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Broad reviews
Alternative splice form analysis
Alternative splicedA0transcripts as cancer markers
PAID
Alternative splicing and genome complexity
PAID
Substances that can changeA0alternative splice-site selection
PAID
Correlation between intron length and alternative splicing
Alternative splicing: increasing diversity in the proteomic world
PAID
DNA motif detection
Computational identification of transcriptional regulatory elements in DNA sequence
A survey of motif discovery methods in an integrated framework
How does DNA sequence motif discovery work?
Computer analysis of nucleic acid regulatory sequences
Detecting cis-regulatory modules by modeling correlated structures in genomic sequences
Gene expression
Overview on quantitative capabilities of several techniques for measuring gene expression levels
Gene expression databases and data mining
An overview of advances in gene expression profiling studies over the last decade and areas that need further research
MicroRNA
microRNA biogenesis and post transcriptional regulation
Plant microRNA: characteristics, identification and methods of study
Fundamental concepts, progress and recent trends in the study of microRNA
microRNA genomics, function, regulation in plants and animals
Computational tools for microRNA gene and target identification
Regulatory pathways in microRNA processing and its role in cancer
microRNAs and small interfering RNAs
Biogenesis of small RNAs
PAID
Major protein components of microRNA pathway: Dicer, Argonaute, RISC RNA-binding proteins, Exportin
Current tools, strategies and applications of microRNA study from a bioengineering perspective
PAID
Experimental methods for microRNA target identification
Evolution of microRNA genes in plants
The importance of coding regions in post-transcriptional regulation
Experimental strategies for microRNA research
Multiple sequence alignment
Alignment of amino acid sequences
PAID
Multiple sequence alignment: available methods, their advantages and limitations
PAID
An overview of multiple sequence alignment
PAID
Multiple sequence alignments: essential tool for sequence analysis
PAID
Next generation sequencing
Solutions to biological problems through sequencing
A window into third-generation sequencing
Bioinformatics challenges of new sequencing technology
Review on applications of NGS
Statistical analyses of next generation sequence data: An overview
Next generation sequencing: applications beyond genomes
Potential impact of next-generation sequencing (NGS) technologies on genomics
Uncovering the immunological repertoire through next-generation sequencing
The power of NGS technologies to delineate the genome organization in cancer: from mutations to structural variations and epigenetic alterations
Pathways
Pathway analysis of genomic data: concepts, methods and prospects for future development
PAID
Targeting the extracellular signal-regulated kinase pathway in cancer therapy
Use of pathway information in molecular epidemiology
Bioinformatics applications for pathway analysis of microarray data
PAID
Emerging applications of network and pathway analysis in drug discovery and development
PAID
Biological pathway construction and analysis
Pathway analysis tools and toxicogenomics reference databases for risk assessment
PAID
Pathway and ontology analysis
PAID
Significance of Wnt pathway in human cancers
PAID
Integrated pathway-genome databases and their role in drug discovery
PAID
The final common pathway of cancer
Primer designing
PCR primer designing and trouble shooting
PAID
General concepts for PCR primer designing
Optimization and troubleshooting in PCR
Recent Advances in the Polymerase Chain Reaction
PAID
Sequencing of PCR-amplified DNA
Amplifying DNA with arbitrary oligonucleotide primers
Promoter prediction
An introduction to promoters, their types and activities in detail
The transcriptional initiation process: review
PAID
A description on RNA polymerase II core promoter elements
Functional characterization of core promoter elements
Compilation and analysis of E.coli promoter DNA sequences
PAID
Effects of a polymorphism in the human tumor necrosis factor alpha promoter on transcriptional activation
The organization, promoter analysis and expression of the human PPARG gene
Origin and evolution of CpG islands: a review
A novel method for prokaryotic promoter prediction based on DNA stability
Dragon Promoter Finder: recognition of vertebrate RNA polymerase II promoters
Promoter2.0: for the recognition of pol II promoter sequences
Interpolated markov chains for eukaryotic promoter recognition
Large scale human promoter mapping using CpG islands
Identification and analysis of eukaryotic promoters: recent computational approaches
PAID
Predicting Pol II promoter sequences using transcription factor binding sites
PAID
TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies
The Eukaryotic Promoter Database EPD
SCPD: a promoter database of the yeast Saccharomyces cerevisiae
MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and CHIP-chip experimental data
PlantProm: a database of plant promoter sequences
Promoter Extraction from GenBank (PEG): automatic extraction of eukaryotic promoter sequences in large sets of genes
Osteo-Promoter Database (OPD) - promoter analysis in skeletal cells
Protein structure prediction
Ab initio structure prediction
Structure prediction and model quality assessment
Threading approach for proteins with low homology
Advances in homology protein structure modeling
Introduction to homology modeling (wikipedia)
Homology Modeling
An article on ab initio structure prediction: progress and prospects
Protein homology detection by HMM - HMM comparison
PAID
Homology modeling of proteins - powerpoint presentation
Advances in template based protein modeling
Ab initio structure prediction- current scenario
Protein-protein interactions
Principles of protein-protein interactions
Protein-protein interactions: in vivo and in vitro detection methods
PAID
Methods for the detection and analysis of protein-protein interactions
PAID
Protein-protein interactions: detection and analysis methods
Moleacular interactions: models and tools
Protein-protein interaction networks: from interactions to networks
Genome-wide protein interaction maps using two-hybrid systems
PAID
Bioinformatics of large-scale protein interaction networks
RNA structure prediction
Overview of RNA structure prediction
Revolutions in RNA secondary structure prediction
PAID
Principles of free energy minimization and comparative approaches of RNA structure prediction
PAID
Structure prediction by free energy minimization
PAID
Analysis of RNA sequence using covariance models
Statistical sampling algorithm for RNA structure prediction
Stochastic context free grammars (SCFG) based approach to predict RNA structure
Computational RNA three-dimensional modeling: Briding the gap in RNA structure prediction
PAID
Computational approaches for modeling nucleic acids
PAID
Computational tools for prediction and design of DNA and RNA structures
PAID
SNP analysis
Genotyping single nucleotide polymorphisms: a review
PAID
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