software / tool

DeepSCENIC: transfer learning from sequence-to-function models enables causal gene regulatory network inference

DeepSCENIC uses transfer learning from sequence-to-function models to infer causal gene regulatory networks from single-cell multiome data.

MetaboCensoR: A Shiny Application for Data Filtering in Untargeted LC-MS Metabolomics to Enhance Interpretability

MetaboCensoR filters untargeted LC-MS metabolomics data to reduce redundancy and improve downstream analysis while retaining known analytes.

NeuralRNN: a unified framework for recurrent neural network methods in cognitive neuroscience

NeuralRNN unifies RNN methods for cognitive neuroscience tasks by providing a single framework for model implementation, comparison, and extension.

Comparison of the Distribution of Fitness Effects Across Primates

Across 38 catarrhine subspecies, the population-scaled distribution of fitness effects (DFE) tracks effective population size while the unscaled deleterious DFE appears conserved, with no detectable epistasis.

inteRelate: flexible and thorough relating of genomic interval datasets through comparative overlap analysis

inteRelate compares genomic features by analyzing their overlap with a common feature, testing heterogeneity and identifying differing overlap rates across biological contexts.

Leveraging collaborations between researchers, wildlife managers and citizen-volunteers to monitor endangered carnivore populations across space and time

The paper presents a collaborative framework for monitoring dhole populations using fecal DNA and SECR models, showing stable densities in some areas and highlighting the role of citizen-volunteers in conservation.

PanGBank: a large-scale resource of precomputed microbial pangenomes built with PPanGGOLiN

Precomputed PPanGGOLiN pangenomes for over 4,600 prokaryotic species (Genome Taxonomy Database clusters), with plasticity regions and modules, downloadable via web, API and command line for projection onto new genomes.

Integrated Spatial Metabolomics and Proteomics from the Same Tissue Section Using a Conductive ITO-PET Slide

This paper develops an ITO-PET slide that enables sequential MALDI-MSI and LCM-LC-MS analysis of the same tissue section, demonstrating comparable performance to conventional slides across multiple tissues.

CalFluxTools: An R package for analysis of high-throughput calcium oscillation screening data

CalFluxTools automates analysis of calcium flux data from high-throughput screens, providing quality control, statistical tests, and machine learning predictions for toxicity assessment.

ProtPipe2: Multi-Platform Downstream Proteomics Analysis Tool

ProtPipe2 provides a unified framework for downstream proteomics analysis across mass spectrometry, Olink, and SomaScan platforms, enabling consistent workflows and reusable analyses.

MakeMyFigure: An Interactive Platform for Reproducible Quantitative Data Visualization, Analysis, and Scientific Figure Construction

MakeMyFigure enables reproducible scientific figure creation by integrating data analysis, visualization, and figure assembly in a single workflow with automated documentation.

MaSkel and napari-MaSkel: fast morphological skeleton feature extraction from segmentation masks

The paper introduces MaSkel and napari-MaSkel, tools for fast skeletonization and graph-based feature extraction from segmentation masks, using an optimized Lee94 thinning algorithm.

MAT-classifier: A memory-efficient pipeline for accurate genus level profiling from ancient metagenomic data

Per-genus Bowtie2 or BWA-aln alignments in place of MALT cut alignment-stage memory from about 140 GB (aMeta) to about 7 GB and gave higher simulated-data AUC (0.87 vs 0.79).

Structure-based Antibody Renumbering

This paper introduces SAbR, a structure-based method for antibody renumbering that outperforms sequence-based methods on de novo-designed molecules and shows high agreement with sequence-based approaches on benchmark structures.

Dosing and Delivery of Bacteriophage Therapy In a Murine Wound Infection Model

This study evaluates phage therapy dosing and delivery in a mouse wound infection model, finding topical high-dose repeated administration effective and developing a sustained-release hydrogel system.

A Unified 3D Generative Model for Synthesizable Structure-Based Drug Design

This paper introduces LDDM, a generative model for drug design that produces synthetically accessible compounds validated experimentally for five protein targets.

An atlas of transcription factor cooperation reveals how motif readers shape regulatory output

The paper develops ARES to analyze TF binding data and finds that motif readers, not canonical TFs, determine regulatory outcomes.

sabinaMBM: An R package for Multiscale Bayesian species distribution Modelling using INLA

The paper introduces sabinaMBM, an R package for multiscale Bayesian species distribution modeling that improves out-of-sample discrimination and uncertainty propagation across scales.

Incomplete references leave bulk deconvolution targets non-identifiable, but identification has a computable precision price

With an incomplete deconvolution reference, operator history changes estimates and associations, and the target is not point-identified; fitdrop scores remedies on shrinkage, coverage, certification and false certification, and prices measurements.

BoneGraph: A Domain-Specialised, Self-Correcting Reasoning System for Bone Science Retrieval, Grounded Inference, and Image Mechanics

BoneGraph combines a SPECTER2-indexed bone corpus, knowledge graph, deterministic physics checks, and user-taught rules in a local five-tab system; oracle passages raise accuracy 42% to 78%.

Benchmarking of bulk transcriptomic harmonization tools in a multi-platform B-cell lymphoma cohort identifies feature-specific quantile normalization and surrogate variable analysis as top-performing methods

Across 7,174 multi-platform lymphoma transcriptomes, only surrogate variable analysis and feature-specific quantile normalization corrected batch effects while keeping subtype and normal B-cell differences; top-scoring MNN erased biomarker correlations.

Unlocking Sensitive Data with SPHERE in the Age of AI

SPHERE enables the use of sensitive datasets in AI and open science by creating synthetic twins that preserve statistical properties and privacy.

Gelato streamlines reproducible and auditable assembly of Western blot figures

Gelato is a Fiji/ImageJ plugin that simplifies Western blot figure preparation, enabling reproducibility, auditability, and reducing errors in reporting.

From Prompt to Pipeline: A Comparative Evaluation of Large Language Model Coding Agents for Reproducible Bioinformatics Pipeline Construction

This paper evaluates three agentic coding systems for constructing bioinformatics pipelines and finds they produce plausible but incomplete implementations requiring expert review.

KSTAR v1.2: A faster and more and accessible KSTAR for kinase activity inference

KSTAR v1.2 improves speed and accessibility for kinase activity inference from phosphoproteomic data without compromising accuracy.

TrIdent - An R package to automate transductomics analysis of virus-like particle mediated DNA mobilization

TrIdent automates transductomics analysis by identifying DNA mobilized by virus-like particles, showing high agreement with manual classifications and revealing enriched bacterial families in murine gut transductomes.

Rsearch: An R interface to VSEARCH supporting visualization and parameter tuning

Rsearch runs VSEARCH from R with quality plots, trimming optimizers and phyloseq conversion; on a 16S mock community it matched DADA2's abundance accuracy with fewer, more prevalent OTUs.

Interaction Profiles as a Universal Language for Generative Molecular Design with ShEPhERD-2

This paper introduces ShEPhERD-2, a 3D generative model that creates drug-like molecules based on interaction profiles, demonstrating its versatility across multiple design tasks.

eCOMET: An R package for evaluating metabolic diversity and enrichment from LC-MS/MS data to test ecological hypotheses from individuals to ecosystems

eCOMET integrates metabolomics tools and provides statistical analysis for ecological studies, enabling researchers to assess metabolic diversity and test ecological hypotheses.

Automatic Quality Control and Error Correction in MRI linear registration via a Residual Parameter Prediction Network for T1w MRI

A 3D ResNet18 trained on synthetically misaligned T1w scans predicts residual affine parameters, correcting synthetic misalignments to 0.778 mm residual RMSE and flagging failed registrations better than RegQCNET or DARQ.