REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats

Autor: Egor Dolzhenko, Ben Weisburd, Kristina Ibañez, Indhu-Shree Rajan-Babu, Christine Anyansi, Mark F. Bennett, Kimberley Billingsley, Ashley Carroll, Samuel Clamons, Matt C. Danzi, Viraj Deshpande, Jinhui Ding, Sarah Fazal, Andreas Halman, Bharati Jadhav, Yunjiang Qiu, Phillip A. Richmond, Christopher T. Saunders, Konrad Scheffler, Joke J. F. A. van Vugt, Ramona R. A. J. Zwamborn, Genomics England Research Consortium, Samuel S. Chong, Jan M. Friedman, Arianna Tucci, Heidi L. Rehm, Michael A. Eberle

Publikováno v: Genome Medicine, Vol 14, Iss 1, Pp 1-10 (2022)

Abstract Background Expansions of short tandem repeats are the cause of many neurogenetic disorders including familial amyotrophic lateral sclerosis, Huntington disease, and many others. Multiple methods have been recently developed that can identify

Externí odkaz: https://doaj.org/article/018b5e0870b648eca3506644f3e08453

A regression-based differential expression detection algorithm for microarray studies with ultra-low sample size.

Autor: Daniel Vasiliu, Samuel Clamons, Molly McDonough, Brian Rabe, Margaret Saha

Publikováno v: PLoS ONE, Vol 10, Iss 3, p e0118198 (2015)

Global gene expression analysis using microarrays and, more recently, RNA-seq, has allowed investigators to understand biological processes at a system level. However, the identification of differentially expressed genes in experiments with small sam

Externí odkaz: https://doaj.org/article/10d7d76dc1db4b459bdbbaf0332a5f21

Enabling community-based metrology for wood-degrading fungi

Autor: Drew Endy, Pamela A. Silver, Marina Luccioni, Katarzyna P. Adamala, Samuel Clamons, Rohinton T. Kamakaka, Rolando Perez, Finn Stirling, Nathaniel J. Gaut

Publikováno v: Fungal Biology and Biotechnology, Vol 7, Iss 1, Pp 1-15 (2020)
Fungal Biology and Biotechnology
Fungal biology and biotechnology, vol 7, iss 1

Background Lignocellulosic biomass could support a greatly-expanded bioeconomy. Current strategies for using biomass typically rely on single-cell organisms and extensive ancillary equipment to produce precursors for downstream manufacturing processe

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d8a13b9f83598bcf3649bf8731f35755
http://link.springer.com/article/10.1186/s40694-020-00092-2

How to model DNA replication in stochastic models of synthetic gene circuits (and why)

Autor: Samuel Clamons, Richard M. Murray

Biocircuit modeling sometimes requires explicit tracking of a self-replicating DNA species. The most obvious, straightforward way to model a replicating DNA is structurally unstable and leads to pathological model behavior. We describe a simple, stab

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::81ca474fbbec8208136d9953f7d2cf5f
https://doi.org/10.1101/2021.09.26.461880

A Regression-Based Differential Expression Detection Algorithm for Microarray Studies with Ultra-Low Sample Size

Autor: Brian A. Rabe, Daniel Vasiliu, Samuel Clamons, Margaret S. Saha, Molly J. McDonough

Publikováno v: PLoS ONE
PLoS ONE, Vol 10, Iss 3, p e0118198 (2015)

Global gene expression analysis using microarrays and, more recently, RNA-seq, has allowed investigators to understand biological processes at a system level. However, the identification of differentially expressed genes in experiments with small sam

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2b4e49eb541184e90073c06ce54a5495
http://europepmc.org/articles/PMC4349782