Szpiech Lab

Population Genetics | Evolutionary Genomics

Research Papers [Google Scholar]

Preprints

  1. KD Makova*†, BD Pickett*, RS Harris*, GA Hartley*, M Cechova*, K Pal, S Nurk, D-A Yoo, Q Li, P Hebbar, BC McGrath, F Antonacci, M Aubel, A Biddanda, M Borchers, E Bomberg, GG Bouffard, SY Brooks, L Carbone, L Carrel, A Carroll, P-C Chang, C-S Chin, DE Cook, SJC Craig, L de Gennaro, M Diekhans, A Dutra, GH Garcia, PGS Grady, RE Green, D Haddad, P Hallast, WT Harvey, G Hickey, DA Hillis, SJ Hoyt, H Jeong, K Kamali, SLK Pond, TM LaPolice, C Lee, AP Lewis, Y-HE Loh, P Masterson, RC McCoy, P Medvedev, KH Miga, KM Munson, E Pak, B Paten, BJ Pinto, T Potapova, A Rhie, JL Rocha, F Ryabov, OA Ryder, S Sacco, K Shafin, VA Shepelev, V Slon, SJ Solar, JM Storer, PH Sudmant, Sweetalana, A Sweeten, MG Tassia, F Thibaud-Nissen, M Ventura, MA Wilson, AC Young, H Zeng, X Zhang, ZA Szpiech, CD Huber, JL Gerton, SV Yi, MC Schatz, IA Alexandrov, S Koren, RJ O’Neill, E Eichler†, AM Phillippy†. (2023) The complete sequence and comparative analysis of ape sex chromosomes. bioRxiv doi: 10.1101/2023.11.30.569198.[preprint]

  2. C Steux and ZA Szpiech†. (2023) The maintenance of deleterious variation in wild Chinese rhesus macaques. bioRxiv doi: 10.1101/2023.10.04.560901.[preprint]

  3. BA Assis†*, AP Sullivan*, S Marciniak, CM Bergey, V Garcia, ZA Szpiech, T Langkilde†, GH Perry†. (2023) Genomic signatures of adaptation in native lizards exposed to human-introduced fire ants. bioRxiv doi: 10.1101/2023.09.24.559217.[preprint]

  4. AV Leon-Apodaca, M Kumar, A del Castillo, G Conroy, RW Lamont, S Ogbourne, KM Cairns, L Borburgh, L Behrendorff, S Subramanian†, ZA Szpiech†. (2023) Genomic consequences of isolation and inbreeding in an island dingo population. bioRxiv doi: 10.1101/2023.09.15.557950. [preprint]

Published

  1. ZA Szpiech†. (2024) selscan 2.0: scanning for sweeps in unphased data. Bioinformatics 40: btae006. [link][pdf][supplement][software]

  2. AW Wood*, ZA Szpiech, I Lovette, BT Smith, DPL Toews*†. (2023) Genomes of the extinct Bachman’s Warbler show high divergence and no evidence of admixture with other extant Vermivora Warblers. Current Biology 33: 2823-2829. [link][pdf][news]

  3. DJ Cotter†, EF Hofgard, J Novembre, ZA Szpiech, NA Rosenberg. (2023) A rarefaction approach for measuring popuation differences in rare and common variation. Genetics 224: iyad070. [link][pdf]

  4. R Laurent, ZA Szpiech, SS da Costa, V Thourzeau, CA Fortes-Lima, F Dessarps-Freichey, L Lémée, J Utgé, NA Rosenberg, M Baptista, P Verdu†. (2023) A genetic and linguistic analysis of the admixture histories of the islands of Cabo Verde. eLife 12: e79827. [link][pdf][news (fr)][news (fr)][news (fr)]

  5. LS Stevison†, NP Bailey, ZA Szpiech, TE Novak, DJ Melnick, BJ Evans, JD Wall. (2022) Evolution of genes involved in the unusual genitals of the bear macaque, Macaca arctoides. Ecology and Evolution 12: e8897. [link][pdf]

     preLights Recommended 
  6. M DeGiorgio*† and ZA Szpiech*†. (2022) A spatially aware likelihood test to detect sweeps from haplotype distributions. PLoS Genetics 18: e1010134. [link][pdf]

  7. ZA Szpiech†, TE Novak*, NP Bailey*, LS Stevison†. (2021) Application of a novel haplotype-based scan for local adaptation to study high-altitude adaptation in rhesus macaques. Evolution Letters 5: 408-421. [link][pdf]

  8. D Taliun*, DN Harris*, MD Kessler*, J Carlson*, ZA Szpiech*, R Torres*, SAG Taliun*, A Corvelo*, 169 co-authors, Trans-Omics for Precision Medicine (TOPMed) Program, TOPMed Population Genetics Working Group, GJ Papanicolaou, DA Nickerson, SR Browning, MC Zody, S Zöllner, JG Wilson, LA Cupples, CC Laurie, CE Jaquish, RD Hernandez, TD O'Connor, GR Abecasis†. (2021) Sequencing of 53,831 diverse human genomes from the NHLBI TOPMed Program. Nature 590: 290-299. [link][pdf]

  9. ZA Szpiech†, ACY Mak, MJ White, D Hu, C Eng, EG Burchard, RD Hernandez†. (2019) Ancestry-dependent accumulation of deleterious homozygotes in runs of homozygosity. American Journal of Human Genetics 105: 747-762. [link][pdf][code]

  10. R Torres, ZA Szpiech, RD Hernandez†. (2018) Human demographic history has amplified the effects of background selection across the genome. PLoS Genetics 14: e1007387. [link][pdf]

  11. TJ Pemberton† and ZA Szpiech. (2018) Relationship between deleterious variation, genomic autozygosity, and disease risk: insights from the 1000 Genomes Project. American Journal of Human Genetics 102: 658-675. [link][pdf]

     Faculty Opinions Recommended 
  12. ACY Mak*†, MJ White*, WL Eckalbar*, ZA Szpiech*, SS Oh, M Pino-Yanes, D Hu, S Huntsman, J Galanter, DG Torgerson, AC Wu, BE Himes, S Germer, JM Vogel, KL Bunting, C Eng, S Salazar, KL Keys, TA Nguyen, P-Y Kwok, AM Levin, JC Celedon, E Forno, H Hakonarson, PM Sleiman, A Dahlin, KG Tantisira, ST Weiss, D Serebrisky, E Brigino-Buenaventura, HJ Farber, K Meade, MA Lenoir, PC Avila, S Sen, SM Thyne, W Rodriguez-Cintron, CA Winkler, A Moreno-Estrada, K Sandoval, JR Rodriguez-Santana, R Kumar, LK Williams, N Ahituv, E Ziv, MA Seibold, RB Darnell, N Zaitlen, RD Hernandez, EG Burchard, The Trans-Omics for Precision Medicine Whole Genome Sequencing Program. (2018) Whole genome sequencing of pharmacogenetic drug response in racially diverse children with asthma. American Journal of Respiratory and Critital Care Medicine 197: 1552-1564. [link][pdf][editorial]

  13. A Blant*, M Kwong*, ZA Szpiech, TJ Pemberton†. (2017) Weighted likelihood inference of genomic autozygosity patterns in dense genotype data. BMC Genomics 18: 928. [link][pdf][data]

  14. KA White, DG Ruiz, ZA Szpiech, NB Strauli, MP Jacobson, RD Hernandez, DL Barber†. (2017) Cancer-associated arginine-to-histidine mutations confer a gain in pH sensing to mutant proteins. Science Signaling 10: eaam9931. [link][pdf]

  15. ZA Szpiech†, NB Strauli, KA White, DG Ruiz, MP Jacobson, DL Barber, RD Hernandez†. (2017) Prominent features of the amino acid mutation landscape in cancer. PLoS ONE 12: e0183273. [link][pdf]

  16. ZA Szpiech†, A Blant, TJ Pemberton. (2017) GARLIC: Genomic Autozygosity Regions Likelihood-based Inference and Classification. Bioinformatics 33: 2059-2062. [link][pdf][software]

  17. SS Shringarpure†, RA Mathias, RD Hernandez, TD O'Conner, ZA Szpiech, R Torres, FM De La Vega, CD Bustamante, KC Barnes, MA Taub†, on behalf of the CAAPA consortium. (2017) Comparing multi- and single-sample variant calls to improve variant call sets from deep coverage whole-genome sequencing data. Bioinformatics 33: 1147-1153. [link][pdf]

     Faculty Opinions Recommended 
  18. Y Nédélec*, J Sanz-Remon*, G Baharian*, ZA Szpiech, A Pacis, A Dumaine, J-C Grenier, A Freiman, AJ Sams, S Herbet, AP Sabourin, F Luca, R Blekhman, RD Hernandez, R Pique-Regi, J Tung, V Yotova, LB Barreiro†. (2016) Genetic ancestry and natural selection drive population differences in immune responses to pathogens in humans. Cell 167: 657-669. [link][pdf]

  19. ZA Szpiech and RD Hernandez. (2016) Selective Sweeps. In: Kliman, RM (ed.), Encyclopedia of Evolutionary Biology. vol 4, pp. 23-32. Oxford: Academic Press.

  20. ZA Szpiech† and RD Hernandez. (2014) selscan: an efficient multi-threaded program to perform EHH-based scans for positive selection. Molecular Biology and Evolution 31: 2824-2827. [link][pdf][git]

  21. AM Thompson, MC Maher, LH Uricchio, ZA Szpiech and RD Hernandez†. (2014) Comparing evolutionary rates using an exact test for 2 x 2 tables with continuous cell entries. arXiv 1404.2992 [q-bio.PE]. [preprint]

  22. CJ Ryan, P Cimermanc̆ic̆, ZA Szpiech, A Sali, RD Hernandez, NJ Krogan†. (2013) High-resolution network biology: connecting sequence with function. Nature Reviews Genetics 14: 865-879. [link][pdf]

     AJHG Featured Article    Faculty Opinions Recommended 
  23. ZA Szpiech†, J Xu, TJ Pemberton, W Peng, S Zöllner, NA Rosenberg*, JZ Li.* (2013) Long runs of homozygosity are enriched for deleterious variation. American Journal of Human Genetics 93: 90-102. [link][pdf][supplement][data]

  24. ZA Szpiech† and NA Rosenberg. (2011) On the size distribution of private microsatellite alleles. Theoretical Population Biology 80: 100-113. [link][pdf]

  25. NA Rosenberg†, L Huang*, EM Jewett*, ZA Szpiech*, I Jankovic*, M Boehnke. (2010) Genome-wide association studies in diverse populations. Nature Reviews Genetics 11: 356-366. [link][pdf]

  26. C Wang†, ZA Szpiech, JH Degnan, M Jakobsson, TJ Pemberton, JA Hardy, AB Singleton, NA Rosenberg. (2009) Comparing spatial maps of human population-genetic variation using Procrustes analysis. Statistical Applications in Genetics and Molecular Biology 9: 13. [link][pdf]

  27. ZA Szpiech†, M Jakobsson, NA Rosenberg. (2008) ADZE: a rarefaction approach for counting alleles private to combinations of populations. Bioinformatics 24: 2498-2504. [link][pdf][git]

     Faculty Opinions Recommended 
  28. M Jakobsson*, SW Scholz*, P Scheet*, JR Gibbs, JM VanLiere, H-C Fung, ZA Szpiech, JH Degnan, K Wang, R Guerreiro, JM Bras, JC Schymick, DG Hernandez, BJ Traynor, J Simon-Sanchez, M Matarin, A Britton, J van de Leemput, I Rafferty, M Bucan, HM Cann, JA Hardy, NA Rosenberg†, AB Singleton†. (2008) Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451: 998-1003. [link][pdf]

    (* indicates equal contributions)