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Bioinformatic and Statistical Methodology

  1. Wang H, Torous W, Gong B, Purdom E (2023) "Visualizing scRNA-Seq Data at Population Scale with GloScope" BioRXiv preprint
  2. Roux de Bezieux H, Street K, Fischer S, Van den Berge K, Chance R, Risso D, Gillis J, Ngai J, Purdom E, and Dudoit S (2024) "Improving replicability in single-cell RNA-Seq cell type discovery with Dune" BMC Bioinformatics 25: 198 link
  3. Gong B, Zhou Y, and Purdom E (2021) "Cobolt: integrative analysis of multimodal single-cell sequencing data" Genome Biology 22, Article number: 351 link
  4. Hicks SC, Liu R, Ni Y, Purdom E, Risso D (2021) "mbkmeans: fast clustering for single cell data using mini-batch k-means" PLOS Computational Biology 17(1): e1008625 link
  5. Varoquaux N., Purdom E. (2020) "A pipeline to analyse time-course gene expression data" F1000Research 9:1447 link
  6. Gong B., Purdom E. (2019) MethCP: Differentially Methylated Region Detection with Change Point Models. In: Cowen L. (eds) Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467. link
  7. El Karoui N and Purdom E (2019) "The bootstrap, covariance matrices and PCA in moderate and high-dimensions" Proceedings of Machine Learning Research: The 22nd International Conference on Artificial Intelligence and Statistics. 89:2115-2124. link
  8. Cole MB, Risso D, Wagner A, DeTomaso D, Ngai J, Purdom E, Dudoit S, Yosef N (2019) "Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq" Cell Systems 8(4): 315-328. link
  9. Risso D, Purvis L, Fletcher R, Das D, Ngai J, Dudoit S, Purdom E (2018) "clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets" PLoS Comput Biol. 2018 Sep 4;14(9):e1006378 link
  10. Street K, Risso D, Fletcher RB, Das D, Ngai J, Yosef N, Purdom E, and Dudoit S (2018) "Slingshot: Cell lineage and pseudotime inference for single-cell transcriptomics" BMC Genomics 19(1): 477. link
  11. El Karoui N, and Purdom E (2018) "Can we trust the bootstrap in high-dimension?" Journal of Machine Learning Research 19 (2018) 1-66 link
  12. 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
  13. Johnson M and Purdom E (2017) "Clustering of mRNA-Seq data based on alternative splicing patterns," Biostatistics (2017) 18 (2): 295-307. link
  14. 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
  15. 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
  16. Purdom E (2012) "Annotation-Free Estimates of Gene-Expression from mRNA-Seq," Technical Report 825, Department of Statistics, UC Berkeley link
  17. 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
  18. 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
  19. 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
  20. Purdom E. (2008) "Analyzing Data with Graphs: Metagenomic Data and the Phylogenetic Tree" Technical Report 766, Department of Statistics, UC Berkeley. link
  21. 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
  22. Purdom E and Holmes S. (2005) "Error Distribution for Gene Expression Data", Statistical Applications in Genetics and Molecular Biology 4(1): Article 16.

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Applied and Collaborative

  1. BRAIN Initiative Cell Census Network (BICCN) (2021) "A multimodal cell census and atlas of the mammalian primary motor cortex" Nature 598: 86–102. link
  2. Yao Z, Liu H, Xie F, Fischer S, et al (2021) "An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types" Nature 598: 103-110. link
  3. Brann DH, Tsukahara T, Weinreb C, Lipovsek M, Van den Berge K, Gong B, Chance R, Macaulay IC, Chou H-J, Fletcher RB, Das D, Street K, Roux de Bezieux H, Choi YG, Risso D, Dudoit S, Purdom E, Mill J, Hachem RA, Matsunami H, Logan DW, Goldstein BJ, Grubb MS, Ngai J, Datta SR (2020) "Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia" Science Advances 6: eabc5801 link
  4. Gao C, Montoya L, Xu L, Madera M, Hollingsworth J, Purdom E, Singan V, Vogel J, Hutmacher RB, Dahlberg JA, Coleman-Derr D, Lemaux PG, and Taylor JW (2020) "Fungal community assembly in drought-stressed sorghum shows stochasticity, selection, and universal ecological dynamics" Nature Communications 11:34. link
  5. Varoquaux N, Cole B, Gao C, Pierroz G, Baker CR, Patel D, Madera M, Jeffers T, Hollingsworth J, Sievert J, Yoshinaga Y, Owiti JA, Singan VR, DeGraaf S, Xu L, Blow MJ, Harrison MJ, Visel A, Jansson C, Niyogi KK, Hutmacher R, Coleman-Derr D, O'Malley RC, Taylor JW, Dahlberg J, Vogel JP, Lemaux PG, and Purdom E (2019) "Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses" PNAS, 116(52): 27124-27132. link
  6. Harirchian P, Lee J, Hilz S, Sedgewick AJ, Perez White BE, Kesling MJ, Mully T, Golovato J, Gray M, Mauro TM, Purdom E, Kim EA, Sbitany H, Bhutani T, Vaske CJ, Benz SC, Cho RJ, and Cheng JB (2019) "A20 and ABIN1 Suppression of a Keratinocyte Inflammatory Program with a Shared Single-Cell Expression Signature in Diverse Human Rashes," Journal of Investigative Dermatology, 139(6), 1264-1273. link
  7. Gao C, Montoya L, Xu L, Madera M, Hollingsworth J, Purdom E, Hutmacher RB, Dahlberg JA, Coleman-Derr D, Lemaux PG, and Taylor JW (2018) "Strong succession in arbuscular mycorrhizal fungal communities" The ISME Journal link
  8. Cheng JB, Sedgewick AJ, Finnegan AI, Harirchian P, Lee J, Kwon S, Fassett MS, Golovato J, Gray M, Ghadially R, Liao W, White BEP, Mauro TM, Mully T, Kim EA, Sbitany H, Neuhaus IM, Grekin RC, Yu SS, Gray JW, Purdom E, Paus R, Vaske CJ, Benz SC, Song JS, Cho RJ (2018). "Transcriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell Resolution" Cell Reports, 25(4), 871-883. link
  9. Cho RJ, Alexandrov LB, den Breems NY, Atanasova VS, Farshchian M, Purdom E, Nguyen TN, Coarfa C, Rajapakshe K, Prisco M, Sahu J, Tassone P, Greenawalt EJ, Collisson EA, Wu W, Yao H, Su X, Guttmann-Gruber C, Hofbauer PN, Hashmi R, Fuentes I, Benz SC, Golovato J, Ehli EA, Davis CM, Davies GE, Covington KR, Murrell DF, Salas-Alanis JC, Palisson F, Bruckner AL, Robinson W, Has C, Bruckner-Tuderman L, Titeux M, Jonkman MF, Rashidghamat E, Lwin SM, Mellerio JE, McGrath JA, Bauer JW, Hovnanian A, Tsai KY, South AP (2018) "APOBEC mutation drives early-onset squamous cell carcinomas in recessive dystrophic epidermolysis bullosa" Science Translational Medicine 10 (455): eaas9668 link
  10. Gadye L, Das D, Sanchez MA, Street K, Baudhuin A, Wagner A, Cole MB, Choi YG, Yosef N, Purdom E, Dudoit S, Risso D, Ngai J, and Fletcher RB (2017) "Injury Activates Transient Olfactory Stem Cell States with Diverse Lineage Capacities" Cell Stem Cell 21(6): 775-790 link
  11. 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 11: 2691-2704 link
  12. 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
  13. 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
  14. 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
  15. 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)
    Xenograft specific cdfs: Human cdf, Mouse cdf
  16. 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
  17. 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
  18. The Cancer Genome Atlas Research Network (2011) "Integrated genomic analyses of ovarian carcinoma," Nature. 474(7353):609-15. link
  19. 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
  20. 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
  21. 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
  22. The Cancer Genome Atlas Research Network (2008) "Comprehensive Genomic Characterization Defines Human Glioblastoma Genes and Core Pathways" Nature 455(7216): 1061-1068. link
  23. 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
  24. 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
  25. 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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  1. Purdom E (2020) Statistical Methods for Data Science Online book
  2. 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. Cobolt: Joint analysis of multimodal single-cell sequencing data
    (python package available on Github)
  2. moanin: An R Package for Time Course RNASeq Data Analysis
    (available on Bioconductor)
  3. mbkmeans: Mini-batch K-means Clustering for Single-Cell RNA-seq
    (available on Bioconductor)
  4. Dune: Improving replicability in single-cell RNA-Seq cell type discovery
    (available on Bioconductor)
  5. methCP: An R package for Differentially Methylated Region Detection by Boying Gong
    (available on Github)
  6. Slingshot: Lineage Inference for Single-cell Data by Kelly Street
    (available on Bioconductor)
  7. clusterExperiment : a package for clustering of single-cell sequencing data and other high-throughput experiments with large numbers of samples by Elizabeth Purdom and Davide Risso
    (Available as a bioconductor package and also available on github)
  8. DoubleExpSeq: Differential Exon Usage Test for RNA-Seq data via Empirical Bayes Shrinkage of the Dispersion Parameter by Sean Ruddy
    (R package, available on CRAN)
  9. cancerTiming: Estimation of temporal ordering of cancer abnormalities. by Elizabeth Purdom
    (R package, available on CRAN and GitHub )
  10. FIRMA available in the R package aroma.affymetrix, by Elizabeth Purdom
    (available on

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Last updated 08/2021