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Transcriptional Perturbations in Graft Rejection.

Vitalone MJ, Sigdel TK, Salomonis N, Sarwal RD, Hsieh SC, Sarwal MM.

Transplantation. 2015 Sep;99(9):1882-1893.


Reactive oxygen species-mediated therapeutic response and resistance in glioblastoma.

Singer E, Judkins J, Salomonis N, Matlaf L, Soteropoulos P, McAllister S, Soroceanu L.

Cell Death Dis. 2015 Jan 15;6:e1601. doi: 10.1038/cddis.2014.566.


The kSORT assay to detect renal transplant patients at high risk for acute rejection: results of the multicenter AART study.

Roedder S, Sigdel T, Salomonis N, Hsieh S, Dai H, Bestard O, Metes D, Zeevi A, Gritsch A, Cheeseman J, Macedo C, Peddy R, Medeiros M, Vincenti F, Asher N, Salvatierra O, Shapiro R, Kirk A, Reed EF, Sarwal MM.

PLoS Med. 2014 Nov 11;11(11):e1001759. doi: 10.1371/journal.pmed.1001759. eCollection 2014 Nov. Erratum in: PLoS Med. 2015 Feb;12(2):e1001790. Zeevi, Andrea [corrected to Zeevi, Adriana]; Reed, Elaine [corrected to Reed, Elaine F].


Systems-level perspective of sudden infant death syndrome.

Salomonis N.

Pediatr Res. 2014 Sep;76(3):220-9. doi: 10.1038/pr.2014.90. Epub 2014 Jun 25.


Alternative splicing of MBD2 supports self-renewal in human pluripotent stem cells.

Lu Y, Loh YH, Li H, Cesana M, Ficarro SB, Parikh JR, Salomonis N, Toh CX, Andreadis ST, Luckey CJ, Collins JJ, Daley GQ, Marto JA.

Cell Stem Cell. 2014 Jul 3;15(1):92-101. doi: 10.1016/j.stem.2014.04.002. Epub 2014 May 8.


Long non-coding RNA and alternative splicing modulations in Parkinson's leukocytes identified by RNA sequencing.

Soreq L, Guffanti A, Salomonis N, Simchovitz A, Israel Z, Bergman H, Soreq H.

PLoS Comput Biol. 2014 Mar 20;10(3):e1003517. doi: 10.1371/journal.pcbi.1003517. eCollection 2014 Mar.


MAAMD: a workflow to standardize meta-analyses and comparison of affymetrix microarray data.

Gan Z, Wang J, Salomonis N, Stowe JC, Haddad GG, McCulloch AD, Altintas I, Zambon AC.

BMC Bioinformatics. 2014 Mar 12;15:69. doi: 10.1186/1471-2105-15-69.


The identification of novel potential injury mechanisms and candidate biomarkers in renal allograft rejection by quantitative proteomics.

Sigdel TK, Salomonis N, Nicora CD, Ryu S, He J, Dinh V, Orton DJ, Moore RJ, Hsieh SC, Dai H, Thien-Vu M, Xiao W, Smith RD, Qian WJ, Camp DG 2nd, Sarwal MM.

Mol Cell Proteomics. 2014 Feb;13(2):621-31. doi: 10.1074/mcp.M113.030577. Epub 2013 Dec 12.


A robust method to derive functional neural crest cells from human pluripotent stem cells.

Kreitzer FR, Salomonis N, Sheehan A, Huang M, Park JS, Spindler MJ, Lizarraga P, Weiss WA, So PL, Conklin BR.

Am J Stem Cells. 2013 Jun 30;2(2):119-31. Print 2013.


Whole-Genome rVISTA: a tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data.

Dubchak I, Munoz M, Poliakov A, Salomonis N, Minovitsky S, Bodmer R, Zambon AC.

Bioinformatics. 2013 Aug 15;29(16):2059-61. doi: 10.1093/bioinformatics/btt318. Epub 2013 Jun 4.


Small RNA sequencing-microarray analyses in Parkinson leukocytes reveal deep brain stimulation-induced splicing changes that classify brain region transcriptomes.

Soreq L, Salomonis N, Bronstein M, Greenberg DS, Israel Z, Bergman H, Soreq H.

Front Mol Neurosci. 2013 May 13;6:10. doi: 10.3389/fnmol.2013.00010. eCollection 2013.


AKAP13 Rho-GEF and PKD-binding domain deficient mice develop normally but have an abnormal response to β-adrenergic-induced cardiac hypertrophy.

Spindler MJ, Burmeister BT, Huang Y, Hsiao EC, Salomonis N, Scott MJ, Srivastava D, Carnegie GK, Conklin BR.

PLoS One. 2013 Apr 26;8(4):e62705. doi: 10.1371/journal.pone.0062705. Print 2013.


GO-Elite: a flexible solution for pathway and ontology over-representation.

Zambon AC, Gaj S, Ho I, Hanspers K, Vranizan K, Evelo CT, Conklin BR, Pico AR, Salomonis N.

Bioinformatics. 2012 Aug 15;28(16):2209-10. doi: 10.1093/bioinformatics/bts366. Epub 2012 Jun 27.


Mosaic: making biological sense of complex networks.

Zhang C, Hanspers K, Kuchinsky A, Salomonis N, Xu D, Pico AR.

Bioinformatics. 2012 Jul 15;28(14):1943-4. doi: 10.1093/bioinformatics/bts278. Epub 2012 May 9.


Deficiency of the lipid synthesis enzyme, DGAT1, extends longevity in mice.

Streeper RS, Grueter CA, Salomonis N, Cases S, Levin MC, Koliwad SK, Zhou P, Hirschey MD, Verdin E, Farese RV Jr.

Aging (Albany NY). 2012 Jan;4(1):13-27.


Stem cell pluripotency: alternative modes of transcription regulation.

Salomonis N, Conklin BR.

Cell Cycle. 2010 Aug 15;9(16):3133-4. doi: 10.4161/cc.9.16.12888. Epub 2010 Aug 2. No abstract available.


AltAnalyze and DomainGraph: analyzing and visualizing exon expression data.

Emig D, Salomonis N, Baumbach J, Lengauer T, Conklin BR, Albrecht M.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W755-62. doi: 10.1093/nar/gkq405. Epub 2010 May 31.


Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation.

Salomonis N, Schlieve CR, Pereira L, Wahlquist C, Colas A, Zambon AC, Vranizan K, Spindler MJ, Pico AR, Cline MS, Clark TA, Williams A, Blume JE, Samal E, Mercola M, Merrill BJ, Conklin BR.

Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10514-9. doi: 10.1073/pnas.0912260107. Epub 2010 May 24.


G(i)-coupled GPCR signaling controls the formation and organization of human pluripotent colonies.

Nakamura K, Salomonis N, Tomoda K, Yamanaka S, Conklin BR.

PLoS One. 2009 Nov 10;4(11):e7780. doi: 10.1371/journal.pone.0007780.


Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors.

Salomonis N, Nelson B, Vranizan K, Pico AR, Hanspers K, Kuchinsky A, Ta L, Mercola M, Conklin BR.

PLoS Comput Biol. 2009 Nov;5(11):e1000553. doi: 10.1371/journal.pcbi.1000553. Epub 2009 Nov 6.

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