Zobrazeno 1 - 10
of 14
pro vyhledávání: '"Christopher Pockrandt"'
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:
Amde Selassie Shifera, Christopher Pockrandt, Natalia Rincon, Yuchen Ge, Jennifer Lu, Steven L. Salzberg, Charles Eberhart, Jennifer E. Thorne, Ales Varabyou, Anne E. Jedlicka, Karen Sun, Alan L. Scott
Publikováno v:
F1000Research, Vol 10 (2021)
Background: Metagenomic sequencing has the potential to identify a wide range of pathogens in human tissue samples. Sarcoidosis is a complex disorder whose etiology remains unknown and for which a variety of infectious causes have been hypothesized.
Externí odkaz:
https://doaj.org/article/2007947481804759b89e87f38c8b1796
Publikováno v:
BMC Biotechnology, Vol 19, Iss 1, Pp 1-7 (2019)
Abstract Background Natural variations in a genome can drastically alter the CRISPR-Cas9 off-target landscape by creating or removing sites. Despite the resulting potential side-effects from such unaccounted for sites, current off-target detection pi
Externí odkaz:
https://doaj.org/article/55f4d2c5b2be44949d621446f89d79f8
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
The original CHESS database of human genes was assembled from nearly 10,000 RNA sequencing experiments in 53 human body sites produced by the Genotype-Tissue Expression (GTEx) project, and then augmented with genes from other databases to yield a com
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::26cb2390259bcb782b79850651274db3
https://doi.org/10.1101/2022.12.21.521274
https://doi.org/10.1101/2022.12.21.521274
Publikováno v:
Bioinformatics
SummaryPhyloCSF++ is an efficient and parallelized C++ implementation of the popular PhyloCSF method to distinguish protein-coding and non-coding regions in a genome based on multiple sequence alignments. It can score alignments or produce browser tr
Publikováno v:
Journal of Open Source Software. 7:4908
Kraken and KrakenUniq are widely-used tools for classifying metagenomics sequences. A key requirement for these systems is a database containing all k-mers from all genomes that the users want to be able to detect, where k = 31 by default. This datab
Autor:
Jennifer Lu, Natalia Rincon, Derrick E. Wood, Florian P. Breitwieser, Christopher Pockrandt, Ben Langmead, Steven L. Salzberg, Martin Steinegger
Publikováno v:
Nat Protoc
Metagenomic experiments expose the wide range of microscopic organisms in any microbial environment through high-throughput DNA sequencing. The computational analysis of the sequencing data is critical for the accurate and complete characterization o
Publikováno v:
BMC Biotechnology, Vol 19, Iss 1, Pp 1-7 (2019)
BMC Biotechnology
BMC Biotechnology
Background Natural variations in a genome can drastically alter the CRISPR-Cas9 off-target landscape by creating or removing sites. Despite the resulting potential side-effects from such unaccounted for sites, current off-target detection pipelines a
Publikováno v:
bioRxiv
Genetics
Genetics
The ability to detect recombination in pathogen genomes is crucial to the accuracy of phylogenetic analysis and consequently to forecasting the spread of infectious diseases and to developing therapeutics and public health policies. However, previous
Publikováno v:
Bioinformatics
Motivation Computing the uniqueness of k-mers for each position of a genome while allowing for up to e mismatches is computationally challenging. However, it is crucial for many biological applications such as the design of guide RNA for CRISPR exper