Results 31 to 40 of about 11,725 (260)
Hardware Accelerated Sequence Alignment with Traceback
International Journal of Reconfigurable Computing, 2009 Biological sequence alignment is an essential tool used in molecular biology and biomedical applications. The growing volume of genetic data and the complexity of sequence alignment present a challenge in obtaining alignment results in a timely manner ...
Scott Lloyd, Quinn O. Snell
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BMC Bioinformatics, 2010 Background Protein alignments are an essential tool for many bioinformatics analyses. While sequence alignments are accurate for proteins of high sequence similarity, they become unreliable as they approach the so-called 'twilight zone' where sequence ...
Bastolla Ugo +3 more
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Identifying and seeing beyond multiple sequence alignment errors using intra-molecular protein covariation. [PDF]
PLoS ONE, 2010 BACKGROUND: There is currently no way to verify the quality of a multiple sequence alignment that is independent of the assumptions used to build it. Sequence alignments are typically evaluated by a number of established criteria: sequence conservation ...
Russell J Dickson +3 more
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Population Ecology, EarlyView.Population size and dynamics fundamentally shape speciation by influencing genetic drift, founder events, and adaptive potential. Small populations may speciate rapidly due to stronger drift, whereas large populations harbor more genetic diversity, which can alter divergence trajectories. We highlight theoretical models that incorporate population size
Ryo Yamaguchi +3 more
wiley +1 more source
Reticular alignment: A progressive corner-cutting method for multiple sequence alignment
BMC Bioinformatics, 2010 Background In this paper, we introduce a progressive corner cutting method called Reticular Alignment for multiple sequence alignment. Unlike previous corner-cutting methods, our approach does not define a compact part of the dynamic programming table ...
Novák Ádám +3 more
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From omics to AI—mapping the pathogenic pathways in type 2 diabetes
FEBS Letters, EarlyView.Integrating multi‐omics data with AI‐based modelling (unsupervised and supervised machine learning) identify optimal patient clusters, informing AI‐driven accurate risk stratification. Digital twins simulate individual trajectories in real time, guiding precision medicine by matching patients to targeted therapies.
Siobhán O'Sullivan +2 more
wiley +1 more source
ERBIN limits epithelial cell plasticity via suppression of TGF‐β signaling
FEBS Letters, EarlyView.In breast and lung cancer patients, low ERBIN expression correlates with poor clinical outcomes. Here, we show that ERBIN inhibits TGF‐β‐induced epithelial‐to‐mesenchymal transition in NMuMG breast and A549 lung adenocarcinoma cell lines. ERBIN suppresses TGF‐β/SMAD signaling and reduces TGF‐β‐induced ERK phosphorylation.
Chao Li +3 more
wiley +1 more source
The effect of sequence quality on sequence alignment [PDF]
Bioinformatics, 2008 Abstract Motivation: The nucleotide sequencing process produces not only the sequence of nucleotides, but also associated quality values. Quality values provide valuable information, but are primarily used only for trimming sequences and generally ignored in subsequent analyses.
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Contact-based sequence alignment [PDF]
Nucleic Acids Research, 2004 This paper introduces the novel method of contact-based protein sequence alignment, where structural information in the form of contact mutation probabilities is incorporated into an alignment routine using contact-mutation matrices (CAO: Contact Accepted mutatiOn).
Kuang Lin +3 more
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gpALIGNER: A Fast Algorithm for Global Pairwise Alignment of DNA Sequences [PDF]
Iranian Journal of Chemistry & Chemical Engineering, 2011 Bioinformatics, through the sequencing of the full genomes for many species, is increasingly relying on efficient global alignment tools exhibiting both high sensitivity and specificity.
Mostafa Hadian Dehkordi +2 more
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