Results 51 to 60 of about 429,505 (261)

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

Data‐driven discovery of gene expression markers distinguishing pediatric acute lymphoblastic leukemia subtypes

Molecular Oncology, EarlyView.
This study investigates gene expression differences between two major pediatric acute lymphoblastic leukemia (ALL) subtypes, B‐cell precursor ALL, and T‐cell ALL, using a data‐driven approach consisting of biostatistics and machine learning methods. Following analysis of a discovery dataset, we find a set of 14 expression markers differentiating the ...
Mona Nourbakhsh, Nikola Tom, Anna Schrøder Lassen, Helene Brasch Lind Petersen, Ulrik Kristoffer Stoltze, Karin Wadt, Kjeld Schmiegelow, Matteo Tiberti, Elena Papaleo   +8 more
wiley   +1 more source

CMSA: a heterogeneous CPU/GPU computing system for multiple similar RNA/DNA sequence alignment

BMC Bioinformatics, 2017
Background The multiple sequence alignment (MSA) is a classic and powerful technique for sequence analysis in bioinformatics. With the rapid growth of biological datasets, MSA parallelization becomes necessary to keep its running time in an acceptable ...
Xi Chen, Chen Wang, Shanjiang Tang, Ce Yu, Quan Zou   +4 more
doaj   +1 more source

Unraveling LINE‐1 retrotransposition in head and neck squamous cell carcinoma

Molecular Oncology, EarlyView.
The novel RetroTest method allows the detection of L1 activation in clinical samples with low DNA input, providing global L1 activity and the identification of the L1 source element. We applied RetroTest to a real‐world cohort of HNSCC patients where we reported an early L1 activation, with more than 60% of T1 patients showing L1 activity.
Jenifer Brea‐Iglesias, Ana Oitabén, Sonia Zumalave, Bernardo Rodriguez‐Martin, María Gallardo‐Gómez, Martín Santamarina, Ana Pequeño‐Valtierra, Laura Juaneda‐Magdalena, Ramón García‐Escudero, José Luis López‐Cedrún, Máximo Fraga, José M. C. Tubio, Mónica Martínez‐Fernández   +12 more
wiley   +1 more source

Designing universal primers for the isolation of DNA sequences encoding Proanthocyanidins biosynthetic enzymes in Crataegus aronia

BMC Research Notes, 2012
Background Hawthorn is the common name of all plant species in the genus Crataegus, which belongs to the Rosaceae family. Crataegus are considered useful medicinal plants because of their high content of proanthocyanidins (PAs) and other related ...
Zuiter Afnan, Sawwan Jammal, Al Abdallat Ayed   +2 more
doaj   +1 more source

Tumor clusters with divergent inflammation and human retroelement expression determine the clinical outcome of patients with serous ovarian cancer

Molecular Oncology, EarlyView.
Analysis of treatment‐naïve high‐grade serous ovarian carcinoma (HGSOC) and control tissues for ERVs, LINE‐1 (L1), inflammation, and immune checkpoints identified five clusters with diverse patient recurrence‐free survivals. An inflammation score was calculated and correlated with retroelement expression, where one novel cluster (Triple‐I) with high ...
Laura Glossner, Markus Eckstein, Christoph Mark, Matthias W. Beckmann, Arndt Hartmann, Pamela L. Strissel, Reiner Strick   +6 more
wiley   +1 more source

Machine learning for identifying liver and pancreas cancers through comprehensive serum glycopeptide spectra analysis: a case‐control study

Molecular Oncology, EarlyView.
This study presents a novel AI‐based diagnostic approach—comprehensive serum glycopeptide spectra analysis (CSGSA)—that integrates tumor markers and enriched glycopeptides from serum. Using a neural network model, this method accurately distinguishes liver and pancreatic cancers from healthy individuals.
Motoyuki Kohjima, Yuko Takami, Ken Kawabe, Kazuhiro Tanabe, Chihiro Hayashi, Mikio Mikami, Tetsuya Kusumoto   +6 more
wiley   +1 more source

IBBOMSA: An Improved Biogeography-based Approach for Multiple Sequence Alignment

Evolutionary Bioinformatics, 2016
In bioinformatics, multiple sequence alignment (MSA) is an NP-hard problem. Hence, nature-inspired techniques can better approximate the solution. In the current study, a novel biogeography-based optimization (NBBO) is proposed to solve an MSA problem ...
Rohit Kumar Yadav, Haider Banka
doaj   +2 more sources

Vertical decomposition with Genetic Algorithm for Multiple Sequence Alignment

BMC Bioinformatics, 2011
Background Many Bioinformatics studies begin with a multiple sequence alignment as the foundation for their research. This is because multiple sequence alignment can be a useful technique for studying molecular evolution and analyzing sequence structure ...
Essam Daryl, Sarker Ruhul, Naznin Farhana   +2 more
doaj   +1 more source

Decrypting cancer's spatial code: from single cells to tissue niches

Molecular Oncology, EarlyView.
Spatial transcriptomics maps gene activity across tissues, offering powerful insights into how cancer cells are organised, switch states and interact with their surroundings. This review outlines emerging computational, artificial intelligence (AI) and geospatial approaches to define cell states, uncover tumour niches and integrate spatial data with ...
Cenk Celik, Shi Pan, Eloise Withnell, Hou Wang Lam, Maria Secrier   +4 more
wiley   +1 more source