User profiles for F. William Townes

F. William Townes

Assistant Professor of Statistics and Data Science, Carnegie Mellon University
Verified email at andrew.cmu.edu
Cited by 1076

Missing data and technical variability in single-cell RNA-sequencing experiments

SC Hicks, FW Townes, M Teng, RA Irizarry - Biostatistics, 2018 - academic.oup.com
Until recently, high-throughput gene expression technology, such as RNA-Sequencing (RNA-seq)
required hundreds of thousands of cells to produce reliable measurements. Recent …

[HTML][HTML] Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model

FW Townes, SC Hicks, MJ Aryee, RA Irizarry - Genome biology, 2019 - Springer
Single-cell RNA-Seq (scRNA-Seq) profiles gene expression of individual cells. Recent
scRNA-Seq datasets have incorporated unique molecular identifiers (UMIs). Using negative …

[HTML][HTML] Alignment of spatial genomics data using deep Gaussian processes

A Jones, FW Townes, D Li, BE Engelhardt - Nature Methods, 2023 - nature.com
Spatially resolved genomic technologies have allowed us to study the physical organization
of cells and tissues, and promise an understanding of local interactions between cells. …

[HTML][HTML] Nonnegative spatial factorization applied to spatial genomics

FW Townes, BE Engelhardt - Nature methods, 2023 - nature.com
Nonnegative matrix factorization (NMF) is widely used to analyze high-dimensional count
data because, in contrast to real-valued alternatives such as factor analysis, it produces an …

[HTML][HTML] Cerebellar contributions to a brainwide network for flexible behavior in mice

…, S Bergeler, M Kislin, F William Townes… - Communications …, 2023 - nature.com
The cerebellum regulates nonmotor behavior, but the routes of influence are not well
characterized. Here we report a necessary role for the posterior cerebellum in guiding a reversal …

[HTML][HTML] Quantile normalization of single-cell RNA-seq read counts without unique molecular identifiers

FW Townes, RA Irizarry - Genome biology, 2020 - Springer
Single-cell RNA-seq (scRNA-seq) profiles gene expression of individual cells. Unique
molecular identifiers (UMIs) remove duplicates in read counts resulting from polymerase chain …

Contrastive latent variable modeling with application to case-control sequencing experiments

A Jones, FW Townes, D Li… - The Annals of Applied …, 2022 - projecteuclid.org
… S z f j + W tj … We find that, in both the CGLVM and CPLVM, the subspaces defined by S
and W picked up on the directions of shared and foreground-specific variation, respectively (Figure …

Nonnegative spatial factorization

FW Townes, BE Engelhardt - arXiv preprint arXiv:2110.06122, 2021 - arxiv.org
Gaussian processes are widely used for the analysis of spatial data due to their
nonparametric flexibility and ability to quantify uncertainty, and recently developed scalable …

[HTML][HTML] Predicting subnational ebola virus disease epidemic dynamics from sociodemographic indicators

…, Y Gurmu, A Ablorh, J Bobb, FW Townes… - PloS one, 2016 - journals.plos.org
Background The recent Ebola virus disease (EVD) outbreak in West Africa has spread wider
than any previous human EVD epidemic. While individual-level risk factors that contribute to …

Expression QTLs in single-cell sequencing data

ADH Gewirtz, FW Townes, BE Engelhardt - bioRxiv, 2022 - biorxiv.org
Single nucleotide polymorphisms (SNPs) are important drivers of gene expression variation
and downstream phenotypes including disease risk. Single-cell RNA-sequencing (scRNA-…