Exon
View article: Supplementary Data for: Scalp Tape-Strip RNA Sequencing Captures Disease and Treatment-Responsive Signatures in Alopecia Areata
Supplementary Data for: Scalp Tape-Strip RNA Sequencing Captures Disease and Treatment-Responsive Signatures in Alopecia Areata Open
This dataset accompanies the manuscript “Scalp Tape-Strip RNA Sequencing Captures Disease and Treatment-Responsive Signatures in Alopecia Areata”. It provides the processed transcriptomic data and analysis scripts used to characterize the …
View article: Investigating HLA haplotypes as a potential risk factor for nodding syndrome: A case-control study in the Mahenge area, Tanzania
Investigating HLA haplotypes as a potential risk factor for nodding syndrome: A case-control study in the Mahenge area, Tanzania Open
Background Nodding syndrome (NS) is a disabling childhood-onset epilepsy occurring in onchocerciasis-endemic regions. High Onchocerca volvulus microfilarial loads in childhood are a key risk factor, but not all heavily infected individuals…
View article: Cardioprotective role of RBFox1 in myocardial infarction-induced heart failure
Cardioprotective role of RBFox1 in myocardial infarction-induced heart failure Open
Aims Alternative mRNA splicing is a significant part of transcriptome reprogramming during the pathological manifestation of heart diseases. Earlier studies have identified a muscle-specific isoform of RBFox1 (RNA binding fox-1 homolog 1) …
View article: A Novel Case of IRF2BP2 Deficiency Presenting as a CVID-Like Disorder With Prominent Autoinflammatory Features and Dyslipidaemia
A Novel Case of IRF2BP2 Deficiency Presenting as a CVID-Like Disorder With Prominent Autoinflammatory Features and Dyslipidaemia Open
Background Interferon regulatory factor-2–binding protein-2 (IRF2BP2) is a nuclear transcriptional co-regulator originally characterised as a co-repressor of IRF2 but now recognised to exert broader functions as both a co-repressor and co-…
View article: Supplementary Table 2 from Relationship between <i>ABO</i> Blood Group Alleles and Pancreatic Cancer Is Modulated by Secretor (<i>FUT2</i>) Genotype, but Not Lewis Antigen (<i>FUT3</i>) Genotype
Supplementary Table 2 from Relationship between <i>ABO</i> Blood Group Alleles and Pancreatic Cancer Is Modulated by Secretor (<i>FUT2</i>) Genotype, but Not Lewis Antigen (<i>FUT3</i>) Genotype Open
Table S2 lists eight SNPs that characterize ABO blood groups, secretor status, and Lewis antigen.
View article: Genome-wide identification and expression profiling of bHLH transcription factors associated with ferulic acid biosynthesis in Angelica sinensis
Genome-wide identification and expression profiling of bHLH transcription factors associated with ferulic acid biosynthesis in Angelica sinensis Open
This study identifies 148 bHLH transcription factors in Angelica sinensis and reveals four putative candidates associated with ferulic acid biosynthesis, providing a genetic foundation for metabolic engineering to enhance the plant’s medic…
View article: Absence of the LRRK2 mutation in Emirati Parkinson’s disease patients in contrast to other Arab populations
Absence of the LRRK2 mutation in Emirati Parkinson’s disease patients in contrast to other Arab populations Open
Background The role of genetic factors in the pathogenesis of Parkinson’s disease (PD) is characterized by heterogeneity in specific genetic variations and their prevalence across different populations and geographic locations. Objective T…
View article: Infantile‐Onset Ascending Hereditary Spastic Paraplegia due to a Homozygous <scp> <i>ALS2</i> </scp> Exons 24–25 Deletion: Expanding the Genotypic <scp> <i>Spectrum</i> </scp>
Infantile‐Onset Ascending Hereditary Spastic Paraplegia due to a Homozygous <span> <i>ALS2</i> </span> Exons 24–25 Deletion: Expanding the Genotypic <span> <i>Spectrum</i> </span> Open
We describe a novel homozygous intragenic deletion in the ALS2 gene in an 8‐year‐old boy with Infantile‐onset Ascending Hereditary Spastic Paraplegia (IAHSP) and oculomotor apraxia, thereby contributing to the expanding genetic landscape o…
View article: Clinical and molecular genetic analysis of a Chinese patient with Cockayne syndrome caused by ERCC8 gene synonymous variant at splicing site and exon 1 deletion
Clinical and molecular genetic analysis of a Chinese patient with Cockayne syndrome caused by ERCC8 gene synonymous variant at splicing site and exon 1 deletion Open
Background Cockayne Syndrome (CS) is a rare autosomal recessive genetic disease, mainly caused by ERCC8 and ERCC6 gene defect. However, many of its molecular characteristics remain unclear. In this study, molecular genetic analysis was per…
View article: Transcription start sites experience a high influx of heritable variants fueled by early development
Transcription start sites experience a high influx of heritable variants fueled by early development Open
Mutations drive evolution and genetic diversity, with the most consequential mutations occurring in coding exons and regulatory regions. However, the impact of transcription on germline mutagenesis remains poorly understood. Here, we ident…
View article: Cell type-resolved long-read transcriptomics of the human cortex reveals pervasive alternative splicing and disease-relevant isoforms
Cell type-resolved long-read transcriptomics of the human cortex reveals pervasive alternative splicing and disease-relevant isoforms Open
Alternative splicing generates extensive transcriptomic diversity in the human brain, but the full cell type-resolved landscape of isoform variation remains unresolved due to the constraints of short-read sequencing. Here, we integrated fl…
View article: Reviewer #3 (Public review): TSvelo: Comprehensive RNA velocity by modeling the cascade of gene regulation, transcription and splicing
Reviewer #3 (Public review): TSvelo: Comprehensive RNA velocity by modeling the cascade of gene regulation, transcription and splicing Open
View article: TSvelo: Comprehensive RNA velocity by modeling the cascade of gene regulation, transcription and splicing
TSvelo: Comprehensive RNA velocity by modeling the cascade of gene regulation, transcription and splicing Open
RNA velocity approaches fit gene dynamics and infer cell fate by modeling the splicing process using single-cell RNA sequencing (scRNA-seq) data. However, due to short time scale of splicing, high noise and large complexity of data, existi…
View article: Supplementary Figure 4 from <i>ALK</i> Amplification and Rearrangements Are Recurrent Targetable Events in Congenital and Adult Glioblastoma
Supplementary Figure 4 from <i>ALK</i> Amplification and Rearrangements Are Recurrent Targetable Events in Congenital and Adult Glioblastoma Open
Supplementary Figure 4: Characterization of the lung cancer recurrent DCTN1-ALK fusion identified in cGBM (case ALK.232). A. Integrative Genomic Viewer (IGV) screenshot of the DCTN1-ALK variant.B. Predicted sequence of DCTN1-ALK fusion (DC…
View article: Clinical cases of biventricular arrhythmogenic cardiomyopathy with a variant in the DES gene
Clinical cases of biventricular arrhythmogenic cardiomyopathy with a variant in the DES gene Open
Mutations in the DES gene, which encodes the desmin protein, are associated with various forms of skeletal and/or cardiac myopathies. Arrhythmogenic cardiomyopathy (ACM) due to a DES gene mutation is a rare form of desminopathy. In this ar…
View article: Molecular mechanisms of TTC21B gene mutations in nephronophthisis type 12 and genetic prevention through PGT
Molecular mechanisms of TTC21B gene mutations in nephronophthisis type 12 and genetic prevention through PGT Open
Objective To elucidate the pathogenic mechanism of nephronophthisis type 12 (NPHP12) caused by compound heterozygous mutations in the TTC21B gene and to implement preimplantation genetic testing (PGT) for clinical prevention. Methods We re…
View article: Author response: TSvelo: Comprehensive RNA velocity by modeling the cascade of gene regulation, transcription and splicing
Author response: TSvelo: Comprehensive RNA velocity by modeling the cascade of gene regulation, transcription and splicing Open
View article: Supplementary Figure S3 from <i>KIT</i> and <i>PDGFRA</i> Mutations and Survival of Gastrointestinal Stromal Tumor Patients Treated with Adjuvant Imatinib in a Randomized Trial
Supplementary Figure S3 from <i>KIT</i> and <i>PDGFRA</i> Mutations and Survival of Gastrointestinal Stromal Tumor Patients Treated with Adjuvant Imatinib in a Randomized Trial Open
Kaplan-Meier estimates of recurrence-free survival (A, C, E) and overall survival (B, D, F) of patients with KIT exon 11 insertion or duplication mutation (A, B), patients with PDGFRA exon 18 D842V mutation (C, D), and patients with no det…
View article: Supplementary Figure S13 from Multiomic Mapping of Acquired Chromosome 1 Copy-Number and Structural Variants to Identify Therapeutic Vulnerabilities in Multiple Myeloma
Supplementary Figure S13 from Multiomic Mapping of Acquired Chromosome 1 Copy-Number and Structural Variants to Identify Therapeutic Vulnerabilities in Multiple Myeloma Open
CRISPR dependencies on chromosome 1. Nineteen myeloma cell lines and 15 random non-myeloma cell lines were identified and CERES dependencies for genes located on chr1 recorded. A total of 1701 genes were analyzed. Cell lines did not cluste…
View article: eLife Assessment: TSvelo: Comprehensive RNA velocity by modeling the cascade of gene regulation, transcription and splicing
eLife Assessment: TSvelo: Comprehensive RNA velocity by modeling the cascade of gene regulation, transcription and splicing Open
View article: Cancer-associated snaR-A noncoding RNA interacts with core splicing machinery and disrupts processing of mRNA subpopulations
Cancer-associated snaR-A noncoding RNA interacts with core splicing machinery and disrupts processing of mRNA subpopulations Open
Expansion of RNA polymerase III (Pol III) activity in cancer can activate the transcription of typically silent small RNA genes, including snaR-A (small NF90-associated RNA isoform A), a hominid-specific noncoding RNA that promotes cell pr…
View article: Figure S2 from BBT-176, a Novel Fourth-Generation Tyrosine Kinase Inhibitor for Osimertinib-Resistant EGFR Mutations in Non–Small Cell Lung Cancer
Figure S2 from BBT-176, a Novel Fourth-Generation Tyrosine Kinase Inhibitor for Osimertinib-Resistant EGFR Mutations in Non–Small Cell Lung Cancer Open
Supplementary Figure 2. Activity of BBT-176 in EGFR WT and EGFR exon 20 insertion models.
View article: Supplementary Figure S2 from <i>KIT</i> and <i>PDGFRA</i> Mutations and Survival of Gastrointestinal Stromal Tumor Patients Treated with Adjuvant Imatinib in a Randomized Trial
Supplementary Figure S2 from <i>KIT</i> and <i>PDGFRA</i> Mutations and Survival of Gastrointestinal Stromal Tumor Patients Treated with Adjuvant Imatinib in a Randomized Trial Open
Kaplan-Meier estimates of recurrence-free survival of patients with KIT exon 11 substitution mutation (A) and patients with KIT exon 9 mutation (B). The 5-year and 10-year survival rates are shown. Censored patients are indicated with a bar
View article: Supplementary Figure 5 from Clinicopathologic, Genomic, and Immunophenotypic Landscape of <i>ATM</i> Mutations in Non–Small Cell Lung Cancer
Supplementary Figure 5 from Clinicopathologic, Genomic, and Immunophenotypic Landscape of <i>ATM</i> Mutations in Non–Small Cell Lung Cancer Open
Supplementary Figure 5. (A) Median distance of each missense mutation from the closest intron start. (B) Median distance of each missense mutation from the closest intron end. (C) Proportion of cases with ATM loss and ATM intact expression…
View article: Supplementary Figure S1 from <i>KIT</i> and <i>PDGFRA</i> Mutations and Survival of Gastrointestinal Stromal Tumor Patients Treated with Adjuvant Imatinib in a Randomized Trial
Supplementary Figure S1 from <i>KIT</i> and <i>PDGFRA</i> Mutations and Survival of Gastrointestinal Stromal Tumor Patients Treated with Adjuvant Imatinib in a Randomized Trial Open
Kaplan-Meier estimates of recurrence-free survival (A, C) and overall survival (B, D) of patients with KIT exon 11 deletion mutation (A, B) and patients with KIT exon 11 indel mutation (C, D)
View article: Correlation analysis between EGFR gene mutation status, ALK positivity and demographic data, tumor biomarkers, radiological and pathological features in patients with lung adenocarcinoma
Correlation analysis between EGFR gene mutation status, ALK positivity and demographic data, tumor biomarkers, radiological and pathological features in patients with lung adenocarcinoma Open
Objective This study aimed to explore the relationship between EGFR mutations, ALK positivity, and demographic, tumor, radiological, and pathological characteristics in lung adenocarcinoma patients. Methods This study included 626 patients…
View article: Reviewer #2 (Public review): TSvelo: Comprehensive RNA velocity by modeling the cascade of gene regulation, transcription and splicing
Reviewer #2 (Public review): TSvelo: Comprehensive RNA velocity by modeling the cascade of gene regulation, transcription and splicing Open
View article: DIS3 licenses B cells for plasma cell differentiation in humans
DIS3 licenses B cells for plasma cell differentiation in humans Open
DIS3 is the main catalytic subunit of the nuclear RNA exosome, a complex playing a crucial role in RNA processing and the degradation of various noncoding RNA substrates. In mice, DIS3 is essential for genomic rearrangements during B cell …
View article: Reviewer #1 (Public review): TSvelo: Comprehensive RNA velocity by modeling the cascade of gene regulation, transcription and splicing
Reviewer #1 (Public review): TSvelo: Comprehensive RNA velocity by modeling the cascade of gene regulation, transcription and splicing Open
View article: TSvelo: Comprehensive RNA velocity by modeling the cascade of gene regulation, transcription and splicing
TSvelo: Comprehensive RNA velocity by modeling the cascade of gene regulation, transcription and splicing Open
RNA velocity approaches fit gene dynamics and infer cell fate by modeling the splicing process using single-cell RNA sequencing (scRNA-seq) data. However, due to short time scale of splicing, high noise and large complexity of data, existi…