ISMB/ECCB 2017 proceedings
CATS (Coordinates of Atoms by Taylor Series): protein design with backbone flexibility in all locally feasible directions
Deep learning-based subdivision approach for large scale macromolecules structure recovery from electron cryo tomograms
Large-scale structure prediction by improved contact predictions and model quality assessment
SnapDock—template-based docking by Geometric Hashing
Deep learning with word embeddings improves biomedical named entity recognition
BIOSSES: a semantic sentence similarity estimation system for the biomedical domain
Rectified factor networks for biclustering of omics data
Applying meta-analysis to genotype-tissue expression data from multiple tissues to identify eQTLs and increase the number of eGenes
Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference
DextMP: deep dive into text for predicting moonlighting proteins
Chromatin accessibility prediction via convolutional long short-term memory networks with k -mer embedding
HopLand: single-cell pseudotime recovery using continuous Hopfield network-based modeling of Waddington's epigenetic landscape
Improving the performance of minimizers and winnowing schemes
Modelling haplotypes with respect to reference cohort variation graphs
Abundance estimation and differential testing on strain level in metagenomics data
deBGR: an efficient and near-exact representation of the weighted de Bruijn graph
Improved data-driven likelihood factorizations for transcript abundance estimation
Tumor phylogeny inference using tree-constrained importance sampling
Discovery and genotyping of novel sequence insertions in many sequenced individuals
Incorporating interaction networks into the determination of functionally related hit genes in genomic experiments with Markov random fields
Alignment of dynamic networks
Predicting multicellular function through multi-layer tissue networks
A new method to study the change of miRNA-mRNA interactions due to environmental exposures
Multiple network-constrained regressions expand insights into influenza vaccination responses
Image-based spatiotemporal causality inference for protein signaling networks
Denoising genome-wide histone ChIP-seq with convolutional neural networks
TITER: predicting translation initiation sites by deep learning
Direct AUC optimization of regulatory motifs
Exploiting sequence-based features for predicting enhancer-promoter interactions
miniMDS: 3D structural inference from high-resolution Hi-C data
DeepBound: accurate identification of transcript boundaries via deep convolutional neural fields
Integrative deep models for alternative splicing
Efficient approximations of RNA kinetics landscape using non-redundant sampling
A scalable moment-closure approximation for large-scale biochemical reaction networks
Estimation of time-varying growth, uptake and excretion rates from dynamic metabolomics data
popFBA: tackling intratumour heterogeneity with Flux Balance Analysis
Efficient simulation of intrinsic, extrinsic and external noise in biochemical systems
Association testing of bisulfite-sequencing methylation data via a Laplace approximation
Molecular signatures that can be transferred across different omics platforms
Identification of associations between genotypes and longitudinal phenotypes via temporally-constrained group sparse canonical correlation analysis
Predicting phenotypes from microarrays using amplified, initially marginal, eigenvector regression
Systematic identification of feature combinations for predicting drug response with Bayesian multi-view multi-task linear regression
Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes
Increasing the power of meta-analysis of genome-wide association studies to detect heterogeneous effects
When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants
swga: a primer design toolkit for selective whole genome amplification
Tagging SNP-set selection with maximum information based on linkage disequilibrium structure in genome-wide association studies
Pseudoalignment for metagenomic read assignment
RNAscClust: clustering RNA sequences using structure conservation and graph based motifs
Computational modeling of in vivo and in vitro protein-DNA interactions by multiple instance learning
A network model predicts the intensity of residue-protein thermal coupling
Fast, clash-free RNA conformational morphing using molecular junctions
QRank: a novel quantile regression tool for eQTL discovery
Quantifying circular RNA expression from RNA-seq data using model-based framework
Meta-analytic framework for liquid association
Fast admixture analysis and population tree estimation for SNP and NGS data
SANA: simulated annealing far outperforms many other search algorithms for biological network alignment
Stepwise inference of likely dynamic flux distributions from metabolic time series data
VCNet: vector-based gene co-expression network construction and its application to RNA-seq data
Morphologically constrained spectral unmixing by dictionary learning for multiplex fluorescence microscopy
DNA Compass: a secure, client-side site for navigating personal genetic information
Dynamix: dynamic visualization by automatic selection of informative tracks from hundreds of genomic datasets
SynMap2 and SynMap3D: web-based whole-genome synteny browsers
HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps
GenomeScope: fast reference-free genome profiling from short reads
ResistoMap—online visualization of human gut microbiota antibiotic resistome
poRe GUIs for parallel and real-time processing of MinION sequence data
ConKit: a python interface to contact predictions
Aozan: an automated post-sequencing data-processing pipeline
DLTree: efficient and accurate phylogeny reconstruction using the dynamical language method
rMATS-DVR: rMATS discovery of differential variants in RNA
The RNASeq-er API—a gateway to systematically updated analysis of public RNA-seq data
SIApopr: a computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution
Constructing linkage maps in the genomics era with MapDisto 2.0
MaBoSS 2.0: an environment for stochastic Boolean modeling
SmartR: an open-source platform for interactive visual analytics for translational research data
Estimating gene regulatory networks with pandaR
MetCCS predictor: a web server for predicting collision cross-section values of metabolites in ion mobility-mass spectrometry based metabolomics
PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data
HLA-MA: simple yet powerful matching of samples using HLA typing results
Message from the ISCB: 2017 ISCB Innovator Award Given to Aviv Regev
Message from the ISCB: 2017 ISCB Accomplishment by a Senior Scientist Award Given to Pavel Pevzner
Message from the ISCB: 2017 ISCB Overton Prize Awarded to Christoph Bock
Message from the ISCB: 2017 Outstanding Contributions to ISCB Award Given to Fran Lewitter