Matthew Stephens

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 33

Top Topics

Genome Wide Association

Dna Methylation

Top Venues

Nature genetics

bioRxiv : the preprint server for biology

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences

This page only lists publications with an associated author ORCID identifier.

Publications

Siming Zhao, Wesley Crouse, Sheng Qian, Kaixuan Luo, Matthew Stephens, Xin He
Adjusting for genetic confounders in transcriptome-wide association studies improves discovery of risk genes of complex traits. Nature genetics 56 (2) (2024)
Eric Weine, Peter Carbonetto, Matthew Stephens
Accelerated dimensionality reduction of single-cell RNA sequencing data with fastglmpca. bioRxiv : the preprint server for biology (2024)
Siming Zhao, Wesley Crouse, Sheng Qian, Kaixuan Luo, Matthew Stephens, Xin He
Adjusting for genetic confounders in transcriptome-wide association studies improves discovery of risk genes of complex traits. Nature genetics 56 (2) (2024)
Eric Weine, Peter Carbonetto, Matthew Stephens
Accelerated dimensionality reduction of single-cell RNA sequencing data with fastglmpca. bioRxiv : the preprint server for biology (2024)
Eric Weine, Peter Carbonetto, Matthew Stephens
Accelerated dimensionality reduction of single-cell RNA sequencing data with fastglmpca. bioRxiv : the preprint server for biology (2024)
Siming Zhao, Wesley Crouse, Sheng Qian, Kaixuan Luo, Matthew Stephens, Xin He
Adjusting for genetic confounders in transcriptome-wide association studies improves discovery of risk genes of complex traits. Nature genetics 56 (2) (2024)
Eric Weine, Peter Carbonetto, Matthew Stephens
Accelerated dimensionality reduction of single-cell RNA sequencing data with fastglmpca. bioRxiv : the preprint server for biology (2024)
Siming Zhao, Wesley Crouse, Sheng Qian, Kaixuan Luo, Matthew Stephens, Xin He
Adjusting for genetic confounders in transcriptome-wide association studies improves discovery of risk genes of complex traits. Nature genetics 56 (2) (2024)
Siming Zhao, Wesley Crouse, Sheng Qian, Kaixuan Luo, Matthew Stephens, Xin He
Adjusting for genetic confounders in transcriptome-wide association studies improves discovery of risk genes of complex traits. Nature genetics (2024)
Siming Zhao, Wesley Crouse, Sheng Qian, Kaixuan Luo, Matthew Stephens, Xin He
Adjusting for genetic confounders in transcriptome-wide association studies improves discovery of risk genes of complex traits. Nature genetics 56 (2) (2024)
Siming Zhao, Wesley Crouse, Sheng Qian, Kaixuan Luo, Matthew Stephens, Xin He
Adjusting for genetic confounders in transcriptome-wide association studies improves discovery of risk genes of complex traits. Nature genetics 56 (2) (2024)
Eric Weine, Peter Carbonetto, Matthew Stephens
Accelerated dimensionality reduction of single-cell RNA sequencing data with fastglmpca. bioRxiv : the preprint server for biology (2024)
Eric Weine, Peter Carbonetto, Matthew Stephens
Accelerated dimensionality reduction of single-cell RNA sequencing data with fastglmpca. bioRxiv : the preprint server for biology (2024)
Matthew Stephens
The Bayesian lens and Bayesian blinkers. Philosophical transactions. Series A, Mathematical, physical, and engineering sciences 381 (2247) (2023)
Matthew Stephens
The Bayesian lens and Bayesian blinkers. Philosophical transactions. Series A, Mathematical, physical, and engineering sciences 381 (2247) (2023)
Yuxin Zou, Peter Carbonetto, Dongyue Xie, Gao Wang, Matthew Stephens
Fast and flexible joint fine-mapping of multiple traits via the Sum of Single Effects model. bioRxiv : the preprint server for biology (2023)
Fabio Morgante, Peter Carbonetto, Gao Wang, Yuxin Zou, Abhishek K Sarkar, Matthew Stephens
A flexible empirical Bayes approach to multivariate multiple regression, and its improved accuracy in predicting multi-tissue gene expression from genotypes. PLoS genetics 19 (7) (2023)
Matthew Stephens
The Bayesian lens and Bayesian blinkers. Philosophical transactions. Series A, Mathematical, physical, and engineering sciences 381 (2247) (2023)
Yusha Liu, Peter Carbonetto, Jason Willwerscheid, Scott A Oakes, Kay F Macleod, Matthew Stephens
Dissecting tumor transcriptional heterogeneity from single-cell RNA-seq data by generalized binary covariance decomposition. bioRxiv : the preprint server for biology (2023)
Peter Carbonetto, Kaixuan Luo, Abhishek K Sarkar, Anthony Hung, Karl Tayeb, Sebastian Pott, Matthew Stephens
Interpreting structure in sequence count data with differential expression analysis allowing for grades of membership. bioRxiv : the preprint server for biology (2023)
Yuxin Zou, Peter Carbonetto, Gao Wang, Matthew Stephens
Fine-mapping from summary data with the "Sum of Single Effects" model. PLoS genetics 18 (7) (2022)
Abhishek K Sarkar, Matthew Stephens
Separating measurement and expression models clarifies confusion in single-cell RNA sequencing analysis. Nature genetics 53 (6) (2021)
Jean Morrison, Nicholas Knoblauch, Joseph H Marcus, Matthew Stephens, Xin He
Mendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics. Nature genetics 52 (7) (2020)
Sarah Kim-Hellmuth, François Aguet, Meritxell Oliva, Manuel Muñoz-Aguirre, Silva Kasela, Valentin Wucher, Stephane E Castel, Andrew R Hamel, Ana Viñuela, Amy L Roberts, Serghei Mangul, Xiaoquan Wen, Gao Wang, Alvaro N Barbeira, Diego Garrido-Martín, Brian B Nadel, Yuxin Zou, Rodrigo Bonazzola, Jie Quan, Andrew Anand Brown, Angel Martinez-Perez, José Manuel Soria, null null, Gad A Getz, Emmanouil T Dermitzakis, Kerrin S Small, Matthew Stephens, Hualin S Xi, Hae Kyung Im, Roderic Guigo, Ayellet V Segrè, Barbara E Stranger, Kristin G Ardlie, Tuuli Lappalainen
Cell type-specific genetic regulation of gene expression across human tissues. Science (New York, N.Y.) 369 (6509) (2020)
Chiaowen Joyce Hsiao, PoYuan Tung, John D Blischak, Jonathan E Burnett, Kenneth A Barr, Kushal K Dey, Matthew Stephens, Yoav Gilad
Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis. Genome research 30 (4) (2020)
Zijie Zhang, Kaixuan Luo, Zhongyu Zou, Maguanyun Qiu, Jiakun Tian, Laura Sieh, Hailing Shi, Yuxin Zou, Gao Wang, Jean Morrison, Allen C Zhu, Min Qiao, Zhongshan Li, Matthew Stephens, Xin He, Chuan He
Genetic analyses support the contribution of mRNA N6-methyladenosine (m6A) modification to human disease heritability. Nature genetics 52 (9) (2020)
Meritxell Oliva, Manuel Muñoz-Aguirre, Sarah Kim-Hellmuth, Valentin Wucher, Ariel D H Gewirtz, Daniel J Cotter, Princy Parsana, Silva Kasela, Brunilda Balliu, Ana Viñuela, Stephane E Castel, Pejman Mohammadi, François Aguet, Yuxin Zou, Ekaterina A Khramtsova, Andrew D Skol, Diego Garrido-Martín, Ferran Reverter, Andrew Anand Brown, Patrick Evans, Eric R Gamazon, Anthony Payne, Rodrigo Bonazzola, Alvaro N Barbeira, Andrew R Hamel, Angel Martinez-Perez, José Manuel Soria, null null, Brandon L Pierce, Matthew Stephens, Eleazar Eskin, Emmanouil T Dermitzakis, Ayellet V Segrè, Hae Kyung Im, Barbara Elizabeth Engelhardt, Kristin G Ardlie, Stephen B Montgomery, Alexis J Battle, Tuuli Lappalainen, Roderic Guigo, Barbara E Stranger
The impact of sex on gene expression across human tissues. Science (New York, N.Y.) 369 (6509) (2020)
Michael C Turchin, Matthew Stephens
Bayesian multivariate reanalysis of large genetic studies identifies many new associations. PLoS genetics 15 (10) (2019)
Siming Zhao, Jun Liu, Pranav Nanga, Yuwen Liu, A Ercument Cicek, Nicholas Knoblauch, Chuan He, Matthew Stephens, Xin He
Detailed modeling of positive selection improves detection of cancer driver genes. Nature communications 10 (1) (2019)
Alexander E White, Kushal K Dey, Dhananjai Mohan, Matthew Stephens, Trevor D Price
Regional influences on community structure across the tropical-temperate divide. Nature communications 10 (1) (2019)
Xiang Zhu, Matthew Stephens
Large-scale genome-wide enrichment analyses identify new trait-associated genes and pathways across 31 human phenotypes. Nature communications 9 (1) (2018)
Sarah M Urbut, Gao Wang, Peter Carbonetto, Matthew Stephens
Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions. Nature genetics 51 (1) (2018)
David Gerard, Luis Felipe Ventorim Ferrão, Antonio Augusto Franco Garcia, Matthew Stephens
Genotyping Polyploids from Messy Sequencing Data. Genetics 210 (3) (2018)