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Paul Marjoram, PhD

TitleProfessor of Research Preventive Medicine
InstitutionUniversity of Southern California
DepartmentPreventive Medicine
AddressSSB 202V 2001 N. Soto Street
Health Sciences Campus
Los Angeles CA 90033
Phone+1 323 442 0111
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    Collapse Research 
    Collapse Research Activities and Funding
    Multi-scale modeling of genetic variation in a developmental network
    NIH/NIGMS U01GM103804Sep 30, 2013 - Jun 30, 2017
    Role: Co-Principal Investigator
    Drosophila Societies: Agent-Based Analysis of Behavioral Plasticity and Genetics
    NIH/NIMH R01MH100879Dec 18, 2012 - Nov 30, 2016
    Role: Principal Investigator
    Design and Analysis of 2 Stage GWAS Study Using Next Generation Sequence Technolo
    NIH/NHGRI U01HG005927Sep 28, 2010 - Aug 31, 2013
    Role: Principal Investigator
    Statistical Methods for Relating Sequence Data to Phenotype
    NIH/NIMH R01MH084678Sep 25, 2008 - Jun 30, 2012
    Role: Principal Investigator
    Computational Methods for Fine Mapping
    NIH/NIGMS R01GM069890Sep 1, 2004 - Aug 31, 2009
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Signor SA, Abbasi M, Marjoram P, Nuzhdin SV. Conservation of social effects (?) between two species of Drosophila despite reversal of sexual dimorphism. Ecol Evol. 2017 Dec; 7(23):10031-10041. PMID: 29238534.
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    2. Gursky VV, Kozlov KN, Kulakovskiy IV, Zubair A, Marjoram P, Lawrie DS, Nuzhdin SV, Samsonova MG. Translating natural genetic variation to gene expression in a computational model of the Drosophila gap gene regulatory network. PLoS One. 2017; 12(9):e0184657. PMID: 28898266.
      View in: PubMed
    3. Foley BR, Marjoram P, Nuzhdin SV. Basic reversal-learning capacity in flies suggests rudiments of complex cognition. PLoS One. 2017; 12(8):e0181749. PMID: 28813432.
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    4. Foley BR, Marjoram P. Sure enough: efficient Bayesian learning and choice. Anim Cogn. 2017 Sep; 20(5):867-880. PMID: 28669114.
      View in: PubMed
    5. Signor SA, Abbasi M, Marjoram P, Nuzhdin SV. Social effects for locomotion vary between environments in Drosophila melanogaster females. Evolution. 2017 07; 71(7):1765-1775. PMID: 28489252.
      View in: PubMed
    6. Zhao J, Salomon MP, Shibata D, Curtis C, Siegmund K, Marjoram P. Early mutation bursts in colorectal tumors. PLoS One. 2017; 12(3):e0172516. PMID: 28257429.
      View in: PubMed
    7. 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 Mar 03; 17:176. PMID: 26940994; PMCID: PMC4776370.
    8. Marjoram P, Hamblin S, Foley B. Simulation-based Bayesian Analysis of Complex Data. Summer Comput Simul Conf (2015). 2015 Dec; 47(10):176-183. PMID: 27840859.
      View in: PubMed
    9. 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. PMID: 26119426; PMCID: PMC4607608 [Available on 11/01/16].
    10. Muchmore P, Marjoram P. Exact likelihood-free Markov chain Monte Carlo for elliptically contoured distributions. Stat Appl Genet Mol Biol. 2015 Aug; 14(4):317-32. PMID: 26167984; PMCID: PMC4607478.
    11. Stram AH, Marjoram P, Chen GK. al3c: high-performance software for parameter inference using Approximate Bayesian Computation. Bioinformatics. 2015 Nov 01; 31(21):3549-51. PMID: 26142186; PMCID: PMC4626746 [Available on 11/01/16].
    12. 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. PMID: 25996864; PMCID: PMC4610401.
    13. 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. PMID: 25665006.
      View in: PubMed
    14. 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 Aug 21; 55(9):6041-5. PMID: 25146985; PMCID: PMC4176415.
    15. 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. PMID: 24907673; PMCID: PMC4138290.
    16. Marjoram P, Zubair A, Nuzhdin SV. Post-GWAS: where next? More samples, more SNPs or more biology? Heredity (Edinb). 2014 Jan; 112(1):79-88. PMID: 23759726; PMCID: PMC3860164.
    17. Marjoram P. Approximation Bayesian Computation. OA Genet. 2013 May 01; 1(3):853. PMID: 25606346.
      View in: PubMed
    18. 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 01; 54(4):2435-43. PMID: 23493294; PMCID: PMC3621577.
    19. Kang CJ, Marjoram P. A sample selection strategy for next-generation sequencing. Genet Epidemiol. 2012 Nov; 36(7):696-709. PMID: 22865643; PMCID: PMC4272568.
    20. 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. PMID: 22948034; PMCID: PMC3461344.
    21. 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. PMID: 22754564; PMCID: PMC3384355.
    22. Chen T, Marjoram P, Sun F, Zhou JX. In this special issue of the Journal of Computational Biology, we take great pleasure in celebrating the landmark birthdays of two leaders in our field. J Comput Biol. 2012 Jun; 19(6):575-6. PMID: 22651813.
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    23. Kang CJ, Marjoram P. Exact coalescent simulation of new haplotype data from existing reference haplotypes. Bioinformatics. 2012 Mar 15; 28(6):838-44. PMID: 22257666; PMCID: PMC3307111.
    24. Yang F, Kang CJ, Marjoram P. Methods for detecting associations between phenotype and aggregations of rare variants. BMC Proc. 2011 Nov 29; 5 Suppl 9:S51. PMID: 22373540.
      View in: PubMed
    25. Jung H, Marjoram P. Choice of summary statistic weights in approximate Bayesian computation. Stat Appl Genet Mol Biol. 2011 Sep 27; 10(1). PMID: 23089822; PMCID: PMC3192002.
    26. 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. PMID: 21840859; PMCID: PMC3189800.
    27. Rakovski C, Weisenberger DJ, Marjoram P, Laird PW, Siegmund KD. Modeling measurement error in tumor characterization studies. BMC Bioinformatics. 2011 Jul 13; 12:284. PMID: 21752297; PMCID: PMC3213130.
    28. 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 01; 12(7):735-42. PMID: 21637295; PMCID: PMC3128970.
    29. 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. PMID: 21738754; PMCID: PMC3125304.
    30. 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. PMID: 21368315; PMCID: PMC3144384.
    31. 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. PMID: 21309924.
      View in: PubMed
    32. Hong YJ, Marjoram P, Shibata D, Siegmund KD. Using DNA methylation patterns to infer tumor ancestry. PLoS One. 2010 Aug 09; 5(8):e12002. PMID: 20711251; PMCID: PMC2918495.
    33. 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 03; 465(7298):627-31. PMID: 20336072; PMCID: PMC3023908.
    34. Shtir C, Pique-Regi R, Siegmund K, Morrison J, Schumacher F, Marjoram P. Copy number variation in the Framingham Heart Study. BMC Proc. 2009 Dec 15; 3 Suppl 7:S133. PMID: 20018000; PMCID: PMC2795907.
    35. 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 Nov 10; 10:71. PMID: 19903357; PMCID: PMC3087512.
    36. 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. PMID: 19602725; PMCID: PMC2757189.
    37. Siegmund KD, Marjoram P, Tavaré S, Shibata D. Many colorectal cancers are "flat" clonal expansions. Cell Cycle. 2009 Jul 15; 8(14):2187-93. PMID: 19556889; PMCID: PMC4145878.
    38. 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. PMID: 19261858; PMCID: PMC2651202.
    39. Chen GK, Marjoram P, Wall JD. Fast and flexible simulation of DNA sequence data. Genome Res. 2009 Jan; 19(1):136-42. PMID: 19029539; PMCID: PMC2612967.
    40. Jiang R, Tavaré S, Marjoram P. Population genetic inference from resequencing data. Genetics. 2009 Jan; 181(1):187-97. PMID: 18984575; PMCID: PMC2621167.
    41. Joyce P, Marjoram P. Approximately sufficient statistics and bayesian computation. Stat Appl Genet Mol Biol. 2008; 7(1):Article26. PMID: 18764775.
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    42. 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. PMID: 18597664.
      View in: PubMed
    43. 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. PMID: 18430959; PMCID: PMC2323826.
    44. Jung H, Zhao K, Marjoram P. Cladistic analysis of genotype data-application to GAW15 Problem 3. BMC Proc. 2007; 1 Suppl 1:S125. PMID: 18466467; PMCID: PMC2367549.
    45. 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. PMID: 18466510; PMCID: PMC2367554.
    46. 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. PMID: 17932707.
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    47. 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. PMID: 17623264.
      View in: PubMed
    48. 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. PMID: 17238287; PMCID: PMC1779303.
    49. Marjoram P, Tavaré S. Modern computational approaches for analysing molecular genetic variation data. Nat Rev Genet. 2006 Oct; 7(10):759-70. PMID: 16983372.
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    50. 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. PMID: 16980396; PMCID: PMC1667054.
    51. Marjoram P, Chang J, Laird PW, Siegmund KD. Cluster analysis for DNA methylation profiles having a detection threshold. BMC Bioinformatics. 2006 Jul 26; 7:361. PMID: 16872497; PMCID: PMC1555616.
    52. Jiang R, Marjoram P, Borevitz JO, Tavaré S. Inferring population parameters from single-feature polymorphism data. Genetics. 2006 Aug; 173(4):2257-67. PMID: 16702439; PMCID: PMC1569697.
    53. Marjoram P, Wall JD. Fast "coalescent" simulation. BMC Genet. 2006 Mar 15; 7:16. PMID: 16539698; PMCID: PMC1458357.
    54. 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. PMID: 16510789; PMCID: PMC1526505.
    55. Molitor J, Zhao K, Marjoram P. Fine mapping--19th century style. BMC Genet. 2005 Dec 30; 6 Suppl 1:S63. PMID: 16451676; PMCID: PMC1866719.
    56. 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. PMID: 16299388; PMCID: PMC1456404.
    57. 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. PMID: 16292355; PMCID: PMC1283159.
    58. 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. PMID: 16219764.
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    59. 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. PMID: 16172218.
      View in: PubMed
    60. 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. PMID: 15654103; PMCID: PMC1449527.
    61. 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. PMID: 15579712; PMCID: PMC1448803.
    62. 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. PMID: 15225679.
      View in: PubMed
    63. Molitor J, Marjoram P, Conti D, Thomas D. A survey of current Bayesian gene mapping methods. Hum Genomics. 2004 Aug; 1(5):371-4. PMID: 15588497; PMCID: PMC3525098.
    64. 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. PMID: 15250027; PMCID: PMC1182018.
    65. 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. PMID: 15107828.
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    66. 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. PMID: 14654066.
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    67. 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. PMID: 14663152; PMCID: PMC307566.
    68. 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. PMID: 14631555; PMCID: PMC1180401.
    69. 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. PMID: 12916018.
      View in: PubMed
    70. 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 01; 59(2):450-9. PMID: 12909328.
      View in: PubMed
    71. 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. PMID: 12826286.
      View in: PubMed
    72. Thomas DC, Stram DO, Conti D, Molitor J, Marjoram P. Bayesian spatial modeling of haplotype associations. Hum Hered. 2003; 56(1-3):32-40. PMID: 14614236.
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    73. 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. PMID: 11371600.
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    74. Markovtsova L, Marjoram P, Tavaré S. The effects of rate variation on ancestral inference in the coalescent. Genetics. 2000 Nov; 156(3):1427-36. PMID: 11063714; PMCID: PMC1461332.
    75. Markovtsova L, Marjoram P, Tavaré S. The age of a unique event polymorphism. Genetics. 2000 Sep; 156(1):401-9. PMID: 10978303; PMCID: PMC1461247.
    76. 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. PMID: 9931325.
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    77. Griffiths RC, Marjoram P. Ancestral inference from samples of DNA sequences with recombination. J Comput Biol. 1996; 3(4):479-502. PMID: 9018600.
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    78. 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. PMID: 8150290; PMCID: PMC1205816.
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