software / tool

LocusBlend blends linkage disequilibrium colors for up to three index variants in LocusZoom and LocusCompare plots, helping separate independent signals at complex Alzheimer's disease loci.

Panomap maps raw nanopore signals to pangenome variation graphs, improving mapping accuracy and reducing reference bias compared to linear-reference methods.

PepCL updates peptide-MHC predictors with new assay data while preserving prior MS knowledge, improving prediction across alleles in clinical contexts.

The paper designs and optimizes a phosphorylation-controlled transcription factor switch that outperforms existing ERK-responsive biosensors in selectivity and sensitivity.

This paper develops an LLM interface for scientific simulations, achieving high accuracy and reproducibility in converting natural language descriptions to structured inputs for photon transport simulations.

Survey of 46,185 A. baumannii assemblies and NCBI entries added 168 novel capsule loci, expanding the Kaptive typing database to 409 K loci with 1010 annotated protein clusters.

HapNet automates haplotype network construction and visualization from FASTA files, incorporating population metadata for population-aware analysis.

The paper introduces siibra, a software tool suite that integrates diverse brain data into a Multilevel Human Brain Atlas, enabling interoperable analysis and visualization.

This paper uses an agent-based model to show that Registered Reports are often unattractive under realistic academic conditions due to career incentives and competition.

cf-Cabernet improves cfDNA methylation sequencing by repairing nicks before end repair, preserving methylation information and outperforming standard methods.

This paper introduces Fetal Twin, a mechanistic computational model of fetal physiology to study heart-rate-variability biomarkers, revealing artifacts in beat detection and fidelity requirements for accurate biomarker interpretation.

An open, instruction-free EEG plus eye-tracking task battery for autism families (344 to 587 participants per task so far), with timing-validated integrated recordings that enable gaze-locked ERP analysis.

This paper examines the uptake and implementation of multiverse-style analyses across 613 studies, finding widespread use primarily in psychology, social sciences, and medicine.

A normalizing flow over backbone internal-coordinate angles generates protein ensembles comparable to BioEmu in one step and doubles as a differentiable coarse-grained potential for Langevin dynamics.

ArrayAnalysis provides an interactive web and desktop platform for analyzing microarray and RNA-seq data, offering tools for preprocessing, differential expression, and visualization to support both novice and expert users.

This paper develops a computational framework to design crisscross DNA megastructures, optimizing handle assignment and expanding handle libraries to enable large-scale fabrication.

A 3D-printed OpenFlexure Microscope adapted for humid incubators, with relocated electronics, ASA printing and 22 Ω current-limiting resistors, records 48-hour label-free docetaxel responses that CellPhe can analyse.

This paper develops an algorithm called Algostim to synchronize neuromuscular electrical stimulation with breathing in mice with cervical spinal cord injury, showing improved chest movement with synchronized stimulation.

Standardized Snakemake pipelines on GitHub Actions fetch open sequence data, curate it, and publish daily or weekly updated phylogenies for 21 viruses and Mycobacterium tuberculosis.

The paper identifies a new PCR artifact called 'PCR leaping' and develops a DNA library screening method using it for natural product discovery.

The paper introduces CGUI-CLD, a web-based platform for covalent ligand docking that automates ligand preparation and simulation using AutoDock4.

The paper introduces a method to prioritize targets in Perturb-seq by assessing the dependability of perturbation effects using generalizability theory, improving target identification reliability.

This paper introduces a neural model that uses low-dimensional representations of module reuse to accelerate learning, showing consistency with primate behavioral and neural data.

The paper introduces a method to infer isoform-level kinetics of nonsense-mediated mRNA decay using short-read NR-seq data, revealing variability in NMD efficiency and decay rates of transcripts with and without PTCs.

The paper introduces RomicsProcessor, a reproducible-by-design tool for multi-omics and spatial-omics analysis that enforces FAIR principles and ensures computational reproducibility.

This paper develops an individual-based model of academic career progression, finding that multiple factors compound to slow women's advancement and showing that gender parity at high ranks requires equalizing hiring rates across gender, rank, and discipline.

Radiant DIA is a fast and cost-effective search engine for proteomics that maintains accuracy and sensitivity, enabling efficient analysis of large-scale datasets.

This study characterizes the orientation dependence of R2' in white matter, develops a new Myelin-Blood model, and shows it improves R2' fitting compared to existing models.

Model Context Protocol tools over Virtual Fly Brain's graph let Claude answer 25/30 Drosophila neuroscience tasks precisely, vs 14/30 with web search, 2/30 bare.

This paper presents a method to achieve programmable and dynamic DNA localisation at synthetic cell membranes using RNA linkers and enzymatic degradation.