Publications
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Bioinformatic and Statistical Methodology

  1. Street K, Risso D, Fletcher RB, Das D, Ngai J, Yosef N, Purdom E, and Dudoit S (under revision) "Slingshot: Cell lineage and pseudotime inference for single-cell transcriptomics" biorXiv link
  2. Perraudeau F, Risso D, Street K, Purdom E, and Dudoit S (2017) "Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference" F1000Research 6:1158. link
  3. El Karoui N, and Purdom E (under review) "The bootstrap, covariance matrices and PCA in moderate and high-dimensions" arXiv link
  4. El Karoui N, and Purdom E (under review) "Can we trust the bootstrap in high-dimension?" original tech report, updated arXiv link
  5. Johnson M and Purdom E (2017) "Clustering of mRNA-Seq data based on alternative splicing patterns," Biostatistics (2017) 18 (2): 295-307. link
  6. Ruddy S, Johnson M, Purdom E (2016) "Shrinkage of dispersion parameters in the binomial family, with application to differential exon skipping," Annals of Applied Statistics 10: 690-725 link
  7. Purdom E, Ho C, Grasso CS, Quist MJ, Cho RJ, and Spellman P (2013) "Methods and challenges in timing chromosomal abnormalities within cancer samples," Bioinformatics. 29(24):3113-20. link
  8. Purdom E (2012) "Annotation-Free Estimates of Gene-Expression from mRNA-Seq," Technical Report 825, Department of Statistics, UC Berkeley link
  9. Purdom E (2011) "Analysis Of A Data Matrix And A Graph: Metagenomic Data And The Phylogenetic Tree", Ann. Appl. Stat. 5(4): 2326-2358. link
  10. Wang XV, Verhaak RGW, Purdom E, Spellman PT, Speed TP (2011). "Unifying gene expression measures from multiple platforms using factor analysis" PloS one, 6(3) link
  11. Bullard J, Purdom E, Hansen K, Dudoit S. (2010) "Evaluation of Statistical Methods for Normalization and Differential Expression in mRNA-Seq Experiments", BMC Bioinformatics 11:94. link
  12. Purdom E. (2008) "Analyzing Data with Graphs: Metagenomic Data and the Phylogenetic Tree" Technical Report 766, Department of Statistics, UC Berkeley. link
  13. Purdom E, Simpson K, Robinson M, Conboy J, Lapuk A. and Speed T. (2008) "FIRMA: A Method for Detection of Alternative Splicing from Exon Array Data" Bioinformatics 24(15): 1707-1714. link Data
  14. Purdom E and Holmes S. (2005) "Error Distribution for Gene Expression Data", Statistical Applications in Genetics and Molecular Biology 4(1): Article 16. http://www.bepress.com/sagmb/vol4/iss1/art16

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Applied and Collaborative

  1. Naylor D, DeGraaf S, Purdom E, and Coleman-Derr D (2017) "Drought and host selection influence bacterial community dynamics in the grass root microbiome" ISME Journal Jul 28. doi: 10.1038/ismej.2017.118. [Epub ahead of print] link
  2. Fletcher RB, Das D, Gadye L, Street KN, Baudhuin A, Wagner A, Cole MB, Flores Q, Choi YG, Yosef N, Purdom E, Dudoit S, Risso D and Ngai J (2017) "Deconstructing Olfactory Stem Cell Trajectories at Single Cell Resolution" Cell Stem Cell 20(6):817-830. link
  3. Sanborn Z, Chung J, Purdom E, Wang NJ, Kakavand H, Wilmott J, Butler T, Thompson JF, Mann GJ, Haydu LE, Saw RP, Busam KJ, Lo R, Collisson EA, Hur JS, Spellman P, Cleaver JE, Gray JW, Huh N, Murali R, Scolyer RA, Bastian BC, Cho RJ (2015) "Phylogenetic analyses of melanoma reveal complex patterns of metastatic dissemination" PNAS 112: 10995-11000 link
  4. Zheng CL, Wang NJ, Chung J, Moslehi H, Sanborn JZ, Hur JS, Collisson EA, Vemula SS, Naujokas A, Chiotti KE, Cheng JB, Fassihi H, Blumberg AJ, Bailey CV, Fudem GM, Mihm FG, Cunningham BB, Neuhaus IM, Liao W, Oh DH, Cleaver JE, LeBoit PE, Costello JF, Lehmann AR, Gray JW, Spellman PT, Arron ST, Huh N, Purdom E, Cho RJ (2014) "Transcription Restores DNA Repair to Heterochromatin, Determining Regional Mutation Rates in Cancer Genomes" Cell Reports 9(4): 1228-1234. link
  5. Purdom E, Restall C, Busuttil RA, Schluter H, Boussioutas A, Thompson EW, Anderson RL, Speed TP, Haviv I. (2013) "Determining epithelial contribution to in vivo mesenchymal tumour expression signature using species-specific microarray profiling analysis of xenografts." Genetics Research. 95(1):14-29.link
    Xenograft specific cdfs: Human cdf, Mouse cdf
  6. Couvillion M, Bounova G, Purdom E, Speed T, and Collins K. (2013) "A Tetrahymena Piwi bound to mature tRNA 3' fragments activates the exonuclease Xrn2 for RNA processing in the nucleus" Molecular Cell. 48:509-20. link
  7. Heiser LM, Sadanandam A, Kuo WL, Benz SC, Goldstein TC, Ng S, Gibb WJ, Wang NJ, Ziyad S, Tong F, Bayani N, Hu Z, Billig JI, Dueregger A, Lewis S, Jakkula L, Korkola JE, Durinck S, Pepin F, Guan Y, Purdom E, Neuvial P, Bengtsson H, Wood KW, Smith PG, Vassilev LT, Hennessy BT, Greshock J, Bachman KE, Hardwicke MA, Park JW, Marton LJ, Wolf DM, Collisson EA, Neve RM, Mills GB, Speed TP, Feiler HS, Wooster RF, Haussler D, Stuart JM, Gray JW, and Spellman PT (2012). "Subtype and pathway specific responses to anticancer compounds in breast cancer,"" Proc Natl Acad Sci U S A. 109(8):2724-9. link
  8. The Cancer Genome Atlas Research Network (2011) "Integrated genomic analyses of ovarian carcinoma," Nature. 474(7353):609-15. link
  9. Durinck S, Ho C, Wang NJ, Liao W, Jakkula LR, Collisson EA, Pons J, Chan SW, Lam ET, Chu C, Park K, Hong SW, Hur JS, Huh N, Neuhaus IM, Yu SS, Grekin RC, Mauro TM, Cleaver JE, Kwok PY, LeBoit PE, Getz G, Cibulskis K, Aster JC, Huang H, Purdom E, Li J, Bolund L, Arron ST, Gray JW, Spellman PT, and Cho RJ (2011). "Temporal Dissection of Tumorigenesis in Primary Cancers." Cancer Discovery. 1:137-143. link
  10. Lapuk A, Marr H, Jakkula L, Pedro H, Bhattacharya S, Purdom E, Hu Z, Simpson K, Pachter L, Durinck S, Wang N, Parvin B, Fontenay G, Speed T, Garbe J, Stampfer M, Bayandorian H, Dorton S, Clark TA, Schweitzer A, Wyrobek A, Feiler H, Spellman P, Conboy J, Gray JW. (2010) "Exon-level microarray analyses identify alternative splicing programs in breast cancer", Molecular Cancer Research 8(7):961-74 link
  11. Verhaak R, Hoadley K, Purdom E, Wang V, Qi Y, Wilkerson M, Miller CR , Ding L, Golub T, Mesirov JP, Alexe G, Lawrence M, O'Kelly M, Tamayo P, Weir BA, Gabriel S, Winckler W, Gupta S, Jakkula L, Feiler HS, Hodgson JG, James CD, Sarkaria JN, Brennan C, Kahn,A, Spellman PT, Wilson RK, Speed TP, Gray JW, Meyerson M, Getz G, Perou C, Hayes DN and The Cancer Genome Atlas Research Network (2010) "Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1", Cancer Cell 17(1): 98-110. link
  12. The Cancer Genome Atlas Research Network (2008) "Comprehensive Genomic Characterization Defines Human Glioblastoma Genes and Core Pathways" Nature 455(7216): 1061-1068. link
  13. Bik E, Eckburg P, Gill S, Nelson K, Purdom E, Francois F, Perez-Perez G, Blaser M, and Relman D. (2006) "Molecular Analysis of the Bacterial Microbiota in the Human Stomach", PNAS 103(1): 732-737. link
  14. Eckburg P, Bik E, Bernstein C, Purdom E, Dethlefsen L, Sargent M, Gill S, Nelson K, and Relman D. (2005) "Diversity of the Human Intestinal Microbial Flora", Science 308: 1635-1638. link
  15. Xu T, Xhu C.-T, Purdom E, Dang D, Ilsley D, Guo Y, Weber J, Holmes S.P. and Lee P.P (2004) "Microarray Analysis Reveals Differences in Gene Expression of Circulating CD8+ T Cells in Melanoma Patients and Healthy Donors", Cancer Research 64: 3661-3667. link

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Reviews

  1. Purdom E and Mukherjee S. (2011) "Transcriptomic Technologies and Statistical Data Analysis" in Handbook of Statistical Systems Biology. (eds M. P. H. Stumpf, D. J. Balding and M. Girolami), Wiley & Sons, Ltd, Chichester, UK, 135-162. link

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Related Software

  1. clusterExperiment : a package for clustering of single-cell sequencing data and other high-throughput experiments with large numbers of samples. (Available as a bioconductor package and also available on github)
  2. DoubleExpSeq: Differential Exon Usage Test for RNA-Seq data via Empirical Bayes Shrinkage of the Dispersion Parameter (R package, available on CRAN)
  3. cancerTiming: Estimation of temporal ordering of cancer abnormalities. (R package, available on CRAN and GitHub )
  4. FIRMA available in the R package aroma.affymetrix, available on www.aroma-project.org

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Last updated 08/2016