Publications and Preprints

    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]

    R Torres, ZA Szpiech, RD Hernandez. (2018) Human demographic history has amplified the effects of background selection across the genome. bioRxiv doi: 10.1101/181859. [preprint]

    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 In Press. doi: 10.1164/rccm.201712-2529OC. [link]

    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)