Zachary Szpiech
Assistant Professor of Biology
Research Summary
Population and evolutionary genetics, with applications to medical genetics, anthropology, and conservation
Huck Graduate Students
Huck Affiliations
Links
Most Recent Publications
Genomic signatures of adaptation in native lizards exposed to human-introduced fire ants
Braulio A. Assis, Alexis P. Sullivan, Stephanie Marciniak, Christina M. Bergey, Vanessa Garcia, Zachary A. Szpiech, Tracy Langkilde, George H. Perry, 2025, Nature Communications
Differentiating mechanism from outcome for ancestry-assortative mating in admixed human populations
Dashiell J. Massey, Zachary A. Szpiech, Amy Goldberg, 2025, Genetics
Recently Delisted Songbird Harbors Extensive Genomic Evidence of Inbreeding, Potentially Complicating Future Recovery
Anna María Calderón, Andrew W. Wood, Zachary A. Szpiech, David P.L. Toews, 2024, Evolutionary Applications
Genomic Consequences of Isolation and Inbreeding in an Island Dingo Population
Ana V. Leon-Apodaca, Manoharan Kumar, Andres Del Castillo, Gabriel C. Conroy, Robert W. Lamont, Steven Ogbourne, Kylie M. Cairns, Liz Borburgh, Linda Behrendorff, Sankar Subramanian, Zachary A. Szpiech, 2024, Genome Biology and Evolution
The Maintenance of Deleterious Variation in Wild Chinese Rhesus Macaques
Camille Steux, Zachary A. Szpiech, 2024, Genome Biology and Evolution
The complete sequence and comparative analysis of ape sex chromosomes
Kateryna D. Makova, Brandon Pickett, R Harris, Gabrielle Hartley, Monika Cechova, Karol Pal, Sergey Nurk, DongAhn Yoo, Qiuhui Li, Prajna Hebbar, B McGrath, Francesca Antonacci, Margaux Aubel, Arjun Biddanda, Matthew Borchers, Erich Bornberg-Bauer, Gerard Bouffard, Shelise Brooks, Lucia Carbone, Laura Carrel, Andrew Carroll, Pi-Chuan Chang, Chen-Shan Chin, Daniel Cook, S Craig, Luciana de Gennaro, Mark Diekhans, Amalia Dutra, Gage Garcia, Patrick Grady, Richard Green, Diana Haddad, Pille Hallast, William Harvey, Glenn Hickey, David Hillis, Savannah Hoyt, Hyeonsoo Jeong, Kaivan Kamali, Sergei Pond, Troy LaPolice, Charles Lee, Alexandra Lewis, Yong-Hwee Loh, Patrick Masterson, Kelly McGarvey, Rajiv McCoy, P Medvedev, Karen Miga, Katherine Munson, Evgenia Pak, Benedict Paten, Brendan Pinto, Tamara Potapova, Arang Rhie, Joana Rocha, Fedor Ryabov, Oliver Ryder, Samuel Sacco, Kishwar Shafin, Valery Shepelev, Viviane Slon, Steven Solar, Jessica Storer, Peter Sudmant, Sweetalana, Sweetalana, Alex Sweeten, Michael Tassia, Françoise Thibaud-Nissen, Thibaud-Nissen, Fran\ccoise, Mario Ventura, Melissa Wilson, Alice Young, Huiqing Zeng, Xinru Zhang, Z Szpiech, Christian D. Huber, Jennifer Gerton, Soojin Yi, Michael Schatz, Ivan Alexandrov, Sergey Koren, Rachel J. O’Neill, Rachel O'Neill, Evan Eichler, Adam Phillippy, 2024, Nature on p. 410-411
Selscan 2.0: Scanning for sweeps in unphased data
Zachary A. Szpiech, 2024, Bioinformatics
Genomes of the extinct Bachman's warbler show high divergence and no evidence of admixture with other extant Vermivora warblers
Andrew W. Wood, Zachary A. Szpiech, Irby J. Lovette, Brian Tilston Smith, David Toews, 2023, Current Biology on p. 2823-2829.e4
A rarefaction approach for measuring population differences in rare and common variation
Daniel J. Cotter, Elyssa F. Hofgard, John Novembre, Zachary A. Szpiech, Noah A. Rosenberg, 2023, Genetics
A genetic and linguistic analysis of the admixture histories of the islands of Cabo Verde
Romain Laurent, Zachary A. Szpiech, Sergio S. da Costa, Valentin Thouzeau, Cesar A. Fortes-Lima, Françoise Dessarps-Freichey, Laure Lémée, José Utgé, Noah A. Rosenberg, Marlyse Baptista, Paul Verdu, 2023, eLife
Most-Cited Papers
Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program
Daniel Taliun, Daniel N. Harris, Michael D. Kessler, Jedidiah Carlson, Zachary A. Szpiech, Raul Torres, Sarah A.Gagliano Taliun, André Corvelo, Stephanie M. Gogarten, Hyun Min Kang, Achilleas N. Pitsillides, Jonathon LeFaive, Seung been Lee, Xiaowen Tian, Brian L. Browning, Sayantan Das, Anne Katrin Emde, Wayne E. Clarke, Douglas P. Loesch, Amol C. Shetty, Thomas W. Blackwell, Albert V. Smith, Quenna Wong, Xiaoming Liu, Matthew P. Conomos, Dean M. Bobo, François Aguet, Christine Albert, Alvaro Alonso, Kristin G. Ardlie, Dan E. Arking, Stella Aslibekyan, Paul L. Auer, John Barnard, R. Graham Barr, Lucas Barwick, Lewis C. Becker, Rebecca L. Beer, Emelia J. Benjamin, Lawrence F. Bielak, John Blangero, Michael Boehnke, Donald W. Bowden, Jennifer A. Brody, Esteban G. Burchard, Brian E. Cade, James F. Casella, Brandon Chalazan, Daniel I. Chasman, Yii Der Ida Chen, 2021, Nature on p. 290-299
Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens
Yohann Nédélec, Joaquín Sanz, Golshid Baharian, Zachary A. Szpiech, Alain Pacis, Anne Dumaine, Jean Christophe Grenier, Andrew Freiman, Aaron J. Sams, Steven Hebert, Ariane Pagé Sabourin, Francesca Luca, Ran Blekhman, Ryan D. Hernandez, Roger Pique-Regi, Jenny Tung, Vania Yotova, Luis B. Barreiro, 2016, Cell on p. 657-669.e21
Whole-Genome sequencing of pharmacogenetic drug response in racially diverse children with asthma
Angel C.Y. Mak, Marquitta J. White, Walter L. Eckalbar, Zachary A. Szpiech, Sam S. Oh, Maria Pino-Yanes, Donglei Hu, Paǵe Goddard, Scott Huntsman, Joshua Galanter, Ann Chen Wu, Blanca E. Himes, Soren Germer, Julia M. Vogel, Karen L. Bunting, Celeste Eng, Sandra Salazar, Kevin L. Keys, Jennifer Liberto, Thomas J. Nuckton, Thomas A. Nguyen, Dara G. Torgerson, Pui Yan Kwok, Albert M. Levin, Juan C. Celedón, Erick Forno, Hakon Hakonarson, Patrick M. Sleiman, Amber Dahlin, Kelan G. Tantisira, Scott T. Weiss, Denise Serebrisky, Emerita Brigino-Buenaventura, Harold J. Farber, Kelley Meade, Michael A. Lenoir, Pedro C. Avila, Saunak Sen, Shannon M. Thyne, William Rodriguez-Cintron, Cheryl A. Winkler, Andŕes Moreno-Estrada, Karla Sandoval, Jose R. Rodriguez-Santana, Rajesh Kumar, L. Keoki Williams, Nadav Ahituv, Elad Ziv, Max A. Seibold, Robert B. Darnell, Noah Zaitlen, Ryan D. Hernandez, Esteban G. Burchard, 2018, American Review of Respiratory Disease on p. 1552-1564
Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations
Michelle Daya, Nicholas Rafaels, Tonya M. Brunetti, Sameer Chavan, Albert M. Levin, Aniket Shetty, Christopher R. Gignoux, Meher Preethi Boorgula, Genevieve Wojcik, Monica Campbell, Candelaria Vergara, Dara G. Torgerson, Victor E. Ortega, Ayo Doumatey, Henry Richard Johnston, Nathalie Acevedo, Maria Ilma Araujo, Pedro C. Avila, Gillian Belbin, Eugene Bleecker, Carlos Bustamante, Luis Caraballo, Alvaro Cruz, Georgia M. Dunston, Celeste Eng, Mezbah U. Faruque, Trevor S. Ferguson, Camila Figueiredo, Jean G. Ford, Weiniu Gan, Pierre Antoine Gourraud, Nadia N. Hansel, Ryan D. Hernandez, Edwin Francisco Herrera-Paz, Silvia Jiménez, Eimear E. Kenny, Jennifer Knight-Madden, Rajesh Kumar, Leslie A. Lange, Ethan M. Lange, Antoine Lizee, Pissamai Maul, Trevor Maul, Alvaro Mayorga, Deborah Meyers, Dan L. Nicolae, Timothy D. O’Connor, Ricardo Riccio Oliveira, Christopher O. Olopade, Zachary A. Szpiech, 2019, Nature Communications
Cancer-associated arginine-to-histidine mutations confer a gain in pH sensing to mutant proteins
Katharine A. White, Diego Garrido Ruiz, Zachary A. Szpiech, Nicolas B. Strauli, Ryan D. Hernandez, Matthew P. Jacobson, Diane L. Barber, 2017, Science's STKE : signal transduction knowledge environment
Human demographic history has amplified the effects of background selection across the genome
Raul Torres, Zachary A. Szpiech, Ryan D. Hernandez, 2018, PLoS Genetics
Application of a novel haplotype-based scan for local adaptation to study high-altitude adaptation in rhesus macaques
Zachary A. Szpiech, Taylor E. Novak, Nick P. Bailey, Laurie S. Stevison, 2021, Evolution Letters on p. 408-421
The complete sequence and comparative analysis of ape sex chromosomes
Kateryna D. Makova, Brandon Pickett, R Harris, Gabrielle Hartley, Monika Cechova, Karol Pal, Sergey Nurk, DongAhn Yoo, Qiuhui Li, Prajna Hebbar, B McGrath, Francesca Antonacci, Margaux Aubel, Arjun Biddanda, Matthew Borchers, Erich Bornberg-Bauer, Gerard Bouffard, Shelise Brooks, Lucia Carbone, Laura Carrel, Andrew Carroll, Pi-Chuan Chang, Chen-Shan Chin, Daniel Cook, S Craig, Luciana de Gennaro, Mark Diekhans, Amalia Dutra, Gage Garcia, Patrick Grady, Richard Green, Diana Haddad, Pille Hallast, William Harvey, Glenn Hickey, David Hillis, Savannah Hoyt, Hyeonsoo Jeong, Kaivan Kamali, Sergei Pond, Troy LaPolice, Charles Lee, Alexandra Lewis, Yong-Hwee Loh, Patrick Masterson, Kelly McGarvey, Rajiv McCoy, P Medvedev, Karen Miga, Katherine Munson, Evgenia Pak, Benedict Paten, Brendan Pinto, Tamara Potapova, Arang Rhie, Joana Rocha, Fedor Ryabov, Oliver Ryder, Samuel Sacco, Kishwar Shafin, Valery Shepelev, Viviane Slon, Steven Solar, Jessica Storer, Peter Sudmant, Sweetalana, Sweetalana, Alex Sweeten, Michael Tassia, Françoise Thibaud-Nissen, Thibaud-Nissen, Fran\ccoise, Mario Ventura, Melissa Wilson, Alice Young, Huiqing Zeng, Xinru Zhang, Z Szpiech, Christian D. Huber, Jennifer Gerton, Soojin Yi, Michael Schatz, Ivan Alexandrov, Sergey Koren, Rachel J. O’Neill, Rachel O'Neill, Evan Eichler, Adam Phillippy, 2024, Nature on p. 410-411
Ancestry-Dependent Enrichment of Deleterious Homozygotes in Runs of Homozygosity
Zachary A. Szpiech, Angel C.Y. Mak, Marquitta J. White, Donglei Hu, Celeste Eng, Esteban G. Burchard, Ryan D. Hernandez, 2019, American Journal of Human Genetics on p. 747-762
Prominent features of the amino acid mutation landscape in cancer
Zachary A. Szpiech, Nicolas B. Strauli, Katharine A. White, Diego Garrido Ruiz, Matthew P. Jacobson, Diane L. Barber, Ryan D. Hernandez, 2017, PLoS One
News Articles Featuring Zachary Szpiech
Apr 09, 2025
Complete genome sequences of six ape species unveiled
Differences among the DNA of seven ape species — including humans — are greater than originally thought, according to an international team led by researchers at Penn State, the National Human Genome Research Institute, and the University of Washington.
Full Article
Apr 09, 2025
Complete genome sequences of six ape species unveiled
Previously inaccessible regions reveal novel insights that may advance understanding of evolution and conservation genetics for endangered apes as well as human health.
Full Article
Dec 11, 2024
Once-endangered Kirtland’s warblers show extensive signs of inbreeding in genome
The genome of a once-endangered songbird shows extensive signs of inbreeding, according to a new study by Penn State researchers.
Full Article
May 29, 2024
Complete X and Y chromosome sequences of living great ape species determined
Newly generated, complete “end-to-end” reference genomes for the sex chromosomes of five great ape species and one lesser ape species — produced by an international collaborative team led by researchers at Penn State, the National Human Genome Research Institute and the University of Washington — highlight extremely rapid changes on the male-specific Y chromosome among ape species.
Full Article
Jun 23, 2023
Extinct warbler’s genome sequenced from museum specimens
The Bachman’s warbler, a songbird that was last seen in North America nearly 40 years ago, was a distinct species and not a hybrid of its two living sister species, according a new study in which the full genomes of seven museum specimens of the bird were sequenced.
Full Article