MOTIVATION: Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to each genomic feature, for example to each exon or each gene. The process of counting reads is called read summarization. Read summarization is required for a great variety of genomic analyses but has so far received relatively little attention in the literature. RESULTS: We present featureCounts, a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments. featureCounts implements highly efficient chromosome hashing and feature blocking techniques. It is considerably faster than existing methods (by an order of magnitude for gene-level summarization) and requires far less computer memory. It works with either single or paired-end reads and provides a wide range of options appropriate for different sequencing applications. AVAILABILITY AND IMPLEMENTATION: featureCounts is available under GNU General Public License as part of the Subread (http://subread.sourceforge.net) or Rsubread (http://www.bioconductor.org) software packages.

featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features

Functional analysis of large gene lists, derived in most cases from emerging high-throughput genomic, proteomic and bioinformatics scanning approaches, is still a challenging and daunting task. The gene-annotation enrichment analysis is a promising high-throughput strategy that increases the likelihood for investigators to identify biological processes most pertinent to their study. Approximately 68 bioinformatics enrichment tools that are currently available in the community are collected in this survey. Tools are uniquely categorized into three major classes, according to their underlying enrichment algorithms. The comprehensive collections, unique tool classifications and associated questions/issues will provide a more comprehensive and up-to-date view regarding the advantages, pitfalls and recent trends in a simpler tool-class level rather than by a tool-by-tool approach. Thus, the survey will help tool designers/developers and experienced end users understand the underlying algorithms and pertinent details of particular tool categories/tools, enabling them to make the best choices for their particular research interests.

/pdf/bioinformatics-enrichment-tools-paths-toward-the-2yo1xl3r2j.pdf

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.

/pdf/integrative-analysis-of-111-reference-human-epigenomes-4bavnjaon6.pdf

Integrative analysis of 111 reference human epigenomes

We present GOseq, an application for performing Gene Ontology (GO) analysis on RNA-seq data. GO analysis is widely used to reduce complexity and highlight biological processes in genome-wide expression studies, but standard methods give biased results on RNA-seq data due to over-detection of differential expression for long and highly expressed transcripts. Application of GOseq to a prostate cancer data set shows that GOseq dramatically changes the results, highlighting categories more consistent with the known biology.

/pdf/gene-ontology-analysis-for-rna-seq-accounting-for-selection-456k6bns5w.pdf

Gene ontology analysis for RNA-seq: accounting for selection bias

Outcomes of high-throughput biological experiments are typically interpreted by statistical testing for enriched gene functional categories defined by the Gene Ontology (GO). The resulting lists of GO terms may be large and highly redundant, and thus difficult to interpret.

REVIGO is a Web server that summarizes long, unintelligible lists of GO terms by finding a representative subset of the terms using a simple clustering algorithm that relies on semantic similarity measures. Furthermore, REVIGO visualizes this non-redundant GO term set in multiple ways to assist in interpretation: multidimensional scaling and graph-based visualizations accurately render the subdivisions and the semantic relationships in the data, while treemaps and tag clouds are also offered as alternative views. REVIGO is freely available at http://revigo.irb.hr/.

/pdf/revigo-summarizes-and-visualizes-long-lists-of-gene-ontology-3taarmiz8n.pdf

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

Purpose: DEM is widely used in the analysis of spatio-temporal correlation and clustering, and plays an important role in geographic big data mining. To assist researchers in selecting the most suitable dataset according to the application requirements, a comparative analysis of the accuracy of the highest resolution or the latest version of four freely available DEMs was conducted in this study.[Method: 19 relatively uniformly distributed runway elevation data were used as reference data, and line-based method was adopted to quantitatively analyze DEM elevation accuracy. Based on elevation datum unification, the elevation error at each checkpoint can be calculated. And the error statistical indicators were selected based on the error distribution.Conclusion: The experimental results show that the errors of various DEMs do not follow normal distribution. For ASTER GDEM with the lowest accuracy, there has relatively evident offsets exist in elevation. The accuracy of SRTM DEM and AW3D30 DSM are relative higher. And then, TanDEM-X 90 m has the smallest error statistical indicators and steepest probability density function, indicating its high accuracy and overall sound representation of the topographic relief.

Accuracy Assessment of SRTM DEM, ASTER GDEM, AW3D30 DSM, and TanDEM-X 90 m DEM Based on Runway Elevation Data

Research on Classroom Teaching Behavior Analysis System Based on Artificial Intelligence Technology

A novel AC turning on behavior model based on survival analysis

Sperm is formed through spermiogenesis, a highly complex process involving chromatin condensation that results in cessation of transcription. mRNAs required for spermiogenesis are transcribed at earlier stages and translated in a delayed fashion during spermatid formation. However, it remains unknown that how these repressed mRNAs are stabilized.Here we report a Miwi-interacting testis-specific and spermiogenic arrest protein, Ck137956, which we rename Tssa. Deletion of Tssa led to male sterility and absence of sperm formation. The spermiogenesis arrested at the round spermatid stage and numerous spermiogenic mRNAs were down-regulated in Tssa-/- mice. Deletion of Tssa disrupted the localization of Miwi to chromatoid body, a specialized assembly of cytoplasmic messenger ribonucleoproteins (mRNPs) foci present in germ cells. We found that Tssa interacted with Miwi in repressed mRNPs and stabilized Miwi-interacting spermiogenesis-essential mRNAs.Our findings indicate that Tssa is indispensable in male fertility and has critical roles in post-transcriptional regulations by interacting with Miwi during spermiogenesis. 

/pdf/regulation-of-miwi-mediated-mrna-stabilization-by-ck137956-19augn9p.pdf

Regulation of Miwi-mediated mRNA stabilization by Ck137956/Tssa is essential for male fertility

To study the attenuation and dispersion effect of a new protective structure distribution layer constructed with a hollow particle composite material on the shock wave, a similar model field explosion test was carried out in this paper. The numerical simulation of explosion tests under different conditions was carried out by using the finite element program 3D/LS-DYNA and the test results were used for verification. The experimental results showed that under the same charge conditions, the shell-shielding layer above the distribution layer of the hollow-shell particle composite material was greatly deformed and the damage was more serious than that above the distribution layer of yellow sand, which had an obvious attenuation effect on the shock wave. Under the same charge condition, the stress peak at the bottom of the distribution layer of the empty shell particle composite material was 0.47 times that of the distribution layer of yellow sand at the same position; the stress wave rose and the pulse width increased, which had an obvious dispersion effect. The distribution layer constructed by the hollow particle composite material had no obvious overall comminution damage, which improved the secondary anti-explosion ability of the protective structure. Therefore, the distribution layer constructed with the hollow particle composite not only enhanced the energy absorption and wave elimination of the protective structure, but also improved the safety of the protective structure.

Xin Zhou

Papers

Accuracy Assessment of SRTM DEM, ASTER GDEM, AW3D30 DSM, and TanDEM-X 90 m DEM Based on Runway Elevation Data

Research on Classroom Teaching Behavior Analysis System Based on Artificial Intelligence Technology

A novel AC turning on behavior model based on survival analysis

Regulation of Miwi-mediated mRNA stabilization by Ck137956/Tssa is essential for male fertility

Field Test and Numerical Simulation of a New Layered Structure