Ling‐Hong Hung

Interactive Data Integrator for Uniform Data Processing in the MorPhiC Program

The paper introduces an interactive Data Integrator for uniform processing and integration of bulk RNA-seq datasets from the MorPhiC program and external sources.

STARgrid: an open-source pipeline from Visium HD sequencing reads to count matrices

STARgrid is an open-source pipeline that processes Visium HD sequencing data to generate count matrices, showing high agreement with Space Ranger while improving efficiency and resolution.

STAR Suite: Transcriptomics processing in a single binary through AI-assisted development

Open-source STAR binary for five transcriptomic assays runs 3.9- to 6.2-fold faster than Cell Ranger 9.0.1 for scRNA-seq and Perturb-seq, 17- to 41-fold for Flex, with closely concordant counts.

Singe cell RNA sequencing data processing using cloud-based serverless computing

The paper presents a serverless cloud computing approach for scRNA-seq data processing, demonstrating significant speedup for large datasets.

RapidMACS: MACS3-identical peak calling, 50x faster

RapidMACS provides a faster narrow peak caller for ATAC-seq and related data, achieving 3.5 to 51x speed improvements over MACS3 while producing identical output.

Graphical and Interactive Spatial Proteomics Image Analysis Workflow

The paper introduces an interactive spatial proteomics workflow for analyzing imaging data, enabling reproducible and customizable analysis of protein expression and localization in tissues.

Chromap Suite: an open-source single-binary platform for agentic multiomic RNA + ATAC profiling

Chromap Suite provides an open-source, single-binary platform for RNA + ATAC multiomic profiling with improved speed and memory efficiency compared to proprietary tools.

User-friendly scheduler Using a hybrid architecture and supercomputing for big data processing

This paper introduces a user-friendly scheduler for big data processing in bioinformatics, reducing cost and time for bulk RNA sequencing workflows using a hybrid architecture and supercomputing.

Uncovering the Pathophysiological Pattern of Expression from Integrated Analysis across Uniformly Processed RNA Sequencing COVID-19 Datasets

The paper integrates RNA-seq datasets to identify molecular patterns distinguishing acute and chronic phases of COVID-19, revealing pathway signatures for disease progression and PASC diagnosis.

Harmonizing and integrating the NCI Genomic Data Commons through accessible, interactive, and cloud-enabled workflows

The paper converts GDC SOPs into reproducible, containerized workflows to harmonize datasets across repositories and improve data interpretation.

Accelerated and Reproducible Fiji for image processing using GPUs on the cloud

The paper presents a cloud-based Fiji platform with GPU acceleration for image processing, achieving 29x faster execution with reproducible results across AWS and IBM clouds.

Cloud-enabled Fiji for reproducible, integrated and modular image processing

The paper introduces a cloud-enabled platform for reproducible and modular image processing workflows that integrates interactive graphics with software containers.

A graphical, interactive and GPU-enabled workflow to process long-read sequencing data

The paper introduces a GPU-enabled graphical workflow for processing long-read sequencing data, achieving significant speedup and cost reduction in basecalling.

Accessible and interactive RNA sequencing analysis using serverless computing

The paper introduces a serverless computing method that drastically reduces RNA-seq alignment time and provides an interactive interface for real-time parameter adjustment.

Building containerized workflows using the BioDepot-workflow-builder (Bwb)

The paper introduces Bwb, a tool for creating and executing reproducible bioinformatics workflows via a drag-and-drop interface using Docker containers.

Integration of multiple data sources for gene network inference using genetic perturbation data

The paper presents a Bayesian method integrating external data with knockdown data to improve gene network inference in human cell lines.

Holistic optimization of an RNA-seq workflow for multi-threaded environments

The paper optimizes an RNA-seq workflow for multi-threaded environments, achieving significant speed improvements by optimizing all steps, not just alignment.

Hot-starting software containers for bioinformatics analyses

The paper introduces a method to reduce cloud computing costs for bioinformatics by hot-starting software containers, avoiding repetitive initialization steps.

Embedding containerized workflows inside data science notebooks enhances reproducibility

The paper introduces nbdocker, a Jupyter notebook extension that embeds Docker containers to enhance reproducibility of data science workflows.

Accurate informatic modeling of tooth enamel pellicle interactions by training substitution matrices with Mat4Pep

The paper develops a substitution matrix-based method to model tooth enamel pellicle peptide interactions with hydroxyapatite, achieving high discrimination accuracy.

Reproducible Bioconductor Workflows Using Browser-Based Interactive Notebooks And Containers

The paper introduces BiocImageBuilder, a tool that enables reproducible bioinformatics workflows through interactive notebooks and containers.

fastBMA: Scalable Network Inference and Transitive Reduction

fastBMA improves network inference by being faster, more accurate, and scalable, with a transitive reduction method for denser networks.

Software solutions for reproducible RNA-seq workflows

This paper demonstrates that RNA-seq analysis can depend on the computing environment and shows that software containers improve reproducibility.

Rice protein models from the Nutritious Rice for the World Project

The paper generates 10 billion de novo protein models for rice proteins using computational methods, providing centroid models and conformers for benchmarking and functional studies.