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Currently indexing 42,904 bioRxiv papers from 193,370 authors.

Most tweeted bioRxiv papers, last 24 hours

Results 1 through 20 out of 258


1: A method for genome-wide genealogy estimation for thousands of samples

Leo Speidel, Marie Forest et al.

78 tweets (posted 14 Feb 2019) genetics

Knowledge of genome-wide genealogies for thousands of individuals would simplify most evolutionary analyses for humans and other species, but has remained computationally infeasible. We developed a method, Relate, scaling to > 10,000 sequences while simultaneously estimating branch lengths, mutational ages, and variable historical population sizes, as well as allowing for data errors. Application to 1000 Genomes Project haplotypes produces joint genealogical histories for 26 human populations. Highly diverged lineages are present in all groups, but most frequent in Africa. Outside Africa, these mainly reflect ancient introgression from groups related to Neanderthals and Denisovans, while African signals instead reflect unknown events, unique to that continent. Our approach allows more powerful inferences of natural selection than previously possible. We identify multiple novel regions under strong positive selection, and multi-allelic traits including hair colour, BMI, and blood pressure, showing strong evidence of directional selection, varying among human groups.


2: Ohana: detecting selection in multiple populations by modelling ancestral admixture components

Jade Yu Cheng, Fernando Racimo et al.

72 tweets (posted 14 Feb 2019) bioinformatics

One of the most powerful and commonly used methods for detecting local adaptation in the genome is the identification of extreme allele frequency differences between populations. In this paper, we present a new maximum likelihood method for finding regions under positive selection. The method is based on a Gaussian approximation to allele frequency changes and it incorporates admixture between populations. The method can analyze multiple populations simultaneously and retains power to detect selection signatures specifi...


3: Global Signal Regression Strengthens Association between Resting-State Functional Connectivity and Behavior

Jingwei Li, Ru Kong et al.

64 tweets (posted 13 Feb 2019) neuroscience

Global signal regression (GSR) is one of the most debated preprocessing strategies for resting-state functional MRI. GSR effectively removes global artifacts driven by motion and respiration, but also discards globally distributed neural information and introduces negative correlations between certain brain regions. The vast majority of previous studies have focused on the effectiveness of GSR in removing imaging artifacts, as well as its potential biases. Given the growing interest in functional connectivity fingerprin...


4: Novel Algorithms for the Taxonomic Classification of Metagenomic Linked Reads

David C. Danko, Dmitry Meleshko et al.

33 tweets (posted 14 Feb 2019) bioinformatics

We present KrakenLinked, a metagenomic read classifier for Linked-Reads. We have formulated two algorithms for read classification of metagenomic samples using linked reads: tree pruning and taxa promotion. Tree pruning improves specificity while taxa promotion improves sensitivity. Used together the algorithms improve the taxonomic classification of linked-reads compared to short reads, particularly reducing false identification of taxa. We have implemented these algorithms as functions in KrakenUniq which we make avai...


5: EpiMethylTag simultaneously detects ATAC-seq or ChIP-seq signals with DNA methylation

Priscillia Lhoumaud, Gunjan Sethia et al.

30 tweets (posted 14 Feb 2019) genomics

Activation of regulatory elements is thought to be inversely correlated with DNA methylation levels. However, it is difficult to determine whether DNA methylation is compatible with chromatin accessibility or transcription factor (TF) binding if assays are performed separately. We developed a low input, low sequencing depth method, EpiMethylTag that combines ATAC-seq or ChIP-seq (M-ATAC or M-ChIP) with bisulfite conversion, to simultaneously examine accessibility/TF binding and methylation on the same DNA.


6: The genomic basis of mood instability: identification of 46 loci in 363,705 UK Biobank participants, genetic correlation with psychiatric disorders, and association with gene expression and function.

Joey Ward, Elizabeth M. Tunbridge et al.

22 tweets (posted 14 Feb 2019) genetics

Genome-wide association studies (GWAS) of psychiatric phenotypes have tended to focus on categorical diagnoses, but to understand the biology of mental illness it may be more useful to study traits which cut across traditional boundaries. Here we report the results of a GWAS of mood instability (MI) as a trait in a large population cohort (UK Biobank, n=363,705). We also assess the clinical and biological relevance of the findings, including whether genetic associations show enrichment for nervous system pathways. Forty...



Aurelien Roux, Jean Gruenberg et al.

19 tweets (posted 14 Feb 2019) cell biology

Plasma membrane tension strongly affects cell surface processes, such as migration, endocytosis and signalling. However, it is not known whether membrane tension of organelles regulates their functions, notably intracellular traffic. The ESCRT-III complex is the major membrane remodelling complex that drives Intra-Lumenal Vesicle (ILV) formation on endosomal membranes. Here, we made use of a new fluorescent membrane tension probe to show that ESCRT-III subunits are recruited onto endosomal membranes when membrane tensio...


8: Unmatched level of molecular convergence among deeply divergent complex multicellular fungi

Zsolt Merenyi, Arun N Prasanna et al.

18 tweets (posted 14 Feb 2019) evolutionary biology

Convergent evolution is pervasive in nature, but it is poorly understood how various constraints and natural selection limit the diversity of evolvable phenotypes. Here, we report that, despite >650 million years of divergence, the same genes have repeatedly been co-opted for the development of complex multicellularity in the two largest clades of fungi-the Ascomycota and Basidiomycota. Co-opted genes have undergone duplications in both clades, resulting in >81% convergence across shared multicellularity-related familie...


9: Bayesian Estimation of Species Divergence Times Using Correlated Quantitative Characters

Sandra Alvarez-Carretero, Anjali Goswami et al.

17 tweets (posted 11 Oct 2018) evolutionary biology

Discrete morphological data have been widely used to study species evolution, but the use of quantitative (or continuous) morphological characters is less common. Here, we implement a Bayesian method to estimate species divergence times using quantitative characters. Quantitative character evolution is modelled using Brownian diffusion with character correlation and character variation within populations. Through simulations, we demonstrate that ignoring the population variation (or population "noise") and the correlati...


10: Principles of Meiotic Chromosome Assembly

Stephanie A Schalbetter, Geoffrey Fudenberg et al.

15 tweets (posted 13 Oct 2018) molecular biology

During meiotic prophase, chromosomes organise into a series of chromatin loops emanating from a proteinaceous axis, but the mechanisms of assembly remain unclear. Here we elucidate how this elaborate three-dimensional chromosome organisation is underpinned by genomic sequence in Saccharomyces cerevisiae. Entering meiosis, strong cohesin-dependent grid-like Hi-C interaction patterns emerge, reminiscent of mammalian interphase organisation, but with distinct regulation. Meiotic patterns agree with simulations of loop extr...


11: Cannabis use, depression and self-harm: phenotypic and genetic relationships

Karen Hodgson, Jonathan Coleman et al.

14 tweets (posted 14 Feb 2019) genetics

Background and Aims: The use of cannabis has previously been linked to both depression and self-harm, however the role of genetics in this relationship are unclear. We aimed to examine the phenotypic and genetic relationships between these traits. Design: Genetic and cross-sectional phenotypic data collected through UK Biobank, together with consortia genome-wide association study summary statistics. These data were used to assess the phenotypic and genetic relationship between cannabis use, depression and self harm. Se...


12: Exercise twice-a-day potentiates skeletal muscle signalling responses associated with mitochondrial biogenesis in humans, which are independent of lowered muscle glycogen content

Victor Amorim Andrade-Souza, Thaysa Ghiarone et al.

11 tweets (posted 12 Feb 2019) molecular biology

Endurance exercise begun with reduced muscle glycogen stores seems to potentiate skeletal muscle protein abundance and gene expression. However, it is unknown whether this greater signalling responses is due to low muscle glycogen per se or to performing two exercise sessions in close proximity - as a first exercise session is necessary to reduce the muscle glycogen stores. In the present study, we manipulated the recovery duration between a first muscle glycogen-depleting exercise and a second exercise session, such th...


13: SCANVIS: a tool for SCoring, ANnotating and VISualing splice junctions

Phaedra Agius, Heather Geiger et al.

11 tweets (posted 14 Feb 2019) bioinformatics

The association of splicing signatures with disease is a leading area of study for prognosis, diagnosis and therapy, frequently requiring detailed analysis of splicing events across multiple samples. We present a novel fast-performing annotation-dependent tool called SCANVIS for scoring and annotating splice junctions by gene name, junction type and any frame shifts incurred. SCANVIS has a novel and fast visualization technique that distinguishes annotated splice junctions from unannotated ones in the context of nearby ...


14: Speed, accuracy, sensitivity and quality control choices for detecting clinically relevant microbes in whole blood from patients.

James Eric Thornton, George S. Watts et al.

11 tweets (posted 14 Feb 2019) bioinformatics

Infections are a serious health concern worldwide, particularly in vulnerable populations such as the immunocompromised, elderly, and young. Advances in metagenomic sequencing availability, speed, and decreased cost offer the opportunity to supplement or replace culture-based identification of pathogens with DNA sequence-based diagnostics. Adopting metagenomic analysis for clinical use requires that all aspects of the pipeline are optimized and tested, including data analysis. We tested the accuracy, sensitivity, and re...


15: Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues

Adam K Glaser, Nicholas P. Reder et al.

11 tweets (posted 13 Feb 2019) bioengineering

Recent advances in optical clearing and light-sheet microscopy have provided unprecedented access to structural and molecular information from intact tissues. However, current light-sheet microscopes have imposed constraints on the size, shape, number of specimens, and compatibility with various clearing protocols. Here we present a multi-immersion open-top light-sheet microscope that enables simple mounting of multiple specimens processed with a variety of protocols, which will facilitate wider adoption by preclinical ...


16: Potato genotypes differentially alter the expression of Phytophthora infestans effectors during PAMP-mediated resistance induction

Cecile Monique THOMAS, Pauline LE BOULCH et al.

10 tweets (posted 14 Feb 2019) plant biology

Pathogen recognition by plants via pathogen-associated molecular patterns leads to PAMP-triggered immunity. However, pathogens can modulate it via the secretion of effectors. We hypothesize that in potato, induced defense triggered by a Phytophthora infestans concentrated culture filtrate (CCF) could alter both effector expression and disease severity. CCF was sprayed onto three potato genotypes with different resistance levels, before inoculation with P. infestans. Symptoms were scored visually at 1-4 dpi, while the ex...


17: mRNA structure regulates protein expression through changes in functional half-life

David M. Mauger, B. Joseph Cabral et al.

10 tweets (posted 13 Feb 2019) molecular biology

Messenger RNAs (mRNAs) encode information in both their primary sequence and their higher order structure. The independent contributions of factors like codon usage and secondary structure to regulating protein expression are difficult to establish as they are often highly correlated in endogenous sequences. Here, we used two approaches, global inclusion of modified nucleotides and rational sequence design of exogenously delivered constructs to understand the role of mRNA secondary structure independent from codon usage...


18: Ecological Representations

Sabrina Golonka, Andrew D Wilson

10 tweets (posted 15 Jun 2016) animal behavior and cognition

Mainstream cognitive science and neuroscience both rely heavily on the notion of representation in order to explain the full range of our behavioral repertoire. The relevant feature of representation is its ability to designate (stand in for) spatially or temporally distant properties, When we organize our behavior with respect to mental or neural representations, we are (in principle) organizing our behavior with respect to the property it designates. While representational theories are a potentially a powerful foundat...


19: Unpacking conditional neutrality: genomic signatures of selection on conditionally beneficial and conditionally deleterious mutations

Jonathan A Mee, Sam Yeaman

9 tweets (posted 13 Feb 2019) evolutionary biology

It is common to look for signatures of local adaptation in genomes by identifying loci with extreme levels of allele frequency divergence among populations. This approach to finding genes associated with local adaptation often assumes antagonistic pleiotropy, wherein alternative alleles are strongly favoured in alternative environments. Conditional neutrality has been proposed as an alternative to antagonistic pleiotropy, but conditionally neutral polymorphisms are transient and it is unclear how much outlier signal wou...


20: Detection of Base Analogs Incorporated During DNA Replication by Nanopore Sequencing

Daniela Georgieva, Qian Liu et al.

9 tweets (posted 14 Feb 2019) genomics

DNA synthesis is a fundamental requirement for cell proliferation and DNA repair, but no tools exist to identify the location, direction and speed of replication forks with base pair resolution. Mammalian cells have the ability to incorporate thymidine analogs along with the natural A, T, G and C bases during DNA synthesis, which allows for labelling of replicating or repaired DNA. Most sequencing platforms rely on base-pairing to identify the four canonical nucleotides, and are thus unable to distinguish them from thes...