Results 101 to 110 of about 557,186 (345)

GRYFUN: a web application for GO term annotation visualization and analysis in protein sets.

PLoS ONE, 2015
Functional context for biological sequence is provided in the form of annotations. However, within a group of similar sequences there can be annotation heterogeneity in terms of coverage and specificity.
Hugo P Bastos, Lisete Sousa, Luka A Clarke, Francisco M Couto   +3 more
doaj   +1 more source

Treebank-based acquisition of wide-coverage, probabilistic LFG resources: project overview, results and evaluation [PDF]

, 2004
This paper presents an overview of a project to acquire wide-coverage, probabilistic Lexical-Functional Grammar (LFG) resources from treebanks. Our approach is based on an automatic annotation algorithm that annotates “raw” treebank trees with LFG f ...
Burke, Michael, Cahill, Aoife, O'Donovan, Ruth, van Genabith, Josef, Way, Andy   +4 more
core   +1 more source

Protein pyrophosphorylation by inositol pyrophosphates — detection, function, and regulation

FEBS Letters, EarlyView.
Protein pyrophosphorylation is an unusual signaling mechanism that was discovered two decades ago. It can be driven by inositol pyrophosphate messengers and influences various cellular processes. Herein, we summarize the research progress and challenges of this field, covering pathways found to be regulated by this posttranslational modification as ...
Sarah Lampe, Tanmay Kumar Mohanty, Rashna Bhandari, Dorothea Fiedler   +3 more
wiley   +1 more source

SIFTER-T: A scalable and optimized framework for the SIFTER phylogenomic method of probabilistic protein domain annotation

BioTechniques, 2015
Statistical Inference of Function Through Evolutionary Relationships (SIFTER) is a powerful computational platform for probabilistic protein domain annotation. Nevertheless, SIFTER is not widely used, likely due to usability and scalability issues.
Danillo C. Almeida-e-Silva, Ricardo Z.N. Vêncio   +1 more
doaj   +1 more source

Function‐driven design of a surrogate interleukin‐2 receptor ligand

FEBS Letters, EarlyView.
Interleukin (IL)‐2 signaling can be achieved and precisely fine‐tuned through the affinity, distance, and orientation of the heterodimeric receptors with their ligands. We designed a biased IL‐2 surrogate ligand that selectively promotes effector T and natural killer cell activation and differentiation. Interleukin (IL) receptors play a pivotal role in
Ziwei Tang, Zelin Cheng, Teng Li, Fulian Wang, Liangminghui Zhang, Xiuxiu He, Lili Liu, Wei Wang, Aibin Liang, Guang Yang   +9 more
wiley   +1 more source

Time after time – circadian clocks through the lens of oscillator theory

FEBS Letters, EarlyView.
Oscillator theory bridges physics and circadian biology. Damped oscillators require external drivers, while limit cycles emerge from delayed feedback and nonlinearities. Coupling enables tissue‐level coherence, and entrainment aligns internal clocks with environmental cues.
Marta del Olmo, Carolin Ector, Hanspeter Herzel   +2 more
wiley   +1 more source

GNPAnnot: a community annotation system applied to sugarcane sequences : W745 [PDF]

, 2013
A large amount of data is being produced by current genome sequencing projects. Sequence annotations need to be organized into databases and widely accessible.
Bocs, Stéphanie, Charron, Carine, D'Hont, Angélique, Droc, Gaëtan, Garsmeur, Olivier, Guignon, Valentin, Ruiz, Manuel   +6 more
core  

The newfound relationship between extrachromosomal DNAs and excised signal circles

FEBS Letters, EarlyView.
Extrachromosomal DNAs (ecDNAs) contribute to the progression of many human cancers. In addition, circular DNA by‐products of V(D)J recombination, excised signal circles (ESCs), have roles in cancer progression but have largely been overlooked. In this Review, we explore the roles of ecDNAs and ESCs in cancer development, and highlight why these ...
Dylan Casey, Zeqian Gao, Joan Boyes
wiley   +1 more source

HAMAP in 2015: updates to the protein family classification and annotation system [PDF]

, 2017
HAMAP (High-quality Automated and Manual Annotation of Proteins—available at http://hamap.expasy.org/) is a system for the automatic classification and annotation of protein sequences. HAMAP provides annotation of the same quality and detail as UniProtKB/
Auchincloss, Andrea H., Baratin, Delphine, Bougueleret, Lydie, Bridge, Alan, Coudert, Elisabeth, Cuche, Béatrice A., deCastro, Edouard, Keller, Guillaume, Pedruzzi, Ivo, Poux, Sylvain, Redaschi, Nicole, Rivoire, Catherine, Xenarios, Ioannis   +12 more
core  

An upstream open reading frame regulates expression of the mitochondrial protein Slm35 and mitophagy flux

FEBS Letters, EarlyView.
This study reveals how the mitochondrial protein Slm35 is regulated in Saccharomyces cerevisiae. The authors identify stress‐responsive DNA elements and two upstream open reading frames (uORFs) in the 5′ untranslated region of SLM35. One uORF restricts translation, and its mutation increases Slm35 protein levels and mitophagy.
Hernán Romo‐Casanueva, Ariann E. Mendoza‐Martínez, P. Abril Medina‐Flores, Carlos Campero‐Basaldua, Alexander DeLuna, Soledad Funes   +5 more
wiley   +1 more source