Zobrazeno 1 - 10
of 240
pro vyhledávání: '"Bruce A, Stanton"'
Autor:
Lily Taub, Thomas H. Hampton, Sharanya Sarkar, Georgia Doing, Samuel L. Neff, Carson E. Finger, Kiyoshi Ferreira Fukutani, Bruce A. Stanton
Publikováno v:
mSystems, Vol 9, Iss 11 (2024)
ABSTRACT E.PathDash facilitates re-analysis of gene expression data from pathogens clinically relevant to chronic respiratory diseases, including a total of 48 studies, 548 samples, and 404 unique treatment comparisons. The application enables users
Externí odkaz:
https://doaj.org/article/4df9b5f32c51460eb0fa75aea18e143a
Autor:
Samuel L. Neff, Thomas H. Hampton, Katja Koeppen, Sharanya Sarkar, Casey J. Latario, Benjamin D. Ross, Bruce A. Stanton
Publikováno v:
mSystems, Vol 8, Iss 6 (2023)
ABSTRACT Developing software tools that leverage biological data sets to accelerate drug discovery is an important aspect of bioinformatic research. Here, we present a novel example: a web application called Rocket-miR that applies an existing bioinf
Externí odkaz:
https://doaj.org/article/38af883ac4f94636bc3aa24c3f8bf9e5
Autor:
Samuel L. Neff, Thomas H. Hampton, Charles Puerner, Liviu Cengher, Georgia Doing, Alexandra J. Lee, Katja Koeppen, Ambrose L. Cheung, Deborah A. Hogan, Robert A. Cramer, Bruce A. Stanton
Publikováno v:
Scientific Data, Vol 9, Iss 1, Pp 1-14 (2022)
Abstract Researchers studying cystic fibrosis (CF) pathogens have produced numerous RNA-seq datasets which are available in the gene expression omnibus (GEO). Although these studies are publicly available, substantial computational expertise and manu
Externí odkaz:
https://doaj.org/article/5e30a2f3c1034ab18bf4061492bd63f8
Autor:
Georgia Doing, Alexandra J. Lee, Samuel L. Neff, Taylor Reiter, Jacob D. Holt, Bruce A. Stanton, Casey S. Greene, Deborah A. Hogan
Publikováno v:
mSystems, Vol 8, Iss 1 (2023)
ABSTRACT Thousands of Pseudomonas aeruginosa RNA sequencing (RNA-seq) gene expression profiles are publicly available via the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). In this work, the transcriptional profiles
Externí odkaz:
https://doaj.org/article/88e2643156ae4b42b1d30edcecf0e6c2
Publikováno v:
mSystems, Vol 7, Iss 6 (2022)
ABSTRACT The last 20 years have witnessed an explosion in publicly available gene expression and proteomic data and new tools to help researchers analyze these data. Tools typically include statistical approaches to identify differential expression,
Externí odkaz:
https://doaj.org/article/41e79e3cab834f849e5be1844ff25ffd
Autor:
Lily A. Charpentier, Emily F. Dolben, Matthew R. Hendricks, Deborah A. Hogan, Jennifer M. Bomberger, Bruce A. Stanton
Publikováno v:
Membranes, Vol 13, Iss 9, p 752 (2023)
This article reviews the role of outer membrane vesicles (OMVs) in mediating the interaction between Gram-negative bacteria and their human hosts. OMVs are produced by a diverse range of Gram-negative bacteria during infection and play a critical rol
Externí odkaz:
https://doaj.org/article/e67c0166bb3e4493b2ba355ab0705a8c
Autor:
George A. O’Toole, Aurélie Crabbé, Rolf Kümmerli, John J. LiPuma, Jennifer M. Bomberger, Jane C. Davies, Dominique Limoli, Vanessa V. Phelan, James B. Bliska, William H. DePas, Lars E. Dietrich, Thomas H. Hampton, Ryan Hunter, Cezar M. Khursigara, Alexa Price-Whelan, Alix Ashare, Robert A. Cramer, Joanna B. Goldberg, Freya Harrison, Deborah A. Hogan, Michael A. Henson, Dean R. Madden, Jared R. Mayers, Carey Nadell, Dianne Newman, Alice Prince, Damian W. Rivett, Joseph D. Schwartzman, Daniel Schultz, Donald C. Sheppard, Alan R. Smyth, Melanie A. Spero, Bruce A. Stanton, Paul E. Turner, Chris van der Gast, Fiona J. Whelan, Rachel Whitaker, Katrine Whiteson
Publikováno v:
mBio, Vol 12, Iss 5 (2021)
A recent workshop titled “Developing Models to Study Polymicrobial Infections,” sponsored by the Dartmouth Cystic Fibrosis Center (DartCF), explored the development of new models to study the polymicrobial infections associated with the airways o
Externí odkaz:
https://doaj.org/article/1ed07d7593e74bbf8897df772ce78eb2
Autor:
Thomas H. Hampton, Devin Thomas, Christopher van der Gast, George A. O’Toole, Bruce A. Stanton
Publikováno v:
Microbiology Spectrum, Vol 9, Iss 1 (2021)
ABSTRACT Microbial communities in the airways of persons with CF (pwCF) are variable, may include genera that are not typically associated with CF, and their composition can be difficult to correlate with long-term disease outcomes. Leveraging two la
Externí odkaz:
https://doaj.org/article/8c8be97ec91c46cab16cd8657164f6e7
Transfer RNA-Derived Fragments, the Underappreciated Regulatory Small RNAs in Microbial Pathogenesis
Autor:
Zhongyou Li, Bruce A. Stanton
Publikováno v:
Frontiers in Microbiology, Vol 12 (2021)
In eukaryotic organisms, transfer RNA (tRNA)-derived fragments have diverse biological functions. Considering the conserved sequences of tRNAs, it is not surprising that endogenous tRNA fragments in bacteria also play important regulatory roles. Rece
Externí odkaz:
https://doaj.org/article/2496bdce60bf4c10a584b118f3332a0f
Autor:
Zhongyou Li, Katja Koeppen, Victoria I. Holden, Samuel L. Neff, Liviu Cengher, Elora G. Demers, Dallas L. Mould, Bruce A. Stanton, Thomas H. Hampton
Publikováno v:
mSystems, Vol 6, Iss 2 (2021)
ABSTRACT The NCBI Gene Expression Omnibus (GEO) provides tools to query and download transcriptomic data. However, less than 4% of microbial experiments include the sample group annotations required to assess differential gene expression for high-thr
Externí odkaz:
https://doaj.org/article/d6088201743d4d298c3e1530465342c4