Results 21 to 30 of about 557,186 (345)

Functional annotation of regulatory pathways [PDF]

Bioinformatics, 2007
Abstract Motivation: Standardized annotations of biomolecules in interaction networks (e.g. Gene Ontology) provide comprehensive understanding of the function of individual molecules. Extending such annotations to pathways is a critical component of functional characterization of cellular signaling at the systems level ...
Jayesh, Pandey, Mehmet, Koyutürk, Yohan, Kim, Wojciech, Szpankowski, Shankar, Subramaniam, Ananth, Grama   +5 more
openaire   +2 more sources

PINOT: an intuitive resource for integrating protein-protein interactions

Cell Communication and Signaling, 2020
Background The past decade has seen the rise of omics data for the understanding of biological systems in health and disease. This wealth of information includes protein-protein interaction (PPI) data derived from both low- and high-throughput assays ...
James E. Tomkins, Raffaele Ferrari, Nikoleta Vavouraki, John Hardy, Ruth C. Lovering, Patrick A. Lewis, Liam J. McGuffin, Claudia Manzoni   +7 more
doaj   +1 more source

Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing

Biology, 2020
Next-Generation Sequencing (NGS) has made it easier to obtain genome-wide sequence data and it has shifted the research focus into genome annotation. The challenging tasks involved in annotation rely on the currently available tools and techniques to ...
Girum Fitihamlak Ejigu, Jaehee Jung
doaj   +1 more source

Biases in the Experimental Annotations of Protein Function and their Effect on Our Understanding of Protein Function Space [PDF]

, 2013
The ongoing functional annotation of proteins relies upon the work of curators to capture experimental findings from scientific literature and apply them to protein sequence and structure data.
Babbitt, Patricia, Babbitt, PC, Friedberg, I, Ream, DC, Schnoes, AM, Thorman, AW   +5 more
core   +4 more sources

Bacterial riboproteogenomics : the era of N-terminal proteoform existence revealed [PDF]

, 2020
With the rapid increase in the number of sequenced prokaryotic genomes, relying on automated gene annotation became a necessity. Multiple lines of evidence, however, suggest that current bacterial genome annotations may contain inconsistencies and are ...
Fijalkowska, Daria, Fijalkowski, Igor, Van Damme, Petra, Willems, Patrick   +3 more
core   +2 more sources

Phylogenetic molecular function annotation

Journal of Physics: Conference Series, 2009
It is now easier to discover thousands of protein sequences in a new microbial genome than it is to biochemically characterize the specific activity of a single protein of unknown function. The molecular functions of protein sequences have typically been predicted using homology-based computational methods, which rely on the principle that homologous ...
Barbara E, Engelhardt, Michael I, Jordan, Susanna T, Repo, Steven E, Brenner   +3 more
openaire   +2 more sources

Towards Site-Based Protein Functional Annotations [PDF]

2008 IEEE International Conference on Bioinformatics and Biomedicine, 2008
The exact relationship between protein active centres and protein functions is unclear even after decades of intensive study. To improve functional prediction ability based on the local structures, we proposed three different methods. 1. We used Markov Random Field (MRF) to describe protein active region. 2. We developed filtering method that considers
Seak Fei, Lei, Jun, Huan
openaire   +2 more sources

Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. [PDF]

PLoS Genetics, 2006
The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched cDNAs.
Norihiro Maeda, Takeya Kasukawa, Rieko Oyama, Julian Gough, Martin Frith, Pär G Engström, Boris Lenhard, Rajith N Aturaliya, Serge Batalov, Kirk W Beisel, Carol J Bult, Colin F Fletcher, Alistair R R Forrest, Masaaki Furuno, David Hill, Masayoshi Itoh, Mutsumi Kanamori-Katayama, Shintaro Katayama, Masaru Katoh, Tsugumi Kawashima, John Quackenbush, Timothy Ravasi, Brian Z Ring, Kazuhiro Shibata, Koji Sugiura, Yoichi Takenaka, Rohan D Teasdale, Christine A Wells, Yunxia Zhu, Chikatoshi Kai, Jun Kawai, David A Hume, Piero Carninci, Yoshihide Hayashizaki   +33 more
doaj   +2 more sources

Functional annotation of noncoding sequence variants [PDF]

Nature Methods, 2014
Identifying functionally relevant variants against the background of ubiquitous genetic variation is a major challenge in human genetics. For variants in protein-coding regions, our understanding of the genetic code and splicing allows us to identify likely candidates, but interpreting variants outside genic regions is more difficult.
Graham R S Ritchie, Ian Dunham, Eleftheria Zeggini, Paul Flicek   +3 more
openaire   +2 more sources

Annotation Enrichment Analysis: An Alternative Method for Evaluating the Functional Properties of Gene Sets [PDF]

, 2013
Gene annotation databases (compendiums maintained by the scientific community that describe the biological functions performed by individual genes) are commonly used to evaluate the functional properties of experimentally derived gene sets.
Girvan, Michelle, Glass, Kimberly
core   +2 more sources