Faculty

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Paul Marjoram, PhD
Professor of Research Preventive Medicine
Preventive Medicine
SSB 202V 2001 N. Soto Street Health Sciences Campus Los Angeles
+1 323 442 0111

Publications

Salomon MP, Li WL, Edlund CK, Morrison J, Fortini BK, Win AK, Conti DV, Thomas DC, Duggan D, Buchanan DD, Jenkins MA, Hopper JL, Gallinger S, Le Marchand L, Newcomb PA, Casey G, Marjoram P. GWASeq: targeted re-sequencing follow up to GWAS. BMC Genomics. 2016; 17(1):176. View in: PubMed

Stram AH, Marjoram P, Chen GK. al3c: high-performance software for parameter inference using Approximate Bayesian Computation. Bioinformatics. 2015 Nov 1; 31(21):3549-51. View in: PubMed

Kang H, Salomon MP, Sottoriva A, Zhao J, Toy M, Press MF, Curtis C, Marjoram P, Siegmund K, Shibata D. Many private mutations originate from the first few divisions of a human colorectal adenoma. J Pathol. 2015 Nov; 237(3):355-62. View in: PubMed

Muchmore P, Marjoram P. Exact likelihood-free Markov chain Monte Carlo for elliptically contoured distributions. Stat Appl Genet Mol Biol. 2015 Aug 1; 14(4):317-32. View in: PubMed

Foley BR, Saltz JB, Nuzhdin SV, Marjoram P. A Bayesian Approach to Social Structure Uncovers Cryptic Regulation of Group Dynamics in Drosophila melanogaster. Am Nat. 2015 Jun; 185(6):797-808. View in: PubMed

Sottoriva A, Kang H, Ma Z, Graham TA, Salomon MP, Zhao J, Marjoram P, Siegmund K, Press MF, Shibata D, Curtis C. A Big Bang model of human colorectal tumor growth. Nat Genet. 2015 Mar; 47(3):209-16. View in: PubMed

Zhao J, Siegmund KD, Shibata D, Marjoram P. Ancestral inference in tumors: How much can we know? J Theor Biol. 2014 Oct 21; 359:136-45. View in: PubMed

Gao X, Gauderman WJ, Marjoram P, Torres M, Chen YD, Taylor KD, Rotter JI, Varma R. Native american ancestry is associated with severe diabetic retinopathy in latinos. Invest Ophthalmol Vis Sci. 2014 Sep; 55(9):6041-5. View in: PubMed

Marjoram P, Zubair A, Nuzhdin SV. Post-GWAS: where next? Heredity (Edinb). 2014 Jan; 112(1):79-88. View in: PubMed

Gao X, Gauderman WJ, Liu Y, Marjoram P, Torres M, Haritunians T, Kuo JZ, Chen YD, Allingham RR, Hauser MA, Taylor KD, Rotter JI, Varma R. A genome-wide association study of central corneal thickness in Latinos. Invest Ophthalmol Vis Sci. 2013 Apr; 54(4):2435-43. View in: PubMed

Kang CJ, Marjoram P. A sample selection strategy for next-generation sequencing. Genet Epidemiol. 2012 Nov; 36(7):696-709. View in: PubMed

Candelario J, Chen LY, Marjoram P, Reddy S, Comai L. A filtering strategy identifies FOXQ1 as a potential effector of lamin A dysfunction. Aging (Albany NY). 2012 Aug; 4(8):567-77. View in: PubMed

Chen T, Marjoram P, Sun F, Zhou JX. Preface: special issue. J Comput Biol. 2012 Jun; 19(6):575-6. View in: PubMed

Kang CJ, Marjoram P. Exact coalescent simulation of new haplotype data from existing reference haplotypes. Bioinformatics. 2012 Mar 15; 28(6):838-44. View in: PubMed

Gao X, Haritunians T, Marjoram P, McKean-Cowdin R, Torres M, Taylor KD, Rotter JI, Gauderman WJ, Varma R. Genotype Imputation for Latinos Using the HapMap and 1000 Genomes Project Reference Panels. Front Genet. 2012; 3:117. View in: PubMed

Kang CJ, Marjoram P. Inference of population mutation rate and detection of segregating sites from next-generation sequence data. Genetics. 2011 Oct; 189(2):595-605. View in: PubMed

Oh DS, DeMeester SR, Tanaka K, Marjoram P, Kuramochi H, Vallbohmer D, Danenberg K, Chandrasoma PT, DeMeester TR, Hagen JA. The gene expression profile of cardia intestinal metaplasia is similar to that of Barrett's esophagus, not gastric intestinal metaplasia. Dis Esophagus. 2011 Sep; 24(7):516-22. View in: PubMed

Wall JD, Jiang R, Gignoux C, Chen GK, Eng C, Huntsman S, Marjoram P. Genetic variation in Native Americans, inferred from Latino SNP and resequencing data. Mol Biol Evol. 2011 Aug; 28(8):2231-7. View in: PubMed

Dansithong W, Jog SP, Paul S, Mohammadzadeh R, Tring S, Kwok Y, Fry RC, Marjoram P, Comai L, Reddy S. RNA steady-state defects in myotonic dystrophy are linked to nuclear exclusion of SHARP. EMBO Rep. 2011 Jul; 12(7):735-42. View in: PubMed

Jung H, Marjoram P. Choice of summary statistic weights in approximate bayesian computation. Stat Appl Genet Mol Biol. 2011; 10(1). View in: PubMed

Siegmund KD, Marjoram P, Tavaré S, Shibata D. High DNA methylation pattern intratumoral diversity implies weak selection in many human colorectal cancers. PLoS One. 2011; 6(6):e21657. View in: PubMed

Yang F, Kang CJ, Marjoram P. Methods for detecting associations between phenotype and aggregations of rare variants. BMC Proc. 2011; 5 Suppl 9:S51. View in: PubMed

Rakovski C, Weisenberger DJ, Marjoram P, Laird PW, Siegmund KD. Modeling measurement error in tumor characterization studies. BMC Bioinformatics. 2011; 12:284. View in: PubMed

Atwell S, Huang YS, Vilhjálmsson BJ, Willems G, Horton M, Li Y, Meng D, Platt A, Tarone AM, Hu TT, Jiang R, Muliyati NW, Zhang X, Amer MA, Baxter I, Brachi B, Chory J, Dean C, Debieu M, de Meaux J, Ecker JR, Faure N, Kniskern JM, Jones JD, Michael T, Nemri A, Roux F, Salt DE, Tang C, Todesco M, Traw MB, Weigel D, Marjoram P, Borevitz JO, Bergelson J, Nordborg M. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature. 2010 Jun 3; 465(7298):627-31. View in: PubMed

Hong YJ, Marjoram P, Shibata D, Siegmund KD. Using DNA methylation patterns to infer tumor ancestry. PLoS One. 2010; 5(8):e12002. View in: PubMed

Little GH, Saw A, Bai Y, Dow J, Marjoram P, Simkhovich B, Leeka J, Kedes L, Kloner RA, Poizat C. Critical role of nuclear calcium/calmodulin-dependent protein kinase IIdeltaB in cardiomyocyte survival in cardiomyopathy. J Biol Chem. 2009 Sep 11; 284(37):24857-68. View in: PubMed

Siegmund KD, Marjoram P, Tavaré S, Shibata D. Many colorectal cancers are "flat" clonal expansions. Cell Cycle. 2009 Jul 15; 8(14):2187-93. View in: PubMed

Siegmund KD, Marjoram P, Woo YJ, Tavaré S, Shibata D. Inferring clonal expansion and cancer stem cell dynamics from DNA methylation patterns in colorectal cancers. Proc Natl Acad Sci U S A. 2009 Mar 24; 106(12):4828-33. View in: PubMed

Shtir CJ, Marjoram P, Azen S, Conti DV, Le Marchand L, Haiman CA, Varma R. Variation in genetic admixture and population structure among Latinos: the Los Angeles Latino eye study (LALES). BMC Genet. 2009; 10:71. View in: PubMed

Jiang R, Tavaré S, Marjoram P. Population genetic inference from resequencing data. Genetics. 2009 Jan; 181(1):187-97. View in: PubMed

Shtir C, Pique-Regi R, Siegmund K, Morrison J, Schumacher F, Marjoram P. Copy number variation in the Framingham Heart Study. BMC Proc. 2009; 3 Suppl 7:S133. View in: PubMed

Chen GK, Marjoram P, Wall JD. Fast and flexible simulation of DNA sequence data. Genome Res. 2009 Jan; 19(1):136-42. View in: PubMed

Padhukasahasram B, Marjoram P, Wall JD, Bustamante CD, Nordborg M. Exploring population genetic models with recombination using efficient forward-time simulations. Genetics. 2008 Apr; 178(4):2417-27. View in: PubMed

Joyce P, Marjoram P. Approximately sufficient statistics and bayesian computation. Stat Appl Genet Mol Biol. 2008; 7(1):Article26. View in: PubMed

Siegmund KD, Marjoram P, Shibata D. Modeling DNA methylation in a population of cancer cells. Stat Appl Genet Mol Biol. 2008; 7(1):Article 18. View in: PubMed

Simkhovich BZ, Marjoram P, Kleinman MT, Kloner RA. Direct and acute cardiotoxicity of ultrafine particles in young adult and old rat hearts. Basic Res Cardiol. 2007 Nov; 102(6):467-75. View in: PubMed

Vallböhmer D, Marjoram P, Kuramochi H, Shimizu D, Jung H, DeMeester SR, Oh D, Chandrasoma PT, Danenberg KD, DeMeester TR, Danenberg PV, Peters JH. Towards the molecular characterization of disease: comparison of molecular and histological analysis of esophageal epithelia. J Gastrointest Surg. 2007 Sep; 11(9):1095-104. View in: PubMed

Zhao K, Aranzana MJ, Kim S, Lister C, Shindo C, Tang C, Toomajian C, Zheng H, Dean C, Marjoram P, Nordborg M. An Arabidopsis example of association mapping in structured samples. PLoS Genet. 2007 Jan 19; 3(1):e4. View in: PubMed

Jung H, Zhao K, Marjoram P. Cladistic analysis of genotype data-application to GAW15 Problem 3. BMC Proc. 2007; 1 Suppl 1:S125. View in: PubMed

Zhao K, Nordborg M, Marjoram P. Genome-wide association mapping using mixed-models: application to GAW15 Problem 3. BMC Proc. 2007; 1 Suppl 1:S164. View in: PubMed

Padhukasahasram B, Wall JD, Marjoram P, Nordborg M. Estimating recombination rates from single-nucleotide polymorphisms using summary statistics. Genetics. 2006 Nov; 174(3):1517-28. View in: PubMed

Marjoram P, Tavaré S. Modern computational approaches for analysing molecular genetic variation data. Nat Rev Genet. 2006 Oct; 7(10):759-70. View in: PubMed

Jiang R, Marjoram P, Borevitz JO, Tavaré S. Inferring population parameters from single-feature polymorphism data. Genetics. 2006 Aug; 173(4):2257-67. View in: PubMed

Kim S, Zhao K, Jiang R, Molitor J, Borevitz JO, Nordborg M, Marjoram P. Association mapping with single-feature polymorphisms. Genetics. 2006 Jun; 173(2):1125-33. View in: PubMed

Plagnol V, Padhukasahasram B, Wall JD, Marjoram P, Nordborg M. Relative influences of crossing over and gene conversion on the pattern of linkage disequilibrium in Arabidopsis thaliana. Genetics. 2006 Apr; 172(4):2441-8. View in: PubMed

Marjoram P, Chang J, Laird PW, Siegmund KD. Cluster analysis for DNA methylation profiles having a detection threshold. BMC Bioinformatics. 2006; 7:361. View in: PubMed

Marjoram P, Wall JD. Fast "coalescent" simulation. BMC Genet. 2006; 7:16. View in: PubMed

Shi GW, Chen J, Concepcion F, Motamedchaboki K, Marjoram P, Langen R, Chen J. Light causes phosphorylation of nonactivated visual pigments in intact mouse rod photoreceptor cells. J Biol Chem. 2005 Dec 16; 280(50):41184-91. View in: PubMed

Aranzana MJ, Kim S, Zhao K, Bakker E, Horton M, Jakob K, Lister C, Molitor J, Shindo C, Tang C, Toomajian C, Traw B, Zheng H, Bergelson J, Dean C, Marjoram P, Nordborg M. Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet. 2005 Nov; 1(5):e60. View in: PubMed

Brabender J, Marjoram P, Lord RV, Metzger R, Salonga D, Vallböhmer D, Schäfer H, Danenberg KD, Danenberg PV, Selaru FM, Baldus SE, Hölscher AH, Meltzer SJ, Schneider PM. The molecular signature of normal squamous esophageal epithelium identifies the presence of a field effect and can discriminate between patients with Barrett's esophagus and patients with Barrett's-associated adenocarcinoma. Cancer Epidemiol Biomarkers Prev. 2005 Sep; 14(9):2113-7. View in: PubMed

Innan H, Zhang K, Marjoram P, Tavaré S, Rosenberg NA. Statistical tests of the coalescent model based on the haplotype frequency distribution and the number of segregating sites. Genetics. 2005 Mar; 169(3):1763-77. View in: PubMed

Molitor J, Zhao K, Marjoram P. Fine mapping--19th century style. BMC Genet. 2005; 6 Suppl 1:S63. View in: PubMed

Hagenblad J, Tang C, Molitor J, Werner J, Zhao K, Zheng H, Marjoram P, Weigel D, Nordborg M. Haplotype structure and phenotypic associations in the chromosomal regions surrounding two Arabidopsis thaliana flowering time loci. Genetics. 2004 Nov; 168(3):1627-38. View in: PubMed

Wuenschell C, Kunimi M, Castillo C, Marjoram P. Nicotine-responsive genes in cultured embryonic mouse lung buds: interaction of nicotine and superoxide dismutase. Pharmacol Res. 2004 Sep; 50(3):341-50. View in: PubMed

Padhukasahasram B, Marjoram P, Nordborg M. Estimating the rate of gene conversion on human chromosome 21. Am J Hum Genet. 2004 Sep; 75(3):386-97. View in: PubMed

Molitor J, Marjoram P, Conti D, Thomas D. A survey of current Bayesian gene mapping methods. Hum Genomics. 2004 Aug; 1(5):371-4. View in: PubMed

Brabender J, Marjoram P, Salonga D, Metzger R, Schneider PM, Park JM, Schneider S, Hölscher AH, Yin J, Meltzer SJ, Danenberg KD, Danenberg PV, Lord RV. A multigene expression panel for the molecular diagnosis of Barrett's esophagus and Barrett's adenocarcinoma of the esophagus. Oncogene. 2004 Jun 10; 23(27):4780-8. View in: PubMed

Marjoram P, Molitor J, Plagnol V, Tavare S. Markov chain Monte Carlo without likelihoods. Proc Natl Acad Sci U S A. 2003 Dec 23; 100(26):15324-8. View in: PubMed

Simkhovich BZ, Marjoram P, Poizat C, Kedes L, Kloner RA. Age-related changes of cardiac gene expression following myocardial ischemia/reperfusion. Arch Biochem Biophys. 2003 Dec 15; 420(2):268-78. View in: PubMed

Molitor J, Marjoram P, Thomas D. Fine-scale mapping of disease genes with multiple mutations via spatial clustering techniques. Am J Hum Genet. 2003 Dec; 73(6):1368-84. View in: PubMed

Molitor J, Marjoram P, Thomas D. Application of Bayesian spatial statistical methods to analysis of haplotypes effects and gene mapping. Genet Epidemiol. 2003 Sep; 25(2):95-105. View in: PubMed

Simkhovich BZ, Marjoram P, Poizat C, Kedes L, Kloner RA. Brief episode of ischemia activates protective genetic program in rat heart: a gene chip study. Cardiovasc Res. 2003 Aug 1; 59(2):450-9. View in: PubMed

Simkhovich BZ, Kloner RA, Poizat C, Marjoram P, Kedes LH. Gene expression profiling--a new approach in the study of myocardial ischemia. Cardiovasc Pathol. 2003 Jul-Aug; 12(4):180-5. View in: PubMed

Thomas DC, Stram DO, Conti D, Molitor J, Marjoram P. Bayesian spatial modeling of haplotype associations. Hum Hered. 2003; 56(1-3):32-40. View in: PubMed

Markovtsova L, Marjoram P, Tavare S. On a test of Depaulis and Veuille. Mol Biol Evol. 2001 Jun; 18(6):1132-3; author reply 1136-8. View in: PubMed

Markovtsova L, Marjoram P, Tavaré S. The effects of rate variation on ancestral inference in the coalescent. Genetics. 2000 Nov; 156(3):1427-36. View in: PubMed

Markovtsova L, Marjoram P, Tavaré S. The age of a unique event polymorphism. Genetics. 2000 Sep; 156(1):401-9. View in: PubMed

Leeflang EP, Tavaré S, Marjoram P, Neal CO, Srinidhi J, MacFarlane H, MacDonald ME, Gusella JF, de Young M, Wexler NS, Arnheim N. Analysis of germline mutation spectra at the Huntington's disease locus supports a mitotic mutation mechanism. Hum Mol Genet. 1999 Feb; 8(2):173-83. View in: PubMed

Griffiths RC, Marjoram P. Ancestral inference from samples of DNA sequences with recombination. J Comput Biol. 1996; 3(4):479-502. View in: PubMed

Marjoram P, Donnelly P. Pairwise comparisons of mitochondrial DNA sequences in subdivided populations and implications for early human evolution. Genetics. 1994 Feb; 136(2):673-83. View in: PubMed

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