Predicting transcription factor affinities to DNA from a biophysical model
Reliable prediction of Drosha processing sites improves microRNA gene prediction
Complementary intron sequence motifs associated with human exon repetition: a role for intragenic, inter-transcript interactions in gene expression
Striped Smith–Waterman speeds database searches six times over other SIMD implementations
QOMA: quasi-optimal multiple alignment of protein sequences
Tree and rate estimation by local evaluation of heterochronous nucleotide data
In silico grouping of peptide/HLA class I complexes using structural interaction characteristics
Interpretation of ANOVA models for microarray data using PCA
A framework for gene expression analysis
Dependence network modeling for biomarker identification
Modular organization of protein interaction networks
CGI: a new approach for prioritizing genes by combining gene expression and protein–protein interaction data
Network neighborhood analysis with the multi-node topological overlap measure
SAGA: a subgraph matching tool for biological graphs
GenoProfiler: batch processing of high-throughput capillary fingerprinting data
PEAKS: identification of regulatory motifs by their position in DNA sequences
Detecting protein dissimilarities in multiple alignments using Bayesian variable selection
AGScan: a pluggable microarray image quantification software based on the ImageJ library
KGraph: a system for visualizing and evaluating complex genetic associations
LdCompare: rapid computation of single- and multiple-marker r 2 and genetic coverage
WHAP: haplotype-based association analysis
Using GOstats to test gene lists for GO term association
Sungear: interactive visualization and functional analysis of genomic datasets
ProteomeCommons.org IO Framework: reading and writing multiple proteomics data formats
PrepMS: TOF MS data graphical preprocessing tool
ECCB 2006
ECCB 2006 Organization
Simulating multiplexed SNP discovery rates using base-specific cleavage and mass spectrometry
ISIS: interaction sites identified from sequence
Incremental window-based protein sequence alignment algorithms
Multiple alignment by sequence annealing
Tandem repeats over the edit distance
Designing patterns for profile HMM search
Simultaneous alignment and annotation of cis-regulatory regions
A comparative genome approach to marker ordering
Genetic code symmetry and efficient design of GC-constrained coding sequences
Merging microarray cell synchronization experiments through curve alignment
Family relationships: should consensus reign?—consensus clustering for protein families
Optimization of probe coverage for high-resolution oligonucleotide aCGH
Discovering tightly regulated and differentially expressed gene sets in whole genome expression data
A supervised approach for identifying discriminating genotype patterns and its application to breast cancer data
Electrostatic potentials of proteins in water: a structured continuum approach
Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family
Phylogenetic reconstruction from non-genomic data
Inferring phylogeny from whole genomes
Efficient parsimony-based methods for phylogenetic network reconstruction
Using median sets for inferring phylogenetic trees
Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates
Efficient inference on known phylogenetic trees using Poisson regression
Identifying HLA supertypes by learning distance functions
Learning probabilistic models of cis-regulatory modules that represent logical and spatial aspects
Rediscovering secondary structures as network motifs—an unsupervised learning approach
Identification of conserved protein complexes based on a model of protein network evolution
Biological network comparison using graphlet degree distribution
Similarities and differences of gene expression in yeast stress conditions
TOPP—the OpenMS proteomics pipeline
Difference detection in LC-MS data for protein biomarker discovery
Vorolign—fast structural alignment using Voronoi contacts
Prediction and simulation of motion in pairs of transmembrane α-helices
Using an alignment of fragment strings for comparing protein structures
A tale of two tails: why are terminal residues of proteins exposed?
A novel pattern recognition algorithm to classify membrane protein unfolding pathways with high-throughput single-molecule force spectroscopy
EBIMed—text crunching to gather facts for proteins from Medline