An Applications-focused Review of Comparative Genomics Tools: Capabilities, Limitations and Future Challenges. - Patrick S. G. Chain; Stefan Kurtz; Enno Ohlebusch; Tom Slezak (Briefings Bioinform., 2003)

Finishing Repetitive Regions Automatically with Dupfinisher. - Cliff Han; Patrick S. G. Chain (BIOCOMP, 2006)

Array2BIO: from microarray expression data to functional annotation of co-regulated genes. - Gabriela G. Loots; Patrick S. G. Chain; Shalini Mabery; Amy Rasley; Emilio Garcia; Ivan Ovcharenko (BMC Bioinform., 2006)

Rapid evaluation and quality control of next generation sequencing data with FaQCs. - Chien-Chi Lo; Patrick S. G. Chain (BMC Bioinform., 2014)

ADEPT, a dynamic next generation sequencing data error-detection program with trimming. - Shihai Feng; Chien-Chi Lo; Po-E Li; Patrick S. G. Chain (BMC Bioinform., 2016)

Leveraging Ontologies within the National Microbiome Data Collaborative. - William D. Duncan; Faiza Ahmed; Fnu Anubhav; Jeffrey Baumes; Jonathan Beezley; Mark Borkum; Lisa M. Bramer; Shane Canon; Patrick S. G. Chain; Danielle Christianson; Yuri Corilo; Karen Davenport; et al. (ICBO, 2021)

A public website for the automated assessment and validation of SARS-CoV-2 diagnostic PCR assays. - Po-E Li; Adán Myers y Gutiérrez; Karen Davenport; Mark Flynn; Bin Hu 025; Chien-Chi Lo; Elais Player Jackson; Migun Shakya; Yan Xu; Jason D. Gans; Patrick S. G. Chain (Bioinform., 2021)

Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale. - Bin Hu 025; Shane Canon; Emiley A. Eloe-Fadrosh; Fnu Anubhav; Michal Babinski; Yuri Corilo; Karen Davenport; William D. Duncan; Kjiersten Fagnan; Mark Flynn; Brian Foster; David Hays; et al. (Frontiers Bioinform., 2021)

EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts. - Chien-Chi Lo; Migun Shakya; Ryan Connor; Karen Davenport; Mark Flynn; Adán Myers y Gutiérrez; Bin Hu 025; Po-E Li; Elais Player Jackson; Yan Xu; Patrick S. G. Chain (Bioinform., 2022)