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Items: 1 to 50 of 83

1.

Mutational signatures in colon cancer.

Pandey P, Yang Z, Shibata D, Marjoram P, Siegmund KD.

BMC Res Notes. 2019 Dec 3;12(1):788. doi: 10.1186/s13104-019-4820-0.

2.

HiLDA: a statistical approach to investigate differences in mutational signatures.

Yang Z, Pandey P, Shibata D, Conti DV, Marjoram P, Siegmund KD.

PeerJ. 2019 Aug 28;7:e7557. doi: 10.7717/peerj.7557. eCollection 2019.

3.

Bayesian model selection for the Drosophila gap gene network.

Zubair A, Rosen IG, Nuzhdin SV, Marjoram P.

BMC Bioinformatics. 2019 Jun 13;20(1):327. doi: 10.1186/s12859-019-2888-0.

4.

WhoGEM: an admixture-based prediction machine accurately predicts quantitative functional traits in plants.

Gentzbittel L, Ben C, Mazurier M, Shin MG, Lorenz T, Rickauer M, Marjoram P, Nuzhdin SV, Tatarinova TV.

Genome Biol. 2019 May 28;20(1):106. doi: 10.1186/s13059-019-1697-0.

5.

Threshold response to stochasticity in morphogenesis.

Courcoubetis G, Ali S, Nuzhdin SV, Marjoram P, Haas S.

PLoS One. 2019 Jan 30;14(1):e0210088. doi: 10.1371/journal.pone.0210088. eCollection 2019.

6.

Conservation of social effects (Ψ) between two species of Drosophila despite reversal of sexual dimorphism.

Signor SA, Abbasi M, Marjoram P, Nuzhdin SV.

Ecol Evol. 2017 Oct 22;7(23):10031-10041. doi: 10.1002/ece3.3523. eCollection 2017 Dec.

7.

Translating natural genetic variation to gene expression in a computational model of the Drosophila gap gene regulatory network.

Gursky VV, Kozlov KN, Kulakovskiy IV, Zubair A, Marjoram P, Lawrie DS, Nuzhdin SV, Samsonova MG.

PLoS One. 2017 Sep 12;12(9):e0184657. doi: 10.1371/journal.pone.0184657. eCollection 2017.

8.

Basic reversal-learning capacity in flies suggests rudiments of complex cognition.

Foley BR, Marjoram P, Nuzhdin SV.

PLoS One. 2017 Aug 16;12(8):e0181749. doi: 10.1371/journal.pone.0181749. eCollection 2017.

9.

Sure enough: efficient Bayesian learning and choice.

Foley BR, Marjoram P.

Anim Cogn. 2017 Sep;20(5):867-880. doi: 10.1007/s10071-017-1107-5. Epub 2017 Jul 1.

10.

Social effects for locomotion vary between environments in Drosophila melanogaster females.

Signor SA, Abbasi M, Marjoram P, Nuzhdin SV.

Evolution. 2017 Jul;71(7):1765-1775. doi: 10.1111/evo.13266. Epub 2017 May 24.

PMID:
28489252
11.

Early mutation bursts in colorectal tumors.

Zhao J, Salomon MP, Shibata D, Curtis C, Siegmund K, Marjoram P.

PLoS One. 2017 Mar 3;12(3):e0172516. doi: 10.1371/journal.pone.0172516. eCollection 2017.

12.

GWASeq: targeted re-sequencing follow up to GWAS.

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.

BMC Genomics. 2016 Mar 3;17:176. doi: 10.1186/s12864-016-2459-y.

13.

Exact likelihood-free Markov chain Monte Carlo for elliptically contoured distributions.

Muchmore P, Marjoram P.

Stat Appl Genet Mol Biol. 2015 Aug;14(4):317-32. doi: 10.1515/sagmb-2014-0063.

14.

al3c: high-performance software for parameter inference using Approximate Bayesian Computation.

Stram AH, Marjoram P, Chen GK.

Bioinformatics. 2015 Nov 1;31(21):3549-51. doi: 10.1093/bioinformatics/btv393. Epub 2015 Jul 2.

15.

Simulation-based Bayesian Analysis of Complex Data.

Marjoram P, Hamblin S, Foley B.

Summer Comput Simul Conf (2015). 2015 Dec;47(10):176-183.

16.

Many private mutations originate from the first few divisions of a human colorectal adenoma.

Kang H, Salomon MP, Sottoriva A, Zhao J, Toy M, Press MF, Curtis C, Marjoram P, Siegmund K, Shibata D.

J Pathol. 2015 Nov;237(3):355-62. doi: 10.1002/path.4581. Epub 2015 Aug 3.

17.

A Bayesian Approach to Social Structure Uncovers Cryptic Regulation of Group Dynamics in Drosophila melanogaster.

Foley BR, Saltz JB, Nuzhdin SV, Marjoram P.

Am Nat. 2015 Jun;185(6):797-808. doi: 10.1086/681084. Epub 2015 Apr 16.

18.

A Big Bang model of human colorectal tumor growth.

Sottoriva A, Kang H, Ma Z, Graham TA, Salomon MP, Zhao J, Marjoram P, Siegmund K, Press MF, Shibata D, Curtis C.

Nat Genet. 2015 Mar;47(3):209-16. doi: 10.1038/ng.3214. Epub 2015 Feb 9.

19.

Native American ancestry is associated with severe diabetic retinopathy in Latinos.

Gao X, Gauderman WJ, Marjoram P, Torres M, Chen YD, Taylor KD, Rotter JI, Varma R.

Invest Ophthalmol Vis Sci. 2014 Aug 21;55(9):6041-5. doi: 10.1167/iovs.14-15044.

20.

Ancestral inference in tumors: how much can we know?

Zhao J, Siegmund KD, Shibata D, Marjoram P.

J Theor Biol. 2014 Oct 21;359:136-45. doi: 10.1016/j.jtbi.2014.05.027. Epub 2014 Jun 5.

21.

Post-GWAS: where next? More samples, more SNPs or more biology?

Marjoram P, Zubair A, Nuzhdin SV.

Heredity (Edinb). 2014 Jan;112(1):79-88. doi: 10.1038/hdy.2013.52. Epub 2013 Jun 12. Review.

22.

Approximation Bayesian Computation.

Marjoram P.

OA Genet. 2013 May 1;1(3):853.

23.

A genome-wide association study of central corneal thickness in Latinos.

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.

Invest Ophthalmol Vis Sci. 2013 Apr 1;54(4):2435-43. doi: 10.1167/iovs.13-11692.

24.

A filtering strategy identifies FOXQ1 as a potential effector of lamin A dysfunction.

Candelario J, Chen LY, Marjoram P, Reddy S, Comai L.

Aging (Albany NY). 2012 Aug;4(8):567-77.

25.

A sample selection strategy for next-generation sequencing.

Kang CJ, Marjoram P.

Genet Epidemiol. 2012 Nov;36(7):696-709. doi: 10.1002/gepi.21664. Epub 2012 Aug 3.

26.

Genotype Imputation for Latinos Using the HapMap and 1000 Genomes Project Reference Panels.

Gao X, Haritunians T, Marjoram P, McKean-Cowdin R, Torres M, Taylor KD, Rotter JI, Gauderman WJ, Varma R.

Front Genet. 2012 Jun 27;3:117. doi: 10.3389/fgene.2012.00117. eCollection 2012.

27.

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.

Chen T, Marjoram P, Sun F, Zhou JX.

J Comput Biol. 2012 Jun;19(6):575-6. doi: 10.1089/cmb.2012.6pre. Epub 2012 May 31. No abstract available.

PMID:
22651813
28.

Methods for detecting associations between phenotype and aggregations of rare variants.

Yang F, Kang CJ, Marjoram P.

BMC Proc. 2011 Nov 29;5 Suppl 9:S51. doi: 10.1186/1753-6561-5-S9-S51.

29.

Exact coalescent simulation of new haplotype data from existing reference haplotypes.

Kang CJ, Marjoram P.

Bioinformatics. 2012 Mar 15;28(6):838-44. doi: 10.1093/bioinformatics/bts033. Epub 2012 Jan 17.

30.

Inference of population mutation rate and detection of segregating sites from next-generation sequence data.

Kang CJ, Marjoram P.

Genetics. 2011 Oct;189(2):595-605. doi: 10.1534/genetics.111.130898. Epub 2011 Aug 11.

31.

Modeling measurement error in tumor characterization studies.

Rakovski C, Weisenberger DJ, Marjoram P, Laird PW, Siegmund KD.

BMC Bioinformatics. 2011 Jul 13;12:284. doi: 10.1186/1471-2105-12-284.

32.

High DNA methylation pattern intratumoral diversity implies weak selection in many human colorectal cancers.

Siegmund KD, Marjoram P, Tavaré S, Shibata D.

PLoS One. 2011;6(6):e21657. doi: 10.1371/journal.pone.0021657. Epub 2011 Jun 28.

33.

RNA steady-state defects in myotonic dystrophy are linked to nuclear exclusion of SHARP.

Dansithong W, Jog SP, Paul S, Mohammadzadeh R, Tring S, Kwok Y, Fry RC, Marjoram P, Comai L, Reddy S.

EMBO Rep. 2011 Jul 1;12(7):735-42. doi: 10.1038/embor.2011.86.

34.

Genetic variation in Native Americans, inferred from Latino SNP and resequencing data.

Wall JD, Jiang R, Gignoux C, Chen GK, Eng C, Huntsman S, Marjoram P.

Mol Biol Evol. 2011 Aug;28(8):2231-7. doi: 10.1093/molbev/msr049. Epub 2011 Mar 2.

35.

The gene expression profile of cardia intestinal metaplasia is similar to that of Barrett's esophagus, not gastric intestinal metaplasia.

Oh DS, DeMeester SR, Tanaka K, Marjoram P, Kuramochi H, Vallbohmer D, Danenberg K, Chandrasoma PT, DeMeester TR, Hagen JA.

Dis Esophagus. 2011 Sep;24(7):516-22. doi: 10.1111/j.1442-2050.2010.01176.x. Epub 2011 Feb 10.

PMID:
21309924
36.

Choice of summary statistic weights in approximate Bayesian computation.

Jung H, Marjoram P.

Stat Appl Genet Mol Biol. 2011 Sep 27;10(1). pii: /j/sagmb.2011.10.issue-1/1544-6115.1586/1544-6115.1586.xml. doi: 10.2202/1544-6115.1586.

37.

Using DNA methylation patterns to infer tumor ancestry.

Hong YJ, Marjoram P, Shibata D, Siegmund KD.

PLoS One. 2010 Aug 9;5(8):e12002. doi: 10.1371/journal.pone.0012002.

38.

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines.

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.

Nature. 2010 Jun 3;465(7298):627-31. doi: 10.1038/nature08800. Epub 2010 Mar 24.

39.

Copy number variation in the Framingham Heart Study.

Shtir C, Pique-Regi R, Siegmund K, Morrison J, Schumacher F, Marjoram P.

BMC Proc. 2009 Dec 15;3 Suppl 7:S133.

40.

Variation in genetic admixture and population structure among Latinos: the Los Angeles Latino eye study (LALES).

Shtir CJ, Marjoram P, Azen S, Conti DV, Le Marchand L, Haiman CA, Varma R.

BMC Genet. 2009 Nov 10;10:71. doi: 10.1186/1471-2156-10-71.

41.

Critical role of nuclear calcium/calmodulin-dependent protein kinase IIdeltaB in cardiomyocyte survival in cardiomyopathy.

Little GH, Saw A, Bai Y, Dow J, Marjoram P, Simkhovich B, Leeka J, Kedes L, Kloner RA, Poizat C.

J Biol Chem. 2009 Sep 11;284(37):24857-68. doi: 10.1074/jbc.M109.003186. Epub 2009 Jul 14.

42.

Many colorectal cancers are "flat" clonal expansions.

Siegmund KD, Marjoram P, Tavaré S, Shibata D.

Cell Cycle. 2009 Jul 15;8(14):2187-93. Epub 2009 Jul 1. Review.

43.

Inferring clonal expansion and cancer stem cell dynamics from DNA methylation patterns in colorectal cancers.

Siegmund KD, Marjoram P, Woo YJ, Tavaré S, Shibata D.

Proc Natl Acad Sci U S A. 2009 Mar 24;106(12):4828-33. doi: 10.1073/pnas.0810276106. Epub 2009 Mar 4.

44.

Fast and flexible simulation of DNA sequence data.

Chen GK, Marjoram P, Wall JD.

Genome Res. 2009 Jan;19(1):136-42. doi: 10.1101/gr.083634.108. Epub 2008 Nov 24.

45.

Population genetic inference from resequencing data.

Jiang R, Tavaré S, Marjoram P.

Genetics. 2009 Jan;181(1):187-97. doi: 10.1534/genetics.107.080630. Epub 2008 Nov 3. Erratum in: Genetics. 2012 Feb;190(2):829-30.

46.

Approximately sufficient statistics and bayesian computation.

Joyce P, Marjoram P.

Stat Appl Genet Mol Biol. 2008;7(1):Article26. doi: 10.2202/1544-6115.1389. Epub 2008 Aug 30.

PMID:
18764775
47.

Modeling DNA methylation in a population of cancer cells.

Siegmund KD, Marjoram P, Shibata D.

Stat Appl Genet Mol Biol. 2008;7(1):Article 18. doi: 10.2202/1544-6115.1374. Epub 2008 Jun 22.

PMID:
18597664
48.

Genome-wide association mapping using mixed-models: application to GAW15 Problem 3.

Zhao K, Nordborg M, Marjoram P.

BMC Proc. 2007;1 Suppl 1:S164. Epub 2007 Dec 18.

49.

Cladistic analysis of genotype data-application to GAW15 Problem 3.

Jung H, Zhao K, Marjoram P.

BMC Proc. 2007;1 Suppl 1:S125. Epub 2007 Dec 18.

50.

Exploring population genetic models with recombination using efficient forward-time simulations.

Padhukasahasram B, Marjoram P, Wall JD, Bustamante CD, Nordborg M.

Genetics. 2008 Apr;178(4):2417-27. doi: 10.1534/genetics.107.085332.

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