Method for identifying transcription factor binding sites in yeast
Combining multiple microarrays in the presence of controlling variables
Ribosomal RNA as molecular barcodes: a simple correlation analysis without sequence alignment
PROXIMO—a new docking algorithm to model protein complexes using data from radical probe mass spectrometry (RP-MS)
Molecular complexes at a glance: automated generation of two-dimensional complex diagrams
Ensemble classifier for protein fold pattern recognition
SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments
How accurately can we control the FDR in analyzing microarray data?
Context-specific infinite mixtures for clustering gene expression profiles across diverse microarray dataset
A Mixture model with random-effects components for clustering correlated gene-expression profiles
A probabilistic dynamical model for quantitative inference of the regulatory mechanism of transcription
Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques
Observing local and global properties of metabolic pathways: ‘load points’ and ‘choke points’ in the metabolic networks
Synchronizing a multicellular system by external input: an artificial control strategy
Combo: a whole genome comparative browser
TSSub: eukaryotic protein subcellular localization by extracting features from profiles
HoSeqI: automated homologous sequence identification in gene family databases
TRFMA: a web-based tool for terminal restriction fragment length polymorphism analysis based on molecular weight
TopoICE-R: 3D visualization modeling the topology of DNA recombination
FCP: functional coverage of the proteome by structures
SHARP2: protein–protein interaction predictions using patch analysis
Analysis assistant for single-molecule force spectroscopy data on membrane proteins—MPTV
Prelude&Fugue, predicting local protein structure, early folding regions and structural weaknesses
BDT: an easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with AutoDock
BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge
ISMB 2006
ISMB 2006 Organization
Automatic clustering of orthologs and inparalogs shared by multiple proteomes
DynaPred: A structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations
ProfilePSTMM: capturing tree-structure motifs in carbohydrate sugar chains
The iRMSD: a local measure of sequence alignment accuracy using structural information
A model-based approach for mining membrane protein crystallization trials
Integrating structured biological data by Kernel Maximum Mean Discrepancy
AClAP, Autonomous hierarchical agglomerative Cluster Analysis based protocol to partition conformational datasets
A top-level ontology of functions and its application in the Open Biomedical Ontologies
Comparative footprinting of DNA-binding proteins
A probabilistic approach to protein backbone tracing in electron density maps
CONTRAfold: RNA secondary structure prediction without physics-based models
springScape: visualisation of microarray and contextual bioinformatic data using spring embedding and an ‘information landscape’
Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles
Dense subgraph computation via stochastic search: application to detect transcriptional modules
Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle
Semi-supervised LC/MS alignment for differential proteomics
Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE
MotifCut: regulatory motifs finding with maximum density subgraphs
Bistable switching and excitable behaviour in the activation of Src at mitosis
Context-specific independence mixture modeling for positional weight matrices
Improved Pruning algorithms and Divide-and-Conquer strategies for Dead-End Elimination, with application to protein design
Predicting the prognosis of breast cancer by integrating clinical and microarray data with Bayesian networks
ZPRED: Predicting the distance to the membrane center for residues in α-helical membrane proteins
Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data
Modelling sequential protein folding under kinetic control
BNTagger: improved tagging SNP selection using Bayesian networks
Finding the evidence for protein-protein interactions from PubMed abstracts
Learning MHC I—peptide binding
Comparative genomics reveals unusually long motifs in mammalian genomes
Distance based algorithms for small biomolecule classification and structural similarity search
Rapid knot detection and application to protein structure prediction
Annotating proteins by mining protein interaction networks
A decompositional approach to parameter estimation in pathway modeling: a case study of the Akt and MAPK pathways and their crosstalk
Finding novel genes in bacterial communities isolated from the environment
A combinatorial pattern discovery approach for the prediction of membrane dipping (re-entrant) loops
Interpreting anonymous DNA samples from mass disasters—probabilistic forensic inference using genetic markers
Peptide sequence tag-based blind identification of post-translational modifications with point process model
Identifying cycling genes by combining sequence homology and expression data
Quantification of transcription factor expression from Arabidopsis images
Mutation parameters from DNA sequence data using graph theoretic measures on lineage trees
Indel seeds for homology search
Efficient identification of DNA hybridization partners in a sequence database
An experimental metagenome data management and analysis system
An equilibrium partitioning model connecting gene expression and cis-motif content
Identification of metabolic units induced by environmental signals
Informative priors based on transcription factor structural class improve de novo motif discovery
Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone
Create and assess protein networks through molecular characteristics of individual proteins
BaCelLo: a balanced subcellular localization predictor
Semi-supervised analysis of gene expression profiles for lineage-specific development in the Caenorhabditis elegans embryo
Decoding non-unique oligonucleotide hybridization experiments of targets related by a phylogenetic tree
Integrating copy number polymorphisms into array CGH analysis using a robust HMM
Relative contributions of structural designability and functional diversity in molecular evolution of duplicates
Integrating image data into biomedical text categorization
On counting position weight matrix matches in a sequence, with application to discriminative motif finding
An ontology for a Robot Scientist
ARTS: accurate recognition of transcription starts in human
A computational approach toward label-free protein quantification using predicted peptide detectability
An integrative approach for causal gene identification and gene regulatory pathway inference
Computational inference of the molecular logic for synaptic connectivity in C. elegans
Novel Unsupervised Feature Filtering of Biological Data
Constructing Near-Perfect Phylogenies with multiple homoplasy events
SNP Function Portal: a web database for exploring the function implication of SNP alleles
Protein classification using ontology classification
Inferring Functional Pathways from Multi-Perturbation Data
Accessing bioscience images from abstract sentences
A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements
Author Index