28 citations
Counting papers with at most 25 authors, so collaboration author lists do not stand in for the people here.
- Fred Hutch Cancer CenterUS22 papers
- University of WashingtonUS10 papers
- Cancer Research CenterUS5 papers
- University of Wisconsin–MadisonUS3 papers
- Cancer Research And BiostatisticsUS2 papers
- University of AlbertaCA2 papers
- University of California, IrvineUS2 papers
- Beijing Institute of TechnologyCN1 paper
- Case Western Reserve UniversityUS1 paper
- Dartmouth CollegeUS1 paper
- Datang Telecom Group (China)CN1 paper
- Department of Mathematical SciencesRU1 paper
25 papers
Mean first passage time of active Brownian particles in two dimensions
Sarafa A. Iyaniwura, Zhiwei Peng
The mean first passage time (MFPT) is a key metric for understanding transport, search, and escape processes in stochastic systems. While well characterized for passive Brownian pa…
ipd: An R Package for Conducting Inference on Predicted Data
Stephen Salerno, Jiacheng Miao, Awan Afiaz +5
Summary: ipd is an open-source R software package for the downstream modeling of an outcome and its associated features where a potentially sizable portion of the outcome data has…
Generalized Data Thinning Using Sufficient Statistics
Ameer Dharamshi, Anna Neufeld, Keshav Motwani +3
Our goal is to develop a general strategy to decompose a random variable into multiple independent random variables, without sacrificing any information about unknown parameter…
Quantitatively visualizing bipartite datasets
Tal Einav, Yuehaw Khoo, Amit Singer
As experiments continue to increase in size and scope, a fundamental challenge of subsequent analyses is to recast the wealth of information into an intuitive and readily-interpret…
A nonconforming primal hybrid finite element method for the two-dimensional vector Laplacian
Mary Barker, Shuhao Cao, Ari Stern
We introduce a nonconforming hybrid finite element method for the two-dimensional vector Laplacian, based on a primal variational principle for which conforming methods are known t…
MINIMALIST: Mutual INformatIon Maximization for Amortized Likelihood Inference from Sampled Trajectories
Giulio Isacchini, Natanael Spisak, Armita Nourmohammad +2
Simulation-based inference enables learning the parameters of a model even when its likelihood cannot be computed in practice. One class of methods uses data simulated with differe…
Lack of evidence for a substantial rate of templated mutagenesis in B cell diversification
Julia Fukuyama, Branden J Olson, Frederick A Matsen
B cell receptor sequences diversify through mutations introduced by purpose-built cellular machinery. A recent paper has concluded that a "templated mutagenesis" process is a major…
An Approximate Quasi-Likelihood Approach for Error-Prone Failure Time Outcomes and Exposures
Lillian A. Boe, Lesley F. Tinker, Pamela A. Shaw
Measurement error arises commonly in clinical research settings that rely on data from electronic health records or large observational cohorts. In particular, self-reported outcom…
Estimation of cell lineage trees by maximum-likelihood phylogenetics
Jean Feng, William S DeWitt, Aaron McKenna +3
CRISPR technology has enabled large-scale cell lineage tracing for complex multicellular organisms by mutating synthetic genomic barcodes during organismal development. However, th…
Gaussian process regression for survival time prediction with genome-wide gene expression
Aaron J. Molstad, Li Hsu, Wei Sun
Predicting the survival time of a cancer patient based on his/her genome-wide gene expression remains a challenging problem. For certain types of cancer, the effects of gene expres…
Non-bifurcating phylogenetic tree inference via the adaptive LASSO
Cheng Zhang, Vu Dinh, Frederick A. Matsen
Phylogenetic tree inference using deep DNA sequencing is reshaping our understanding of rapidly evolving systems, such as the within-host battle between viruses and the immune syst…
Generalizing Tree Probability Estimation via Bayesian Networks
Cheng Zhang, Frederick A. Matsen
Probability estimation is one of the fundamental tasks in statistics and machine learning. However, standard methods for probability estimation on discrete objects do not handle ob…
Simultaneous disease mapping and hot spot detection with application to childhood obesity surveillance from electronic health records
Young-Geun Choi, Lawrence P. Hanrahan, Derek Norton +1
Electronic health records (EHRs) have become a platform for data-driven surveillance on a granular level in recent years. In this paper, we make use of EHRs for early prevention of…
Survival analysis of DNA mutation motifs with penalized proportional hazards
Jean Feng, David A. Shaw, Vladimir N. Minin +2
Antibodies, an essential part of our immune system, develop through an intricate process to bind a wide array of pathogens. This process involves randomly mutating DNA sequences en…
Sequential Double Robustness in Right-Censored Longitudinal Models
Alexander R. Luedtke, Oleg Sofrygin, Mark J. van der Laan +1
Consider estimating the G-formula for the counterfactual mean outcome under a given treatment regime in a longitudinal study. Bang and Robins provided an estimator for this quantit…
Regularized quantile regression under heterogeneous sparsity with application to quantitative genetic traits
Qianchuan He, Linglong Kong, Yanhua Wang +3
Genetic studies often involve quantitative traits. Identifying genetic features that influence quantitative traits can help to uncover the etiology of diseases. Quantile regression…
Cross-validation and Peeling Strategies for Survival Bump Hunting using Recursive Peeling Methods
Jean-Eudes Dazard, Michael Choe, Michael LeBlanc +1
We introduce a framework to build a survival/risk bump hunting model with a censored time-to-event response. Our Survival Bump Hunting (SBH) method is based on a recursive peeling…
Scalable Genomics with R and Bioconductor
Michael Lawrence, Martin Morgan
This paper reviews strategies for solving problems encountered when analyzing large genomic data sets and describes the implementation of those strategies in R by packages from the…
Data Exploration, Quality Control and Testing in Single-Cell qPCR-Based Gene Expression Experiments
Andrew McDavid, Greg Finak, Pratip K. Chattopadyay +5
Cell populations are never truly homogeneous; individual cells exist in biochemical states that define functional differences between them. New technology based on microfluidic arr…
Compression of next-generation sequencing reads aided by highly efficient de novo assembly
Daniel C. Jones, Walter L. Ruzzo, Xinxia Peng +1
We present Quip, a lossless compression algorithm for next-generation sequencing data in the FASTQ and SAM/BAM formats. In addition to implementing reference-based compression, we…
Structured penalties for functional linear models---partially empirical eigenvectors for regression
Timothy W. Randolph, Jaroslaw Harezlak, Ziding Feng
One of the challenges with functional data is incorporating spatial structure, or local correlation, into the analysis. This structure is inherent in the output from an increasing…
Structures and Assumptions: Strategies to Harness Gene Gene and Gene Environment Interactions in GWAS
Charles Kooperberg, Michael LeBlanc, James Y. Dai +1
Genome-wide association studies, in which as many as a million single nucleotide polymorphisms (SNP) are measured on several thousand samples, are quickly becoming a common type of…
Nonparametric spectral analysis with applications to seizure characterization using EEG time series
Li Qin, Yuedong Wang
Understanding the seizure initiation process and its propagation pattern(s) is a critical task in epilepsy research. Characteristics of the pre-seizure electroencephalograms (EEGs)…
Assessing surrogate endpoints in vaccine trials with case-cohort sampling and the Cox model
Li Qin, Peter B. Gilbert, Dean Follmann +1
Assessing immune responses to study vaccines as surrogates of protection plays a central role in vaccine clinical trials. Motivated by three ongoing or pending HIV vaccine efficacy…