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Items: 26

1.

The Immune Landscape of Cancer.

Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CE; Cancer Genome Atlas Research Network, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich L.

Immunity. 2018 Apr 17;48(4):812-830.e14. doi: 10.1016/j.immuni.2018.03.023. Epub 2018 Apr 5.

2.

The Transcription Factor Nfatc2 Regulates β-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets.

Keller MP, Paul PK, Rabaglia ME, Stapleton DS, Schueler KL, Broman AT, Ye SI, Leng N, Brandon CJ, Neto EC, Plaisier CL, Simonett SP, Kebede MA, Sheynkman GM, Klein MA, Baliga NS, Smith LM, Broman KW, Yandell BS, Kendziorski C, Attie AD.

PLoS Genet. 2016 Dec 9;12(12):e1006466. doi: 10.1371/journal.pgen.1006466. eCollection 2016 Dec.

3.

Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis.

Plaisier CL, O'Brien S, Bernard B, Reynolds S, Simon Z, Toledo CM, Ding Y, Reiss DJ, Paddison PJ, Baliga NS.

Cell Syst. 2016 Aug;3(2):172-186. doi: 10.1016/j.cels.2016.06.006. Epub 2016 Jul 14.

4.

Genome-wide CRISPR-Cas9 Screens Reveal Loss of Redundancy between PKMYT1 and WEE1 in Glioblastoma Stem-like Cells.

Toledo CM, Ding Y, Hoellerbauer P, Davis RJ, Basom R, Girard EJ, Lee E, Corrin P, Hart T, Bolouri H, Davison J, Zhang Q, Hardcastle J, Aronow BJ, Plaisier CL, Baliga NS, Moffat J, Lin Q, Li XN, Nam DH, Lee J, Pollard SM, Zhu J, Delrow JJ, Clurman BE, Olson JM, Paddison PJ.

Cell Rep. 2015 Dec 22;13(11):2425-2439. doi: 10.1016/j.celrep.2015.11.021. Epub 2015 Dec 7.

5.

Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions.

Danziger SA, Reiss DJ, Ratushny AV, Smith JJ, Plaisier CL, Aitchison JD, Baliga NS.

BMC Syst Biol. 2015;9 Suppl 2:S1. doi: 10.1186/1752-0509-9-S2-S1. Epub 2015 Apr 15.

6.

cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism.

Reiss DJ, Plaisier CL, Wu WJ, Baliga NS.

Nucleic Acids Res. 2015 Jul 27;43(13):e87. doi: 10.1093/nar/gkv300. Epub 2015 Apr 14.

7.

Evolution of context dependent regulation by expansion of feast/famine regulatory proteins.

Plaisier CL, Lo FY, Ashworth J, Brooks AN, Beer KD, Kaur A, Pan M, Reiss DJ, Facciotti MT, Baliga NS.

BMC Syst Biol. 2014 Nov 14;8:122. doi: 10.1186/s12918-014-0122-2.

8.

Structure-based predictions broadly link transcription factor mutations to gene expression changes in cancers.

Ashworth J, Bernard B, Reynolds S, Plaisier CL, Shmulevich I, Baliga NS.

Nucleic Acids Res. 2014 Dec 1;42(21):12973-83. doi: 10.1093/nar/gku1031. Epub 2014 Nov 5.

9.

Inference of expanded Lrp-like feast/famine transcription factor targets in a non-model organism using protein structure-based prediction.

Ashworth J, Plaisier CL, Lo FY, Reiss DJ, Baliga NS.

PLoS One. 2014 Sep 25;9(9):e107863. doi: 10.1371/journal.pone.0107863. eCollection 2014. Erratum in: PLoS One. 2014;9(11):e114450.

10.

A high-resolution network model for global gene regulation in Mycobacterium tuberculosis.

Peterson EJ, Reiss DJ, Turkarslan S, Minch KJ, Rustad T, Plaisier CL, Longabaugh WJ, Sherman DR, Baliga NS.

Nucleic Acids Res. 2014 Oct;42(18):11291-303. doi: 10.1093/nar/gku777. Epub 2014 Sep 17.

11.

A system-level model for the microbial regulatory genome.

Brooks AN, Reiss DJ, Allard A, Wu WJ, Salvanha DM, Plaisier CL, Chandrasekaran S, Pan M, Kaur A, Baliga NS.

Mol Syst Biol. 2014 Jul 15;10:740. doi: 10.15252/msb.20145160.

12.

Zbtb16 has a role in brown adipocyte bioenergetics.

Plaisier CL, Bennett BJ, He A, Guan B, Lusis AJ, Reue K, Vergnes L.

Nutr Diabetes. 2012 Sep 17;2:e46. doi: 10.1038/nutd.2012.21.

13.

Harnessing the power of human tumor-derived cell lines for the rational design of cancer therapies.

Plaisier CL, Baliga NS.

Pigment Cell Melanoma Res. 2012 Jul;25(4):406-8. doi: 10.1111/j.1755-148X.2012.01020.x. No abstract available.

14.

A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers.

Plaisier CL, Pan M, Baliga NS.

Genome Res. 2012 Nov;22(11):2302-14. doi: 10.1101/gr.133991.111. Epub 2012 Jun 28.

15.

Niche adaptation by expansion and reprogramming of general transcription factors.

Turkarslan S, Reiss DJ, Gibbins G, Su WL, Pan M, Bare JC, Plaisier CL, Baliga NS.

Mol Syst Biol. 2011 Nov 22;7:554. doi: 10.1038/msb.2011.87.

16.

miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling.

Plaisier CL, Bare JC, Baliga NS.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W125-31. doi: 10.1093/nar/gkr374. Epub 2011 May 20.

17.

Systems genetics analysis of gene-by-environment interactions in human cells.

Romanoski CE, Lee S, Kim MJ, Ingram-Drake L, Plaisier CL, Yordanova R, Tilford C, Guan B, He A, Gargalovic PS, Kirchgessner TG, Berliner JA, Lusis AJ.

Am J Hum Genet. 2010 Mar 12;86(3):399-410. doi: 10.1016/j.ajhg.2010.02.002. Epub 2010 Feb 18.

18.

Identification of two common variants contributing to serum apolipoprotein B levels in Mexicans.

Weissglas-Volkov D, Plaisier CL, Huertas-Vazquez A, Cruz-Bautista I, Riaño-Barros D, Herrera-Hernandez M, Riba L, Cantor RM, Sinsheimer JS, Aguilar-Salinas CA, Tusie-Luna T, Pajukanta P.

Arterioscler Thromb Vasc Biol. 2010 Feb;30(2):353-9. doi: 10.1161/ATVBAHA.109.196402. Epub 2009 Dec 3.

19.

A nonsynonymous SNP within PCDH15 is associated with lipid traits in familial combined hyperlipidemia.

Huertas-Vazquez A, Plaisier CL, Geng R, Haas BE, Lee J, Greevenbroek MM, van der Kallen C, de Bruin TW, Taskinen MR, Alagramam KN, Pajukanta P.

Hum Genet. 2010 Jan;127(1):83-9. doi: 10.1007/s00439-009-0749-z. Epub 2009 Oct 9.

20.

A systems genetics approach implicates USF1, FADS3, and other causal candidate genes for familial combined hyperlipidemia.

Plaisier CL, Horvath S, Huertas-Vazquez A, Cruz-Bautista I, Herrera MF, Tusie-Luna T, Aguilar-Salinas C, Pajukanta P.

PLoS Genet. 2009 Sep;5(9):e1000642. doi: 10.1371/journal.pgen.1000642. Epub 2009 Sep 11.

21.

Exclusion of positional candidate gene coding region mutations in the common posterior polymorphous corneal dystrophy 1 candidate gene interval.

Aldave AJ, Yellore VS, Vo RC, Kamal KM, Rayner SA, Plaisier CL, Chen MC, Damani MR, Pham MN, Gorin MB, Sobel E, Papp J.

Cornea. 2009 Aug;28(7):801-7. doi: 10.1097/ICO.0b013e31819672fb.

22.

Reduction of a redox-active ligand drives switching in a Cu(I) pseudorotaxane by a bimolecular mechanism.

McNitt KA, Parimal K, Share AI, Fahrenbach AC, Witlicki EH, Pink M, Bediako DK, Plaisier CL, Le N, Heeringa LP, Vander Griend DA, Flood AH.

J Am Chem Soc. 2009 Jan 28;131(3):1305-13. doi: 10.1021/ja8085593.

PMID:
19125582
23.

Galanin preproprotein is associated with elevated plasma triglycerides.

Plaisier CL, Kyttälä M, Weissglas-Volkov D, Sinsheimer JS, Huertas-Vazquez A, Riba L, Ramírez-Jiménez S, de Bruin TW, Tusié-Luna T, Aouizerat BE, Pullinger CR, Malloy MJ, Kane JP, Cruz-Bautista I, Herrera MF, Aguilar-Salinas C, Kuusisto J, Laakso M, Taskinen MR, van der Kallen CJ, Pajukanta P.

Arterioscler Thromb Vasc Biol. 2009 Jan;29(1):147-52. doi: 10.1161/ATVBAHA.108.178533. Epub 2008 Nov 6.

24.

WW-domain-containing oxidoreductase is associated with low plasma HDL-C levels.

Lee JC, Weissglas-Volkov D, Kyttälä M, Dastani Z, Cantor RM, Sobel EM, Plaisier CL, Engert JC, van Greevenbroek MM, Kane JP, Malloy MJ, Pullinger CR, Huertas-Vazquez A, Aguilar-Salinas CA, Tusie-Luna T, de Bruin TW, Aouizerat BE, van der Kallen CC, Croce CM, Aqeilan RI, Marcil M, Viikari JS, Lehtimäki T, Raitakari OT, Kuusisto J, Laakso M, Taskinen MR, Genest J, Pajukanta P.

Am J Hum Genet. 2008 Aug;83(2):180-92. doi: 10.1016/j.ajhg.2008.07.002.

25.

Estimating ethnic admixture from pedigree data.

Sinsheimer JS, Plaisier CL, Huertas-Vazquez A, Aguilar-Salinas C, Tusie-Luna T, Pajukanta P, Lange K.

Am J Hum Genet. 2008 Mar;82(3):748-55. doi: 10.1016/j.ajhg.2007.12.014.

26.

Targeted mutagenesis using zinc-finger nucleases in Arabidopsis.

Lloyd A, Plaisier CL, Carroll D, Drews GN.

Proc Natl Acad Sci U S A. 2005 Feb 8;102(6):2232-7. Epub 2005 Jan 26.

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