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Items: 19

1.

TOX is a critical regulator of tumour-specific T cell differentiation.

Scott AC, Dündar F, Zumbo P, Chandran SS, Klebanoff CA, Shakiba M, Trivedi P, Menocal L, Appleby H, Camara SJ, Zamarin D, Walther T, Snyder AC, Femia MR, Comen EA, Wen HY, Hellmann MD, Anandasabapathy N, Liu Y, Altorki NK, Lauer P, Levy O, Glickman M, Kaye J, Betel D, Philip M, Schietinger A.

Nature. 2019 Jun 17. doi: 10.1038/s41586-019-1324-y. [Epub ahead of print]

PMID:
31207604
2.

Genome-scale screens identify JNK-JUN signaling as a barrier for pluripotency exit and endoderm differentiation.

Li QV, Dixon G, Verma N, Rosen BP, Gordillo M, Luo R, Xu C, Wang Q, Soh CL, Yang D, Crespo M, Shukla A, Xiang Q, Dündar F, Zumbo P, Witkin M, Koche R, Betel D, Chen S, Massagué J, Garippa R, Evans T, Beer MA, Huangfu D.

Nat Genet. 2019 Jun;51(6):999-1010. doi: 10.1038/s41588-019-0408-9. Epub 2019 May 20.

PMID:
31110351
3.

Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics.

Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O'Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O'Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE.

Cell Syst. 2015 Jul 29;1(1):97-97.e3. doi: 10.1016/j.cels.2015.07.006. Epub 2015 Jul 29. No abstract available.

4.

Modern Methods for Delineating Metagenomic Complexity.

Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O'Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O'Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE.

Cell Syst. 2015 Jul 29;1(1):6-7. doi: 10.1016/j.cels.2015.07.007. Epub 2015 Jul 29. No abstract available.

5.

Features of Circulating Parainfluenza Virus Required for Growth in Human Airway.

Palermo LM, Uppal M, Skrabanek L, Zumbo P, Germer S, Toussaint NC, Rima BK, Huey D, Niewiesk S, Porotto M, Moscona A.

MBio. 2016 Mar 15;7(2):e00235. doi: 10.1128/mBio.00235-16.

6.

Erratum to: Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data.

Rapaport F, Khanin R, Liang Y, Pirun M, Krek A, Zumbo P, Mason CE, Socci ND, Betel D.

Genome Biol. 2015 Nov 23;16:261. doi: 10.1186/s13059-015-0813-z. No abstract available.

7.

Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics.

Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O'Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O'Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE.

Cell Syst. 2015 Jul 29;1(1):72-87. Epub 2015 Mar 3.

8.

Mining the Archives: A Cross-Platform Analysis of Gene Expression Profiles in Archival Formalin-Fixed Paraffin-Embedded Tissues.

Webster AF, Zumbo P, Fostel J, Gandara J, Hester SD, Recio L, Williams A, Wood CE, Yauk CL, Mason CE.

Toxicol Sci. 2015 Dec;148(2):460-72. doi: 10.1093/toxsci/kfv195. Epub 2015 Sep 10.

9.

Detecting and correcting systematic variation in large-scale RNA sequencing data.

Li S, Łabaj PP, Zumbo P, Sykacek P, Shi W, Shi L, Phan J, Wu PY, Wang M, Wang C, Thierry-Mieg D, Thierry-Mieg J, Kreil DP, Mason CE.

Nat Biotechnol. 2014 Sep;32(9):888-95. doi: 10.1038/nbt.3000. Epub 2014 Aug 24.

10.

Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study.

Li S, Tighe SW, Nicolet CM, Grove D, Levy S, Farmerie W, Viale A, Wright C, Schweitzer PA, Gao Y, Kim D, Boland J, Hicks B, Kim R, Chhangawala S, Jafari N, Raghavachari N, Gandara J, Garcia-Reyero N, Hendrickson C, Roberson D, Rosenfeld J, Smith T, Underwood JG, Wang M, Zumbo P, Baldwin DA, Grills GS, Mason CE.

Nat Biotechnol. 2014 Sep;32(9):915-925. doi: 10.1038/nbt.2972. Epub 2014 Aug 24. Erratum in: Nat Biotechnol. 2014 Nov;32(11):1166. Rosenfeld, Jeffrey [corrected to Rosenfeld, Jeffrey A].

11.

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data.

Rapaport F, Khanin R, Liang Y, Pirun M, Krek A, Zumbo P, Mason CE, Socci ND, Betel D.

Genome Biol. 2013;14(9):R95. Erratum in: Genome Biol. 2015;16:261.

12.

A hybrid mechanism of action for BCL6 in B cells defined by formation of functionally distinct complexes at enhancers and promoters.

Hatzi K, Jiang Y, Huang C, Garrett-Bakelman F, Gearhart MD, Giannopoulou EG, Zumbo P, Kirouac K, Bhaskara S, Polo JM, Kormaksson M, MacKerell AD Jr, Xue F, Mason CE, Hiebert SW, Prive GG, Cerchietti L, Bardwell VJ, Elemento O, Melnick A.

Cell Rep. 2013 Aug 15;4(3):578-88. doi: 10.1016/j.celrep.2013.06.016. Epub 2013 Aug 1.

13.

An optimized algorithm for detecting and annotating regional differential methylation.

Li S, Garrett-Bakelman FE, Akalin A, Zumbo P, Levine R, To BL, Lewis ID, Brown AL, D'Andrea RJ, Melnick A, Mason CE.

BMC Bioinformatics. 2013;14 Suppl 5:S10. doi: 10.1186/1471-2105-14-S5-S10. Epub 2013 Apr 10.

14.

Relapse-specific mutations in NT5C2 in childhood acute lymphoblastic leukemia.

Meyer JA, Wang J, Hogan LE, Yang JJ, Dandekar S, Patel JP, Tang Z, Zumbo P, Li S, Zavadil J, Levine RL, Cardozo T, Hunger SP, Raetz EA, Evans WE, Morrison DJ, Mason CE, Carroll WL.

Nat Genet. 2013 Mar;45(3):290-4. doi: 10.1038/ng.2558. Epub 2013 Feb 3.

15.

The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics.

Pipes L, Li S, Bozinoski M, Palermo R, Peng X, Blood P, Kelly S, Weiss JM, Thierry-Mieg J, Thierry-Mieg D, Zumbo P, Chen R, Schroth GP, Mason CE, Katze MG.

Nucleic Acids Res. 2013 Jan;41(Database issue):D906-14. doi: 10.1093/nar/gks1268. Epub 2012 Nov 29.

16.

Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons.

Meyer KD, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey SR.

Cell. 2012 Jun 22;149(7):1635-46. doi: 10.1016/j.cell.2012.05.003. Epub 2012 May 17.

17.

Standardizing the next generation of bioinformatics software development with BioHDF (HDF5).

Mason CE, Zumbo P, Sanders S, Folk M, Robinson D, Aydt R, Gollery M, Welsh M, Olson NE, Smith TM.

Adv Exp Med Biol. 2010;680:693-700. doi: 10.1007/978-1-4419-5913-3_77.

PMID:
20865556
18.

Sex-specific and lineage-specific alternative splicing in primates.

Blekhman R, Marioni JC, Zumbo P, Stephens M, Gilad Y.

Genome Res. 2010 Feb;20(2):180-9. doi: 10.1101/gr.099226.109. Epub 2009 Dec 15.

19.

Genetic diagnosis by whole exome capture and massively parallel DNA sequencing.

Choi M, Scholl UI, Ji W, Liu T, Tikhonova IR, Zumbo P, Nayir A, Bakkaloğlu A, Ozen S, Sanjad S, Nelson-Williams C, Farhi A, Mane S, Lifton RP.

Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):19096-101. doi: 10.1073/pnas.0910672106. Epub 2009 Oct 27.

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