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Bioinformatic and Statistical Methodology

Roux de Bézieux H, Street K, Fischer S, Van den Berge K, Chance R, Risso D et al. Improving replicability in single-cell RNA-seq cell type discovery with dune. BMC Bioinformatics 2024; 25. doi:10.1186/s12859-024-05814-6.
Wang H, Torous W, Gong B, Purdom E. Visualizing scRNA-seq data at population scale with GloScope. bioRxiv 2023. doi:10.1101/2023.05.29.542786.
Gong B, Zhou Y, Purdom E. Cobolt: Integrative analysis of multimodal single-cell sequencing data. Genome Biology 2021; 22: 351.
Hicks SC, Liu R, Ni Y, Purdom E, Risso D. Mbkmeans: Fast clustering for single cell data using mini-batch k-means. PLoS Computational Biology 2021; 17: e1008625.
Varoquaux N, Purdom E. A pipeline to analyse time-course gene expression data. F1000Research 2020; 9. doi:10.12688/f1000research.27262.1.
Cole MB, Risso D, Wagner A, DeTomaso D, Ngai J, Purdom E et al. Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq. Cell Systems 2019; 8: 315–328.e8.
El Karoui N, Purdom E. The non-parametric bootstrap and spectral analysis in moderate and high-dimension. In: Chaudhuri K, Sugiyama M (eds). Proceedings of the twenty-second international conference on artificial intelligence and statistics. PMLR, 2019, pp 2115–2124.
Gong B, Purdom E. MethCP: Differentially methylated region detection with change point models. In: Cowen LJ (ed). Research in computational molecular biology. Springer International Publishing: Cham, 2019, pp 68–84.
El Karoui N, Purdom E. Can we trust the bootstrap in high-dimensions? The case of linear models. Journal of Machine Learning Research 2018; 19: 1–66.
Risso D, Purvis L, Fletcher RB, Das D, Ngai J, Dudoit S et al. clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets. PLoS Computational Biology 2018; 14: 1–16.
Street K, Risso D, Fletcher RB, Das D, Ngai J, Yosef N et al. Slingshot: Cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genomics 2018; 19: 477.
Johnson M, Purdom E. Clustering of mRNA-Seq data based on alternative splicing patterns. Biostatistics 2017. doi:10.1093/biostatistics/kxw044.
Perraudeau F, Risso D, Street K, Purdom E, Dudoit S. Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference. F1000Research 2017; 6. doi:10.12688/f1000research.12122.1.
Ruddy S, Johnson M, Purdom E. Shrinkage of dispersion parameters in the binomial family, with application to differential exon skipping. Annals of Applied Statistics 2016; 10. doi:10.1214/15-AOAS871.
Purdom E, Ho C, Grasso CS, Quist MJ, Cho RJ, Spellman P et al. Methods and challenges in timing chromosomal abnormalities within cancer samples. Bioinformatics 2013; 29: 3113–3120.
Purdom E. Annotation-free estimates of gene-expression from mRNA-seq. Department of Statistics, UC Berkeley, 2012.
Purdom E. Analysis of a data matrix and a graph: Metagenomic data and the phylogenetic tree. Annals of Applied Statistics 2011; 5: 2326–2358.
Wang XV, Verhaak RGW, Purdom E, Spellman PT, Speed TP. Unifying gene expression measures from multiple platforms using factor analysis. PLoS ONE 2011; 6: e17691.
Bullard JH, Purdom E, Hansen KD, Dudoit S. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC bioinformatics 2010; 11: 94.
Purdom E, Simpson KM, Robinson MD, Conboy JG, Lapuk AV, Speed TP. FIRMA: A method for detection of alternative splicing from exon array data. Bioinformatics 2008; 24: 1707–1714.
Purdom E, Holmes SP. Error distribution for gene expression data. Statistical applications in genetics and molecular biology 2005; 4: Article16.

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Applied and Collaborative

Wu D, Hailer AA, Wang S, Yuan M, Chan J, Kurdi AE et al. A single-cell atlas of IL-23 inhibition in cutaneous psoriasis distinguishes clinical response. Science Immunology 2024; 9: eadi2848.
Caddell DF, Pettinga D, Louie K, Bowen BP, Sievert JA, Hollingsworth J et al. Drought shifts sorghum root metabolite and microbiome profiles and enriches for pipecolic acid. Phytobiomes Journal 2023; 7: 449–463.
Gao C, Courty P-E, Varoquaux N, Cole B, Montoya L, Xu L et al. Successional adaptive strategies revealed by correlating arbuscular mycorrhizal fungal abundance with host plant gene expression. Molecular Ecology 2023; 32: 2674–2687.
Van den Berge K, Chou H-J, Kunda D, Risso D, Street K, Purdom E et al. A latent activated olfactory stem cell state revealed by single cell transcriptomic and epigenomic profiling. bioRxiv 2023. doi:10.1101/2023.10.26.564041.
Wu D, Hailer A, Liu Y, Wang S, Purdom E, North J et al. Disruption of a pathologic, skin-resident T17 cell identity in clinically effective IL23 blockade of psoriasis. The Journal of investigative dermatology 2023; 143.
Cook CP, Taylor M, Liu Y, Schmidt R, Sedgewick A, Kim E et al. A single-cell transcriptional gradient in human cutaneous memory t cells restricts Th17/Tc17 identity. Cell Reports Medicine 2022; 3. doi:10.1016/j.xcrm.2022.100715.
Gao C, Xu L, Montoya L, Madera M, Hollingsworth J, Chen L et al. Co-occurrence networks reveal more complexity than community composition in resistance and resilience of microbial communities. Nature Communications 2022; 13: 3867.
Hailer A, Liu Y, Wang H, Taylor M, Cook C, North J et al. RashX: Immune single-cell transcriptional classification of human chronic inflammatory skin disease. The Journal of investigative dermatology 2022; 142.
Liu Y, Wang H, Cook C, Taylor MA, North JP, Hailer A et al. Defining patient-level molecular heterogeneity in psoriasis vulgaris based on single-cell transcriptomics. Frontiers in Immunology 2022; 13. doi:10.3389/fimmu.2022.842651.
Liu Y, Wang H, Taylor M, Cook C, Martı́nez-Berdeja A, North JP et al. Classification of human chronic inflammatory skin disease based on single-cell immune profiling. Science Immunology 2022; 7: eabl9165.
Taylor M, Cook C, Liu Y, Schmidt R, Hailer A, North J et al. A single-cell transcriptional gradient in human cutaneous memory t cells suppresses pathogenic Th17 inflammation. The Journal of investigative dermatology 2022; 142.
Callaway EM, Dong H-W, Ecker JR, Hawrylycz MJ, Huang ZJ, Lein ES et al. A multimodal cell census and atlas of the mammalian primary motor cortex. Nature 2021; 598: 86–102.
Scavuzzo-Duggan T, Varoquaux N, Madera M, Vogel JP, Dahlberg J, Hutmacher R et al. Cell wall compositions of sorghum bicolor leaves and roots remain relatively constant under drought conditions. Frontiers in Plant Science 2021; 12. doi:10.3389/fpls.2021.747225.
Xu L, Dong Z, Chiniquy D, Pierroz G, Deng S, Gao C et al. Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics. Nature Communications 2021; 12: 3209.
Yao Z, Liu H, Xie F, Fischer S, Adkins RS, Aldridge AI et al. A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature 2021; 598: 103–110.
Brann DH, Tsukahara T, Weinreb C, Lipovsek M, Van Den Berge K, Gong B et al. Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia. Science Advances 2020; 6: 1–20.
Gao C, Montoya L, Xu L, Madera M, Hollingsworth J, Purdom E et al. Fungal community assembly in drought-stressed sorghum shows stochasticity, selection, and universal ecological dynamics. Nature Communications 2020; 11: 34.
Gao C, Montoya L, Xu L, Madera M, Hollingsworth J, Purdom E et al. Strong succession in arbuscular mycorrhizal fungal communities. ISME Journal 2019; 13. doi:10.1038/s41396-018-0264-0.
Harirchian P, Lee J, Hilz S, Sedgewick AJ, Perez White BE, Kesling MJ et al. A20 and ABIN1 Suppression of a Keratinocyte Inflammatory Program with a Shared Single-Cell Expression Signature in Diverse Human Rashes. Journal of Investigative Dermatology 2019; 139: 1264–1273.
Pathi A, Smed MK, Pachter L, Purdom E, Wright M, Jewell N et al. The pre-pregnancy rheumatoid arthritis gene expression signature correlates with improvement or worsening of disease activity during pregnancy: A pilot study. Arthritis & Rheumatology 2019; 71.
Varoquaux N, Cole B, Gao C, Pierroz G, Baker CR, Patel D et al. Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses. Proceedings of the National Academy of Sciences of the United States of America 2019; 116: 27124–27132.
Cheng JB, Sedgewick AJ, Finnegan AI, Harirchian P, Lee J, Kwon S et al. Transcriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell Resolution. Cell Reports 2018; 25: 871–883.
Cho RJ, Alexandrov LB, Den Breems NY, Atanasova VS, Farshchian M, Purdom E et al. APOBEC mutation drives early-onset squamous cell carcinomas in recessive dystrophic epidermolysis bullosa. Science Translational Medicine 2018; 10: 1–12.
Fletcher RB, Das D, Gadye L, Street KN, Baudhuin A, Wagner A et al. Deconstructing Olfactory Stem Cell Trajectories at Single-Cell Resolution. Cell Stem Cell 2017; 20: 817–830.e8.
Gadye L, Das D, Sanchez MA, Street K, Baudhuin A, Wagner A et al. Injury Activates Transient Olfactory Stem Cell States with Diverse Lineage Capacities. Cell Stem Cell 2017; 21: 775–790.e9.
Goin DE, Smed MK, Pachter L, Purdom E, Nelson JL, Kjærgaard H et al. Pregnancy-induced gene expression changes in vivo among women with rheumatoid arthritis: A pilot study. Arthritis Research and Therapy 2017; 19. doi:10.1186/s13075-017-1312-2.
Naylor D, Degraaf S, Purdom E, Coleman-Derr D. Drought and host selection influence bacterial community dynamics in the grass root microbiome. ISME Journal 2017; 11. doi:10.1038/ismej.2017.118.
Sanborn JZ, Chung J, Purdom E, Wang NJ, Kakavand H, Wilmott JS et al. Phylogenetic analyses of melanoma reveal complex patterns of metastatic dissemination. Proceedings of the National Academy of Sciences of the United States of America 2015; 112. doi:10.1073/pnas.1508074112.
Zheng CL, Wang NJ, Chung J, Moslehi H, Sanborn JZ, Hur JS et al. Transcription Restores DNA Repair to Heterochromatin, Determining Regional Mutation Rates in Cancer Genomes. Cell Reports 2014; 9: 1228–1234.
Purdom E, Restall C, Busuttil RA, Schluter H, Boussioutas A, Thompson EW et al. Determining epithelial contribution to in vivo mesenchymal tumour expression signature using species-specific microarray profiling analysis of xenografts. Genetics Research 2013; 95. doi:10.1017/S0016672313000013.
Couvillion MT, Bounova G, Purdom E, Speed TP, Collins K. A Tetrahymena Piwi Bound to Mature tRNA 3’ Fragments Activates the Exonuclease Xrn2 for RNA Processing in the Nucleus. Molecular cell 2012; 48: 509–520.
Heiser LM, Sadanandam A, Kuo W-L, Benz SC, Goldstein TC, Ng S et al. Subtype and pathway specific responses to anticancer compounds in breast cancer. Proceedings of the National Academy of Sciences of the United States of America 2012; 109. doi:10.1073/pnas.1018854108.
Bell D, Berchuck A, Birrer M, Chien J, Cramer DW, Dao F et al. Integrated genomic analyses of ovarian carcinoma. Nature 2011; 474. doi:10.1038/nature10166.
Durinck S, Ho C, Wang NJ, Liao W, Jakkula LR, Collisson EA et al. Timing chromosomal abnormalities using mutation data. Genome Biology 2011; 12: P39.
Durinck S, Ho C, Wang NJ, Liao W, Jakkula LR, Collisson EA et al. Temporal Dissection of Tumorigenesis in Primary Cancers. Cancer Discovery 2011; 1: 137–143.
Lapuk A, Marr H, Jakkula L, Pedro H, Bhattacharya S, Purdom E et al. Exon-Level Microarray Analyses Identify Alternative Splicing Programs in Breast Cancer. Molecular Cancer Research 2010; 8: 961–74.
Verhaak RGW, Hoadley KA, Purdom E, Wang V, Qi Y, Wilkerson MD et al. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell 2010; 17: 98–110.
McLendon R, Friedman A, Bigner D, Van Meir EG, Brat DJ, Mastrogianakis GM et al. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 2008; 455. doi:10.1038/nature07385.
Bik EM, Eckburg PB, Gill SR, Nelson KE, Purdom EA, Francois F et al. Molecular analysis of the bacterial microbiota in the human stomach. Proceedings of the National Academy of Sciences of the United States of America 2006; 103. doi:10.1073/pnas.0506655103.
Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M et al. Diversity of the human intestinal microbial flora. Science 2005; 308: 1635–8.
Xu T, Shu C-T, Purdom E, Dang D, Ilsley D, Guo Y et al. Microarray analysis reveals differences in gene expression of circulating CD8(+) T cells in melanoma patients and healthy donors. Cancer Research 2004; 64: 3661–3667.

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Books/Reviews

Purdom E, Mukherjee S. Transcriptomic Technologies and Statistical Data Analysis. In: Handbook of Statistical Systems Biology. Wiley Online Library, 2011, pp 133–162.
Purdom E. Multivariate Kernel Methods in the Analysis of Graphical Structures. 2006.
Purdom E. Statistical methods for data science. https://epurdom.github.io/Stat131A/book/index.html.

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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 www.aroma-project.org)

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Last updated 08/2021