Zachary Szpiech, PhD

InstitutionUniversity of California San Francisco
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    1. Torres R, Szpiech Z, Hernandez RD. Human demographic history has amplified the effects of background selection across the genome. PLoS Genet. 2018 Jun 18; 14(6):e1007387. PMID: 29912945.
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    2. Pemberton TJ, Szpiech Z. Relationship between Deleterious Variation, Genomic Autozygosity, and Disease Risk: Insights from The 1000 Genomes Project. Am J Hum Genet. 2018 Apr 05; 102(4):658-675. PMID: 29551419.
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    3. Mak AC, White MJ, Eckalbar WL, Szpiech Z, Oh SS, Pino-Yanes M, Hu D, Goddard P, Huntsman S, Galanter J, Wu AC, Himes BE, Germer S, Vogel JM, Bunting KL, Eng C, Salazar S, Keys KL, Liberto J, Nuckton TJ, Nguyen TA, Torgerson DG, Kwok PY, Levin AM, Celedón JC, Forno E, Hakonarson H, Sleiman PM, Dahlin A, Tantisira KG, Weiss ST, Serebrisky D, Brigino-Buenaventura E, Farber HJ, Meade K, Lenoir MA, Avila PC, Sen S, Thyne SM, Rodriguez-Cintron W, Winkler CA, Moreno-Estrada A, Sandoval K, Rodriguez-Santana JR, Kumar R, Williams LK, Ahituv N, Ziv E, Seibold MA, Darnell RB, Zaitlen N, Hernandez RD, Burchard EG. Whole Genome Sequencing of Pharmacogenetic Drug Response in Racially Diverse Children with Asthma. Am J Respir Crit Care Med. 2018 Mar 06. PMID: 29509491.
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    4. Blant A, Kwong M, Szpiech Z, Pemberton TJ. Weighted likelihood inference of genomic autozygosity patterns in dense genotype data. BMC Genomics. 2017 Dec 01; 18(1):928. PMID: 29191164.
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    5. White KA, Ruiz DG, Szpiech Z, Strauli NB, Hernandez RD, Jacobson MP, Barber DL. Cancer-associated arginine-to-histidine mutations confer a gain in pH sensing to mutant proteins. Sci Signal. 2017 Sep 05; 10(495). PMID: 28874603.
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    6. Szpiech Z, Strauli NB, White KA, Ruiz DG, Jacobson MP, Barber DL, Hernandez RD. Prominent features of the amino acid mutation landscape in cancer. PLoS One. 2017; 12(8):e0183273. PMID: 28837668.
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    7. Szpiech Z, Blant A, Pemberton TJ. GARLIC: Genomic Autozygosity Regions Likelihood-based Inference and Classification. Bioinformatics. 2017 Jul 01; 33(13):2059-2062. PMID: 28205676.
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    8. Shringarpure SS, Mathias RA, Hernandez RD, O'Connor TD, Szpiech Z, Torres R, De La Vega FM, Bustamante CD, Barnes KC, Taub MA. Using genotype array data to compare multi- and single-sample variant calls and improve variant call sets from deep coverage whole-genome sequencing data. Bioinformatics. 2017 Apr 15; 33(8):1147-1153. PMID: 28035032.
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    9. Nédélec Y, Sanz J, Baharian G, Szpiech Z, Pacis A, Dumaine A, Grenier JC, Freiman A, Sams AJ, Hebert S, Pagé Sabourin A, Luca F, Blekhman R, Hernandez RD, Pique-Regi R, Tung J, Yotova V, Barreiro LB. Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens. Cell. 2016 Oct 20; 167(3):657-669.e21. PMID: 27768889.
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    10. Szpiech Z, Hernandez RD. selscan: an efficient multithreaded program to perform EHH-based scans for positive selection. Mol Biol Evol. 2014 Oct; 31(10):2824-7. PMID: 25015648; PMCID: PMC4166924.
    11. Ryan CJ, Cimermancic P, Szpiech Z, Sali A, Hernandez RD, Krogan NJ. High-resolution network biology: connecting sequence with function. Nat Rev Genet. 2013 Dec; 14(12):865-79. PMID: 24197012; PMCID: PMC4023809.
    12. Szpiech Z, Xu J, Pemberton TJ, Peng W, Zöllner S, Rosenberg NA, Li JZ. Long runs of homozygosity are enriched for deleterious variation. Am J Hum Genet. 2013 Jul 11; 93(1):90-102. PMID: 23746547; PMCID: PMC3710769.
    13. Szpiech Z, Rosenberg NA. On the size distribution of private microsatellite alleles. Theor Popul Biol. 2011 Sep; 80(2):100-13. PMID: 21514313; PMCID: PMC3143247.
    14. Rosenberg NA, Huang L, Jewett EM, Szpiech Z, Jankovic I, Boehnke M. Genome-wide association studies in diverse populations. Nat Rev Genet. 2010 May; 11(5):356-66. PMID: 20395969; PMCID: PMC3079573.
    15. Wang C, Szpiech Z, Degnan JH, Jakobsson M, Pemberton TJ, Hardy JA, Singleton AB, Rosenberg NA. Comparing spatial maps of human population-genetic variation using Procrustes analysis. Stat Appl Genet Mol Biol. 2010; 9:Article 13. PMID: 20196748; PMCID: PMC2861313.
    16. Szpiech Z, Jakobsson M, Rosenberg NA. ADZE: a rarefaction approach for counting alleles private to combinations of populations. Bioinformatics. 2008 Nov 01; 24(21):2498-504. PMID: 18779233; PMCID: PMC2732282.
    17. Jakobsson M, Scholz SW, Scheet P, Gibbs JR, VanLiere JM, Fung HC, Szpiech Z, Degnan JH, Wang K, Guerreiro R, Bras JM, Schymick JC, Hernandez DG, Traynor BJ, Simon-Sanchez J, Matarin M, Britton A, van de Leemput J, Rafferty I, Bucan M, Cann HM, Hardy JA, Rosenberg NA, Singleton AB. Genotype, haplotype and copy-number variation in worldwide human populations. Nature. 2008 Feb 21; 451(7181):998-1003. PMID: 18288195.
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