Terkko Navigator / Bioinformatics (journal)

High-complexity regions in mammalian genomes are enriched for developmental genes

Corrigendum to: Probabilistic identification of bacterial essential genes via insertion density using TraDIS data with Tn5 libraries

Erratum to: abPOA: an SIMD-based C library for fast partial order alignment using adaptive band

Corrigendum to: Utilizing image and caption information for biomedical document classification

Modeling circRNA expression pattern with integrated sequence and epigenetic features demonstrates the potential involvement of H3K79me2 in circRNA expression

CLUE: exact maximal reduction of kinetic models by constrained lumping of differential equations

The topology of data: opportunities for cancer research

MAT2: manifold alignment of single-cell transcriptomes with cell triplets

NeuralPolish: a novel Nanopore polishing method based on alignment matrix construction and orthogonal Bi-GRU Networks

VIRUSBreakend: Viral Integration Recognition Using Single Breakends

Feature-weighted ordinal classification for predicting drug response in multiple myeloma

RVAgene: generative modeling of gene expression time series data

KwARG: parsimonious reconstruction of ancestral recombination graphs with recurrent mutation

ORFLine: a bioinformatic pipeline to prioritize small open reading frames identifies candidate secreted small proteins from lymphocytes

Differential gene expression analysis for multi-subject single-cell RNA-sequencing studies with aggregateBioVar

CLEP: a hybrid data- and knowledge-driven framework for generating patient representations

Alignment free sequence comparison methods and reservoir host prediction

Reactome and the Gene Ontology: digital convergence of data resources

iCircDA-LTR: identification of circRNA–disease associations based on Learning to Rank

Improving deep learning-based protein distance prediction in CASP14

Study of real-valued distance prediction for protein structure prediction with deep learning

Clustering single-cell RNA-seq data by rank constrained similarity learning

Fundamental gene network rewiring at the second order within and across mammalian systems

MetaFusion: a high-confidence metacaller for filtering and prioritizing RNA-seq gene fusion candidates

A novel systematic approach for cancer treatment prognosis and its applications in oropharyngeal cancer with microRNA biomarkers

pDriver: a novel method for unravelling personalized coding and miRNA cancer drivers

Identification of cell-type-specific marker genes from co-expression patterns in tissue samples

Cooperative sequence clustering and decoding for DNA storage system with fountain codes

Protlego: a Python package for the analysis and design of chimeric proteins

Atomic-level evolutionary information improves protein–protein interface scoring

Early cancer detection from genome-wide cell-free DNA fragmentation via shuffled frog leaping algorithm and support vector machine

MicroCellClust: mining rare and highly specific subpopulations from single-cell expression data

GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data

HPOFiller: identifying missing protein–phenotype associations by graph convolutional network

Optimal Bayesian supervised domain adaptation for RNA sequencing data

Fast identification of differential distributions in single-cell RNA-sequencing data with waddR

SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts

ASHLEYS: automated quality control for single-cell Strand-seq data

Protein contact map refinement for improving structure prediction using generative adversarial networks

PrecisionProDB: improving the proteomics performance for precision medicine

VCFShark: how to squeeze a VCF file

ShinyCell: simple and sharable visualization of single-cell gene expression data

EPS: automated feature selection in case–control studies using extreme pseudo-sampling

MaveRegistry: a collaboration platform for multiplexed assays of variant effect

FUNGI: FUsioN Gene Integration toolset

Bioconductor toolchain for reproducible bioinformatics pipelines using Rcwl and RcwlPipelines

Generalized Read-Across prediction using genra-py

PecanPy: a fast, efficient and parallelized Python implementation of node2vec

KEC: unique sequence search by K-mer exclusion

The NRGTEN Python package: an extensible toolkit for coarse-grained normal mode analysis of proteins, nucleic acids, small molecules and their complexes