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Currently indexing 57,506 bioRxiv papers from 264,779 authors.

Most downloaded bioRxiv papers, since beginning of last month

Results 541 through 560 out of 56141


541: The Evolutionary History of Common Genetic Variants Influencing Human Cortical Surface Area

Amanda L Tilot, Ekaterina A. Khramtsova et al.

315 downloads (posted 16 Jul 2019) neuroscience

Structural brain changes along the lineage that led to modern Homo sapiens have contributed to our unique cognitive and social abilities. However, the evolutionarily relevant molecular variants impacting key aspects of neuroanatomy are largely unknown. Here, we integrate evolutionary annotations of the genome at diverse timescales with common variant associations from large-scale neuroimaging genetic screens in living humans, to reveal how selective pressures have shaped neocortical surface area. We show that variation within human gained enhancers active in the developing brain is associated with global surface area as well as that of specific regions. Moreover, we find evidence of recent polygenic selection over the past 2,000 years influencing surface area of multiple cortical regions, including those involved in spoken language and visual processing.


542: A theory of learning to infer

Ishita Dasgupta, Eric Schulz et al.

315 downloads (posted 20 May 2019) animal behavior and cognition

Bayesian theories of cognition assume that people can integrate probabilities rationally. However, several empirical findings contradict this proposition: human probabilistic inferences are prone to systematic deviations from optimality. Puzzlingly, these deviations sometimes go in opposite directions. Whereas some studies suggest that people under-react to prior probabilities (base rate neglect), other studies find that people under-react to the likelihood of the data (conservatism). We argue that these deviations aris...


543: Mozambican genetic variation provides new insights into the Bantu expansion

Armando Semo, Magdalena Gayà-Vidal et al.

314 downloads (posted 10 Jul 2019) genetics

The Bantu expansion, which started in West Central Africa around 5,000 BP, constitutes a major migratory movement involving the joint spread of peoples and languages across sub-Saharan Africa. Despite the rich linguistic and archaeological evidence available, the genetic relationships between different Bantu-speaking populations and the migratory routes they followed during various phases of the expansion remain poorly understood. Here, we analyze the genetic profiles of southwestern and southeastern Bantu-speaking peop...


544: Autocatalytic chemical networks preceded proteins and RNA in evolution

Joana C. Xavier, Wim Hordijk et al.

314 downloads (posted 05 Jul 2019) evolutionary biology

Modern cells embody metabolic networks containing thousands of elements and form autocatalytic molecule sets that produce copies of themselves. How the first self-sustaining metabolic networks arose at life's origin is a major open question. Autocatalytic molecule sets smaller than metabolic networks were proposed as transitory intermediates at the origin of life, but evidence for their role in prebiotic evolution is lacking. Here we identify reflexively autocatalytic food-generated networks (RAFs) - self-sustaining net...


545: Segmentation-Enhanced CycleGAN

Michal Januszewski, Viren Jain

314 downloads (posted 13 Feb 2019) neuroscience

Algorithmic reconstruction of neurons from volume electron microscopy data traditionally requires training machine learning models on dataset-specific ground truth annotations that are expensive and tedious to acquire. We enhanced the training procedure of an unsupervised image-to-image translation method with additional components derived from an automated neuron segmentation approach. We show that this method, Segmentation-Enhanced CycleGAN (SECGAN), enables near perfect reconstruction accuracy on a benchmark connecto...


546: First detection of Infectious Spleen and kidney Necrosis Virus (ISKNV) associated with massive mortalities in farmed tilapia in Africa

Gustavo Ramires, Richard K. Paley et al.

313 downloads (posted 08 Jul 2019) microbiology

In late 2018, unusual patterns of very high mortality (>50% production) were reported in intensive tilapia cage culture systems across Lake Volta. Affected fish showed darkening, erratic swimming and abdominal distension with associated ascites. Histopathological observations of tissues taken from moribund fish at different farms revealed the presence of lesions indicative of viral infection. These included haematopoietic cell nuclear and cytoplasmic pleomorphism with marginalisation of chromatin and fine granulation. T...


547: scAEspy: a unifying tool based on autoencoders for the analysis of single-cell RNA sequencing data

Andrea Tangherloni, Federico Ricciuti et al.

313 downloads (posted 07 Aug 2019) bioinformatics

Autoencoders (AEs) have been effectively used to capture the non-linearities among gene interactions of single-cell RNA sequencing (scRNA-Seq) data. However, their integration with the common scRNA-Seq bioinformatics pipelines still poses a challenge. Here, we introduce scAEspy, a unifying tool that embodies five of the most advanced AEs and different loss functions, including two novel AEs that we developed. scAEspy allows the integration of data generated using different scRNA-Seq platforms. We benchmarked scAEspy aga...


548: Aging-related inflammation driven by cellular senescence enhances NAD consumption via activation of CD38+ macrophages

Anthony Joseph Covarrubias, Abhijit Kale et al.

312 downloads (posted 17 Apr 2019) immunology

Decline in tissue NAD levels during aging has been linked to aging-associated diseases, such as age-related metabolic disease, physical decline, and Alzheimer's disease. However, the mechanism for aging-associated NAD decline remains unclear. Here we report that pro-inflammatory M1 macrophages, but not naive or M2 macrophages, highly express the NAD consuming enzyme CD38 and have enhanced CD38-dependent NADase activity. Furthermore, we show that aging is associated with enhanced inflammation due to increased senescent c...


549: 3D Chromatin Architecture Remodeling during Human Cardiomyocyte Differentiation Reveals A Role Of HERV-H In Demarcating Chromatin Domains

Yanxiao Zhang, Ting Li et al.

312 downloads (posted 04 Dec 2018) genomics

Dynamic restructuring of chromatin architecture has been implicated in cell-type specific gene regulatory programs; yet, how chromatin remodels during lineage specification remains to be elucidated. Through interrogating chromatin reorganization during human cardiomyocyte differentiation, we uncover dynamic chromatin interactions between genes and distal regulatory elements harboring noncoding variants associated with adult and congenital heart diseases. Unexpectedly, we also discover a new class of human pluripotent st...


550: Improved single-cell ATAC-seq reveals chromatin dynamics of in vitro corticogenesis

Ryan M Mulqueen, Brooke A DeRosa et al.

312 downloads (posted 15 May 2019) genomics

Development is a complex process that requires the precise modulation of regulatory gene networks controlled through dynamic changes in the epigenome. Single-cell -omic technologies provide an avenue for understanding the mechanisms of these processes by capturing the progression of epigenetic cell states during the course of cellular differentiation using in vitro or in vivo models. However, current single-cell epigenomic methods are limited in the information garnered per individual cell, which in turn limits their ab...


551: Proteome-wide inference of protein kinase regulatory circuits

Brandon Invergo, Borgthor Petursson et al.

312 downloads (posted 16 Jul 2019) systems biology

Complex networks of regulatory relationships between protein kinases comprise a major component of intracellular signaling. Although many kinase-kinase regulatory relationships have been described in detail, these are biased towards well-studied kinases while the majority of possible relationships remains unexplored. Here, we implement data-driven, unbiased methods to predict human kinase-kinase regulatory relationships and whether they have activating or inhibiting effects. We incorporate high-throughput data, kinase s...


552: nf-core: Community curated bioinformatics pipelines

Philip Ewels, Alexander Peltzer et al.

311 downloads (posted 16 Apr 2019) bioinformatics

The standardization, portability, and reproducibility of analysis pipelines is a renowned problem within the bioinformatics community. Most pipelines are designed for execution on-premise, and the associated software dependencies are tightly coupled with the local compute environment. This leads to poor pipeline portability and reproducibility of the ensuing results - both of which are fundamental requirements for the validation of scientific findings. Here, we introduce nf-core: a framework that provides a community-dr...


553: The immunomodulatory effect of IrSPI, a tick salivary gland serine protease inhibitor involved in Ixodes ricinus tick feeding

Adrien A Blisnick, L. Šimo et al.

311 downloads (posted 17 Jul 2019) animal behavior and cognition

Ticks are strict hematophagous arthropods and are the most important vectors of pathogens affecting both domestic and wild animals worldwide. Moreover, they are second only to mosquitoes as vectors of human pathogens. Hard tick feeding is a slow process—taking up to several days for repletion prior to detachment—and necessitates extended control over the host response. The success of the feeding process depends upon injection of saliva by tick, which not only controls host haemostasis and wound healing, but also subvert...


554: Soil bacterial populations are shaped by recombination and gene-specific selection across a meadow

Alexander Crits-Christoph, Matthew Olm et al.

310 downloads (posted 08 Jul 2019) microbiology

Soil microbial diversity is often studied from the perspective of community composition, but less is known about genetic heterogeneity within species and how population structures are affected by dispersal, recombination, and selection. Genomic inferences about population structure can be made using the millions of sequencing reads that are assembled denovo into consensus genomes from metagenomes, as each read pair describes a short genomic sequence from a cell in the population. Here we track genome-wide population gen...


555: RootNav 2.0: Deep Learning for Automatic Navigation of Complex Plant Root Architectures

Robail Yasrab, Jonathan A. Atkinson et al.

309 downloads (posted 20 Jul 2019) bioinformatics

We present a new image analysis approach that provides fully-automatic extraction of complex root system architectures from a range of plant species in varied imaging setups. Driven by modern deep-learning approaches, RootNav 2.0 replaces previously manual and semi-automatic feature extraction with an extremely deep multi-task Convolutional Neural Network architecture. The network has been designed to explicitly combine local pixel information with global scene information in order to accurately segment small root featu...


556: Cytoplasmic protein granules organize kinase-mediated RAS signaling

Asmin Tulpule, Juan Guan et al.

309 downloads (posted 16 Jul 2019) cancer biology

Understanding how cells spatially organize signaling events is important in normal biology and pathological conditions such as cancer. Here, we uncover a membraneless, protein granule-based subcellular structure that can organize receptor tyrosine kinase (RTK)-mediated RAS/MAPK pathway signaling, which is thought to occur exclusively from lipid-membrane compartments in mammalian cells. De-novo assembly of cytoplasmic protein granules by certain RTKs, including oncogenic gene fusions involving ALK and RET, is dependent o...


557: Cellular dialogues that enable self-organization of dynamic spatial patterns

Yiteng Dang, Douwe Grundel et al.

309 downloads (posted 28 Jul 2019) systems biology

Cells form spatial patterns by coordinating their gene expressions. How a group of mesoscopic numbers (hundreds-to-thousands) of cells, without pre-defined morphogens and spatial organization, self-organizes spatial patterns remains incompletely understood. Of particular importance are dynamic spatial patterns - such as spiral waves that perpetually move and transmit information over macroscopic length-scales. We developed an open-source, expandable software that can simulate a field of cells communicating with any numb...


558: Single cell multi-omics profiling reveals a hierarchical epigenetic landscape during mammalian germ layer specification

Ricard Argelaguet, Hisham Mohammed et al.

309 downloads (posted 13 Jan 2019) developmental biology

Formation of the three primary germ layers during gastrulation is an essential step in the establishment of the vertebrate body plan. Recent studies employing single cell RNA-sequencing have identified major transcriptional changes associated with germ layer specification. Global epigenetic reprogramming accompanies these changes, but the role of the epigenome in regulating early cell fate choice remains unresolved, and the coordination between different epigenetic layers is unclear. Here we describe the first single ce...


559: Characterizing the temporal dynamics of gene expression in single cells with sci-fate

Junyue Cao, Wei Zhou et al.

309 downloads (posted 11 Jun 2019) genomics

Gene expression is a dynamic process on multiple scales, e.g. the cell cycle, response to stimuli, normal differentiation and development, etc. However, nearly all techniques for profiling gene expression in single cells fail to directly capture these temporal dynamics, which limits the scope of biology that can be effectively investigated. Towards addressing this, we developed sci-fate, a new technique that combines S4U labeling of newly synthesized mRNA with single cell combinatorial indexing (sci-), in order to concu...


560: Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe

Rosa Fregel, Fernado L. Mendez et al.

309 downloads (posted 21 Sep 2017) genetics

The extent to which prehistoric migrations of farmers influenced the genetic pool of western North Africans remains unclear. Archaeological evidence suggests the Neolithization process may have happened through the adoption of innovations by local Epipaleolithic communities, or by demic diffusion from the Eastern Mediterranean shores or Iberia. Here, we present the first analysis of individuals' genome sequences from early and late Neolithic sites in Morocco, as well as Early Neolithic individuals from southern Iberia. ...