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Items: 47

1.

The 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 Jun 4. pii: MCB.00175-18. doi: 10.1128/MCB.00175-18. [Epub ahead of print]

PMID:
29866654
2.

Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates.

Norton SS, Vaquero-Garcia J, Lahens NF, Grant GR, Barash Y.

Bioinformatics. 2018 May 1;34(9):1488-1497. doi: 10.1093/bioinformatics/btx790.

PMID:
29236961
3.

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.

PMID:
29107558
4.

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
5.

Transcriptome analysis of hypoxic cancer cells uncovers intron retention in EIF2B5 as a mechanism to inhibit translation.

Brady LK, Wang H, Radens CM, Bi Y, Radovich M, Maity A, Ivan C, Ivan M, Barash Y, Koumenis C.

PLoS Biol. 2017 Sep 29;15(9):e2002623. doi: 10.1371/journal.pbio.2002623. eCollection 2017 Sep.

6.

Phosphoproteomics reveals that glycogen synthase kinase-3 phosphorylates multiple splicing factors and is associated with alternative splicing.

Shinde MY, Sidoli S, Kulej K, Mallory MJ, Radens CM, Reicherter AL, Myers RL, Barash Y, Lynch KW, Garcia BA, Klein PS.

J Biol Chem. 2017 Nov 3;292(44):18240-18255. doi: 10.1074/jbc.M117.813527. Epub 2017 Sep 15.

7.

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.

8.

PRiMeUM: A Model for Predicting Risk of Metastasis in Uveal Melanoma.

Vaquero-Garcia J, Lalonde E, Ewens KG, Ebrahimzadeh J, Richard-Yutz J, Shields CL, Barrera A, Green CJ, Barash Y, Ganguly A.

Invest Ophthalmol Vis Sci. 2017 Aug 1;58(10):4096-4105. doi: 10.1167/iovs.17-22255.

PMID:
28828481
9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease.

Xiong HY, Alipanahi B, Lee LJ, Bretschneider H, Merico D, Yuen RK, Hua Y, Gueroussov S, Najafabadi HS, Hughes TR, Morris Q, Barash Y, Krainer AR, Jojic N, Scherer SW, Blencowe BJ, Frey BJ.

Science. 2015 Jan 9;347(6218):1254806. doi: 10.1126/science.1254806. Epub 2014 Dec 18.

15.

Splicing code modeling.

Barash Y, Vaquero-Garcia J.

Adv Exp Med Biol. 2014;825:451-66. doi: 10.1007/978-1-4939-1221-6_13. Review.

PMID:
25201114
16.

Predicting alternative splicing.

Barash Y, Garcia JV.

Methods Mol Biol. 2014;1126:411-23. doi: 10.1007/978-1-62703-980-2_28.

PMID:
24549679
17.

The magnetic penetration depth influenced by the proximity to the surface.

Barash YS.

J Phys Condens Matter. 2014 Jan 29;26(4):045702. doi: 10.1088/0953-8984/26/4/045702. Epub 2014 Jan 6.

PMID:
24390056
18.

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.

19.

AVISPA: a web tool for the prediction and analysis of alternative splicing.

Barash Y, Vaquero-Garcia J, González-Vallinas J, Xiong HY, Gao W, Lee LJ, Frey BJ.

Genome Biol. 2013;14(10):R114.

20.

Determination of molecular markers for BRCA1 and BRCA2 heterozygosity using gene expression profiling.

Salmon AY, Salmon-Divon M, Zahavi T, Barash Y, Levy-Drummer RS, Jacob-Hirsch J, Peretz T.

Cancer Prev Res (Phila). 2013 Feb;6(2):82-90. doi: 10.1158/1940-6207.CAPR-12-0105. Epub 2013 Jan 22.

21.

Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context.

Xiong HY, Barash Y, Frey BJ.

Bioinformatics. 2011 Sep 15;27(18):2554-62. doi: 10.1093/bioinformatics/btr444. Epub 2011 Jul 29.

PMID:
21803804
22.

An illuminated view of molecular biology.

Barash Y, Wang X.

Genome Biol. 2010;11(8):307. doi: 10.1186/gb-2010-11-8-307. Epub 2010 Aug 26.

23.

Model-based detection of alternative splicing signals.

Barash Y, Blencowe BJ, Frey BJ.

Bioinformatics. 2010 Jun 15;26(12):i325-33. doi: 10.1093/bioinformatics/btq200.

24.

Deciphering the splicing code.

Barash Y, Calarco JA, Gao W, Pan Q, Wang X, Shai O, Blencowe BJ, Frey BJ.

Nature. 2010 May 6;465(7294):53-9. doi: 10.1038/nature09000.

PMID:
20445623
25.

Electric field stimulation integrated into perfusion bioreactor for cardiac tissue engineering.

Barash Y, Dvir T, Tandeitnik P, Ruvinov E, Guterman H, Cohen S.

Tissue Eng Part C Methods. 2010 Dec;16(6):1417-26. doi: 10.1089/ten.TEC.2010.0068. Epub 2010 May 10.

PMID:
20367291
26.

Low-energy subgap states and the magnetic flux periodicity in d-wave superconducting rings.

Barash YS.

Phys Rev Lett. 2008 May 2;100(17):177003. Epub 2008 May 1.

PMID:
18518325
27.

A systematic analysis of intronic sequences downstream of 5' splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation.

Aznarez I, Barash Y, Shai O, He D, Zielenski J, Tsui LC, Parkinson J, Frey BJ, Rommens JM, Blencowe BJ.

Genome Res. 2008 Aug;18(8):1247-58. doi: 10.1101/gr.073155.107. Epub 2008 May 2.

28.

Epitaxial integration of the highly spin-polarized ferromagnetic semiconductor EuO with silicon and GaN.

Schmehl A, Vaithyanathan V, Herrnberger A, Thiel S, Richter C, Liberati M, Heeg T, Röckerath M, Kourkoutis LF, Mühlbauer S, Böni P, Muller DA, Barash Y, Schubert J, Idzerda Y, Mannhart J, Schlom DG.

Nat Mater. 2007 Nov;6(11):882-7. Epub 2007 Sep 16.

PMID:
17873862
29.

Functional coordination of alternative splicing in the mammalian central nervous system.

Fagnani M, Barash Y, Ip JY, Misquitta C, Pan Q, Saltzman AL, Shai O, Lee L, Rozenhek A, Mohammad N, Willaime-Morawek S, Babak T, Zhang W, Hughes TR, van der Kooy D, Frey BJ, Blencowe BJ.

Genome Biol. 2007;8(6):R108.

30.

0-pi transitions in Josephson junctions with antiferromagnetic interlayers.

Andersen BM, Bobkova IV, Hirschfeld PJ, Barash YS.

Phys Rev Lett. 2006 Mar 24;96(11):117005. Epub 2006 Mar 24.

PMID:
16605855
31.

Thalassomonas loyana sp. nov., a causative agent of the white plague-like disease of corals on the Eilat coral reef.

Thompson FL, Barash Y, Sawabe T, Sharon G, Swings J, Rosenberg E.

Int J Syst Evol Microbiol. 2006 Feb;56(Pt 2):365-8.

PMID:
16449441
32.

Spin-dependent quasiparticle reflection and bound States at interfaces with itinerant antiferromagnets.

Bobkova IV, Hirschfeld PJ, Barash YS.

Phys Rev Lett. 2005 Jan 28;94(3):037005. Epub 2005 Jan 26.

PMID:
15698311
33.

CIS: compound importance sampling method for protein-DNA binding site p-value estimation.

Barash Y, Elidan G, Kaplan T, Friedman N.

Bioinformatics. 2005 Mar 1;21(5):596-600. Epub 2004 Sep 28.

PMID:
15454407
34.

Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression.

Marion RM, Regev A, Segal E, Barash Y, Koller D, Friedman N, O'Shea EK.

Proc Natl Acad Sci U S A. 2004 Oct 5;101(40):14315-22. Epub 2004 Sep 7.

35.

Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays.

Barash Y, Dehan E, Krupsky M, Franklin W, Geraci M, Friedman N, Kaminski N.

Bioinformatics. 2004 Apr 12;20(6):839-46. Epub 2004 Jan 29.

PMID:
14751998
36.

Context-specific Bayesian clustering for gene expression data.

Barash Y, Friedman N.

J Comput Biol. 2002;9(2):169-91.

PMID:
12015876
37.

Transcriptional profiling of non-small cell lung cancer using oligonucleotide microarrays.

Cojocaru G, Friedman N, Krupsky M, Yaron P, Simansky D, Yellin A, Rechavi G, Barash Y, Ben-Dor A, Yakhini Z, Kaminski N.

Chest. 2002 Mar;121(3 Suppl):44S. No abstract available.

PMID:
11893681
38.

Soluble tumor necrosis factor receptor levels in familial Mediterranean fever.

Dror Y, Hahn T, Barash Y.

J Rheumatol. 1998 Dec;25(12):2481-2. No abstract available.

PMID:
9858459
39.

Low-Temperature Anomaly in the Josephson Critical Current of Junctions in d-Wave Superconductors.

Barash YS, Burkhardt H, Rainer D.

Phys Rev Lett. 1996 Nov 4;77(19):4070-4073. No abstract available.

PMID:
10062380
40.

Low-temperature properties and specific anisotropy of pure anisotropically paired superconductors.

Barash YS, Svidzinsky AA.

Phys Rev B Condens Matter. 1996 Jun 1;53(22):15254-15264. No abstract available.

PMID:
9983322
41.

Upper critical field for an unconventional superconducting film: A kink due to the boundary conditions.

Barash YS, Galaktionov AV, Svidzinsky AA.

Phys Rev B Condens Matter. 1995 Oct 1;52(14):10344-10358. No abstract available.

PMID:
9980086
42.

[Systemic lupus erythematosus in children in Israel].

Brik R, Padeh S, Mukamel M, Navon P, Uziel Y, Kornmehl P, Taub D, Barash Y.

Harefuah. 1995 Oct;129(7-8):233-5, 296, 295. Hebrew.

PMID:
8549958
43.

Comment on "Superconducting Pairing Symmetry and Josephson Tunneling"

Barash YS, Galaktionov AV, Zaikin AD.

Phys Rev Lett. 1995 Aug 21;75(8):1676. No abstract available.

PMID:
10060359
44.

Charge transport in junctions between d-wave superconductors.

Barash YS, Galaktionov AV, Zaikin AD.

Phys Rev B Condens Matter. 1995 Jul 1;52(1):665-682. No abstract available.

PMID:
9979645
45.

Frequency and wave-vector dependence of the fluctuation electromagnetic response near the superconducting transition.

Barash YS, Galaktionov AV.

Phys Rev B Condens Matter. 1993 Sep 1;48(9):6284-6292. No abstract available.

PMID:
10009174
46.

Homozygosity for autosomal dominant Marfan syndrome.

Chemke J, Nisani R, Feigl A, Garty R, Cooper M, Bårash Y, Duksin D.

J Med Genet. 1984 Jun;21(3):173-7.

47.

Renal glomerular and tubular function following acute insulin deprivation in juvenile diabetes mellitus.

Barash Y, Aladjem M, Sack J, Bistritzer T, Theodor R, Orda S, Boichis H.

Nephron. 1982;31(1):65-7.

PMID:
7050753

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