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Currently indexing 57,822 bioRxiv papers from 266,142 authors.

Most downloaded bioRxiv papers, since beginning of last month

Results 341 through 360 out of 56442


341: Nanopore native RNA sequencing of a human poly(A) transcriptome

Rachael E. Workman, Alison Tang et al.

441 downloads (posted 09 Nov 2018) genomics

High throughput RNA sequencing technologies have dramatically advanced our understanding of transcriptome complexity and regulation. However, these cDNA-based methods lose information contained in biological RNA because the copied reads are short or because modifications are not carried forward in cDNA. Here we address these limitations using a native poly(A) RNA sequencing strategy developed by Oxford Nanopore Technologies (ONT). Our study focused on poly(A) RNA isolated from the human cell line GM12878, from which we sequenced approximately 9.9 million individual aligned strands. These native RNA sequence reads had an N50 length of 1334 bases, and a maximum length of 22,000 bases. A total of 78,199 high-confidence isoforms were identified by combining long nanopore reads with short higher accuracy Illumina reads. Among these isoforms, over 50% are not present in GENCODE v24. We describe strategies for assessing 3'poly(A) tail length, base modifications and transcript haplotypes using this single molecule technology. Together, these nanopore-based techniques are poised to deliver new insights into RNA biology.


342: JBrowse Connect: A server API to connect JBrowse instances and users

Ian Holmes, Robert Buels et al.

440 downloads (posted 11 Jul 2019) bioinformatics

We describe JBrowse Connect, an optional expansion to JBrowse that allows live messaging via WebSockets, notifications for new annotation tracks, heavy-duty analyses initiated by the user from within the browser, and other dynamic features. We present JBlast, an example application of JBrowse Connect that allows users to specify and execute BLAST searches, managed by a Galaxy instance, as well as tracking job progress and viewing results, all in the context of the browser.


343: Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules

Camille Sessegolo, Corinne Cruaud et al.

439 downloads (posted 12 Mar 2019) bioinformatics

Our vision of DNA transcription and splicing has changed dramatically with the introduction of short-read sequencing. These high-throughput sequencing technologies promised to unravel the complexity of any transcriptome. Generally gene expression levels are well-captured using these technologies, but there are still remaining caveats due to the limited read length and the fact that RNA molecules had to be reverse transcribed before sequencing. Oxford Nanopore Technologies has recently launched a portable sequencer which...


344: Recombinase system-dependent copackaging strategy for highly efficient neurocircuit tracing

Pei Sun, Sen Jin et al.

438 downloads (posted 17 Jul 2019) neuroscience

Despite significant progresses in dissecting neural circuits with recombinant adeno-associated viruses (rAAVs), compatible and efficient gene expressions of multiple vectors within the same cell still remains challenging. Here, we developed MAP-ENVIVIDERS, a recombinase system-dependent (including Cre-lox/Flp-FRT recombinase systems) viral copackaging strategy to ameliorate mutual suppression and enhance compatibility among different rAAVs to improve neurocircuit tracing. For neuron labeling with wild-type and Cre-drive...


345: Diabetic Retinopathy detection through integration of Deep Learning classification framework

Alexander Rakhlin

438 downloads (posted 27 Nov 2017) pathology

This document represents a brief account of ongoing project for Diabetic Retinopathy Detection (DRD) through integration of state-of the art Deep Learning methods. We make use of deep Convolutional Neural Networks (CNNs), which have proven revolutionary in multiple fields of computer vision including medical imaging, and we bring their power to the diagnosis of eye fundus images. For training our models we used publicly available Kaggle data set. For testing we used portion of Kaggle data withheld from training and Mess...


346: Variable prediction accuracy of polygenic scores within an ancestry group

Hakhamanesh Mostafavi, Arbel Harpak et al.

438 downloads (posted 07 May 2019) genetics

Fields as diverse as human genetics and sociology are increasingly using polygenic scores based on genome-wide association studies (GWAS) for phenotypic prediction. However, recent work has shown that polygenic scores have limited portability across groups of different genetic ancestries, restricting the contexts in which they can be used reliably and potentially creating serious inequities in future clinical applications. Using the UK Biobank data, we demonstrate that even within a single ancestry group, the prediction...


347: MULTI-seq: Scalable sample multiplexing for single-cell RNA sequencing using lipid-tagged indices

Christopher S McGinnis, David M Patterson et al.

436 downloads (posted 08 Aug 2018) genomics

We describe MULTI-seq: A rapid, modular, and universal scRNA-seq sample multiplexing strategy using lipid-tagged indices. MULTI-seq reagents can barcode any cell type from any species with an accessible plasma membrane. The method is compatible with enzymatic tissue dissociation, and also preserves viability and endogenous gene expression patterns. We leverage these features to multiplex the analysis of multiple solid tissues comprising human and mouse cells isolated from patient-derived xenograft mouse models. We also ...


348: Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images

Juan C Caicedo, Jonathan Roth et al.

436 downloads (posted 31 May 2018) bioinformatics

Identifying nuclei is often a critical first step in analyzing microscopy images of cells, and classical image processing algorithms are most commonly used for this task. Recent developments in deep learning can yield superior accuracy, but typical evaluation metrics for nucleus segmentation do not satisfactorily capture error modes that are relevant in cellular images. We present an evaluation framework to measure accuracy, types of errors, and computational efficiency; and use it to compare deep learning strategies an...


349: Unraveling the polygenic architecture of complex traits using blood eQTL meta-analysis

Urmo V├Ása, Annique Claringbould et al.

435 downloads (posted 19 Oct 2018) genomics

While many disease-associated variants have been identified through genome-wide association studies, their downstream molecular consequences remain unclear. To identify these effects, we performed cis- and trans-expression quantitative trait locus (eQTL) analysis in blood from 31,684 individuals through the eQTLGen Consortium. We observed that cis-eQTLs can be detected for 88% of the studied genes, but that they have a different genetic architecture compared to disease-associated variants, limiting our ability to use ci...


350: Ribosolve: Rapid determination of three-dimensional RNA-only structures

Kalli Kappel, Kaiming Zhang et al.

433 downloads (posted 31 Jul 2019) biophysics

The discovery and design of biologically important RNA molecules is dramatically outpacing three-dimensional structural characterization. To address this challenge, we present Ribosolve, a hybrid method integrating moderate-resolution cryo-EM maps, chemical mapping, and Rosetta computational modeling, and demonstrate its application to thirteen previously unknown 119- to 338-nucleotide protein-free RNA-only structures: full-length Tetrahymena ribozyme, hc16 ligase with and without substrate, full-length V. cholerae and ...


351: Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle

Elias T Friman, Cedric Deluz et al.

432 downloads (posted 11 Jul 2019) genomics

The pioneer activity of transcription factors allows for opening of inaccessible regulatory elements and has been extensively studied in the context of cellular differentiation and reprogramming. In contrast, the function of pioneer activity in self-renewing cell divisions and across the cell cycle is poorly understood. Here we assessed the interplay between OCT4 and SOX2 in controlling chromatin accessibility of mouse embryonic stem cells. We found that OCT4 and SOX2 operate in a largely independent manner even at co-o...


352: DeepC: Predicting chromatin interactions using megabase scaled deep neural networks and transfer learning.

Ron Schwessinger, Matthew Gosden et al.

432 downloads (posted 04 Aug 2019) genomics

Understanding 3D genome structure requires high throughput, genome-wide approaches. However, assays for all vs. all chromatin interaction mapping are expensive and time consuming, which severely restricts their usage for large-scale mutagenesis screens or for mapping the impact of sequence variants. Computational models sophisticated enough to grasp the determinants of chromatin folding provide a unique window into the functional determinants of 3D genome structure as well as the effects of genome variation. A chromatin...


353: Free circular introns with an unusual branchpoint in neuronal projections

Sean R. Eddy, Harleen Saini et al.

431 downloads (posted 30 Apr 2019) cell biology

The polarized structure of axons and dendrites in neuronal cells depends in part on RNA localization. Previous studies have looked at which polyadenylated RNAs are enriched in neuronal projections or at synapses, but less is known about the distribution of non-adenylated RNAs. By physically dissecting projections from cell bodies of primary rat hippocampal neurons and sequencing total RNA, we found an unexpected set of free circular introns with a non-canonical branchpoint enriched in neuronal projections. These introns...


354: Measuring glycolytic flux in single yeast cells with an orthogonal synthetic biosensor

Francisca Monteiro, Georg Hubmann et al.

431 downloads (posted 25 Jun 2019) synthetic biology

Metabolic heterogeneity between individual cells of a population harbors offers significant challenges for fundamental and applied research. Identifying metabolic heterogeneity and investigating its emergence requires tools to zoom into metabolism of individual cells. While methods exist to measure metabolite levels in single cells, we lack capability to measure metabolic flux, i.e. the ultimate functional output of metabolic activity, on the single-cell level. Here, combining promoter engineering, computational protein...


355: scAlign: a tool for alignment, integration and rare cell identification from scRNA-seq data

Nelson Johansen, Gerald Quon

431 downloads (posted 22 Dec 2018) bioinformatics

scRNA-seq dataset integration occurs in different contexts, such as the identification of cell type-specific differences in gene expression across conditions or species, or batch effect correction. We present scAlign, an unsupervised deep learning method for data integration that can incorporate partial, overlapping or a complete set of cell labels, and estimate per-cell differences in gene expression across datasets. scAlign performance is state-of-the-art and robust to cross-dataset variation in cell type-specific exp...


356: Modeling Zero-Inflated Count Data With glmmTMB

Mollie E. Brooks, Kasper Kristensen et al.

431 downloads (posted 01 May 2017) ecology

Ecological phenomena are often measured in the form of count data. These data can be analyzed using generalized linear mixed models (GLMMs) when observations are correlated in ways that require random effects. However, count data are often zero-inflated, containing more zeros than would be expected from the standard error distributions used in GLMMs, e.g., parasite counts may be exactly zero for hosts with effective immune defenses but vary according to a negative binomial distribution for non-resistant hosts. We presen...


357: Humans are primarily model-based and not model-free learners in the two-stage task

Carolina Feher da Silva, Todd A Hare

431 downloads (posted 27 Jun 2019) neuroscience

Distinct model-free and model-based learning processes are thought to drive both typical and dysfunctional behaviors. Data from two-stage decision tasks have seemingly shown that human behavior is driven by both processes operating in parallel. However, in this study, we show that more detailed task instructions lead participants to make primarily model-based choices that show little, if any, model-free influence. We also demonstrate that behavior in the two-stage task may falsely appear to be driven by a combination of...


358: The origin of the Gravettians: genomic evidence from a 36,000-year-old Eastern European

E. Andrew Bennett, Sandrine Prat et al.

430 downloads (posted 28 Jun 2019) genetics

The Gravettian technocomplex was present in Europe from more than 30,000 years ago until the Last Glacial Maximum, but the source of this industry and the people who manufactured it remain unsettled. We use genome-wide analysis of a ~36,000-year-old Eastern European individual (BuranKaya3A) from Buran-Kaya III in Crimea, the earliest documented occurrence of the Gravettian, to investigate relationships between population structures of Upper Palaeolithic Europe and the origin and spread of the culture. We show BuranKaya3...


359: TBtools, a Toolkit for Biologists integrating various biological data handling tools with a user-friendly interface

Chengjie Chen, Rui Xia et al.

430 downloads (posted 27 Mar 2018) bioinformatics

Various softwares or pipelines have been developed for biological information mining from high-throughput sequencing (HTS) data, and most of them relies on programming and command-line environment with which most biologists are unfamiliar. Bioinformatic tools with an user-friendly interface are preferred by wet-lab biologists. Here, we describe TBtools, a Toolkit for Biologists integrating various HTS-data handling tools with a user-friendly interface. It includes a large collection of functions, which facilitate many s...


360: A complete Cannabis chromosome assembly and adaptive admixture for elevated cannabidiol (CBD) content

Christopher J Grassa, Jonathan P Wenger et al.

429 downloads (posted 31 Oct 2018) genomics

Cannabis has been cultivated for millennia with distinct cultivars providing either fiber and grain or tetrahydrocannabinol. Recent demand for cannabidiol rather than tetrahydrocannabinol has favored the breeding of admixed cultivars with extremely high cannabidiol content. Despite several draft Cannabis genomes, the genomic structure of cannabinoid synthase loci has remained elusive. A genetic map derived from a tetrahydrocannabinol/cannabidiol segregating population and a complete chromosome assembly from a high-canna...