software / tool

This paper evaluates segmentation models for low- and ultralow-dose cryoEM images, finding that model choice significantly affects downstream quantitative measurements.

This paper develops an inflammation-driven epigenetic clock to track disease progression and rejuvenation using DNA methylation data.

iSBEM automates ROI targeting in SBF-SEM using XRM maps, improving acquisition throughput while maintaining targeting precision in biological specimens.

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

This paper designs a DNA-based nanoscale Jitterbug transformer that reconfigures its structure in response to chemical and optical signals, maintaining a Poissons ratio of -1.

CellSTIC decodes hierarchical cell-cell communication in spatial multi-omics data by integrating multimodal evidence and organizing interactions into a hierarchical semantic representation.

The paper introduces MitoBEAP, an R package for analysing next-generation sequencing data from mitochondrial base-edited samples to assess off-target effects.

NeuroCaptain v2 enables interactive 3D fNIRS optode design and registration with improved cross-subject placement consistency.

SWARM improves detection of RNA modifications by reducing false positives and reveals new splicing-related pseudouridylation patterns.

This paper introduces ReCLIP, a transformer-based framework that models protein-protein interactions at the residue level, showing high accuracy in predicting mutation effects and peptide-MHC binding.

sEEG-Suite provides a semi-automated pipeline for sEEG contact localization and anatomical labeling within Brainstorm, improving accuracy and efficiency in epileptic network mapping.

LipidCruncher processes, visualizes, and analyzes lipidomic data with quality controls, enabling efficient and rigorous analysis of lipid profiles.

The paper introduces CLASH, a method to quantify how genetic variation, methylation, and CTCF occupancy affect chromatin loop strength across individuals.

KhufuEnv is an open-source toolkit for building genomic analysis pipelines, demonstrating rapid QTL identification and ROH calculation on published datasets.

This paper introduces a top-down mass spectrometry workflow with DMTm technology and a new software platform to achieve deeper proteoform sequencing and improved sequence coverage.

TabularQual provides a spreadsheet-based format for annotating logical models, with tools to convert between spreadsheets and SBML-qual, enhancing model reuse and interoperability.

The paper introduces two Bioconductor packages for multi-state QTL analysis, providing tools for data storage, analysis, and simulation.

RAD is a demultiplexer for single-cell long-read sequencing that improves speed and sensitivity over existing methods while supporting complex read structures.

This paper introduces Shred-seq, a method to scan large-scale deletions in the human genome, revealing essential regions including noncoding sequences and establishing a lower bound for viability.

TRaP provides an open-source framework for reproducible Raman spectral preprocessing across different systems, enabling consistent and transparent analysis workflows.

ATI_Box simplifies CNN-based image segmentation for researchers without coding skills by integrating annotation, training, and analysis into a single platform.

The paper introduces YSA, an open-source GUI for analyzing HD-MEA recordings, enabling efficient visualization and exploration of seizure dynamics in neural data.

DropSynth-Gold uses Golden Gate assembly in emulsions to enable longer and more complex gene library synthesis with comparable fidelity to previous methods.

ALARMIST identifies multicellular communication motifs in spatial transcriptomics data, revealing microenvironmental drivers of tumor progression in lung and brain cancers.

barbieQ is an R package for analysing barcode count data from clonal tracking experiments, providing statistical tests for differential barcode proportion and occurrence.

This study examines how auditory stimuli modulate the pupil light reflex in autistic and non-autistic children, finding similar cross-modal effects across groups.

The paper introduces Autopipe, a platform that enables reproducible and shareable bioinformatics pipelines generated from natural-language prompts using LLMs.

BrightEyes-FFS provides an open-source platform for analyzing fluorescence fluctuation spectroscopy data with small detector arrays, offering tools for data processing, correlation analysis, and model fitting.

PEPE efficiently extracts multimodal protein embeddings from language models, enabling scalable and memory-efficient generation of large embedding datasets for downstream biological tasks.