software / tool

MSK-Morph automates the transformation of template musculoskeletal models into subject-specific bone geometries using medical imaging data.

MicrobeMS is a MATLAB toolbox for microbial identification using MALDI-ToF MS, enabling database compilation, spectrum analysis, and identification tasks.

SPIFEE is a pipeline that improves the analysis of live-cell fluorescence microscopy data by reducing noise and extracting features more accurately and objectively.

VIDEO is a web-based tool that integrates and visualizes chromatin accessibility, TF binding, and motif occurrence in tissue-specific genes to explore gene regulation in Drosophila.

The paper introduces plyxp, an R package that provides a grammar for efficiently manipulating annotated matrix data in the Bioconductor ecosystem.

This paper develops two codon optimization tools using classical and AI methods, showing they outperform existing tools in protein expression.

The paper develops epiVIP, a deep learning framework to predict HLA-I peptide abundance from (sc)RNA-seq data, showing that peptide abundance and non-selfness jointly determine antigenicity and predict tumor reactivity and survival.

scLASER simulates and detects time-dependent cellular dynamics in longitudinal studies, showing higher sensitivity than traditional methods in rare cell types and non-linear patterns.

LIVIA is a browser-based tool that assesses and visualizes predicted protein interactions by computing confidence metrics and providing 3D visualization options.

This study identifies ten forms of social capital that science undergraduates use to access research experiences, highlighting the role of institutions and proactive behaviors.

The paper proposes a model of hippocampal pyramidal neurons that use predictive learning through dendritic compartments and synaptic plasticity to encode spatial and behaviorally relevant features.

This paper develops a sample processing pipeline for spatial transcriptomics of murine musculoskeletal tissues, achieving high-quality transcript detection across multiple tissue types using the Xenium Prime 5K platform.

COCOA.jl identifies concordant and kinetic modules in biochemical networks, enabling analysis of concentration robustness with improved scalability.

This paper introduces PALMS, a Python tool for simulating Pavlovian learning models, including attentional approaches, and evaluates its utility through experimental simulations.

The paper introduces a unified SDE framework for efficient stochastic transcription trace generation, showing high accuracy with reduced computational cost.

This study evaluates a course redesign in a graduate genomics course, finding improved perceived navigability but persistent challenges in course coherence.

BRIDGE generates virtual spatial transcriptomes from histology images, improving cancer diagnosis accuracy in few-shot settings and outperforming existing models.

This paper synthesizes global DNA-based methods for detecting marine invasive species, finding that metabarcoding and single-species PCR are most common, with COI as the most widely used marker.

The paper introduces immuneKG, a knowledge graph framework for immune-mediated diseases, achieving high performance in target discovery using a graph neural network and novel features.

This paper introduces BPL, a compiler-verified language for biology protocols, and demonstrates its ability to convert natural language SOPs into reproducible, physically valid protocols with high fidelity.

BandHiC reduces memory usage for Hi-C matrices by 99% using a banded storage strategy while enabling efficient analysis of ultra-high-resolution data.

The paper introduces PEPR-GNN, a graph neural network framework to model regulome responses during genetic perturbations using Multiome Perturb-Seq data.

anndataR enables interoperability between R and Python by allowing native reading and writing of H5AD files in R, with compatibility testing and conversion to R single-cell objects.

The paper presents a Python Dash App and cPanel workflow to automate metabolomics data analysis and visualization, enabling interactive statistical analysis and result sharing.

This paper provides processing guidelines for helical reconstruction of amyloids using cryoSPARC, highlighting current capabilities and limitations while advocating for amyloid-specific parameter optimization.

This paper introduces Genie 3, a diffusion model that improves protein design by combining SE(3)-equivariance with hallucination, achieving state-of-the-art results in binder design and motif scaffolding.

The paper introduces NIBS-DAS, a template for structuring, managing, and analyzing NIBS data to improve data sharing and standardization.

AMRgen is an R package that links antimicrobial resistance genotypes to phenotypes through data harmonization, analysis, and visualization, using surveillance data from priority pathogens.

The paper redesigns an existing MOA-seq analysis pipeline using Nextflow to improve scalability and efficiency, resulting in a containerized and reproducible workflow.

Segzoo simplifies genome annotation analysis by automating data retrieval and analysis, providing a single visualization of results.