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Paul Marjoram, PhD

Professor of Research Population and Public Health Sciences

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Phone +1 323 442 0111
Email pmarjora@usc.edu
CTSI Profile

Publications

  • Longitudinal hierarchical Bayesian models of covariate effects on airway and alveolar nitric oxide Sci Rep. 2023 04 01; 13(1):5346. . View in PubMed
  • Genomic diversity and genome-wide association analysis related to yield and fatty acid composition of wild American oil palm Plant Sci. 2021 Mar; 304:110731. . View in PubMed
  • Bayesian parameter estimation for automatic annotation of gene functions using observational data and phylogenetic trees PLoS Comput Biol. 2021 02; 17(2):e1007948. . View in PubMed
  • Functional human genes typically exhibit epigenetic conservation PLoS One. 2021; 16(9):e0253250. . View in PubMed
  • Hierarchical Bayesian estimation of covariate effects on airway and alveolar nitric oxide Sci Rep. 2021 08 25; 11(1):17180. . View in PubMed
  • Epigenetic Conservation Is a Beacon of Function: An Analysis Using Methcon5 Software for Studying Gene Methylation JCO Clin Cancer Inform. 2020 02; 4:100-107. . View in PubMed
  • Impact of different fixed flow sampling protocols on flow-independent exhaled nitric oxide parameter estimates using the Bayesian dynamic two-compartment model Physiol Rep. 2020 01; 8(1):e14336. . View in PubMed
  • iMutSig: a web application to identify the most similar mutational signature using shiny F1000Res. 2020; 9:586. . View in PubMed
  • Mutational signatures in colon cancer BMC Res Notes. 2019 Dec 03; 12(1):788. . View in PubMed
  • Bayesian model selection for the Drosophila gap gene network BMC Bioinformatics. 2019 Jun 13; 20(1):327. . View in PubMed
  • WhoGEM: an admixture-based prediction machine accurately predicts quantitative functional traits in plants Genome Biol. 2019 05 28; 20(1):106. . View in PubMed
  • Threshold response to stochasticity in morphogenesis PLoS One. 2019; 14(1):e0210088. . View in PubMed
  • HiLDA: a statistical approach to investigate differences in mutational signatures PeerJ. 2019; 7:e7557. . View in PubMed
  • slurmR: A lightweight wrapper for HPC with Slurm J Open Source Softw. 2019; 4(42). . View in PubMed
  • fmcmc: A friendly MCMC framework J Open Source Softw. 2019; 4(39). . View in PubMed
  • Sure enough: efficient Bayesian learning and choice Anim Cogn. 2017 Sep; 20(5):867-880. . View in PubMed
  • Social effects for locomotion vary between environments in Drosophila melanogaster females Evolution. 2017 Jul; 71(7):1765-1775. . View in PubMed
  • Ecol Evol. 2017 12; 7(23):10031-10041. . View in PubMed
  • Early mutation bursts in colorectal tumors PLoS One. 2017; 12(3):e0172516. . View in PubMed
  • Basic reversal-learning capacity in flies suggests rudiments of complex cognition PLoS One. 2017; 12(8):e0181749. . View in PubMed
  • Translating natural genetic variation to gene expression in a computational model of the Drosophila gap gene regulatory network PLoS One. 2017; 12(9):e0184657. . View in PubMed
  • GWASeq: targeted re-sequencing follow up to GWAS BMC Genomics. 2016 Mar 03; 17:176. . View in PubMed
  • 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
  • al3c: high-performance software for parameter inference using Approximate Bayesian Computation Bioinformatics. 2015 Nov 01; 31(21):3549-51. . View in PubMed
  • Exact likelihood-free Markov chain Monte Carlo for elliptically contoured distributions Stat Appl Genet Mol Biol. 2015 Aug; 14(4):317-32. . View in PubMed
  • 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
  • A Big Bang model of human colorectal tumor growth Nat Genet. 2015 Mar; 47(3):209-16. . View in PubMed
  • Simulation-based Bayesian Analysis of Complex Data Summer Comput Simul Conf (2015). 2015 Dec; 47(10):176-183. . View in PubMed
  • Ancestral inference in tumors: how much can we know? J Theor Biol. 2014 Oct 21; 359:136-45.. View in PubMed
  • Native American ancestry is associated with severe diabetic retinopathy in Latinos Invest Ophthalmol Vis Sci. 2014 Aug 21; 55(9):6041-5. . View in PubMed
  • Post-GWAS: where next? Heredity (Edinb). 2014 Jan; 112(1):79-88.. View in PubMed
  • Approximation Bayesian Computation OA Genet. 2013 May 01; 1(3):853. . View in PubMed
  • A genome-wide association study of central corneal thickness in Latinos Invest Ophthalmol Vis Sci. 2013 Apr 01; 54(4):2435-43. . View in PubMed
  • A sample selection strategy for next-generation sequencing Genet Epidemiol. 2012 Nov; 36(7):696-709. . View in PubMed
  • 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
  • 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. . View in PubMed
  • Exact coalescent simulation of new haplotype data from existing reference haplotypes Bioinformatics. 2012 Mar 15; 28(6):838-44. . View in PubMed
  • Genotype Imputation for Latinos Using the HapMap and 1000 Genomes Project Reference Panels Front Genet. 2012; 3:117. . View in PubMed
  • Methods for detecting associations between phenotype and aggregations of rare variants BMC Proc. 2011 Nov 29; 5 Suppl 9:S51. . View in PubMed
  • 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
  • Choice of summary statistic weights in approximate Bayesian computation Stat Appl Genet Mol Biol. 2011 Sep 27; 10(1). . View in PubMed
  • 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
  • Genetic variation in Native Americans, inferred from Latino SNP and resequencing data Mol Biol Evol. 2011 Aug; 28(8):2231-7. . View in PubMed
  • Modeling measurement error in tumor characterization studies BMC Bioinformatics. 2011 Jul 13; 12:284. . View in PubMed
  • RNA steady-state defects in myotonic dystrophy are linked to nuclear exclusion of SHARP EMBO Rep. 2011 Jul 01; 12(7):735-42. . View in PubMed
  • High DNA methylation pattern intratumoral diversity implies weak selection in many human colorectal cancers PLoS One. 2011; 6(6):e21657. . View in PubMed
  • Using DNA methylation patterns to infer tumor ancestry PLoS One. 2010 Aug 09; 5(8):e12002. . View in PubMed
  • Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines Nature. 2010 Jun 03; 465(7298):627-31. . View in PubMed
  • Copy number variation in the Framingham Heart Study BMC Proc. 2009 Dec 15; 3 Suppl 7:S133. . View in PubMed
  • Variation in genetic admixture and population structure among Latinos: the Los Angeles Latino eye study (LALES) BMC Genet. 2009 Nov 10; 10:71. . View in PubMed
  • 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
  • Many colorectal cancers are “flat” clonal expansions Cell Cycle. 2009 Jul 15; 8(14):2187-93. . View in PubMed
  • 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
  • Population genetic inference from resequencing data Genetics. 2009 Jan; 181(1):187-97. . View in PubMed
  • Fast and flexible simulation of DNA sequence data Genome Res. 2009 Jan; 19(1):136-42. . View in PubMed
  • Exploring population genetic models with recombination using efficient forward-time simulations Genetics. 2008 Apr; 178(4):2417-27. . View in PubMed
  • Modeling DNA methylation in a population of cancer cells Stat Appl Genet Mol Biol. 2008; 7(1):Article 18. . View in PubMed
  • Approximately sufficient statistics and bayesian computation Stat Appl Genet Mol Biol. 2008; 7(1):Article26. . View in PubMed
  • 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
  • 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
  • An Arabidopsis example of association mapping in structured samples PLoS Genet. 2007 Jan 19; 3(1):e4. . View in PubMed
  • Cladistic analysis of genotype data-application to GAW15 Problem 3 BMC Proc. 2007; 1 Suppl 1:S125. . View in PubMed
  • Genome-wide association mapping using mixed-models: application to GAW15 Problem 3 BMC Proc. 2007; 1 Suppl 1:S164. . View in PubMed
  • Estimating recombination rates from single-nucleotide polymorphisms using summary statistics Genetics. 2006 Nov; 174(3):1517-28. . View in PubMed
  • Modern computational approaches for analysing molecular genetic variation data Nat Rev Genet. 2006 Oct; 7(10):759-70. . View in PubMed
  • Inferring population parameters from single-feature polymorphism data Genetics. 2006 Aug; 173(4):2257-67. . View in PubMed
  • Cluster analysis for DNA methylation profiles having a detection threshold BMC Bioinformatics. 2006 Jul 26; 7:361. . View in PubMed
  • Association mapping with single-feature polymorphisms Genetics. 2006 Jun; 173(2):1125-33. . View in PubMed
  • 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
  • Fast “coalescent” simulation BMC Genet. 2006 Mar 15; 7:16. . View in PubMed
  • Fine mapping–19th century style BMC Genet. 2005 Dec 30; 6 Suppl 1:S63. . View in PubMed
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • Estimating the rate of gene conversion on human chromosome 21 Am J Hum Genet. 2004 Sep; 75(3):386-97. . View in PubMed
  • A survey of current Bayesian gene mapping methods Hum Genomics. 2004 Aug; 1(5):371-4. . View in PubMed
  • 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
  • Markov chain Monte Carlo without likelihoods Proc Natl Acad Sci U S A. 2003 Dec 23; 100(26):15324-8. . View in PubMed
  • Age-related changes of cardiac gene expression following myocardial ischemia/reperfusion Arch Biochem Biophys. 2003 Dec 15; 420(2):268-78. . View in PubMed
  • 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
  • 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
  • Brief episode of ischemia activates protective genetic program in rat heart: a gene chip study Cardiovasc Res. 2003 Aug 01; 59(2):450-9. . View in PubMed
  • Gene expression profiling–a new approach in the study of myocardial ischemia Cardiovasc Pathol. 2003 Jul-Aug; 12(4):180-5. . View in PubMed
  • Bayesian spatial modeling of haplotype associations Hum Hered. 2003; 56(1-3):32-40. . View in PubMed
  • On a test of Depaulis and Veuille Mol Biol Evol. 2001 Jun; 18(6):1132-3; author reply 1136-8. . View in PubMed
  • The effects of rate variation on ancestral inference in the coalescent Genetics. 2000 Nov; 156(3):1427-36. . View in PubMed
  • The age of a unique event polymorphism Genetics. 2000 Sep; 156(1):401-9. . View in PubMed
  • 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
  • Ancestral inference from samples of DNA sequences with recombination J Comput Biol. 1996; 3(4):479-502. . View in PubMed
  • 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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