software / tool

LVentiView automates 3D left ventricular mesh reconstruction and analysis from cardiac MRI, achieving accuracy comparable to expert manual segmentation.

The paper introduces Decima, a model that predicts cell type- and condition-specific gene expression from DNA sequence using single-cell RNA sequencing data.

InsectMorphoAI automates insect length, volume, and biomass estimation from 2D images using two methods, achieving high accuracy and enabling efficient ecological research.

This paper introduces a novel reaction-diffusion architecture called JAPI for engineering self-organized patterns in mammalian cells, demonstrating its ability to generate spatial patterns with fewer parameters than classical diffusion-based systems.

The paper introduces a cost-effective reverse transcriptase, MarathonRT, and compares its performance with commercial enzymes for tRNA sequencing library preparation.

This paper introduces Dynamic Resource Theory to explain self-organization in resource-constrained systems, showing how complexity and adaptability emerge through thermodynamic and variational principles.

AreTomo3 and DenoisET form an automated GPU pipeline that reconstructs cryo-electron tomograms with tile-based contrast transfer function correction, screens their quality, and denoises them during acquisition.

The paper develops the genC pipeline to estimate taxonomically resolved organic carbon sources in lake sediments and finds that environmental conditions, especially warming, drive OC variation, with terrestrial sources dominating.

This paper introduces a generative AI framework to design target-specific siRNAs for RNAi-based drug design, showing improved specificity and reduced off-target effects compared to existing methods.

This study uses single-cell multi-omics to analyze immune reconstitution failure in HIV patients, identifying genetic and epigenetic factors and developing a predictive model.

The paper introduces OMEGA, a low-cost method for assembling large gene libraries from oligopools, achieving high sequence recovery and uniformity.

ZipStrain enables rapid and precise strain-resolved metagenomics by analyzing 2,754 human samples to identify strain-sharing gradients and gene variation.

The paper develops a method to identify conserved causative genes across species using multi-species GWAS data, finding that conserved genes are more frequently associated with trait variation than expected by chance.

PATTY corrects open chromatin bias in CUT&Tag data using ATAC-seq and machine learning, improving detection of histone modifications and cell clustering in single-cell analyses.

This study compares seven automated tools for generating draft genome-scale metabolic models (GEMs) in multicellular eukaryotes, finding no single tool consistently outperforms others.

MARRVEL-MCP enables natural language variant interpretation by allowing LLMs to autonomously construct workflows using curated genomic tools, improving performance over models without tool access.

SelNeTime infers effective population size and selection intensity from genomic time series data using an improved HMM approach with Beta with Spikes approximation.

NanoCortex provides a unified agentic framework for nanopore sequencing analysis, improving usability over general-purpose models by integrating data processing and biological interpretation.

geneML improves fungal gene prediction accuracy and recall using deep learning, outperforming existing tools and enabling faster, more comprehensive genome annotation.

This study analyzes the credentials of 40 individuals who became research-intensive biomedical faculty, finding that research independence and mentorship were key, while high-prestige publications and grants were not essential.

PlasmidLM is a DNA language model that generates plasmid constructs from component specifications, achieving high fidelity and viability in generated sequences.

Shiny AMMOA provides an interactive platform for analyzing multi-omics datasets from murine aging studies, enabling integrative analysis and visualization of transcriptomic, proteomic, and metabolomic data.

SuBMIT generates input files for molecular dynamics simulations of coarse-grained structure-based models using GROMACS and OpenMM/OpenSMOG.

TRINUS decouples cell lineage identity from niche pressure to uncover interaction syntax in spatial transcriptomics data, showing improved clustering and domain detection across biological systems.

The paper introduces MaxSBM, a MaxQuant module for identifying sequence-based modifiers like SUMO, improving peptide identification rates and spectral annotation.

VX provides a genome and transcriptome viewer with an embedded API and analysis framework enabling script and AI agent interaction.

ProteomeLM predicts protein-protein interactions and gene essentiality across species using a proteome-scale language model, outperforming existing methods in speed and accuracy.

This paper demonstrates how integrating AbSolution, ENCORE, and R packages can automate reproducibility in interactive applications by enabling single-step export of data, code, and documentation.

cadmus retrieves and processes full-text biomedical literature, achieving high retrieval rates and demonstrating improved coverage of biomedical concepts compared to abstracts.

StringTie3 improves total RNA-seq assembly by resolving nascent and mature transcripts, reducing errors and enhancing precision and sensitivity in both short- and long-read data.