Results 71 to 80 of about 1,171,841 (304)

leeHom: adaptor trimming and merging for Illumina sequencing reads [PDF]

Nucleic Acids Research, 2014
Abstract The sequencing of libraries containing molecules shorter than the read length, such as in ancient or forensic applications, may result in the production of reads that include the adaptor, and in paired reads that overlap one another.
Renaud, G. ; https://orcid.org/0000-0002-0630-027X, Stenzel, U., Kelso, J. ; https://orcid.org/0000-0002-3618-322X   +2 more
openaire   +3 more sources

The performance of metagenomic next-generation sequencing in diagnosing pulmonary infectious diseases using authentic clinical specimens: The Illumina platform versus the Beijing Genomics Institute platform

Frontiers in Pharmacology, 2023
Introduction: Metagenomic next-generation sequencing (mNGS) has been increasingly used to detect infectious organisms and is rapidly moving from research to clinical laboratories.
Shuangyu Han, Zhan Zhao, Lei Yang, Jie Huang, Yubao Wang, Jing Feng   +5 more
doaj   +1 more source

Spatial and single‐nuclei transcriptomics reveals idiosyncratic and generic patterns in papillary and anaplastic thyroid cancers

Molecular Oncology, EarlyView.
Matched spatial transcriptomics and single‐nuclei RNA‐seq were generated for anaplastic and BRAFV600E papillary thyroid cancers revealing generic and tumor‐specific states occurring in cancer cells and in the tumor microenvironment. In this context, cancer dedifferentiation mirrored organoid maturation through ordered thyroid marker gain/loss ...
Adrien Tourneur, Joel Rodrigues Vitória, Manuel Saiselet, Ligia Craciun, Denis Larsimont, Anne Lefort, Frédérick Libert, Carine Maenhaut, Sabine Costagliola, Maxime Tarabichi, Mirian Romitti, Vincent Detours   +11 more
wiley   +1 more source

Comparison of different sequencing techniques for identification of SARS-CoV-2 variants of concern with multiplex real-time PCR.

PLoS ONE, 2022
As different SARS-CoV-2 variants emerge and with the continuous evolvement of sub lineages of the delta variant, it is crucial that all countries carry out sequencing of at least >1% of their infections, in order to detect emergence of variants with ...
Diyanath Ranasinghe, Tibutius Thanesh Pramanayagam Jayadas, Deshni Jayathilaka, Chandima Jeewandara, Osanda Dissanayake, Dinuka Guruge, Dinuka Ariyaratne, Dumni Gunasinghe, Laksiri Gomes, Ayesha Wijesinghe, Ruwan Wijayamuni, Gathsaurie Neelika Malavige   +11 more
doaj   +1 more source

Epigenetic silencing of the liver‐specific lncRNA LUNAR promotes liver cancer progression via NOTCH activation

Molecular Oncology, EarlyView.
LUNAR is a liver‐specific long noncoding RNA (lncRNA) that is highly expressed in normal liver but becomes epigenetically silenced in hepatocellular carcinoma through promoter hypermethylation. Loss of LUNAR is associated with NOTCH activation, epithelial–mesenchymal transition, and metastasis, whereas restoring LUNAR restrains metastatic progression ...
Se Ha Jang, Hyung Seok Kim, Geum Ok Baek, Moon Gyeong Yoon, Su In Lee, Jee‐Yeong Jeong, Ji Eun Han, Soon Sun Kim, Jae Youn Cheong, Jung Woo Eun   +9 more
wiley   +1 more source

CEACAM1 participation in breast cancer progression

Molecular Oncology, EarlyView.
In invasive breast cancer (BC), CEACAM1 shifts from an apical to a uniform membranous/cytoplasmic pattern, or is lost, as tumors dedifferentiate, inversely tracking the Ki‐67 proliferative index. In MCF‐7 cells, only CEACAM1‐4L suppresses proliferation, repressing cell cycle and growth factor genes.
Mykola Lyndin, Irina Kube‐Golovin, Anatolii Romaniuk, Gunther Wennemuth   +3 more
wiley   +1 more source

Bayexer: an accurate and fast Bayesian demultiplexer for Illumina sequences [PDF]

Bioinformatics, 2015
Abstract Summary: Demultiplexing is used after high-throughput sequencing to in silico assign reads to the samples of origin based on the sequenced reads of the indices. Existing demultiplexing tools based on the similarity between the read index and the reference index sequences may fail to provide satisfactory results on low-quality ...
Haisi Yi, Zhe Li, Tao Li, Jindong Zhao
openaire   +2 more sources

Pharmacological chromatin remodeling enhances response to estrogen therapy in ER+ breast cancer

Molecular Oncology, EarlyView.
Estrogen therapy elicits clinical benefit in ~ 30% of patients with endocrine‐resistant estrogen receptor (ER)‐positive breast cancer. Based on findings that ER transcriptional activation underlies response to estrogen therapy, we tested the effects of epigenetic dysregulation via pharmacological inhibition of histone deacetylases (HDACi).
Anneka L. Johnson Thomas, Barbara Karakyriakou, Patricia C. Muskus, Alyssa M. Roberts, Justin Rendleman, Alexa Warren, Hanxu Lu, Kimberly A. Birmingham, Malone K. Friedman, Abigail E. Goen, Huijuan Yang, Owen M. Wilkins, Fred W. Kolling, Eugene Demidenko, Julie M. Jorns, Brock C. Christensen, Todd W. Miller   +16 more
wiley   +1 more source

Reliable variant calling during runtime of Illumina sequencing [PDF]

Scientific Reports, 2018
Abstract The sequential paradigm of data acquisition and analysis in next-generation sequencing leads to high turnaround times for the generation of interpretable results. We combined a novel real-time read mapping algorithm with fast variant calling to obtain reliable variant calls still during the sequencing process.
Loka, Tobias P., Tausch, Simon H., Renard, Bernhard Y.   +2 more
openaire   +2 more sources

Solution-based targeted genomic enrichment for precious DNA samples

BMC Biotechnology, 2012
Background Solution-based targeted genomic enrichment (TGE) protocols permit selective sequencing of genomic regions of interest on a massively parallel scale.
Shearer Aiden, Hildebrand Michael S, Smith Richard JH   +2 more
doaj   +1 more source