Results 61 to 70 of about 308,842 (252)

HMMploidy: inference of ploidy levels from short-read sequencing data [PDF]

Peer Community Journal, 2021
Abstract The inference of ploidy levels from genomic data is important to understand molecular mechanisms underpinning genome evolution. However, current methods based on allele frequency and sequencing depth variation do not have power to infer ploidy levels at low-and mid-depth sequencing data, as they do not ...
Soraggi S, Rhodes J, Altinkaya I, Tarrant O, Balloux F, Fisher MC, Fumagalli M.   +6 more
europepmc   +4 more sources

TRAIL‐PEG‐Apt‐PLGA nanosystem as an aptamer‐targeted drug delivery system potential for triple‐negative breast cancer therapy using in vivo mouse model

Molecular Oncology, EarlyView.
Aptamers are used both therapeutically and as targeting agents in cancer treatment. We developed an aptamer‐targeted PLGA–TRAIL nanosystem that exhibited superior therapeutic efficacy in NOD/SCID breast cancer models. This nanosystem represents a novel biotechnological drug candidate for suppressing resistance development in breast cancer.
Gulen Melike Demirbolat, Aslihan Kucuk, Omer Erdogan, Samed Ozer, Bensu Kozan, Tugba Cuceli, Erkan Gumus, Evrim Cevik, Ozge Cevik   +8 more
wiley   +1 more source

AREM: Aligning Short Reads from ChIP-Sequencing by Expectation Maximization [PDF]

Journal of Computational Biology, 2011
Abstract High-throughput sequencing coupled to chromatin immunoprecipitation (ChIP-Seq) is widely used in characterizing genome-wide binding patterns of transcription factors, cofactors, chromatin modifiers, and other DNA binding proteins.
Daniel Newkirk, Jacob Biesinger, Alvin Chon, Kyoko Yokomori, Xiaohui Xie   +4 more
openaire   +2 more sources

Tumour–host interactions in Drosophila: mechanisms in the tumour micro‐ and macroenvironment

Molecular Oncology, EarlyView.
This review examines how tumour–host crosstalk takes place at multiple levels of biological organisation, from local cell competition and immune crosstalk to organism‐wide metabolic and physiological collapse. Here, we integrate findings from Drosophila melanogaster studies that reveal conserved mechanisms through which tumours hijack host systems to ...
José Teles‐Reis, Tor Erik Rusten
wiley   +1 more source

Short-read, high-throughput sequencing technology for STR genotyping

BioTechniques, 2012
DNA-based methods for human identification principally rely upon genotyping of short tandem repeat (STR) loci. Electrophoretic-based techniques for variable-length classification of STRs are universally utilized, but are limited in that they have relatively low throughput and do not yield nucleotide sequence information.
Daniel M, Bornman, Mark E, Hester, Jared M, Schuetter, Manjula D, Kasoji, Angela, Minard-Smith, Curt A, Barden, Scott C, Nelson, Gene D, Godbold, Christine H, Baker, Boyu, Yang, Jacquelyn E, Walther, Ivan E, Tornes, Pearlly S, Yan, Benjamin, Rodriguez, Ralf, Bundschuh, Michael L, Dickens, Brian A, Young, Seth A, Faith   +17 more
openaire   +2 more sources

Benchmarking of sequencing technologies defines optimal strategies for genetic variants detection in a human genome

Genome Biology
Background Advances in sequencing technologies continue to improve the resolution and completeness with which human genetic variation can be characterized.
Robert J. M. Eveleigh, Sarah J. Reiling, Jose Hector Galvez, Mathieu Bourgey, Jiannis Ragoussis, Guillaume Bourque   +5 more
doaj   +1 more source

Subtype‐specific enhancer RNAs define transcriptional regulators and prognosis in breast cancers

Molecular Oncology, EarlyView.
This study employed machine learning methodologies to perform the subtype‐specific classification of RNA‐seq data sets, which are mapped on enhancers from TCGA‐derived breast cancer patients. Their integration with gene expression (referred to as ProxCReAM eRNAs) and chromatin accessibility profiles has the potential to identify lineage‐specific and ...
Aamena Y. Patel, Peyman Zarrineh, Nathnael T. Tuffa, Jigar H. Sheth, Sumitra Mohan, Mudassar Iqbal, Sankari Nagarajan   +6 more
wiley   +1 more source

Genomic surveillance of multidrug-resistant organisms based on long-read sequencing

Genome Medicine
Background Multidrug-resistant organisms (MDRO) pose a significant threat to public health worldwide. The ability to identify antimicrobial resistance determinants, to assess changes in molecular types, and to detect transmission are essential for ...
Fabian Landman, Casper Jamin, Angela de Haan, Sandra Witteveen, Jeroen Bos, Han G. J. van der Heide, Leo M. Schouls, Antoni P. A. Hendrickx, Dutch CPE/MRSA surveillance study group   +8 more
doaj   +1 more source

EDNRB‐dependent endothelin signaling reduces proliferation and promotes proneural‐to‐mesenchymal transition in gliomas

Molecular Oncology, EarlyView.
Glioma cells mainly express the endothelin receptor EDNRB, while EDNRA is restricted to a perivascular tumor subpopulation. Endothelin signaling reduces glioma cell proliferation while promoting migration and a proneural‐to‐mesenchymal transition associated with poor prognosis. This pathway activates Ca2+, K+, ERK, and STAT3 signalings and is regulated
Donovan Pineau, Leonor Garcia, Hugo Arnold, Antonija Hanžek, Maialen Arrieta, Laurent R Gauthier, Christine Granotier‐Beckers, François D Boussin, Amaury Herbet, Marie Hautière, Valentin Asei‐Ceschino, Clémentin Jacques, Laura Brard, Thomas Harnois, Valérie Coronas, Bruno Constantin, Aurélien Chatelier, Jean Chemin, Serge Urbach, Martial Seveno, Szimonetta Hideg, Chantal Ripoll, Kasandra Aguilar‐Cázarez, Min Zheng, Guo‐Hao Huang, Sheng‐Qing Lv, Lei Zhang, Philippe Rondard, Laurent Prezeau, Jean‐Philippe Pin, Hugues Duffau, Luc Bauchet, Valérie Rigau, Franck Denat, Charles Truillet, Didier Boquet, Jean‐Philippe Hugnot   +36 more
wiley   +1 more source

Long-read genome and RNA sequencing resolve a pathogenic intronic germline LINE-1 insertion in APC

npj Genomic Medicine
Familial adenomatous polyposis (FAP) is caused by pathogenic germline variants in the tumor suppressor gene APC. Confirmation of diagnosis was not achieved by cancer gene panel and exome sequencing or custom array-CGH in a family with suspected FAP ...
Alexandra A. Baumann, Lisanne I. Knol, Marie Arlt, Tim Hutschenreiter, Anja Richter, Thomas J. Widmann, Marcus Franke, Karl Hackmann, Sylke Winkler, Daniela Richter, Isabel Spier, Stefan Aretz, Daniela Aust, Joseph Porrmann, Doreen William, Evelin Schröck, Hanno Glimm, Arne Jahn   +17 more
doaj   +1 more source