- PBSIM2: a simulator for long read sequencers with a novel generative model of quality scores
- Neighbourhoods in the Yeast Regulatory Network in Different Physiological States
- BERTMeSH: Deep Contextual Representation Learning for Large-scale High-performance MeSH Indexing with Full Text
- BP4RNAseq: a babysitter package for retrospective and newly generated RNA-seq data analyses using both alignment-based and alignment-free quantification method
- COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology
- Fold recognition by scoring protein maps using the congruence coefficient
- DPDDI: a deep predictor for drug-drug interactions
- GraphAligner: rapid and versatile sequence-to-graph alignment
- GraphAligner: rapid and versatile sequence-to-graph alignment
- A web-based system for creating, viewing, and editing precursor mass spectrometry ground truth data
- Knockoff Boosted Tree for Model-Free Variable Selection
- IsoResolve: Predicting Splice Isoform Functions by Integrating Gene and Isoform-level Features with Domain Adaptation
- Bedtk: Finding Interval Overlap with Implicit Interval Tree
- Prioritizing transcriptomic and epigenomic experiments by using an optimization strategy that leverages imputed data
- Bacnet: A user-friendly platform for building multi-omics websites
- Theoretical characterisation of strand cross-correlation in ChIP-seq
- MapGL: inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony
- SAPPHIRE: a neural network based classifier for σ70 promoter prediction in Pseudomonas
- An embedded gene selection method using knockoffs optimizing neural network
- MMAP: A Cloud Computing Platform for Mining the Maximum Accuracy of Predicting Phenotypes from Genotypes
Whats new in Bioinformatics
Genome Biology
- GraphAligner: rapid and versatile sequence-to-graph alignment
- Haplotype threading: accurate polyploid phasing from long reads
- Chromatin regulates expression of small RNAs to help maintain transposon methylome homeostasis in Arabidopsis
- Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph
- Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs
- Ultrasensitive deletion detection links mitochondrial DNA replication, disease, and aging
- Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation
- AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination
- Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
- Primo: integration of multiple GWAS and omics QTL summary statistics for elucidation of molecular mechanisms of trait-associated SNPs and detection of pleiotropy in complex traits