Challenges and opportunities in understanding microbial communities with metagenome assembly (accompanied by IPython Notebook tutorial)

by Howe, Adina, Chain, Patrick S. G.
Published in Front Microbiol (2015)

Rapid evaluation and quality control of next generation sequencing data with FaQCs

by Lo, Chien-Chi, Chain, Patrick S G
Published in BMC Bioinformatics (2014)

Improved Assemblies Using a Source-Agnostic Pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of Contigs

by Scholz, Matthew, Lo, Chien-Chi, Chain, Patrick S. G.
Published 2014

Advances and Challenges in Metatranscriptomic Analysis

by Shakya, Migun, Lo, Chien-Chi, Chain, Patrick S. G.
Published in Front Genet (2019)

Genomic Analysis of Diverse Members of the Fungal Genus Monosporascus Reveals Novel Lineages, Unique Genome Content and a Potential Bacterial Associate

by Robinson, Aaron J., Natvig, Donald O., Chain, Patrick S. G.
Published in G3 (Bethesda) (2020)

Epigenetic regulation of gene expression in Shiga toxin-producing Escherichia coli: Transcriptomic data

by Carter, Michelle Qiu, Hu, Bin, Chain, Patrick S.G.
Published in Data Brief (2021)

Recruiting Human Microbiome Shotgun Data to Site-Specific Reference Genomes

by Xie, Gary, Lo, Chien-Chi, Scholz, Matthew, Chain, Patrick S. G.
Published 2014

Building International Genomics Collaboration for Global Health Security

by Cui, Helen H., Erkkila, Tracy, Chain, Patrick S. G., Vuyisich, Momchilo
Published in Front Public Health (2015)

oriT-Directed Cloning of Defined Large Regions from Bacterial Genomes: Identification of the Sinorhizobium meliloti pExo Megaplasmid Replicator Region

by Chain, Patrick S. G., Hernandez-Lucas, Ismael, Golding, Brian, Finan, Turlough M.
Published 2000

ADEPT, a dynamic next generation sequencing data error-detection program with trimming

by Feng, Shihai, Lo, Chien-Chi, Li, Po-E, Chain, Patrick S. G.
Published in BMC Bioinformatics (2016)

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures

by Freitas, Tracey Allen K., Li, Po-E, Scholz, Matthew B., Chain, Patrick S. G.
Published in Nucleic Acids Res (2015)

“Candidatus Nitrosotenuis aquarius,” an Ammonia-Oxidizing Archaeon from a Freshwater Aquarium Biofilter

by Sauder, Laura A., Engel, Katja, Lo, Chien-Chi, Chain, Patrick, Neufeld, Josh D.
Published in Appl Environ Microbiol (2018)

Array2BIO: from microarray expression data to functional annotation of co-regulated genes

by Rasley Amy, Mabery Shalini, Chain Patrick SG, Loots Gabriela G, Garcia Emilio, Ovcharenko Ivan
Published 2006-06-01

Array2BIO: from microarray expression data to functional annotation of co-regulated genes

by Loots, Gabriela G, Chain, Patrick SG, Mabery, Shalini, Rasley, Amy, Garcia, Emilio, Ovcharenko, Ivan
Published 2006

Complete Genome Sequence of the Plant Growth-Promoting Endophyte Burkholderia phytofirmans Strain PsJN

by Weilharter, Alexandra, Mitter, Birgit, Shin, Maria V., Chain, Patrick S. G., Nowak, Jerzy, Sessitsch, Angela
Published 2011

CRP-Mediated Carbon Catabolite Regulation of Yersinia pestis Biofilm Formation Is Enhanced by the Carbon Storage Regulator Protein, CsrA

by Willias, Stephan P., Chauhan, Sadhana, Lo, Chien-Chi, Chain, Patrick S. G., Motin, Vladimir L.
Published in PLoS One (2015)

Complete Genome Sequence of Francisella philomiragia ATCC 25017

by Zeytun, Ahmet, Malfatti, Stephanie A., Vergez, Lisa M., Shin, Maria, Garcia, Emilio, Chain, Patrick S. G.
Published 2012

The Genome Sequence of Yersinia pestis Bacteriophage φA1122 Reveals an Intimate History with the Coliphage T3 and T7 Genomes

by Garcia, Emilio, Elliott, Jeffrey M., Ramanculov, Erlan, Chain, Patrick S. G., Chu, May C., Molineux, Ian J.
Published 2003

Identification of MglA-Regulated Genes Reveals Novel Virulence Factors in Francisella tularensis

by Brotcke, Anna, Weiss, David S., Kim, Charles C., Chain, Patrick, Malfatti, Stephanie, Garcia, Emilio, Monack, Denise M.
Published 2006

Under-detection of endospore-forming Firmicutes in metagenomic data

by Filippidou, Sevasti, Junier, Thomas, Wunderlin, Tina, Lo, Chien-Chi, Li, Po-E, Chain, Patrick S., Junier, Pilar
Published in Comput Struct Biotechnol J (2015)