software / tool

Maximizing the conditional likelihood in spatially explicit capture-recapture models estimates spatial relative density and population growth rates rapidly while remaining robust to unmodeled individual detection heterogeneity.

This paper introduces a universal method for wave-optical PSF calculations in microscopy, supported by a MATLAB software package, and demonstrates its application across multiple imaging techniques.

This paper develops Plasmo3Net, a CNN-based algorithm for detecting malaria parasites in thin blood smears, achieving high accuracy and precision.

This paper introduces TCRDiff, a conditional diffusion model for generating antigen-specific TCR sequences, validated through in vitro assays.

Seqwin identifies microbial signature sequences by analyzing large genome collections, outperforming existing methods in efficiency and quality.

ALPINE classifies gene-editing outcomes from long-read amplicon sequencing into 10+ categories, including DNA repair vector integrations, with high accuracy.

damidBind provides tools for differential DamID analysis and data exploration to identify differentially bound loci and transcribed genes between cell types.

MicroGrowAgents is an agentic AI system that designs microbial growth media using structured knowledge and experimental design, identifying optimal conditions for Methylorubrum extorquens AM1.

This paper introduces SCRIVENER, a bacterial mating-based DNA assembly platform that enables high-throughput, low-error DNA construction of up to 23 kb constructs.

The paper benchmarks molecular fingerprints across multiple datasets and tasks, finding that count and unfolded variants improve specificity and alignment with structural references.

The paper updates a yeast reference transcriptome using direct RNA sequencing to improve UTR annotation and provides a reusable pipeline for future updates.

The paper develops a population model of motor evoked potentials from TMS to enable in-silico testing and tuning of closed-loop procedures without experimental data.

CoalMiner generates coalescent models for fastsimcoal2 to improve demographic inference by exploring model space efficiently.

Re-annotated MitoCore (SBML3, UniProt, EC, Human-GEM gene rules) supports sMOMENT proteomics integration, reducing thrombocyte ATP prediction error by 89% relative to the original model.

AnimalTA provides a flexible, open-source tool for video tracking data importation, correction, and analysis across different tracking programs.

The paper introduces and benchmarks two droplet-based single-nucleus assays for chromatin accessibility and gene expression, showing they are cost-effective and produce high-quality data.

MBIOME provides an open-source workflow for amplicon-based microbiome analysis, validated across sequencing platforms and showing improved flexibility and taxonomic resolution.

SC-Framework provides a unified, containerized environment for single-cell data analysis to improve reproducibility and scalability.

OpenGerminal replaces PyRosetta with open-source tools and benchmarks IgLM versus AbLang1 in the Germinal antibody design pipeline, achieving higher cofolding pass rates with equivalent structural confidence.

The paper re-architected a variant caller into a client-server system to improve agent-driven variant calling efficiency and reliability.

The paper introduces MassSpectrum Analyzer, a tool for refining proteomic search parameters and re-scoring peptides with modifications, improving detection of highly modified peptides and quantifying fragmentation patterns.

The paper identifies simplex-shaped neural manifolds for number representation in the human medial temporal lobe and finds similarities with large language models.

ProteoMeter integrates multi-PTM and limited proteolysis data to map proteomic changes to residue level, demonstrating its use in analyzing HCoV-229E infection.

bMINTY provides a structured, portable framework for managing post-alignment sequencing data and metadata to enhance reproducibility and reuse of scientific findings.

UTRGen is a unified framework for designing mRNA 5' UTRs that integrates sequence generation, prediction, and function-guided optimization, achieving state-of-the-art performance across multiple tasks.

VicMAG visualizes circular metagenome-assembled genomes to highlight virulence and antimicrobial resistance genes in bacterial communities.

This paper evaluates five AI frameworks on real scientific tasks, finding they excel in hypothesis generation and reporting but struggle with depth and reliability in real-world research.

IsoformSwitchAnalyzeR v2 identifies and analyzes functional isoform switches in long-read and single-cell sequencing data, showing disease-relevant changes in Alzheimer's and glioblastoma.

TandemTwister is a tool for tandem repeat genotyping and visualization, showing high accuracy and speed across sequencing technologies and datasets.

QutRNA2 improves tRNA modification detection using Nanopore sequencing with GPU acceleration, achieving faster performance and identifying modifications in human and mouse tRNAs.