Terkko Navigator / Bioinformatics (journal)

Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs

MOOMIN– Mathematical explOration of ’Omics data on a MetabolIc Network

Context awareness and embedding for biomedical event extraction

Topology-independent and global protein structure alignment through an FFT-based algorithm

ArtiFuse—computational validation of fusion gene detection tools without relying on simulated reads

RAG-Web: RNA structure prediction/design using RNA-As-Graphs

DNA Rchitect: an R based visualizer for network analysis of chromatin interaction data

Predicting the effects of SNPs on transcription factor binding affinity

gwasrapidd: an R package to query, download and wrangle GWAS catalog data

circMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs

VirtualCytometry: a webserver for evaluating immune cell differentiation using single-cell RNA sequencing data

Non-parametric individual treatment effect estimation for survival data with random forests

Discovering protein drug targets using knowledge graph embeddings

Gaussian mixture copulas for high-dimensional clustering and dependency-based subtyping

Bayesian estimation of genetic regulatory effects in high-throughput reporter assays

DEEPCON: protein contact prediction using dilated convolutional neural networks with dropout

P-value evaluation, variability index and biomarker categorization for adaptively weighted Fisher’s meta-analysis method in omics applications

ACTINN: automated identification of cell types in single cell RNA sequencing

DeepGOPlus: improved protein function prediction from sequence

Identifying small-effect genetic associations overlooked by the conventional fixed-effect model in a large-scale meta-analysis of coronary artery disease

pourRNA—a time- and memory-efficient approach for the guided exploration of RNA energy landscapes

BioNorm: deep learning-based event normalization for the curation of reaction databases

ISoLDE: a data-driven statistical method for the inference of allelic imbalance in datasets with reciprocal crosses

THETA: a new genotypic approach for predicting HIV-1 CRF02-AG coreceptor usage

Haplotype-aware graph indexes

MetaBMF: a scalable binning algorithm for large-scale reference-free metagenomic studies

Bayesian inference of distributed time delay in transcriptional and translational regulation

DR-SIP: protocols for higher order structure modeling with distance restraints- and cyclic symmetry-imposed packing

Efficient parameterization of large-scale dynamic models based on relative measurements

GSMA: an approach to identify robust global and test Gene Signatures using Meta-Analysis

Estimating and testing the microbial causal mediation effect with high-dimensional and compositional microbiome data

How sequence alignment scores correspond to probability models

QPARSE: searching for long-looped or multimeric G-quadruplexes potentially distinctive and druggable

Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network

ATEN: And/Or tree ensemble for inferring accurate Boolean network topology and dynamics

The influence of heterogeneous codon frequencies along sequences on the estimation of molecular adaptation

Identifying emerging phenomenon in long temporal phenotyping experiments

MM-6mAPred: identifying DNA N6-methyladenine sites based on Markov model

Identification of expression signatures for non-small-cell lung carcinoma subtype classification

Comparison of single and module-based methods for modeling gene regulatory networks

Look4TRs: a de novo tool for detecting simple tandem repeats using self-supervised hidden Markov models

Artificial intelligence-based multi-objective optimization protocol for protein structure refinement

MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome

ROBOKOP: an abstraction layer and user interface for knowledge graphs to support question answering

DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data

BLANT—fast graphlet sampling tool

scRNABatchQC: multi-samples quality control for single cell RNA-seq data

OncodriveCLUSTL: a sequence-based clustering method to identify cancer drivers

Sequence tube maps: making graph genomes intuitive to commuters

Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit