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Currently indexing 48,092 bioRxiv papers from 215,637 authors.

Most tweeted bioRxiv papers, last 24 hours

Results 1 through 20 out of 390


1: Intelligible speech synthesis from neural decoding of spoken sentences

Gopala K Anumanchipalli, Josh Chartier et al.

280 tweets (posted 29 Nov 2018) neuroscience

The ability to read out, or decode, mental content from brain activity has significant practical and scientific implications. For example, technology that translates cortical activity into speech would be transformative for people unable to communicate as a result of neurological impairment. Decoding speech from neural activity is challenging because speaking requires extremely precise and dynamic control of multiple vocal tract articulators on the order of milliseconds. Here, we designed a neural decoder that explicitly leverages the continuous kinematic and sound representations encoded in cortical activity to generate fluent and intelligible speech. A recurrent neural network first decoded vocal tract physiological signals from direct cortical recordings, and then transformed them to acoustic speech output. Robust decoding performance was achieved with as little as 25 minutes of training data. Naive listeners were able to accurately identify these decoded sentences. Additionally, speech decoding was not only effective for audibly produced speech, but also when participants silently mimed speech. These results advance the development of speech neuroprosthetic technology to restore spoken communication in patients with disabling neurological disorders.


2: deSALT: fast and accurate long transcriptomic read alignment with de Bruijn graph-based index

Bo Liu, Yadong Liu et al.

74 tweets (posted 17 Apr 2019) bioinformatics

Long-read RNA sequencing (RNA-Seq) is promising to transcriptomics studies, however, the alignment of the reads is still a fundamental but non-trivial task due to the sequencing errors and complicated gene structures. We propose deSALT, a tailored two-pass long RNA-seq read alignment approach, which constructs graph-based alignment skeletons to sensitively infer exons, and use them to generate spliced reference sequence to produce refined alignments. deSALT addresses several difficult issues, such as small exons, seriou...


3: Whole genome phylogenies reflect long-tailed distributions of recombination rates in many bacterial species

Thomas Sakoparnig, Chris Field et al.

66 tweets (posted 07 Apr 2019) evolutionary biology

Although homologous recombination is accepted to be common in bacteria, so far it has been challenging to accurately quantify its impact on genome evolution within bacterial species. We here introduce methods that use the statistics of single-nucleotide polymorphism (SNP) splits in the core genome alignment of a set of strains to show that, for many bacterial species, recombination dominates genome evolution. Each genomic locus has been overwritten so many times by recombination that it is impossible to reconstruct the ...


4: Neighbor predation linked to natural competence fosters the transfer of large genomic regions in Vibrio cholerae

Noemie Matthey, Sandrine Stutzmann et al.

45 tweets (posted 24 Apr 2019) microbiology

Natural competence for transformation is a primary mode of horizontal gene transfer (HGT). Competent bacteria are able to absorb free DNA from their surroundings and exchange this DNA against pieces of their own genome when sufficiently homologous. And while it is known that transformation contributes to evolution and pathogen emergence in bacteria, there are still questions regarding the general prevalence of non-degraded DNA with sufficient coding capacity. In this context, we previously showed that the naturally comp...


5: Distinct Structural Features of the Lon Protease Drive Conserved Hand-over-Hand Substrate Translocation

Mia Shin, Ananya Asmita et al.

44 tweets (posted 24 Apr 2019) molecular biology

Hand-over-hand translocation is emerging as the conserved mechanism by which ATP hydrolysis drives substrate translocation within the classical clade of AAA+ proteins. However, the operating principles of the distantly related HCLR clade, which includes the important quality control protease Lon, remains poorly defined. We determined a cryo-electron microscopy structure of Y. pestis Lon trapped in the act of processing substrate. This structure revealed that sequential ATP hydrolysis and hand-over-hand substrate translo...


6: Population imaging of neural activity in awake behaving mice in multiple brain regions

Kiryl D. Piatkevich, Seth Bensussen et al.

36 tweets (posted 23 Apr 2019) neuroscience

A longstanding goal in neuroscience has been to image membrane voltage, with high temporal precision and sensitivity, in awake behaving mammals. Here, we report a genetically encoded voltage indicator, SomArchon, which exhibits millisecond response times and compatibility with optogenetic control, and which increases the sensitivity, signal-to-noise ratio, and number of neurons observable, by manyfold over previous reagents. SomArchon only requires conventional one-photon microscopy to achieve these high performance cha...


7: Targeting the trypanosome kinetochore with CLK1 protein kinase inhibitors

Manuel Saldivia, Srinivasa P.S. Rao et al.

32 tweets (posted 24 Apr 2019) microbiology

The kinetochore is a macromolecular structure that assembles on the centromeres of chromosomes and provides the major attachment point for spindle microtubules during mitosis. In Trypanosoma brucei the proteins that make up the kinetochore are highly divergent, with the inner kinetochore comprising at least 20 distinct and essential proteins (KKT1-20) that include four protein kinases, CLK1 (KKT10), CLK2 (KKT19), KKT2 and KKT3. We performed a phenotypic screen of T. brucei bloodstream forms with a Novartis kinase-focuse...


8: Recovery of trait heritability from whole genome sequence data

Pierrick Wainschtein, Deepti P Jain et al.

30 tweets (posted 25 Mar 2019) genetics

Heritability, the proportion of phenotypic variance explained by genetic factors, can be estimated from pedigree data, but such estimates are uninformative with respect to the underlying genetic architecture. Analyses of data from genome-wide association studies (GWAS) on unrelated individuals have shown that for human traits and disease, approximately one-third to two-thirds of heritability is captured by common SNPs. It is not known whether the remaining heritability is due to the imperfect tagging of causal variants ...


9: A phenome-wide association and Mendelian Randomisation study of polygenic risk for depression in UK Biobank

Xueyi Shen, David M. Howard et al.

29 tweets (posted 24 Apr 2019) genetics

Depression is the leading cause of worldwide disability but there remains considerable uncertainty regarding its neural and behavioural associations. Depression is known to be heritable with a polygenic architecture, and results from genome-wide associations studies are providing summary statistics with increasing polygenic signal that can be used to estimate genetic risk scores for prediction in independent samples. This provides a timely opportunity to identify traits that are associated with polygenic risk of depress...


10: recount-brain: a curated repository of human brain RNA-seq datasets metadata

Ashkaun Razmara, Shannon E Ellis et al.

27 tweets (posted 24 Apr 2019) genomics

The usability of publicly-available gene expression data is often limited by the availability of high-quality, standardized biological phenotype and experimental condition information ("metadata"). We released the recount2 project, which involved re-processing ~70,000 samples in the Sequencing Read Archive (SRA), Genotype-Tissue Expression (GTEx), and The Cancer Genome Atlas (TCGA) projects. While samples from the latter two projects are well-characterized with extensive metadata, the ~50,000 RNA-seq samples from SRA in...


11: Investigating the role of behaviour in the genetic risk for schizophrenia

Jessye Maxwell, Adam Socrates et al.

25 tweets (posted 18 Apr 2019) genetics

The notion that behaviour may be on a causal path from genetics to psychiatric disorders, such as schizophrenia, highlights a potential for practical interventions. Motivated by this, we test the association between schizophrenia (SCZ) polygenic risk scores (PRS) and 420 behavioural traits (personality, psychological, lifestyle, nutritional) in a psychiatrically healthy sub-cohort of the UK Biobank. Higher schizophrenia PRS was associated with a range of traits, including lower verbal-numerical reasoning (P = 6x10-61), ...



Michael Skocik, John Collins et al.

23 tweets (posted 03 Oct 2016) neuroscience

Machine learning is a powerful set of techniques that has enhanced the abilities of neuroscientists to interpret information collected through EEG, fMRI, MEG, and PET data. With these new techniques come new dangers of overfitting that are not well understood by the neuroscience community. In this article, we use Support Vector Machine (SVM) classifiers, and genetic algorithms to demonstrate the ease by which overfitting can occur, despite the use of cross validation. We demonstrate that comparable and non-generalizable...


13: Reconstructing the transcriptional ontogeny of maize and sorghum supports an inverse hourglass model of inflorescence development

Samuel Leiboff, Sarah Hake

22 tweets (posted 23 Apr 2019) plant biology

Assembling meaningful comparisons between species is a major limitation in studying the evolution of organismal form. To understand development in maize and sorghum, closely-related species with architecturally distinct inflorescences, we collected RNAseq profiles encompassing inflorescence body plan specification in both species. We reconstructed molecular ontogenies from 40 B73 maize tassels and 47 BTx623 sorghum panicles and separated them into transcriptional stages. To discover new markers of inflorescence developm...


14: The Community Simulator: A Python package for microbial ecology

Robert Marsland, Wenping Cui et al.

20 tweets (posted 22 Apr 2019) ecology

Natural microbial communities contain hundreds to thousands of interacting species. For this reason, computational simulations are playing an increasingly important role in microbial ecology. In this manuscript, we present a new open-source, freely available Python package called Community Simulator for simulating microbial population dynamics in a reproducible, transparent and scalable way. The package includes five major elements: tools for preparing the initial states and environmental conditions for a set of samples...


15: ELIMAKI locus is required for mechanosensing and proprioception in birch trees

Juan Alonso Serra, Xueping Shi et al.

19 tweets (posted 24 Apr 2019) plant biology

The remarkable vertical and radial growth observed in tree species, encompasses a major physical challenge for wood forming tissues. To compensate with increasing size and weight, cambium-derived radial growth increases the stem width, thereby supporting the aerial body of trees. This feedback appears to be part of a so-called 'proprioception' (1, 2) mechanism that controls plant size and biomass allocation. Yet, how trees experience or respond to mechanical stress derived from their own vertical loading, remains unknow...


16: Neo-sex chromosomes and demography shape genetic diversity in the Critically Endangered Raso lark

Elisa G Dierickx, Simon Yung Wa Sin et al.

19 tweets (posted 24 Apr 2019) genomics

Generally small effective population sizes expose island species to inbreeding and loss of genetic variation. The Raso lark has been restricted to a single islet for ~500 years, with a population size of a few hundred. To investigate the factors shaping genetic diversity in the species, we assembled a reference genome for the related Eurasian skylark and then assessed genomic diversity and demographic history using RAD-seq data (26 Raso lark samples and 52 samples from its two most closely related mainland species). Gen...


17: The identification of temporal communities through trajectory clustering correlates with single-trial behavioural fluctuations in neuroimaging data

William Hedley Thompson, Jessey Wright et al.

18 tweets (posted 23 Apr 2019) neuroscience

Interacting sets of nodes and fluctuations in their interaction are important properties of a dynamic network system. In some cases the edges reflecting these interactions are directly quantifiable from the data collected, however in many cases (such as functional magnetic resonance imaging (fMRI) data) the edges must be inferred from statistical relations between the nodes. Here we present a new method, called temporal communities by trajectory clustering (TCTC), that derives time-varying communities directly from time...


18: An antisense oligonucleotide leads to suppressed transcriptional elongation of Hdac2 and long-term memory enhancement

Celeste B Greer, Shane Poplawski et al.

18 tweets (posted 24 Apr 2019) pharmacology and toxicology

The memory suppressor gene histone deacetylase 2 (Hdac2) is a target of small molecule inhibitors under investigation for their effects on cognitive enhancement and treating disorders of memory. The therapeutic compounds currently available are not completely specific to the Hdac2 isoform, and have short half-lives. Antisense oligonucleotides (ASOs) are FDA-approved to treat several diseases. They are a class of drugs that base pair with their target RNA and their effects are extremely long lasting compared to small mol...


19: HAMAP rules as SPARQL - A portable annotation pipeline for genomes and proteomes

Jerven Bolleman, Edouard de Castro et al.

17 tweets (posted 24 Apr 2019) bioinformatics

Motivation: Genome and proteome annotation pipelines are generally custom built and therefore not easily reusable by other groups, which leads to duplication of effort, increased costs, and suboptimal results. One cost-effective way to increase the data quality in public databases is to encourage the adoption of annotation standards and technological solutions that enable the sharing of biological knowledge and tools for genome and proteome annotation. Results: We have translated the rules of our HAMAP proteome annotati...


20: Statistical modeling, estimation, and remediation of sample index hopping in multiplexed droplet-based single-cell RNA-seq data

Rick Farouni, Hamed S Najafabadi

17 tweets (posted 24 Apr 2019) bioinformatics

Sample index hopping can substantially confound the analysis of multiplexed sequencing data due to the resulting erroneous assignment of some, or even all, of the sequencing reads generated by a cDNA fragment in a given sample to other samples. In those target samples, the data cross-contamination artifact takes the form of phantom molecules, molecules that exist only in the data by virtue of read misassignment. Phantom molecules should be a cause of great concern in droplet-based single cell RNA-seq experiments since t...