Ian H Holmes

Apollo 3 is a new manual genome annotation tool that integrates with JBrowse 2, enabling multi-genome editing and synteny visualization.

The paper develops variational inference methods for amino acid coevolution models, showing improved efficiency and accuracy over existing approaches.

The paper compares nested birth-death processes with neural networks for modeling protein evolution, finding the former more parameter-efficient and competitive.

This paper compares state-space models and transformers for predicting RNA-Seq read coverage, finding Mamba-based models slightly outperform transformers in accuracy but not in downstream SNP classification.

JBrowse 2 is a genome browser with enhanced views for structural variation and synteny, offering modular design and multiple usage options.

JBrowse Jupyter provides a Python interface to JBrowse 2 for interactive genomic visualization within Jupyter notebooks.

CellScape generates editable 2D molecular cartoons from atomic coordinates and combines them into cellular scenes using vector graphics.

CNVpytor is a Python-based tool for detecting and analyzing CNVs/CNAs from whole genome sequencing data, offering improved speed, functionality, and visualization compared to CNVnator.

The paper improves nanopore sequencing accuracy by combining two neural network basecallers using a consensus approach, achieving higher accuracy than existing basecallers.

The paper introduces a method to approximate indel evolution using differential equations derived from Pair HMMs, showing improved alignment distribution fits over a broader range of parameters.

JBrowse Connect enables live messaging, notifications, and user-initiated analyses in JBrowse via WebSockets, with JBlast as an example application for BLAST searches integrated with Galaxy.

Machine Boss streamlines the creation of bioinformatics HMMs by providing tools for automata manipulation, enabling rapid prototyping similar to regular expression construction.

Apollo is an open-source software tool that enables researchers to collaboratively annotate and refine genomic features through a graphical interface.

The paper introduces k-BOOM, a Bayesian method for merging ontologies by estimating logical relationships from mappings, applied to build a unified disease ontology.

BioMake improves upon GNU Make by adding cluster support, MD5 signatures, and Prolog extensions for better bioinformatics workflow management.

WTFgenes provides a static web tool for gene set analysis using hypergeometric and model-based methods, running in the browser without server resources.

Historian improves ancestral sequence reconstruction and evolutionary rate estimation by combining an efficient ProtPal algorithm with heuristics from other tools.