Results 71 to 80 of about 225,232 (252)

A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics

Microbiology Spectrum
Shotgun metagenomics enables the reconstruction of complex microbial communities at a high level of detail. Such an approach can be conducted using both short-read and long-read sequencing data, as well as a combination of both.
Raphael Eisenhofer, Joseph Nesme, Luisa Santos-Bay, Adam Koziol, Søren Johannes Sørensen, Antton Alberdi, Ostaizka Aizpurua   +6 more
doaj   +1 more source

In vitro models of cancer‐associated fibroblast heterogeneity uncover subtype‐specific effects of CRISPR perturbations

Molecular Oncology, EarlyView.
Development of therapies targeting cancer‐associated fibroblasts (CAFs) necessitates preclinical model systems that faithfully represent CAF–tumor biology. We established an in vitro coculture system of patient‐derived pancreatic CAFs and tumor cell lines and demonstrated its recapitulation of primary CAF–tumor biology with single‐cell transcriptomics ...
Elysia Saputra, Shamsudheen Karuthedath Vellarikkal, Lixia Li, Hong Sun, Khoa Nguyen, Amber Montano, Suchitra Natarajan, Federica Piccioni, Alex Michael Tamburino, Xin Yu, Aleksandra Katarzyna Olow   +10 more
wiley   +1 more source

Stranded Mapping from Long Reads v2

, 2018
This protocol demonstrates how to convert raw long reads produced using a strand-specific sequencing protocol (e.g. ONT's strand-switching protocol) into strand-specific mapped reads. The general ides is to use LAST to identify the adapter orientation relative to the genome, and then use that information to split BAM files up and recombine them to ...
openaire   +1 more source

Dual targeting of RET and SRC synergizes in RET fusion‐positive cancer cells

Molecular Oncology, EarlyView.
Despite the strong activity of selective RET tyrosine kinase inhibitors (TKIs), resistance of RET fusion‐positive (RET+) lung cancer and thyroid cancer frequently occurs and is mainly driven by RET‐independent bypass mechanisms. Son et al. show that SRC TKIs significantly inhibit PAK and AKT survival signaling and enhance the efficacy of RET TKIs in ...
Juhyeon Son, Lily L. Remsing Rix, Bin Fang, Eric A. Welsh, Nicole V. Bremer, Valentina Foglizzo, Paola Roa, Nickole Sigcha‐Coello, Yi Liao, Eric B. Haura, Alexander Drilon, John M. Koomen, Emiliano Cocco, Uwe Rix   +13 more
wiley   +1 more source

Long-read technologies identify a hidden LINE-1/ERV1 insertion in IQCB1 as causative variant for Senior-Løken syndrome

npj Genomic Medicine
Senior-Løken syndrome is a rare ciliopathy characterized by retinal dystrophy and nephronophthisis. This autosomal recessive inherited disease is caused by pathogenic variants in several genes, including IQCB1.
Suzanne E. de Bruijn, L. Ingeborgh van den Born, Ronny Derks, Lonneke Haer-Wigman, Luke O’Gorman, Frans P. M. Cremers, Ronald van Beek, Alexander Hoischen, Susanne Roosing, Kornelia Neveling   +9 more
doaj   +1 more source

Short-Read and Long-Read Whole Genome Sequencing for SARS-CoV-2 Variants Identification

Viruses
Genomic surveillance of SARS-CoV-2 is crucial for detecting emerging variants and informing public health responses. Various sequencing technologies are used for whole genome sequencing of SARS-CoV-2.
Mengfei Peng, Morgan L. Davis, Meghan L. Bentz, Alex Burgin, Mark Burroughs, Jasmine Padilla, Sarah Nobles, Yvette Unoarumhi, Kevin Tang   +8 more
doaj   +1 more source

Cis‐regulatory and long noncoding RNA alterations in breast cancer – current insights, biomarker utility, and the critical need for functional validation

Molecular Oncology, EarlyView.
The noncoding region of the genome plays a key role in regulating gene expression, and mutations within these regions are capable of altering it. Researchers have identified multiple functional noncoding mutations associated with increased cancer risk in the genome of breast cancer patients.
Arnau Cuy Saqués, Aracele Martinez‐Mendez, John Crown, Alex Eustace   +3 more
wiley   +1 more source

De novo assembly of middle-sized genome using MinION and Illumina sequencers

BMC Genomics, 2018
Background The plastid acquisition by secondary endosymbiosis is a driving force for the algal evolution, and the comparative genomics was required to examine the genomic change of symbiont.
Ryuhei Minei, Ryo Hoshina, Atsushi Ogura
doaj   +1 more source

Detection of circulating tumor DNA in colorectal cancer patients using a methylation‐specific droplet digital PCR multiplex

Molecular Oncology, EarlyView.
We developed a cost‐effective methylation‐specific droplet digital PCR multiplex assay containing tissue‐conserved and tumor‐specific methylation markers. The assay can detect circulating tumor DNA with high accuracy in patients with localized and metastatic colorectal cancer.
Luisa Matos do Canto, Louise Raunkilde, Jan Lindebjerg, Mads Malik Aagaard, Christina Therkildsen, Jakob Kleif, Lars Henrik Jensen, Torben Frøstrup Hansen, Rikke Fredslund Andersen   +8 more
wiley   +1 more source

Accelerating 3D genomics data analysis with Microcket

Communications Biology
The three-dimensional (3D) organization of genome is fundamental to cell biology. To explore 3D genome, emerging high-throughput approaches have produced billions of sequencing reads, which is challenging and time-consuming to analyze.
Yu Zhao, Mengqi Yang, Fanglei Gong, Yuqi Pan, Minghui Hu, Qin Peng, Leina Lu, Xiaowen Lyu, Kun Sun   +8 more
doaj   +1 more source