Paul Hoffman
A5078971011- IPv6, Mobility, Handover, Networks, Security
- Mobile Agent-Based Network Management
- Network Packet Processing and Optimization
- Single-cell and spatial transcriptomics
- Genomics and Phylogenetic Studies
- Network Security and Intrusion Detection
- RNA Research and Splicing
- Genetic Associations and Epidemiology
- Digital Rights Management and Security
- Distributed and Parallel Computing Systems
- Wheat and Barley Genetics and Pathology
- Service-Oriented Architecture and Web Services
- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Chromatin Dynamics
- Genetic diversity and population structure
- Clinical Reasoning and Diagnostic Skills
- Genomics and Rare Diseases
- RNA modifications and cancer
- Internet Traffic Analysis and Secure E-voting
- Natural Language Processing Techniques
- Cancer Genomics and Diagnostics
- Simulation Techniques and Applications
- Chromosomal and Genetic Variations
- Library Science and Information Systems
- Immune cells in cancer
University of Pittsburgh
1991-2023
New York University
2020-2023
New York Genome Center
2018-2022
Thermo Fisher Scientific (Sweden)
2020
Columbia University
1964-2019
University of Minnesota
2015-2019
Harvard University
2019
Regional Medical Center
2019
Massachusetts Eye and Ear Infirmary
2019
University of Minnesota System
2018
The simultaneous measurement of multiple modalities represents an exciting frontier for single-cell genomics and necessitates computational methods that can define cellular states based on multimodal data. Here, we introduce "weighted-nearest neighbor" analysis, unsupervised framework to learn the relative utility each data type in cell, enabling integrative analysis modalities. We apply our procedure a CITE-seq dataset 211,000 human peripheral blood mononuclear cells (PBMCs) with panels...
The Genotype-Tissue Expression (GTEx) project dissects how genetic variation affects gene expression and splicing.
Many complex human phenotypes exhibit sex-differentiated characteristics. However, the molecular mechanisms underlying these differences remain largely unknown. We generated a catalog of sex in gene expression and genetic regulation across 44 tissue sources surveyed by Genotype-Tissue Expression project (GTEx, v8 release). demonstrate that influences levels cellular composition samples body. A total 37% all genes sex-biased at least one tissue. identify cis quantitative trait loci (eQTLs)...
Cell type composition, estimated from bulk tissue, maps the cellular specificity of genetic variants.
Telomere length within an individual varies in a correlated manner across most tissues.
Abstract The simultaneous measurement of multiple modalities, known as multimodal analysis, represents an exciting frontier for single-cell genomics and necessitates new computational methods that can define cellular states based on data types. Here, we introduce ‘weighted-nearest neighbor’ unsupervised framework to learn the relative utility each type in cell, enabling integrative analysis modalities. We apply our procedure a CITE-seq dataset hundreds thousands human white blood cells...
Single cell transcriptomics (scRNA-seq) has transformed our ability to discover and annotate types states, but deep biological understanding requires more than a taxonomic listing of clusters. As new methods arise measure distinct cellular modalities, including high-dimensional immunophenotypes, chromatin accessibility, spatial positioning, key analytical challenge is integrate these datasets into harmonized atlas that can be used better understand identity function. Here, we develop...
Abstract The Genotype-Tissue Expression (GTEx) project was established to characterize genetic effects on the transcriptome across human tissues, and link these regulatory mechanisms trait disease associations. Here, we present analyses of v8 data, based 17,382 RNA-sequencing samples from 54 tissues 948 post-mortem donors. We comprehensively associations for gene expression splicing in cis trans , showing that are found almost all genes, describe underlying molecular their contribution...
Abstract Mapping single-cell sequencing profiles to comprehensive reference datasets represents a powerful alternative unsupervised analysis. Reference datasets, however, are predominantly constructed from RNA-seq data, and cannot be used annotate that do not measure gene expression. Here we introduce ‘bridge integration’, method harmonize singlecell across modalities by leveraging multi-omic dataset as molecular bridge. Each cell in the comprises an element ‘dictionary’, which can...
Outliers in the human transcriptome reveal functional effects of rare genetic variants.
Abstract Allele expression (AE) analysis robustly measures cis -regulatory effects. Here, we present and demonstrate the utility of a vast AE resource generated from GTEx v8 release, containing 15,253 samples spanning 54 human tissues for total 431 million measurements at SNP level 153 haplotype level. In addition, develop an extension our tool phASER that allows effect sizes variants to be estimated using haplotype-level data. This is largest date, are able make data publicly available. We...