin Xiao, Vadim Zalunin, Lisa A Purcell, Kim D Pruitt
Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows. Viruses 16 (3) (2024)
Ryan Connor, Migun Shakya, David A Yarmosh, Wolfgang Maier, Ross Martin, Rebecca Bradford, J Rodney Brister, Patrick S G Chain, Courtney A Copeland, Julia di Iulio, Bin Hu, Philip Ebert, Jonathan Gunti, Yumi Jin, Kenneth S Katz, Andrey Kochergin, Tré LaRosa, Jiani Li, Po-E Li, Chien-Chi Lo, Sujatha Rashid, Evguenia S Maiorova, Chunlin Xiao, Vadim Zalunin, Lisa A Purcell, Kim D Pruitt
Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows. Viruses 16 (3) (2024)
James D Brunner, Aaron J Robinson, Patrick S G Chain
Combining compositional data sets introduces error in covariance network reconstruction. ISME communications 4 (1) (2024)
James D Brunner, Aaron J Robinson, Patrick S G Chain
Combining compositional data sets introduces error in covariance network reconstruction. ISME communications 4 (1) (2024)
Ryan Connor, Migun Shakya, David A Yarmosh, Wolfgang Maier, Ross Martin, Rebecca Bradford, J Rodney Brister, Patrick S G Chain, Courtney A Copeland, Julia di Iulio, Bin Hu, Philip Ebert, Jonathan Gunti, Yumi Jin, Kenneth S Katz, Andrey Kochergin, Tré LaRosa, Jiani Li, Po-E Li, Chien-Chi Lo, Sujatha Rashid, Evguenia S Maiorova, Chunlin Xiao, Vadim Zalunin, Lisa A Purcell, Kim D Pruitt
Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows. Viruses 16 (3) (2024)
Ryan Connor, Migun Shakya, David A Yarmosh, Wolfgang Maier, Ross Martin, Rebecca Bradford, J Rodney Brister, Patrick S G Chain, Courtney A Copeland, Julia di Iulio, Bin Hu, Philip Ebert, Jonathan Gunti, Yumi Jin, Kenneth S Katz, Andrey Kochergin, Tré LaRosa, Jiani Li, Po-E Li, Chien-Chi Lo, Sujatha Rashid, Evguenia S Maiorova, Chunlin Xiao, Vadim Zalunin, Lisa A Purcell, Kim D Pruitt
Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows. Viruses 16 (3) (2024)
Ryan Connor, Migun Shakya, David A Yarmosh, Wolfgang Maier, Ross Martin, Rebecca Bradford, J Rodney Brister, Patrick S G Chain, Courtney A Copeland, Julia di Iulio, Bin Hu, Philip Ebert, Jonathan Gunti, Yumi Jin, Kenneth S Katz, Andrey Kochergin, Tré LaRosa, Jiani Li, Po-E Li, Chien-Chi Lo, Sujatha Rashid, Evguenia S Maiorova, Chunlin Xiao, Vadim Zalunin, Lisa A Purcell, Kim D Pruitt
Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows. Viruses 16 (3) (2024)
Reid Longley, Aaron J Robinson, Olivia A Asher, Earl A Middlebrook, Gregory M Bonito, Patrick S G Chain
Signatures of Mollicutes-related endobacteria in publicly available Mucoromycota genomes. mSphere (2024)
Ryan Connor, Migun Shakya, David A Yarmosh, Wolfgang Maier, Ross Martin, Rebecca Bradford, J Rodney Brister, Patrick S G Chain, Courtney A Copeland, Julia di Iulio, Bin Hu, Philip Ebert, Jonathan Gunti, Yumi Jin, Kenneth S Katz, Andrey Kochergin, Tré LaRosa, Jiani Li, Po-E Li, Chien-Chi Lo, Sujatha Rashid, Evguenia S Maiorova, Chunlin Xiao, Vadim Zalunin, Lisa A Purcell, Kim D Pruitt
Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows. Viruses 16 (3) (2024)
Ryan Connor, Migun Shakya, David A Yarmosh, Wolfgang Maier, Ross Martin, Rebecca Bradford, J Rodney Brister, Patrick S G Chain, Courtney A Copeland, Julia di Iulio, Bin Hu, Philip Ebert, Jonathan Gunti, Yumi Jin, Kenneth S Katz, Andrey Kochergin, Tré LaRosa, Jiani Li, Po-E Li, Chien-Chi Lo, Sujatha Rashid, Evguenia S Maiorova, Chunlin Xiao, Vadim Zalunin, Lisa A Purcell, Kim D Pruitt
Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows. Viruses 16 (3) (2024)
Emiley A Eloe-Fadrosh, Christopher John Mungall, Mark Andrew Miller, Montana L Smith, Sujay Sanjeev Patil, Julia M Kelliher, Leah Y D Johnson, Francisca E Rodriguez, Patrick S G Chain, Bin Hu, Michael B Thornton, Lee Ann McCue, Alice Carolyn McHardy, Nomi L Harris, T B K Reddy, Supratim Mukherjee, Christopher I Hunter, Ramona L Walls, Lynn M Schriml
A Practical Approach to Using the Genomic Standards Consortium MIxS Reporting Standard for Comparative Genomics and Metagenomics. Methods in molecular biology (Clifton, N.J.) 2802 (2024)
Michelle Qiu Carter, Beatriz Quiñones, Xiaohua He, Antares Pham, Diana Carychao, Michael B Cooley, Chien-Chi Lo, Patrick S G Chain, Rebecca L Lindsey, James L Bono
Genomic and Phenotypic Characterization of Shiga Toxin-Producing Escherichia albertii Strains Isolated from Wild Birds in a Major Agricultural Region in California. Microorganisms 11 (11) (2023)
Antonio Pedro Camargo, Simon Roux, Frederik Schulz, Michal Babinski, Yan Xu, Bin Hu, Patrick S G Chain, Stephen Nayfach, Nikos C Kyrpides
Identification of mobile genetic elements with geNomad. Nature biotechnology (2023)
Reid Longley, Aaron J Robinson, Julian A Liber, Abigail E Bryson, Demosthenes P Morales, Kurt M LaButti, Robert Riley, Stephen J Mondo, Alan Kuo, Yuko Yoshinaga, Christopher Daum, Kerrie W Barry, Igor V Grigoriev, Alessandro Desirò, Patrick S G Chain, Gregory M Bonito
Comparative genomics of Mollicutes-related endobacteria supports a late invasion into Mucoromycota fungi. Communications biology 6 (1) (2023)
Ryan Connor, David A Yarmosh, Wolfgang Maier, Migun Shakya, Ross Martin, Rebecca Bradford, J Rodney Brister, Patrick S G Chain, Courtney A Copeland, Julia di Iulio, Bin Hu, Philip J Ebert, Jonathan Gunti, Yumi Jin, Kenneth S Katz, Andrey Kochergin, Tré LaRosa, Jiani Li, Po-E Li, Chien-Chi Lo, Sujatha Rashid, Evguenia S Maiorova, Chunlin Xiao, Vadim Zalunin, Kim D Pruitt
Towards increased accuracy and reproducibility in SARS-CoV-2 next generation sequence analysis for public health surveillance. bioRxiv : the preprint server for biology (2022)
Tim Mercer, Neil Almond, Michael A Crone, Patrick S G Chain, Alina Deshpande, Deepa Eveleigh, Paul S Freemont, Sebastien Fuchs, Russell Garlick, Jim Huggett, Martin Kammel, Po-E Li, Mojca Milavec, Elizabeth M Marlowe, Denise M O'Sullivan, Mark Page, Gary A Pestano, Sara A Suliman, Birgitte Simen, John J Sninsky, Lynne Sopchak, Cristina M Tato, Peter M Vallone, Jo Vandesompele, Thomas J White, Heinz Zeichhardt, Marc L Salit
The Coronavirus Standards Working Group's roadmap for improved population testing. Nature biotechnology 40 (11) (2022)
Michelle Qiu Carter, Nicole Laniohan, Chien-Chi Lo, Patrick S G Chain
Comparative Genomics Applied to Systematically Assess Pathogenicity Potential in Shiga Toxin-Producing Escherichia coli O145:H28. Microorganisms 10 (5) (2022)
Ashley Thommana, Migun Shakya, Jaykumar Gandhi, Christian K Fung, Patrick S G Chain, Irina Maljkovic Berry, Matthew A Conte
Intrahost SARS-CoV-2 k-mer Identification Method (iSKIM) for Rapid Detection of Mutations of Concern Reveals Emergence of Global Mutation Patterns. Viruses 14 (10) (2022)
Andrew William Bartlow, Zachary R Stromberg, Cheryl D Gleasner, Bin Hu, Karen W Davenport, Shailja Jakhar, Po-E Li, Molly Vosburg, Madhavi Garimella, Patrick S G Chain, Tracy H Erkkila, Jeanne M Fair, Harshini Mukundan
Comparing variability in diagnosis of upper respiratory tract infections in patients using syndromic, next generation sequencing, and PCR-based methods. PLOS global public health 2 (7) (2022)
Thierry Kuhn, Matteo Buffi, Saskia Bindschedler, Patrick S G Chain, Diego Gonzalez, Claire E Stanley, Lukas Y Wick, Pilar Junier, Xiang-Yi Li Richter
Design and construction of 3D printed devices to investigate active and passive bacterial dispersal on hydrated surfaces. BMC biology 20 (1) (2022)
Po-E Li, Adán Myers Y Gutiérrez, Karen Davenport, Mark Flynn, Bin Hu, Chien-Chi Lo, Elais Player Jackson, Migun Shakya, Yan Xu, Jason D Gans, Patrick S G Chain
A public website for the automated assessment and validation of SARS-CoV-2 diagnostic PCR assays. Bioinformatics (Oxford, England) 37 (7) (2021)
Jessica Z Kubicek-Sutherland, Gary Xie, Migun Shakya, Priya K Dighe, Lindsey L Jacobs, Hajnalka E Daligault, Karen W Davenport, Loreen Rose Stromberg, Zachary R Stromberg, Qiuying Cheng, Prakasha Kempaiah, John Michael Ong'echa, Vincent Otieno, Evans Raballah, Samuel B Anyona, Collins Ouma, Patrick S G Chain, Douglas J Perkins, Harshini Mukundan, Benjamin H McMahon, Norman A Doggett
Comparative genomic and phenotypic characterization of invasive non-typhoidal Salmonella isolates from Siaya, Kenya. PLoS neglected tropical diseases 15 (2) (2021)
Aaron J Robinson, Geoffrey L House, Demosthenes P Morales, Julia M Kelliher, La Verne Gallegos-Graves, Erick S LeBrun, Karen W Davenport, Fabio Palmieri, Andrea Lohberger, Danae Bregnard, Aislinn Estoppey, Matteo Buffi, Christophe Paul, Thomas Junier, Vincent Hervé, Guillaume Cailleau, Simone Lupini, Hang N Nguyen, Amy O Zheng, Luciana Jandelli Gimenes, Saskia Bindschedller, Debora F Rodrigues, James H Werner, Jamey D Young, Pilar Junier, Patrick S G Chain
Widespread bacterial diversity within the bacteriome of fungi. Communications biology 4 (1) (2021)
Alison E Murray, Chien-Chi Lo, Hajnalka E Daligault, Nicole E Avalon, Robert W Read, Karen W Davenport, Mary L Higham, Yuliya A Kunde, Armand E K Dichosa, Bill J Baker, Patrick S G Chain
Discovery of an Antarctic Ascidian-Associated Uncultivated Verrucomicrobia with Antimelanoma Palmerolide Biosynthetic Potential. mSphere (2021)
Erick S LeBrun, Meghali Nighot, Viszwapriya Dharmaprakash, Anand Kumar, Chien-Chi Lo, Patrick S G Chain, Thomas Y Ma
The Gut Microbiome and Alcoholic Liver Disease: Ethanol Consumption Drives Consistent and Reproducible Alteration in Gut Microbiota in Mice. Life (Basel, Switzerland) 11 (1) (2020)
Aaron J Robinson, Donald O Natvig, Patrick S G Chain
Genomic Analysis of Diverse Members of the Fungal Genus Monosporascus Reveals Novel Lineages, Unique Genome Content and a Potential Bacterial Associate. G3 (Bethesda, Md.) 10 (8) (2020)