DNAscent v2: detecting replication forks in nanopore sequencing data with deep learning
BMC Genomics, 2021 Background Measuring DNA replication dynamics with high throughput and single-molecule resolution is critical for understanding both the basic biology behind how cells replicate their DNA and how DNA replication can be used as a therapeutic target for ...
Michael A. Boemo
doaj +1 more source
Estimating T-cell repertoire diversity: limitations of classical estimators and a new approach [PDF]
, 2015 A highly diverse T-cell receptor (TCR) repertoire is a fundamental property of an effective immune system, and is associated with efficient control of viral infections and other pathogens. However, direct measurement of total TCR diversity is impossible.
Asquith, RE, Bangham, C, Laydon, D
core +1 more source
Bottom‐Up Programming of Cell States in Cancer Organoids with Defined Synthetic Adhesion Cues
Advanced Materials, EarlyView.A bottom‐up biomaterial platform is developed to program transcriptomic states in pancreatic cancer organoids by tuning adhesion cues within synthetic matrices. By combining a Design of Experiments framework with multiobjective optimization, matrix compositions are identified that enrich specific cellular programs like EMT.
Ali Nadernezhad +6 more
wiley +1 more source
Targeted Amplicon Sequencing for Single-Nucleotide-Polymorphism Genotyping of Attaching and Effacing Escherichia coli O26:H11 Cattle Strains via a High-Throughput Library Preparation Technique [PDF]
Applied and Environmental Microbiology, 2016 ABSTRACT Enterohemorrhagic Escherichia coli (EHEC) O26:H11, a serotype within Shiga toxin-producing E. coli (STEC) that causes severe human disease, has been considered to have evolved from attaching and effacing E. coli (AEEC) O26:H11 through the acquisition
Sarah A. Ison +8 more
openaire +3 more sources
A saturated genetic linkage map of autotetraploid alfalfa (Medicago sativa L.) developed using genotyping-by-sequencing is highly syntenous with the Medicago truncatula genome. [PDF]
, 2014 A genetic linkage map is a valuable tool for quantitative trait locus mapping, map-based gene cloning, comparative mapping, and whole-genome assembly. Alfalfa, one of the most important forage crops in the world, is autotetraploid, allogamous, and highly
Acharya, Ananta +5 more
core +2 more sources
Plant Methods, 2018 The recent development of next-generation sequencing DNA marker technologies, such as genotyping-by-sequencing (GBS), generates thousands of informative single nucleotide polymorphism markers in almost any species, regardless of genomic resources.
C. Anderson +8 more
semanticscholar +1 more source
Advanced Robotics Research, EarlyView.To address challenges in high‐throughput intestinal sampling with sealed containment and target drug delivery, we developed a dual‐functional ingestible passive capsule with a dual‐triggered control system based on pH‐response and mechanical actuation.
Libing Huang +9 more
wiley +1 more source
Double-digest RADseq loci using standard Illumina indexes improve deep and shallow phylogenetic resolution of Lophodermium, a widespread fungal endophyte of pine needles. [PDF]
, 2018 The phylogenetic and population genetic structure of symbiotic microorganisms may correlate with important ecological traits that can be difficult to directly measure, such as host preferences or dispersal rates.
Oono, Ryoko, Salas-Lizana, Rodolfo
core +1 more source
BARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing
BMC Bioinformatics, 2018 Current high-throughput sequencing platforms provide capacity to sequence multiple samples in parallel. Different samples are labeled by attaching a short sample specific nucleotide sequence, barcode, to each DNA molecule prior pooling them into a mix ...
P. Somervuo +5 more
semanticscholar +1 more source
Advanced Science, EarlyView.Ectodermal tissue excised from Xenopus embryos self‐organizes into a three‐dimensional mucociliary organoid. Here, we generate a neural variant, termed neurobot, by implanting neural precursor cells. Neurobots develop mature neurons, adopt distinct morphologies, exhibit more complex motility, and respond differentially to neuroactive compounds. Imaging
Haleh Fotowat +6 more
wiley +1 more source