Publications and Preprints

    R Torres, ZA Szpiech, RD Hernandez. (2017) Human demographic history has amplified the effects of background selection across the genome. bioRxiv doi: https://doi.org/10.1101/181859. [preprint]

    ACY Mak*, MJ White*, ZA Szpiech*, WL Eckalbar*, 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. (2017) Whole genome sequencing of pharmacogenetic drug response in racial and ethnically diverse children with asthma. bioRxiv doi: https://doi.org/10.1101/128116. [preprint]

    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]

    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]

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

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

    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]

     F1000 Recommended Article 
    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]

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

    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]

    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]

    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    F1000 Recommended Article 
    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]

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

    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]

    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]

    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][software]

     F1000 Recommended Article 
    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)