Long-TREC: The Long-Reads Transcriptomics European Consortium. The next generation transcriptome biology revealed by single molecule sequencing technologies

Informazioni relative al progetto

LongTREC

ID dell’accordo di sovvenzione: 101072892

DOI

10.3030/101072892

Progetto chiuso

Data della firma CE 14 Luglio 2022

Data di avvio 1 Ottobre 2022

Data di completamento 30 Settembre 2026

Finanziato da

• Marie Skłodowska-Curie Actions (MSCA)

Costo totale

Nessun dato

Contributo UE

€ 2 621 931,00

Coordinato da

AGENCIA ESTATAL CONSEJO SUPERIOR DE INVESTIGACIONES CIENTIFICAS
Spain

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Risultati finali

Documents, reports (9)

Interim report including links to a protocol repository

Updated report on the state of library preparation, sequencing and mapping algorithm developments, including links to a protocol repository (i.e. protocols.io) and GitHub for code of novel mapping algorithms

Interim report on the state of algorithm developments in WP4 applied to use cases

Updated progress report on the state of algorithm developments in WP4, including a list of links to GitHub repositories containing code

Initial report on the state of algorithm developments in WP5
Interim report on the state of algorithm developed in WP5 and pipelines comparison

Updated progress report on the state of algorithm developments in WP5 and comparison of pipelines

Initial progress report on the state of algorithm developments in WP3

Progress report on the state of algorithm developments in WP3

Progress report on the state of library preparation, sequencing and mapping algorithm

Progress report on the state of library preparation, sequencing, and mapping algorithm developments.

Interim report on the state of algorithm developed in WP3, including benchmarks

Updated progress report on the state of algorithm developments in WP3, including a list of links to a GitHub repository containing code

Progress report on the state of algorithm developments in WP4
LongTREC website and social network profiles

Pubblicazioni

Peer reviewed articles (16)

Quality assessment of long read data in multisample lrRNA-seq experiments using SQANTI-reads

Autori: Netanya Keil, Carolina Monzó, Lauren McIntyre, Ana Conesa
Pubblicato in: Genome Research, Numero 35, 2026, ISSN 1088-9051
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/GR.280021.124

Handling biological replicates in long-read RNA sequencing data by joining or not joining

Autori: Fabian Jetzinger, Alejandro Paniagua, Stanley Cormack, Jorge Mestre-Tomás, José Manuel Morante-Redolat, Isabel Fariñas, Luis Ferrández-Peral, Stefan Götz, Carolina Monzó, Ana Conesa
Pubblicato in: Nature Communications, Numero 17, 2026, ISSN 2041-1723
Editore: Springer Science and Business Media LLC
DOI: 10.1038/S41467-026-77367-6

TUSCO: benchmarking transcriptome reconstruction with endogenous single-isoform controls

Autori: Tianyuan Liu, Alejandro Paniagua, Fabian Jetzinger, Luis Ferrández-Peral, Adam Frankish, Ana Conesa
Pubblicato in: Nature Communications, Numero 17, 2026, ISSN 2041-1723
Editore: Springer Science and Business Media LLC
DOI: 10.1038/S41467-026-72089-1

Cell culture differentiation and proliferation conditions influence the<i>in vitro</i>regeneration of the human airway epithelium

Autori: Elisa Redman; Morgane Fierville; Amélie Cavard; Magali Plaisant; Marie-Jeanne Arguel; Sandra Ruiz Garcia; Eamon M McAndrew; Cédric Girard-Riboulleau; Kevin Lebrigand; Virginie Magnone; Gilles Ponzio; Delphine Gras; Pascal Chanez; Sophie Abelanet; Pascal Barbry; Brice Marcet; Laure-Emmanuelle Zaragosi
Pubblicato in: American Journal of Respiratory Cell and Molecular Biology, 2024
Editore: OXFORD ACADEMIC
DOI: 10.1165/RCMB.2023-0356MA

Transcriptomics in the era of long-read sequencing

Autori: Carolina Monzó; Tianyuan Liu; Ana Conesa
Pubblicato in: Nature Reviews Genetics, 2025, ISSN 1471-0064
Editore: Springer Nature
DOI: 10.1038/S41576-025-00828-Z

IsoTools 2.0: Software for Comprehensive Analysis of Long-read Transcriptome Sequencing Data

Autori: Yalan Bi, Tom Lukas Lankenau, Matthias Lienhard, Ralf Herwig
Pubblicato in: Journal of Molecular Biology, 2025, ISSN 0022-2836
Editore: Elsevier BV
DOI: 10.1016/j.jmb.2025.169049

Icarust, a real-time simulator for Oxford Nanopore adaptive sampling

Autori: Rory Munro, Satrio Wibowo, Alexander Payne, Matthew Loose
Pubblicato in: Bioinformatics, Numero 40, 2024, ISSN 1367-4811
Editore: Oxford University Press (OUP)
DOI: 10.1093/bioinformatics/btae141

Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of<i>SF3B1</i>mutations

Autori: Alicja Pacholewska, Matthias Lienhard, Mirko Brüggemann, Heike Hänel, Lorina Bilalli, Anja Königs, Felix Heß, Kerstin Becker, Karl Köhrer, Jesko Kaiser, Holger Gohlke, Norbert Gattermann, Michael Hallek, Carmen D. Herling, Julian König, Christina Grimm, Ralf Herwig, Kathi Zarnack, Michal R. Schweiger
Pubblicato in: Genome Research, Numero 34, 2024, ISSN 1088-9051
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/GR.279327.124

The promise of long-read RNA-seq: reducing bias in analyses of allele imbalance

Autori: Nadja Nolte, Marko Petek, Pablo Angulo Lara, Logan Mulroney, Francesco Nicassio, Fabio Marroni, Lauren McIntyre
Pubblicato in: NAR Genomics and Bioinformatics, Numero 8, 2026, ISSN 2631-9268
Editore: Oxford University Press (OUP)
DOI: 10.1093/NARGAB/LQAG071

Evidence-based unification of potato gene models with the UniTato collaborative genome browser

Autori: Maja Zagorščak, Jan Zrimec, Carissa Bleker, Nadja Nolte, Mojca Juteršek, Živa Ramšak, Kristina Gruden, Marko Petek
Pubblicato in: Frontiers in Plant Science, Numero 15, 2024, ISSN 1664-462X
Editore: Frontiers Media SA
DOI: 10.3389/FPLS.2024.1352253

Long-read metagenomic and metatranscriptomic datasets from marine plankton

Autori: Carmen Lafuente Sanz, Corinne Da Silva, Corinne Cruaud, Stefan Engelen, Karine Labadie, Jean-Marc Aury, France Denoeud
Pubblicato in: Scientific Data, 2026, ISSN 2052-4463
Editore: Springer Science and Business Media LLC
DOI: 10.1038/S41597-026-08292-Y

Multiparent recombinant inbred lines crossed to a tester provide novel insights into sources of <i>cis</i> and <i>trans</i> regulation of gene expression

Autori: Fabio Marroni, Alison M Morse, Adalena V Nanni, Nadja Nolte, Patricka Williams-Simon, Luis G León-Novelo, Rita M Graze, Paul Schmidt, Elizabeth King, Lauren M McIntyre
Pubblicato in: GENETICS, Numero 232, 2026, ISSN 1943-2631
Editore: Oxford University Press (OUP)
DOI: 10.1093/GENETICS/IYAF257

Toward the use of nanopore RNA sequencing technologies in the clinic: challenges and opportunities

Autori: Xanthi-Lida Katopodi, Oguzhan Begik, Eva Maria Novoa
Pubblicato in: Nucleic Acids Research, Numero 53, 2025, ISSN 0305-1048
Editore: Oxford University Press (OUP)
DOI: 10.1093/NAR/GKAF128

LongPolyASE: an end-to-end framework for allele-specific gene and isoform analysis in polyploids using long-read RNA-seq

Autori: Nadja Nolte, Kristina Gruden, Marko Petek
Pubblicato in: Plant Methods, 2026, ISSN 1746-4811
Editore: Springer Science and Business Media LLC
DOI: 10.1186/S13007-026-01569-8

Quality assessment of long read data in multisample lrRNA-seq experiments using SQANTI-reads

Autori: Netanya Keil, Carolina Monzó, Lauren McIntyre, Ana Conesa
Pubblicato in: Genome Research, Numero 35, 2025, ISSN 1088-9051
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/GR.280021.124

Profiling the epigenome using long-read sequencing

Autori: Tianyuan Liu, Ana Conesa
Pubblicato in: Nature Genetics, Numero 57, 2025, ISSN 1061-4036
Editore: Springer Science and Business Media LLC
DOI: 10.1038/s41588-024-02038-5

Book chapters (1)

Machine Learning-Enhanced Resource Optimization for Bioinformatics Workflows in the Cloud

Autori: Robert Nica, Fabian Jetzinger, Stefan Götz, Germán Moltó
Pubblicato in: Lecture Notes in Computer Science, Euro-Par 2026: Parallel Processing, 2026
Editore: Springer Nature Switzerland
DOI: 10.1007/978-3-032-35251-4_23