Terkko Navigator / Bioinformatics (journal)

Boosting the extraction of elementary flux modes in genome-scale metabolic networks using the linear programming approach

FastTargetPred: a program enabling the fast prediction of putative protein targets for input chemical databases

RNAIndel: discovering somatic coding indels from tumor RNA-Seq data

Capybara: equivalence ClAss enumeration of coPhylogenY event-BAsed ReconciliAtions

Higher-order Markov models for metagenomic sequence classification

HiGwas: how to compute longitudinal GWAS data in population designs

Unipept CLI 2.0: adding support for visualizations and functional annotations

scTPA: a web tool for single-cell transcriptome analysis of pathway activation signatures

ThETA: transcriptome-driven efficacy estimates for gene-based TArget discovery

ProteinFishing: a protein complex generator within the ModelX toolsuite

PLIDflow: an open-source workflow for the online analysis of protein–ligand docking using galaxy

Stereo3D: using stereo images to enrich 3D visualization

MetaviralSPAdes: assembly of viruses from metagenomic data

SOMM4mC: a second-order Markov model for DNA N4-methylcytosine site prediction in six species

BioStructures.jl: read, write and manipulate macromolecular structures in Julia

iBioProVis: interactive visualization and analysis of compound bioactivity space

EasyVS: a user-friendly web-based tool for molecule library selection and structure-based virtual screening

ipcoal: an interactive Python package for simulating and analyzing genealogies and sequences on a species tree or network

Deshrinking ridge regression for genome-wide association studies

HPOLabeler: improving prediction of human protein–phenotype associations by learning to rank

DeepNano-blitz: a fast base caller for MinION nanopore sequencers

GDASC: a GPU parallel-based web server for detecting hidden batch factors

pepFunk: a tool for peptide-centric functional analysis of metaproteomic human gut microbiome studies

An in silico model of LINE-1-mediated neoplastic evolution

Optimization of co-evolution analysis through phylogenetic profiling reveals pathway-specific signals

CiteFuse enables multi-modal analysis of CITE-seq data

Testing hypotheses about the microbiome using the linear decomposition model (LDM)

genozip: a fast and efficient compression tool for VCF files

rScudo: an R package for classification of molecular profiles using rank-based signatures

COVID-2019-associated overexpressed Prevotella proteins mediated host–pathogen interactions and their role in coronavirus outbreak

PathWalks: identifying pathway communities using a disease-related map of integrated information

grünifai: interactive multiparameter optimization of molecules in a continuous vector space

GM-DockZn: a geometry matching-based docking algorithm for zinc proteins

Bayesian structural equation modeling in multiple omics data with application to circadian genes

HiC-Hiker: a probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C

SHOGUN: a modular, accurate and scalable framework for microbiome quantification

PRIME: a probabilistic imputation method to reduce dropout effects in single-cell RNA sequencing

PPTPP: a novel therapeutic peptide prediction method using physicochemical property encoding and adaptive feature representation learning

aPCoA: covariate adjusted principal coordinates analysis

OpenBioLink: a benchmarking framework for large-scale biomedical link prediction

Targeted domain assembly for fast functional profiling of metagenomic datasets with S3A

A reformulation of pLSA for uncertainty estimation and hypothesis testing in bio-imaging

Can ODE gene regulatory models neglect time lag or measurement scaling?

Learning context-aware structural representations to predict antigen and antibody binding interfaces

Codon optimization: a mathematical programing approach

A novel normalization and differential abundance test framework for microbiome data

A phylogenetic C interpreter for TNT

BEM: Mining Coregulation Patterns in Transcriptomics via Boolean Matrix Factorization

Meta-analysis of Caenorhabditis elegans single-cell developmental data reveals multi-frequency oscillation in gene activation

An efficient approach based on multi-sources information to predict circRNA–disease associations using deep convolutional neural network