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Author Index

ISMB/ECCB 2019 PROCEEDINGS PAPERS COMMITTEE

Learning a mixture of microbial networks using minorization–maximization

ISMB/ECCB 2019 Proceedings

ShaKer: RNA SHAPE prediction using graph kernel

Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotype

Multifaceted protein–protein interaction prediction based on Siamese residual RCNN

Weighted elastic net for unsupervised domain adaptation with application to age prediction from DNA methylation data

Statistical compression of protein sequences and inference of marginal probability landscapes over competing alignments using finite state models and Dirichlet priors

MCS2: minimal coordinated supports for fast enumeration of minimal cut sets in metabolic networks

TADA: phylogenetic augmentation of microbiome samples enhances phenotype classification

MOLI: multi-omics late integration with deep neural networks for drug response prediction

DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning

Prediction of mRNA subcellular localization using deep recurrent neural networks

PRISM: methylation pattern-based, reference-free inference of subclonal makeup

Inference of clonal selection in cancer populations using single-cell sequencing data

scOrange—a tool for hands-on training of concepts from single-cell data analytics

Reconstructing signaling pathways using regular language constrained paths

hicGAN infers super resolution Hi-C data with generative adversarial networks

Robust network inference using response logic

Precise modelling and interpretation of bioactivities of ligands targeting G protein-coupled receptors

Inheritance and variability of kinetic gene expression parameters in microbial cells: modeling and inference from lineage tree data

Efficient haplotype matching between a query and a panel for genealogical search

A divide-and-conquer method for scalable phylogenetic network inference from multilocus data

pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework

Inferring signalling dynamics by integrating interventional with observational data

FunDMDeep-m6A: identification and prioritization of functional differential m6A methylation genes

Enhancing the drug discovery process: Bayesian inference for the analysis and comparison of dose–response experiments

Efficient merging of genome profile alignments

Large scale microbiome profiling in the cloud

Alignment-free filtering for cfNA fusion fragments

Identifying and ranking potential driver genes of Alzheimer’s disease using multiview evidence aggregation

SCRIBER: accurate and partner type-specific prediction of protein-binding residues from proteins sequences

Learning signaling networks from combinatorial perturbations by exploiting siRNA off-target effects

TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain

Bayesian metabolic flux analysis reveals intracellular flux couplings

Unsupervised segmentation of mass spectrometric ion images characterizes morphology of tissues

Collaborative intra-tumor heterogeneity detection

Adversarial domain adaptation for cross data source macromolecule in situ structural classification in cellular electron cryo-tomograms

LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search

Block HSIC Lasso: model-free biomarker detection for ultra-high dimensional data

Large-scale inference of competing endogenous RNA networks with sparse partial correlation

A joint method for marker-free alignment of tilt series in electron tomography

TreeMerge: a new method for improving the scalability of species tree estimation methods

Locality-sensitive hashing for the edit distance

NPS: scoring and evaluating the statistical significance of peptidic natural product–spectrum matches

Estimating the predictability of cancer evolution

Large-scale mammalian genome rearrangements coincide with chromatin interactions

Predicting drug-induced transcriptome responses of a wide range of human cell lines by a novel tensor-train decomposition algorithm

Rotation equivariant and invariant neural networks for microscopy image analysis