Matthew Stephens

ScholarGPS® ID: 58541487697511

Affiliation

University of Chicago, Chicago, United States

Affiliation History

Field

Life Sciences

Discipline

Genetics

Top Specialties

Metrics Summary

Publication Count

Predicted Citations

34,014

Predicted h-index

Ranking

Publications and Citation History

Publications based on Top Specialties

Types of Publication

Publications
Books
Patents
NIH/NSF

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Adjusting for genetic confounders in transcriptome-wide association studies improves discovery of risk genes of complex traits (journal article) Zhao, Siming \| Crouse, Wesley \| Qian, Sheng \| Luo, Kaixuan \| Stephens, Matthew \| He, Xin Nature Genetics, volume 56, issue 2, pages 336-347 (2024). 10.1038/s41588-023-01648-9 Cited by (5) \| Cite \| Source
A pairwise cytokine code explains the organism-wide response to sepsis (journal article) Takahama, Michihiro \| Patil, Ashwini \| Richey, Gabriella \| Cipurko, Denis \| Johnson, Katherine \| Carbonetto, Peter \| Plaster, Madison \| Pandey, Surya \| Cheronis, Katerina \| Ueda, Tatsuki \| ... \| Chevrier, Nicolas Nature Immunology, volume 25, issue 2, pages 226-239 (2024). 10.1038/s41590-023-01722-8 Cited by (5) \| Cite \| Source
GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership (journal article) Carbonetto, Peter \| Luo, Kaixuan \| Sarkar, Abhishek \| Hung, Anthony \| Tayeb, Karl \| Pott, Sebastian \| Stephens, Matthew Genome Biology, volume 24, issue 1 (2023). 10.1186/s13059-023-03067-9 Cited by (2) \| Cite \| Source
A flexible empirical Bayes approach to multivariate multiple regression, and its improved accuracy in predicting multi-tissue gene expression from genotypes (journal article) Morgante, Fabio \| Carbonetto, Peter \| Wang, Gao \| Zou, Yuxin \| Sarkar, Abhishek \| Stephens, Matthew PLOS Genetics, volume 19, issue 7, pages e1010539- (2023). 10.1371/journal.pgen.1010539 Cite \| Source
The Bayesian lens and Bayesian blinkers (journal article) Stephens, Matthew Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, volume 381, issue 2247 (2023). 10.1098/rsta.2022.0144 Cited by (3) \| Cite \| Source
Fine-mapping from summary data with the “Sum of Single Effects” model (journal article) Zou, Yuxin \| Carbonetto, Peter \| Wang, Gao \| Stephens, Matthew PLOS Genetics, volume 18, issue 7, pages e1010299- (2022). 10.1371/journal.pgen.1010299 Cited by (66) \| Cite \| Source
Fine-mapping studies distinguish genetic risks for childhood- and adult-onset asthma in the HLA region (journal article) Clay, Selene M. \| Schoettler, Nathan \| Goldstein, Andrew M. \| Carbonetto, Peter \| Dapas, Matthew \| Altman, Matthew C. \| Rosasco, Mario G. \| Gern, James E. \| Jackson, Daniel J. \| Im, Hae Kyung \| ... \| Ober, Carole Genome Medicine, volume 14, issue 1 (2022). 10.1186/s13073-022-01058-2 Cited by (4) \| Cite \| Source
Separating measurement and expression models clarifies confusion in single-cell RNA sequencing analysis (journal article) Sarkar, Abhishek \| Stephens, Matthew Nature Genetics, volume 53, issue 6, pages 770-777 (2021). 10.1038/s41588-021-00873-4 Cited by (75) \| Cite \| Source
Dynamic effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes (journal article) Ward, Michelle C \| Banovich, Nicholas E \| Sarkar, Abhishek \| Stephens, Matthew \| Gilad, Yoav eLife, volume 10 (2021). 10.7554/eLife.57345 Cited by (27) \| Cite \| Source
Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls (journal article) Gerard, David \| Stephens, Matthew Statistica Sinica (2021). 10.5705/ss.202018.0345 Cited by (3) \| Cite \| Source
A Simple New Approach to Variable Selection in Regression, with Application to Genetic Fine Mapping (journal article) Wang, Gao \| Sarkar, Abhishek \| Carbonetto, Peter \| Stephens, Matthew Journal of the Royal Statistical Society Series B: Statistical Methodology, volume 82, issue 5, pages 1273-1300 (2020). 10.1111/rssb.12388 Cited by (297) \| Cite \| Source
Genetic analyses support the contribution of mRNA N6-methyladenosine (m6A) modification to human disease heritability (journal article) Zhang, Zijie \| Luo, Kaixuan \| Zou, Zhongyu \| Qiu, Maguanyun \| Tian, Jiakun \| Sieh, Laura \| Shi, Hailing \| Zou, Yuxin \| Wang, Gao \| Morrison, Jean \| ... \| He, Chuan Nature Genetics, volume 52, issue 9, pages 939-949 (2020). 10.1038/s41588-020-0644-z Cited by (115) \| Cite \| Source
Mendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics (journal article) Morrison, Jean \| Knoblauch, Nicholas \| Marcus, Joseph H. \| Stephens, Matthew \| He, Xin Nature Genetics, volume 52, issue 7, pages 740-747 (2020). 10.1038/s41588-020-0631-4 Cited by (276) \| Cite \| Source
A Fast Algorithm for Maximum Likelihood Estimation of Mixture Proportions Using Sequential Quadratic Programming (journal article) Kim, Youngseok \| Carbonetto, Peter \| Stephens, Matthew \| Anitescu, Mihai Journal of Computational and Graphical Statistics, volume 29, issue 2, pages 261-273 (2020). 10.1080/10618600.2019.1689985 Cited by (9) \| Cite \| Source
Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis (journal article) Hsiao, Chiaowen Joyce \| Tung, PoYuan \| Blischak, John D. \| Burnett, Jonathan E. \| Barr, Kenneth A. \| Dey, Kushal K. \| Stephens, Matthew \| Gilad, Yoav Genome Research, volume 30, issue 4, pages 611-621 (2020). 10.1101/gr.247759.118 Cited by (45) \| Cite \| Source
Empirical Bayes shrinkage and false discovery rate estimation, allowing for unwanted variation (journal article) Gerard, David \| Stephens, Matthew Biostatistics, volume 21, issue 1, pages 15-32 (2020). 10.1093/biostatistics/kxy029 Cited by (9) \| Cite \| Source \| Open Access
Bayesian multivariate reanalysis of large genetic studies identifies many new associations (journal article) Turchin, Michael C. \| Stephens, Matthew PLOS Genetics, volume 15, issue 10, pages e1008431- (2019). 10.1371/journal.pgen.1008431 Cited by (8) \| Cite \| Source
Detailed modeling of positive selection improves detection of cancer driver genes (journal article) Zhao, Siming \| Liu, Jun \| Nanga, Pranav \| Liu, Yuwen \| Cicek, A. Ercument \| Knoblauch, Nicholas \| He, Chuan \| Stephens, Matthew \| He, Xin Nature Communications, volume 10, issue 1 (2019). 10.1038/s41467-019-11284-9 Cited by (46) \| Cite \| Source
Regional influences on community structure across the tropical-temperate divide (journal article) White, Alexander E. \| Dey, Kushal K. \| Mohan, Dhananjai \| Stephens, Matthew \| Price, Trevor D. Nature Communications, volume 10, issue 1 (2019). 10.1038/s41467-019-10253-6 Cited by (37) \| Cite \| Source
Discovery and characterization of variance QTLs in human induced pluripotent stem cells (journal article) Sarkar, Abhishek K. \| Tung, Po-Yuan \| Blischak, John D. \| Burnett, Jonathan E. \| Li, Yang I. \| Stephens, Matthew \| Gilad, Yoav PLOS Genetics, volume 15, issue 4, pages e1008045- (2019). 10.1371/journal.pgen.1008045 Cited by (40) \| Cite \| Source

Title	Investigators	Year	Cost	Agency
Statistical analysis of gene expression quantitative trait loci (eQTL)	Stephens, Matthew	2015	$377,765	NATIONAL INSTITUTE OF MENTAL HEALTH
Statistical analysis of gene expression quantitative trait loci (eQTL)	Stephens, Matthew	2014	$377,765	NATIONAL INSTITUTE OF MENTAL HEALTH
Statistical analysis of gene expression quantitative trait loci (eQTL)	Stephens, Matthew	2013	$392,265	NATIONAL INSTITUTE OF MENTAL HEALTH
Multipoint and significance methods for genome-wide association studies	Stephens, Matthew	2008	$293,132	NATIONAL HEART, LUNG, AND BLOOD INSTITUTE
Multipoint and significance methods for genome-wide association studies	Stephens, Matthew	2007	$294,206	NATIONAL HEART, LUNG, AND BLOOD INSTITUTE