Created by
Shodhaka
Contributors
Share your knowledge / experiences
Home |
Other web-portals
Resources
Post-analysis categorization
Literature search
Post-survey categorization
Features validated in most cases
Gene expression
Pathways
Primer designing
Protein-protein interactions (commonly used resources)
Features not validated
DNA motif detection
MicroRNA
Multiple sequence alignment
Next generation sequencing
Simple lists
Gene ID conversion
Promoter prediction
Protein-protein interactions (all resources)
Protein structure prediction
SNP analysis
Under preparation
Alternative splice form analysis
Microarray data analysis
Basic concepts
Broad reviews
Other reviews
Case studies
Comparison of resources
Case studies
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
The motif tool assessment platform
Discovery of cis-elements between sorghum and 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
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
Analysis of fish IL-1beta and derived peptide sequences indicates conserved structures with species-specific IL-1 receptor binding: implications for pharmacological design
Comparative genomics and functional roles of the ATP-dependent proteases Lon and Clp during cytosolic protein degradation
Antibacterial peptides derived from caprine whey proteins, by digestion with human gastrointestinal juice
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
Differential identification of Salmonella enterica subsp. enterica serovar Gallinarum biovars Gallinarum and Pullorum based on polymorphic regions of glgC and speC genes
Next generation sequencing
A highly annotated whole-genome sequence of a Korean individual
FREE
Variant discovery through NGS
FREE
The first complete genome of an individual by massively parallel DNA sequencing
FREE
Comparative genomics based on transcriptome sequencing
FREE
The effect of NGS technology on complex trait research
FREE
Variant discovery by characterization of twenty sequenced human genomes
FREE
Genetic diagnosis of Duchenne and Becker muscular dystrophy using next-generation sequencing technology: comprehensive mutational search in a single platform
FREE
Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences
FREE
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
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 (An Oxford Journals article)
PromH: promoters identification using orthologous genomic sequences (An Oxford Journals article)
PromoSer: a large-scale mammalian promoter and TSS identification service (An Oxford Journals article)
Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment (Downloadable PDF file)
Human pol II promoter prediction: time series descriptors and machine learning (An Oxford Journals article)
PromoterExplorer: An effective promoter identification method based on the AdaBoost algorithm (An Oxford Journals article)
EnsemPro: An ensemble approach to predict TSS in human genomic DNA sequences (A ScienceDirect article)
Promoter prediction and analysis in human, mouse and rat
Promoter prediction for 13,744 genes in humans
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
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
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
Grow and let grow!
copyright © shodhaka life sciences private limited; all rights reserved
Grow and let grow!