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Volume 28, Issue 12, June 2012
On the calculation of signal transduction ability of signaling transduction pathways in intracellular communication: systematic approach
Bioinformatics, Volume 28, Issue 12, June 2012, Pages 1604–1611, https://doi.org/10.1093/bioinformatics/bts159
Estimating the order of mutations during tumorigenesis from tumor genome sequencing data
Bioinformatics, Volume 28, Issue 12, June 2012, Pages 1555–1561, https://doi.org/10.1093/bioinformatics/bts168
Automated gene-model curation using global discriminative learning
Bioinformatics, Volume 28, Issue 12, June 2012, Pages 1571–1578, https://doi.org/10.1093/bioinformatics/bts176
optiCall: a robust genotype-calling algorithm for rare, low-frequency and common variants
Bioinformatics, Volume 28, Issue 12, June 2012, Pages 1598–1603, https://doi.org/10.1093/bioinformatics/bts180
Ranking viruses: measures of positional importance within networks define core viruses for rational polyvalent vaccine development
Bioinformatics, Volume 28, Issue 12, June 2012, Pages 1624–1632, https://doi.org/10.1093/bioinformatics/bts181
Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles
Bioinformatics, Volume 28, Issue 12, June 2012, Pages 1579–1585, https://doi.org/10.1093/bioinformatics/bts182
ChemSpot: a hybrid system for chemical named entity recognition
Bioinformatics, Volume 28, Issue 12, June 2012, Pages 1633–1640, https://doi.org/10.1093/bioinformatics/bts183
RFMapp: ribosome flow model application
Bioinformatics, Volume 28, Issue 12, June 2012, Pages 1663–1664, https://doi.org/10.1093/bioinformatics/bts185
TSSi—an R package for transcription start site identification from 5′ mRNA tag data
Bioinformatics, Volume 28, Issue 12, June 2012, Pages 1641–1642, https://doi.org/10.1093/bioinformatics/bts189
Stability of gene rankings from RNAi screens
Bioinformatics, Volume 28, Issue 12, June 2012, Pages 1612–1618, https://doi.org/10.1093/bioinformatics/bts192
A hybrid approach to protein differential expression in mass spectrometry-based proteomics
Bioinformatics, Volume 28, Issue 12, June 2012, Pages 1586–1591, https://doi.org/10.1093/bioinformatics/bts193
MMFPh: a maximal motif finder for phosphoproteomics datasets
Bioinformatics, Volume 28, Issue 12, June 2012, Pages 1562–1570, https://doi.org/10.1093/bioinformatics/bts195
Tachyon search speeds up retrieval of similar sequences by several orders of magnitude
Bioinformatics, Volume 28, Issue 12, June 2012, Pages 1645–1646, https://doi.org/10.1093/bioinformatics/bts197
Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
Bioinformatics, Volume 28, Issue 12, June 2012, Pages 1647–1649, https://doi.org/10.1093/bioinformatics/bts199
DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol
Bioinformatics, Volume 28, Issue 12, June 2012, Pages 1655–1657, https://doi.org/10.1093/bioinformatics/bts200
NuST: analysis of the interplay between nucleoid organization and gene expression
Bioinformatics, Volume 28, Issue 12, June 2012, Pages 1643–1644, https://doi.org/10.1093/bioinformatics/bts201
Recognition models to predict DNA-binding specificities of homeodomain proteins
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i84–i89, https://doi.org/10.1093/bioinformatics/bts202
Statistical model-based testing to evaluate the recurrence of genomic aberrations
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i115–i120, https://doi.org/10.1093/bioinformatics/bts203
Lineage-based identification of cellular states and expression programs
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i250–i257, https://doi.org/10.1093/bioinformatics/bts204
Matching experiments across species using expression values and textual information
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i258–i264, https://doi.org/10.1093/bioinformatics/bts205
NOrMAL: accurate nucleosome positioning using a modified Gaussian mixture model
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i242–i249, https://doi.org/10.1093/bioinformatics/bts206
Fast alignment of fragmentation trees
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i265–i273, https://doi.org/10.1093/bioinformatics/bts207
Weighted pooling—practical and cost-effective techniques for pooled high-throughput sequencing
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i197–i206, https://doi.org/10.1093/bioinformatics/bts208
MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i75–i83, https://doi.org/10.1093/bioinformatics/bts209
Identification of sequence–structure RNA binding motifs for SELEX-derived aptamers
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i215–i223, https://doi.org/10.1093/bioinformatics/bts210
How networks change with time
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i40–i48, https://doi.org/10.1093/bioinformatics/bts211
A single source k-shortest paths algorithm to infer regulatory pathways in a gene network
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i49–i58, https://doi.org/10.1093/bioinformatics/bts212
A conditional neural fields model for protein threading
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i59–i66, https://doi.org/10.1093/bioinformatics/bts213
Dissect: detection and characterization of novel structural alterations in transcribed sequences
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i179–i187, https://doi.org/10.1093/bioinformatics/bts214
Extending ontologies by finding siblings using set expansion techniques
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i292–i300, https://doi.org/10.1093/bioinformatics/bts215
Novel domain combinations in proteins encoded by chimeric transcripts
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i67–i74, https://doi.org/10.1093/bioinformatics/bts216
GenomeRing: alignment visualization based on SuperGenome coordinates
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i7–i15, https://doi.org/10.1093/bioinformatics/bts217
DACTAL: divide-and-conquer trees (almost) without alignments
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i274–i282, https://doi.org/10.1093/bioinformatics/bts218
SEQuel: improving the accuracy of genome assemblies
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i188–i196, https://doi.org/10.1093/bioinformatics/bts219
Joint stage recognition and anatomical annotation of drosophila gene expression patterns
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i16–i24, https://doi.org/10.1093/bioinformatics/bts220
Improved synapse detection for mGRASP-assisted brain connectivity mapping
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i25–i31, https://doi.org/10.1093/bioinformatics/bts221
Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networks
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i233–i241, https://doi.org/10.1093/bioinformatics/bts222
Minimum message length inference of secondary structure from protein coordinate data
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i97–i105, https://doi.org/10.1093/bioinformatics/bts223
GraphClust: alignment-free structural clustering of local RNA secondary structures
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i224–i232, https://doi.org/10.1093/bioinformatics/bts224
Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i283–i291, https://doi.org/10.1093/bioinformatics/bts225
Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i207–i214, https://doi.org/10.1093/bioinformatics/bts226
Leveraging input and output structures for joint mapping of epistatic and marginal eQTLs
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i137–i146, https://doi.org/10.1093/bioinformatics/bts227
Identifying disease sensitive and quantitative trait-relevant biomarkers from multidimensional heterogeneous imaging genetics data via sparse multimodal multitask learning
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i127–i136, https://doi.org/10.1093/bioinformatics/bts228
Data-driven integration of epidemiological and toxicological data to select candidate interacting genes and environmental factors in association with disease
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i121–i126, https://doi.org/10.1093/bioinformatics/bts229
Protein subcellular location pattern classification in cellular images using latent discriminative models
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i32–i39, https://doi.org/10.1093/bioinformatics/bts230
Detection of allele-specific methylation through a generalized heterogeneous epigenome model
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i163–i171, https://doi.org/10.1093/bioinformatics/bts231
Ranking of multidimensional drug profiling data by fractional-adjusted bi-partitional scores
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i106–i114, https://doi.org/10.1093/bioinformatics/bts232
Ranking models of transmembrane β-barrel proteins using Z-coordinate predictions
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i90–i96, https://doi.org/10.1093/bioinformatics/bts233
DELISHUS: an efficient and exact algorithm for genome-wide detection of deletion polymorphism in autism
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i154–i162, https://doi.org/10.1093/bioinformatics/bts234
Incorporating prior information into association studies
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i147–i153, https://doi.org/10.1093/bioinformatics/bts235
Xenome—a tool for classifying reads from xenograft samples
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i172–i178, https://doi.org/10.1093/bioinformatics/bts236
PSI-Search: iterative HOE-reduced profile SSEARCH searching
Bioinformatics, Volume 28, Issue 12, June 2012, Pages 1650–1651, https://doi.org/10.1093/bioinformatics/bts240
Utilizing RNA-Seq data for de novo coexpression network inference
Bioinformatics, Volume 28, Issue 12, June 2012, Pages 1592–1597, https://doi.org/10.1093/bioinformatics/bts245
FindGeo: a tool for determining metal coordination geometry
Bioinformatics, Volume 28, Issue 12, June 2012, Pages 1658–1660, https://doi.org/10.1093/bioinformatics/bts246
Improving the TFold test for differential shotgun proteomics
Bioinformatics, Volume 28, Issue 12, June 2012, Pages 1652–1654, https://doi.org/10.1093/bioinformatics/bts247
DecoyFinder: an easy-to-use python GUI application for building target-specific decoy sets
Bioinformatics, Volume 28, Issue 12, June 2012, Pages 1661–1662, https://doi.org/10.1093/bioinformatics/bts249
Truncated branch and bound achieves efficient constraint-based genetic design
Bioinformatics, Volume 28, Issue 12, June 2012, Pages 1619–1623, https://doi.org/10.1093/bioinformatics/bts255
graph2tab, a library to convert experimental workflow graphs into tabular formats
Bioinformatics, Volume 28, Issue 12, June 2012, Pages 1665–1667, https://doi.org/10.1093/bioinformatics/bts258
Editorial
Bioinformatics, Volume 28, Issue 12, June 2012, Page i1, https://doi.org/10.1093/bioinformatics/bts281
ISMB 2012 PROCEEDINGS PAPERS COMMITTEE
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i2–i6, https://doi.org/10.1093/bioinformatics/bts287
AUTHOR INDEX
Bioinformatics, Volume 28, Issue 12, June 2012, Page i301, https://doi.org/10.1093/bioinformatics/bts324
