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Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium.

Salomonis N, Dexheimer PJ, Omberg L, Schroll R, Bush S, Huo J, Schriml L, Ho Sui S, Keddache M, Mayhew C, Shanmukhappa SK, Wells J, Daily K, Hubler S, Wang Y, Zambidis E, Margolin A, Hide W, Hatzopoulos AK, Malik P, Cancelas JA, Aronow BJ, Lutzko C.

Stem Cell Reports. 2016 Jul 12;7(1):110-25. doi: 10.1016/j.stemcr.2016.05.006. Epub 2016 Jun 9.


Intragraft Antiviral-Specific Gene Expression as a Distinctive Transcriptional Signature for Studies in Polyomavirus-Associated Nephropathy.

Sigdel TK, Bestard O, Salomonis N, Hsieh SC, Torras J, Naesens M, Tran TQ, Roedder S, Sarwal MM.

Transplantation. 2016 May 2. [Epub ahead of print]


DNMT3A Haploinsufficiency Transforms FLT3ITD Myeloproliferative Disease into a Rapid, Spontaneous, and Fully Penetrant Acute Myeloid Leukemia.

Meyer SE, Qin T, Muench DE, Masuda K, Venkatasubramanian M, Orr E, Suarez L, Gore SD, Delwel R, Paietta E, Tallman MS, Fernandez H, Melnick A, Le Beau MM, Kogan S, Salomonis N, Figueroa ME, Grimes HL.

Cancer Discov. 2016 May;6(5):501-15. doi: 10.1158/2159-8290.CD-16-0008. Epub 2016 Mar 25.


MBNL1-mediated regulation of differentiation RNAs promotes myofibroblast transformation and the fibrotic response.

Davis J, Salomonis N, Ghearing N, Lin SC, Kwong JQ, Mohan A, Swanson MS, Molkentin JD.

Nat Commun. 2015 Dec 16;6:10084. doi: 10.1038/ncomms10084.


Systems biology evaluation of cell-free amniotic fluid transcriptome of term and preterm infants to detect fetal maturity.

Kamath-Rayne BD, Du Y, Hughes M, Wagner EA, Muglia LJ, DeFranco EA, Whitsett JA, Salomonis N, Xu Y.

BMC Med Genomics. 2015 Oct 22;8:67. doi: 10.1186/s12920-015-0138-5.


Analyzing alternative splicing data of splice junction arrays from Parkinson patients' leukocytes before and after deep brain stimulation as compared with control donors.

Soreq L, Salomonis N, Israel Z, Bergman H, Soreq H.

Genom Data. 2015 Jul 16;5:340-3. doi: 10.1016/j.gdata.2015.07.014. eCollection 2015 Sep.


Whole transcriptome RNA sequencing data from blood leukocytes derived from Parkinson's disease patients prior to and following deep brain stimulation treatment.

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

Genom Data. 2014 Nov 22;3:57-60. doi: 10.1016/j.gdata.2014.11.009. eCollection 2015 Mar.


Intrinsic Age-Dependent Changes and Cell-Cell Contacts Regulate Nephron Progenitor Lifespan.

Chen S, Brunskill EW, Potter SS, Dexheimer PJ, Salomonis N, Aronow BJ, Hong CI, Zhang T, Kopan R.

Dev Cell. 2015 Oct 12;35(1):49-62. doi: 10.1016/j.devcel.2015.09.009.


Transcriptional Perturbations in Graft Rejection.

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

Transplantation. 2015 Sep;99(9):1882-93. doi: 10.1097/TP.0000000000000809.


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. Review.


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. Erratum in: PLoS Comput Biol. 2014 May;10(5):e1003647.


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.

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