Susanne Pfeifer
Assistant Professor, School of Life Sciences
Asst Professor, Biodesign Center for Mechanisms of Evolution
Associate Professor, School of Life Sciences Biomedicine and Biotechnology
Associate Professor, Center for Evolution and Medicine
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School of Life Sciences LSC 340 Tempe, AZ 85281
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Mail code: 4501Campus: Tempe
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Long Bio
Susanne Pfeifer is an Assistant Professor in the ASU School of Life Sciences, the Center for Evolution & Medicine, and the Center for Mechanisms of Evolution.
The Pfeifer lab is interested in studying genetic and evolutionary processes by combining large-scale, high-throughput sequence data analysis and model-based statistical inference with two main foci: (i) to elucidate the causes and consequences of mutation and recombination rate variation (with a focus on primates) and (ii) to understand how natural selection shapes patterns of genetic variation in populations (with particular interest in understanding the process of adaptation during rapid environmental change).
Education
Susanne Pfeifer earned a B.Sc. and M.Sc. from the Max Plank Institute for Computer Science & Saarland University (Germany). She earned her D.Phil. in Statistics at the University of Oxford (UK) advised by Gil McVean, working on the statistical challenges involved in the estimation of variation in mutation and recombination rates from high throughput sequencing data, with direct applications to primate population genetics in a collaboration with Molly Przeworski’s Lab at the University of Chicago and Peter Donnelly’s Lab at the Wellcome Trust Centre for Human Genetics in Oxford. She completed her postdoctoral work as a Vienna International Postdoctoral Program fellow at the Center for Integrative Bioinformatics in Vienna (Austria) and worked as a research associate at the Swiss Institute for Technology (Switzerland).
Research Website URL
Google Scholar URL
Research Interests
Research in the Pfeifer Lab is focused on analysing high-throughput sequencing data to learn about genetic and evolutionary processes. In particular, we focus on three topics within evolutionary genomics, also intersecting broadly with other related fields:
- Anthropological - mutation and recombination rate variation in primates
- Ecological - adaptation due to recent environmental change
- Clinical - virus evolution
Please refer to our lab webpage for additional details.
Research Group
Publications
Recent, representative publications: (lab members indicated; * authors contributed equally)
- M. Milhaven and S.P. Pfeifer. 2022. Performance comparison of six popular short-read simulators. Heredity, online ahead of print.
- K. Walker, D. Kalra, R. Lowdon, G. Chen, D. Molik, D.C. Soto, F. Dabbaghie, A.A. Khleifat, M. Mahmoud, L.F. Paulin, M. Sohail Raza, S.P. Pfeifer, D. Paiva Agustinho, E. Aliyev, P. Avdeyev, E.R. Barrozo, S. Behera, K. Billingsley, L. Chuin Chong, D. Choubey, W. De Coster, Y. Fu, A.R. Gener, T. Hefferon, D. Morgan Henke, W. Höps, A. Illarionova, M.D. Jochum, M. Jose, R.K. Kesharwani, S. Rohit Raj Kolora, J. Kubica, P. Lakra, D. Lattimer, C.-S. Liew, B.-W. Lo, C. Lo, A. Lötter, S. Majidian, S.Kumar Mendem, R. Mondal, H. Ohmiya, N. Parvin, C. Peralta, C.-L. Poon, R. Prabhakaran, M. Saitou, A. Sammi, P. Sanio, N. Sapoval, N. Syed, T. Treangen, G. Wang, T. Xu, J. Yang, S. Zhang, W. Zhou, F.J. Sedlazeck, B. Busby. 2022. The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms. F1000 Res., 11: 530.
- A.A. Howell*, C.J. Versoza*, G. Cerna, T. Johnston, S. Kakde, K. Karuku, M. Kowal, J. Monahan, J. Murray, T. Nguyen, A. Sanchez Carreon, A. Streiff, B. Su, F. Youkhana, S. Munig, Z. Patel, M. So, M. Sy, S. Weiss, S.P. Pfeifer. 2022. Phylogenomic analyses and host range prediction of cluster P mycobacteriophages. G3 (Bethesda), 12(11): e0054022.
- C.J. Versoza*, A.A. Howell*, T. Aftab, M. Blanco, A. Brar, E. Chaffee, N. Howell, W. Leach, J. Lobatos, M. Luca, M. Maddineni, R. Mirji, C. Mitra, M. Strasser, S. Munig, Z. Patel, M. So, M. Sy, S. Weiss, S.P. Pfeifer. 2022. Comparative genomics of closely-related Gordonia terrae cluster DR bacteriophages. Viruses, 14(8): 1647.
- C.J. Versoza*, A.A. Howell*, T. Aftab, M. Blanco, A. Brar, E. Chaffee, N. Howell, W. Leach, J. Lobatos, M. Luca, M. Maddineni, R. Mirji, C. Mitra, M. Strasser, S. Munig, Z. Patel, M. So, M. Sy, S. Weiss, C.D. Herren, M. Smith Caldas, S.P. Pfeifer. 2022. Complete genome sequence of the Gordonia bacteriophage BiggityBass. Microbiol. Resour. Announc. 11(9): e00469-22.
- A.A. Howell*, C.J. Versoza*, G. Cerna, T. Johnston, S. Kakde, K. Karuku, M. Kowal, J. Monahan, J. Murray, T. Nguyen, A. Sanchez Carreon, E. Song, A. Streiff, B. Su, F. Youkhana, S. Munig, Z. Patel, M. So, M. Sy, S. Weiss, Y. Zhou, S.P. Pfeifer. 2022. Complete genome sequence of the cluster P mycobacteriophage Phegasus. Microbiol. Resour. Announc. 11(9): e00540-22.
- P. Johri, C.F. Aquadro, M. Beaumont, B. Charlesworth, L. Excoffier, A. Eyre-Walker, P. Keightley, M. Lynch, G. McVean, B.A. Payseur, S.P. Pfeifer, W. Stephan, J.D. Jensen. 2022. Recommendations for improving statistical inference in population genomics. PLoS Biology, 20(5): e3001669.
- S. Sabin, A.Y. Morales-Arce, S.P. Pfeifer, J.D. Jensen. 2022. The impact of frequently neglected model violations on bacterial recombination rate estimation: a case study in Mycobacterium canetti and Mycobacterium tuberculosis. G3 (Bethesda), 12(5): jkac055.
- C.J. Versoza and S.P. Pfeifer. 2022. Computational prediction of bacteriophage host ranges. Microorganisms, 10(1): 149.
- L.A. Bergeron, S. Besenbacher, T.N. Turner, C.J. Versoza, R.J. Wang, A.L. Price, E. Armstrong, M. Riera, J. Carlson, H. Chen, M.W. Hahn, K. Harris, A.S.L.N.M. Kleppe, E.H. López-Nandam, P. Moorjani, S.P. Pfeifer, G.P. Tiley, A.D. Yoder, G. Zhang and M.H. Schierup. 2022. The mutationathon highlights the importance of reaching standardization in estimates of pedigree-based germline mutation rates. eLife, 11: e73577.
- S.P. Pfeifer. 2021. Studying mutation rate evolution in primates – the effects of computational pipeline and parameter choices. GigaScience, 10(10): giab069.
- C.J. Versoza*, J.A. Rivera*, E.B. Rosenblum, C. Vital García, J. Jaime Zúñiga-Vega, D.K. Hews, S.P. Pfeifer. 2021. The recombination landscapes of spiny lizards (genus Sceloporus). G3 (Bethesda), 12(2): jkab402.
- A. Crane*, C.J. Versoza*, T. Hua, R. Kapoor, L. Lloyd, R. Mehta, J. Menolascino, A. Morais, S. Munig, Z. Patel, D. Sackett, B. Schmit, M. Sy, S.P. Pfeifer. 2021. Phylogenetic relationships and codon usage bias amongst cluster K mycobacteriophages. G3 (Bethesda), 11(11): jkab291.
- M. Milhaven, E. Hastings, D. Brister, L. Cevallos, S. Chilukuri, A. Diyya, A. Garg, R. Hernandez, D. Kelly, K. Lazo, J. Le, G. Maag, P.D. Marfatia, R. Mehta, A. Nejad, J. Porche, A. Queiroz, D. Sackett, P. Santos Molina, T. Slade, M. So, K. Thakur, A. Urquidez Negrete, S. Wackett, S. Weiss, L. McCarthy, K. Wheaton, A.D. Rudner, J.P. McCutcheon, S.P. Pfeifer. 2021. Complete genome sequence of the Microbacterium bacteriophage Erla. Microbiol. Resour. Announc., 10(3): e01354-20.
- S.P. Pfeifer. Spontaneous mutation rates. In The Molecular Evolutionary Clock. Theory and Practice. Springer Nature.
- A. Crane, J. Abaidoo, G. Beltran, D. Fry, C. Furey, N. Green, R. Johal, B. La Rosa, C. Lopez Jimenez, L. Luong, G. Maag, J. Porche, L. Reyes, A. Robinson, S. Sabbara, L. Soto Herrera, A. Urquidez Negrete, P. Wilson, K. Geiler-Samerotte, S.P. Pfeifer. 2020. The complete genome sequence of the Staphylococcus bacteriophage Metroid. G3 (Bethesda), 10(9): 2975-2979.
- S.P. Pfeifer. 2020. A fine-scale genetic map for vervet monkeys. Mol. Biol. Evol., 37(7): 1855-1865.
- M. Apata and S.P. Pfeifer. 2020. Recent population genomic insights in to the genetic basis of arsenic tolerance in humans: the difficulties of identifying positively selected loci in strongly bottlenecked populations. Heredity, 124(2): 253-262.
- R.B. Harris, K. Irwin, M.R. Jones, S. Laurent, R.D.H. Barrett, M.W. Nachman, J.M. Good, C.R. Linnen, J.D. Jensen, S.P. Pfeifer. 2020. The population genetics of crypsis in vertebrates: recent insights from mice, hares, and lizards. Heredity, 124(1): 1-14.
- R.D.H. Barrett*, S. Laurent*, R. Mallarino*, S.P. Pfeifer, C.C. Xu, M. Foll, K. Wakamatsu, J. Duke-Cohan, J.D. Jensen, H.E. Hoekstra. 2019. Linking genetic variation to survival in wild mice. Science, 363(6426): 499-504.
- L.A.P. Tran, S.P. Pfeifer. 2018. Germline mutation rates in Old World monkeys. eLS, John Wiley & Sons, Ltd: Chichester.
- S.P. Pfeifer. 2017. Direct estimate of the spontaneous germ line mutation rate in African green monkeys. Evolution, 71(12): 2858-2870.
- S.P. Pfeifer. 2017. The demographic and adaptive history of the African green monkey. Mol. Biol. Evol., 34(5): 1055-1065.
- S.P. Pfeifer. 2017. From next-generation resequencing reads to a high quality variant data set. Heredity, 118(2): 111-124.
Courses
2023 Fall
| Course Number | Course Title |
|---|---|
| BIO 492 | Honors Directed Study |
| BIO 493 | Honors Thesis |
| BIO 494 | Special Topics |
| BIO 495 | Undergraduate Research |
| MBB 495 | Undergraduate Research |
| BIO 498 | Pro-Seminar |
| BIO 498 | Pro-Seminar |
2023 Spring
| Course Number | Course Title |
|---|---|
| BIO 493 | Honors Thesis |
| BIO 494 | Special Topics |
| MBB 495 | Undergraduate Research |
| BIO 495 | Undergraduate Research |
| BIO 415 | Statistical Models for Biology |
| BIO 415 | Statistical Models for Biology |
| BIO 514 | Statistical Models for Biology |
| BIO 514 | Statistical Models for Biology |
2022 Fall
| Course Number | Course Title |
|---|---|
| BIO 492 | Honors Directed Study |
| BIO 493 | Honors Thesis |
| BIO 494 | Special Topics |
| BIO 495 | Undergraduate Research |
| MBB 495 | Undergraduate Research |
| BIO 498 | Pro-Seminar |
| BIO 498 | Pro-Seminar |
2022 Spring
| Course Number | Course Title |
|---|---|
| BIO 493 | Honors Thesis |
| BIO 494 | Special Topics |
| MBB 495 | Undergraduate Research |
| BIO 495 | Undergraduate Research |
| BIO 498 | Pro-Seminar |
| BIO 498 | Pro-Seminar |
2021 Fall
| Course Number | Course Title |
|---|---|
| BIO 492 | Honors Directed Study |
| BIO 495 | Undergraduate Research |
| MBB 495 | Undergraduate Research |
2021 Spring
| Course Number | Course Title |
|---|---|
| BIO 494 | Special Topics |
| MBB 495 | Undergraduate Research |
| BIO 495 | Undergraduate Research |
| BIO 498 | Pro-Seminar |
| BIO 498 | Pro-Seminar |
2020 Fall
| Course Number | Course Title |
|---|---|
| BIO 494 | Special Topics |
| BIO 495 | Undergraduate Research |
| MBB 495 | Undergraduate Research |
| BIO 498 | Pro-Seminar |
| BIO 498 | Pro-Seminar |
2020 Spring
| Course Number | Course Title |
|---|---|
| BIO 498 | Pro-Seminar |
| BIO 498 | Pro-Seminar |
2019 Fall
| Course Number | Course Title |
|---|---|
| BIO 498 | Pro-Seminar |
| BIO 498 | Pro-Seminar |
2019 Spring
| Course Number | Course Title |
|---|---|
| BIO 498 | Pro-Seminar |
| BIO 598 | Special Topics |
| EVO 598 | Special Topics |
2018 Fall
| Course Number | Course Title |
|---|---|
| BIO 494 | Special Topics |
| BIO 598 | Special Topics |
| EVO 598 | Special Topics |