| Year |
Citation |
Score |
| 2021 |
Schirman D, Yakhini Z, Pilpel Y, Dahan O. A broad analysis of splicing regulation in yeast using a large library of synthetic introns. Plos Genetics. 17: e1009805. PMID 34570750 DOI: 10.1371/journal.pgen.1009805 |
0.312 |
|
| 2020 |
Slomka S, Françoise I, Hornung G, Asraf O, Biniashvili T, Pilpel Y, Dahan O. Experimental Evolution of Reveals the Evolutionary Dynamics of Horizontal Gene Transfer and Suggests Adaptive and Neutral Effects. Genetics. PMID 32847815 DOI: 10.1534/Genetics.120.303401 |
0.372 |
|
| 2019 |
Mikl M, Hamburg A, Pilpel Y, Segal E. Dissecting splicing decisions and cell-to-cell variability with designed sequence libraries. Nature Communications. 10: 4572. PMID 31594945 DOI: 10.1038/S41467-019-12642-3 |
0.351 |
|
| 2019 |
Frumkin I, Yofe I, Bar-Ziv R, Gurvich Y, Lu YY, Voichek Y, Towers R, Schirman D, Krebber H, Pilpel Y. Evolution of intron splicing towards optimized gene expression is based on various Cis- and Trans-molecular mechanisms. Plos Biology. 17: e3000423. PMID 31442222 DOI: 10.1371/Journal.Pbio.3000423 |
0.414 |
|
| 2019 |
Cohen-Zontag O, Baez C, Lim LQJ, Olender T, Schirman D, Dahary D, Pilpel Y, Gerst JE. A secretion-enhancing cis regulatory targeting element (SECReTE) involved in mRNA localization and protein synthesis. Plos Genetics. 15: e1008248. PMID 31260446 DOI: 10.1371/Journal.Pgen.1008248 |
0.326 |
|
| 2018 |
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, ... ... Pilpel Y, et al. Deterministic Somatic Cell Reprogramming Involves Continuous Transcriptional Changes Governed by Myc and Epigenetic-Driven Modules. Cell Stem Cell. PMID 30554962 DOI: 10.1016/J.Stem.2018.11.014 |
0.359 |
|
| 2018 |
Rak R, Dahan O, Pilpel Y. Repertoires of tRNAs: The Couplers of Genomics and Proteomics. Annual Review of Cell and Developmental Biology. PMID 30125138 DOI: 10.1146/Annurev-Cellbio-100617-062754 |
0.456 |
|
| 2018 |
Bar-Yaacov D, Pilpel Y, Dahan O. RNA editing in bacteria: occurrence, regulation and significance. Rna Biology. 1-5. PMID 30071181 DOI: 10.1080/15476286.2018.1481698 |
0.305 |
|
| 2018 |
Schirman D, Frumkin I, Pilpel Y. Does cancer strive to minimize the cost of gene expression? Oncotarget. 9: 27909-27910. PMID 29963249 DOI: 10.18632/Oncotarget.22657 |
0.318 |
|
| 2018 |
Frumkin I, Lajoie MJ, Gregg CJ, Hornung G, Church GM, Pilpel Y. Codon usage of highly expressed genes affects proteome-wide translation efficiency. Proceedings of the National Academy of Sciences of the United States of America. PMID 29735666 DOI: 10.1073/Pnas.1719375115 |
0.488 |
|
| 2017 |
Bar-Yaacov D, Mordret E, Towers R, Biniashvili T, Soyris C, Schwartz S, Dahan O, Pilpel Y. RNA editing in bacteria recodes multiple proteins and regulates an evolutionarily conserved toxin-antitoxin system. Genome Research. PMID 28864459 DOI: 10.1101/Gr.222760.117 |
0.356 |
|
| 2016 |
Frumkin I, Schirman D, Rotman A, Li F, Zahavi L, Mordret E, Asraf O, Wu S, Levy SF, Pilpel Y. Gene Architectures that Minimize Cost of Gene Expression. Molecular Cell. PMID 27989436 DOI: 10.1016/J.Molcel.2016.11.007 |
0.403 |
|
| 2016 |
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, et al. Mitochondrial 16S rRNA Is Methylated by tRNA Methyltransferase TRMT61B in All Vertebrates. Plos Biology. 14: e1002557. PMID 27631568 DOI: 10.1371/Journal.Pbio.1002557 |
0.311 |
|
| 2016 |
Sagi D, Rak R, Gingold H, Adir I, Maayan G, Dahan O, Broday L, Pilpel Y, Rechavi O. Tissue- and Time-Specific Expression of Otherwise Identical tRNA Genes. Plos Genetics. 12: e1006264. PMID 27560950 DOI: 10.1371/Journal.Pgen.1006264 |
0.478 |
|
| 2016 |
Karmon A, Pilpel Y. Biological causal links on physiological and evolutionary time scales. Elife. 5. PMID 27113916 DOI: 10.7554/Elife.14424 |
0.336 |
|
| 2016 |
Hoffman Y, Bublik DR, P Ugalde A, Elkon R, Biniashvili T, Agami R, Oren M, Pilpel Y. 3'UTR Shortening Potentiates MicroRNA-Based Repression of Pro-differentiation Genes in Proliferating Human Cells. Plos Genetics. 12: e1005879. PMID 26908102 DOI: 10.1371/Journal.Pgen.1005879 |
0.367 |
|
| 2015 |
Hoffman Y, Pilpel Y. Gene expression. MicroRNAs silence the noisy genome. Science (New York, N.Y.). 348: 41-2. PMID 25838367 DOI: 10.1126/Science.Aaa9841 |
0.371 |
|
| 2014 |
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, ... ... Pilpel Y, et al. A dual program for translation regulation in cellular proliferation and differentiation. Cell. 158: 1281-92. PMID 25215487 DOI: 10.1016/J.Cell.2014.08.011 |
0.426 |
|
| 2014 |
Hoffman Y, Pilpel Y, Oren M. microRNAs and Alu elements in the p53-Mdm2-Mdm4 regulatory network. Journal of Molecular Cell Biology. 6: 192-7. PMID 24868102 DOI: 10.1093/Jmcb/Mju020 |
0.366 |
|
| 2014 |
Bloom-Ackermann Z, Navon S, Gingold H, Towers R, Pilpel Y, Dahan O. A comprehensive tRNA deletion library unravels the genetic architecture of the tRNA pool. Plos Genetics. 10: e1004084. PMID 24453985 DOI: 10.1371/Journal.Pgen.1004084 |
0.45 |
|
| 2014 |
Minis A, Dahary D, Manor O, Leshkowitz D, Pilpel Y, Yaron A. Subcellular transcriptomics-dissection of the mRNA composition in the axonal compartment of sensory neurons. Developmental Neurobiology. 74: 365-81. PMID 24127433 DOI: 10.1002/Dneu.22140 |
0.338 |
|
| 2013 |
Yona AH, Bloom-Ackermann Z, Frumkin I, Hanson-Smith V, Charpak-Amikam Y, Feng Q, Boeke JD, Dahan O, Pilpel Y. tRNA genes rapidly change in evolution to meet novel translational demands. Elife. 2: e01339. PMID 24363105 DOI: 10.7554/Elife.01339 |
0.425 |
|
| 2013 |
Shalem O, Carey L, Zeevi D, Sharon E, Keren L, Weinberger A, Dahan O, Pilpel Y, Segal E. Measurements of the impact of 3' end sequences on gene expression reveal wide range and sequence dependent effects. Plos Computational Biology. 9: e1002934. PMID 23505350 DOI: 10.1371/Journal.Pcbi.1002934 |
0.43 |
|
| 2013 |
Hoffman Y, Dahary D, Bublik DR, Oren M, Pilpel Y. The majority of endogenous microRNA targets within Alu elements avoid the microRNA machinery. Bioinformatics (Oxford, England). 29: 894-902. PMID 23361327 DOI: 10.1093/Bioinformatics/Btt044 |
0.32 |
|
| 2013 |
Yona AH, Bloom-Ackermann Z, Frumkin I, Hanson-Smith V, Charpak-Amikam Y, Feng Q, Boeke JD, Dahan O, Pilpel Y. Author response: tRNA genes rapidly change in evolution to meet novel translational demands Elife. DOI: 10.7554/Elife.01339.017 |
0.405 |
|
| 2012 |
Dori-Bachash M, Shalem O, Manor YS, Pilpel Y, Tirosh I. Widespread promoter-mediated coordination of transcription and mRNA degradation. Genome Biology. 13: R114. PMID 23237624 DOI: 10.1186/Gb-2012-13-12-R114 |
0.388 |
|
| 2012 |
Salari R, Wojtowicz D, Zheng J, Levens D, Pilpel Y, Przytycka TM. Teasing apart translational and transcriptional components of stochastic variations in eukaryotic gene expression. Plos Computational Biology. 8: e1002644. PMID 22956896 DOI: 10.1371/Journal.Pcbi.1002644 |
0.42 |
|
| 2012 |
Gingold H, Dahan O, Pilpel Y. Dynamic changes in translational efficiency are deduced from codon usage of the transcriptome. Nucleic Acids Research. 40: 10053-63. PMID 22941644 DOI: 10.1093/Nar/Gks772 |
0.41 |
|
| 2012 |
Salari R, Wojtowicz D, Zheng J, Levens D, Pilpel Y, Przytycka TM. Correction: Teasing Apart Translational and Transcriptional Components of Stochastic Variations in Eukaryotic Gene Expression Plos Computational Biology. 8. DOI: 10.1371/annotation/4498943d-525d-4ac1-8375-ae78e67ea0c8 |
0.334 |
|
| 2011 |
Shalem O, Groisman B, Choder M, Dahan O, Pilpel Y. Transcriptome kinetics is governed by a genome-wide coupling of mRNA production and degradation: a role for RNA Pol II. Plos Genetics. 7: e1002273. PMID 21931566 DOI: 10.1371/Journal.Pgen.1002273 |
0.359 |
|
| 2011 |
Pilpel Y. Noise in biological systems: pros, cons, and mechanisms of control. Methods in Molecular Biology (Clifton, N.J.). 759: 407-25. PMID 21863500 DOI: 10.1007/978-1-61779-173-4_23 |
0.37 |
|
| 2011 |
Dahan O, Gingold H, Pilpel Y. Regulatory mechanisms and networks couple the different phases of gene expression. Trends in Genetics : Tig. 27: 316-22. PMID 21763027 DOI: 10.1016/J.Tig.2011.05.008 |
0.383 |
|
| 2011 |
Gingold H, Pilpel Y. Determinants of translation efficiency and accuracy. Molecular Systems Biology. 7: 481. PMID 21487400 DOI: 10.1038/Msb.2011.14 |
0.445 |
|
| 2011 |
Mitchell A, Pilpel Y. A mathematical model for adaptive prediction of environmental changes by microorganisms. Proceedings of the National Academy of Sciences of the United States of America. 108: 7271-6. PMID 21487001 DOI: 10.1073/Pnas.1019754108 |
0.3 |
|
| 2011 |
Limor-Waisberg K, Carmi A, Scherz A, Pilpel Y, Furman I. Specialization versus adaptation: two strategies employed by cyanophages to enhance their translation efficiencies. Nucleic Acids Research. 39: 6016-28. PMID 21470965 DOI: 10.1093/Nar/Gkr169 |
0.353 |
|
| 2011 |
Navon S, Pilpel Y. The role of codon selection in regulation of translation efficiency deduced from synthetic libraries. Genome Biology. 12: R12. PMID 21284851 DOI: 10.1186/Gb-2011-12-2-R12 |
0.371 |
|
| 2010 |
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, ... ... Pilpel Y, et al. EGF decreases the abundance of microRNAs that restrain oncogenic transcription factors. Science Signaling. 3: ra43. PMID 20516477 DOI: 10.1126/Scisignal.2000876 |
0.384 |
|
| 2010 |
Shen-Orr SS, Pilpel Y, Hunter CP. Composition and regulation of maternal and zygotic transcriptomes reflects species-specific reproductive mode. Genome Biology. 11: R58. PMID 20515465 DOI: 10.1186/Gb-2010-11-6-R58 |
0.43 |
|
| 2010 |
Shalgi R, Pilpel Y, Oren M. Repression of transposable-elements - a microRNA anti-cancer defense mechanism? Trends in Genetics : Tig. 26: 253-9. PMID 20417576 DOI: 10.1016/J.Tig.2010.03.006 |
0.301 |
|
| 2010 |
Tuller T, Carmi A, Vestsigian K, Navon S, Dorfan Y, Zaborske J, Pan T, Dahan O, Furman I, Pilpel Y. An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Cell. 141: 344-54. PMID 20403328 DOI: 10.1016/J.Cell.2010.03.031 |
0.376 |
|
| 2010 |
Rodríguez Martínez M, Soriano J, Tlusty T, Pilpel Y, Furman I. Messenger RNA fluctuations and regulatory RNAs shape the dynamics of a negative feedback loop. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 81: 031924. PMID 20365787 DOI: 10.1103/Physreve.81.031924 |
0.325 |
|
| 2009 |
Mitchell A, Romano GH, Groisman B, Yona A, Dekel E, Kupiec M, Dahan O, Pilpel Y. Adaptive prediction of environmental changes by microorganisms. Nature. 460: 220-4. PMID 19536156 DOI: 10.1038/Nature08112 |
0.333 |
|
| 2009 |
Kafri R, Springer M, Pilpel Y. Genetic redundancy: new tricks for old genes. Cell. 136: 389-92. PMID 19203571 DOI: 10.1016/J.Cell.2009.01.027 |
0.401 |
|
| 2008 |
Brosh R, Shalgi R, Liran A, Landan G, Korotayev K, Nguyen GH, Enerly E, Johnsen H, Buganim Y, Solomon H, Goldstein I, Madar S, Goldfinger N, Børresen-Dale AL, Ginsberg D, ... ... Pilpel Y, et al. p53-Repressed miRNAs are involved with E2F in a feed-forward loop promoting proliferation. Molecular Systems Biology. 4: 229. PMID 19034270 DOI: 10.1038/Msb.2008.65 |
0.313 |
|
| 2008 |
Shalem O, Dahan O, Levo M, Martinez MR, Furman I, Segal E, Pilpel Y. Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation. Molecular Systems Biology. 4: 223. PMID 18854817 DOI: 10.1038/Msb.2008.59 |
0.396 |
|
| 2008 |
Lapidot M, Michal L, Mizrahi-Man O, Pilpel Y. Functional characterization of variations on regulatory motifs. Plos Genetics. 4: e1000018. PMID 18369443 DOI: 10.1371/Journal.Pgen.1000018 |
0.387 |
|
| 2008 |
Kafri R, Dahan O, Levy J, Pilpel Y. Preferential protection of protein interaction network hubs in yeast: evolved functionality of genetic redundancy. Proceedings of the National Academy of Sciences of the United States of America. 105: 1243-8. PMID 18216251 DOI: 10.1073/Pnas.0711043105 |
0.334 |
|
| 2007 |
Man O, Pilpel Y. Differential translation efficiency of orthologous genes is involved in phenotypic divergence of yeast species. Nature Genetics. 39: 415-21. PMID 17277776 DOI: 10.1038/Ng1967 |
0.734 |
|
| 2007 |
Man O, Pilpel Y. Erratum: Corrigendum: Differential translation efficiency of orthologous genes is involved in phenotypic divergence of yeast species Nature Genetics. 39: 688-688. DOI: 10.1038/Ng0507-688A |
0.712 |
|
| 2006 |
Lapidot M, Pilpel Y. Genome-wide natural antisense transcription: coupling its regulation to its different regulatory mechanisms. Embo Reports. 7: 1216-22. PMID 17139297 DOI: 10.1038/Sj.Embor.7400857 |
0.442 |
|
| 2006 |
Kafri R, Levy M, Pilpel Y. The regulatory utilization of genetic redundancy through responsive backup circuits. Proceedings of the National Academy of Sciences of the United States of America. 103: 11653-8. PMID 16861297 DOI: 10.1073/Pnas.0604883103 |
0.428 |
|
| 2006 |
Furman I, Pilpel Y. Promoting human promoters. Molecular Systems Biology. 2: 2006.0030. PMID 16760901 DOI: 10.1038/Msb4100072 |
0.45 |
|
| 2006 |
Bar-Even A, Paulsson J, Maheshri N, Carmi M, O'Shea E, Pilpel Y, Barkai N. Noise in protein expression scales with natural protein abundance. Nature Genetics. 38: 636-43. PMID 16715097 DOI: 10.1038/Ng1807 |
0.421 |
|
| 2006 |
Xi Y, Shalgi R, Fodstad O, Pilpel Y, Ju J. Differentially regulated micro-RNAs and actively translated messenger RNA transcripts by tumor suppressor p53 in colon cancer. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 12: 2014-24. PMID 16609010 DOI: 10.1158/1078-0432.Ccr-05-1853 |
0.342 |
|
| 2005 |
Tabach Y, Milyavsky M, Shats I, Brosh R, Zuk O, Yitzhaky A, Mantovani R, Domany E, Rotter V, Pilpel Y. The promoters of human cell cycle genes integrate signals from two tumor suppressive pathways during cellular transformation. Molecular Systems Biology. 1: 2005.0022. PMID 16729057 DOI: 10.1038/Msb4100030 |
0.4 |
|
| 2005 |
Shalgi R, Lapidot M, Shamir R, Pilpel Y. A catalog of stability-associated sequence elements in 3' UTRs of yeast mRNAs. Genome Biology. 6: R86. PMID 16207357 DOI: 10.1186/Gb-2005-6-10-R86 |
0.354 |
|
| 2005 |
Kafri R, Bar-Even A, Pilpel Y. Transcription control reprogramming in genetic backup circuits. Nature Genetics. 37: 295-9. PMID 15723064 DOI: 10.1038/Ng1523 |
0.377 |
|
| 2005 |
Garten Y, Kaplan S, Pilpel Y. Extraction of transcription regulatory signals from genome-wide DNA-protein interaction data. Nucleic Acids Research. 33: 605-15. PMID 15684410 DOI: 10.1093/Nar/Gki166 |
0.433 |
|
| 2003 |
Lapidot M, Pilpel Y. Comprehensive quantitative analyses of the effects of promoter sequence elements on mRNA transcription. Nucleic Acids Research. 31: 3824-8. PMID 12824429 DOI: 10.1093/Nar/Gkg593 |
0.338 |
|
| 2002 |
Sudarsanam P, Pilpel Y, Church GM. Genome-wide co-occurrence of promoter elements reveals a cis-regulatory cassette of rRNA transcription motifs in Saccharomyces cerevisiae. Genome Research. 12: 1723-31. PMID 12421759 DOI: 10.1101/Gr.301202 |
0.431 |
|
| 2002 |
Zhu Z, Pilpel Y, Church GM. Computational identification of transcription factor binding sites via a transcription-factor-centric clustering (TFCC) algorithm. Journal of Molecular Biology. 318: 71-81. PMID 12054769 DOI: 10.1016/S0022-2836(02)00026-8 |
0.363 |
|
| 2002 |
Cohen BA, Pilpel Y, Mitra RD, Church GM. Discrimination between paralogs using microarray analysis: application to the Yap1p and Yap2p transcriptional networks. Molecular Biology of the Cell. 13: 1608-14. PMID 12006656 DOI: 10.1091/Mbc.01-10-0472 |
0.456 |
|
| 2001 |
Pilpel Y, Sudarsanam P, Church GM. Identifying regulatory networks by combinatorial analysis of promoter elements. Nature Genetics. 29: 153-9. PMID 11547334 DOI: 10.1038/Ng724 |
0.38 |
|
| 2001 |
Fuchs T, Glusman G, Horn-Saban S, Lancet D, Pilpel Y. The human olfactory subgenome: from sequence to structure and evolution. Human Genetics. 108: 1-13. PMID 11214901 DOI: 10.1007/S004390000436 |
0.391 |
|
| 2001 |
Lapidot M, Pilpel Y, Gilad Y, Falcovitz A, Sharon D, Haaf T, Lancet D. Mouse-human orthology relationships in an olfactory receptor gene cluster. Genomics. 71: 296-306. PMID 11170746 DOI: 10.1006/Geno.2000.6431 |
0.365 |
|
| 2000 |
Glusman G, Bahar A, Sharon D, Pilpel Y, White J, Lancet D. The olfactory receptor gene superfamily: data mining, classification, and nomenclature. Mammalian Genome : Official Journal of the International Mammalian Genome Society. 11: 1016-23. PMID 11063259 DOI: 10.1007/S003350010196 |
0.392 |
|
| 2000 |
Conticello SG, Pilpel Y, Glusman G, Fainzilber M. Position-specific codon conservation in hypervariable gene families. Trends in Genetics : Tig. 16: 57-9. PMID 10652528 DOI: 10.1016/S0168-9525(99)01956-3 |
0.352 |
|
| 1999 |
Sharon D, Glusman G, Pilpel Y, Khen M, Gruetzner F, Haaf T, Lancet D. Primate evolution of an olfactory receptor cluster: diversification by gene conversion and recent emergence of pseudogenes. Genomics. 61: 24-36. PMID 10512677 DOI: 10.1006/Geno.1999.5900 |
0.349 |
|
| 1999 |
Pilpel Y, Lancet D. Olfaction. Good reception in fruitfly antennae. Nature. 398: 285, 287. PMID 10192327 DOI: 10.1038/18552 |
0.322 |
|
| 1998 |
Sharon D, Glusman G, Pilpel Y, Horn-Saban S, Lancet D. Genome dynamics, evolution, and protein modeling in the olfactory receptor gene superfamily. Annals of the New York Academy of Sciences. 855: 182-93. PMID 9929603 DOI: 10.1111/J.1749-6632.1998.Tb10564.X |
0.395 |
|
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