Created by
Share your knowledge / experiences
About Startbioinfo |
Other web-portals |
BdataA |
Categories of resources
Post-analysis categorization
Literature search
Post-survey categorization
Features validated in most cases
Gene expression
MicroRNA
Pathways
Primer designing
Protein-protein interactions (commonly used resources)
Protein structure prediction
SNP analysis
Features not validated
Alternative splice form analysis
DNA motif detection
Microbiology
Multiple sequence alignment
Next generation sequencing
Simple lists
Carbohydrates
Gene ID conversion
Lipids
Long non-coding RNA
PiRNA
Promoter prediction
Protein-protein interactions (all resources)
RNA structure prediction
SNP analysis
Preliminary lists
Antibodies
Biomarkers
Cell lines
Clinical trials
DNA/RNA structures
Disease-gene relationships
Enzymes
Functional analysis
Gene Ontology specific analysis
Gene/protein unified information
Genetics
Genomes and Genomics
Mass spectrometry
Microarray data analysis
Molecular docking
Nomenclature
Organelles
Orthologs
Pharmacokinetics and Pharmacodynamics
Phylogeny/Taxonomy
Protein domains
Protein localization
Protein-nucleic acid interactions
Secretome
Small molecules
Spectral analysis
Text-mining
Toxicology
Transcription factors and binding sites
Suggested Readings
Basic concepts
Broad reviews
Other reviews
Case studies
Comparison of resources
Intuitive browsing
Multi-level categories
Alphabetical list
Case studies
Alternative splice form analysis
The types and prevalence ofA0alternative spliceA0forms
PAID
EpigeneticA0featuresA0are significantlyA0associatedA0withA0alternativeA0splicing
Disturbances ofA0alternative splicingA0in cancer
Alternative splicingA0and breast cancer
Alternative splicingA0in cancer: noise, functional, or systematic?
Alternative splicing: an emerging topic in molecular and clinical oncology
DNA motif detection
A novel ensemble method for fine-grained integration of generic motif finders
Higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling
MTAP-the motif tool assessment platform
Discovery ofA0cis-elements betweenA0sorghumA0and rice using co-expression and evolutionary conservation
Computational prediction of transcription-factor binding site locations
Discovery of transcription factor binding sites in a set of sequences from co-regulated genes
Gene expression
Gene expression signature involved with epithelial-mesenchymal transformation
Hypoxic gene expression and tumor growth
Sonic Hedgehog pathway stimulates prostate tumor growth
Transcriptional regulation of Elf-1
Downstream targets of HOXB4 in a cell line model of primitive hematopoietic progenitor cells
Mechanisms of regulatation of cytoskeletal gene expression in macrophages
Quantitative PCR tissue expression profiling of the human SGLT2 gene and related family members
Gene expression profiling in mouse model identifies potential biomarkers for Down Syndrome screening
Biomarker discovery in breast cancer
A comprehensive genome-scale reconstruction of Escherichia coli metabolism
MicroRNA
Role of mir-2861 in osteoblast differentiation in mice
Case study on microRNA and mRNA expression
microRNA-196 as a potential candidate in the treatment of hepatitis-C infection
miRNA-328 as a decoy in cancer suppression
Role of miR-34c in stress induced anxiety
Multiple sequence alignment
Evolution of duplications in the transferrin family of proteins
PAID
Conserved structures with species-specific IL-1 receptor binding: new avenues for pharmacological design
PAID
Comparative genomics and functional roles of the ATP-dependent proteases Lon and Clp during cytosolic protein degradation
PAID
Antibacterial peptides derived from caprine whey proteins, by digestion with human gastrointestinal juice
PAID
Identification of novel conserved functional motifs across most Influenza A viral strains
Multiple-locus, variable number of tandem repeat analysis (MLVA) of the fish-pathogen Francisella noatunensis
Exon-intron structure of the Xist gene in elephant, armadillo, and the ancestor of placental mammals
Phylogenetic and functional analysis of the vertebrate cytochrome p450 2 family
Issues in bioinformatics benchmarking: the case study of multiple sequence alignment
Next generation sequencing
A highly annotated whole-genome sequence of a Korean individual
Variant discovery through NGS
The first complete genome of an individual by massively parallel DNA sequencing
Comparative genomics based on transcriptome sequencing
The effect of NGS technology on complex trait research
Variant discovery by characterization of twenty sequenced human genomes
Genetic diagnosis of Duchenne and Becker muscular dystrophy using next-generation sequencing technology
Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences
Pathways
Gene expression and pathway analysis of ovarian cancer
Pathway analysis of expression data: deciphering functional building blocks of complex diseases
MicroRNAs target gene and signaling pathway by bioinformatics analysis in the cardiac hypertrophy
PAID
Microarray data mining for biological pathway analysis
Genome-wide gene and pathway analysis
Pathway analysis of breast cancer
Common variants conferring risk of schizophrenia: a pathway analysis of GWAS data
Integrating pathway analysis and genetics of gene expression for genome-wide association studies
Using genome-wide pathway analysis to unravel the etiology of complex diseases
Gene expression meta-analysis identifies metastatic pathways and transcription factors in breast cancer
Mining literature for a comprehensive pathway analysis
Discovering molecular pathways from protein interaction and gene expression data
Primer designing
Primer design for a prokaryotic differential display RT-PCR
Detection of specific polymerase chain reaction product by utilizing the 5 prime---> 3 prime exonuclease activity of Thermus aquaticus DNA polymerase
Multiplex detection of four pathogenic retroviruses using molecular beacons
Simple, sensitive, and specific detection of human immunodeficiency virus type 1 in clinical specimens by polymerase chain reaction with nested primers
Genotyping ocular strains of Chlamydia trachomatis by single-tube nested PCR
Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands
Multiplex PCR design strategy used for the simultaneous amplification of 10 Y chromosome short tandem repeat (STR) loci
In situ PCR: protocols and applications
Amplification of human minisatellites by the polymerase chain reaction: towards DNA fingerprinting of single cells
Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies
Analysis of nonspecific DNA synthesis during in-situ PCR and solution-phase PCR
Rapid detection of Spanish (delta beta)zero-thalassemia deletion by polymerase chain reaction
RAPD and other PCR-based analyses of plant genomes using DNA extracted from small leaf disks
Optimization of long-distance PCR using a transposon-based model system
Multiplex automated primer extension analysis: simultaneous genotyping of several polymorphisms
Promoter prediction
CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences
PromH: promoters identification using orthologous genomic sequences
PromoSer: a large-scale mammalian promoter and TSS identification service
Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment
Human pol II promoter prediction: time series descriptors and machine learning
PromoterExplorer: an effective promoter identification method based on the AdaBoost algorithm
EnsemPro: an ensemble approach to predict TSS in human genomic DNA sequences
Promoter prediction and analysis in human, mouse and rat
Promoter prediction for 13,744 genes in humans
Protein structure prediction
Issues in high-throughput comparative modelling: a case study using the ubiquitin E2 conjugating enzymes
PAID
A case study using Phyre server
PAID
Modelling of human cytochrome P450 1A2
PAID
Protein-protein interactions
Computational analysis of HIV-1 resistance based on gene expression profiles and the virus-host interaction network
Identifying causal genes and dysregulated pathways in complex diseases
Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology
A comparative study of cancer proteins in the human protein-protein interaction network
Multi-level reproducibility of signature hubs in human interactome for breast cancer metastasis
Detection of molecular paths associated with insulitis and type 1 diabetes in non-obese diabetic mouse
Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts
Mycobacterium tuberculosis interactome analysis unravels potential pathways to drug resistance
CGI: a new approach for prioritizing genes by combining gene expression and protein-protein interaction data
Protein-protein interactions more conserved within species than across species
Gene function prediction by a combined analysis of gene expression data and protein-protein interaction data
PAID
Functional modules by relating protein interaction networks and gene expression
Discovering molecular pathways from protein interaction and gene expression data
Protein-protein interaction map is a key gateway into liver regeneration
Building protein interaction maps for Down's syndrome
RNA structure prediction
RNA tertiary structure prediction with ModeRNA, program for comparative modeling of RNA 3D structures
Predicted changes in the pre-mRNA secondary structure vary in their association with exon skipping
PAID
Structure prediction using Mfold
Structure prediction using Vienna RNA package
PAID
SNP analysis
Introduction of SNP markers in diagnosis of Wilson disease
Describes identification of SNP in protamine1 gene
Explains how the SNP resulted in an amino acid change in the PRM1 gene
Disclaimer
copyright © Dr. Kshitish Acharya K; all rights reserved
