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View article: Exploring a Circulating <scp>miRNA</scp> Signature for <scp>PMM2</scp> ‐ <scp>CDG</scp> : Initial Insights Toward Diagnosis, Stratification, and Monitoring
Exploring a Circulating <span>miRNA</span> Signature for <span>PMM2</span> ‐ <span>CDG</span> : Initial Insights Toward Diagnosis, Stratification, and Monitoring Open
Phosphomannomutase deficiency (PMM2‐CDG) is the most common congenital disorder of glycosylation, characterized by variable early‐onset neurological (hypotonia, cerebellar syndrome, developmental delay) and multi‐organ manifestations. Alth…
View article: CapTrap-seq: Advancing zebrafish transcriptomic research through high-fidelity full-length RNA sequencing
CapTrap-seq: Advancing zebrafish transcriptomic research through high-fidelity full-length RNA sequencing Open
Zebrafish is a valuable model organism thanks to its genetic and anatomical similarities to humans, offering a more relevant system for studying human biology and disease than in vitro or non-vertebrate models. However, its use in large-sc…
View article: Long-read transcriptomics of a diverse human cohort reveals widespread ancestry bias in gene annotation
Long-read transcriptomics of a diverse human cohort reveals widespread ancestry bias in gene annotation Open
Accurate gene annotations are fundamental for interpreting genetic variation, cellular function, and disease mechanisms. However, current human gene annotations are largely derived from transcriptomic data of individuals with European ance…
View article: GENCODE 2025: reference gene annotation for human and mouse
GENCODE 2025: reference gene annotation for human and mouse Open
GENCODE produces comprehensive reference gene annotation for human and mouse. Entering its twentieth year, the project remains highly active as new technologies and methodologies allow us to catalog the genome at ever-increasing granularit…
View article: GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing
GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing Open
Accurate and complete gene annotations are indispensable for understanding how genome sequences encode biological functions. For twenty years, the GENCODE consortium has developed reference annotations for the human and mouse genomes, beco…
View article: CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing
CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing Open
View article: Systematic assessment of long-read RNA-seq methods for transcript identification and quantification
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification Open
View article: CapTrap-Seq cDNA library preparation for full-length RNA sequencing
CapTrap-Seq cDNA library preparation for full-length RNA sequencing Open
Long-read RNA sequencing is crucial for generating precise and comprehensive annotations of eukaryotic genomes. Despite advancements in throughput and accuracy, achieving reliable end-to-end identification of RNA transcripts remains a chal…
View article: 5' Capping protocol to add 5’ cap structures to exogenous synthetic RNA references (spike-ins)
5' Capping protocol to add 5’ cap structures to exogenous synthetic RNA references (spike-ins) Open
Exogenous spike-ins like SIRV and ERCC mixes lack the typical 7-Methylguanosine (m7G) cap structure found in natural eukaryotic RNA transcripts, rendering them incompatible with certain library preparation protocols. This method details th…
View article: Correction: Profiling subcellular localization of nuclear-encoded mitochondrial gene products in zebrafish
Correction: Profiling subcellular localization of nuclear-encoded mitochondrial gene products in zebrafish Open
The vast majority (99%) of mitochondrial proteins are encoded by the nuclear genome, synthesized in the cytosol and imported into the organelle. Here we study the principles of mitochondrial import in vivo from the RNA perspective using ze…
View article: The status of the human gene catalogue
The status of the human gene catalogue Open
View article: Systematic assessment of long-read RNA-seq methods for transcript identification and quantification
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification Open
The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from …
View article: CapTrap-Seq: A platform-agnostic and quantitative approach for high-fidelity full-length RNA transcript sequencing
CapTrap-Seq: A platform-agnostic and quantitative approach for high-fidelity full-length RNA transcript sequencing Open
Long-read RNA sequencing is essential to produce accurate and exhaustive annotation of eukaryotic genomes. Despite advancements in throughput and accuracy, achieving reliable end-to-end identification of RNA transcripts remains a challenge…
View article: Artificial intelligence, big data and heart transplantation: Actualities
Artificial intelligence, big data and heart transplantation: Actualities Open
View article: The status of the human gene catalogue
The status of the human gene catalogue Open
Scientists have been trying to identify all of the genes in the human genome since the initial draft of the genome was published in 2001. Over the intervening years, much progress has been made in identifying protein-coding genes, and the …
View article: GENCODE: reference annotation for the human and mouse genomes in 2023
GENCODE: reference annotation for the human and mouse genomes in 2023 Open
GENCODE produces high quality gene and transcript annotation for the human and mouse genomes. All GENCODE annotation is supported by experimental data and serves as a reference for genome biology and clinical genomics. The GENCODE consorti…
View article: Big Data in cardiac surgery: real world and perspectives
Big Data in cardiac surgery: real world and perspectives Open
Big Data, and the derived analysis techniques, such as artificial intelligence and machine learning, have been considered a revolution in the modern practice of medicine. Big Data comes from multiple sources, encompassing electronic health…
View article: Profiling subcellular localization of nuclear-encoded mitochondrial gene products in zebrafish
Profiling subcellular localization of nuclear-encoded mitochondrial gene products in zebrafish Open
Most mitochondrial proteins are encoded by nuclear genes, synthetized in the cytosol and targeted into the organelle. To characterize the spatial organization of mitochondrial gene products in zebrafish ( Danio rerio ), we sequenced RNA fr…
View article: RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing
RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing Open
View article: Additional file 2 of RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing
Additional file 2 of RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing Open
Additional file 2: Tables S1-S12. Supporting Tables.
View article: Profiling subcellular localization of nuclear-encoded mitochondrial gene products in zebrafish
Profiling subcellular localization of nuclear-encoded mitochondrial gene products in zebrafish Open
Most mitochondrial proteins are encoded by nuclear genes, synthetized in the cytosol and targeted into the organelle. The import of some, but not all, nuclear-encoded mitochondrial proteins begins with translation of messenger RNAs (mRNAs)…
View article: Eculizumab in patients with severe coronavirus disease 2019 (COVID-19) requiring continuous positive airway pressure ventilator support: Retrospective cohort study
Eculizumab in patients with severe coronavirus disease 2019 (COVID-19) requiring continuous positive airway pressure ventilator support: Retrospective cohort study Open
Background Complement activation contributes to lung dysfunction in coronavirus disease 2019 (COVID-19). We assessed whether C5 blockade with eculizumab could improve disease outcome. Methods In this single-centre, academic, unblinded stud…
View article: Cardiac Toxicity Associated with Cancer Immunotherapy and Biological Drugs
Cardiac Toxicity Associated with Cancer Immunotherapy and Biological Drugs Open
Cancer immunotherapy significantly contributed to an improvement in the prognosis of cancer patients. Immunotherapy, including human epidermal growth factor receptor 2 (HER2)-targeted therapies, immune checkpoint inhibitors (ICI), and chim…
View article: Systematic assessment of long-read RNA-seq methods for transcript identification and quantification
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification Open
View article: From research to rapid response: mass COVID-19 testing by volunteers at the Centre for Genomic Regulation
From research to rapid response: mass COVID-19 testing by volunteers at the Centre for Genomic Regulation Open
The COVID-19 pandemic has posed and is continuously posing enormous societal and health challenges worldwide. The research community has mobilized to develop novel projects to find a cure or a vaccine, as well as to contribute to mass test…
View article: GENCODE 2021
GENCODE 2021 Open
The GENCODE project annotates human and mouse genes and transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology and clinical genomics. GENCODE annotation processes make …
View article: RATTLE: Reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing
RATTLE: Reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing Open
Nanopore sequencing enables the efficient and unbiased measurement of transcriptomes from any sample. However, current methods for transcript identification and quantification rely of mapping reads to a reference genome, which precludes th…
View article: GENCODE reference annotation for the human and mouse genomes
GENCODE reference annotation for the human and mouse genomes Open
The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics. Over the last 15 years, the GENCODE…