Paul Marjoram

Paul Marjoram

Professor of Research Population and Public Health Sciences
SSB 202V 2001 N. Soto Street Health Sciences Campus Los Angeles

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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Affiliated Faculty at UPC