Avery Davis Bell
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View article: Allelic variation at tRNA genes in three nematode species indicates mutation load despite strong purifying selection
Allelic variation at tRNA genes in three nematode species indicates mutation load despite strong purifying selection Open
Cytosolic transfer RNAs, which are encoded as hundreds of genes in nuclear genomes, experience exceptionally high mutation rates and have been hypothesized to confer substantial mutational load in natural populations. Although this phenome…
Coloured feeder balls and mirrors increase exploring behaviour in captive common marmosets (Callithrix jacchus) Open
The influence of visual enrichment on the behaviour and welfare of captive animals is still little studied for many species due to variations in ability to distinguish colours. Common marmosets make an interesting model of study because al…
The Impact of Puzzle Feeders, Ice-Pops and Artificial Seaweed on Captive Harbour Seals (Phoca vitulina) Behaviour Open
Environmental enrichment is used in zoos and aquaria to improve animal welfare through the stimulation of naturalistic behaviours and reduction of stereotypic behaviours. This study investigated the impact of new enrichment items on the be…
The regulatory architecture of gene expression variation in <i>C. elegans</i> revealed by multi-strain allele-specific analysis Open
An outstanding question in the evolution of gene expression is the composition of the underlying regulatory architecture and the processes that shape it. Mutations affecting a gene’s expression may reside locally in cis or distally in tran…
A web application for gene-based queries of CaeNDR RNA-seq data Open
Variation in gene expression is a feature of all living systems and has recently been characterized extensively among wild strains of the model organism Caenorhabditis elegans. To enable researchers to query gene expression and gene expres…
Diversification of small RNA pathways underlies germline RNA interference incompetence in wild <i>Caenorhabditis elegans</i> strains Open
The discovery that experimental delivery of dsRNA can induce gene silencing at target genes revolutionized genetics research, by both uncovering essential biological processes and creating new tools for developmental geneticists. However, …
Generating multiple stage-matched C. elegans hybrids and parental strains simultaneously v1 Open
Here we provide a protocol for generating RNA from synchronized C. elegans F1s from crosses of multiple wild strains to a common reference strain (for example, for allele specific expression analysis). This protocol, which comprises 9 sequ…
Beyond the reference: gene expression variation and transcriptional response to RNA interference in <i>Caenorhabditis elegans</i> Open
Though natural systems harbor genetic and phenotypic variation, research in model organisms is often restricted to a reference strain. Focusing on a reference strain yields a great depth of knowledge but potentially at the cost of breadth …
Beyond the reference: gene expression variation and transcriptional response to RNAi in <i>C. elegans</i> Open
A universal feature of living systems is that natural variation in genotype underpins variation in phenotype. Yet, research in model organisms is often constrained to a single genetic background, the reference strain. Further, genomic stud…
Supplemental data files: Beyond the reference: gene expression variation and transcriptional response to RNAi in C. elegans Open
This dataset holds all non-GEO-hosted supplemental data files for manuscript "Beyond the reference: gene expression variation and transcriptional response to RNAi in C. elegans". Please see the linked preprint/publication for full details.…
Supplemental data files: Beyond the reference: gene expression variation and transcriptional response to RNAi in C. elegans Open
This dataset holds all non-GEO-hosted supplemental data files for manuscript "Beyond the reference: gene expression variation and transcriptional response to RNAi in C. elegans". Please see the linked preprint/publication for full details.…
A method for low-coverage single-gamete sequence analysis demonstrates adherence to Mendel’s first law across a large sample of human sperm Open
Recently published single-cell sequencing data from individual human sperm ( n =41,189; 969–3377 cells from each of 25 donors) offer an opportunity to investigate questions of inheritance with improved statistical power, but require new me…
Author response: A method for low-coverage single-gamete sequence analysis demonstrates adherence to Mendel’s first law across a large sample of human sperm Open
Article Figures and data Abstract Editor's evaluation eLife digest Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract Recently …
Strict adherence to Mendel’s First Law across a large sample of human sperm genomes Open
Mendel’s Law of Segregation states that the offspring of a diploid, heterozygous parent will inherit either allele with equal probability. While the vast majority of loci adhere to this rule, research in model and non-model organisms has u…
Diversification of small RNA pathways underlies germline RNAi incompetence in wild <i>C. elegans</i> strains Open
The discovery that experimental delivery of dsRNA can induce gene silencing at target genes revolutionized genetics research, by both uncovering essential biological processes and creating new tools for developmental geneticists. However, …
Data and analysis script, reply to Matters Arising, Insights into variation in meiosis from 31,228 human sperm genomes Open
Data and scripts accompanying reply to Veller et al. Matters Arising concerning Bell et al 2020 "Insights into variation in meiosis from 31,228 human sperm genomes" Please refer to the readme.txt file for complete details! The script spseq…
Data and analysis script, reply to Matters Arising, Insights into variation in meiosis from 31,228 human sperm genomes Open
Data and scripts accompanying reply to Veller et al. Matters Arising concerning Bell et al 2020 "Insights into variation in meiosis from 31,228 human sperm genomes" Please refer to the readme.txt file for complete details! The script spseq…
Sperm-seq wet lab protocol: sperm preparation and droplet-based sequencing library generation Open
Sperm-seq is a high-throughput, droplet-based single-sperm sequencing technology capable of generating thousands of cell-barcoded single-sperm sequencing libraries at one time. This protocol describes Sperm-seq library generation, featurin…
Insights about variation in meiosis from tens of thousands of human sperm genomes Open
Meiosis is the specialized cell division that creates sperm and egg cells, and so is critical for reproduction. Even so, meiotic processes and outcomes are highly variable. For example, crossover rates and locations vary among individual h…
Insights about variation in meiosis from 31,228 human sperm genomes Open
Meiosis, while critical for reproduction, is also highly variable and error prone: crossover rates vary among humans and individual gametes, and chromosome nondisjunction leads to aneuploidy, a leading cause of miscarriage. To study variat…
Recombination and aneuploidy data for: Insights about variation in meiosis from 31,228 human sperm genomes Open
This repository holds crossover and aneuploidy data for 31,228 human sperm genomes sequenced with Sperm-seq. Data are described in the preprint/paper "Insights about variation in meiosis from 31,228 human sperm genomes." Several levels of …
Recombination and aneuploidy data for: Insights about variation in meiosis from 31,228 human sperm genomes Open
This repository holds crossover and aneuploidy data for 31,228 human sperm genomes sequenced with Sperm-seq. Data are described in the preprint/paper "Insights about variation in meiosis from 31,228 human sperm genomes." Several levels of …
Recombination and aneuploidy data for: Insights about variation in meiosis from 31,228 human sperm genomes Open
This repository holds crossover and aneuploidy data for 31,228 human sperm genomes sequenced with Sperm-seq. Data are described in the preprint/paper "Insights about variation in meiosis from 31,228 human sperm genomes." Several levels of …
Analysis scripts for: Insights about variation in meiosis from 31,228 human sperm genomes Open
This repository holds scripts that call crossovers, determine ploidy, and perform various other analyses for data generated via Sperm-seq. The methods from the preprint/paper ("Insights about variation in meiosis from 31,228 human sperm ge…
Curated compendium of human transcriptional biomarker data Open
Genome-wide transcriptional profiles provide broad insights into cellular activity. One important use of such data isto identify relationships between transcription levels and patient outcomes. These translational insights can guide the de…