Terkko Navigator / Bioinformatics (journal)

CMF-Impute: an accurate imputation tool for single cell RNA-seq data

UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase

Integration of gene interaction information into a reweighted Lasso-Cox model for accurate survival prediction

MorphOT: transport-based interpolation between EM maps with UCSF ChimeraX

struct: an R/Bioconductor-based framework for standardized metabolomics data analysis and beyond

New computational model for miRNA-mediated repression reveals novel regulatory roles of miRNA bindings inside the coding region

RCSB Protein Data Bank 1D tools and services

IDDkin: network-based influence deep diffusion model for enhancing prediction of kinase inhibitors

A unifying framework for rare variant association testing in family-based designs, including higher criticism approaches, SKATs, and burden tests

Virxicon: a lexicon of viral sequences

Atlas: automatic modeling of regulation of bacterial gene expression and metabolism using rule-based languages

DeepNOG: fast and accurate protein orthologous group assignment

CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes

Collecting and managing taxonomic data with NCBI-taxonomist

SugarPy facilitates the universal, discovery-driven analysis of intact glycopeptides

SneakySnake: a fast and accurate universal genome pre-alignment filter for CPUs, GPUs and FPGAs

LFQC: A lossless compression algorithm for FASTQ files

Methrix: an R/Bioconductor package for systematic aggregation and analysis of bisulfite sequencing data

High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides

Data-driven noise modeling of digital DNA melting analysis enables prediction of sequence discriminating power

Corrigendum to: HALPER facilitates the identification of regulatory element orthologs across species

Minimally overlapping words for sequence similarity search

Comment on‘Hayai-Annotation Plants: an ultrafast and comprehensive functional gene annotation system in plants’: the importance of taking the GO graph structure into account

PStrain: an iterative microbial strains profiling algorithm for shotgun metagenomic sequencing data

Issues of Z-factor and an approach to avoid them for quality control in high-throughput screening studies

crisscrosslinkeR: identification and visualization of protein–RNA and protein–protein interactions from crosslinking mass spectrometry

SVIM-asm: structural variant detection from haploid and diploid genome assemblies

Heterogeneous graph inference with matrix completion for computational drug repositioning

Rapid screening and detection of inter-type viral recombinants using phylo-k-mers

A Bayesian linear mixed model for prediction of complex traits

LBERT: Lexically-aware Transformers based Bidirectional Encoder Representation model for learning Universal Bio-Entity Relations

LDpred2: better, faster, stronger

PETAL: a Python tool for deep analysis of biological pathways

Improved protein model quality assessment by integrating sequential and pairwise features using deep learning

A library of coiled-coil domains: from regular bundles to peculiar twists

Helixer: cross-species gene annotation of large eukaryotic genomes using deep learning

aCLImatise: automated generation of tool definitions for bioinformatics workflows

IsoMaTrix: a framework to visualize the isoclines of matrix games and quantify uncertainty in structured populations

On biases of attention in scientific discovery

DeMaSk: a deep mutational scanning substitution matrix and its use for variant impact prediction

Impact of lossy compression of nanopore raw signal data on basecalling and consensus accuracy

MobiDB-lite 3.0: fast consensus annotation of intrinsic disorder flavors in proteins

Complete populations of virtual patients for in silico clinical trials

CAFE 5 models variation in evolutionary rates among gene families

MOVICS: an R package for multi-omics integration and visualization in cancer subtyping

dittoSeq: universal user-friendly single-cell and bulk RNA sequencing visualization toolkit

DeepPurpose: a deep learning library for drug–target interaction prediction

Autoregressive modeling and diagnostics for qPCR amplification

Sparse Project VCF: efficient encoding of population genotype matrices

Prioritizing genes for systematic variant effect mapping