Bioinformatics 101: Bioinformatics Journals

Here are some of the journals that I check on a weekly basis.  I would strongly recommend subscribing to the relevant RSS feeds (using something like Google Reader).

Bioinformatics / Computational Biology:

• Bioinformatics
• PLoS Computational Biology
• BMC Bioinformatics

Genomics:

• Genome Research
• Genome Biology
• Nucleic Acids Research
• PLoS Genetics
• BMC Genomics

Other Journals:

• Nature Methods and Nature Biotechnology - not specific for bioinformatics articles, but many important programs / protocols are published here
• PLOS ONE - general subject journal, but it has some good bioinformatics articles
• peerJ - similar to PLOS ONE, but utilizes a membership system (so, you pay by author instead of by article)
• Nature, Science, PNAS, etc.

Tutorials / Blogs:

• OpenHelix - tutorials for popular programs; some free, some require subscription
• Open Helix Blog - this covers tutorials and FAQs for common bioinformatics tools. I mostly read it for the Friday SNPpets (collection of popular weekly twitter feeds)
• Omixon Blog - Bioinformatics company that provides free tutorials for common tools
• Core Genomics - "personal blog written by James Hadfield who runs a Genomics core facility Cambridge" - lots of interesting technical details about next-generation sequencing
• MassGenomics - medical genomics blog by Dan Koboldt, a staff scientist at the Genome Institute at Washington University. Consistently great article reviewers.
• Genomes Unzipped - popular blog run by several genomics researchers. I would argue that it was made popular by Daniel McArthur (who doesn't post there as often now), but there are still other contributors that keep the blog up to date.
• Getting Genetics Done - a well-maintained blog written mostly by Stephen Turner (Bioinformatics Core director at University of Virginia). Focuses mostly on providing technical suggestions.
• List of Bioinformatics Workshops
• NIH Bioinformatics Support System - probably doesn't have a feed, but contains useful tutorials

Bioinformatics 101: RNA Sequence Analysis

miRNA Resources:

• MirBase
• free database of miRNA sequences
• TarBase
• free database of experimentally validated miRNA targets
• miRecords
• database of miRNA-target interactions
• IPA miRNA-target analysis
• commercial database that includes free databases as well as a proprietary list of miRNA-target interactions found using text-mining of the literature
• TargetScan
• free tool to predict miRNA targets
• sylArray
• tool to predict miRNA targets from gene expression data.  Uses gene ranking, so it doesn't require mRNA differential expression (although you will need to check that the miRNA regulator is differentially expressed)

In general, I think you really need both miRNA expression and mRNA expression data to get reliable results when trying to identify miRNA-target interactions

RNA-Seq Splicing Events:

• JunctionSeq - extends DEXSeq to include junction coverage (including junctions not defined among isoforms in reference database).  Strictly speaking, it only calls differential exon and junction coverage (and provides a statistic at the gene-level), but the junction coverage can be helpful in identifying some other types of splicing events.
• MATS - Provides differential splicing for skipped exon (SE), alternative 5' splice site (A5SS), alternative 3' splice site (A3SS), mutually exclusive exons (MXE), and retained intron (IR)
• MISO - Provides single-sample and differential splicing for skipped exon (SE), alternative 5' splice site (A5SS), alternative 3' splice site (A3SS), mutually exclusive exons (MXE), retained intron (IR), tandem 3' UTRs (TandemUTR), alternative first exon (AFE), and alternative last exon (ALE)

RNA Secondary Structure:

• Mfold
• RNAfold

RNA Domain Homology:

• Rfam
• may be helpful in predicting function of a non-coding RNA of unknown function

de novo Assembly Algorithms (RNA-Seq):

• Oases
• Trans-ABySS
• Trinity
• eXpress - mRNA quantification tool that works with both de novo assembly transcripts (as well as transcripts from direct genome alignment)

RNA-Seq QC

• FASTX-Toolkit - popular suite of tools to quantify and manipulate sequences .fastq and .fasta files
• samtools - popular suite of tools to quantify and reformat .sam/.bam files
• Picard - Java-based implementation of samtools; CollectRNASeqMetrics can produce a coverage plot (normalized per start to end of transcript)
• RSeQC - package to produce a variety of RNA-Seq QC figures

General RNA-Seq Analysis

• Wikipedia list of RNA-Seq bioinformatics tools
• Please see Gene Expression Analysis for tools for statistical analysis of RNA-Seq data

Bioinformatics 101: Literature / Text Mining

Search Engines:

• PubMed
• popular, free tool provided by NCBI to search biomedical journal articles
• includes links to connected NCBI resources (GEO, RefSeq, etc.)
• Google Scholar
• popular, free tool to search the scientific literature
• provides citation information
• allows authors to create their own bibliographies (which provide author-level citation metrics) 

Gene-Centric Information:

• NCBI Gene
• free tool curated by the NCBI
• includes literature citations, Gene Ontology categories, alternative and official gene symbols, etc.
• iHOP (Information Hyperlinked Over Proteins)
• free text-mining program that predicts interactions between genes
• PolySearch
• free text-mining program that predicts interactions between genes, diseases, drugs, metabolites, SNPs, pathways, and/or tissues
• IPA (Ingenuity Pathway Analysis)
• commercial program curating information about genes, metabolites, etc.
• most popular use is for functional enrichment analysis, but it can also be used as a general tool for searching the literature