Publications | ||||||
Methodology | Applied | Books/Reviews | Software | Home Page | ||||||
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.
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.
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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Last updated 08/2021 |