SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads
Y Xie, G Wu, J Tang, R Luo, J Patterson, S Liu… - …, 2014 - academic.oup.com
Motivation: Transcriptome sequencing has long been the favored method for quickly and
inexpensively obtaining a large number of gene sequences from an organism with no …
inexpensively obtaining a large number of gene sequences from an organism with no …
[HTML][HTML] Characterization of the gut microbiome using 16S or shotgun metagenomics
The advent of next generation sequencing (NGS) has enabled investigations of the gut
microbiome with unprecedented resolution and throughput. This has stimulated the development …
microbiome with unprecedented resolution and throughput. This has stimulated the development …
Effect of oral capsule–vs colonoscopy-delivered fecal microbiota transplantation on recurrent Clostridium difficile infection: a randomized clinical trial
Importance Fecal microbiota transplantation (FMT) is effective in preventing recurrentClostridium
difficileinfection (RCDI). However, it is not known whether clinical efficacy differs by …
difficileinfection (RCDI). However, it is not known whether clinical efficacy differs by …
[HTML][HTML] Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes
…, M Melkonian, N Miles, H Myburg, J Patterson… - PloS one, 2012 - journals.plos.org
Next-generation sequencing plays a central role in the characterization and quantification of
transcriptomes. Although numerous metrics are purported to quantify the quality of RNA, …
transcriptomes. Although numerous metrics are purported to quantify the quality of RNA, …
Metagenomic analysis of microbiome in colon tissue from subjects with inflammatory bowel diseases reveals interplay of viruses and bacteria
Inflammatory bowel diseases (IBD), Crohn's disease and ulcerative colitis, are poorly
understood disorders affecting the intestinal tract. The current model for disease suggests that …
understood disorders affecting the intestinal tract. The current model for disease suggests that …
Branched evolution and genomic intratumor heterogeneity in the pathogenesis of cutaneous T-cell lymphoma
A Iyer, D Hennessey, S O'Keefe, J Patterson… - Blood …, 2020 - ashpublications.org
Mycosis fungoides (MF) is a slowly progressive cutaneous T-cell lymphoma (CTCL) for
which there is no cure. In the early plaque stage, the disease is indolent, but development of …
which there is no cure. In the early plaque stage, the disease is indolent, but development of …
[HTML][HTML] Impact of sequencing depth and technology on de novo RNA-Seq assembly
J Patterson, EJ Carpenter, Z Zhu, D An, X Liang… - BMC genomics, 2019 - Springer
Background RNA-Seq data is inherently nonuniform for different transcripts because of
differences in gene expression. This makes it challenging to decide how much data should be …
differences in gene expression. This makes it challenging to decide how much data should be …
Effective fecal microbiota transplantation for recurrent Clostridioides difficile infection in humans is associated with increased signalling in the bile acid-farnesoid X …
Full article: Effective fecal microbiota transplantation for recurrent Clostridioides difficile
infection in humans is associated with increased signalling in the bile acid-farnesoid X receptor-…
infection in humans is associated with increased signalling in the bile acid-farnesoid X receptor-…
Skin colonization by circulating neoplastic clones in cutaneous T-cell lymphoma
…, D Hennessey, S O'Keefe, J Patterson… - Blood, The Journal …, 2019 - ashpublications.org
Mycosis fungoides (MF) is a mature T-cell lymphoma currently thought to develop primarily
in the skin by a clonal expansion of a transformed, resident memory T cell. However, this …
in the skin by a clonal expansion of a transformed, resident memory T cell. However, this …
[HTML][HTML] Pet dogs (Canis lupus familiaris) release their trapped and distressed owners: Individual variation and evidence of emotional contagion
J Van Bourg, JE Patterson, CDL Wynne - PLoS One, 2020 - journals.plos.org
Domestic dogs have assisted humans for millennia. However, the extent to which these
helpful behaviors are prosocially motivated remains unclear. To assess the propensity of pet …
helpful behaviors are prosocially motivated remains unclear. To assess the propensity of pet …