Zobrazeno 1 - 10
of 432
pro vyhledávání: '"Steven L. Salzberg"'
Autor:
Ales Varabyou, Markus J. Sommer, Beril Erdogdu, Ida Shinder, Ilia Minkin, Kuan-Hao Chao, Sukhwan Park, Jakob Heinz, Christopher Pockrandt, Alaina Shumate, Natalia Rincon, Daniela Puiu, Martin Steinegger, Steven L. Salzberg, Mihaela Pertea
Publikováno v:
Genome Biology, Vol 24, Iss 1, Pp 1-16 (2023)
Abstract CHESS 3 represents an improved human gene catalog based on nearly 10,000 RNA-seq experiments across 54 body sites. It significantly improves current genome annotation by integrating the latest reference data and algorithms, machine learning
Externí odkaz:
https://doaj.org/article/20e94c3931d244779a6859df07d6e08f
Autor:
Pritpal Kaur, Loren Moon, Divya Srikumaran, Steven L. Salzberg, Jennifer Lu, Patricia J. Simner, Uri S. Soiberman
Publikováno v:
Journal of Clinical Medicine, Vol 13, Iss 12, p 3399 (2024)
Objectives: This study aims to assess the presence of pathogenic microorganisms in the corneal epithelial layer of keratoconus patients. Methods: DNA was extracted from corneal epithelial samples procured from ten individual keratoconus eyes and thre
Externí odkaz:
https://doaj.org/article/b7f1660feede48a08f4e06e654a4bab0
Autor:
Abraham Gihawi, Yuchen Ge, Jennifer Lu, Daniela Puiu, Amanda Xu, Colin S. Cooper, Daniel S. Brewer, Mihaela Pertea, Steven L. Salzberg
Publikováno v:
mBio, Vol 14, Iss 5 (2023)
ABSTRACT We re-analyzed the data from a recent large-scale study that reported strong correlations between DNA signatures of microbial organisms and 33 different cancer types and that created machine-learning predictors with near-perfect accuracy at
Externí odkaz:
https://doaj.org/article/83d404f30353408bbe8bb9679a67fc75
Autor:
Victoria L. Sork, Shawn J. Cokus, Sorel T. Fitz-Gibbon, Aleksey V. Zimin, Daniela Puiu, Jesse A. Garcia, Paul F. Gugger, Claudia L. Henriquez, Ying Zhen, Kirk E. Lohmueller, Matteo Pellegrini, Steven L. Salzberg
Publikováno v:
Nature Communications, Vol 13, Iss 1, Pp 1-15 (2022)
The genus Quercus (oaks) has diversified into over 450 species which often play dominant roles in the ecosystems in which they occur. Here the authors present a genome and methylome for a California endemic oak, Quercus lobata, and describe features
Externí odkaz:
https://doaj.org/article/9f631944a7bc4470b05eb062f2f94740
Publikováno v:
The Journal of Clinical Investigation, Vol 132, Iss 7 (2022)
Next-generation sequencing (NGS) technology has advanced our understanding of the human microbiome by allowing for the discovery and characterization of unculturable microbes with prediction of their function. Key NGS methods include 16S rRNA gene se
Externí odkaz:
https://doaj.org/article/bcfb46e6f36d40a3990c801ad690e03f
Autor:
Alison D. Scott, Aleksey V. Zimin, Daniela Puiu, Rachael Workman, Monica Britton, Sumaira Zaman, Madison Caballero, Andrew C. Read, Adam J. Bogdanove, Emily Burns, Jill Wegrzyn, Winston Timp, Steven L. Salzberg, David B. Neale
Publikováno v:
G3: Genes, Genomes, Genetics, Vol 10, Iss 11, Pp 3907-3919 (2020)
The giant sequoia (Sequoiadendron giganteum) of California are massive, long-lived trees that grow along the U.S. Sierra Nevada mountains. Genomic data are limited in giant sequoia and producing a reference genome sequence has been an important goal
Externí odkaz:
https://doaj.org/article/860ce952a2d64d18803fdd70720cf46d
Autor:
Steven L. Salzberg, Derrick E. Wood
Publikováno v:
Frontiers in Bioinformatics, Vol 1 (2021)
Ten years ago, the dramatic rise in the number of microbial genomes led to an inflection point, when the approach of finding short, exact matches in a comprehensive database became just as accurate as older, slower approaches. The new idea led to a m
Externí odkaz:
https://doaj.org/article/e6200e23191f450db669fbbddf965e8c
Autor:
Jennifer Lu, Steven L. Salzberg
Publikováno v:
Microbiome, Vol 8, Iss 1, Pp 1-11 (2020)
Abstract Background For decades, 16S ribosomal RNA sequencing has been the primary means for identifying the bacterial species present in a sample with unknown composition. One of the most widely used tools for this purpose today is the QIIME (Quanti
Externí odkaz:
https://doaj.org/article/c9a5f4f43e294608bcabe6884db3e1d6
Autor:
Alaina Shumate, Aleksey V. Zimin, Rachel M. Sherman, Daniela Puiu, Justin M. Wagner, Nathan D. Olson, Mihaela Pertea, Marc L. Salit, Justin M. Zook, Steven L. Salzberg
Publikováno v:
Genome Biology, Vol 21, Iss 1, Pp 1-18 (2020)
Abstract Background Thousands of experiments and studies use the human reference genome as a resource each year. This single reference genome, GRCh38, is a mosaic created from a small number of individuals, representing a very small sample of the hum
Externí odkaz:
https://doaj.org/article/34b6a666474a481a80ed46ff3264dec4
Autor:
Martin Steinegger, Steven L. Salzberg
Publikováno v:
Genome Biology, Vol 21, Iss 1, Pp 1-12 (2020)
Abstract Genomic analyses are sensitive to contamination in public databases caused by incorrectly labeled reference sequences. Here, we describe Conterminator, an efficient method to detect and remove incorrectly labeled sequences by an exhaustive a
Externí odkaz:
https://doaj.org/article/0c58db75fd8a487eb02d1ef019ea16a4