Metagenomic sequencing of clinical samples provides a promising technique for direct pathogen detection and characterization in biosurveillance. Taxonomic analysis at the strain level can be used to resolve serotypes Sigma was developed strain-level identification quantification pathogens using their reference genomes based on metagenomic analysis.Sigma not only accurate inferences, but also three unique capabilities: (i) quantifies statistical uncertainty its which includes hypothesis...

Abstract Motivation : Metagenomic sequencing allows reconstruction of microbial genomes directly from environmental samples. Omega ( o verlap-graph me ta g enome a ssembler) was developed for assembling and scaffolding Illumina data communities. Results found overlaps between reads using prefix/suffix hash table. The overlap graph simplified by removing transitive edges trimming short branches. Unitigs were generated based on minimum cost flow analysis the then merged to contigs scaffolds...

Spasmolytic polypeptide-expressing metaplasia (SPEM) is a regenerative lesion in the gastric mucosa and potential precursor to intestinal metaplasia/gastric adenocarcinoma chronic inflammatory setting. The goal of these studies was define transcriptional changes associated with SPEM at individual cell level response acute drug injury damage mucosa.Epithelial cells were isolated from corpus healthy stomachs drug-induced inflammation-induced lesions. Single RNA sequencing (scRNA-seq) performed...

Detailed characterization of post-translational modifications (PTMs) proteins in microbial communities remains a significant challenge. Here we directly identify and quantify broad range PTMs (hydroxylation, methylation, citrullination, acetylation, phosphorylation, methylthiolation, S-nitrosylation nitration) natural community from an acid mine drainage site. Approximately 29% the identified dominant Leptospirillum group II bacteria are modified, 43% modified carry multiple PTM types. Most...

The transcription initiation landscape of eukaryotic genes is complex and highly dynamic. In eukaryotes, can generate multiple transcript variants that differ in 5' boundaries due to usages alternative start sites (TSSs), the abundance isoforms are variable. Due a large number complexity TSSs, it not feasible depict details all using text-format genome annotation files. Therefore, necessary provide data visualization TSSs represent quantitative TSS maps core promoters (CPs). addition,...

Metagenomics is the application of modern genomic techniques to investigate members a microbial community directly in their natural environments and widely used many studies survey communities organisms that live diverse ecosystems. In order understand metagenomic profile one densest interaction spaces for millions people, public transit system, MetaSUB international Consortium has collected sequenced metagenomes from subways different cities across world. collaboration with CAMDA, made...

Abstract Summary: Sipros/ProRata is an open-source software package for end-to-end data analysis in a wide variety of community proteomics measurements. A database-searching program, Sipros 3.0, was developed accurate general-purpose protein identification and broad-range post-translational modification searches. Hybrid Message Passing Interface/OpenMP parallelism the new architecture allowed its computation to be scalable from desktops supercomputers. The upgraded ProRata 3.0 performs...

Tracking antigen-specific T cell responses over time within individuals is difficult because of lack knowledge TCR sequences, limitations in sample size, and assay sensitivities. We hypothesized that analyses high-throughput sequencing clonotypes could provide functional readouts individuals' immunological histories. Using sequencing, we develop a database TCRβ sequences from large cohorts mice before (naive) after smallpox vaccination. computationally identify 315 vaccine-associated (VATS)...

Abstract Motivation Reprogramming somatic cells into neurons holds great promise to model neuronal development and disease. The efficiency success rate of reprogramming, however, may vary between different conversion platforms cell types, thereby necessitating an unbiased, systematic approach estimate identity converted cells. Recent studies have demonstrated that long genes (>100 kb from transcription start end) are highly enriched in neurons, which provides opportunity identify...

Change-point detection is a challenging problem that has number of applications across various real-world domains. The primary objective CPD to identify specific time points where the underlying system undergoes transitions between different states, each characterized by its distinct data distribution. Precise identification change in series omics can provide insights into dynamic and temporal characteristics inherent complex biological systems. Many change-point methods have traditionally...

Phylogenetic studies have provided detailed knowledge on the evolutionary mechanisms of genes and species in Bacteria Archaea. However, evolution cellular functions, represented by metabolic pathways biological processes, has not been systematically characterized. Many clades prokaryotic tree life now covered sequenced genomes GenBank. This enables a large-scale functional phylogenomics study many computationally inferred functions across all prokaryotes. A total 14,727 GenBank were...

Unlike many mutants that are completely viable or inviable, the CLB2-dbΔ clb5Δ mutant of Saccharomyces cerevisiae is inviable in glucose but partially on slower growth media such as raffinose. On raffinose, cells can bud and divide each cycle there a chance cell will fail to (telophase arrest), causing it exit cycle. This effect gives rise stochastic phenotype cannot be explained by deterministic model. We measure inter-bud times wild type growing raffinose compute statistics distributions...

Transcription initiation is regulated in a highly organized fashion to ensure proper cellular functions. Accurate identification of transcription start sites (TSSs) and quantitative characterization activities are fundamental steps for studies transcriptions core promoter structures. Several high-throughput techniques have been developed sequence the very 5'end RNA transcripts (TSS sequencing) on genome scale. Bioinformatics tools essential processing, analysis, visualization TSS sequencing...

Interspecies hybridization is prevalent in various eukaryotic lineages and plays important roles phenotypic diversification, adaptation, speciation. To better understand the changes that occurred different subgenomes of a hybrid species how they facilitate we completed chromosome-level de novo assemblies all chromosomes for recently formed yeast, Saccharomyces bayanus strain CBS380, using Nanopore MinION long-read sequencing. We characterized S. genome compared it with its parent species,...

In biochemical systems some of the chemical species are present with only small numbers molecules. this situation discrete and stochastic simulation approaches more relevant than continuous deterministic ones. The fundamental Gillespie's algorithm (SSA) accounts for every reaction event, which occurs a probability determined by configuration system. This approach requires considerable computational effort models many channels species. order to improve efficiency, tau-leaping methods...

Machine learning (ML) techniques discover knowledge from large amounts of data. Modeling in ML is becoming essential to software systems practice. The accuracy and efficiency models have been focused on research communities, while there less attention validating the qualities models. Validating applications a challenging time-consuming process for developers since prediction heavily relies generated are written by relatively more data-driven programming based black box frameworks. All...

Diverse microbiome communities drive biogeochemical processes and evolution of animals in their ecosystems. Many projects have demonstrated the power using metagenomics to understand structures factors influencing function microbiomes environments. In order characterize effects from composition for human health, diseases, even ecosystems, one must first relationship microbes environment different samples. Running machine learning model with metagenomic sequencing data is encouraged this...

Abstract Background Recent advances in sequencing technologies have driven studies identifying the microbiome as a key regulator of overall health and disease host. Both 16S amplicon whole genome shotgun are currently being used to investigate this relationship, however, choice technology often depends on nature experimental design study. In principle, outputs rendered by analysis pipelines heavily influenced data input; it is then important consider that genomic features produced different...

The diversity within different microbiome communities that drive biogeochemical processes influences many phenotypes. Analyses of these and their by countless projects have revealed an important role metagenomics in understanding the complex relation between microbes environments. This relationship can be understood context composition specific known These compositions then used as a template for predicting status similar Machine learning has been applied key component to this predictive...

For biochemical systems, where some chemical species are represented by small numbers of molecules, discrete and stochastic approaches more appropriate than continuous deterministic approaches. The approach using ordinary differential equations is adequate for understanding the average behavior cells, while accurately captures noisy events in growth-division cycle. Since emergence simulation algorithm (SSA) Gillespie, alternative algorithms have been developed whose goal to improve...