Michaël Ryan
A5063865589- RNA modifications and cancer
- RNA Research and Splicing
- Cancer Genomics and Diagnostics
- Retinopathy of Prematurity Studies
- Bioinformatics and Genomic Networks
- Genomics and Rare Diseases
- Genomics and Chromatin Dynamics
- Epigenetics and DNA Methylation
- DNA Repair Mechanisms
- Neonatal and fetal brain pathology
- Gene expression and cancer classification
- Political Economy and Marxism
- Neonatal Respiratory Health Research
- Molecular Biology Techniques and Applications
- Genetics, Bioinformatics, and Biomedical Research
- Critical Theory and Philosophy
- Poetry Analysis and Criticism
- Ferroptosis and cancer prognosis
- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Retinal Diseases and Treatments
- Bladder and Urothelial Cancer Treatments
- Russia and Soviet political economy
- Philosophy, Ethics, and Existentialism
- Global Health Care Issues
University of South Carolina
2024
Cornell University
1979-2021
Weill Cornell Medicine
2021
Health and Safety Authority
2021
Trinity College Dublin
2017-2021
Health Information and Quality Authority
2021
In Silico Biosciences (United States)
2011-2020
MacEwan University
2020
The University of Texas MD Anderson Cancer Center
2010-2019
National University of Ireland, Maynooth
2010-2019
The Cancer Genome Atlas (TCGA) cancer genomics dataset includes over 10,000 tumor-normal exome pairs across 33 different types, in total >400 TB of raw data files requiring analysis. Here we describe the Multi-Center Mutation Calling Multiple Cancers project, our effort to generate a comprehensive encyclopedia somatic mutation calls for TCGA enable robust cross-tumor-type analyses. Our approach accounts variance and batch effects introduced by rapid advancement DNA extraction,...
Hotspot mutations in splicing factor genes have been recently reported at high frequency hematological malignancies, suggesting the importance of RNA cancer. We analyzed whole-exome sequencing data across 33 tumor types The Cancer Genome Atlas (TCGA), and we identified 119 with significant non-silent mutation patterns, including over-representation, recurrent loss function (tumor suppressor-like), or hotspot profile (oncogene-like). Furthermore, analysis revealed altered events associated...
Highlights•An overview of PanCancer Atlas analyses on oncogenic molecular processes•Germline genome affects somatic genomic landscape in a pathway-dependent fashion•Genome mutations impact expression, signaling, and multi-omic profiles•Mutation burdens drivers influence immune-cell composition microenvironmentSummaryThe Cancer Genome (TCGA) has catalyzed systematic characterization diverse alterations underlying human cancers. At this historic junction marking the completion over 11,000...
The role of enhancers, a key class non-coding regulatory DNA elements, in cancer development has increasingly been appreciated. Here, we present the detection and characterization large number expressed enhancers genome-wide analysis 8928 tumor samples across 33 types using TCGA RNA-seq data. Compared with matched normal tissues, global enhancer activation was observed most cancers. Across types, activity positively associated aneuploidy, but not mutation load, suggesting hypothesis centered...
Long noncoding RNAs (lncRNAs) are commonly dysregulated in tumors, but only a handful known to play pathophysiological roles cancer. We inferred lncRNAs that dysregulate cancer pathways, oncogenes, and tumor suppressors (cancer genes) by modeling their effects on the activity of transcription factors, RNA-binding proteins, microRNAs 5,185 TCGA tumors 1,019 ENCODE assays. Our predictions included hundreds candidate onco- tumor-suppressor lncRNAs) whose somatic alterations account for...
For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for large-scale discovery of splice-site-creating (SCMs) across 8,656 TCGA tumors. We report 1,964 originally mis-annotated clear evidence creating alternative splice junctions. TP53 and GATA3 26 18 SCMs, respectively, ATRX has 5 from lower-grade gliomas. Mutations in 11 genes, including...
SpliceSeq is a resource for RNA-Seq data that provides clear view of alternative splicing and identifies potential functional changes result from splice variation. It displays intuitive visualizations prioritized lists results highlight events their biological consequences. unambiguously aligns reads to gene graphs, facilitating accurate analysis large, complex transcript variants cannot be adequately represented in other formats.SpliceSeq freely available at...
Abstract Summary: Advances in sequencing technology have greatly reduced the costs incurred collecting raw data. Academic laboratories and researchers therefore now access to very large datasets of genomic alterations but limited time computational resources analyse their potential biological importance. Here, we provide a web-based application, Cancer-Related Analysis Variants Toolkit, designed with an easy-to-use interface facilitate high-throughput assessment prioritization genes missense...
Abstract Summary: Thousands of cancer exomes are currently being sequenced, yielding millions non-synonymous single nucleotide variants (SNVs) possible relevance to disease etiology. Here, we provide a software toolkit prioritize SNVs based on their predicted contribution tumorigenesis. It includes database precomputed, predictive features covering all positions in the annotated human exome and can be used either stand-alone or as part larger variant discovery pipeline. Availability...
Insertion/deletion variants (indels) alter protein sequence and length, yet are highly prevalent in healthy populations, presenting a challenge to bioinformatics classifiers. Commonly used features—DNA conservation, indel occurrence repeat regions—are useful for inference of damage. However, these features can cause false positives when predicting the impact indels on disease. Existing methods classification suffer from low specificities, severely limiting clinical utility. Here, we further...
This report investigates the mechanisms by which mammalian cells coordinate DNA replication with transcription and chromatin assembly. In yeast, initiates within nucleosome-free regions, but studies in have not revealed a similar relationship. Here, we used genome-wide massively parallel sequencing to map initiation events, thereby creating database of all sites nonrepetitive two human cell lines. Mining this that genomic regions transcribed at moderate levels were generally associated high...
PURPOSE The modern researcher is confronted with hundreds of published methods to interpret genetic variants. There are databases genes and variants, phenotype-genotype relationships, algorithms that score rank genes, in silico variant effect prediction tools. Because prioritization a multifactorial problem, welcome development the field has been emergence decision support frameworks, which make it easier integrate multiple resources an interactive environment. Current frameworks typically...
Mammalian DNA replication starts at distinct chromosomal sites in a tissue-specific pattern coordinated with transcription, but previous studies have not yet identified chromatin modification that correlates the initiation of particular genomic locations. Here we report fraction human genome are associated high frequency dimethylation histone H3 lysine K79 (H3K79Me2). H3K79Me2-containing exhibited highest genome-wide enrichment for events observed any examined thus far (23.39% H3K79Me2 peaks...
Cancer sequencing studies are increasingly comprehensive and well powered, returning long lists of somatic mutations that can be difficult to sort interpret. Diligent analysis quality control require multiple computational tools distinct utility producing disparate output, creating additional challenges for the investigator. The Cancer-Related Analysis Variants Toolkit (CRAVAT) is an evolving suite informatics mutation interpretation includes mapping control, impact prediction extensive...
<ns4:p>Clustered heat maps are the most frequently used graphics for visualization and interpretation of genome-scale molecular profiling data in biology. Construction a map generally requires assistance biostatistician or bioinformatics analyst capable working R similar programming language to transform study data, perform hierarchical clustering, generate map. Our web-based Interactive Heat Map Builder can be by investigators with no experience high-caliber, publication quality maps....
Clustered heat maps are the most frequently used graphics for visualization and interpretation of genome-scale molecular profiling data in biology. Construction a map generally requires assistance biostatistician or bioinformatics analyst capable working R similar programming language to transform study data, perform hierarchical clustering, generate map. Our web-based Interactive Heat Map Builder can be by investigators with no experience high-caliber, publication quality maps. Preparation...