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Items: 16

1.

Tumor-derived IFN triggers chronic pathway agonism and sensitivity to ADAR loss.

Liu H, Golji J, Brodeur LK, Chung FS, Chen JT, deBeaumont RS, Bullock CP, Jones MD, Kerr G, Li L, Rakiec DP, Schlabach MR, Sovath S, Growney JD, Pagliarini RA, Ruddy DA, MacIsaac KD, Korn JM, McDonald ER 3rd.

Nat Med. 2019 Jan;25(1):95-102. doi: 10.1038/s41591-018-0302-5. Epub 2018 Dec 17.

PMID:
30559422
2.

Genomic Analysis of Nasopharyngeal Carcinoma Reveals TME-Based Subtypes.

Zhang L, MacIsaac KD, Zhou T, Huang PY, Xin C, Dobson JR, Yu K, Chiang DY, Fan Y, Pelletier M, Wang Y, Jaeger S, Krishnamurthy Radhakrishnan V, JeBailey L, Skewes-Cox P, Zhang J, Fang W, Huang Y, Zhao H, Zhao Y, Li E, Peng B, Huang A, Dranoff G, Hammerman PS, Engelman J, Bitter H, Zeng YX, Yao Y.

Mol Cancer Res. 2017 Dec;15(12):1722-1732. doi: 10.1158/1541-7786.MCR-17-0134. Epub 2017 Aug 29.

3.

Inhibition of RORγT Skews TCRα Gene Rearrangement and Limits T Cell Repertoire Diversity.

Guo Y, MacIsaac KD, Chen Y, Miller RJ, Jain R, Joyce-Shaikh B, Ferguson H, Wang IM, Cristescu R, Mudgett J, Engstrom L, Piers KJ, Baltus GA, Barr K, Zhang H, Mehmet H, Hegde LG, Hu X, Carter LL, Aicher TD, Glick G, Zaller D, Hawwari A, Correll CC, Jones DC, Cua DJ.

Cell Rep. 2016 Dec 20;17(12):3206-3218. doi: 10.1016/j.celrep.2016.11.073.

4.

Phenotypic responses of differentiated asthmatic human airway epithelial cultures to rhinovirus.

Bai J, Smock SL, Jackson GR Jr, MacIsaac KD, Huang Y, Mankus C, Oldach J, Roberts B, Ma YL, Klappenbach JA, Crackower MA, Alves SE, Hayden PJ.

PLoS One. 2015 Feb 23;10(2):e0118286. doi: 10.1371/journal.pone.0118286. eCollection 2015.

5.

Pre-treatment whole blood gene expression is associated with 14-week response assessed by dynamic contrast enhanced magnetic resonance imaging in infliximab-treated rheumatoid arthritis patients.

MacIsaac KD, Baumgartner R, Kang J, Loboda A, Peterfy C, DiCarlo J, Riek J, Beals C.

PLoS One. 2014 Dec 12;9(12):e113937. doi: 10.1371/journal.pone.0113937. eCollection 2014.

6.

Genomic and systems approaches to translational biomarker discovery in immunological diseases.

MacIsaac KD, Wang IM, Menetski J, Roberts C.

Drug Discov Today. 2014 Feb;19(2):133-9. doi: 10.1016/j.drudis.2013.10.002. Epub 2013 Oct 11. Review.

PMID:
24126144
7.

A quantitative atlas of polyadenylation in five mammals.

Derti A, Garrett-Engele P, Macisaac KD, Stevens RC, Sriram S, Chen R, Rohl CA, Johnson JM, Babak T.

Genome Res. 2012 Jun;22(6):1173-83. doi: 10.1101/gr.132563.111. Epub 2012 Mar 27.

8.

Sequence analysis of chromatin immunoprecipitation data for transcription factors.

Macisaac KD, Fraenkel E.

Methods Mol Biol. 2010;674:179-93. doi: 10.1007/978-1-60761-854-6_11.

9.

A quantitative model of transcriptional regulation reveals the influence of binding location on expression.

MacIsaac KD, Lo KA, Gordon W, Motola S, Mazor T, Fraenkel E.

PLoS Comput Biol. 2010 Apr 29;6(4):e1000773. doi: 10.1371/journal.pcbi.1000773.

10.

Tissue-specific transcriptional regulation has diverged significantly between human and mouse.

Odom DT, Dowell RD, Jacobsen ES, Gordon W, Danford TW, MacIsaac KD, Rolfe PA, Conboy CM, Gifford DK, Fraenkel E.

Nat Genet. 2007 Jun;39(6):730-2. Epub 2007 May 21.

11.

Foxp3 occupancy and regulation of key target genes during T-cell stimulation.

Marson A, Kretschmer K, Frampton GM, Jacobsen ES, Polansky JK, MacIsaac KD, Levine SS, Fraenkel E, von Boehmer H, Young RA.

Nature. 2007 Feb 22;445(7130):931-5. Epub 2007 Jan 21.

12.

High-resolution computational models of genome binding events.

Qi Y, Rolfe A, MacIsaac KD, Gerber GK, Pokholok D, Zeitlinger J, Danford T, Dowell RD, Fraenkel E, Jaakkola TS, Young RA, Gifford DK.

Nat Biotechnol. 2006 Aug;24(8):963-70. Erratum in: Nat Biotechnol. 2006 Oct;24(10):1293.

PMID:
16900145
13.

Practical strategies for discovering regulatory DNA sequence motifs.

MacIsaac KD, Fraenkel E.

PLoS Comput Biol. 2006 Apr;2(4):e36. No abstract available.

14.

An improved map of conserved regulatory sites for Saccharomyces cerevisiae.

MacIsaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD, Fraenkel E.

BMC Bioinformatics. 2006 Mar 7;7:113.

15.

A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data.

Macisaac KD, Gordon DB, Nekludova L, Odom DT, Schreiber J, Gifford DK, Young RA, Fraenkel E.

Bioinformatics. 2006 Feb 15;22(4):423-9. Epub 2005 Dec 6.

PMID:
16332710
16.

Transcriptional regulatory code of a eukaryotic genome.

Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA.

Nature. 2004 Sep 2;431(7004):99-104.

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