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Items: 27

1.

Targeted deep sequencing of the PEAR1 locus for platelet aggregation in European and African American families.

Keramati AR, Yanek LR, Iyer K, Taub MA, Ruczinski I, Becker DM, Becker LC, Faraday N, Mathias RA.

Platelets. 2018 Mar 19:1-7. doi: 10.1080/09537104.2018.1447659. [Epub ahead of print]

PMID:
29553866
2.

Analysis of sequence data to identify potential risk variants for oral clefts in multiplex families.

Holzinger ER, Li Q, Parker MM, Hetmanski JB, Marazita ML, Mangold E, Ludwig KU, Taub MA, Begum F, Murray JC, Albacha-Hejazi H, Alqosayer K, Al-Souki G, Albasha Hejazi A, Scott AF, Beaty TH, Bailey-Wilson JE.

Mol Genet Genomic Med. 2017 Aug 9;5(5):570-579. doi: 10.1002/mgg3.320. eCollection 2017 Sep.

3.

Identifying Genetic Sources of Phenotypic Heterogeneity in Orofacial Clefts by Targeted Sequencing.

Carlson JC, Taub MA, Feingold E, Beaty TH, Murray JC, Marazita ML, Leslie EJ.

Birth Defects Res. 2017 Jul 17;109(13):1030-1038. doi: 10.1002/bdr2.23605.

PMID:
28762674
4.

Reproducible RNA-seq analysis using recount2.

Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD, Jaffe AE, Langmead B, Leek JT.

Nat Biotechnol. 2017 Apr 11;35(4):319-321. doi: 10.1038/nbt.3838. No abstract available.

PMID:
28398307
5.

Integrity of Induced Pluripotent Stem Cell (iPSC) Derived Megakaryocytes as Assessed by Genetic and Transcriptomic Analysis.

Kammers K, Taub MA, Ruczinski I, Martin J, Yanek LR, Frazee A, Gao Y, Hoyle D, Faraday N, Becker DM, Cheng L, Wang ZZ, Leek JT, Becker LC, Mathias RA.

PLoS One. 2017 Jan 20;12(1):e0167794. doi: 10.1371/journal.pone.0167794. eCollection 2017.

6.

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.

7.

Evidence for SNP-SNP interaction identified through targeted sequencing of cleft case-parent trios.

Xiao Y, Taub MA, Ruczinski I, Begum F, Hetmanski JB, Schwender H, Leslie EJ, Koboldt DC, Murray JC, Marazita ML, Beaty TH.

Genet Epidemiol. 2017 Apr;41(3):244-250. doi: 10.1002/gepi.22023. Epub 2016 Dec 26.

8.

High-specificity bioinformatics framework for epigenomic profiling of discordant twins reveals specific and shared markers for ACPA and ACPA-positive rheumatoid arthritis.

Gomez-Cabrero D, Almgren M, Sjöholm LK, Hensvold AH, Ringh MV, Tryggvadottir R, Kere J, Scheynius A, Acevedo N, Reinius L, Taub MA, Montano C, Aryee MJ, Feinberg JI, Feinberg AP, Tegnér J, Klareskog L, Catrina AI, Ekström TJ.

Genome Med. 2016 Nov 22;8(1):124.

9.

A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome.

Mathias RA, Taub MA, Gignoux CR, Fu W, Musharoff S, O'Connor TD, Vergara C, Torgerson DG, Pino-Yanes M, Shringarpure SS, Huang L, Rafaels N, Boorgula MP, Johnston HR, Ortega VE, Levin AM, Song W, Torres R, Padhukasahasram B, Eng C, Mejia-Mejia DA, Ferguson T, Qin ZS, Scott AF, Yazdanbakhsh M, Wilson JG, Marrugo J, Lange LA, Kumar R, Avila PC, Williams LK, Watson H, Ware LB, Olopade C, Olopade O, Oliveira R, Ober C, Nicolae DL, Meyers D, Mayorga A, Knight-Madden J, Hartert T, Hansel NN, Foreman MG, Ford JG, Faruque MU, Dunston GM, Caraballo L, Burchard EG, Bleecker E, Araujo MI, Herrera-Paz EF, Gietzen K, Grus WE, Bamshad M, Bustamante CD, Kenny EE, Hernandez RD, Beaty TH, Ruczinski I, Akey J; CAAPA, Barnes KC.

Nat Commun. 2016 Oct 11;7:12522. doi: 10.1038/ncomms12522.

10.

Challenges and disparities in the application of personalized genomic medicine to populations with African ancestry.

Kessler MD, Yerges-Armstrong L, Taub MA, Shetty AC, Maloney K, Jeng LJ, Ruczinski I, Levin AM, Williams LK, Beaty TH, Mathias RA, Barnes KC; Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA), O'Connor TD.

Nat Commun. 2016 Oct 11;7:12521. doi: 10.1038/ncomms12521.

11.

Association of DNA Methylation Differences With Schizophrenia in an Epigenome-Wide Association Study.

Montano C, Taub MA, Jaffe A, Briem E, Feinberg JI, Trygvadottir R, Idrizi A, Runarsson A, Berndsen B, Gur RC, Moore TM, Perry RT, Fugman D, Sabunciyan S, Yolken RH, Hyde TM, Kleinman JE, Sobell JL, Pato CN, Pato MT, Go RC, Nimgaonkar V, Weinberger DR, Braff D, Gur RE, Fallin MD, Feinberg AP.

JAMA Psychiatry. 2016 May 1;73(5):506-14. doi: 10.1001/jamapsychiatry.2016.0144.

PMID:
27074206
12.

Identification of Rare Variants in ATP8B4 as a Risk Factor for Systemic Sclerosis by Whole-Exome Sequencing.

Gao L, Emond MJ, Louie T, Cheadle C, Berger AE, Rafaels N, Vergara C, Kim Y, Taub MA, Ruczinski I, Mathai SC, Rich SS, Nickerson DA, Hummers LK, Bamshad MJ, Hassoun PM, Mathias RA; National Heart, Lung, and Blood Institute GO Exome Sequencing Project, Barnes KC.

Arthritis Rheumatol. 2016 Jan;68(1):191-200. doi: 10.1002/art.39449.

13.

Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci.

Leslie EJ, Taub MA, Liu H, Steinberg KM, Koboldt DC, Zhang Q, Carlson JC, Hetmanski JB, Wang H, Larson DE, Fulton RS, Kousa YA, Fakhouri WD, Naji A, Ruczinski I, Begum F, Parker MM, Busch T, Standley J, Rigdon J, Hecht JT, Scott AF, Wehby GL, Christensen K, Czeizel AE, Deleyiannis FW, Schutte BC, Wilson RK, Cornell RA, Lidral AC, Weinstock GM, Beaty TH, Marazita ML, Murray JC.

Am J Hum Genet. 2015 Mar 5;96(3):397-411. doi: 10.1016/j.ajhg.2015.01.004. Epub 2015 Feb 19.

14.

Analytic power and sample size calculation for the genotypic transmission/disequilibrium test in case-parent trio studies.

Neumann C, Taub MA, Younkin SG, Beaty TH, Ruczinski I, Schwender H.

Biom J. 2014 Nov;56(6):1076-92. doi: 10.1002/bimj.201300148. Epub 2014 Aug 14.

15.

Detecting disease variants in case-parent trio studies using the bioconductor software package trio.

Schwender H, Li Q, Neumann C, Taub MA, Younkin SG, Berger P, Scharpf RB, Beaty TH, Ruczinski I.

Genet Epidemiol. 2014 Sep;38(6):516-22. doi: 10.1002/gepi.21836. Epub 2014 Jul 21.

16.

Whole exome sequencing of distant relatives in multiplex families implicates rare variants in candidate genes for oral clefts.

Bureau A, Parker MM, Ruczinski I, Taub MA, Marazita ML, Murray JC, Mangold E, Noethen MM, Ludwig KU, Hetmanski JB, Bailey-Wilson JE, Cropp CD, Li Q, Szymczak S, Albacha-Hejazi H, Alqosayer K, Field LL, Wu-Chou YH, Doheny KF, Ling H, Scott AF, Beaty TH.

Genetics. 2014 Jul;197(3):1039-44. doi: 10.1534/genetics.114.165225. Epub 2014 May 2.

17.

On multi-marker tests for association in case-control studies.

Taub MA, Schwender HR, Younkin SG, Louis TA, Ruczinski I.

Front Genet. 2013 Dec 16;4:252. doi: 10.3389/fgene.2013.00252. eCollection 2013.

18.

Measuring cell-type specific differential methylation in human brain tissue.

Montaño CM, Irizarry RA, Kaufmann WE, Talbot K, Gur RE, Feinberg AP, Taub MA.

Genome Biol. 2013 Aug 30;14(8):R94. doi: 10.1186/gb-2013-14-8-r94.

19.

Confirming genes influencing risk to cleft lip with/without cleft palate in a case-parent trio study.

Beaty TH, Taub MA, Scott AF, Murray JC, Marazita ML, Schwender H, Parker MM, Hetmanski JB, Balakrishnan P, Mansilla MA, Mangold E, Ludwig KU, Noethen MM, Rubini M, Elcioglu N, Ruczinski I.

Hum Genet. 2013 Jul;132(7):771-81. doi: 10.1007/s00439-013-1283-6. Epub 2013 Mar 20.

20.

A statistical approach to selecting and confirming validation targets in -omics experiments.

Leek JT, Taub MA, Rasgon JL.

BMC Bioinformatics. 2012 Jun 27;13:150.

21.

Incorporating genotype uncertainties into the genotypic TDT for main effects and gene-environment interactions.

Taub MA, Schwender H, Beaty TH, Louis TA, Ruczinski I.

Genet Epidemiol. 2012 Apr;36(3):225-34. doi: 10.1002/gepi.21615.

22.

Examining markers in 8q24 to explain differences in evidence for association with cleft lip with/without cleft palate between Asians and Europeans.

Murray T, Taub MA, Ruczinski I, Scott AF, Hetmanski JB, Schwender H, Patel P, Zhang TX, Munger RG, Wilcox AJ, Ye X, Wang H, Wu T, Wu-Chou YH, Shi B, Jee SH, Chong S, Yeow V, Murray JC, Marazita ML, Beaty TH.

Genet Epidemiol. 2012 May;36(4):392-9. doi: 10.1002/gepi.21633. Epub 2012 Apr 16.

23.

Rapid testing of SNPs and gene-environment interactions in case-parent trio data based on exact analytic parameter estimation.

Schwender H, Taub MA, Beaty TH, Marazita ML, Ruczinski I.

Biometrics. 2012 Sep;68(3):766-73. doi: 10.1111/j.1541-0420.2011.01713.x. Epub 2011 Dec 7.

24.

Cooperation between referees and authors increases peer review accuracy.

Leek JT, Taub MA, Pineda FJ.

PLoS One. 2011;6(11):e26895. doi: 10.1371/journal.pone.0026895. Epub 2011 Nov 9.

25.

Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis.

Niranjan TS, Adamczyk A, Bravo HC, Taub MA, Wheelan SJ, Irizarry R, Wang T.

Genome Biol. 2011 Sep 28;12(9):R93. doi: 10.1186/gb-2011-12-9-r93.

26.

Overcoming bias and systematic errors in next generation sequencing data.

Taub MA, Corrada Bravo H, Irizarry RA.

Genome Med. 2010 Dec 10;2(12):87. doi: 10.1186/gm208.

27.

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