software / tool

MC-Bayes: A Python-based wrapper for MotionCor3 processing of EER files compatible with Bayesian polishing

MC-Bayes provides a Python wrapper for MotionCor3 to process EER files for Bayesian polishing, enabling faster motion correction on GPU systems compared to CPU-based methods.

jazzPanda: spatially aware marker gene detection for imaging-based spatial transcriptomics

Binning transcript and cell coordinates into spatial vectors lets jazzPanda call smaller, spatially concordant marker sets than Wilcoxon or t-tests on Xenium/CosMx data, while modelling replicates and negative-control background.

ATLAS: Population-Level Disease Locus Discovery via Differential Attention in Genomic Language Models

Contrasting a pretrained genomic language model's attention between case and control haplotypes ranked HBB first on chromosome 11 and recovered more known β-thalassemia variants than GWAS, without per-variant tests.

BRIDGE: A Computational Workflow from Single Neurons to Network of Mean-Field Models

BRIDGE is a Python pipeline that reconstructs and validates mean-field models from single neuron dynamics, enabling reproducible and reusable large-scale brain simulations.

Plant DNA Designer: A Computational Framework for Multi-Objective Codon Optimisation and Synthetic Gene Design in Crop Biotechnology

Plant DNA Designer optimizes synthetic gene design for crops by balancing multiple molecular objectives, outperforming existing tools in safety and GC content while maintaining moderate CAI.

CARS: A General Force Field for Carotenoids

The paper introduces CARS, a transferable force field for carotenoids that improves simulation accuracy across diverse chemical structures and outperforms existing force fields.

Hoike: A Joint-Embedding Predictive Architecture for Transcriptome Data Generation with Diffusion Models

Hoike generates condition-specific bulk transcriptomes using a joint-embedding predictive architecture and diffusion models, conditioned on normal tissue profiles.

A structured study of cross-condition prediction of transcriptional responses to gene perturbations

This study introduces TranScouter, a framework for predicting transcriptional responses to gene perturbations across different biological conditions, showing competitive performance in both seen and unseen perturbation scenarios.

DetectGxT: detecting gene-by-treatment interactions on molecular count phenotypes accounting for allelic additivity

R package DetectGxT fits allelic-additivity nonlinear models with optional donor or polygenic random effects, raising simulated power to detect gene-by-treatment interaction QTLs over linear regression.

Semi-automated annotation refinement accelerates cell type identification in brain spatial and single-cell studies

SAHA provides a statistical framework for rapid cell type annotation by transferring labels from reference datasets to query datasets without integration.

A Cell Viability and Utility Index (CVUI) for wildlife fibroblast biobanking: framework development and preliminary empirical validation

The paper introduces the Cell Viability and Utility Index (CVUI) to assess cell culture quality in wildlife biobanking, validated across 154 culture rounds from 46 species.

Evolutionary Design of Membrane-Lytic Antimicrobial Peptides with Mixture of Experts

This paper introduces AMPainterV2, a model that designs membrane-lytic antimicrobial peptides using generative adversarial imitation learning, achieving active peptides with improved activity and miniaturization.

Automatic Body Morphometric Analysis of Adult Zebrafish Using MicroCT

This study develops fully automated methods using FIJI/ImageJ to compute body morphometric measures from microCT scans of adult zebrafish, improving throughput and reducing variability.

Building optimized single-cell reference atlases with scAtlasTb

The paper introduces scAtlasTb, a framework for building and optimizing single-cell reference atlases, demonstrating its application on three Human Cell Atlas projects.

SVkhor: a unified framework for structural variant integration across long-read, short-read, and optical genome mapping data

SVkhor normalizes, merges and integrates long-read, short-read and optical-mapping structural variant calls; on HG002 it retained 98.6% of naive concatenation's true positives with 58.2% fewer false positives.

AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates

AniAnns annotates tandem repeat arrays by leveraging high ANI between repeat units, improving annotation accuracy and speed across plant and animal genomes.

eyeris: A flexible, extensible, and reproducible pupillometry preprocessing framework in R

eyeris provides a reproducible pupillometry preprocessing framework that enhances FAIR principles and open science practices in pupillometry research.

Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet

The paper introduces Verkko-Fillet, a tool for refining genome assemblies, and applies it to produce a telomere-to-telomere giraffe genome.

BackBone Builder (B3): A modular Golden Gate standard with a compatible Agrobacterium parts library

The paper introduces B3, a modular Golden Gate system for assembling Agrobacterium binary vector backbones, enabling efficient and flexible construction of over 370,000 possible constructs.

A complete diploid human genome benchmark for personalized genomics

T2T-HG002v1.1, a complete diploid HG002 assembly lacking detectable errors over 99.4% of its length, enables genome-based benchmarking of assemblies, sequencing reads, and phased variant calls.

Updating the RZooRoH package for the analysis of inbreeding, identity-by-descent and relatedness from genomic data

The paper updates the RZooRoH package to improve computational efficiency and interpretability in analyzing inbreeding, identity-by-descent, and relatedness from genomic data.

De novo Autogenic Engineered Living Functional Materials

This paper introduces a platform for creating de novo autogenic engineered living materials using CsgA-like proteins from extremophilic bacteria, demonstrating tunable mechanical properties and programmable functionalities.

CyFj11: FlowJo v11 Workspace Import and Legacy Format Export for R-Based Flow Cytometry Analysis

CyFj11 enables importing FlowJo v11 workspaces into R and exporting R-based gates back to FlowJo, ensuring interoperability between gating tools and statistical analysis environments.

Fast remote nucleotide sequence alignment with Riboseek

Riboseek is a fast and sensitive sequence alignment tool for RNA and DNA that uses di-mers for alignment, outperforming BLASTN and nhmmer in speed and sensitivity.

A nuclear targeting approach enables efficient transgenesis in the milkweed bug Oncopeltus fasciatus

This paper develops an efficient transgenesis system in the milkweed bug Oncopeltus fasciatus using nuclear targeting and piggyBac, enabling genetic manipulations and expanding its use as a model organism.

Continual integration of single-cell multimodal data with MIRACLE

MIRACLE enables efficient continual integration of single-cell multimodal data, updating cell atlases with new data without reintegration, and identifies novel cell types and transfers labels across datasets.

vOMIX-MEGA: An ultra-fast end-to-end pipeline for terabyte-scale viral metagenomics analysis.

vOMIX-MEGA processes terabyte-scale viral metagenomic data faster and more efficiently than existing pipelines, achieving faster runtime and higher accuracy.

jaxon: a differentiable, GPU-native simulator for peripheral-nerve fiber models

jaxon provides a differentiable, GPU-accelerated simulator for peripheral-nerve fiber models, achieving high speedup and precision in simulating and optimizing extracellular stimulation parameters.

Structured Schemas for Provenance-Rich, LLM-Assisted QSP Model Calibration

The paper introduces MAPLE, a framework that uses structured schemas to improve LLM-assisted QSP model calibration by ensuring data provenance and reducing hallucination.

Rich structure alphabets enable highest accuracy protein search

The paper introduces Reseek, a protein structure search algorithm achieving the highest accuracy with practical scalability for large databases.