software / tool

Multi-agentic system for primer design in qPCR and LAMP diagnostics tests

This study develops an AI-orchestrated workflow using multiple agents to automate primer design for qPCR and LAMP assays by integrating bioinformatics tools and databases.

stably: error-controlled stability selection for biomarker panel discovery

stably (Python) applies error-controlled stability selection to DIA-NN output; its 17-protein pancreatic cancer panel reached held-out AUC 0.93 versus 0.82 for a published two-protein panel rescored on the same data.

MRSIPrep: A Standardized Post-Quantification Framework for Preprocessing Whole-Brain Magnetic Resonance Spectroscopic Imaging

MRSIPrep provides a standardized post-quantification framework for whole-brain MRSI to improve reproducibility across datasets and applications.

A Turing-Style Test for In-Silico Antibodies: How Sampling Mode Makes WGAN-GP Beat VAE in the Wet Lab

This paper compares GANs and VAEs for generating viable antibody sequences, finding GANs outperform VAEs when sampling strategies are optimized.

FetchPA: a guided, end-to-end solution for local ATAC-Seq data processing and analyses

FetchPA provides an end-to-end ATAC-Seq analysis pipeline for users without bioinformatics expertise, enabling local and public data processing and differential accessibility analysis.

Autonomous AI-Driven Nanoscale Spatial Mapping Reveals Novel Targets and Ternary Architectures in 5xFAD Alzheimer's Disease Model

The paper uses AI to analyze spatial data from Alzheimer's mouse models, revealing new protein interactions and synaptic structures linked to disease.

Whole-body 3D kinematics of freely behaving Drosophila

Seven high-speed cameras, a hybrid 2D/3D network and body-model inverse kinematics track 50 keypoints on freely moving flies; height and speed peak together at all running speeds.

QuantiTrack: A unified software to study protein dynamics in living cells

QuantiTrack, a MATLAB GUI, unifies single-molecule detection, tracking, quality control and mobility analyses; for glucocorticoid receptor, hormone washout cut bound fraction, dwell times and low-mobility occupancy.

Ryder: Epigenome normalization using a two-tier model and internal reference regions

Ryder normalizes epigenomic bigWig tracks against stable internal reference regions such as invariant CTCF sites, correcting background and signal separately, recovering expected perturbation effects that depth-only normalization obscured.

Fully automated open-source analysis and interactive visualization of magnetic resonance spectroscopic imaging (MRSI) data in Osprey-MRSI

The paper introduces Osprey-MRSI, an open-source software package for fully automated MRSI data analysis and visualization, validated across multiple vendors and sites.

A foundation model learns the sequence and functional grammar of fully human heavy-chain-only antibodies

The paper develops a foundation model trained on fully human heavy-chain-only antibodies, showing it captures sequence and functional constraints distinct from conventional antibody models.

ProteoformTracker: an interactive tool for planning proteoform detectability in top-down and middle-down proteomics

ProteoformTracker models MS signals and evaluates proteoform detectability in top-down and middle-down proteomics for experimental planning.

Transparent Weighting of Heterogeneous Evidence for Auditable Candidate Prioritization

Analytic Hierarchy Process weights merge fold-change, FDR and protein-interaction centrality into a traceable composite ranking of 143 triple-negative breast cancer exosomal protein candidates.

A precise atlas of the human subcortex

FOCUS, a 100 µm atlas of 180 manually segmented subcortical grey and white matter regions and 77 hand-built tracts, registered to MNI 2009b space for warping to individual brains.

An intersectional expression platform for gene complementation using RNA-fragment end joining (REJ)

This paper introduces an RNA-fragment end joining (REJ) platform for gene complementation that enables precise and efficient splicing of RNA units into functional mRNAs.

An interpretable peptide-HLA model emergently learns binding energetics and structure

The paper introduces an interpretable model for predicting peptide-HLA binding that matches state-of-the-art performance using only sequence data.

Scalable context-dependent single-cell eQTL mapping reveals disease-relevant regulatory variation beyond static models

The paper introduces CASTIE, a method for context-dependent eQTL mapping in single-cell data, identifying regulatory variants missed by static models and linking them to disease traits.

A structural antibody benchmark for leakage-aware deep-learning evaluation

The paper introduces SABLE, a benchmark for evaluating deep-learning methods in antibody structure prediction, with leakage-controlled test sets and versioned resources.

AlphaPeptTools: scverse-native analysis of mass spectrometry-based proteomics

AlphaPeptTools provides a scverse-native Python package for analyzing MS-based proteomics data, enabling scalable analysis and integration with other modalities.

Toward standardized behavioral analysis in IntelliCage experiments

The paper introduces ic-analysis, an open-source toolkit for standardized IntelliCage behavioral analysis, demonstrating its ability to recover behavioral differences in a synthetic experiment.

HARIBOSS++: An Integrated Platform for RNA-Targeted Drug Design

HARIBOSS++ is an updated platform for RNA-targeted drug design that includes expanded data and analysis tools for RNA-small molecule interactions.

pydreg: a fast Python package for identifying active cis-regulatory elements from nascent transcription

pydreg is a Python port of dREG that improves runtime and memory efficiency while maintaining similar performance in identifying active cis-regulatory elements.

CasanovoGUI: a cross-platform desktop application for deep learning-based de novo peptide sequencing with Casanovo

CasanovoGUI provides a user-friendly desktop interface for Casanovo, a deep learning model for de novo peptide sequencing, simplifying setup and result interpretation.

tTEscanR: A user-friendly integrative R package for quantifying and visualizing translation efficiency from sequencing data in diverse biological systems

tTEscanR quantifies and visualizes translation efficiency from transcriptomic data across diverse biological systems, revealing translational regulatory programs in cancer, aging, and neurodegeneration.

TLS-Sim: An Open-Source Toolkit for Individualized Transcranial Light Stimulation Modeling with Deep-Learning-Accelerated Simulation

TLS-Sim provides a toolkit for individualized transcranial light stimulation modeling using deep-learning-accelerated Monte Carlo simulations to improve efficiency and accuracy.

RNA-guided transcriptional repression by TIGR-Tas systems

TIGRFinder annotated 6,685 TIGR arrays; cryo-EM structures show inactive RuvC domains, and E. coli reporter assays show CsTasR and MbTasA repress transcription in a guide-dependent manner.

scPyviewer: a Python-native interactive viewer from AnnData single-cell data

scPyviewer provides a Python-native interactive viewer for AnnData single-cell data, matching R Shiny tools' features and outperforming them in speed and memory efficiency.

FlashDeconv reveals resolution horizons in atlas-scale spatial transcriptomics

Leverage-weighted sketching plus sparse spatial regularization deconvolves 1.6 million Visium HD bins in 153 seconds on commodity hardware, revealing tissue-specific resolution limits where cell-type co-localization can reverse sign.

Using stochastic dynamic programming for making decisions about invasive species

This paper provides a practical guide to using stochastic dynamic programming for invasive species management, with examples and R implementations.

Plateau-gated one-shot plasticity supports continual recognition memory

This paper develops a model of continual recognition memory using plateau-gated one-shot plasticity, showing it outperforms Hebbian controls in accuracy and memory retention.