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TDP-43 loss induces cryptic polyadenylation in ALS/FTD.

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MaxChien1996/replace_UG_in_first_800_bp_of_ELK1_extended_3_prime_UTR

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CommonMindConsortium/RAPiD-nf

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frattalab/rna_seq_snakemake

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frattalab/PAPA

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SamBryce-Smith/bulk_polyatail_reads

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frattalab/tdp43-apa

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iRNA-COSI/APAeval

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SamBryce-Smith/peka

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frattalab/rna_seq_single_steps

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SamBryce-Smith/bedops_parse_star_junctions

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Zenodo 15210472

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Zenodo 15210438

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Zenodo 15538003

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Tools found in the code: BCFtools, BEDTools, Biopython, broom, data.table, DESeq2, edgeR, ggplot2, ggpubr, Keras, Matplotlib, NumPy, pandas, patchwork, pysam, rstatix, SAMtools, scikit-learn, SciPy, seaborn, Snakemake, STAR, tidyverse

Overview

Authors: Sam Bryce-Smith, Anna-Leigh Brown, Max Z Y J Chien, Dario Dattilo, Puja R Mehta, Francesca Mattedi, Simone Barattucci, Alla Mikheenko, Matteo Zanovello, Flaminia Pellegrini, Sara Emad El-Agamy, Matthew Yome, Sarah E Kargbo-Hill, Yue A Qi, Kai Sun, Eugeni Ryadnov, Yixuan Wan, NYGC ALS Consortium, Jose Norberto S Vargas, Nicol Birsa
and 7 other authorsTowfique Raj, Jack Humphrey, Matthew Keuss, Oscar G Wilkins, Michael Ward, Maria Secrier, Pietro Fratta
Journal: Nature neuroscience
Published: 21 October 2025
Type: Research article
Status: code verified (how the code is found and verified)
DOI: 10.1038/s41593-025-02050-w
License: CC BY
Institutions: National Hospital for Neurology and Neurosurgery (United Kingdom), UCL Queen Square Institute of Neurology (United Kingdom), University College London (United Kingdom), The Francis Crick Institute (United Kingdom), National Institutes of Health (United States), National Institute of Neurological Disorders and Stroke (United States), Icahn School of Medicine at Mount Sinai (United States)
Categories: genetics / omics (modality), human (organism), other condition (population), Alzheimer's / dementia (population), cellular / molecular (subfield)

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