Zobrazeno 1 - 10
of 19
pro vyhledávání: '"Ales Varabyou"'
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:
Markus J Sommer, Sooyoung Cha, Ales Varabyou, Natalia Rincon, Sukhwan Park, Ilia Minkin, Mihaela Pertea, Martin Steinegger, Steven L Salzberg
Publikováno v:
eLife, Vol 11 (2022)
Recently developed methods to predict three-dimensional protein structure with high accuracy have opened new avenues for genome and proteome research. We explore a new hypothesis in genome annotation, namely whether computationally predicted structur
Externí odkaz:
https://doaj.org/article/c835503456a64f098e302b3d3173af99
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
Autor:
Mihaela Pertea, Alaina Shumate, Geo Pertea, Ales Varabyou, Florian P. Breitwieser, Yu-Chi Chang, Anil K. Madugundu, Akhilesh Pandey, Steven L. Salzberg
Publikováno v:
Genome Biology, Vol 19, Iss 1, Pp 1-14 (2018)
Abstract We assembled the sequences from deep RNA sequencing experiments by the Genotype-Tissue Expression (GTEx) project, to create a new catalog of human genes and transcripts, called CHESS. The new database contains 42,611 genes, of which 20,352 a
Externí odkaz:
https://doaj.org/article/0d297fa94d774476af3c4ddcee1850d7
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
Autor:
Markus J Sommer, Sooyoung Cha, Ales Varabyou, Natalia Rincon, Sukhwan Park, Ilia Minkin, Mihaela Pertea, Martin Steinegger, Steven L Salzberg
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::4df0175a777683d30b6dee47c8cad30c
https://doi.org/10.7554/elife.82556.sa2
https://doi.org/10.7554/elife.82556.sa2
Autor:
Markus J. Sommer, Sooyoung Cha, Ales Varabyou, Natalia Rincon, Sukhwan Park, Ilia Minkin, Mihaela Pertea, Martin Steinegger, Steven L. Salzberg
We explore a new hypothesis in genome annotation, namely whether computationally predicted protein structures can help to identify which of multiple possible gene isoforms represents a functional protein product. Guided by structure predictions, we e
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::a601ccad6f91f2013a4b623ec813d737
https://doi.org/10.1101/2022.06.08.495354
https://doi.org/10.1101/2022.06.08.495354
Autor:
Sommer, Markus J., Sooyoung Cha, Ales Varabyou, Rincon, Natalia, Sukhwan Park, Ilia Minkin, Pertea, Mihaela, Steinegger, Martin, Salzberg, Steven L.
Publikováno v:
eLife; 12/15/2022, p1-21, 21p
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:
Genome Res
RNA sequencing is widely used to measure gene expression across a vast range of animal and plant tissues and conditions. Most studies of computational methods for gene expression analysis use simulated data to evaluate the accuracy of these methods.