Estimating the order of mutations during tumorigenesis from tumor genome sequencing data
MMFPh
Automated gene-model curation using global discriminative learning
Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles
A hybrid approach to protein differential expression in mass spectrometry-based proteomics
Utilizing RNA-Seq data for de novo coexpression network inference
optiCall
On the calculation of signal transduction ability of signaling transduction pathways in intracellular communication
Stability of gene rankings from RNAi screens
Truncated branch and bound achieves efficient constraint-based genetic design
Ranking viruses
ChemSpot
TSSi—an R package for transcription start site identification from 5′ mRNA tag data
NuST
Tachyon search speeds up retrieval of similar sequences by several orders of magnitude
Geneious Basic
PSI-Search
Improving the TFold test for differential shotgun proteomics
DelPhi web server v2
FindGeo
DecoyFinder
RFMapp
graph2tab, a library to convert experimental workflow graphs into tabular formats
Editorial
ISMB 2012 PROCEEDINGS PAPERS COMMITTEE
GenomeRing
Joint stage recognition and anatomical annotation of drosophila gene expression patterns
Improved synapse detection for mGRASP-assisted brain connectivity mapping
Protein subcellular location pattern classification in cellular images using latent discriminative models
How networks change with time
A single source k-shortest paths algorithm to infer regulatory pathways in a gene network
A conditional neural fields model for protein threading
Novel domain combinations in proteins encoded by chimeric transcripts
MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins
Recognition models to predict DNA-binding specificities of homeodomain proteins
Ranking models of transmembrane β-barrel proteins using Z-coordinate predictions
Minimum message length inference of secondary structure from protein coordinate data
Ranking of multidimensional drug profiling data by fractional-adjusted bi-partitional scores
Statistical model-based testing to evaluate the recurrence of genomic aberrations
Data-driven integration of epidemiological and toxicological data to select candidate interacting genes and environmental factors in association with disease
Identifying disease sensitive and quantitative trait-relevant biomarkers from multidimensional heterogeneous imaging genetics data via sparse multimodal multitask learning
Leveraging input and output structures for joint mapping of epistatic and marginal eQTLs
Incorporating prior information into association studies
DELISHUS
Detection of allele-specific methylation through a generalized heterogeneous epigenome model
Xenome—a tool for classifying reads from xenograft samples
Dissect
SEQuel
Weighted pooling—practical and cost-effective techniques for pooled high-throughput sequencing
Towards 3D structure prediction of large RNA molecules
Identification of sequence–structure RNA binding motifs for SELEX-derived aptamers
GraphClust
Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networks
NORMAL
Lineage-based identification of cellular states and expression programs
Matching experiments across species using expression values and textual information
Fast alignment of fragmentation trees
DACTAL
Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss
Extending ontologies by finding siblings using set expansion techniques
AUTHOR INDEX