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Items: 33

1.

Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq.

Cole MB, Risso D, Wagner A, DeTomaso D, Ngai J, Purdom E, Dudoit S, Yosef N.

Cell Syst. 2019 Apr 24;8(4):315-328.e8. doi: 10.1016/j.cels.2019.03.010.

PMID:
31022373
2.

A20 and ABIN1 Suppression of a Keratinocyte Inflammatory Program with a Shared Single-Cell Expression Signature in Diverse Human Rashes.

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, Cheng JB.

J Invest Dermatol. 2019 Jun;139(6):1264-1273. doi: 10.1016/j.jid.2018.10.046. Epub 2018 Dec 10.

PMID:
30543901
3.

Transcriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell Resolution.

Cheng JB, Sedgewick AJ, Finnegan AI, Harirchian P, Lee J, Kwon S, Fassett MS, Golovato J, Gray M, Ghadially R, Liao W, Perez White BE, 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.

Cell Rep. 2018 Oct 23;25(4):871-883. doi: 10.1016/j.celrep.2018.09.006.

4.

clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets.

Risso D, Purvis L, Fletcher RB, Das D, Ngai J, Dudoit S, Purdom E.

PLoS Comput Biol. 2018 Sep 4;14(9):e1006378. doi: 10.1371/journal.pcbi.1006378. eCollection 2018 Sep. Erratum in: PLoS Comput Biol. 2019 Jan 11;15(1):e1006727.

5.

Strong succession in arbuscular mycorrhizal fungal communities.

Gao C, Montoya L, Xu L, Madera M, Hollingsworth J, Purdom E, Hutmacher RB, Dahlberg JA, Coleman-Derr D, Lemaux PG, Taylor JW.

ISME J. 2019 Jan;13(1):214-226. doi: 10.1038/s41396-018-0264-0. Epub 2018 Aug 31.

6.

APOBEC mutation drives early-onset squamous cell carcinomas in recessive dystrophic epidermolysis bullosa.

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 JP, 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.

Sci Transl Med. 2018 Aug 22;10(455). pii: eaas9668. doi: 10.1126/scitranslmed.aas9668.

PMID:
30135250
7.

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.

Street K, Risso D, Fletcher RB, Das D, Ngai J, Yosef N, Purdom E, Dudoit S.

BMC Genomics. 2018 Jun 19;19(1):477. doi: 10.1186/s12864-018-4772-0.

8.

Injury Activates Transient Olfactory Stem Cell States with Diverse Lineage Capacities.

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, Fletcher RB.

Cell Stem Cell. 2017 Dec 7;21(6):775-790.e9. doi: 10.1016/j.stem.2017.10.014. Epub 2017 Nov 22.

9.

Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference.

Perraudeau F, Risso D, Street K, Purdom E, Dudoit S.

F1000Res. 2017 Jul 21;6:1158. doi: 10.12688/f1000research.12122.1. eCollection 2017.

10.

Drought and host selection influence bacterial community dynamics in the grass root microbiome.

Naylor D, DeGraaf S, Purdom E, Coleman-Derr D.

ISME J. 2017 Dec;11(12):2691-2704. doi: 10.1038/ismej.2017.118. Epub 2017 Jul 28.

11.

Pregnancy-induced gene expression changes in vivo among women with rheumatoid arthritis: a pilot study.

Goin DE, Smed MK, Pachter L, Purdom E, Nelson JL, Kjærgaard H, Olsen J, Hetland ML, Zoffmann V, Ottesen B, Jawaheer D.

Arthritis Res Ther. 2017 May 25;19(1):104. doi: 10.1186/s13075-017-1312-2.

12.

Deconstructing Olfactory Stem Cell Trajectories at Single-Cell Resolution.

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, Ngai J.

Cell Stem Cell. 2017 Jun 1;20(6):817-830.e8. doi: 10.1016/j.stem.2017.04.003. Epub 2017 May 11.

13.

Clustering of mRNA-Seq data based on alternative splicing patterns.

Johnson M, Purdom E.

Biostatistics. 2017 Apr 1;18(2):295-307. doi: 10.1093/biostatistics/kxw044.

14.

Phylogenetic analyses of melanoma reveal complex patterns of metastatic dissemination.

Sanborn JZ, Chung J, Purdom E, Wang NJ, Kakavand H, Wilmott JS, Butler T, Thompson JF, Mann GJ, Haydu LE, Saw RP, Busam KJ, Lo RS, Collisson EA, Hur JS, Spellman PT, Cleaver JE, Gray JW, Huh N, Murali R, Scolyer RA, Bastian BC, Cho RJ.

Proc Natl Acad Sci U S A. 2015 Sep 1;112(35):10995-1000. doi: 10.1073/pnas.1508074112. Epub 2015 Aug 18.

15.

Transcription restores DNA repair to heterochromatin, determining regional mutation rates in cancer genomes.

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.

Cell Rep. 2014 Nov 20;9(4):1228-34. doi: 10.1016/j.celrep.2014.10.031. Epub 2014 Nov 20.

16.

Methods and challenges in timing chromosomal abnormalities within cancer samples.

Purdom E, Ho C, Grasso CS, Quist MJ, Cho RJ, Spellman P.

Bioinformatics. 2013 Dec 15;29(24):3113-20. doi: 10.1093/bioinformatics/btt546. Epub 2013 Sep 23.

17.

Determining epithelial contribution to in vivo mesenchymal tumour expression signature using species-specific microarray profiling analysis of xenografts.

Purdom E, Restall C, Busuttil RA, Schluter H, Boussioutas A, Thompson EW, Anderson RL, Speed TP, Haviv I.

Genet Res (Camb). 2013 Feb;95(1):14-29. doi: 10.1017/S0016672313000013. Epub 2013 Mar 18.

PMID:
23497823
18.

A Tetrahymena Piwi bound to mature tRNA 3' fragments activates the exonuclease Xrn2 for RNA processing in the nucleus.

Couvillion MT, Bounova G, Purdom E, Speed TP, Collins K.

Mol Cell. 2012 Nov 30;48(4):509-20. doi: 10.1016/j.molcel.2012.09.010. Epub 2012 Oct 18.

19.

Subtype and pathway specific responses to anticancer compounds in breast cancer.

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, Spellman PT.

Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):2724-9. doi: 10.1073/pnas.1018854108. Epub 2011 Oct 14.

20.

Temporal dissection of tumorigenesis in primary cancers.

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, Cho RJ.

Cancer Discov. 2011 Jul;1(2):137-43. doi: 10.1158/2159-8290.CD-11-0028. Epub 2011 Jun 29.

21.

Unifying gene expression measures from multiple platforms using factor analysis.

Wang XV, Verhaak RG, Purdom E, Spellman PT, Speed TP.

PLoS One. 2011 Mar 11;6(3):e17691. doi: 10.1371/journal.pone.0017691.

22.

Exon-level microarray analyses identify alternative splicing programs in breast cancer.

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.

Mol Cancer Res. 2010 Jul;8(7):961-74. doi: 10.1158/1541-7786.MCR-09-0528. Epub 2010 Jul 6.

23.

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments.

Bullard JH, Purdom E, Hansen KD, Dudoit S.

BMC Bioinformatics. 2010 Feb 18;11:94. doi: 10.1186/1471-2105-11-94.

24.

Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1.

Verhaak RG, Hoadley KA, Purdom E, Wang V, Qi Y, Wilkerson MD, 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 CM, Hayes DN; Cancer Genome Atlas Research Network.

Cancer Cell. 2010 Jan 19;17(1):98-110. doi: 10.1016/j.ccr.2009.12.020.

25.

FIRMA: a method for detection of alternative splicing from exon array data.

Purdom E, Simpson KM, Robinson MD, Conboy JG, Lapuk AV, Speed TP.

Bioinformatics. 2008 Aug 1;24(15):1707-14. doi: 10.1093/bioinformatics/btn284. Epub 2008 Jun 23.

26.

Pneumosinus dilatans.

Nowlin TP 4th, Hall DJ, Purdom EB, Holtel MR.

Ear Nose Throat J. 2007 May;86(5):290-1.

PMID:
17580810
27.

Acute airway obstruction from a thyroglossal duct cyst.

Purdom E, Robitschek J, Littlefield PD, Cable B.

Otolaryngol Head Neck Surg. 2007 Feb;136(2):317-8. No abstract available.

PMID:
17275565
28.

Error distribution for gene expression data.

Purdom E, Holmes SP.

Stat Appl Genet Mol Biol. 2005;4:Article16. Epub 2005 Jul 12.

PMID:
16646833
29.

Molecular analysis of the bacterial microbiota in the human stomach.

Bik EM, Eckburg PB, Gill SR, Nelson KE, Purdom EA, Francois F, Perez-Perez G, Blaser MJ, Relman DA.

Proc Natl Acad Sci U S A. 2006 Jan 17;103(3):732-7. Epub 2006 Jan 4.

30.
31.

Diversity of the human intestinal microbial flora.

Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA.

Science. 2005 Jun 10;308(5728):1635-8. Epub 2005 Apr 14.

32.

Microarray analysis reveals differences in gene expression of circulating CD8(+) T cells in melanoma patients and healthy donors.

Xu T, Shu CT, Purdom E, Dang D, Ilsley D, Guo Y, Weber J, Holmes SP, Lee PP.

Cancer Res. 2004 May 15;64(10):3661-7.

33.

The use of radioisotopes as tracers in cigarette smoke.

WOLFF WA, PURDOM EG, ISENHOWER JA.

N C Med J. 1954 Apr;15(4):159-63. No abstract available.

PMID:
13154697

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