Terkko Navigator / Bioinformatics (journal)

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

dv-trio: a family-based variant calling pipeline using DeepVariant

IgGeneUsage: differential gene usage in immune repertoires

immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking

HLPpred-Fuse: improved and robust prediction of hemolytic peptide and its activity by fusing multiple feature representation

nanoTRON: a Picasso module for MLP-based classification of super-resolution data

Supervised learning is an accurate method for network-based gene classification

Feature set optimization in biomarker discovery from genome-scale data

Discovery of disease- and drug-specific pathways through community structures of a literature network

Potential covalent drugs targeting the main protease of the SARS-CoV-2 coronavirus

CRiSP: accurate structure prediction of disulfide-rich peptides with cystine-specific sequence alignment and machine learning

Fast and robust ancestry prediction using principal component analysis

powmic: an R package for power assessment in microbiome case–control studies

A blind and independent benchmark study for detecting differeally methylated regions in plants

LogoJS: a Javascript package for creating sequence logos and embedding them in web applications

TCRBuilder: multi-state T-cell receptor structure prediction

M2IA: a web server for microbiome and metabolome integrative analysis

Projected t-SNE for batch correction

DeCoDe: degenerate codon design for complete protein-coding DNA libraries

Exploring high-dimensional biological data with sparse contrastive principal component analysis

Interpretable factor models of single-cell RNA-seq via variational autoencoders

tugHall: a simulator of cancer-cell evolution based on the hallmarks of cancer and tumor-related genes

GlycoGlyph: a glycan visualizing, drawing and naming application

VISAR: an interactive tool for dissecting chemical features learned by deep neural network QSAR models

primirTSS: an R package for identifying cell-specific microRNA transcription start sites

Reconstructing ribosomal genes from large scale total RNA meta-transcriptomic data

NIHBA: a network interdiction approach for metabolic engineering design

GraphBin: refined binning of metagenomic contigs using assembly graphs