Matthew Stephens

114.6k total citations · 28 hit papers
132 papers, 75.0k citations indexed

About

Matthew Stephens is a scholar working on Genetics, Molecular Biology and Cancer Research. According to data from OpenAlex, Matthew Stephens has authored 132 papers receiving a total of 75.0k indexed citations (citations by other indexed papers that have themselves been cited), including 83 papers in Genetics, 61 papers in Molecular Biology and 12 papers in Cancer Research. Recurrent topics in Matthew Stephens's work include Genetic Mapping and Diversity in Plants and Animals (41 papers), Genetic Associations and Epidemiology (37 papers) and Genetic and phenotypic traits in livestock (35 papers). Matthew Stephens is often cited by papers focused on Genetic Mapping and Diversity in Plants and Animals (41 papers), Genetic Associations and Epidemiology (37 papers) and Genetic and phenotypic traits in livestock (35 papers). Matthew Stephens collaborates with scholars based in United States, United Kingdom and France. Matthew Stephens's co-authors include Jonathan K. Pritchard, Peter Donnelly, Daniel Falush, Nicholas Smith, Xiang Zhou, Paul Scheet, Yoav Gilad, Melissa J. Hubisz, John C. Marioni and Peter Carbonetto and has published in prestigious journals such as Nature, Science and Proceedings of the National Academy of Sciences.

In The Last Decade

Matthew Stephens

129 papers receiving 73.2k citations

Hit Papers

Inference of Population Structure Using Multilocus Genoty... 2000 2026 2008 2017 2000 2003 2001 2003 2007 5.0k 10.0k 15.0k 20.0k 25.0k
What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

  1. Inference of Population Structure Using Multilocus Genotype Data
    2000 27.5k citations Jonathan K. Pritchard, Matthew Stephens et al. Genetics profile →
  2. Inference of Population Structure Using Multilocus Genotype Data: Linked Loci and Correlated Allele Frequencies
    2003 6.6k citations Daniel Falush, Matthew Stephens et al. Genetics profile →
  3. A New Statistical Method for Haplotype Reconstruction from Population Data
    2001 6.4k citations Matthew Stephens, Peter Donnelly et al. profile →
  4. A Comparison of Bayesian Methods for Haplotype Reconstruction from Population Genotype Data
    2003 3.1k citations Matthew Stephens, Peter Donnelly profile →
  5. Inference of population structure using multilocus genotype data: dominant markers and null alleles
    2007 2.8k citations Daniel Falush, Matthew Stephens et al. profile →
  6. Inferring weak population structure with the assistance of sample group information
    2009 2.8k citations Daniel Falush, Matthew Stephens et al. profile →
  7. Genome-wide efficient mixed-model analysis for association studies
    2012 2.1k citations Xiang Zhou, Matthew Stephens Nature Genetics profile →
  8. RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
    2008 2.1k citations John C. Marioni, Matthew Stephens et al. Genome Research profile →
  9. Association Mapping in Structured Populations
    2000 1.5k citations Jonathan K. Pritchard, Matthew Stephens et al. profile →
  10. A Fast and Flexible Statistical Model for Large-Scale Population Genotype Data: Applications to Inferring Missing Genotypes and Haplotypic Phase
    2006 1.4k citations Paul Scheet, Matthew Stephens profile →
  11. fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets
    2014 1.1k citations Anil Raj, Matthew Stephens et al. Genetics profile →
  12. Accounting for Decay of Linkage Disequilibrium in Haplotype Inference and Missing-Data Imputation
    2005 1.1k citations Matthew Stephens, Paul Scheet profile →
  13. Fast and accurate genotype imputation in genome-wide association studies through pre-phasing
    2012 990 citations Matthew Stephens et al. Nature Genetics profile →
  14. Understanding mechanisms underlying human gene expression variation with RNA sequencing
    2010 908 citations Joseph K. Pickrell, John C. Marioni et al. Nature profile →
  15. Genes mirror geography within Europe
    2008 887 citations John Novembre, Matthew Stephens et al. Nature profile →
  16. Traces of Human Migrations in Helicobacter pylori Populations
    2003 742 citations Daniel Falush, Thierry Wirth et al. Science profile →
  17. Modeling Linkage Disequilibrium and Identifying Recombination Hotspots Using Single-Nucleotide Polymorphism Data
    2003 692 citations Matthew Stephens et al. Genetics profile →
  18. Dealing With Label Switching in Mixture Models
    2000 675 citations Matthew Stephens Journal of the Royal Statistical Society Series B (Statistical Methodology) profile →
  19. Genotype Imputation with Thousands of Genomes
    2011 561 citations Matthew Stephens et al. profile →
  20. Efficient multivariate linear mixed model algorithms for genome-wide association studies
    2014 555 citations Xiang Zhou, Matthew Stephens profile →
  21. Polygenic Modeling with Bayesian Sparse Linear Mixed Models
    2013 531 citations Xiang Zhou, Peter Carbonetto et al. PLoS Genetics profile →
  22. False discovery rates: a new deal
    2016 501 citations Matthew Stephens Biostatistics profile →
  23. DNase I sensitivity QTLs are a major determinant of human expression variation
    2012 429 citations Jacob F. Degner, Athma A. Pai et al. Nature profile →
  24. Visualizing spatial population structure with estimated effective migration surfaces
    2015 392 citations John Novembre, Matthew Stephens et al. Nature Genetics profile →
  25. A Simple New Approach to Variable Selection in Regression, with Application to Genetic Fine Mapping
    2020 371 citations Gao Wang, Abhishek Sarkar et al. Journal of the Royal Statistical Society Series B (Statistical Methodology) profile →
  26. Mendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics
    2020 332 citations Matthew Stephens et al. Nature Genetics profile →
  27. A Multivariate Genome-Wide Association Analysis of 10 LDL Subfractions, and Their Response to Statin Treatment, in 1868 Caucasians
    2015 324 citations Matthew Stephens et al. profile →
  28. Fine-mapping from summary data with the “Sum of Single Effects” model
    2022 109 citations Peter Carbonetto, Gao Wang et al. PLoS Genetics profile →

Peers — A (Enhanced Table)

Peers by citation overlap · career bar shows stage (early→late) cites · hero ref

Name h Career Trend Papers Cites
Matthew Stephens United States 66 43.7k 21.8k 15.7k 12.0k 9.2k 132 75.0k
Jonathan K. Pritchard United States 92 47.6k 1.1× 24.9k 1.1× 15.7k 1.0× 11.6k 1.0× 8.8k 1.0× 182 77.5k
Peter Donnelly United Kingdom 66 35.2k 0.8× 17.6k 0.8× 11.3k 0.7× 8.2k 0.7× 6.5k 0.7× 208 61.2k
Laurent Excoffier Switzerland 85 45.6k 1.0× 18.0k 0.8× 10.7k 0.7× 19.0k 1.6× 13.4k 1.5× 185 70.9k
David Posada Spain 55 18.5k 0.4× 18.9k 0.9× 12.5k 0.8× 15.4k 1.3× 13.0k 1.4× 164 56.6k
Alexei J. Drummond New Zealand 60 23.4k 0.5× 21.8k 1.0× 10.5k 0.7× 15.5k 1.3× 18.9k 2.1× 108 70.3k
Arndt von Haeseler Austria 58 14.1k 0.3× 28.4k 1.3× 13.2k 0.8× 13.8k 1.1× 12.4k 1.3× 192 61.8k
Marc A. Suchard United States 78 17.0k 0.4× 18.9k 0.9× 10.9k 0.7× 12.6k 1.0× 15.6k 1.7× 300 64.7k
Rasmus Nielsen United States 97 23.7k 0.5× 17.9k 0.8× 6.8k 0.4× 7.0k 0.6× 5.9k 0.6× 293 43.5k
Makoto Kimura Japan 77 27.9k 0.6× 27.5k 1.3× 11.2k 0.7× 12.5k 1.0× 9.0k 1.0× 362 64.2k
Masatoshi Nei United States 82 43.8k 1.0× 28.4k 1.3× 23.2k 1.5× 16.4k 1.4× 15.6k 1.7× 199 88.0k

Countries citing papers authored by Matthew Stephens

Since Specialization
Citations

This map shows the geographic impact of Matthew Stephens's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Matthew Stephens with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Matthew Stephens more than expected).

Fields of papers citing papers by Matthew Stephens

Since Specialization
Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Matthew Stephens. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Matthew Stephens. The network helps show where Matthew Stephens may publish in the future.

Co-authorship network of co-authors of Matthew Stephens

This figure shows the co-authorship network connecting the top 25 collaborators of Matthew Stephens. A scholar is included among the top collaborators of Matthew Stephens based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with Matthew Stephens. Matthew Stephens is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

20 of 20 papers shown
1.
Wang, Gao, Abhishek Sarkar, Peter Carbonetto, & Matthew Stephens. (2020). A Simple New Approach to Variable Selection in Regression, with Application to Genetic Fine Mapping. Journal of the Royal Statistical Society Series B (Statistical Methodology). 82(5). 1273–1300. 371 indexed citations breakdown →
2.
Sarkar, Abhishek, Po‐Yuan Tung, John Blischak, et al.. (2019). Discovery and characterization of variance QTLs in human induced pluripotent stem cells. PLoS Genetics. 15(4). e1008045–e1008045. 44 indexed citations
3.
Al-Asadi, Hussein, Kushal K. Dey, John Novembre, & Matthew Stephens. (2018). Inference and visualization of DNA damage patterns using a grade of membership model. Bioinformatics. 35(8). 1292–1298. 4 indexed citations
4.
Gerard, David, Luís Felipe V. Ferrão, Antônio Augusto Franco Garcia, & Matthew Stephens. (2018). Genotyping Polyploids from Messy Sequencing Data. Genetics. 210(3). 789–807. 122 indexed citations
5.
Smith, Joel, Graham Coop, Matthew Stephens, & John Novembre. (2018). Estimating Time to the Common Ancestor for a Beneficial Allele. Molecular Biology and Evolution. 35(4). 1003–1017. 37 indexed citations
6.
Ward, Michelle C., Siming Zhao, Kaixuan Luo, et al.. (2018). Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs. eLife. 7. 17 indexed citations
7.
Urbut, Sarah, Gao Wang, Peter Carbonetto, & Matthew Stephens. (2018). Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions. Nature Genetics. 51(1). 187–195. 184 indexed citations
8.
Stephens, Matthew, et al.. (2016). Variance adaptive shrinkage ( vash ): flexible empirical Bayes estimation of variances. Bioinformatics. 32(22). 3428–3434. 6 indexed citations
9.
Shiraishi, Yuichi, et al.. (2015). A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures. PLoS Genetics. 11(12). e1005657–e1005657. 65 indexed citations
10.
Raj, Anil, Matthew Stephens, & Jonathan K. Pritchard. (2014). fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets. Genetics. 197(2). 573–589. 1149 indexed citations breakdown →
11.
Zhou, Xiang, Carolyn E Cain, Marsha Myrthil, et al.. (2014). Epigenetic modifications are associated with inter-species gene expression variation in primates. Genome biology. 15(12). 547–547. 53 indexed citations
12.
Degner, Jacob F., Athma A. Pai, Roger Piqué-Regi, et al.. (2012). DNase I sensitivity QTLs are a major determinant of human expression variation. Nature. 482(7385). 390–394. 429 indexed citations breakdown →
13.
Maranville, Joseph, Francesca Luca, Allison L. Richards, et al.. (2011). Interactions between Glucocorticoid Treatment and Cis-Regulatory Polymorphisms Contribute to Cellular Response Phenotypes. PLoS Genetics. 7(7). e1002162–e1002162. 83 indexed citations
14.
Perry, George H., Páll Melsted, John C. Marioni, et al.. (2011). Comparative RNA sequencing reveals substantial genetic variation in endangered primates. Genome Research. 22(4). 602–610. 102 indexed citations
15.
Scheet, Paul & Matthew Stephens. (2008). Linkage Disequilibrium-Based Quality Control for Large-Scale Genetic Studies. PLoS Genetics. 4(8). e1000147–e1000147. 16 indexed citations
16.
Gottardo, Raphaël, Julian Besag, Matthew Stephens, & Alejandro Murua. (2005). Probabilistic segmentation and intensity estimation for microarray images. Biostatistics. 7(1). 85–99. 22 indexed citations
17.
Ptak, Susan E., Amy D. Roeder, Matthew Stephens, et al.. (2004). Absence of the TAP2 Human Recombination Hotspot in Chimpanzees. PLoS Biology. 2(6). e155–e155. 105 indexed citations
18.
Falush, Daniel, Thierry Wirth, Bodo Linz, et al.. (2003). Traces of Human Migrations in Helicobacter pylori Populations. Science. 299(5612). 1582–1585. 742 indexed citations breakdown →
19.
Falush, Daniel, et al.. (2003). Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies.. Genomics. 6 indexed citations
20.
Pritchard, Jonathan K., Matthew Stephens, & Peter Donnelly. (2000). Inference of Population Structure Using Multilocus Genotype Data. Genetics. 155(2). 945–959. 27461 indexed citations breakdown →

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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