Results 151 to 160 of about 4,504,319 (408)
Molecular and functional profiling unravels targetable vulnerabilities in colorectal cancer
Molecular Oncology, EarlyView.We used whole exome and RNA‐sequencing to profile divergent genomic and transcriptomic landscapes of microsatellite stable (MSS) and microsatellite instable (MSI) colorectal cancer. Alterations were classified using a computational score for integrative cancer variant annotation and prioritization.
Efstathios‐Iason Vlachavas +15 more
wiley +1 more source
Anchor points for genome alignment based on Filtered Spaced Word Matches [PDF]
arXiv, 2017 Alignment of large genomic sequences is a fundamental task in computational genome analysis. Most methods for genomic alignment use high-scoring local alignments as {\em anchor points} to reduce the search space of the alignment procedure. Speed and quality of these methods therefore depend on the underlying anchor points.
arxiv
Global Network Alignment [PDF]
, 2010 Motivation: High-throughput methods for detecting molecular interactions have lead to a plethora of biological network data with much more yet to come, stimulating the development of techniques for biological network alignment.
Natasa Przulj, Oleksii Kuchaiev
core +1 more source
Multiple sequence alignment modeling: methods and applications
Briefings Bioinform., 2016 This review provides an overview on the development of Multiple sequence alignment (MSA) methods and their main applications. It is focused on progress made over the past decade. The three first sections review recent algorithmic developments for protein,
Maria Chatzou +6 more
semanticscholar +1 more source
Peripheral blood proteome biomarkers distinguish immunosuppressive features of cancer progression
Molecular Oncology, EarlyView.Immune status significantly influences cancer progression. This study used plasma proteomics to analyze benign 67NR and malignant 4T1 breast tumor models at early and late tumor stages. Immune‐related proteins–osteopontin (Spp1), lactotransferrin (Ltf), calreticulin (Calr) and peroxiredoxin 2 (Prdx2)–were associated with systemic myeloid‐derived ...
Yeon Ji Park +6 more
wiley +1 more source
Fractal MapReduce decomposition of sequence alignment
Algorithms for Molecular Biology, 2012 Background The dramatic fall in the cost of genomic sequencing, and the increasing convenience of distributed cloud computing resources, positions the MapReduce coding pattern as a cornerstone of scalable bioinformatics algorithm development.
Almeida Jonas S +3 more
doaj +1 more source
Improving spliced alignment for identification of ortholog groups and multiple CDS alignment [PDF]
arXiv, 2017 The Spliced Alignment Problem (SAP) that consists in finding an optimal semi-global alignment of a spliced RNA sequence on an unspliced genomic sequence has been largely considered for the prediction and the annotation of gene structures in genomes.
arxiv
msa: an R package for multiple sequence alignment
Bioinform., 2015 UNLABELLED Although the R platform and the add-on packages of the Bioconductor project are widely used in bioinformatics, the standard task of multiple sequence alignment has been neglected so far.
Ulrich Bodenhofer +3 more
semanticscholar +1 more source
Stochastic variation in the FOXM1 transcription program mediates replication stress tolerance
Molecular Oncology, EarlyView.Cellular heterogeneity is a major cause of drug resistance in cancer. Segeren et al. used single‐cell transcriptomics to investigate gene expression events that correlate with sensitivity to the DNA‐damaging drugs gemcitabine and prexasertib. They show that dampened expression of transcription factor FOXM1 and its target genes protected cells against ...
Hendrika A. Segeren +4 more
wiley +1 more source
MAVID: Constrained ancestral alignment of multiple sequences [PDF]
arXiv, 2003 We describe a new global multiple alignment program capable of aligning a large number of genomic regions. Our progressive alignment approach incorporates the following ideas: maximum-likelihood inference of ancestral sequences, automatic guide-tree construction, protein based anchoring of ab-initio gene predictions, and constraints derived from a ...
arxiv