Results 91 to 100 of about 1,259,867 (328)

Metric Learning for Temporal Sequence Alignment [PDF]

, 2014
In this paper, we propose to learn a Mahalanobis distance to perform alignment of multivariate time series. The learning examples for this task are time series for which the true alignment is known.
Arlot, Sylvain, Bach, Francis, Garreau, Damien, Lajugie, Rémi   +3 more
core   +3 more sources

Multidimensional OMICs reveal ARID1A orchestrated control of DNA damage, splicing, and cell cycle in normal‐like and malignant urothelial cells

Molecular Oncology, EarlyView.
Loss of the frequently mutated chromatin remodeler ARID1A, a subunit of the SWI/SNF cBAF complex, results in less open chromatin, alternative splicing, and the failure to stop cells from progressing through the cell cycle after DNA damage in bladder (cancer) cells. Created in BioRender. Epigenetic regulators, such as the SWI/SNF complex, with important
Rebecca M. Schlösser, Florian Krumbach, Eyleen Corrales, Geoffroy Andrieux, Christian Preisinger, Franziska Liss, Alexandra Golzmann, Melanie Boerries, Kerstin Becker, Ruth Knüchel, Stefan Garczyk, Bernhard Lüscher   +11 more
wiley   +1 more source

Multi‐omic characterization of consensus molecular subtype 1 (CMS1) colorectal cancer with dampened immune response improves precision medicine

Molecular Oncology, EarlyView.
This study highlights the importance of multi‐omic analyses in characterizing colorectal cancers. Indeed, our analysis revealed a rare CMS1 exhibiting dampened immune activation, including reduced PD‐1 expression, moderate CD8+ T‐cell infiltration, and suppressed JAK/STAT pathway.
Livia Concetti, Manuel Scimeca, Julia Bischof, Jonathan Woodsmith, Massimiliano Agostini, Cristina Fiorani, Yufang Shi, Eleonora Candi, Gerry Melino, Alessandro Mauriello, Giuseppe S. Sica   +10 more
wiley   +1 more source

Three-Way Alignment Improves Multiple Sequence Alignment of Highly Diverged Sequences

Algorithms
The standard approach for constructing a phylogenetic tree from a set of sequences consists of two key stages. First, a multiple sequence alignment (MSA) of the sequences is computed.
Mahbubeh Askari Rad, Alibek Kruglikov, Xuhua Xia   +2 more
doaj   +1 more source

Meta-alignment of biological sequences

, 2023
Les seqüències són una de les estructures de dades més versàtils que existeixen. De forma relativament senzilla, en una seqüència de símbols es pot emmagatzemar informació de qualsevol tipus. L'anàlisi sistemàtic de seqüències es un àrea molt rica de l'algorísmica amb numeroses aproximacions desenvolupades amb éxit.
openaire   +4 more sources

Chemoresistome mapping in individual breast cancer patients unravels diversity in dynamic transcriptional adaptation

Molecular Oncology, EarlyView.
This study used longitudinal transcriptomics and gene‐pattern classification to uncover patient‐specific mechanisms of chemotherapy resistance in breast cancer. Findings reveal preexisting drug‐tolerant states in primary tumors and diverse gene rewiring patterns across patients, converging on a few dysregulated functional modules. Despite receiving the
Maya Dadiani, Gilgi Friedlander, Gili Perry, Nora Balint‐Lahat, Shlomit Gilad, Dana Morzaev‐Sulzbach, Anjana Shenoy, Noa Bossel Ben‐Moshe, Anya Pavlovsky, Rinat Bernstein‐Molho, Eytan Domany, Iris Barshack, Tamar Geiger, Bella Kaufman, Einav Nili Gal‐Yam   +14 more
wiley   +1 more source

Optimizing Data Parallelism for FM-Based Short-Read Alignment on the Heterogeneous Non-Uniform Memory Access Architectures

Future Internet
Sequence alignment is a critical factor in the variant analysis of genomic research. Since the FM (Ferrainas–Manzini) index was developed, it has proven to be a model in a compact format with efficient pattern matching and high-speed query searching ...
Shaolong Chen, Yunzi Dai, Liwei Liu, Xinting Yu   +3 more
doaj   +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, Grüneberg Alexander, Maass Wolfgang, Vinga Susana   +3 more
doaj   +1 more source

Expression and DNA methylation of 20S proteasome subunits as prognostic and resistance markers in cancer

Molecular Oncology, EarlyView.
Comprehensive analysis of genomic mutations, gene expression, DNA methylation, and pathway analysis of TCGA data was carried out to define cancer types in which proteasome subunits expression is associated with worse survival. Albeit the effect of specific proteasome subunits on cellular function, the main role of the proteasome is better evaluated ...
Ruba Al‐Abdulla, Simone Venz, Ruslan Al‐Ali, Martin Wendlandt, Mandy Radefeldt, Elke Krüger   +5 more
wiley   +1 more source

FPGA-based protein sequence alignment : A review

EPJ Web of Conferences, 2017
Sequence alignment have been optimized using several techniques in order to accelerate the computation time to obtain the optimal score by implementing DP-based algorithm into hardware such as FPGA-based platform.
Md. Isa Mohd. Nazrin, Ku Muhsen Ku Noor Dhaniah, Saiful Nurdin Dayana, Ahmad Muhammad Imran, Zainol Murad Sohiful Anuar, Mohyar Shaiful Nizam, Harun Azizi, Hussin Razaidi   +7 more
doaj   +1 more source