software / tool

AutoRNAseq provides an automated bulk RNA-seq analysis pipeline to ensure consistent and reproducible processing across experiments.

Metaxa is a transformer-based model for classifying long Nanopore reads, outperforming existing tools on out-of-sample data and across different sequencing chemistries.

This paper adapts a modernized BERT-style model to genomic sequence modeling, achieving strong efficiency and performance, and releases it as an open baseline.

Using the share of AMELY-specific among all sex-specific amelogenin peptides (RAMELY), enamel proteomes are sexed consistently across four search engines, tolerating false-positive AMELY hits without manual checks.

The paper introduces MiCSPARC, a cryo-EM pipeline for microtubule structure determination, achieving high-resolution reconstructions of decorated and undecorated microtubules.

This paper develops a computational framework to model how task-induced changes in brain dynamics relate to cognitive individual differences using rsfMRI and tfMRI data.

BioEngine enables biologists to run, adapt, and deploy bioimage AI models on various hardware by interacting with an AI agent through a user-friendly interface.

The paper introduces DIMPLE, a scalable qPCR primer design algorithm that enables 10,000+ primers in a single reaction, achieving low VAF detection and multiplex applications.

FlowWeb provides a web-based platform for flow cytometry analysis, offering automated workflows and visualization tools comparable to commercial software.

The paper presents a VR dataset of 33 upper limb gestures for VR-AOT, designed to support standardized and flexible implementation in neurorehabilitation and motor learning.

The paper describes the creation of CASMDB, a database of metabolite annotations for 1D 1H NMR-based metabolomics, enabling accurate simulation and visualization of spectra.

REPLAY automates DNA replication timing analysis from Repli-seq data, providing a reproducible and user-friendly tool without requiring programming expertise.

The paper introduces DBCO-modified PCR primers for enzyme-free click chemistry ligation in nanopore amplicon sequencing, achieving higher pore occupation and reads than commercial solutions.

This study compares four proteomics software tools for hair proteome analysis, finding differences in peptide identification, protein inference, functional annotation, and quantification across tools and extraction methods.

The paper introduces KELPE, a cell line with dual genomic landing pads for efficient screening of synthetic gene circuits in pluripotent stem cells.

TernTables automates clinical data analysis and table generation, using statistical rules and transparency tools to improve reproducibility and reduce administrative barriers in biomedical research.

EasyCAPS is a web tool that integrates dCAPS primer design with CRISPR-Cas9 strategies to improve genotyping and gene editing efficiency.

CGAgentX develops transferable coarse-grained models using an agentic AI framework with specialized agents that autonomously optimize parameters to match experimental and simulation data.

The paper introduces RICE, a method to quantify chimeric RNA expression, validates it with qPCR and siRNA, and applies it to prostate cancer data to identify differentially expressed chimeric RNAs.

The paper introduces EntDetect, a tool to detect non-covalent lasso entanglements in protein structures, simulations, and mass spectrometry data, and demonstrates its application in identifying misfolded states.

This paper introduces SMILE, a diffusion model for converting H&E stains to multiplex IHC images, showing superior performance in pancreatic islet analysis and breast cancer stain conversion.

The paper uses Nota to identify genes involved in cannabis sex determination by analyzing transcriptomic data from silver-treated plants.

NetMHCIIphosPan predicts HLA class II antigen presentation of phosphorylated peptides using immunopeptidomics data, outperforming existing tools.

NAViFluX is a web-based platform for analyzing and designing genome-scale metabolic networks, enabling interactive visualization, refinement, and flux analysis of metabolic models.

ADAR-Sense is a web tool for designing ADAR-based RNA sensors with customizable parameters, enabling efficient and flexible sensor creation for various applications.

GANGE is a deep-learning system that generates accurate genomic sequences from low-coverage, error-prone reads, reducing sequencing costs and enabling regulomics research without genome data.

This paper identifies key challenges in passive acoustic monitoring software through expert assessment and proposes strategies to improve scalability and usability.

The paper introduces IC-TFCE, an algorithm that improves the computational efficiency of threshold-free cluster enhancement for functional connectivity analysis, achieving significant speedups for large-scale analyses.

trackDJ is an R package that simplifies the creation of publication-quality epigenomic figures through a user-friendly interface and high-level plotting functions.

The paper introduces ioNERDSS, a Python tool that converts 3D atomic structures into coarse-grained models for simulating macromolecular self-assembly.