Cloud computing
Cross species analysis of microarray expression data
Gene regulation in the intraerythrocytic cycle of Plasmodium falciparum
Protein function annotation from sequence : prediction of residues interacting with RNA
A local multiple alignment method for detection of non-coding RNA sequences
ModLink+ : improving fold recognition by using protein–protein interactions
Identification of computational hot spots in protein interfaces : combining solvent accessibility and inter-residue potentials improves the accuracy
Enrichment constrained time-dependent clustering analysis for finding meaningful temporal transcription modules
A stochastic model for the evolution of metabolic networks with neighbor dependence
Bayesian inference of protein–protein interactions from biological literature
Application and evaluation of automated semantic annotation of gene expression experiments
WebGBrowse—a web server for GBrowse
CROC : finding chromosomal clusters in eukaryotic genomes
MapView : visualization of short reads alignment on a desktop computer
BEsTRF : a tool for optimal resolution of terminal-restriction fragment length polymorphism analysis based on user-defined primer–enzyme–sequence databases
BIPA : a database for protein–nucleic acid interaction in 3D structures
A graphical algorithm for fast computation of identity coefficients and generalized kinship coefficients
Fluctuation AnaLysis CalculatOR : a web tool for the determination of mutation rate using Luria–Delbrück fluctuation analysis
ELISA-BASE : an integrated bioinformatics tool for analyzing and tracking ELISA microarray data
ProtVirDB : a database of protozoan virulent proteins
ISMB/ECCB 2009 Stockholm
Erratum
Editorial
ISMB/ECCB 2009 Proceedings papers committee
Constrained mixture estimation for analysis and robust classification of clinical time series
Graph theoretical approach to study eQTL : a case study of Plasmodium falciparum
A Classifier-based approach to identify genetic similarities between diseases
Model-based clustering of array CGH data
Viruses selectively mutate their CD8+ T-cell epitopes—a large-scale immunomic analysis
Family classification without domain chaining
Identifying novel constrained elements by exploiting biased substitution patterns
From disease ontology to disease-ontology lite : statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations
Alignment of the UMLS semantic network with BioTop : methodology and assessment
Ontology quality assurance through analysis of term transformations
Computing galled networks from real data
Genotype–phenotype associations : substitution models to detect evolutionary associations between phenotypic variables and genotypic evolutionary rate
Modeling stochasticity and robustness in gene regulatory networks
Grouped graphical Granger modeling for gene expression regulatory networks discovery
Clustered alignments of gene-expression time series data
KELLER : estimating time-varying interactions between genes
Predicting functionality of protein–DNA interactions by integrating diverse evidence
Probabilistic retrieval and visualization of biologically relevant microarray experiments
Proteome coverage prediction with infinite Markov models
Fewer permutations, more accurate P-values
A general computational method for robustness analysis with applications to synthetic gene networks
E-zyme : predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs
Multi-locus match probability in a finite population : a fundamental difference between the Moran and Wright–Fisher models
Speeding up HMM algorithms for genetic linkage analysis via chain reductions of the state space
A multivariate regression approach to association analysis of a quantitative trait network
Inference of locus-specific ancestry in closely related populations
A geometric approach for classification and comparison of structural variants
Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data
Domain-oriented edge-based alignment of protein interaction networks
Network-based prediction of metabolic enzymes' subcellular localization
IsoRankN : spectral methods for global alignment of multiple protein networks
Global alignment of protein–protein interaction networks by graph matching methods
PICKY : a novel SVD-based NMR spectra peak picking method
A framework to refine particle clusters produced by EMAN
Pokefind : a novel topological filter for use with protein structure prediction
REPETITA : detection and discrimination of the periodicity of protein solenoid repeats by discrete Fourier transform
Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation
A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery
Toward a gold standard for promoter prediction evaluation
DISCOVER : a feature-based discriminative method for motif search in complex genomes
Predictions of RNA secondary structure by combining homologous sequence information
Assessing phylogenetic motif models for predicting transcription factor binding sites
Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancy
Efficient exact motif discovery
A partition function algorithm for interacting nucleic acid strands
Predicting and understanding the stability of G-quadruplexes
Author Index