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Items: 1 to 50 of 96

1.

Dissecting splicing decisions and cell-to-cell variability with designed sequence libraries.

Mikl M, Hamburg A, Pilpel Y, Segal E.

Nat Commun. 2019 Oct 8;10(1):4572. doi: 10.1038/s41467-019-12642-3.

2.

Evolution of intron splicing towards optimized gene expression is based on various Cis- and Trans-molecular mechanisms.

Frumkin I, Yofe I, Bar-Ziv R, Gurvich Y, Lu YY, Voichek Y, Towers R, Schirman D, Krebber H, Pilpel Y.

PLoS Biol. 2019 Aug 23;17(8):e3000423. doi: 10.1371/journal.pbio.3000423. eCollection 2019 Aug.

3.

Systematic Detection of Amino Acid Substitutions in Proteomes Reveals Mechanistic Basis of Ribosome Errors and Selection for Translation Fidelity.

Mordret E, Dahan O, Asraf O, Rak R, Yehonadav A, Barnabas GD, Cox J, Geiger T, Lindner AB, Pilpel Y.

Mol Cell. 2019 Aug 8;75(3):427-441.e5. doi: 10.1016/j.molcel.2019.06.041. Epub 2019 Jul 25.

PMID:
31353208
4.

A secretion-enhancing cis regulatory targeting element (SECReTE) involved in mRNA localization and protein synthesis.

Cohen-Zontag O, Baez C, Lim LQJ, Olender T, Schirman D, Dahary D, Pilpel Y, Gerst JE.

PLoS Genet. 2019 Jul 1;15(7):e1008248. doi: 10.1371/journal.pgen.1008248. eCollection 2019 Jul.

5.

Evolthon: A community endeavor to evolve lab evolution.

Kaminski Strauss S, Schirman D, Jona G, Brooks AN, Kunjapur AM, Nguyen Ba AN, Flint A, Solt A, Mershin A, Dixit A, Yona AH, Csörgő B, Busby BP, Hennig BP, Pál C, Schraivogel D, Schultz D, Wernick DG, Agashe D, Levi D, Zabezhinsky D, Russ D, Sass E, Tamar E, Herz E, Levy ED, Church GM, Yelin I, Nachman I, Gerst JE, Georgeson JM, Adamala KP, Steinmetz LM, Rübsam M, Ralser M, Klutstein M, Desai MM, Walunjkar N, Yin N, Aharon Hefetz N, Jakimo N, Snitser O, Adini O, Kumar P, Soo Hoo Smith R, Zeidan R, Hazan R, Rak R, Kishony R, Johnson S, Nouriel S, Vonesch SC, Foster S, Dagan T, Wein T, Karydis T, Wannier TM, Stiles T, Olin-Sandoval V, Mueller WF, Bar-On YM, Dahan O, Pilpel Y.

PLoS Biol. 2019 Mar 29;17(3):e3000182. doi: 10.1371/journal.pbio.3000182. eCollection 2019 Mar.

6.

Deterministic Somatic Cell Reprogramming Involves Continuous Transcriptional Changes Governed by Myc and Epigenetic-Driven Modules.

Zviran A, Mor N, Rais Y, Gingold H, Peles S, Chomsky E, Viukov S, Buenrostro JD, Scognamiglio R, Weinberger L, Manor YS, Krupalnik V, Zerbib M, Hezroni H, Jaitin DA, Larastiaso D, Gilad S, Benjamin S, Gafni O, Mousa A, Ayyash M, Sheban D, Bayerl J, Aguilera-Castrejon A, Massarwa R, Maza I, Hanna S, Stelzer Y, Ulitsky I, Greenleaf WJ, Tanay A, Trumpp A, Amit I, Pilpel Y, Novershtern N, Hanna JH.

Cell Stem Cell. 2019 Feb 7;24(2):328-341.e9. doi: 10.1016/j.stem.2018.11.014. Epub 2018 Dec 13.

PMID:
30554962
7.

Metabolic Syndrome is a Risk Factor for Post-Operative Adhesions: Need for Novel Treatment Strategies.

Pilpel Y, Pines G, Birkenfeld A, Bornstein SR, Miller R.

Horm Metab Res. 2019 Jan;51(1):35-41. doi: 10.1055/a-0798-3931. Epub 2018 Nov 29. Review.

PMID:
30497091
8.

Repertoires of tRNAs: The Couplers of Genomics and Proteomics.

Rak R, Dahan O, Pilpel Y.

Annu Rev Cell Dev Biol. 2018 Oct 6;34:239-264. doi: 10.1146/annurev-cellbio-100617-062754. Epub 2018 Aug 20. Review.

PMID:
30125138
9.

RNA editing in bacteria: occurrence, regulation and significance.

Bar-Yaacov D, Pilpel Y, Dahan O.

RNA Biol. 2018;15(7):863-867. doi: 10.1080/15476286.2018.1481698. Epub 2018 Aug 2.

10.

Does cancer strive to minimize the cost of gene expression?

Schirman D, Frumkin I, Pilpel Y.

Oncotarget. 2018 Jun 15;9(46):27909-27910. doi: 10.18632/oncotarget.22657. eCollection 2018 Jun 15. No abstract available.

11.

Codon usage of highly expressed genes affects proteome-wide translation efficiency.

Frumkin I, Lajoie MJ, Gregg CJ, Hornung G, Church GM, Pilpel Y.

Proc Natl Acad Sci U S A. 2018 May 22;115(21):E4940-E4949. doi: 10.1073/pnas.1719375115. Epub 2018 May 7.

12.

Meiotic Recombination: Genetics' Good Old Scalpel.

Slomka S, Pilpel Y.

Cell. 2018 Jan 25;172(3):391-392. doi: 10.1016/j.cell.2018.01.017.

13.

RNA editing in bacteria recodes multiple proteins and regulates an evolutionarily conserved toxin-antitoxin system.

Bar-Yaacov D, Mordret E, Towers R, Biniashvili T, Soyris C, Schwartz S, Dahan O, Pilpel Y.

Genome Res. 2017 Oct;27(10):1696-1703. doi: 10.1101/gr.222760.117. Epub 2017 Sep 1.

14.

Editorial overview: Systems biology for biotechnology.

Heinemann M, Pilpel Y.

Curr Opin Biotechnol. 2017 Aug;46:iv-v. doi: 10.1016/j.copbio.2017.07.001. Epub 2017 Jul 19. No abstract available.

PMID:
28734757
15.

Correction: Mitochondrial 16S rRNA Is Methylated by tRNA Methyltransferase TRMT61B in All Vertebrates.

Bar-Yaacov D, Frumkin I, Yashiro Y, Chujo T, Ishigami Y, Chemla Y, Blumberg A, Schlesinger O, Bieri P, Greber B, Ban N, Zarivach R, Alfonta L, Pilpel Y, Suzuki T, Mishmar D.

PLoS Biol. 2017 Jan 19;15(1):e1002594. doi: 10.1371/journal.pbio.1002594. eCollection 2017 Jan.

16.

Gene Architectures that Minimize Cost of Gene Expression.

Frumkin I, Schirman D, Rotman A, Li F, Zahavi L, Mordret E, Asraf O, Wu S, Levy SF, Pilpel Y.

Mol Cell. 2017 Jan 5;65(1):142-153. doi: 10.1016/j.molcel.2016.11.007. Epub 2016 Dec 15.

17.

Mitochondrial 16S rRNA Is Methylated by tRNA Methyltransferase TRMT61B in All Vertebrates.

Bar-Yaacov D, Frumkin I, Yashiro Y, Chujo T, Ishigami Y, Chemla Y, Blumberg A, Schlesinger O, Bieri P, Greber B, Ban N, Zarivach R, Alfonta L, Pilpel Y, Suzuki T, Mishmar D.

PLoS Biol. 2016 Sep 15;14(9):e1002557. doi: 10.1371/journal.pbio.1002557. eCollection 2016 Sep. Erratum in: PLoS Biol. 2017 Jan 19;15(1):e1002594.

18.

Tissue- and Time-Specific Expression of Otherwise Identical tRNA Genes.

Sagi D, Rak R, Gingold H, Adir I, Maayan G, Dahan O, Broday L, Pilpel Y, Rechavi O.

PLoS Genet. 2016 Aug 25;12(8):e1006264. doi: 10.1371/journal.pgen.1006264. eCollection 2016 Aug.

19.

Rapid evolutionary adaptation to growth on an 'unfamiliar' carbon source.

Tamari Z, Yona AH, Pilpel Y, Barkai N.

BMC Genomics. 2016 Aug 24;17:674. doi: 10.1186/s12864-016-3010-x.

20.

Biological causal links on physiological and evolutionary time scales.

Karmon A, Pilpel Y.

Elife. 2016 Apr 26;5:e14424. doi: 10.7554/eLife.14424.

21.

3'UTR Shortening Potentiates MicroRNA-Based Repression of Pro-differentiation Genes in Proliferating Human Cells.

Hoffman Y, Bublik DR, Ugalde AP, Elkon R, Biniashvili T, Agami R, Oren M, Pilpel Y.

PLoS Genet. 2016 Feb 23;12(2):e1005879. doi: 10.1371/journal.pgen.1005879. eCollection 2016 Feb. Erratum in: PLoS Genet. 2016 Aug;12(8):e1006254.

22.

A relay race on the evolutionary adaptation spectrum.

Yona AH, Frumkin I, Pilpel Y.

Cell. 2015 Oct 22;163(3):549-59. doi: 10.1016/j.cell.2015.10.005. Epub 2015 Oct 22. Review.

23.

The Lamarckian chicken and the Darwinian egg.

Pilpel Y, Rechavi O.

Biol Direct. 2015 Jul 1;10:34. doi: 10.1186/s13062-015-0062-9.

24.

Gene expression. MicroRNAs silence the noisy genome.

Hoffman Y, Pilpel Y.

Science. 2015 Apr 3;348(6230):41-2. doi: 10.1126/science.aaa9841. No abstract available.

PMID:
25838367
25.

A dual program for translation regulation in cellular proliferation and differentiation.

Gingold H, Tehler D, Christoffersen NR, Nielsen MM, Asmar F, Kooistra SM, Christophersen NS, Christensen LL, Borre M, Sørensen KD, Andersen LD, Andersen CL, Hulleman E, Wurdinger T, Ralfkiær E, Helin K, Grønbæk K, Ørntoft T, Waszak SM, Dahan O, Pedersen JS, Lund AH, Pilpel Y.

Cell. 2014 Sep 11;158(6):1281-1292. doi: 10.1016/j.cell.2014.08.011.

26.

mRNA-programmed translation pauses in the targeting of E. coli membrane proteins.

Fluman N, Navon S, Bibi E, Pilpel Y.

Elife. 2014 Aug 18;3. doi: 10.7554/eLife.03440.

27.

microRNAs and Alu elements in the p53-Mdm2-Mdm4 regulatory network.

Hoffman Y, Pilpel Y, Oren M.

J Mol Cell Biol. 2014 Jun;6(3):192-7. doi: 10.1093/jmcb/mju020. Review.

28.

A comprehensive tRNA deletion library unravels the genetic architecture of the tRNA pool.

Bloom-Ackermann Z, Navon S, Gingold H, Towers R, Pilpel Y, Dahan O.

PLoS Genet. 2014 Jan;10(1):e1004084. doi: 10.1371/journal.pgen.1004084. Epub 2014 Jan 16.

29.

tRNA genes rapidly change in evolution to meet novel translational demands.

Yona AH, Bloom-Ackermann Z, Frumkin I, Hanson-Smith V, Charpak-Amikam Y, Feng Q, Boeke JD, Dahan O, Pilpel Y.

Elife. 2013 Dec 20;2:e01339. doi: 10.7554/eLife.01339.

30.

miR-661 downregulates both Mdm2 and Mdm4 to activate p53.

Hoffman Y, Bublik DR, Pilpel Y, Oren M.

Cell Death Differ. 2014 Feb;21(2):302-9. doi: 10.1038/cdd.2013.146. Epub 2013 Oct 18.

31.

Subcellular transcriptomics-dissection of the mRNA composition in the axonal compartment of sensory neurons.

Minis A, Dahary D, Manor O, Leshkowitz D, Pilpel Y, Yaron A.

Dev Neurobiol. 2014 Mar;74(3):365-81. doi: 10.1002/dneu.22140. Epub 2013 Nov 18.

32.

Measurements of the impact of 3' end sequences on gene expression reveal wide range and sequence dependent effects.

Shalem O, Carey L, Zeevi D, Sharon E, Keren L, Weinberger A, Dahan O, Pilpel Y, Segal E.

PLoS Comput Biol. 2013;9(3):e1002934. doi: 10.1371/journal.pcbi.1002934. Epub 2013 Mar 7.

33.

The majority of endogenous microRNA targets within Alu elements avoid the microRNA machinery.

Hoffman Y, Dahary D, Bublik DR, Oren M, Pilpel Y.

Bioinformatics. 2013 Apr 1;29(7):894-902. doi: 10.1093/bioinformatics/btt044. Epub 2013 Jan 29.

PMID:
23361327
34.

Widespread promoter-mediated coordination of transcription and mRNA degradation.

Dori-Bachash M, Shalem O, Manor YS, Pilpel Y, Tirosh I.

Genome Biol. 2012 Dec 13;13(12):R114. doi: 10.1186/gb-2012-13-12-r114.

35.

Chromosomal duplication is a transient evolutionary solution to stress.

Yona AH, Manor YS, Herbst RH, Romano GH, Mitchell A, Kupiec M, Pilpel Y, Dahan O.

Proc Natl Acad Sci U S A. 2012 Dec 18;109(51):21010-5. doi: 10.1073/pnas.1211150109. Epub 2012 Nov 29.

36.

Teasing apart translational and transcriptional components of stochastic variations in eukaryotic gene expression.

Salari R, Wojtowicz D, Zheng J, Levens D, Pilpel Y, Przytycka TM.

PLoS Comput Biol. 2012;8(8):e1002644. doi: 10.1371/journal.pcbi.1002644. Epub 2012 Aug 30. Erratum in: PLoS Comput Biol. 2012;8(10): doi/10.1371/annotation/4498943d-525d-4ac1-8375-ae78e67ea0c8.

37.

Dynamic changes in translational efficiency are deduced from codon usage of the transcriptome.

Gingold H, Dahan O, Pilpel Y.

Nucleic Acids Res. 2012 Nov 1;40(20):10053-63. doi: 10.1093/nar/gks772. Epub 2012 Aug 31.

38.

Axonal transcription factors signal retrogradely in lesioned peripheral nerve.

Ben-Yaakov K, Dagan SY, Segal-Ruder Y, Shalem O, Vuppalanchi D, Willis DE, Yudin D, Rishal I, Rother F, Bader M, Blesch A, Pilpel Y, Twiss JL, Fainzilber M.

EMBO J. 2012 Mar 21;31(6):1350-63. doi: 10.1038/emboj.2011.494. Epub 2012 Jan 13.

39.

Transcriptome kinetics is governed by a genome-wide coupling of mRNA production and degradation: a role for RNA Pol II.

Shalem O, Groisman B, Choder M, Dahan O, Pilpel Y.

PLoS Genet. 2011 Sep;7(9):e1002273. doi: 10.1371/journal.pgen.1002273. Epub 2011 Sep 8. Erratum in: PLoS Genet. 2011 Sep;7(9). doi: 10.1371/annotation/7919492c-3e4b-4363-96da-f75281c1340c.

40.

Noise in biological systems: pros, cons, and mechanisms of control.

Pilpel Y.

Methods Mol Biol. 2011;759:407-25. doi: 10.1007/978-1-61779-173-4_23. Review.

PMID:
21863500
41.

Regulatory mechanisms and networks couple the different phases of gene expression.

Dahan O, Gingold H, Pilpel Y.

Trends Genet. 2011 Aug;27(8):316-22. doi: 10.1016/j.tig.2011.05.008. Epub 2011 Jul 15. Review.

PMID:
21763027
42.

Determinants of translation efficiency and accuracy.

Gingold H, Pilpel Y.

Mol Syst Biol. 2011 Apr 12;7:481. doi: 10.1038/msb.2011.14. Review.

43.

A mathematical model for adaptive prediction of environmental changes by microorganisms.

Mitchell A, Pilpel Y.

Proc Natl Acad Sci U S A. 2011 Apr 26;108(17):7271-6. doi: 10.1073/pnas.1019754108. Epub 2011 Apr 12.

44.

Specialization versus adaptation: two strategies employed by cyanophages to enhance their translation efficiencies.

Limor-Waisberg K, Carmi A, Scherz A, Pilpel Y, Furman I.

Nucleic Acids Res. 2011 Aug;39(14):6016-28. doi: 10.1093/nar/gkr169. Epub 2011 Apr 5.

45.

The role of codon selection in regulation of translation efficiency deduced from synthetic libraries.

Navon S, Pilpel Y.

Genome Biol. 2011;12(2):R12. doi: 10.1186/gb-2011-12-2-r12. Epub 2011 Feb 1.

46.

CpG Islands as a putative source for animal miRNAs: evolutionary and functional implications.

Dahary D, Shalgi R, Pilpel Y.

Mol Biol Evol. 2011 May;28(5):1545-51. doi: 10.1093/molbev/msq315. Epub 2010 Nov 22.

PMID:
21097999
47.

Signaling to transcription networks in the neuronal retrograde injury response.

Michaelevski I, Segal-Ruder Y, Rozenbaum M, Medzihradszky KF, Shalem O, Coppola G, Horn-Saban S, Ben-Yaakov K, Dagan SY, Rishal I, Geschwind DH, Pilpel Y, Burlingame AL, Fainzilber M.

Sci Signal. 2010 Jul 13;3(130):ra53. doi: 10.1126/scisignal.2000952.

48.

EGF decreases the abundance of microRNAs that restrain oncogenic transcription factors.

Avraham R, Sas-Chen A, Manor O, Steinfeld I, Shalgi R, Tarcic G, Bossel N, Zeisel A, Amit I, Zwang Y, Enerly E, Russnes HG, Biagioni F, Mottolese M, Strano S, Blandino G, Børresen-Dale AL, Pilpel Y, Yakhini Z, Segal E, Yarden Y.

Sci Signal. 2010 Jun 1;3(124):ra43. doi: 10.1126/scisignal.2000876.

49.

Composition and regulation of maternal and zygotic transcriptomes reflects species-specific reproductive mode.

Shen-Orr SS, Pilpel Y, Hunter CP.

Genome Biol. 2010;11(6):R58. doi: 10.1186/gb-2010-11-6-r58. Epub 2010 Jun 1.

50.

Repression of transposable-elements - a microRNA anti-cancer defense mechanism?

Shalgi R, Pilpel Y, Oren M.

Trends Genet. 2010 Jun;26(6):253-9. doi: 10.1016/j.tig.2010.03.006. Epub 2010 Apr 22.

PMID:
20417576

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