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Visualitza Recerca: articles, congressos, llibres per matèria "Biologia computacional -- Mètodes"

Ara mostrant els elements 1-9 de 9

ASPic-GeneID: a lightweight pipeline for gene prediction and alternative isoforms detection

Alioto, Tyler; Picardi, Ernesto; Guigó Serra, Roderic; Pesole, Graziano (Hindawi, 2013)

New genomes are being sequenced at an increasingly rapid rate, far outpacing the rate at which manual gene annotation can be performed. Automated genome annotation is thus necessitated by this growth in genome projects; ...
Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely-expressed human genes

Castelo Valdueza, Robert; Reymond, Alexandre; Wyss, Carine; Cámara, Francisco; Parra Farré, Genís; Antonarakis, Stylianos E.; Guigó Serra, Roderic; Eyras Jiménez, Eduardo (Oxford University Press, 2005)

The recent availability of the chicken genome sequence poses the question of whether there are human protein-coding genes conserved in chicken that are currently not included in the human gene catalog. Here, we show, using ...
A comprehensive model of the phototransduction cascade in mouse rod cells

Invergo, Brandon M., 1982-; Dell'Orco, Daniele; Montanucci, Ludovica, 1978-; Koch, Karl-Wilhelm; Bertranpetit, Jaume, 1952- (Royal Society of Chemistry, 2014)

Vertebrate visual phototransduction is perhaps the most well-studied G-protein signaling pathway. A wealth of available biochemical and electrophysiological data has resulted in a rich history of mathematical modeling of ...
Fast computation and applications of genome mappability

Derrien, Thomas; Estellé, Jordi; Marco Sola, Santiago; Knowles, David G.; Raineri, Emanuele; Guigó Serra, Roderic; Ribeca, Paolo (Public Library of Science (PLoS), 2012)

We present a fast mapping-based algorithm to compute the mappability of each region of a reference genome up to a specified number of mismatches. Knowing the mappability of a genome is crucial for the interpretation of ...
A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments

Esnaola, Mikel; Puig, Pedro; González, David; Castelo Valdueza, Robert; González Ruiz, Juan Ramón (BioMed Central, 2013)

Background: High-throughput RNA sequencing (RNA-seq) offers unprecedented power to capture the real dynamics of gene expression. Experimental designs with extensive biological replication present a unique opportunity to ...
Gene finding in the chicken genome

Eyras Jiménez, Eduardo; Reymond, Alexandre; Castelo Valdueza, Robert; Bye, Jacqueline M.; Cámara, Francisco; Flicek, Paul; Huckle, Elizabeth J.; Parra Farré, Genís; Shteynberg, David D.; Wyss, Carine; Rogers, Jane; Antonarakis, Stylianos E.; Birney, Ewan; Guigó Serra, Roderic; Brent, Michael R. (BioMed Central, 2005)

Background: Despite the continuous production of genome sequence for a number of organisms,/nreliable, comprehensive, and cost effective gene prediction remains problematic. This is particularly/ntrue for genomes for which ...
How to analyze many contingency tables simultaneously in genetic association studies

Dickhaus, Thorsten; Straßburger, Klaus; Schunk, Daniel; Morcillo Suárez, Carlos, 1969-; Illig, Thomas; Navarro i Cuartiellas, Arcadi, 1969- (De Gruyter, 2012)

We study exact tests for (2 x 2) and (2 x 3) contingency tables, in particular exact chi-squared tests and exact tests of Fisher type. In practice, these tests are typically carried out without randomization, leading to ...
Identifying protein-coding genes in genomic sequences

Harrow, Jennifer; Nagy, Alinda; Reymond, Alexandre; Alioto, Tyler; Patthy, Laszlo; Antonarakis, Stylianos E.; Guigó Serra, Roderic (BioMed Central, 2009)

The vast majority of the biology of a newly sequenced genome is inferred from the set of encoded proteins. Predicting this set is therefore invariably the first step after the completion of the genome DNA sequence. Here ...
Transcription factor map alignment of promoter regions

Blanco, Enrique; Messeguer, Xavier; Smith, Temple F.; Guigó Serra, Roderic (Public Library of Science (PLoS), 2006)

We address the problem of comparing and characterizing the promoter regions of genes with similar expression patterns. This remains a challenging problem in sequence analysis, because often the promoter regions of co-expressed ...