Tài liệu miễn phí Sinh học
Download Tài liệu học tập miễn phí Sinh học
Detecting pore-lining regions in transmembrane protein sequences
Alpha-helical transmembrane channel and transporter proteins play vital roles in a diverse range of essential biological processes and are crucial in facilitating the passage of ions and molecules across the lipid bilayer.
12/29/2020 4:32:43 PM +00:00
Re-visiting protein-centric two-tier classification of existing DNA-protein complexes
Precise DNA-protein interactions play most important and vital role in maintaining the normal physiological functioning of the cell, as it controls many high fidelity cellular processes. Detailed study of the nature of these interactions has paved the way for understanding the mechanisms behind the biological processes in which they are involved.
12/29/2020 4:32:35 PM +00:00
Minimalist ensemble algorithms for genome-wide protein localization prediction
Computational prediction of protein subcellular localization can greatly help to elucidate its functions. Despite the existence of dozens of protein localization prediction algorithms, the prediction accuracy and coverage are still low.
12/29/2020 4:32:28 PM +00:00
Molecular evolution of dihydrouridine synthases
Dihydrouridine (D) is a modified base found in conserved positions in the D-loop of tRNA in Bacteria, Eukaryota, and some Archaea. Despite the abundant occurrence of D, little is known about its biochemical roles in mediating tRNA function. It is assumed that D may destabilize the structure of tRNA and thus enhance its conformational flexibility.
12/29/2020 4:32:20 PM +00:00
PREMIM and EMIM: Tools for estimation of maternal, imprinting and interaction effects using multinomial modelling
Here we present two new computer tools, PREMIM and EMIM, for the estimation of parental and child genetic effects, based on genotype data from a variety of different child-parent configurations.
12/29/2020 4:32:05 PM +00:00
Surprising results on phylogenetic tree building methods based on molecular sequences
We analyze phylogenetic tree building methods from molecular sequences (PTMS). These are methods which base their construction solely on sequences, coding DNA or amino acids.
12/29/2020 4:31:58 PM +00:00
QuartetS-DB: A large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence
The concept of orthology is key to decoding evolutionary relationships among genes across different species using comparative genomics. QuartetS is a recently reported algorithm for large-scale orthology detection.
12/29/2020 4:31:49 PM +00:00
EGNAS: An exhaustive DNA sequence design algorithm
The molecular recognition based on the complementary base pairing of deoxyribonucleic acid (DNA) is the fundamental principle in the fields of genetics, DNA nanotechnology and DNA computing. We present an exhaustive DNA sequence design algorithm that allows to generate sets containing a maximum number of sequences with defined properties.
12/29/2020 4:31:42 PM +00:00
A Bayesian model for classifying all differentially expressed proteins simultaneously in 2D PAGE gels
Two-dimensional polyacrylamide gel electrophoresis (2D PAGE) is commonly used to identify differentially expressed proteins under two or more experimental or observational conditions.
12/29/2020 4:31:36 PM +00:00
Down-weighting overlapping genes improves gene set analysis
The identification of gene sets that are significantly impacted in a given condition based on microarray data is a crucial step in current life science research. Most gene set analysis methods treat genes equally, regardless how specific they are to a given gene set.
12/29/2020 4:31:29 PM +00:00
Bios2mds: An R package for comparing orthologous protein families by metric multidimensional scaling
The distance matrix computed from multiple alignments of homologous sequences is widely used by distance-based phylogenetic methods to provide information on the evolution of protein families. This matrix can also be visualized in a low dimensional space by metric multidimensional scaling (MDS).
12/29/2020 4:31:22 PM +00:00
Simulating gene-gene and gene-environment interactions in complex diseases: Gene-Environment iNteraction Simulator 2
The analysis of complex diseases is an important problem in human genetics. Because multifactoriality is expected to play a pivotal role, many studies are currently focused on collecting information on the genetic and environmental factors that potentially influence these diseases.
12/29/2020 4:31:16 PM +00:00
ROCS: A reproducibility index and confidence score for interaction proteomics studies
Affinity-Purification Mass-Spectrometry (AP-MS) provides a powerful means of identifying protein complexes and interactions. Several important challenges exist in interpreting the results of AP-MS experiments.
12/29/2020 4:31:08 PM +00:00
PollenCALC: Software for estimation of pollen compatibility of self-incompatible allo- and autotetraploid species
Self-incompatibility (SI) is a biological mechanism to avoid inbreeding in allogamous plants. In grasses, this mechanism is controlled by a two-locus system (S-Z). Calculation of male and female gamete frequencies is complex for tetraploid species.
12/29/2020 4:31:01 PM +00:00
On the hypothesis-free testing of metabolite ratios in genome-wide and metabolome-wide association studies
Genome-wide association studies (GWAS) with metabolic traits and metabolome-wide association studies (MWAS) with traits of biomedical relevance are powerful tools to identify the contribution of genetic, environmental and lifestyle factors to the etiology of complex diseases.
12/29/2020 4:30:55 PM +00:00
Predicting protein-ATP binding sites from primary sequence through fusing bi-profile sampling of multi-view features
Adenosine-5′-triphosphate (ATP) is one of multifunctional nucleotides and plays an important role in cell biology as a coenzyme interacting with proteins. Revealing the binding sites between protein and ATP is significantly important to understand the functionality of the proteins and the mechanisms of protein-ATP complex.
12/29/2020 4:30:49 PM +00:00
OLSVis: An animated, interactive visual browser for bio-ontologies
More than one million terms from biomedical ontologies and controlled vocabularies are available through the Ontology Lookup Service (OLS). Although OLS provides ample possibility for querying and browsing terms, the visualization of parts of the ontology graphs is rather limited and inflexible.
12/29/2020 4:30:42 PM +00:00
Detection and correction of probe-level artefacts on microarrays
A recent large-scale analysis of Gene Expression Omnibus (GEO) data found frequent evidence for spatial defects in a substantial fraction of Affymetrix microarrays in the GEO. Nevertheless, in contrast to quality assessment, artefact detection is not widely used in standard gene expression analysis pipelines.
12/29/2020 4:30:35 PM +00:00
Molecular ecological network analyses
Understanding the interaction among different species within a community and their responses to environmental changes is a central goal in ecology. However, defining the network structure in a microbial community is very challenging due to their extremely high diversity and as-yet uncultivated status.
12/29/2020 4:30:28 PM +00:00
TreeSnatcher plus: Capturing phylogenetic trees from images
Figures of phylogenetic trees are widely used to illustrate the result of evolutionary analyses. However, one cannot easily extract a machine-readable representation from such images. Therefore, new software emerges that helps to preserve phylogenies digitally for future research.
12/29/2020 4:30:21 PM +00:00
Profile-based short linear protein motif discovery
Short linear protein motifs are attracting increasing attention as functionally independent sites, typically 3–10 amino acids in length that are enriched in disordered regions of proteins. Multiple methods have recently been proposed to discover over-represented motifs within a set of proteins based on simple regular expressions.
12/29/2020 4:30:15 PM +00:00
MetaMapp: Mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity
Exposure to environmental tobacco smoke (ETS) leads to higher rates of pulmonary diseases and infections in children. To study the biochemical changes that may precede lung diseases, metabolomic effects on fetal and maternal lungs and plasma from rats exposed to ETS were compared to filtered air control animals.
12/29/2020 4:30:05 PM +00:00
SIS: A program to generate draft genome sequence scaffolds for prokaryotes
Decreasing costs of DNA sequencing have made prokaryotic draft genome sequences increasingly common. A contig scaffold is an ordering of contigs in the correct orientation. A scaffold can help genome comparisons and guide gap closure efforts.
12/29/2020 4:29:58 PM +00:00
DIPSBC - data integration platform for systems biology collaborations
Modern biomedical research is often organized in collaborations involving labs worldwide. In particular in systems biology, complex molecular systems are analyzed that require the generation and interpretation of heterogeneous data for their explanation, for example ranging from gene expression studies and mass spectrometry measurements to experimental techniques for detecting molecular interactions and functional assays.
12/29/2020 4:29:50 PM +00:00
Augmented annotation and orthologue analysis for Oryctolagus cuniculus: Better Bunny
The rabbit is an important model organism used in a wide range of biomedical research. However, the rabbit genome is still sparsely annotated, thus prohibiting extensive functional analysis of gene sets derived from whole-genome experiments.
12/29/2020 4:29:44 PM +00:00
Inferring high-confidence human protein-protein interactions
As numerous experimental factors drive the acquisition, identification, and interpretation of proteinprotein interactions (PPIs), aggregated assemblies of human PPI data invariably contain experiment-dependent noise.
12/29/2020 4:29:37 PM +00:00
Metaprotein expression modeling for label-free quantitative proteomics
Label-free quantitative proteomics holds a great deal of promise for the future study of both medicine and biology. However, the data generated is extremely intricate in its correlation structure, and its proper analysis is complex. There are issues with missing identifications.
12/29/2020 4:29:29 PM +00:00
A Bayesian variable selection procedure to rank overlapping gene sets
Genome-wide expression profiling using microarrays or sequence-based technologies allows us to identify genes and genetic pathways whose expression patterns influence complex traits. Different methods to prioritize gene sets, such as the genes in a given molecular pathway, have been described.
12/29/2020 4:29:22 PM +00:00
A unified computational model for revealing and predicting subtle subtypes of cancers
Gene expression profiling technologies have gradually become a community standard tool for clinical applications. For example, gene expression data has been analyzed to reveal novel disease subtypes (class discovery) and assign particular samples to well-defined classes (class prediction).
12/29/2020 4:29:16 PM +00:00
The MULTICOM toolbox for protein structure prediction
As genome sequencing is becoming routine in biomedical research, the total number of protein sequences is increasing exponentially, recently reaching over 108 million. However, only a tiny portion of these proteins (i.e. ~75,000 or < 0.07%) have solved tertiary structures determined by experimental techniques.
12/29/2020 4:29:09 PM +00:00