Nature Search

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

This Registered Report presents the results of the Long-read RNA-Seq Genome Annotation Assessment Project, which is a community effort for benchmarking long-read methods for transcriptome analyses, including transcript isoform detection, quantification and de novo transcript detection.

Francisco J. Pardo-Palacios
Dingjie Wang
Angela N. Brooks
ResearchOpen Access07 Jun 2024
Nature Methods

Volume: 21, P: 1349-1363
Clinical and immunopathological evaluation and its comparison with IHC consensus molecular subtypes of colorectal cancer

Eduardo Feliciangeli
Ana Albaladejo-González
Ginés Luengo-Gil
ResearchOpen Access01 Jul 2025
Scientific Reports

Volume: 15, P: 1-22
acorde unravels functionally interpretable networks of isoform co-usage from single cell data

Alternative splicing (AS) is a highly-regulated post-transcriptional mechanism known to modulate isoform expression within genes and contribute to cell-type identity. Here, the authors present acorde, a pipeline that successfully leverages bulk long reads and single-cell data to confidently detect alternative isoform co-expression relationships.

Angeles Arzalluz-Luque
Pedro Salguero
Ana Conesa
ResearchOpen Access05 Apr 2022
Nature Communications

Volume: 13, P: 1-18
Overexpression of the vascular brassinosteroid receptor BRL3 confers drought resistance without penalizing plant growth

Drought resistant plants typically have reduced growth. Here the authors show that overexpression of the BRL3 brassinosteroid receptor confers drought tolerance and accumulation of osmoprotectant metabolites without penalizing growth, demonstrating that drought response and growth can be uncoupled.

Norma Fàbregas
Fidel Lozano-Elena
Ana I. Caño-Delgado
ResearchOpen Access08 Nov 2018
Nature Communications

Volume: 9, P: 1-13
Structures of T7 bacteriophage portal and tail suggest a viral DNA retention and ejection mechanism

The genome of double-stranded DNA bacteriophages is delivered to host cells through the viral portal and tail structures. Here the authors describe structures of the bacteriophage T7 portal and the 1.5 MDa tail complex formed by the portal protein, adaptor protein and nozzle, providing insight into how the portal and tail machinery work during DNA packaging and ejection.

Ana Cuervo
Montserrat Fàbrega-Ferrer
Miquel Coll
ResearchOpen Access20 Aug 2019
Nature Communications

Volume: 10, P: 1-11
SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms

SQANTI3 offers a flexible tool for quality control, curation and annotation of long-read RNA sequencing data.

Francisco J. Pardo-Palacios
Angeles Arzalluz-Luque
Ana Conesa
ResearchOpen Access20 Mar 2024
Nature Methods

Volume: 21, P: 793-797
Single-cell long-read targeted sequencing reveals transcriptional variation in ovarian cancer

Long-read sequencing allows the detection of RNA isoforms, but is hampered by low throughput and potential artefacts. Here, the authors develop the scTaILoR-seq hybridisation capture method for long-read RNA sequencing to improve transcript detection, and use this method to detect isoforms at the single-cell level in ovarian cancer.

Ashley Byrne
Daniel Le
William Stephenson
ResearchOpen Access12 Aug 2024
Nature Communications

Volume: 15, P: 1-13
Enhanced SREBP2-driven cholesterol biosynthesis by PKCλ/ι deficiency in intestinal epithelial cells promotes aggressive serrated tumorigenesis

The underlying mechanisms driving colorectal cancer (CRC) through the serrated route are largely unknown. Here, the authors show that reduced aPKC levels increase cholesterol biosynthesis to promote aggressiveness in serrated tumours and targeting this pathway reduces tumourigenesis in preclinical models of serrated CRC.

Yu Muta
Juan F. Linares
Jorge Moscat
ResearchOpen Access13 Dec 2023
Nature Communications

Volume: 14, P: 1-20
Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures

Differential gene expression experiments yield quantitative insight into biological activity and may be important in disease classification and treatment. Here, the authors analyse external spike-in RNA controls to provide a standard method to assess and compare experiment performance.

Sarah A. Munro
Steven P. Lund
Marc Salit
Research25 Sept 2014
Nature Communications

Volume: 5, P: 1-10
Independent phenotypic plasticity axes define distinct obesity sub-types

Yang et al. show that neuronatin (NNAT) can explain part of the phenotypic variation of complex traits, independently of genetics or the environment. Such NNAT-dependent variations can stratify human cohorts into four metabolic sub-types, including two distinct types of obesity.

Chih-Hsiang Yang
Luca Fagnocchi
J. Andrew Pospisilik
ResearchOpen Access12 Sept 2022
Nature Metabolism

Volume: 4, P: 1150-1165
Impact of SARS-CoV-2 infection therapies on the risk of venous thromboembolism and cardiovascular events from the SEMI-COVID-19 Registry

Crhistian-Mario Oblitas
Pablo Demelo-Rodríguez
Hector Meijide Míguez
ResearchOpen Access05 Mar 2025
Scientific Reports

Volume: 15, P: 1-13
Harmonization of quality metrics and power calculation in multi-omic studies

Multi-omics studies are popular but lack rigorous criteria for experimental design. We define Figures of Merit across omics to comparatively describe their performance, and present new algorithms for sample size calculation in multi-omics experiments aiming either at feature selection or sample classification.

Sonia Tarazona
Leandro Balzano-Nogueira
Ana Conesa
ResearchOpen Access18 Jun 2020
Nature Communications

Volume: 11, P: 1-13
Profiling the epigenome using long-read sequencing

Long-read sequencing technologies have revolutionized genomics and transcriptomics, and more recently enabled comprehensive epigenomic profiling. These advances now also allow investigation of the relationship between chromatin states and transcriptional dynamics.

Tianyuan Liu
Ana Conesa
Reviews08 Jan 2025
Nature Genetics

Volume: 57, P: 27-41
A machine learning approach to identify patients at risk for long-term consequences after pulmonary embolism

Stephan Nopp
Clemens Spielvogel
H. M. Bui
ResearchOpen Access24 Sept 2025
Scientific Reports

Volume: 15, P: 1-12
Programmed cell death pathways coordinate neutrophil and macrophage clearance in zebrafish and are differentially exploited by Salmonella Typhimurium

Juan M. Lozano-Gil
Annamaria Pedoto
Sylwia D. Tyrkalska
ResearchOpen Access08 Dec 2025
Cell Death & Disease

Volume: 17, P: 1-13
Transcriptomics in the era of long-read sequencing

Advances in long-read sequencing are driving the implementation of these technologies for transcriptome profiling. The authors provide a comprehensive guide to long-read RNA sequencing, including experimental and computational tools, current applications, challenges and opportunities.

Carolina Monzó
Tianyuan Liu
Ana Conesa
Reviews28 Mar 2025
Nature Reviews Genetics

Volume: 26, P: 681-701
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

The Sequencing Quality Control (SEQC) consortium shows that junction discovery and differential gene expression profiling with RNA-seq can be robust but transcript-level and absolute measurements remain challenging.

Zhenqiang Su
Paweł P Łabaj
Leming Shi
Research24 Aug 2014
Nature Biotechnology

Volume: 32, P: 903-914
Mortality reduction in older COVID-19-patients hospitalized in Spain during the second pandemic wave from the SEMI-COVID-19 Registry

José-Manuel Casas-Rojo
Juan-Miguel Antón-Santos
Hector Meijide Míguez
ResearchOpen Access18 Oct 2023
Scientific Reports

Volume: 13, P: 1-18
Discovery of Z1362873773: a novel fascin inhibitor from a large chemical library for colorectal cancer

Alejandro Rodríguez-Martínez
Lucía Giraldo-Ruiz
Horacio Pérez-Sánchez
ResearchOpen Access28 Apr 2025
Scientific Reports

Volume: 15, P: 1-15
NFKB2 polymorphisms associate with the risk of developing rheumatoid arthritis and response to TNF inhibitors: Results from the REPAIR consortium

Jose Manuel Sánchez-Maldonado
Manuel Martínez-Bueno
Juan Sainz
ResearchOpen Access09 Mar 2020
Scientific Reports

Volume: 10, P: 1-13
GAIT-GM integrative cross-omics analyses reveal cholinergic defects in a C. elegans model of Parkinson’s disease

Lauren M. McIntyre
Francisco Huertas
Danielle E. Mor
ResearchOpen Access28 Feb 2022
Scientific Reports

Volume: 12, P: 1-9
Correction: Polymorphisms at phase I-metabolizing enzyme and hormone receptor loci influence the response to anti-TNF therapy in rheumatoid arthritis patients

Luz M. Canet
Jose M. Sánchez-Maldonado
Juan Sainz
Amendments and Corrections14 Feb 2019
The Pharmacogenomics Journal

Volume: 19, P: 582
Steering research on mRNA splicing in cancer towards clinical translation

Although splicing factors are altered in cancer through mutations and copy number variations, their exact role remains challenging to define. In this Roadmap, Anczukow, Thomas-Tikhonenko and colleagues explore recent advances in splicing biology and provide guidance on leveraging these insights to facilitate the clinical application of compounds that target or exploit aberrant splicing patterns in cancer.

Olga Anczukow
Frédéric H.-T. Allain
Andrei Thomas-Tikhonenko
Reviews09 Oct 2024
Nature Reviews Cancer

Volume: 24, P: 887-905
Unravelling genotype-phenotype correlations in Stargardt disease using patient-derived retinal organoids

Avril Watson
Rachel Queen
Majlinda Lako
ResearchOpen Access19 Feb 2025
Cell Death & Disease

Volume: 16, P: 1-15
Undisclosed, unmet and neglected challenges in multi-omics studies

Multi-omics studies have been increasingly used to better understand biological samples and infer molecular interactions. Nevertheless, a number of challenges must still be addressed to take full advantage of multi-omics data and to avoid reaching potentially incorrect conclusions.

Sonia Tarazona
Angeles Arzalluz-Luque
Ana Conesa
Reviews21 Jun 2021
Nature Computational Science

Volume: 1, P: 395-402
Development and validation of a clinical score to estimate progression to severe or critical state in COVID-19 pneumonia hospitalized patients

Francisco Gude
Vanessa Riveiro
Luis Valdés
ResearchOpen Access13 Nov 2020
Scientific Reports

Volume: 10, P: 1-10
Polymorphisms at phase I-metabolizing enzyme and hormone receptor loci influence the response to anti-TNF therapy in rheumatoid arthritis patients

Luz M. Canet
Jose M. Sánchez-Maldonado
Juan Sainz
Research05 Oct 2018
The Pharmacogenomics Journal

Volume: 19, P: 83-96
One-year breakthrough SARS-CoV-2 infection and correlates of protection in fully vaccinated hematological patients

José Luis Piñana
Lourdes Vazquez
Rodrigo Martino
ResearchOpen Access05 Jan 2023
Blood Cancer Journal

Volume: 13, P: 1-14
Author Correction: Influence of chromium hyperdoping on the electronic structure of CH₃NH₃PbI₃ perovskite: a first-principles insight

Gregorio García
Pablo Palacios
Perla Wahnón
Amendments and CorrectionsOpen Access03 May 2018
Scientific Reports

Volume: 8, P: 1
A network approach to elucidate and prioritize microbial dark matter in microbial communities

Tatyana Zamkovaya
Jamie S. Foster
Ana Conesa
ResearchOpen Access22 Sept 2020
The ISME Journal

Volume: 15, P: 228-244
Multi-omic analysis unveils biological pathways in peripheral immune system associated to minimal hepatic encephalopathy appearance in cirrhotic patients

Teresa Rubio
Vicente Felipo
Carmina Montoliu
ResearchOpen Access21 Jan 2021
Scientific Reports

Volume: 11, P: 1-14
Transcriptional profiling of the mutualistic bacterium Vibrio fischeri and an hfq mutant under modeled microgravity

Alexandrea A. Duscher
Ana Conesa
Jamie S. Foster
ResearchOpen Access18 Dec 2018
npj Microgravity

Volume: 4, P: 1-10
Assessment of unconventional antimicrobial compounds for the control of ‘Candidatus Liberibacter asiaticus’, the causative agent of citrus greening disease

Christopher L. Gardner
Danilo R. da Silva
Claudio F. Gonzalez
ResearchOpen Access25 Mar 2020
Scientific Reports

Volume: 10, P: 1-15
XTEND: Extending the depth of field in cryo soft X-ray tomography

Joaquín Otón
Eva Pereiro
José M. Carazo
ResearchOpen Access04 Apr 2017
Scientific Reports

Volume: 7, P: 1-12
Influence of chromium hyperdoping on the electronic structure of CH₃NH₃PbI₃ perovskite: a first-principles insight

Gregorio García
Pablo Palacios
Perla Wahnón
ResearchOpen Access06 Feb 2018
Scientific Reports

Volume: 8, P: 1-12
STATegra, a comprehensive multi-omics dataset of B-cell differentiation in mouse

David Gomez-Cabrero
Sonia Tarazona
Ana Conesa
ResearchOpen Access31 Oct 2019
Scientific Data

Volume: 6, P: 1-15
A multi-omics dataset of heat-shock response in the yeast RNA binding protein Mip6

Carme Nuño-Cabanes
Manuel Ugidos
Ana Conesa
ResearchOpen Access27 Feb 2020
Scientific Data

Volume: 7, P: 1-10
Clinical characterization and outcomes of 85 patients with neurosarcoidosis

Manuel Ramos-Casals
Roberto Pérez-Alvarez
A. Sisó-Almirall
ResearchOpen Access02 Jul 2021
Scientific Reports

Volume: 11, P: 1-14
Analysis of the common genetic component of large-vessel vasculitides through a meta-Immunochip strategy

F. David Carmona
Patrick Coit
Steven R. Ytterberg
ResearchOpen Access09 Mar 2017
Scientific Reports

Volume: 7, P: 1-11
Making multi-omics data accessible to researchers

A special collection on multi-omics data sharing, launched today at Scientific Data, offers to the scientific community a compendium of multi-omics datasets ready for reuse, which showcase the diversity of multi-omics projects and highlights innovative approaches for preprocessing, quality control, hosting and access.

Ana Conesa
Stephan Beck
Comments & OpinionOpen Access31 Oct 2019
Scientific Data

Volume: 6, P: 1-4
Correction: Corrigendum: Analysis of the common genetic component of large-vessel vasculitides through a meta-Immunochip strategy

F. David Carmona
Patrick Coit
Steven R. Ytterberg
Amendments and CorrectionsOpen Access05 Apr 2017
Scientific Reports

Volume: 7, P: 1

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