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All Top News in Life Sciences
Top Bioinformatics News
EBI
We can learn a lot from other species
Butterfly genome reveals a promiscuous past
SwissProt and TrEMBL Protein database release
Gene Ontology Annotation (UniProt-GOA) Database updated
EMBO welcomes new members
The latest Ensembl update (e!67) has been released
ChEBI release 91 is now available, with 28,093 fully annotated entities
IntAct Release 153
InterPro 37.0 released
A matter of priorities: Bacteria evolved way to safeguard crucial genetic material
NCBI Gene DB
RefSeq genome annotation in GFF3 format (v.1.20)
Links Between RefSeqs and Vega
Changes in reporting of clone names
Phasing out use of hypothetical in Gene and RefSeq protein names
CCDS human update (HsGRCh37.3) is public in Gene
Celera assembly no longer appearing in Gene
Readthrough genes
Words excluded from queries
Policy change in reporting gene location only on top level genome-level RefSeqs
Ensembl matches for Pongo abelii (Sumatran orangutan)
NCBI dbGaP
New | phs000257.v2.p1 | Human Gut Microbiome in Crohn's Disease
Update | phs000096.v4.p1 | Additional imputed genotype data added | HAPO Maternal Glycemia and Birthweight GEI Study
New | phs000418.v1.p1 | Temporal Dissection of Tumorigenesis in Primary Cancers
New | phs000456.v1.p1 | Risk Assessment of Cerebrovascular Events (RACE) Study
New | phs000443.v1.p1 | Molecular Profiling of Cancer
New | phs000478.v1.p1 | Strabismus, CCDD and Other Anomalies
New | phs000298.v1.p1 | ARRA Autism Sequencing Collaboration
Bioinformatics Articles
Bioinformatics
Predicting giant transmembrane {beta}-barrel architecture
1001 Proteomes: a functional proteomics portal for the analysis of Arabidopsis thaliana accessions
CONTRA: copy number analysis for targeted resequencing
Probabilistic suffix array: efficient modeling and prediction of protein families
Fulcrum: condensing redundant reads from high-throughput sequencing studies
A subspace method for the detection of transcription factor binding sites
PhyLAT: a phylogenetic local alignment tool
Fast protein binding site comparisons using visual words representation
Matrix eQTL: ultra fast eQTL analysis via large matrix operations
Fast and accurate inference of local ancestry in Latino populations
BMC Bioinformatics
Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community
Statistical analysis of real-time PCR data
Tavaxy: Integrating Taverna and Galaxy workflows with cloud computing support
Readjoiner: a fast and memory efficient string graph-basedsequence assembler
Cancer bioinformatics: A new approach to systems clinical medicine
A comparison of feature selection and classification methods in DNA methylation studies using the Illumina Infinium platform
WGCNA: an R package for weighted gene co-expressionnetwork analysis
A comparative evaluation of sequence classification programs
Methods for visual mining of genomic and proteomic data atlases
GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction
JCBC
IDENTIFICATION OF SHORTENED 3′ UNTRANSLATED REGIONS FROM EXPRESSION ARRAYS
STRUCTURE FLUCTUATIONS AND CONFORMATIONAL CHANGES IN PROTEIN BINDING
SHEEP: A TOOL FOR DESCRIPTION OF β-SHEETS IN PROTEIN 3D STRUCTURES
DEPPDB — DNA ELECTROSTATIC POTENTIAL PROPERTIES DATABASE: ELECTROSTATIC PROPERTIES OF GENOME DNA ELEMENTS
ANALYSIS OF CONTEXT-DEPENDENT ERRORS FOR ILLUMINA SEQUENCING
PRACTICALITY AND TIME COMPLEXITY OF A SPARSIFIED RNA FOLDING ALGORITHM
DERIVED SNP ALLELES ARE USED MORE FREQUENTLY THAN ANCESTRAL ALLELES AS RISK-ASSOCIATED VARIANTS IN COMMON HUMAN DISEASES
VirE2-DEPENDENT PORES FOR ssDNA TRANSFER ACROSS ARTIFICIAL AND CELL MEMBRANES
EVALUATING MIXTURE MODELS FOR BUILDING RNA KNOWLEDGE-BASED POTENTIALS
FLEXIBLE AND ROBUST NETWORKS
Briefings in Bioinformatics
Bioinformatics tools and database resources for systems genetics analysis in mice--a short review and an evaluation of future needs
LEPSCAN--a web server for searching latent periodicity in DNA sequences
Learning transcriptional regulation on a genome scale: a theoretical analysis based on gene expression data
How to cluster gene expression dynamics in response to environmental signals
Dissection of human MiRNA regulatory influence to subpathway
Calculating transcription factor binding maps for chromatin
Biological network motif detection: principles and practice
GO-function: deriving biologically relevant functions from statistically significant functions
Detecting coevolving positions in a molecule: why and how to account for phylogeny
A toolbox for developing bioinformatics software
JBRA
A new algorithm for quantifying binding site pattern similarity with applications for Next Generation Sequencing
An effective graph-based clustering technique to identify coherent patterns from gene expression data
Large margin classifiers and Random Forests for integrated biological prediction
Combining gene expression and interaction network data to improve kidney lesion score prediction
Detecting molecular selection on single amino acid replacements
Computational analysis of adaptive antigenic mutations of the human influenza hemagglutinin for vaccine strain selection
Evolution of bacterial ribosomal protein L1
Application of nanotechnology in cancer: a review
New encoded single-indicator sequences based on physico-chemical parameters for efficient exon identification
Discovering best candidates for Hepatocellular Carcinoma (HCC) by in-silico techniques and tools
Database
CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations
The gene-specific codon counting database: a genome-based catalog of one-, two-, three-, four- and five-codon combinations present in Saccharomyces cerevisiae genes
AntiFam: a tool to help identify spurious ORFs in protein annotation
PRIDE: Quality control in a proteomics data repository
A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework
Aptamer base: a collaborative knowledge base to describe aptamers and SELEX experiments
Tetrahymena genome database Wiki: a community-maintained model organism database
Tracking and coordinating an international curation effort for the CCDS Project
Community gene annotation in practice
Argo: an integrative, interactive, text mining-based workbench supporting curation
BioMedical Informatics
Relation mining experiments in the pharmacogenomics domain
Ontology-guided feature engineering for clinical text classification
COnto–Diff: generation of complex evolution mappings for life science ontologies
Decision-making model for early diagnosis of congestive heart failure using rough set and decision tree approaches
Using PharmGKB to train text mining approaches for identifying potential gene targets for pharmacogenomic studies
Standardizing clinical laboratory data for secondary use
A SNPshot of PubMed to associate genetic variants with drugs, diseases, and adverse reactions
A knowledge-driven conditional approach to extract pharmacogenomics specific drug–gene relationships from free text
Development of a benchmark corpus to support the automatic extraction of drug-related adverse effects from medical case reports
Measuring the level of activity in community built bio-ontologies
Computational Biology
A Generalized Linear Model for Peak Calling in ChIP-Seq Data
Combinatorics of the Breakage-Fusion-Bridge Mechanism
Mapping Reads on a Genomic Sequence: An Algorithmic Overwiew and a Practical Comparative Analysis
Nonadaptive Algorithms for Threshold Group Testing with Inhibitors and Error-Tolerance
Discovery of Protein Complexes with Core-Attachment Structures from Tandem Affinity Purification (TAP) Data
Exploiting Genome Structure in Association Analysis
Identifying Contributors of DNA Mixtures by Means of Quantitative Information of STR Typing
HarmonyDOCK: The Structural Analysis of Poses in Protein-Ligand Docking
Prediction of siRNA Potency Using Sparse Logistic Regression
Biological Cluster Evaluation for Gene Function Prediction
OMICS
Identification of Differentially Expressed Proteins in Curcumin-Treated Prostate Cancer Cell Lines
Impact of Velvet Complex on Transcriptome and Penicillin G Production in Glucose-Limited Chemostat Cultures of a β-Lactam High-Producing Penicillium chrysogenum Strain
Purification of the COP9 Signalosome Complex and Binding Partners from Human T Cells
Proteome Differences Between Male and Female Fetal Cells in Amniotic Fluid
Assessing Differential Expression Measurements by Highly Parallel Pyrosequencing and DNA Microarrays: A Comparative Study
Metabolomics Reveals Differential Levels of Oral Metabolites in HIV-Infected Patients: Toward Novel Diagnostic Targets
Balanced Caloric Macronutrient Composition Downregulates Immunological Gene Expression in Human Blood Cells—Adipose Tissue Diverges
ChIP-seq and Functional Analysis of the SOX2 Gene in Colorectal Cancers
Diving Through the “-Omics”: The Case for Deep Phenotyping and Systems Epidemiology
Can Soy Phytoestrogens Decrease DNA Methylation in BRCA1 and BRCA2 Oncosuppressor Genes in Breast Cancer?
Top Bioinformatics Blogs
Macromolecular Modeling
Weekly literature review
Weekly literature review
Rosetta 3.4 released
Mobile apps for structural biology and protein design
Weekly literature review
ByteSizeBio
Job opening: Scientific Curator at the Jackson Laboratory
Crowdsourcing Genomics II: Unveiling HINdeR and Phrux
Repost: the Scope(s) of Substance
The Inside Poop
It’s a smORF world, after all?
The Mind Wobbles
Google Scholar Citations and Microsoft Academic Search: first impressions
A new journal, a new bogus review: again, the culprits are banned
What should you think about when you think about standards?
The more things change, the more they stay the same
How can socks facilitate scientific outreach?
Blue Collar Bioinformatics
Extending the GATK for custom variant comparisons using Clojure
Making next-generation sequencing analysis pipelines easier with BioCloudCentral and Galaxy integration
Parallel approaches in next-generation sequencing analysis pipelines
Distributed exome analysis pipeline with CloudBioLinux and CloudMan
Summarizing next-gen sequencing variation statistics with Hadoop using Cascalog
Programming4Scientists
How to…optimise Matlab
Scripting for science papers
“Should I switch to Python?”
Writing code for a big scientific collaboration
The ‘programming for scientists’ link montage
The ‘Programming for Scientists’ training montage
The ‘Programming for Scientists’ software project primer
How to explain programming to your Mum
BioinfoBlog
Introduction to Unix systems for Evolutionary Biologists – slides online
Planning a 8-hours “Introduction to Linux” course with trello
Origins of Evolutionary Innovations, chapter 5
Origins of Evolutionary Innovations, chapter 4
The genotype space – how does it looks like?
Bioinformatics Patents
Secondary structure defining database and methods for determining identity and geographic origin of an unknown bioagent thereby
Methods for producing uniquely distinct nucleic acid tags
Time to event data analysis method and system
Method for detection of autoimmune diseases
Differential filtering of genetic data
Biosensor remote collection packaging system with bioinformatics processing
Secondary structure defining database and methods for determining identity and geographic origin of an unknown bioagent thereby
Engineering intracellular sialylation pathways
Polymer encapsulated aluminum particulates
Efficiently determining condition relevant modifiable lifestyle attributes
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