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Items: 21

1.

Deep profiling and custom databases improve detection of proteoforms generated by alternative splicing.

Agosto LM, Gazzara MR, Radens CM, Sidoli S, Baeza J, Garcia BA, Lynch KW.

Genome Res. 2019 Nov 14. doi: 10.1101/gr.248435.119. [Epub ahead of print]

PMID:
31727681
2.

Retention of CD19 intron 2 contributes to CART-19 resistance in leukemias with subclonal frameshift mutations in CD19.

Asnani M, Hayer KE, Naqvi AS, Zheng S, Yang SY, Oldridge D, Ibrahim F, Maragkakis M, Gazzara MR, Black KL, Bagashev A, Taylor D, Mourelatos Z, Grupp SA, Barrett D, Maris JM, Sotillo E, Barash Y, Thomas-Tikhonenko A.

Leukemia. 2019 Oct 7. doi: 10.1038/s41375-019-0580-z. [Epub ahead of print] No abstract available.

PMID:
31591467
3.

RNA Binding Protein CELF2 Regulates Signal-Induced Alternative Polyadenylation by Competing with Enhancers of the Polyadenylation Machinery.

Chatrikhi R, Mallory MJ, Gazzara MR, Agosto LM, Zhu WS, Litterman AJ, Ansel KM, Lynch KW.

Cell Rep. 2019 Sep 10;28(11):2795-2806.e3. doi: 10.1016/j.celrep.2019.08.022.

4.

An ancient germ cell-specific RNA-binding protein protects the germline from cryptic splice site poisoning.

Ehrmann I, Crichton JH, Gazzara MR, James K, Liu Y, Grellscheid SN, Curk T, de Rooij D, Steyn JS, Cockell S, Adams IR, Barash Y, Elliott DJ.

Elife. 2019 Jan 24;8. pii: e39304. doi: 10.7554/eLife.39304.

5.

FCNN-based axon segmentation for convection-enhanced delivery optimization.

Vidotto M, De Momi E, Gazzara M, Mattos LS, Ferrigno G, Moccia S.

Int J Comput Assist Radiol Surg. 2019 Mar;14(3):493-499. doi: 10.1007/s11548-018-01911-z. Epub 2019 Jan 7.

PMID:
30613910
6.

Aberrant splicing in B-cell acute lymphoblastic leukemia.

Black KL, Naqvi AS, Asnani M, Hayer KE, Yang SY, Gillespie E, Bagashev A, Pillai V, Tasian SK, Gazzara MR, Carroll M, Taylor D, Lynch KW, Barash Y, Thomas-Tikhonenko A.

Nucleic Acids Res. 2019 Jan 25;47(2):1043. doi: 10.1093/nar/gky1231. No abstract available.

7.

Aberrant splicing in B-cell acute lymphoblastic leukemia.

Black KL, Naqvi AS, Asnani M, Hayer KE, Yang SY, Gillespie E, Bagashev A, Pillai V, Tasian SK, Gazzara MR, Carroll M, Taylor D, Lynch KW, Barash Y, Thomas-Tikhonenko A.

Nucleic Acids Res. 2018 Nov 30;46(21):11357-11369. doi: 10.1093/nar/gky946. Erratum in: Nucleic Acids Res. 2019 Jan 25;47(2):1043.

8.

Co-regulatory activity of hnRNP K and NS1-BP in influenza and human mRNA splicing.

Thompson MG, Muñoz-Moreno R, Bhat P, Roytenberg R, Lindberg J, Gazzara MR, Mallory MJ, Zhang K, García-Sastre A, Fontoura BMA, Lynch KW.

Nat Commun. 2018 Jun 19;9(1):2407. doi: 10.1038/s41467-018-04779-4.

9.

Poly(C)-Binding Protein Pcbp2 Enables Differentiation of Definitive Erythropoiesis by Directing Functional Splicing of the Runx1 Transcript.

Ghanem LR, Kromer A, Silverman IM, Ji X, Gazzara M, Nguyen N, Aguilar G, Martinelli M, Barash Y, Liebhaber SA.

Mol Cell Biol. 2018 Jul 30;38(16). pii: e00175-18. doi: 10.1128/MCB.00175-18. Print 2018 Aug 15.

10.

MAJIQ-SPEL: Web-tool to interrogate classical and complex splicing variations from RNA-Seq data.

Green CJ, Gazzara MR, Barash Y.

Bioinformatics. 2017 Sep 11. doi: 10.1093/bioinformatics/btx565. [Epub ahead of print]

PMID:
28968636
11.

Integrative deep models for alternative splicing.

Jha A, Gazzara MR, Barash Y.

Bioinformatics. 2017 Jul 15;33(14):i274-i282. doi: 10.1093/bioinformatics/btx268.

12.

Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomes.

Gazzara MR, Mallory MJ, Roytenberg R, Lindberg JP, Jha A, Lynch KW, Barash Y.

Genome Res. 2017 Aug;27(8):1360-1370. doi: 10.1101/gr.220517.117. Epub 2017 May 16.

13.

A SLM2 Feedback Pathway Controls Cortical Network Activity and Mouse Behavior.

Ehrmann I, Gazzara MR, Pagliarini V, Dalgliesh C, Kheirollahi-Chadegani M, Xu Y, Cesari E, Danilenko M, Maclennan M, Lowdon K, Vogel T, Keskivali-Bond P, Wells S, Cater H, Fort P, Santibanez-Koref M, Middei S, Sette C, Clowry GJ, Barash Y, Cunningham MO, Elliott DJ.

Cell Rep. 2016 Dec 20;17(12):3269-3280. doi: 10.1016/j.celrep.2016.12.002.

14.

Position-dependent activity of CELF2 in the regulation of splicing and implications for signal-responsive regulation in T cells.

Ajith S, Gazzara MR, Cole BS, Shankarling G, Martinez NM, Mallory MJ, Lynch KW.

RNA Biol. 2016 Jun 2;13(6):569-81. doi: 10.1080/15476286.2016.1176663. Epub 2016 Apr 20.

15.

A new view of transcriptome complexity and regulation through the lens of local splicing variations.

Vaquero-Garcia J, Barrera A, Gazzara MR, González-Vallinas J, Lahens NF, Hogenesch JB, Lynch KW, Barash Y.

Elife. 2016 Feb 1;5:e11752. doi: 10.7554/eLife.11752.

16.

Convergence of Acquired Mutations and Alternative Splicing of CD19 Enables Resistance to CART-19 Immunotherapy.

Sotillo E, Barrett DM, Black KL, Bagashev A, Oldridge D, Wu G, Sussman R, Lanauze C, Ruella M, Gazzara MR, Martinez NM, Harrington CT, Chung EY, Perazzelli J, Hofmann TJ, Maude SL, Raman P, Barrera A, Gill S, Lacey SF, Melenhorst JJ, Allman D, Jacoby E, Fry T, Mackall C, Barash Y, Lynch KW, Maris JM, Grupp SA, Thomas-Tikhonenko A.

Cancer Discov. 2015 Dec;5(12):1282-95. doi: 10.1158/2159-8290.CD-15-1020. Epub 2015 Oct 29.

17.

Widespread JNK-dependent alternative splicing induces a positive feedback loop through CELF2-mediated regulation of MKK7 during T-cell activation.

Martinez NM, Agosto L, Qiu J, Mallory MJ, Gazzara MR, Barash Y, Fu XD, Lynch KW.

Genes Dev. 2015 Oct 1;29(19):2054-66. doi: 10.1101/gad.267245.115.

18.

Induced transcription and stability of CELF2 mRNA drives widespread alternative splicing during T-cell signaling.

Mallory MJ, Allon SJ, Qiu J, Gazzara MR, Tapescu I, Martinez NM, Fu XD, Lynch KW.

Proc Natl Acad Sci U S A. 2015 Apr 28;112(17):E2139-48. doi: 10.1073/pnas.1423695112. Epub 2015 Apr 13.

19.

In silico to in vivo splicing analysis using splicing code models.

Gazzara MR, Vaquero-Garcia J, Lynch KW, Barash Y.

Methods. 2014 May 1;67(1):3-12. doi: 10.1016/j.ymeth.2013.11.006. Epub 2013 Dec 7.

20.

Contrasting dynamics of a mutator allele in asexual populations of differing size.

Raynes Y, Gazzara MR, Sniegowski PD.

Evolution. 2012 Jul;66(7):2329-34. doi: 10.1111/j.1558-5646.2011.01577.x. Epub 2012 Mar 4.

21.

Mutator dynamics in sexual and asexual experimental populations of yeast.

Raynes Y, Gazzara MR, Sniegowski PD.

BMC Evol Biol. 2011 Jun 7;11:158. doi: 10.1186/1471-2148-11-158.

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