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Items: 17

1.

Human demographic history has amplified the effects of background selection across the genome.

Torres R, Szpiech ZA, Hernandez RD.

PLoS Genet. 2018 Jun 18;14(6):e1007387. doi: 10.1371/journal.pgen.1007387. [Epub ahead of print]

2.

Relationship between Deleterious Variation, Genomic Autozygosity, and Disease Risk: Insights from The 1000 Genomes Project.

Pemberton TJ, Szpiech ZA.

Am J Hum Genet. 2018 Apr 5;102(4):658-675. doi: 10.1016/j.ajhg.2018.02.013. Epub 2018 Mar 15.

PMID:
29551419
3.

Whole-Genome Sequencing of Pharmacogenetic Drug Response in Racially Diverse Children with Asthma.

Mak ACY, White MJ, Eckalbar WL, Szpiech ZA, 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; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium.

Am J Respir Crit Care Med. 2018 Jun 15;197(12):1552-1564. doi: 10.1164/rccm.201712-2529OC.

PMID:
29509491
4.

Weighted likelihood inference of genomic autozygosity patterns in dense genotype data.

Blant A, Kwong M, Szpiech ZA, Pemberton TJ.

BMC Genomics. 2017 Dec 1;18(1):928. doi: 10.1186/s12864-017-4312-3.

5.

Cancer-associated arginine-to-histidine mutations confer a gain in pH sensing to mutant proteins.

White KA, Ruiz DG, Szpiech ZA, Strauli NB, Hernandez RD, Jacobson MP, Barber DL.

Sci Signal. 2017 Sep 5;10(495). pii: eaam9931. doi: 10.1126/scisignal.aam9931.

6.

Prominent features of the amino acid mutation landscape in cancer.

Szpiech ZA, Strauli NB, White KA, Ruiz DG, Jacobson MP, Barber DL, Hernandez RD.

PLoS One. 2017 Aug 24;12(8):e0183273. doi: 10.1371/journal.pone.0183273. eCollection 2017.

7.

GARLIC: Genomic Autozygosity Regions Likelihood-based Inference and Classification.

Szpiech ZA, Blant A, Pemberton TJ.

Bioinformatics. 2017 Jul 1;33(13):2059-2062. doi: 10.1093/bioinformatics/btx102.

8.

Using genotype array data to compare multi- and single-sample variant calls and improve variant call sets from deep coverage whole-genome sequencing data.

Shringarpure SS, Mathias RA, Hernandez RD, O'Connor TD, Szpiech ZA, Torres R, De La Vega FM, Bustamante CD, Barnes KC, Taub MA; CAAPA Consortium.

Bioinformatics. 2017 Apr 15;33(8):1147-1153. doi: 10.1093/bioinformatics/btw786.

9.

Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens.

Nédélec Y, Sanz J, Baharian G, Szpiech ZA, 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.

Cell. 2016 Oct 20;167(3):657-669.e21. doi: 10.1016/j.cell.2016.09.025.

10.

selscan: an efficient multithreaded program to perform EHH-based scans for positive selection.

Szpiech ZA, Hernandez RD.

Mol Biol Evol. 2014 Oct;31(10):2824-7. doi: 10.1093/molbev/msu211. Epub 2014 Jul 10.

11.

High-resolution network biology: connecting sequence with function.

Ryan CJ, Cimermančič P, Szpiech ZA, Sali A, Hernandez RD, Krogan NJ.

Nat Rev Genet. 2013 Dec;14(12):865-79. doi: 10.1038/nrg3574. Epub 2013 Nov 7. Review.

12.

Long runs of homozygosity are enriched for deleterious variation.

Szpiech ZA, Xu J, Pemberton TJ, Peng W, Zöllner S, Rosenberg NA, Li JZ.

Am J Hum Genet. 2013 Jul 11;93(1):90-102. doi: 10.1016/j.ajhg.2013.05.003. Epub 2013 Jun 6.

13.

On the size distribution of private microsatellite alleles.

Szpiech ZA, Rosenberg NA.

Theor Popul Biol. 2011 Sep;80(2):100-13. doi: 10.1016/j.tpb.2011.03.006. Epub 2011 Apr 15.

14.

Genome-wide association studies in diverse populations.

Rosenberg NA, Huang L, Jewett EM, Szpiech ZA, Jankovic I, Boehnke M.

Nat Rev Genet. 2010 May;11(5):356-66. doi: 10.1038/nrg2760. Review.

15.

Comparing spatial maps of human population-genetic variation using Procrustes analysis.

Wang C, Szpiech ZA, Degnan JH, Jakobsson M, Pemberton TJ, Hardy JA, Singleton AB, Rosenberg NA.

Stat Appl Genet Mol Biol. 2010;9:Article 13. doi: 10.2202/1544-6115.1493. Epub 2010 Jan 27.

16.

ADZE: a rarefaction approach for counting alleles private to combinations of populations.

Szpiech ZA, Jakobsson M, Rosenberg NA.

Bioinformatics. 2008 Nov 1;24(21):2498-504. doi: 10.1093/bioinformatics/btn478. Epub 2008 Sep 8.

17.

Genotype, haplotype and copy-number variation in worldwide human populations.

Jakobsson M, Scholz SW, Scheet P, Gibbs JR, VanLiere JM, Fung HC, Szpiech ZA, 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.

Nature. 2008 Feb 21;451(7181):998-1003. doi: 10.1038/nature06742.

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