A5029455059- Single-cell and spatial transcriptomics
- Gene expression and cancer classification
- Epigenetics and DNA Methylation
- RNA modifications and cancer
- Molecular Biology Techniques and Applications
- RNA Research and Splicing
- Cell Image Analysis Techniques
- Cancer-related molecular mechanisms research
- Genomics and Phylogenetic Studies
- Genomics and Chromatin Dynamics
- Bioinformatics and Genomic Networks
- Cancer Genomics and Diagnostics
- Gene Regulatory Network Analysis
- RNA and protein synthesis mechanisms
- MicroRNA in disease regulation
- Genetics, Aging, and Longevity in Model Organisms
- Extracellular vesicles in disease
- Immune cells in cancer
- CRISPR and Genetic Engineering
- Invertebrate Immune Response Mechanisms
- Research on Leishmaniasis Studies
- Cancer Immunotherapy and Biomarkers
- Genetic Syndromes and Imprinting
- Scientific Computing and Data Management
- Cancer-related gene regulation
University of Zurich
2016-2025
SIB Swiss Institute of Bioinformatics
2016-2025
University Hospital of Zurich
2022
ETH Zurich
2022
University of California, San Francisco
2022
Swiss Insurance Association
2021
University of Port Harcourt
2021
Life Science Zurich
2013-2020
Rutgers, The State University of New Jersey
2008-2018
Carolinas Healthcare System
2017-2018
Summary: It is expected that emerging digital gene expression (DGE) technologies will overtake microarray in the near future for many functional genomics applications. One of fundamental data analysis tasks, especially studies, involves determining whether there evidence counts a transcript or exon are significantly different across experimental conditions. edgeR Bioconductor software package examining differential replicated count data. An overdispersed Poisson model used to account both...
Abstract The fine detail provided by sequencing-based transcriptome surveys suggests that RNA-seq is likely to become the platform of choice for interrogating steady state RNA. In order discover biologically important changes in expression, we show normalization continues be an essential step analysis. We outline a simple and effective method performing dramatically improved results inferring differential expression simulated publicly available data sets.
<ns4:p>High-throughput sequencing of cDNA (RNA-seq) is used extensively to characterize the transcriptome cells. Many transcriptomic studies aim at comparing either abundance levels or composition between given conditions, and as a first step, reads must be basis for quantification features interest, such genes transcripts. Several different approaches have been proposed, ranging from simple counting that overlap genomic regions more complex estimation underlying transcript abundances. In...
In Saccharomyces cerevisiae , more than 80% of the ∼6200 predicted genes are nonessential, implying that genome is buffered from phenotypic consequences genetic perturbation. To evaluate function, we developed a method for systematic construction double mutants, termed synthetic array (SGA) analysis, in which query mutation crossed to an ∼4700 deletion mutants. Inviable double-mutant meiotic progeny identify functional relationships between genes. SGA analysis with roles cytoskeletal...
<ns4:p>High-throughput sequencing of cDNA (RNA-seq) is used extensively to characterize the transcriptome cells. Many transcriptomic studies aim at comparing either abundance levels or composition between given conditions, and as a first step, reads must be basis for quantification features interest, such genes transcripts. Various approaches have been proposed, ranging from simple counting that overlap genomic regions more complex estimation underlying transcript abundances. In this paper,...
We derive a quantile-adjusted conditional maximum likelihood estimator for the dispersion parameter of negative binomial distribution and compare its performance, in terms bias, to various other methods. Our estimation scheme outperforms all methods very small samples, typical those from serial analysis gene expression studies, motivating data this study. The impact on hypothesis testing is studied. an "exact" test that standard approximate asymptotic tests.
Article13 March 2007Open Access Large-scale mapping of human protein–protein interactions by mass spectrometry Rob M Ewing Protana (now Transition Therapeutics), Toronto, Ontario, Canada Infochromics, MaRS Discovery District, Search for more papers this author Peter Chu CanadaPresent address: Faculty Health Sciences, McMaster University, Hamilton, Fred Elisma Medicine, The Ottawa Institute Systems Biology, University Ottawa, BMI, Hongyan Li Department York Paul Taylor Hospital Sick Children...
Abstract Motivation: Digital gene expression (DGE) technologies measure by counting sequence tags. They are sensitive for measuring on a genomic scale, without the need prior knowledge of genome sequence. As cost sequencing DNA decreases, number DGE datasets is expected to grow dramatically. Various tests differential have been proposed replicated data using binomial, Poisson, negative binomial or pseudo-likelihood (PL) models counts, but none these usable when replicates very small....
Signaling pathways transmit information through protein interaction networks that are dynamically regulated by complex extracellular cues. We developed LUMIER (for luminescence-based mammalian interactome mapping), an automated high-throughput technology, to map protein-protein systematically in cells and applied it the transforming growth factorâβ (TGFβ) pathway. Analysis using self-organizing maps k -means clustering identified links of TGFβ pathway p21-activated kinase (PAK) network,...
Doublets are prevalent in single-cell sequencing data and can lead to artifactual findings. A number of strategies have therefore been proposed detect them. Building on the strengths existing approaches, we developed
Among the many educational materials produced by European Society of Human Reproduction and Embryology (ESHRE) are guidelines. ESHRE guidelines may be developed for reasons but their intent is always to promote best quality practices in reproductive medicine. In an era which preimplantation genetic diagnosis (PGD) has become a reality, we must strive maintain its efficacy credibility offering safest most effective treatment available. The dominant motivators development current comprehensive...
For effective exposition of biological information, especially with regard to analysis large-scale data types, researchers need immediate access multiple categorical knowledge bases and summary information presented them on collections genes, as opposed the typical one gene at a time. We present here web-based tool (FunSpec) for statistical evaluation groups genes proteins (e.g. co-regulated protein complexes, genetic interactors) respect existing annotations functional roles, biochemical...
A popular approach for comparing gene expression levels between (replicated) conditions of RNA sequencing data relies on counting reads that map to features interest. Within such count-based methods, many flexible and advanced statistical approaches now exist offer the ability adjust covariates (e.g. batch effects). Often, these methods include some sort ‘sharing information’ across improve inferences in small samples. It is important achieve an appropriate tradeoff power protection against...
<ns4:p>High-dimensional mass and flow cytometry (HDCyto) experiments have become a method of choice for high-throughput interrogation characterization cell populations. Here, we present an updated R-based pipeline differential analyses HDCyto data, largely based on Bioconductor packages. We computationally define populations using FlowSOM clustering, facilitate optional but reproducible strategy manual merging algorithm-generated clusters. Our workflow offers different analysis paths,...
High dimensional mass and flow cytometry (HDCyto) experiments have become a method of choice for high throughput interrogation characterization cell populations.Here, we present an R-based pipeline differential analyses HDCyto data, largely based on Bioconductor packages. We computationally define populations using FlowSOM clustering, facilitate optional but reproducible strategy manual merging algorithm-generated clusters. Our workflow offers different analysis paths, including association...
Abstract Recent technological developments in high‐dimensional flow cytometry and mass (CyTOF) have made it possible to detect expression levels of dozens protein markers thousands cells per second, allowing cell populations be characterized unprecedented detail. Traditional data analysis by “manual gating” can inefficient unreliable these settings, which has led the development a large number automated methods. Methods designed for unsupervised use specialized clustering algorithms define...