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Items: 43

1.

Deep-learning augmented RNA-seq analysis of transcript splicing.

Zhang Z, Pan Z, Ying Y, Xie Z, Adhikari S, Phillips J, Carstens RP, Black DL, Wu Y, Xing Y.

Nat Methods. 2019 Apr;16(4):307-310. doi: 10.1038/s41592-019-0351-9. Epub 2019 Mar 25.

PMID:
30923373
2.

Esrp1-Regulated Splicing of Arhgef11 Isoforms Is Required for Epithelial Tight Junction Integrity.

Lee S, Cieply B, Yang Y, Peart N, Glaser C, Chan P, Carstens RP.

Cell Rep. 2018 Nov 27;25(9):2417-2430.e5. doi: 10.1016/j.celrep.2018.10.097.

3.

Alternative splicing rewires Hippo signaling pathway in hepatocytes to promote liver regeneration.

Bangru S, Arif W, Seimetz J, Bhate A, Chen J, Rashan EH, Carstens RP, Anakk S, Kalsotra A.

Nat Struct Mol Biol. 2018 Oct;25(10):928-939. doi: 10.1038/s41594-018-0129-2. Epub 2018 Sep 24.

4.

Mutations in the Epithelial Cadherin-p120-Catenin Complex Cause Mendelian Non-Syndromic Cleft Lip with or without Cleft Palate.

Cox LL, Cox TC, Moreno Uribe LM, Zhu Y, Richter CT, Nidey N, Standley JM, Deng M, Blue E, Chong JX, Yang Y, Carstens RP, Anand D, Lachke SA, Smith JD, Dorschner MO, Bedell B, Kirk E, Hing AV, Venselaar H, Valencia-Ramirez LC, Bamshad MJ, Glass IA, Cooper JA, Haan E, Nickerson DA, van Bokhoven H, Zhou H, Krahn KN, Buckley MF, Murray JC, Lidral AC, Roscioli T.

Am J Hum Genet. 2018 Jun 7;102(6):1143-1157. doi: 10.1016/j.ajhg.2018.04.009. Epub 2018 May 24.

5.

Aggressive triple negative breast cancers have unique molecular signature on the basis of mitochondrial genetic and functional defects.

Guha M, Srinivasan S, Raman P, Jiang Y, Kaufman BA, Taylor D, Dong D, Chakrabarti R, Picard M, Carstens RP, Kijima Y, Feldman M, Avadhani NG.

Biochim Biophys Acta Mol Basis Dis. 2018 Apr;1864(4 Pt A):1060-1071. doi: 10.1016/j.bbadis.2018.01.002. Epub 2018 Jan 5.

6.

ESRP1 Mutations Cause Hearing Loss due to Defects in Alternative Splicing that Disrupt Cochlear Development.

Rohacek AM, Bebee TW, Tilton RK, Radens CM, McDermott-Roe C, Peart N, Kaur M, Zaykaner M, Cieply B, Musunuru K, Barash Y, Germiller JA, Krantz ID, Carstens RP, Epstein DJ.

Dev Cell. 2017 Nov 6;43(3):318-331.e5. doi: 10.1016/j.devcel.2017.09.026. Epub 2017 Oct 26.

7.
8.

Ablation of the epithelial-specific splicing factor Esrp1 results in ureteric branching defects and reduced nephron number.

Bebee TW, Sims-Lucas S, Park JW, Bushnell D, Cieply B, Xing Y, Bates CM, Carstens RP.

Dev Dyn. 2016 Oct;245(10):991-1000. doi: 10.1002/dvdy.24431. Epub 2016 Jul 28.

9.

Multiphasic and Dynamic Changes in Alternative Splicing during Induction of Pluripotency Are Coordinated by Numerous RNA-Binding Proteins.

Cieply B, Park JW, Nakauka-Ddamba A, Bebee TW, Guo Y, Shang X, Lengner CJ, Xing Y, Carstens RP.

Cell Rep. 2016 Apr 12;15(2):247-55. doi: 10.1016/j.celrep.2016.03.025. Epub 2016 Mar 31.

10.

Determination of a Comprehensive Alternative Splicing Regulatory Network and Combinatorial Regulation by Key Factors during the Epithelial-to-Mesenchymal Transition.

Yang Y, Park JW, Bebee TW, Warzecha CC, Guo Y, Shang X, Xing Y, Carstens RP.

Mol Cell Biol. 2016 May 16;36(11):1704-19. doi: 10.1128/MCB.00019-16. Print 2016 Jun 1.

11.

ESRP2 controls an adult splicing programme in hepatocytes to support postnatal liver maturation.

Bhate A, Parker DJ, Bebee TW, Ahn J, Arif W, Rashan EH, Chorghade S, Chau A, Lee JH, Anakk S, Carstens RP, Xiao X, Kalsotra A.

Nat Commun. 2015 Nov 4;6:8768. doi: 10.1038/ncomms9768.

12.

The splicing regulators Esrp1 and Esrp2 direct an epithelial splicing program essential for mammalian development.

Bebee TW, Park JW, Sheridan KI, Warzecha CC, Cieply BW, Rohacek AM, Xing Y, Carstens RP.

Elife. 2015 Sep 15;4. doi: 10.7554/eLife.08954.

13.

Functional roles of alternative splicing factors in human disease.

Cieply B, Carstens RP.

Wiley Interdiscip Rev RNA. 2015 May-Jun;6(3):311-26. doi: 10.1002/wrna.1276. Epub 2015 Jan 28. Review.

14.

Genome-wide activities of RNA binding proteins that regulate cellular changes in the epithelial to mesenchymal transition (EMT).

Bebee TW, Cieply BW, Carstens RP.

Adv Exp Med Biol. 2014;825:267-302. doi: 10.1007/978-1-4939-1221-6_8. Review.

PMID:
25201109
15.

Networking in an alternative splicing world.

Carstens RP.

Mol Cell. 2014 Jun 19;54(6):903-4. doi: 10.1016/j.molcel.2014.06.014.

16.

Exo70 isoform switching upon epithelial-mesenchymal transition mediates cancer cell invasion.

Lu H, Liu J, Liu S, Zeng J, Ding D, Carstens RP, Cong Y, Xu X, Guo W.

Dev Cell. 2013 Dec 9;27(5):560-73. doi: 10.1016/j.devcel.2013.10.020.

17.

The RNA binding protein RBM38 (RNPC1) regulates splicing during late erythroid differentiation.

Heinicke LA, Nabet B, Shen S, Jiang P, van Zalen S, Cieply B, Russell JE, Xing Y, Carstens RP.

PLoS One. 2013 Oct 18;8(10):e78031. doi: 10.1371/journal.pone.0078031. eCollection 2013.

18.

Mitochondrial retrograde signaling induces epithelial-mesenchymal transition and generates breast cancer stem cells.

Guha M, Srinivasan S, Ruthel G, Kashina AK, Carstens RP, Mendoza A, Khanna C, Van Winkle T, Avadhani NG.

Oncogene. 2014 Nov 6;33(45):5238-50. doi: 10.1038/onc.2013.467. Epub 2013 Nov 4.

19.

A compendium of RNA-binding motifs for decoding gene regulation.

Ray D, Kazan H, Cook KB, Weirauch MT, Najafabadi HS, Li X, Gueroussov S, Albu M, Zheng H, Yang A, Na H, Irimia M, Matzat LH, Dale RK, Smith SA, Yarosh CA, Kelly SM, Nabet B, Mecenas D, Li W, Laishram RS, Qiao M, Lipshitz HD, Piano F, Corbett AH, Carstens RP, Frey BJ, Anderson RA, Lynch KW, Penalva LO, Lei EP, Fraser AG, Blencowe BJ, Morris QD, Hughes TR.

Nature. 2013 Jul 11;499(7457):172-7. doi: 10.1038/nature12311.

20.

Splicing program of human MENA produces a previously undescribed isoform associated with invasive, mesenchymal-like breast tumors.

Di Modugno F, Iapicca P, Boudreau A, Mottolese M, Terrenato I, Perracchio L, Carstens RP, Santoni A, Bissell MJ, Nisticò P.

Proc Natl Acad Sci U S A. 2012 Nov 20;109(47):19280-5. doi: 10.1073/pnas.1214394109. Epub 2012 Nov 5.

21.

Complex changes in alternative pre-mRNA splicing play a central role in the epithelial-to-mesenchymal transition (EMT).

Warzecha CC, Carstens RP.

Semin Cancer Biol. 2012 Oct;22(5-6):417-27. doi: 10.1016/j.semcancer.2012.04.003. Epub 2012 Apr 23. Review.

22.

Dynamic fluorescent and luminescent reporters for cell-based splicing screens.

Warzecha CC, Hovhannisyan R, Carstens RP.

Methods Mol Biol. 2012;867:273-87. doi: 10.1007/978-1-61779-767-5_18.

PMID:
22454068
23.

Genome-wide determination of a broad ESRP-regulated posttranscriptional network by high-throughput sequencing.

Dittmar KA, Jiang P, Park JW, Amirikian K, Wan J, Shen S, Xing Y, Carstens RP.

Mol Cell Biol. 2012 Apr;32(8):1468-82. doi: 10.1128/MCB.06536-11. Epub 2012 Feb 21.

24.

MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data.

Shen S, Park JW, Huang J, Dittmar KA, Lu ZX, Zhou Q, Carstens RP, Xing Y.

Nucleic Acids Res. 2012 Apr;40(8):e61. doi: 10.1093/nar/gkr1291. Epub 2012 Jan 20.

25.

An ESRP-regulated splicing programme is abrogated during the epithelial-mesenchymal transition.

Warzecha CC, Jiang P, Amirikian K, Dittmar KA, Lu H, Shen S, Guo W, Xing Y, Carstens RP.

EMBO J. 2010 Oct 6;29(19):3286-300. doi: 10.1038/emboj.2010.195. Epub 2010 Aug 13.

26.

MADS+: discovery of differential splicing events from Affymetrix exon junction array data.

Shen S, Warzecha CC, Carstens RP, Xing Y.

Bioinformatics. 2010 Jan 15;26(2):268-9. doi: 10.1093/bioinformatics/btp643. Epub 2009 Nov 17.

27.

The epithelial splicing factors ESRP1 and ESRP2 positively and negatively regulate diverse types of alternative splicing events.

Warzecha CC, Shen S, Xing Y, Carstens RP.

RNA Biol. 2009 Nov-Dec;6(5):546-62. Epub 2009 Nov 22.

28.

Identification of a putative network of actin-associated cytoskeletal proteins in glomerular podocytes defined by co-purified mRNAs.

Nabet B, Tsai A, Tobias JW, Carstens RP.

PLoS One. 2009 Aug 4;4(8):e6491. doi: 10.1371/journal.pone.0006491.

29.

ESRP1 and ESRP2 are epithelial cell-type-specific regulators of FGFR2 splicing.

Warzecha CC, Sato TK, Nabet B, Hogenesch JB, Carstens RP.

Mol Cell. 2009 Mar 13;33(5):591-601. doi: 10.1016/j.molcel.2009.01.025.

30.
32.
33.

Identification of RNA-binding proteins that regulate FGFR2 splicing through the use of sensitive and specific dual color fluorescence minigene assays.

Newman EA, Muh SJ, Hovhannisyan RH, Warzecha CC, Jones RB, McKeehan WL, Carstens RP.

RNA. 2006 Jun;12(6):1129-41. Epub 2006 Apr 7.

34.
35.

Characterization of sequences and mechanisms through which ISE/ISS-3 regulates FGFR2 splicing.

Hovhannisyan RH, Warzecha CC, Carstens RP.

Nucleic Acids Res. 2006 Jan 12;34(1):373-85. Print 2006.

37.
38.
40.

A novel isoform ratio switch of the polypyrimidine tract binding protein.

Wagner EJ, Carstens RP, Garcia-Blanco MA.

Electrophoresis. 1999 Apr-May;20(4-5):1082-6.

PMID:
10344288
41.
42.

Alternative splicing of fibroblast growth factor receptor 2 (FGF-R2) in human prostate cancer.

Carstens RP, Eaton JV, Krigman HR, Walther PJ, Garcia-Blanco MA.

Oncogene. 1997 Dec 18;15(25):3059-65.

43.

Identification of RNA splicing errors resulting in human ornithine transcarbamylase deficiency.

Carstens RP, Fenton WA, Rosenberg LR.

Am J Hum Genet. 1991 Jun;48(6):1105-14.

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