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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
Other reviews
DNA motif detection
Regulatory sequence analysis tools
A survey of DNA motif finding algorithms
Gene expression
Microarray analysis of gene expression
Gene expression profiling by microarray
Gene expression profiling by Serial Analysis of Gene Expression (SAGE)
Gene expression profiling in asthma research
Gene expression arrays in cancer research
Application of SAGE in cancer research
Gene expression profiling in breast cancer research
MicroRNA
Role of microRNAs in cardiovascular biology and its therapeutic implications
Integrative computational analytical methods for microRNA target prediction
Role of microRNAs in cancer
Influence of viral microRNAs during replication and infection
Effect of microRNAs during transition phases of plant development
Role of microRNAs in drug response
Significance of microRNAs in mammalian stem cells
Difference between plant and animal microRNAs
Novel function of extracellular or circulating microRNAs as potential clinical biomarkers
Function of microRNAs in response to DNA damage and its application as sensitizers in cancer therapy
microRNAs in normal and diseased lung
Multiple sequence alignment
Recent trends in molecular phylogenetic analysis: where to next?
Upcoming challenges for multiple sequence alignment methods in the high-throughput era
Recent evolutions of multiple sequence alignment algorithms
Multiple sequence alignment: in pursuit of homologous DNA positions
Multiple sequence alignment as a guideline for protein engineering strategies
Integrating protein secondary structure prediction and multiple sequence alignment
Multiple sequence alignment in phylogenetic analysis
Multiple sequence alignment: algorithms and applications
Next generation sequencing
Role of NGS in cancer genomics
FREE
Challenges of sequencing human genomes
FREE
Applications of NGS in pharmacogenomics
FREE
Role of NGS in RNA-seq
FREE
Role of NGS in metagenomics
FREE
Review on cancer genome sequencing
FREE
Advantages of NGS versus the microarray in epigenetic research
FREE
Role of NGS in transcriptomics
FREE
Role of NGS in ChIP-seq
FREE
Review on discovering genetic polymorphisms in next generation sequencing data
FREE
Pathways
Biomarkers in lung cancer
Systems biology visualization tools for drug target discovery
Statistical methods for pathway analysis of genome-wide data for association with complex genetic traits
Immune pathways
Diverse pathways in ovarian cancer
Prognosis in gastric cancer
Two approaches for metabolic pathway analysis?
Primer designing
Optimization of the annealing temperature for DNA amplification in vitro
Ligase chain reaction (LCR): overview and applications
Advances in PCR-based detection of mycoplasmas contaminating cell cultures
Maximizing sensitivity and specificity of PCR by pre-amplification heating
The degenerate primer design problem: theory and applications
Primer design in fluorescent DNA sequencing
Improved primer design for PCR-based, site-directed mutagenesis
Long and Accurate PCR [with trouble shooting]
Long-distance PCR
Applications of the polymerase chain reaction in environmental microbiology
Quantitative analysis of chromosome conformation capture assays (3C-qPCR)
Improved protocols for bisulfite sequencing and fragment analysis of methylated gDNA
A thermodynamic approach to PCR primer design
Optimization of mutation screening systems with temperature gradient gel electrophoresis and PCR
Integrating PCR Theory and Bioinformatics into a Research-oriented Primer Design Exercise
Novel computational methods for increasing PCR primer design effectiveness in directed sequencing
A new approach to primer design for the control of PCR bias in methylation studies
Primer design versus PCR bias in methylation independent PCR amplifications
Cloning, Nucleotide Sequence, and Engineered Expression of Thermus thermophilus DNA Ligase, a Homolog of Escherichia coli DNA Ligase
Role of metal ions in catalysis by HIV integrase analyzed using a quantitative PCR disintegration assay
'Touchdown' PCR to circumvent spurious priming during gene amplification
Primer design versus PCR bias in methylation independent PCR amplifications
Promoter prediction
Rapidly evolving human promoter regions (A Nature Genetics article)
PAID
A chromatin landmark and transcription initiation at most promoters in human cells (A PubMed article)
Sequence features that drive human promoter function and tissue specificity (A CSH Press article)
Invivogen's list of promoters (A list of ubiquitous promoter products)
The promoter of Alzheimer's disease amyloid A4 precursor gene (A PubMed article)
An abundance of bidirectional promoters in the human genome (A CSH Press article)
Promoter prediction analysis on the whole human genome
PAID
Promoter prediction in the human genome with the help of tools and databases
Protein-protein interactions
Protein interactions: general reviews
Role for protein-protein interaction databases in human genetics
Computational reconstruction of protein-protein interaction networks: algorithms and issues
A review on models and algorithms for motif discovery in protein-protein interaction networks
Making the most of high-throughput protein-interaction data
Protein interaction networks in plants
Computational methods for protein-protein interaction and their application
What do we learn from high-throughput protein interaction data?
Protein interaction networks in bacteria
Protein interaction networks from yeast to human
Protein interaction: same network, different hubs
Genome-wide studies of protein-protein interaction
Protein interaction maps for model organisms
Protein-protein interaction maps: a lead towards cellular functions
Use of protein-interaction maps to formulate biological questions
Building a protein interaction map: research in the post-genome era
Protein interaction methods-Toward an Endgame
Protein-protein interaction and enzymatic activity
The value of high quality protein-protein interaction networks for systems biology
Protein interactions and disease
Protein networks in disease
Protein-protein interactions in human disease
Interfering with protein-protein interactions: potential for cancer therapy
Protein interaction prediction
Prediction of protein-protein interaction networks
Protein interaction predictions from diverse sources
Prediction of protein-protein interaction networks
Evaluation of different domain-based methods in protein interaction prediction
Evolution and protein interaction network
Evolution of protein-protein interaction network
Inferring ancestral protein interaction networks
Evolution in protein interaction networks: co-evolution, rewiring and the role of duplication
Protein-protein interactions in structural studies
Protein-protein interaction and quaternary structure
Analyzing protein interaction networks using structural information
Prediction of protein-protein interaction based on structure
Protein interaction and drug discovery
Human protein-protein interaction networks and the value for drug discovery
Protein interaction-targeted drug discovery: evaluating critical issues
SNP analysis
The use of single nucleotide polymorphisms maps in pharmacogenomics
The use of single nucleotide polymorphisms in the isolation of common disease genes
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