Results 101 to 110 of about 296,746 (277)

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, Van den Born L. Ingeborgh, 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

CD47 promotes mitogen‐activated protein kinase and epithelial‐to‐mesenchymal transition molecular programs to drive prometastatic phenotypes in non‐small cell lung cancer

Molecular Oncology, EarlyView.
Beyond its role in immune evasion, this study identified that CD47 drives tumor‐intrinsic signaling in non‐small cell lung cancer (NSCLC). Transcriptomic profiling and functional studies revealed that CD47 regulates cell adhesion, migration, and metastasis through an ERK–EMT signaling axis.
Asa P.Y. Lau, Lilian G. Zhai, Ryunosuke Hoshi, Zackary Rousseau, Abraam Zakhary, Yin Fang Wu, Rola M. Saleeb, Heyu Ni, Kelsie L. Thu   +8 more
wiley   +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

KDM7A and KDM1A inhibition suppresses tumour promoting pathways in prostate cancer

Molecular Oncology, EarlyView.
Treatment resistance is a major challenge for patients with advanced prostate cancer. This study examined an alternative approach to target the major prostate cancer‐promoting pathway by targeting epigenetic factors, whose levels are higher in tumours.
Jennie N Jeyapalan, Veronika M Metzler, Simone de Brot, Corinne L Woodcock, Anna E Harris, Jennifer Lothion‐Roy, Emeli M Nilsson, Atara Ntekim, Michael S Toss, Jenny L Persson, Francesca Khani, Brian D Robinson, Lorraine J Gudas, Emad Rakha, David M Heery, Catrin S Rutland, Nigel P Mongan   +16 more
wiley   +1 more source

Introduction to read mapping v1

, 2018
This is an example of a simple read mapping workflow. It is designed to be performed via the command line on an Ubuntu 16.06 OS. After completing this tutorial you should: 1) Have a practical understanding of how read mapping analyses are performed in
Frank Aylward
core   +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

Stranded Mapping from Long Reads v1

, 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

Heterozygous loss‐of‐function alleles associate the conserved 3′‐5′ exoribonuclease EXOSC10 with hypersensitivity to the anticancer drug 5‐fluorouracil

Molecular Oncology, EarlyView.
EXOSC10, an essential nuclear RNA exosome‐associated 3′‐5′ exoribonuclease, is inhibited by the anticancer drug 5‐fluorouracil (5‐FU), and EXOSC10 depletion increases 5‐FU sensitivity. The colon‐cancer variant EXOSC10S402T, located in a proteolysis motif, is stable and nuclear but nonfunctional in vivo.
Radhika Sain, Yann Le Page, Frédéric Percevault, Emmanuelle Becker, Luc Negroni, Almudena Fernandez, Marta Cantero, Diego Muñoz‐Santos, Lluís Montoliu, Cyrille Garnier, Michael Primig   +10 more
wiley   +1 more source

Introduction to read mapping v2

, 2018
This is an example of a simple read mapping workflow. It is designed to be performed via the command line on an Ubuntu 16.06 OS. After completing this tutorial you should: 1) Have a practical understanding of how read mapping analyses are performed in
Frank Aylward
core   +1 more source

Interpreting the effects of DNA polymerase variants at the structural level

Molecular Oncology, EarlyView.
Using MAVISp and molecular dynamics simulations, we analyzed over 60 000 missense variants in POLE and POLD1 from ClinVar, COSMIC, cBioPortal, and saturation mutagenesis. Identified mechanistic indicators, including stability, binding, and long‐range, enable structural interpretation, providing ACMG‐like evidence for possible reclassification of VUS ...
Matteo Arnaudi, Karolina Krzesińska, Ludovica Beltrame, Pablo Sánchez‐Izquierdo Besora, Matteo Tiberti, Mef Nilbert, Anna Rohlin, Elena Papaleo   +7 more
wiley   +1 more source