Publications

The most up-to-date listing of our papers can be found on Jonathan’s Google Scholar page.

Preprints

In various stages of revision:

1. Dilber E, Liang J, Tan S, Terhorst J. Faster inference of complex demographic models from large allele frequency spectra. bioRxiv. 2024. [bibtex]

   @article{dilber2024faster,
     title = {Faster inference of complex demographic models from large allele frequency spectra},
     author = {Dilber, Enes and Liang, Jiatong and Tan, Sam and Terhorst, Jonathan},
     author+an = {1=bold;2=bold;3=bold},
     journal = {bioRxiv},
     keywords = {submitted},
     year = {2024}
   }
   

2. Erdmann-Pham DD, Terhorst J, Song YS. Exact and arbitrarily accurate non-parametric two-sample tests based on rank spacings. 2020. doi:10.48550/ARXIV.2008.06664 [link] [bibtex]

   @article{https://doi.org/10.48550/arxiv.2008.06664,
     author = {Erdmann-Pham, Dan D. and Terhorst, Jonathan and Song, Yun S.},
     doi = {10.48550/ARXIV.2008.06664},
     keywords = {submitted},
     month = jun,
     publisher = {arXiv},
     title = {Exact and arbitrarily accurate non-parametric two-sample tests based on rank spacings},
     year = {2020},
     bdsk-url-1 = {https://doi.org/10.48550/ARXIV.2008.06664}
   }
   

3. Colbran LL, Terhorst J, Mathieson I. Global patterns of natural selection inferred using ancient DNA. bioRxiv. 2026. doi:10.64898/2026.01.07.697984 [link] [bibtex]

   @article{colbran2026global,
     author = {Colbran, Laura L and Terhorst, Jonathan and Mathieson, Iain},
     date-added = {2026-04-01 12:52:10 -0700},
     date-modified = {2026-04-01 12:52:19 -0700},
     journal = {bioRxiv},
     keywords = {submitted},
     publisher = {Cold Spring Harbor Laboratory},
     title = {Global patterns of natural selection inferred using ancient DNA},
     month = feb,
     doi = {10.64898/2026.01.07.697984},
     year = {2026}
   }
   

4. Do D, Terhorst J. Model selection in ADMIXTURE can be inconsistent: proof of the K=2 phenomenon. bioRxiv. 2026. doi:10.64898/2026.02.27.708651 [link] [bibtex]

   @article{do2026model,
     author = {Do, Dat and Terhorst, Jonathan},
     author+an = {1=bold},
     date-added = {2026-04-01 12:51:09 -0700},
     date-modified = {2026-04-01 12:51:30 -0700},
     journal = {bioRxiv},
     keywords = {submitted},
     publisher = {Cold Spring Harbor Laboratory},
     title = {Model selection in {ADMIXTURE} can be inconsistent: proof of the $K=2$ phenomenon},
     doi = {10.64898/2026.02.27.708651},
     month = mar,
     year = {2026}
   }
   

5. Lee H, Terhorst J. Parameterizing the genetic architecture under stabilizing selection. bioRxiv. 2026. doi:10.64898/2026.03.27.714826 [link] [bibtex]

   @article{lee2026parameterizing,
     author = {Lee, Hanbin and Terhorst, Jonathan},
     author+an = {1=bold},
     date-added = {2026-04-01 12:50:27 -0700},
     date-modified = {2026-04-01 12:50:40 -0700},
     journal = {bioRxiv},
     keywords = {submitted},
     publisher = {Cold Spring Harbor Laboratory},
     title = {Parameterizing the genetic architecture under stabilizing selection},
     doi = {10.64898/2026.03.27.714826},
     month = mar,
     year = {2026}
   }
   

6. Jeffery B, Wong Y, Thornton K, Tsambos G, Bisschop G, Deng Y, et al. Population-scale Ancestral Recombination Graphs with tskit 1.0. 2026. Retrieved: https://arxiv.org/abs/2602.09649 [link] [bibtex]

   @article{jeffery2026tskit,
     archiveprefix = {arXiv},
     author = {Jeffery, Ben and Wong, Yan and Thornton, Kevin and Tsambos, Georgia and Bisschop, Gertjan and Deng, Yun and Ellerman, E. Castedo and Forest, Thomas B. and Fritze, Halley and Goldstein, Daniel and Gorjanc, Gregor and Gower, Graham and Gravel, Simon and Guez, Jeremy and Haller, Benjamin C. and Kern, Andrew D. and Kirk, Lloyd and Krukov, Ivan and Lee, Hanbin and Lehmann, Brieuc and Loay, Hossameldin and Osmond, Matthew M. and Palmer, Duncan S. and Pope, Nathaniel S. and Ragsdale, Aaron P. and Robertson, Duncan and Rodrigues, Murillo F. and van Kemenade, Hugo and Wei{\ss}, Clemens L. and Wohns, Anthony Wilder and Zhan, Shing H. and Zhang, Brian C. and Aspbury, Marianne and Baya, Nikolas A. and Belsare, Saurabh and Biddanda, Arjun and Jim{\'e}nez, Francisco Campuzano and Gladstein, Ariella and Guo, Bing and Karthikeyan, Savita and Kretzschmar, Warren W. and Rebollo, In{\'e}s and Saunack, Kumar and Shemirani, Ruhollah and Simon, Alexis and Smith, Chris and Sukumaran, Jeet and Terhorst, Jonathan and Unneberg, Per and Zhang, Ao and Ralph, Peter and Kelleher, Jerome},
     date-added = {2026-04-01 12:49:47 -0700},
     date-modified = {2026-04-01 12:50:00 -0700},
     eprint = {2602.09649},
     keywords = {submitted},
     primaryclass = {q-bio.PE},
     title = {Population-scale Ancestral Recombination Graphs with tskit 1.0},
     url = {https://arxiv.org/abs/2602.09649},
     year = {2026},
     bdsk-url-1 = {https://arxiv.org/abs/2602.09649}
   }
   

7. Do D, Do L, McKinley SA, Terhorst J, Nguyen XL. Dendrogram of mixing measures: Hierarchical clustering and model selection for finite mixture models. arXiv preprint arXiv:240301684. 2025. [bibtex]

   @article{do2025dendrogram,
     author = {Do, Dat and Do, Linh and McKinley, Scott A and Terhorst, Jonathan and Nguyen, XuanLong},
     author+an = {1=bold},
     date-added = {2025-03-17 11:10:47 -0400},
     date-modified = {2025-03-17 11:13:05 -0400},
     journal = {arXiv preprint arXiv:2403.01684},
     keywords = {submitted},
     title = {Dendrogram of mixing measures: Hierarchical clustering and model selection for finite mixture models},
     year = {2025}
   }
   

8. Do D, Chakraborty S, Terhorst J, Nguyen XL. Dirichlet moment tensors and the correspondence between admixture and mixture of product models. arXiv preprint arXiv:250925441. 2025. [bibtex]

   @article{do2025dirichlet,
     author+an = {1=bold},
     title = {Dirichlet moment tensors and the correspondence between admixture and mixture of product models},
     author = {Do, Dat and Chakraborty, Sunrit and Terhorst, Jonathan and Nguyen, XuanLong},
     journal = {arXiv preprint arXiv:2509.25441},
     keywords = {submitted},
     year = {2025}
   }
   

Published

1. Ki C, Terhorst J. Exact decoding of a sequentially markov coalescent model in genetics. Journal of the American Statistical Association. 2024;119: 2242–2255. doi:10.1080/01621459.2023.2252570 [link] [bibtex]

   @article{ki2024exact,
     title = {Exact decoding of a sequentially markov coalescent model in genetics},
     author+an = {1=bold},
     author = {Ki, Caleb and Terhorst, Jonathan},
     journal = {Journal of the American Statistical Association},
     doi = {10.1080/01621459.2023.2252570},
     keywords = {published},
     volume = {119},
     number = {547},
     pages = {2242--2255},
     year = {2024},
     publisher = {Taylor \& Francis}
   }
   

2. Jin Y, Terhorst J. The solution surface of the Li-Stephens haplotype copying model. Algorithms for Molecular Biology. 2023;18: 12. doi:10.1186/s13015-023-00237-z [link] [bibtex]

   @article{jin2023the-solution,
     author = {Jin, Yifan and Terhorst, Jonathan},
     author+an = {1=bold},
     date = {2023-08-09},
     date-added = {2023-08-09 11:07:39 -0400},
     date-modified = {2023-10-05 12:52:00 -0400},
     doi = {10.1186/s13015-023-00237-z},
     journal = {Algorithms for Molecular Biology},
     keywords = {published},
     number = {1},
     pages = {12},
     title = {The solution surface of the {Li-Stephens} haplotype copying model},
     volume = {18},
     year = {2023},
     bdsk-url-1 = {https://doi.org/10.1186/s13015-023-00237-z}
   }
   

3. Legried B, Terhorst J. Rates of convergence in the two-island and isolation-with-migration models. Theoretical Population Biology. 2022;147: 16–27. doi:10.1016/j.tpb.2022.08.001 [link] [bibtex]

   @article{legried2022rates,
     author = {Legried, Brandon and Terhorst, Jonathan},
     author+an = {1=bold},
     date-added = {2023-05-04 17:06:57 -0400},
     date-modified = {2023-05-04 17:07:17 -0400},
     doi = {10.1016/j.tpb.2022.08.001},
     issn = {0040-5809},
     journal = {Theoretical Population Biology},
     keywords = {published},
     pages = {16-27},
     title = {Rates of convergence in the two-island and isolation-with-migration models},
     volume = {147},
     year = {2022},
     bdsk-url-1 = {https://www.sciencedirect.com/science/article/pii/S004058092200051X},
     bdsk-url-2 = {https://doi.org/10.1016/j.tpb.2022.08.001}
   }
   

4. Fan S, Spence JP, Feng Y, Hansen MEB, Terhorst J, Beltrame MH, et al. Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation. Cell. 2023;186: 923–939.e14. doi:10.1016/j.cell.2023.01.042 [link] [bibtex]

   @article{fan2023whole-genome,
     author = {Fan, Shaohua and Spence, Jeffrey P. and Feng, Yuanqing and Hansen, Matthew E.B. and Terhorst, Jonathan and Beltrame, Marcia H. and Ranciaro, Alessia and Hirbo, Jibril and Beggs, William and Thomas, Neil and Nyambo, Thomas and Mpoloka, Sununguko Wata and Mokone, Gaonyadiwe George and Njamnshi, Alfred K. and Fokunang, Charles and Meskel, Dawit Wolde and Belay, Gurja and Song, Yun S. and Tishkoff, Sarah A.},
     date-added = {2023-05-04 17:05:54 -0400},
     date-modified = {2023-05-04 17:06:11 -0400},
     doi = {10.1016/j.cell.2023.01.042},
     journal = {Cell},
     keywords = {published},
     month = mar,
     number = {5},
     pages = {923-939.e14},
     title = {Whole-genome sequencing reveals a complex {African} population demographic history and signatures of local adaptation},
     volume = {186},
     year = {2023},
     bdsk-url-1 = {https://www.sciencedirect.com/science/article/pii/S0092867423001010},
     bdsk-url-2 = {https://doi.org/10.1016/j.cell.2023.01.042}
   }
   

5. Mathieson I, Terhorst J. Direct detection of natural selection in Bronze Age Britain. Genome Research. 2022;32: 2057–2067. doi:10.1101/gr.276862.122 [link] [bibtex]

   @article{mathieson2022direct,
     author = {Mathieson, Iain and Terhorst, Jonathan},
     author+an = {1=star;2=star},
     date-added = {2023-04-03 11:57:38 -0400},
     date-modified = {2023-04-03 12:00:00 -0400},
     doi = {10.1101/gr.276862.122},
     journal = {Genome Research},
     keywords = {published},
     month = nov,
     number = {11-12},
     pages = {2057-2067},
     title = {Direct detection of natural selection in {Bronze Age Britain}},
     volume = {32},
     year = {2022},
     bdsk-url-1 = {https://doi.org/10.1101/gr.276862.122}
   }
   

6. Ki C, Terhorst J. Variational phylodynamic inference using pandemic-scale data. Molecular Biology and Evolution. 2022;39. doi:10.1093/molbev/msac154 [link] [bibtex]

   @article{10.1093/molbev/msac154,
     author = {Ki, Caleb and Terhorst, Jonathan},
     author+an = {1=bold},
     doi = {10.1093/molbev/msac154},
     issn = {1537-1719},
     journal = {Molecular Biology and Evolution},
     keywords = {published},
     month = jul,
     number = {8},
     title = {Variational phylodynamic inference using pandemic-scale data},
     volume = {39},
     year = {2022},
     bdsk-url-1 = {https://doi.org/10.1093/molbev/msac154}
   }
   

7. Maity S, Dutta D, Terhorst J, Sun Y, Banerjee M. A linear adjustment based approach to posterior drift in transfer learning. Biometrika. 2023;111: 31–50. doi:10.1093/biomet/asad029 [link] [bibtex]

   @article{maity2023linear,
     author = {Maity, Subha and Dutta, Diptavo and Terhorst, Jonathan and Sun, Yuekai and Banerjee, Moulinath},
     author+an = {1=bold;2=bold},
     journal = {Biometrika},
     volume = {111},
     number = {1},
     pages = {31-50},
     year = {2023},
     month = jul,
     issn = {1464-3510},
     doi = {10.1093/biomet/asad029},
     keywords = {published},
     title = {{A linear adjustment based approach to posterior drift in transfer learning}},
     bdsk-url-1 = {https://doi.org/10.1093/biomet/asad029}
   }
   

8. Dilber E, Terhorst J. Robust detection of natural selection using a probabilistic model of tree imbalance. Genetics. 2022;220. doi:10.1093/genetics/iyac009 [link] [bibtex]

   @article{dilber2022robust,
     author = {Dilber, Enes and Terhorst, Jonathan},
     author+an = {1=bold},
     date-added = {2022-05-04 17:18:04 -0400},
     date-modified = {2022-05-04 17:18:04 -0400},
     doi = {10.1093/genetics/iyac009},
     journal = {Genetics},
     keywords = {published},
     month = mar,
     number = {3},
     publisher = {Oxford University Press},
     title = {Robust detection of natural selection using a probabilistic model of tree imbalance},
     volume = {220},
     year = {2022},
     bdsk-url-1 = {https://doi.org/10.1093/genetics/iyac009}
   }
   

9. Legried B, Terhorst J. Identifiability and inference of phylogenetic birth–death models. Journal of Theoretical Biology. 2023;568: 111520. doi:10.1016/j.jtbi.2023.111520 [link] [bibtex]

   @article{legried2023identifiability,
     author = {Legried, Brandon and Terhorst, Jonathan},
     author+an = {1=bold},
     doi = {10.1016/j.jtbi.2023.111520},
     issn = {0022-5193},
     journal = {Journal of Theoretical Biology},
     keywords = {published},
     month = jul,
     pages = {111520},
     title = {Identifiability and inference of phylogenetic birth--death models},
     volume = {568},
     year = {2023},
     bdsk-url-1 = {https://doi.org/10.1016/j.jtbi.2023.111520}
   }
   

10. Legried B, Terhorst J. A class of identifiable phylogenetic birth–death models. Proceedings of the National Academy of Sciences. 2022;119: e2119513119. doi:10.1073/pnas.2119513119 [link] [bibtex]

    @article{legried2022class,
      author = {Legried, Brandon and Terhorst, Jonathan},
      author+an = {1=bold},
      doi = {10.1073/pnas.2119513119},
      journal = {Proceedings of the National Academy of Sciences},
      keywords = {published},
      month = aug,
      number = {35},
      pages = {e2119513119},
      publisher = {National Acad Sciences},
      title = {A class of identifiable phylogenetic birth--death models},
      volume = {119},
      year = {2022},
      bdsk-url-1 = {https://doi.org/10.1073/pnas.2119513119}
    }
    

11. Kamm J, Terhorst J, Durbin R, Song YS. Efficiently Inferring the Demographic History of Many Populations With Allele Count Data. Journal of the American Statistical Association. 2020;115: 1472–1487. doi:10.1080/01621459.2019.1635482 [link] [bibtex]

    @article{kamm2020efficiently,
      author = {Kamm, Jack and Terhorst, Jonathan and Durbin, Richard and Song, Yun S.},
      date-added = {2020-10-26 15:40:21 -0400},
      date-modified = {2020-10-26 15:51:46 -0400},
      doi = {10.1080/01621459.2019.1635482},
      journal = {Journal of the American Statistical Association},
      keywords = {published},
      month = jul,
      number = {531},
      pages = {1472-1487},
      publisher = {Taylor \& Francis},
      title = {Efficiently Inferring the Demographic History of Many Populations With Allele Count Data},
      volume = {115},
      year = {2020},
      bdsk-url-1 = {https://doi.org/10.1080/01621459.2019.1635482}
    }
    

12. Plumb G, Terhorst J, Sankararaman S, Talwalkar A. Explaining Groups of Points in Low-Dimensional Representations. In: III HD, Singh A, editors. Proceedings of the 37th International Conference on Machine Learning. PMLR; 2020. pp. 7762–7771. Retrieved: https://proceedings.mlr.press/v119/plumb20a.html [link] [bibtex]

    @inproceedings{pmlr-v119-plumb20a,
      author = {Plumb, Gregory and Terhorst, Jonathan and Sankararaman, Sriram and Talwalkar, Ameet},
      author+an = {1=bold},
      booktitle = {Proceedings of the 37th International Conference on Machine Learning},
      editor = {III, Hal Daum{\'e} and Singh, Aarti},
      keywords = {published},
      month = jul,
      pages = {7762--7771},
      pdf = {http://proceedings.mlr.press/v119/plumb20a/plumb20a.pdf},
      publisher = {PMLR},
      series = {Proceedings of Machine Learning Research},
      title = {Explaining Groups of Points in Low-Dimensional Representations},
      url = {https://proceedings.mlr.press/v119/plumb20a.html},
      volume = {119},
      year = {2020},
      bdsk-url-1 = {https://proceedings.mlr.press/v119/plumb20a.html}
    }
    

13. Gao Z, Terhorst J, Van Hout CV, Stoev S. U-PASS: unified power analysis and forensics for qualitative traits in genetic association studies. Bioinformatics. 2019;36: 974–975. doi:10.1093/bioinformatics/btz637 [link] [bibtex]

    @article{gao2019u-pass:,
      author = {Gao, Zheng and Terhorst, Jonathan and Van Hout, Cristopher V. and Stoev, Stilian},
      author+an = {1=bold},
      date-modified = {2020-10-26 15:51:49 -0400},
      doi = {10.1093/bioinformatics/btz637},
      issn = {1367-4803},
      journal = {Bioinformatics},
      keywords = {published},
      month = aug,
      number = {3},
      pages = {974-975},
      title = {{U-PASS: unified power analysis and forensics for qualitative traits in genetic association studies}},
      volume = {36},
      year = {2019},
      bdsk-url-1 = {https://doi.org/10.1093/bioinformatics/btz637}
    }
    

14. Spence JP, Steinrücken M, Terhorst J, Song YS. Inference of population history using coalescent HMMs: review and outlook. Current Opinion in Genetics & Development. 2018;53: 70–76. doi:10.1016/j.gde.2018.07.002 [link] [bibtex]

    @article{spence2018inference,
      author = {Spence, Jeffrey P. and Steinr{\"u}cken, Matthias and Terhorst, Jonathan and Song, Yun S.},
      date-modified = {2020-10-26 15:51:49 -0400},
      doi = {10.1016/j.gde.2018.07.002},
      issn = {0959-437X},
      journal = {Current Opinion in Genetics \& Development},
      keywords = {published},
      month = dec,
      note = {Genetics of Human Origins},
      pages = {70 - 76},
      title = {Inference of population history using coalescent {HMMs}: review and outlook},
      volume = {53},
      year = {2018},
      bdsk-url-1 = {http://www.sciencedirect.com/science/article/pii/S0959437X18300765},
      bdsk-url-2 = {https://doi.org/10.1016/j.gde.2018.07.002}
    }
    

15. Palamara P, Terhorst J, Song YS, Price AL. High-throughput inference of pairwise coalescence times identifies signals of selection and enriched disease heritability. Nature Genetics. 2018;50: 1311. doi:10.1038/s41588-018-0177-x [link] [bibtex]

    @article{palamara2018high-throughput,
      author = {Palamara, Pier and Terhorst, Jonathan and Song, Yun S. and Price, Alkes L.},
      date-modified = {2020-10-26 15:51:49 -0400},
      doi = {10.1038/s41588-018-0177-x},
      journal = {Nature Genetics},
      keywords = {published},
      month = aug,
      number = {9},
      pages = {1311},
      title = {High-throughput inference of pairwise coalescence times identifies signals of selection and enriched disease heritability.},
      volume = {50},
      year = {2018},
      bdsk-url-1 = {https://doi.org/10.1038/s41588-018-0177-x}
    }
    

16. Moreno-Mayar JV, Potter BA, Vinner L, Steinrücken M, Rasmussen S, Terhorst J, et al. Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans. Nature. 2018. doi:10.1038/nature25173 [link] [bibtex]

    @article{moreno-mayar2018terminal,
      author = {Moreno-Mayar, J. V\'ictor and Potter, Ben A. and Vinner, Lasse and Steinr{\"u}cken, Matthias and Rasmussen, Simon and Terhorst, Jonathan and Kamm, John A. and Albrechtsen, Anders and Malaspinas, Anna-Sapfo and Sikora, Martin and Reuther, Joshua D. and Irish, Joel D. and Malhi, Ripan S. and Orlando, Ludovic and Song, Yun S. and Nielsen, Rasmus and Meltzer, David J. and Willerslev, Eske},
      date-modified = {2021-11-24 11:29:53 -0500},
      day = {03},
      doi = {10.1038/nature25173},
      journal = {Nature},
      keywords = {published},
      month = jan,
      title = {Terminal {Pleistocene Alaskan} genome reveals first founding population of {Native Americans}},
      year = {2018},
      bdsk-url-1 = {https://doi.org/10.1038/nature25173}
    }
    

17. Terhorst J, Kamm JA, Song YS. Robust and scalable inference of population history from hundreds of unphased whole genomes. Nature Genetics. 2017;49: 303–309. doi:10.1038/ng.3748 [link] [bibtex]

    @article{terhorst2017robust,
      author = {Terhorst, Jonathan and Kamm, John A. and Song, Yun S.},
      date-modified = {2020-10-26 15:51:49 -0400},
      doi = {10.1038/ng.3748},
      journal = {Nature Genetics},
      keywords = {published},
      month = jan,
      number = {2},
      pages = {303--309},
      title = {Robust and scalable inference of population history from hundreds of unphased whole genomes},
      volume = {49},
      year = {2017},
      bdsk-url-1 = {https://doi.org/10.1038/ng.3748}
    }
    

18. Kamm JA, Terhorst J, Song YS. Efficient Computation of the Joint Sample Frequency Spectra for Multiple Populations. Journal of Computational and Graphical Statistics. 2017;26: 182–194. doi:10.1080/10618600.2016.1159212 [link] [bibtex]

    @article{kamm2017efficient,
      author = {Kamm, John A. and Terhorst, Jonathan and Song, Yun S.},
      date-modified = {2020-10-26 15:51:49 -0400},
      doi = {10.1080/10618600.2016.1159212},
      journal = {Journal of Computational and Graphical Statistics},
      keywords = {published},
      month = feb,
      number = {1},
      pages = {182-194},
      title = {Efficient Computation of the Joint Sample Frequency Spectra for Multiple Populations},
      volume = {26},
      year = {2017},
      bdsk-url-1 = {https://doi.org/10.1080/10618600.2016.1159212}
    }
    

19. Liu T-Y, Dodson AE, Terhorst J, Song YS, Rine J. Riches of phenotype computationally extracted from microbial colonies. Proceedings of the National Academy of Sciences. 2016;113: E2822–E2831. doi:10.1073/pnas.1523295113 [link] [bibtex]

    @article{liu2016riches,
      author = {Liu, Tzu-Yu and Dodson, Anne E. and Terhorst, Jonathan and Song, Yun S. and Rine, Jasper},
      date-modified = {2020-10-26 15:51:49 -0400},
      doi = {10.1073/pnas.1523295113},
      journal = {Proceedings of the National Academy of Sciences},
      keywords = {published},
      month = may,
      number = {20},
      pages = {E2822-E2831},
      title = {Riches of phenotype computationally extracted from microbial colonies},
      volume = {113},
      year = {2016},
      bdsk-url-1 = {https://doi.org/10.1073/pnas.1523295113}
    }
    

20. Terhorst J, Schlötterer C, Song YS. Multi-locus Analysis of Genomic Time Series Data from Experimental Evolution. PLoS Genetics. 2015;11: 1–29. doi:10.1371/journal.pgen.1005069 [link] [bibtex]

    @article{terhorst2015multi-locus,
      author = {Terhorst, Jonathan and Schl{\"o}tterer, Christian and Song, Yun S.},
      date-modified = {2020-10-26 15:51:49 -0400},
      doi = {10.1371/journal.pgen.1005069},
      journal = {PLoS Genetics},
      keywords = {published},
      month = apr,
      number = {4},
      pages = {1-29},
      title = {Multi-locus Analysis of Genomic Time Series Data from Experimental Evolution},
      volume = {11},
      year = {2015},
      bdsk-url-1 = {https://doi.org/10.1371/journal.pgen.1005069}
    }
    

21. Terhorst J, Song YS. Fundamental limits on the accuracy of demographic inference based on the sample frequency spectrum. Proceedings of the National Academy of Sciences. 2015;112: 7677–7682. doi:10.1073/pnas.1503717112 [link] [bibtex]

    @article{terhorst2015fundamental,
      author = {Terhorst, Jonathan and Song, Yun S.},
      date-modified = {2020-10-26 15:51:49 -0400},
      doi = {10.1073/pnas.1503717112},
      journal = {Proceedings of the National Academy of Sciences},
      keywords = {published},
      month = jun,
      number = {25},
      pages = {7677-7682},
      title = {Fundamental limits on the accuracy of demographic inference based on the sample frequency spectrum},
      volume = {112},
      year = {2015},
      bdsk-url-1 = {https://doi.org/10.1073/pnas.1503717112}
    }
    

22. Talwalkar A, Liptrap J, Newcomb J, Hartl C, Terhorst J, Curtis K, et al. SMaSH: a benchmarking toolkit for human genome variant calling. Bioinformatics. 2014;30: 2787–2795. doi:10.1093/bioinformatics/btu345 [link] [bibtex]

    @article{talwalkar2014smash:,
      author = {Talwalkar, Ameet and Liptrap, Jesse and Newcomb, Julie and Hartl, Christopher and Terhorst, Jonathan and Curtis, Kristal and Bresler, Ma'ayan and Song, Yun S. and Jordan, Michael I. and Patterson, David},
      date-modified = {2020-10-26 15:51:49 -0400},
      doi = {10.1093/bioinformatics/btu345},
      journal = {Bioinformatics},
      keywords = {published},
      month = jun,
      number = {19},
      pages = {2787-2795},
      title = {{{SMaSH}}: a benchmarking toolkit for human genome variant calling},
      volume = {30},
      year = {2014},
      bdsk-url-1 = {https://doi.org/10.1093/bioinformatics/btu345}
    }
    

23. Jaggi M, Smith V, Takac M, Terhorst J, Krishnan S, Hofmann T, et al. Communication-Efficient Distributed Dual Coordinate Ascent. In: Ghahramani Z, Welling M, Cortes C, Lawrence ND, Weinberger KQ, editors. Advances in Neural Information Processing Systems 27. 2014. pp. 3068–3076. [bibtex]

    @incollection{jaggi2014communication-efficient,
      author = {Jaggi, Martin and Smith, Virginia and Takac, Martin and Terhorst, Jonathan and Krishnan, Sanjay and Hofmann, Thomas and Jordan, Michael I},
      booktitle = {Advances in Neural Information Processing Systems 27},
      date-modified = {2020-10-26 15:51:49 -0400},
      editor = {Ghahramani, Z. and Welling, M. and Cortes, C. and Lawrence, N. D. and Weinberger, K. Q.},
      keywords = {published},
      month = nov,
      pages = {3068--3076},
      title = {Communication-Efficient Distributed Dual Coordinate Ascent},
      year = {2014},
      bdsk-url-1 = {http://papers.nips.cc/paper/5599-communication-efficient-distributed-dual-coordinate-ascent.pdf}
    }
    

24. Bloniarz A, Talwalkar A, Terhorst J, Jordan MI, Patterson D, Yu B, et al. Changepoint Analysis for Efficient Variant Calling. In: Sharan R, editor. RECOMB 2014. Cham; 2014. pp. 20–34. doi:10.1007/978-3-319-05269-4_3 [link] [bibtex]

    @incollection{bloniarz2014changepoint,
      address = {Cham},
      author = {Bloniarz, Adam and Talwalkar, Ameet and Terhorst, Jonathan and Jordan, Michael I. and Patterson, David and Yu, Bin and Song, Yun S.},
      booktitle = {RECOMB 2014},
      date-modified = {2020-10-26 15:51:49 -0400},
      doi = {10.1007/978-3-319-05269-4_3},
      editor = {Sharan, Roded},
      isbn = {978-3-319-05269-4},
      keywords = {published},
      month = apr,
      pages = {20--34},
      title = {Changepoint Analysis for Efficient Variant Calling},
      year = {2014},
      bdsk-url-1 = {https://doi.org/10.1007/978-3-319-05269-4_3}
    }
    

25. Xia R, Sheehan S, Zhang Y, Talwalkar A, Zaharia M, Terhorst J, et al. Distributed Pipeline for Genomic Variant Calling. NIPS Workshop on BIG Learning. 2012. [bibtex]

    @inproceedings{xia2012distributed,
      author = {Xia, Richard and Sheehan, Sara and Zhang, Yuchen and Talwalkar, Ameet and Zaharia, Matei and Terhorst, Jonathan and Jordan, Michael and Song, Yun S and Fox, Armando and Patterson, David},
      booktitle = {NIPS Workshop on BIG Learning},
      date-modified = {2022-05-04 17:23:47 -0400},
      keywords = {published},
      month = nov,
      title = {Distributed Pipeline for Genomic Variant Calling},
      year = {2012}
    }
    

26. Terhorst J. Accelerated Bayesian inference of population size history from recombining sequence data. Nature Genetics. 2025;57: 2570–2577. [bibtex]

    @article{terhorst2025accelerated,
      author = {Terhorst, Jonathan},
      date-added = {2026-04-01 12:57:23 -0700},
      date-modified = {2026-04-01 12:57:31 -0700},
      journal = {Nature Genetics},
      keywords = {published},
      number = {10},
      pages = {2570--2577},
      publisher = {Nature Publishing Group US New York},
      title = {Accelerated Bayesian inference of population size history from recombining sequence data},
      volume = {57},
      year = {2025}
    }
    

27. Aragon JAU, Bandyopadhyay E, Fernando AS, Fuente Castro C de la, Welikala AHJ, Biddanda A, et al. Population histories of the Indigenous Adivasi and Sinhalese from Sri Lanka using whole genomes. Current Biology. 2025;35: 2554–2566. doi:10.1016/j.cub.2025.04.039 [link] [bibtex]

    @article{aragon2025population,
      title = {Population histories of the Indigenous Adivasi and Sinhalese from Sri Lanka using whole genomes},
      author = {Aragon, Jose A Urban and Bandyopadhyay, Esha and Fernando, Amali S and de la Fuente Castro, Constanza and Welikala, Anjana HJ and Biddanda, Arjun and Witonsky, David and Sander, Nathan and Kotelawala, Joanne T and Pasupuleti, Nagarjuna and others},
      journal = {Current Biology},
      volume = {35},
      number = {11},
      pages = {2554--2566},
      year = {2025},
      keywords = {published},
      doi = {10.1016/j.cub.2025.04.039},
      publisher = {Elsevier}
    }
    

Unpublished

1. Terhorst J. The Kalmanson Complex. Master's thesis, San Francisco State University. 2011. Retrieved: https://arxiv.org/abs/1102.3177 [link] [bibtex]

   @mastersthesis{terhorst2011the-kalmanson,
     address = {San Francisco, CA},
     author = {Terhorst, Jonathan},
     date-modified = {2020-10-26 15:52:07 -0400},
     keywords = {unpublished},
     month = may,
     school = {San Francisco State University},
     title = {{The Kalmanson Complex}},
     url = {https://arxiv.org/abs/1102.3177},
     year = {2011},
     bdsk-url-1 = {https://arxiv.org/abs/1102.3177}
   }
   

Pre-history

1. Sunding D, Terhorst J. Conserving endangered species through regulation of urban development: the case of California vernal pools. Land Economics. 2014;90: 290–305. doi:10.3368/le.90.2.290 [link] [bibtex]

   @article{sunding2014conserving,
     author = {Sunding, David and Terhorst, Jonathan},
     date-modified = {2021-05-19 12:16:13 -0400},
     doi = {10.3368/le.90.2.290},
     journal = {Land Economics},
     keywords = {old},
     number = {2},
     pages = {290--305},
     title = {Conserving endangered species through regulation of urban development: the case of California vernal pools},
     volume = {90},
     year = {2014},
     bdsk-url-1 = {https://doi.org/10.3368/le.90.2.290}
   }
   

2. Terhorst J, Berkman M. Effect of coal-fired power generation on visibility in a nearby national park. Atmospheric Environment. 2010;44: 2524–2531. doi:10.1016/j.atmosenv.2010.04.022 [link] [bibtex]

   @article{terhorst2010effect,
     author = {Terhorst, Jonathan and Berkman, Mark},
     date-modified = {2021-05-19 12:15:29 -0400},
     doi = {10.1016/j.atmosenv.2010.04.022},
     issn = {1352-2310},
     journal = {Atmospheric Environment},
     keywords = {old},
     number = {21--22},
     pages = {2524 - 2531},
     title = {Effect of coal-fired power generation on visibility in a nearby national park},
     volume = {44},
     year = {2010},
     bdsk-url-1 = {http://dx.doi.org/10.1016/j.atmosenv.2010.04.022}
   }
   

3. Sunding D, Swoboda A, Terhorst J. Federal Land Use Controls and the Planning Anticommons. UC Berkeley, Department of Agricultural and Resource Economics; 2007. Retrieved: https://are.berkeley.edu/ sunding/FederalLandUse.pdf [link] [bibtex]

   @techreport{sunding2007federal,
     author = {Sunding, David and Swoboda, Aaron and Terhorst, Jonathan},
     date-modified = {2021-05-19 12:15:37 -0400},
     institution = {UC Berkeley, Department of Agricultural and Resource Economics},
     keywords = {old},
     title = {Federal Land Use Controls and the Planning Anticommons},
     url = {https://are.berkeley.edu/~sunding/FederalLandUse.pdf},
     year = {2007},
     bdsk-url-1 = {https://are.berkeley.edu/~sunding/FederalLandUse.pdf}
   }