Stephen M. Mount
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View article: Fair molecular feature selection unveils universally tumor lineage-informative methylation sites in colorectal cancer
Fair molecular feature selection unveils universally tumor lineage-informative methylation sites in colorectal cancer Open
Motivation In the era of precision medicine, performing comparative analysis over diverse patient populations is a fundamental step toward tailoring healthcare interventions. However, the aspect of fairly selecting molecular features acros…
View article: REAL-TIME VISUALIZATION OF SPLICEOSOME ASSEMBLY REVEALS BASIC PRINCIPLES OF SPLICE SITE SELECTION
REAL-TIME VISUALIZATION OF SPLICEOSOME ASSEMBLY REVEALS BASIC PRINCIPLES OF SPLICE SITE SELECTION Open
The spliceosome is a megadalton protein-RNA complex which removes introns from pre-mRNA, yet the dynamic early assembly steps have not been structurally resolved. Specifically, how the spliceosome selects the correct 3’ splice site (3’SS) …
View article: Latent Dirichlet allocation mixture models for nucleotide sequence analysis
Latent Dirichlet allocation mixture models for nucleotide sequence analysis Open
Strings of nucleotides carrying biological information are typically described as sequence motifs represented by weight matrices or consensus sequences. However, many signals in DNA or RNA are recognized by multiple factors in temporal seq…
View article: Progerin mRNA expression in non-HGPS patients is correlated with widespread shifts in transcript isoforms
Progerin mRNA expression in non-HGPS patients is correlated with widespread shifts in transcript isoforms Open
Hutchinson–Gilford Progeria Syndrome (HGPS) is a premature aging disease caused primarily by a C1824T mutation in LMNA. This mutation activates a cryptic splice donor site, producing a lamin variant called progerin. Interestingly, progerin…
View article: Fair molecular feature selection unveils universally tumor lineage-informative methylation sites in colorectal cancer
Fair molecular feature selection unveils universally tumor lineage-informative methylation sites in colorectal cancer Open
In the era of precision medicine, performing comparative analysis over diverse patient populations is a fundamental step towards tailoring healthcare interventions. However, the critical aspect of equitably selecting molecular features acr…
View article: scCensus: Off-target scRNA-seq reads reveal meaningful biology
scCensus: Off-target scRNA-seq reads reveal meaningful biology Open
Single-cell RNA-sequencing (scRNA-seq) provides unprecedented insights into cellular heterogeneity. Although scRNA-seq reads from most prevalent and popular tagged-end protocols are expected to arise from the 3′ end of polyadenylated RNAs,…
View article: Supplementary files for "scCensus: Off-target scRNA-seq reads reveal meaningful biology"
Supplementary files for "scCensus: Off-target scRNA-seq reads reveal meaningful biology" Open
The Supplementary files for the manuscript "scCensus: Off-target scRNA-seq reads reveal meaningful biology"
View article: Supplementary files for "scCensus: Off-target scRNA-seq reads reveal meaningful biology"
Supplementary files for "scCensus: Off-target scRNA-seq reads reveal meaningful biology" Open
The Supplementary files for the manuscript "scCensus: Off-target scRNA-seq reads reveal meaningful biology"
View article: Latent Dirichlet Allocation Mixture Models for Nucleotide Sequence Analysis
Latent Dirichlet Allocation Mixture Models for Nucleotide Sequence Analysis Open
Strings of nucleotides that carry biological information are typically described using sequence motifs that can be represented by weight matrices or consensus sequences. However, many biological signals in DNA or RNA are recognized by mult…
View article: Rosaceae fruit transcriptome database (ROFT)—a useful genomic resource for comparing fruits of apple, peach, strawberry, and raspberry
Rosaceae fruit transcriptome database (ROFT)—a useful genomic resource for comparing fruits of apple, peach, strawberry, and raspberry Open
Rosaceae is a large plant family consisting of many economically important fruit crops including peach, apple, pear, strawberry, raspberry, plum, and others. Investigations into their growth and development will promote both basic understa…
View article: Comparison of red raspberry and wild strawberry fruits reveals mechanisms of fruit type specification
Comparison of red raspberry and wild strawberry fruits reveals mechanisms of fruit type specification Open
Belonging to Rosaceae, red raspberry (Rubus idaeus) and wild strawberry (Fragaria vesca) are closely related species with distinct fruit types. While the numerous ovaries become the juicy drupelet fruits in raspberry, their strawberry coun…
View article: Predicting the impact of rare variants on RNA splicing in CAGI6
Predicting the impact of rare variants on RNA splicing in CAGI6 Open
Background Variants which disrupt splicing are a frequent cause of rare disease that have been under-ascertained clinically. Accurate and efficient methods to predict a variant’s impact on splicing are needed to interpret the growing numbe…
View article: Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models
Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models Open
Recent studies exploring the impact of methylation in tumor evolution suggest that while the methylation status of many of the CpG sites are preserved across distinct lineages, others are altered as the cancer progresses. Since changes in …
View article: Analyses of <i>Marsilea vestita</i> genome and transcriptomes do not support widespread intron retention during spermatogenesis
Analyses of <i>Marsilea vestita</i> genome and transcriptomes do not support widespread intron retention during spermatogenesis Open
Intron retention (IR), a form of alternative splicing, plays a key role in post-transcriptional gene regulation. The fate of intron-retaining transcripts varies; for example, they could trigger nonsense-mediated decay or lead to alternativ…
View article: Sex Biases in Cancer and Autoimmune Disease Incidence Are Strongly Positively Correlated with Mitochondrial Gene Expression across Human Tissues
Sex Biases in Cancer and Autoimmune Disease Incidence Are Strongly Positively Correlated with Mitochondrial Gene Expression across Human Tissues Open
Cancer occurs more frequently in men while autoimmune diseases (AIDs) occur more frequently in women. To explore whether these sex biases have a common basis, we collected 167 AID incidence studies from many countries for tissues that have…
View article: Dysregulated Spliceosome Activity Involves Increased Intron Retention Plus Upregulation and Phosphorylation of SF3B1 in Chronic Lymphocytic Leukemia
Dysregulated Spliceosome Activity Involves Increased Intron Retention Plus Upregulation and Phosphorylation of SF3B1 in Chronic Lymphocytic Leukemia Open
Background Alternative splicing (AS) is a fundamental process in eukaryotes contributing to the diversity of mRNA isoforms with variable ratios of intron/exon. SF3B1 is a pivotal protein of the spliceosome machinery. Mutations in the SF3B1…
View article: Comparative transcriptomic analysis of apple and peach fruits: insights into fruit type specification
Comparative transcriptomic analysis of apple and peach fruits: insights into fruit type specification Open
SUMMARY Fruits represent key evolutionary innovations in angiosperms and exhibit diverse types adapted for seed dissemination. However, the mechanisms that underlie fruit type diversity are not understood. The Rosaceae family comprises man…
View article: Sex biases in cancer and autoimmune disease incidence are strongly positively correlated with mitochondrial gene expression across human tissues
Sex biases in cancer and autoimmune disease incidence are strongly positively correlated with mitochondrial gene expression across human tissues Open
Cancer occurs more frequently in men while autoimmune diseases (AIDs) occur more frequently in women. To explore whether these sex biases have a common basis, we collected 167 AID incidence studies from many countries for tissues that have…
View article: An Atlas of Genomic Resources for Studying Rosaceae Fruits and Ornamentals
An Atlas of Genomic Resources for Studying Rosaceae Fruits and Ornamentals Open
Rosaceae, a large plant family of more than 3,000 species, consists of many economically important fruit and ornamental crops, including peach, apple, strawberry, raspberry, cherry, and rose. These horticultural crops are not only importan…
View article: Expanding the scope of plant genome engineering with Cas12a orthologs and highly multiplexable editing systems
Expanding the scope of plant genome engineering with Cas12a orthologs and highly multiplexable editing systems Open
CRISPR-Cas12a is a promising genome editing system for targeting AT-rich genomic regions. Comprehensive genome engineering requires simultaneous targeting of multiple genes at defined locations. Here, to expand the targeting scope of Cas12…
View article: Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models
Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models Open
Recent studies exploring the impact of methylation in tumor evolution suggest that while the methylation status of many of the CpG sites are preserved across distinct lineages, others are altered as the cancer progresses. Since changes in …
View article: Assessing predictions of the impact of variants on splicing in CAGI5
Assessing predictions of the impact of variants on splicing in CAGI5 Open
Precision medicine and sequence-based clinical diagnostics seek to predict disease risk or to identify causative variants from sequencing data. The Critical Assessment of Genome Interpretation (CAGI) is a community experiment consisting of…
View article: Draft Genome Assembly and Annotation of Red Raspberry <i>Rubus Idaeus</i>
Draft Genome Assembly and Annotation of Red Raspberry <i>Rubus Idaeus</i> Open
The red raspberry, Rubus idaeus , is widely distributed in all temperate regions of Europe, Asia, and North America and is a major commercial fruit valued for its taste, high antioxidant and vitamin content. However, Rubus breeding is a lo…
View article: The Splicing Factor <i>RNA-Binding Fox Protein 1</i> Mediates the Cellular Immune Response in <i>Drosophila melanogaster</i>
The Splicing Factor <i>RNA-Binding Fox Protein 1</i> Mediates the Cellular Immune Response in <i>Drosophila melanogaster</i> Open
The uptake and destruction of bacteria by phagocytic cells is an essential defense mechanism in metazoans. To identify novel genes involved in the phagocytosis of Staphylococcus aureus, a major human pathogen, we assessed the phagocytic ca…
View article: Consensus Coexpression Network Analysis Identifies Key Regulators of Flower and Fruit Development in Wild Strawberry
Consensus Coexpression Network Analysis Identifies Key Regulators of Flower and Fruit Development in Wild Strawberry Open
The diploid strawberry, Fragaria vesca, is a developing model system for the economically important Rosaceae family. Strawberry fleshy fruit develops from the floral receptacle and its ripening is nonclimacteric. The external seed configur…
View article: Fast and interpretable alternative splicing and differential gene-level expression analysis using transcriptome segmentation with Yanagi
Fast and interpretable alternative splicing and differential gene-level expression analysis using transcriptome segmentation with Yanagi Open
Introduction: Analysis of differential alternative splicing from RNA-seq data is complicated by the fact that many RNA-seq reads map to multiple transcripts, besides, the annotated transcripts are often a small subset of the possible trans…