Terkko Navigator / Bioinformatics (journal)

Semi-deconvolution of bulk and single-cell RNA-seq data with application to metastatic progression in breast cancer

DECODE: a computational pipeline to discover T cell receptor binding rules

MeConcord: a new metric to quantitatively characterize DNA methylation heterogeneity across reads and CpG sites

The effect of genome graph expressiveness on the discrepancy between genome graph distance and string set distance

QuCo: quartet-based co-estimation of species trees and gene trees

Do-calculus enables estimation of causal effects in partially observed biomolecular pathways

DEMA: a distance-bounded energy-field minimization algorithm to model and layout biomolecular networks with quantitative features

DeepCRISTL: deep transfer learning to predict CRISPR/Cas9 functional and endogenous on-target editing efficiency

Visualizing hierarchies in scRNA-seq data using a density tree-biased autoencoder

Deep kernel learning improves molecular fingerprint prediction from tandem mass spectra

A graph neural network approach for molecule carcinogenicity prediction

Scaling multi-instance support vector machine to breast cancer detection on the BreaKHis dataset

Fast and interpretable genomic data analysis using multiple approximate kernel learning

Bridging the gaps in statistical models of protein alignment

On the reliability and the limits of inference of amino acid sequence alignments

MOJITOO: a fast and universal method for integration of multimodal single-cell data

Phage–bacterial contig association prediction with a convolutional neural network

Quintet Rooting: rooting species trees under the multi-species coalescent model

CALDERA: finding all significant de Bruijn subgraphs for bacterial GWAS

SPARSE: a sparse hypergraph neural network for learning multiple types of latent combinations to accurately predict drug–drug interactions

DeepGOZero: improving protein function prediction from sequence and zero-shot learning based on ontology axioms

MLGL-MP: a Multi-Label Graph Learning framework enhanced by pathway interdependence for Metabolic Pathway prediction

Characterizing domain-specific open educational resources by linking ISCB Communities of Special Interest to Wikipedia

Self-supervised learning of cell type specificity from immunohistochemical images

Synthetic-to-real: instance segmentation of clinical cluster cells with unlabeled synthetic training

An approachable, flexible and practical machine learning workshop for biologists

BITES: balanced individual treatment effect for survival data

High-sensitivity pattern discovery in large, paired multiomic datasets

Sparse and skew hashing of K-mers

Topsy-Turvy: integrating a global view into sequence-based PPI prediction

PhyloPGM: boosting regulatory function prediction accuracy using evolutionary information

2022 ISCB Accomplishments by a Senior Scientist Award: Ron Shamir

DeepMHCII: a novel binding core-aware deep interaction model for accurate MHC-II peptide binding affinity prediction

Computing optimal factories in metabolic networks with negative regulation

CMash: fast, multi-resolution estimation of k-mer-based Jaccard and containment indices

Robust fingerprinting of genomic databases

The minimizer Jaccard estimator is biased and inconsistent

ISMB 2022 proceedings

2022 ISCB Innovator Award: Núria López-Bigas

2022 Outstanding Contributions to ISCB Award: Reinhard Schneider

2022 ISCB Overton Prize: Po-Ru Loh

psupertime: supervised pseudotime analysis for time-series single-cell RNA-seq data

Exploring automatic inconsistency detection for literature-based gene ontology annotation

From drug repositioning to target repositioning: prediction of therapeutic targets using genetically perturbed transcriptomic signatures

A LASSO-based approach to sample sites for phylogenetic tree search

Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations

Syotti: scalable bait design for DNA enrichment

Prediction of recovery from multiple organ dysfunction syndrome in pediatric sepsis patients

ReadBouncer: precise and scalable adaptive sampling for nanopore sequencing

PolarMorphism enables discovery of shared genetic variants across multiple traits from GWAS summary statistics