Tài liệu miễn phí Sinh học
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An integrated network visualization framework towards metabolic engineering applications
Over the last years, several methods for the phenotype simulation of microorganisms, under specified genetic and environmental conditions have been proposed, in the context of Metabolic Engineering (ME). These methods provided insight on the functioning of microbial metabolism and played a key role in the design of genetic modifications that can lead to strains of industrial interest.
12/29/2020 6:45:25 AM +00:00
Prediction of piRNAs using transposon interaction and a support vector machine
Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNA primarily expressed in germ cells that can silence transposons at the post-transcriptional level. Accurate prediction of piRNAs remains a significant challenge.
12/29/2020 6:45:17 AM +00:00
Fast individual ancestry inference from DNA sequence data leveraging allele frequencies for multiple populations
Estimation of individual ancestry from genetic data is useful for the analysis of disease association studies, understanding human population history and interpreting personal genomic variation. New, computationally efficient methods are needed for ancestry inference that can effectively utilize existing information about allele frequencies associated with different human populations and can work directly with DNA sequence reads.
12/29/2020 6:45:10 AM +00:00
JRC GMO-Matrix: A web application to support Genetically Modified Organisms detection strategies
The polymerase chain reaction (PCR) is the current state of the art technique for DNA-based detection of Genetically Modified Organisms (GMOs). A typical control strategy starts by analyzing a sample for the presence of target sequences (GM-elements) known to be present in many GMOs.
12/29/2020 6:45:02 AM +00:00
Unique features of apicoplast DNA gyrases from Toxoplasma gondii and Plasmodium falciparum
DNA gyrase, an enzyme once thought to be unique to bacteria, is also found in some eukaryotic plastids including the apicoplast of Apicomplexa such as Plasmodium falciparum and Toxoplasma gondii which are important disease-causing organisms.
12/29/2020 6:44:53 AM +00:00
Interactive visual exploration of overlapping similar structures for three-dimensional microscope images
Recent advances in microscopy enable the acquisition of large numbers of tomographic images from living tissues. Three-dimensional microscope images are often displayed with volume rendering by adjusting the transfer functions.
12/29/2020 6:44:45 AM +00:00
EPMLR: Sequence-based linear B-cell epitope prediction method using multiple linear regression
B-cell epitopes have been studied extensively due to their immunological applications, such as peptide-based vaccine development, antibody production, and disease diagnosis and therapy. Despite several decades of research, the accurate prediction of linear B-cell epitopes has remained a challenging task.
12/29/2020 6:44:37 AM +00:00
Identification of metabolites from 2D 1 H-13C HSQC NMR using peak correlation plots
Identification of individual components in complex mixtures is an important and sometimes daunting task in several research areas like metabolomics and natural product studies. NMR spectroscopy is an excellent technique for analysis of mixtures of organic compounds and gives a detailed chemical fingerprint of most individual components above the detection limit.
12/29/2020 6:44:30 AM +00:00
Mammalian transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes and are predicted to act as transcriptional activator hubs
Transcriptional hotspots are defined as genomic regions bound by multiple factors. They have been identified recently as cell type specific enhancers regulating developmentally essential genes in many species such as worm, fly and humans.
12/29/2020 6:44:22 AM +00:00
Predicting breast cancer using an expression values weighted clinical classifier
Clinical data, such as patient history, laboratory analysis, ultrasound parameters-which are the basis of day-to-day clinical decision support-are often used to guide the clinical management of cancer in the presence of microarray data. Several data fusion techniques are available to integrate genomics or proteomics data, but only a few studies have created a single prediction model using both gene expression and clinical data.
12/29/2020 6:44:15 AM +00:00
Identifying target processes for microbial electrosynthesis by elementary mode analysis
Microbial electrosynthesis and electro fermentation are techniques that aim to optimize microbial production of chemicals and fuels by regulating the cellular redox balance via interaction with electrodes. While the concept is known for decades major knowledge gaps remain, which make it hard to evaluate its biotechnological potential.
12/29/2020 6:44:07 AM +00:00
DFBAlab: A fast and reliable MATLAB code for dynamic flux balance analysis
Dynamic Flux Balance Analysis (DFBA) is a dynamic simulation framework for biochemical processes. DFBA can be performed using different approaches such as static optimization (SOA), dynamic optimization (DOA), and direct approaches (DA).
12/29/2020 6:43:59 AM +00:00
Kiwi: A tool for integration and visualization of network topology and gene-set analysis
The analysis of high-throughput data in biology is aided by integrative approaches such as gene-set analysis. Gene-sets can represent well-defined biological entities (e.g. metabolites) that interact in networks (e.g. metabolic networks), to exert their function within the cell.
12/29/2020 6:43:52 AM +00:00
A statistical approach to quantification of genetically modified organisms (GMO) using frequency distributions
According to Regulation (EU) No 619/2011, trace amounts of non-authorised genetically modified organisms (GMO) in feed are tolerated within the EU if certain prerequisites are met. Tolerable traces must not exceed the so-called ‘minimum required performance limit’ (MRPL), which was defined according to the mentioned regulation to correspond to 0.1% mass fraction per ingredient.
12/29/2020 6:43:44 AM +00:00
Methodology for the inference of gene function from phenotype data
Biomedical ontologies are increasingly instrumental in the advancement of biological research primarily through their use to efficiently consolidate large amounts of data into structured, accessible sets. However, ontology development and usage can be hampered by the segregation of knowledge by domain that occurs due to independent development and use of the ontologies.
12/29/2020 6:43:36 AM +00:00
ExpaRNA-P: Simultaneous exact pattern matching and folding of RNAs
Identifying sequence-structure motifs common to two RNAs can speed up the comparison of structural RNAs substantially. The core algorithm of the existent approach ExpaRNA solves this problem for a priori known input structures.
12/29/2020 6:43:28 AM +00:00
QUDeX-MS: Hydrogen/deuterium exchange calculation for mass spectra with resolved isotopic fine structure
Hydrogen/deuterium exchange (HDX) coupled to mass spectrometry permits analysis of structure, dynamics, and molecular interactions of proteins. HDX mass spectrometry is confounded by deuterium exchange-associated peaks overlapping with peaks of heavy, natural abundance isotopes, such as carbon-13.
12/29/2020 6:43:20 AM +00:00
Improving statistical inference on pathogen densities estimated by quantitative molecular methods: Malaria gametocytaemia as a case study
Quantitative molecular methods (QMMs) such as quantitative real-time polymerase chain reaction (q-PCR), reverse-transcriptase PCR (qRT-PCR) and quantitative nucleic acid sequence-based amplification (QT-NASBA) are increasingly used to estimate pathogen density in a variety of clinical and epidemiological contexts.
12/29/2020 6:43:12 AM +00:00
MCMC implementation of the optimal Bayesian classifier for non-Gaussian models: Model-based RNA-Seq classification
Sequencing datasets consist of a finite number of reads which map to specific regions of a reference genome. Most effort in modeling these datasets focuses on the detection of univariate differentially expressed genes. However, for classification, we must consider multiple genes and their interactions.
12/29/2020 6:43:04 AM +00:00
Exact reconstruction of gene regulatory networks using compressive sensing
We consider the problem of reconstructing a gene regulatory network structure from limited time series gene expression data, without any a priori knowledge of connectivity. We assume that the network is sparse, meaning the connectivity among genes is much less than full connectivity.
12/29/2020 6:42:56 AM +00:00
Integrating protein structural dynamics and evolutionary analysis with Bio3D
Popular bioinformatics approaches for studying protein functional dynamics include comparisons of crystallographic structures, molecular dynamics simulations and normal mode analysis. However, determining how observed displacements and predicted motions from these traditionally separate analyses relate to each other.
12/29/2020 6:42:48 AM +00:00
Comparative evaluation of gene set analysis approaches for RNA-Seq data
Over the last few years transcriptome sequencing (RNA-Seq) has almost completely taken over microarrays for high-throughput studies of gene expression. Currently, the most popular use of RNA-Seq is to identify genes which are differentially expressed between two or more conditions.
12/29/2020 6:42:40 AM +00:00
Pathomx: An interactive workflow-based tool for the analysis of metabolomic data
Metabolomics is a systems approach to the analysis of cellular processes through small-molecule metabolite profiling. Standardisation of sample handling and acquisition approaches has contributed to reproducibility.
12/29/2020 6:42:33 AM +00:00
CompareSVM: Supervised, Support Vector Machine (SVM) inference of gene regularity networks
Predication of gene regularity network (GRN) from expression data is a challenging task. There are many methods that have been developed to address this challenge ranging from supervised to unsupervised methods. Most promising methods are based on support vector machine (SVM).
12/29/2020 6:42:25 AM +00:00
MPAgenomics: An R package for multi-patient analysis of genomic markers
MPAgenomics, standing for multi-patient analysis (MPA) of genomic markers, is an R-package devoted to: (i) efficient segmentation and (ii) selection of genomic markers from multi-patient copy number and SNP data profiles. It provides wrappers from commonly used packages to streamline their repeated (sometimes difficult) manipulation, offering an easy-to-use pipeline for beginners in R.
12/29/2020 6:42:18 AM +00:00
Computational prediction of protein interactions related to the invasion of erythrocytes by malarial parasites
The invasion of red blood cells (RBCs) by malarial parasites is an essential step in the life cycle of Plasmodium falciparum. Human-parasite surface protein interactions play a critical role in this process.
12/29/2020 6:42:10 AM +00:00
Meta-eQTL: A tool set for flexible eQTL meta-analysis
Increasing number of eQTL (Expression Quantitative Trait Loci) datasets facilitate genetics and systems biology research. Meta-analysis tools are in need to jointly analyze datasets of same or similar issue types to improve statistical power especially in trans-eQTL mapping. Meta-analysis framework is also necessary for ChrX eQTL discovery.
12/29/2020 6:42:03 AM +00:00
SPoRE: A mathematical model to predict double strand breaks and axis protein sites in meiosis
Meiotic recombination between homologous chromosomes provides natural combinations of genetic variations and is a main driving force of evolution. It is initiated via programmed DNA double-strand breaks (DSB) and involves a specific axial chromosomal structure.
12/29/2020 6:41:55 AM +00:00
Pathway activity inference for multiclass disease classification through a mathematical programming optimisation framework
Applying machine learning methods on microarray gene expression profiles for disease classification problems is a popular method to derive biomarkers, i.e. sets of genes that can predict disease state or outcome. Traditional approaches where expression of genes were treated independently suffer from low prediction accuracy and difficulty of biological interpretation.
12/29/2020 6:41:48 AM +00:00
VTBuilder: A tool for the assembly of multi isoform transcriptomes
Within many research areas, such as transcriptomics, the millions of short DNA fragments (reads) produced by current sequencing platforms need to be assembled into transcript sequences before they can be utilized.
12/29/2020 6:41:40 AM +00:00