Journal: Genome biology
1089
Gene name errors are widespread in the scientific literature
- OPEN
- Genome biology
- Published over 4 years ago
- Discuss
The spreadsheet software Microsoft Excel, when used with default settings, is known to convert gene names to dates and floating-point numbers. A programmatic scan of leading genomics journals reveals that approximately one-fifth of papers with supplementary Excel gene lists contain erroneous gene name conversions.
335
Heritable components of the human fecal microbiome are associated with visceral fat
- OPEN
- Genome biology
- Published over 4 years ago
- Discuss
Variation in the human fecal microbiota has previously been associated with body mass index (BMI). Although obesity is a global health burden, the accumulation of abdominal visceral fat is the specific cardio-metabolic disease risk factor. Here, we explore links between the fecal microbiota and abdominal adiposity using body composition as measured by dual-energy X-ray absorptiometry in a large sample of twins from the TwinsUK cohort, comparing fecal 16S rRNA diversity profiles with six adiposity measures.
333
Repeat-induced point mutation in Neurospora crassa causes the highest known mutation rate and mutational burden of any cellular life
- OPEN
- Genome biology
- Published 10 months ago
- Discuss
Repeat-induced point (RIP) mutation in Neurospora crassa degrades transposable elements by targeting repeats with C→T mutations. Whether RIP affects core genomic sequence in important ways is unknown.
270
A novel multi-tissue RNA diagnostic of healthy ageing relates to cognitive health status
- OPEN
- Genome biology
- Published over 5 years ago
- Discuss
Diagnostics of the human ageing process may help predict future healthcare needs or guide preventative measures for tackling diseases of older age. We take a transcriptomics approach to build the first reproducible multi-tissue RNA expression signature by gene-chip profiling tissue from sedentary normal subjects who reached 65 years of age in good health.
269
When will ‘open science’ become simply ‘science’?
- OPEN
- Genome biology
- Published almost 6 years ago
- Discuss
Open science describes the practice of carrying out scientific research in a completely transparent manner, and making the results of that research available to everyone. Isn’t that just ‘science’?
259
Genetic determination of height-mediated mate choice
- OPEN
- Genome biology
- Published about 5 years ago
- Discuss
Numerous studies have reported positive correlations among couples for height. This suggests that humans find individuals of similar height attractive. However, the answer to whether the choice of a mate with a similar phenotype is genetically or environmentally determined has been elusive.
217
The first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures
- OPEN
- Genome biology
- Published over 5 years ago
- Discuss
The cinereous vulture, Aegypius monachus, is the largest bird of prey and plays a key role in the ecosystem by removing carcasses, thus preventing the spread of diseases. Its feeding habits force it to cope with constant exposure to pathogens, making this species an interesting target for discovering functionally selected genetic variants. Furthermore, the presence of two independently evolved vulture groups, Old World and New World vultures, provides a natural experiment in which to investigate convergent evolution due to obligate scavenging.
202
Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle
- OPEN
- Genome biology
- Published over 5 years ago
- Discuss
Domestication of the now-extinct wild aurochs, Bos primigenius, gave rise to the two major domestic extant cattle taxa, B. taurus and B. indicus. While previous genetic studies have shed some light on the evolutionary relationships between European aurochs and modern cattle, important questions remain unanswered, including the phylogenetic status of aurochs, whether gene flow from aurochs into early domestic populations occurred, and which genomic regions were subject to selection processes during and after domestication. Here, we address these questions using whole-genome sequencing data generated from an approximately 6,750-year-old British aurochs bone and genome sequence data from 81 additional cattle plus genome-wide single nucleotide polymorphism data from a diverse panel of 1,225 modern animals.
200
Eleven grand challenges in single-cell data science
- OPEN
- Genome biology
- Published about 1 year ago
- Discuss
The recent boom in microfluidics and combinatorial indexing strategies, combined with low sequencing costs, has empowered single-cell sequencing technology. Thousands-or even millions-of cells analyzed in a single experiment amount to a data revolution in single-cell biology and pose unique data science problems. Here, we outline eleven challenges that will be central to bringing this emerging field of single-cell data science forward. For each challenge, we highlight motivating research questions, review prior work, and formulate open problems. This compendium is for established researchers, newcomers, and students alike, highlighting interesting and rewarding problems for the coming years.
194
Ancient DNA and the rewriting of human history: be sparing with Occam’s razor
- OPEN
- Genome biology
- Published over 5 years ago
- Discuss
Ancient DNA research is revealing a human history far more complex than that inferred from parsimonious models based on modern DNA. Here, we review some of the key events in the peopling of the world in the light of the findings of work on ancient DNA.