Results 91 to 100 of about 1,296,938 (317)
Alignment Metric Accuracy [PDF]
arXiv, 2005 We propose a metric for the space of multiple sequence alignments that can be used to compare two alignments to each other. In the case where one of the alignments is a reference alignment, the resulting accuracy measure improves upon previous approaches, and provides a balanced assessment of the fidelity of both matches and gaps.
arxiv
Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification [PDF]
, 2014 Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the complementary nature
arxiv +1 more source
FEBS Letters, EarlyView.Venom peptides have shown promise in treating pain. Our study uses computer screening to identify a peptide that targets a sodium channel (NaV1.7) linked to chronic pain. We produced the peptide in the laboratory and refined its design, advancing the search for innovative pain therapies.
Gagan Sharma +8 more
wiley +1 more source
An Alignment Algorithm for Sequences [PDF]
arXiv, 2012 This paper describes a new alignment algorithm for sequences that can be used for determination of deletions and substitutions. It provides several solutions out of which the best one can be chosen on the basis of minimization of gaps or other considerations.
arxiv
Sequence Transduction with Recurrent Neural Networks [PDF]
, 2012 Many machine learning tasks can be expressed as the transformation---or \emph{transduction}---of input sequences into output sequences: speech recognition, machine translation, protein secondary structure prediction and text-to-speech to name but a few ...
Graves, Alex
core
Molecular Oncology, EarlyView.Circulating tumor DNA (ctDNA) offers a possibility for different applications in early and late stage breast cancer management. In early breast cancer tumor informed approaches are increasingly used for detecting molecular residual disease (MRD) and early recurrence. In advanced stage, ctDNA provides a possibility for monitoring disease progression and
Eva Valentina Klocker +14 more
wiley +1 more source
Letter Change Bias and Local Uniqueness in Optimal Sequence Alignments [PDF]
, 2013 Considering two optimally aligned random sequences, we investigate the effect on the alignment score caused by changing a random letter in one of the two sequences. Using this idea in conjunction with large deviations theory, we show that in alignments with a low proportion of gaps the optimal alignment is locally unique in most places with high ...
arxiv +1 more source
Unraveling the metastasis‐preventing effect of miR‐200c in vitro and in vivo
Molecular Oncology, EarlyView.Advanced tumors and ineffective cancer treatments can lead to metastases in distant organs. The sole expression of microRNA 200c (miR‐200c) in breast cancer cells is shown to significantly reduce metastasis formation in xenograft mouse models. Various in vitro analyses revealed impeded migratory behavior, upon miR‐200c expression, as one prerequisite ...
Bianca Köhler +12 more
wiley +1 more source
Process-oriented Iterative Multiple Alignment for Medical Process Mining
, 2017 Adapted from biological sequence alignment, trace alignment is a process mining technique used to visualize and analyze workflow data. Any analysis done with this method, however, is affected by the alignment quality.
Burd, Randall S. +4 more
core +1 more source
Molecular Oncology, EarlyView.The LEXOVE prospective study evaluated plasma cell‐free extracellular vesicle (cfEV) dynamics using Bradford assay and dynamic light scattering in metastatic non‐small cell lung cancer patients undergoing first‐line treatments, correlating a ∆cfEV < 20% with improved median progression‐free survival in responders versus non‐responders.
Valerio Gristina +17 more
wiley +1 more source