software / tool

ALBIS: simulation of multi-resolution and multi-dimensional spatial transcriptomics data

ALBIS generates synthetic spatial transcriptomics data across multiple resolutions and dimensions to enable benchmarking of computational methods.

'broadSeq', a benchmarking tool to contrast differential gene expression methods and identify when genomic neighbourhood matters

broadSeq benchmarks differential gene expression methods and shows DELocal identifies distinct genes by considering genomic neighbourhood, particularly for highly expressed genes.

AnnZarro: scalable, interactive exploration of cell-by-cell and gene-by-gene relationships in single-cell data

AnnZarro enables interactive exploration of cell-by-cell and gene-by-gene relationships in single-cell data through a browser-based viewer linked to AnnData objects.

Human-specific CCG-repeat insertion in the RBFOX1 promoter implicated in autism and speech enhances EGR1-responsive activity

A human-specific CCG insertion in the RBFOX1 promoter boosts EGR1-driven reporter activity in HEK293T cells, as does an autism-linked CCG-gaining duplication in PTCHD1.

simSOMA: a cell-lineage based simulator of the somatic VAF spectrum in plants

simSOMA links plant branching topology to meristem cell-lineage dynamics; in simulations, niche size and turnover drive fixation, while terminal organ growth produces most private low-frequency variants.

High-throughput variant libraries and machine learning enable robust target-site selection for toehold-switch design in Detectrons

DeSTAR is a machine learning model that ranks target sites for RNA sensors, improving performance across different transcripts.

MtbAIM: AI/ML-guided endpoint-specific prediction of small-molecule activity across drug-susceptible and drug-resistant Mycobacterium tuberculosis

Tree models on RDKit/Morgan features predict M.tb activity and MIC endpoints for drug-susceptible and resistant isolates, slightly beating pretrained embeddings; released as a Colab tool.

One-Entry Golden Seamless Cloning with a Reusable Donor Streamlines Plant Gene Functional Analysis

The paper introduces a cloning system that simplifies gene cloning and distribution across vectors with reduced background and increased efficiency.

TopFor: Automated Preparation of AMBER-Compatible Parameters for Noncanonical Amino Acids in Peptides

TopFor automates the generation of AMBER-compatible parameters for noncanonical amino acids in peptides, enabling efficient MD simulations and integration into peptide discovery workflows.

Autonomous AI agents discover reverse transcriptases with tandem repeat arrays

The paper uses large language models to discover a novel family of reverse transcriptases with tandem repeat arrays from metagenomic data.

EthoTrace: from behaviour to neural dynamics in a unified analysis framework

EthoTrace is a tool that integrates behavioral annotation and calcium signal analysis in a single workflow for neuroscience studies.

GenDiMug: a generic inclusive multigraph framework to analyze genomic organizations and -omics data at multiple scales

GenDiMug is a multigraph framework for analyzing genomic organization and multi-omics data across scales, revealing gene expression clumping and circadian regulation in a photosynthetic alga.

MetworkPy: A Python Package for Graph- and Information-theoretic Investigation of Metabolic Networks

MetworkPy provides a Python package for objective-free graph- and information-theoretic analysis of genome-scale metabolic models to identify metabolic features perturbed by transcription factors.

TurbOmics: a web-based platform for the analysis of metabolomics data using a multi-omics integrative approach

TurbOmics is a web-based platform that enables multi-omics integration of metabolomics, proteomics, and transcriptomics data, addressing limitations in metabolomics annotation and accessibility.

A modular DNA toolkit for single-molecule biophysics

The paper introduces a modular DNA toolkit for creating long, customizable DNA molecules with user-defined sequences for single-molecule biophysics applications.

qPyCR: A qPCR Data Analyzer for Template Quantification and the Detection of Performance Outliers

qPyCR is a Python tool for analyzing qPCR data that computes Cq values, performs background subtraction, and provides global fitting to quantify template abundance and assess reaction quality.

SCKAnalyzer: A Web Tool for Single-Cycle Kinetics Analysis and Simulation

SCKAnalyzer processes and fits single-cycle kinetics data from biosensors, offering simulation and analysis tools for biomolecular interactions.

sRQA: AN INTEGRATIVE PIPELINE FOR SYMBOLIC RECURRENCE QUANTIFICATION ANALYSIS

The paper introduces sRQA, a software package for symbolic recurrence quantification analysis, validated on simulated and real-world data across multiple domains.

KRAKEN: A provenance-tracked knowledge graph for multiomic and wellness research

A Biolink-compliant graph (∼15 million nodes, ∼113 million edges) adds RefMet and LIPID MAPS metabolite and lipid classifications, plus polygenic score and clinical data element entities, to Translator content.

User-friendly software for high-throughput processing of chlorophyll fluorescence images to assess plant stress responses: fvfmPy and fvfmR packages

The paper introduces fvfmPy and fvfmR, user-friendly tools for automated analysis of chlorophyll fluorescence images to assess plant stress responses, significantly reducing processing time compared to manual methods.

Illuminating dark genes and dark metabolites: calibrated functional association across kingdoms with autoencoders and correlation

VaLPAS pairs a bi-directional autoencoder with correlation for omics guilt-by-association with calibrated confidence; in L. starkeyi its autoencoder linked 176 unidentified metabolites to known-function proteins at ≥50% confidence.

Two Comparators May Be All We Need

Random forests on sequence and 2D chemistry pick the favored protein for a molecule, or the favored molecule for a protein, at 0.71 to 0.78 accuracy on unseen compounds.

A novel analysis pipeline and experimental design for measuring expanded repeat instability

Delta plots from targeted long-read data separate repeat instability frequency, expansion bias and change size; a single-clone assay (SCIA) shows FAN1 knockout raises expansion frequency but shrinks expansions.

msengine: Adaptive Open-Source Signal Extraction for HDX MS

msengine improves HDX-MS signal extraction by adaptively adjusting mass and retention-time boundaries, increasing accepted targets and reducing processing time.

CADENCE: Open-source software for signal conditioning, feature extraction, visualization and analysis of cardiac optical mapping data

CADENCE is an open-source MATLAB-based tool for processing cardiac optical mapping data, offering end-to-end analysis with features for denoising, conduction velocity, alternans, and rotor detection across multiple species and tissue types.

SpatialOmicsLab: an integrated research environment for AI co-scientists in spatial transcriptomics

SpatialOmicsLab provides an integrated environment with AI tools for spatial transcriptomics analysis, outperforming expert workflows in multiple tasks.

fuzzyfold: a high-performance framework for stochastic RNA folding kinetics

The paper introduces fuzzyfold, a Rust-based software framework for stochastic RNA folding kinetics, enabling efficient simulation of long RNA molecules and flexible model integration.

tangermeme: A toolkit for understanding cis-regulatory logic using deep learning models

tangermeme provides tools to interpret deep learning models for cis-regulatory analysis, extracting human-readable insights from genomic predictions.

How to design 1000-plex mass tags using the differential mass defect

This paper explores designing high-plex mass tags using differential mass defect to enable large-scale multiplexing in proteomics.

Super Bloom: Fast and precise filter for streaming k-mer queries

The paper introduces Super Bloom, a Bloom filter variant for streaming k-mer queries, which improves cache efficiency and reduces false positives.