Publications

2019

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    Mikl M., Hamburg A., Pilpel Y. & Segal E. (2019) Nature Communications. 10, 4572.  Abstract
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    Mordret E., Dahan O., Asraf O., Rak R., Yehonadav A., Barnabas G. D., Cox J., Geiger T., Lindner A. B. & Pilpel Y. (2019) Molecular Cell. 75, 3, p. 427-441  Abstract
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    Frumkin I., Yofe I., Bar-Ziv R., Gurvich Y., Lu Y., Voichek Y., Towers R., Schirman D., Krebber H. & Pilpel Y. (2019) PLoS Biology. 17, 8, 3000423.  Abstract
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    Cohen-Zontag O., Baez C., Lim L. Q. J., Olender T., Schirman D., Dahary D., Pilpel Y. & Gerst J. E. (2019) PLoS Genetics. 15, 7, 1008248.  Abstract
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    Dahan, O., Dorfman, B-S., Sayin, S., Rosener, B., Hua, T., Yarden, A. & Mitchell, A. (2019) PLoS Biology. 17, 6,  Abstract
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    Kaminski Strauss S., Schirman D., Jona G., Brooks A. N., Kunjapur A. M., Ba A. N. N., Flint A., Solt A., Mershin A., Dixit A., Yona A. H., Csorgo B., Busby B. P., Hennig B. P., Pal C., Schraivogel D., Schultz D., Wernick D. G., Agashe D., Levi D., Zabezhinsky D., Russ D., Sass E., Tamar E., Herz E., Levy E. D., Church G. M., Yelin I., Nachman I., Gerst J. E., Georgeson J. M., Adamala K. P., Steinmetz L. M., Ruebsam M., Ralser M., Klutstein M., Desai M. M., Walunjkar N., Yin N., Hefetz N. A., Jakimo N., Snitser O., Adini O., Kumar P., Smith R. S. H., Zeidan R., Hazan R., Rak R., Kishony R., Johnson S., Nouriel S., Vonesch S. C., Foster S., Dagan T., Wein T., Karydis T., Wannier T. M., Stiles T., Olin-Sandoval V., Mueller W. F., Bar-On Y. M., Dahan O. & Pilpel Y. (2019) PLoS Biology. 17, 3, p. e3000182 3000182.  Abstract
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    Zviran A., Mor N., Rais Y., Gingold H., Peles S., Chomsky E., Viukov S., Buenrostro J. D., Scognamiglio R., Weinberger L., Manor Y. S., Krupalnik V., Zerbib M., Hezroni H., Jaitin D. A., 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 W. J., Tanay A., Trumpp A., Amit I., Pilpel Y., Novershtern N. & Hanna J. H. (2019) Cell Stem Cell. 24, 2, p. 328-341.e9  Abstract

2018

  1. application/pdf
    Bar-Yaacov D., Pilpel Y. & Dahan O. (2018) RNA Biology. 15, 7, p. 863-867  Abstract
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    Frumkin I., Lajoie M. J., Gregg C. J., Hornung G., Church G. M. & Pilpel Y. (2018) Proceedings Of The National Academy Of Sciences Of The United States Of America-Biological Sciences. 115, 21, p. E4940-E4949  Abstract
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    Rak R., Dahan O. & Pilpel Y. (2018) ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY, VOL 34. Lehmann R.(eds.). Annual Reviews Inc., p. 239-264 (Annual Review of Cell and Developmental Biology).  Abstract
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    Slomka S. & Pilpel Y. (2018) Cell. 172, 3, p. 391-392  Abstract

2017

  1. application/pdf
    Bar-Yaacov D., Mordret E., Towers R., Biniashvili T., Soyris C., Schwartz S., Dahan O. & Pilpel Y. (2017) Genome Research. 27, 10, p. 1696-1703  Abstract
  2. Gene architectures that minimize cost of gene expression
    Frumkin I., Schirman D., Rotman A. & Pilpel Y. (2017) p. 235-236  Abstract
  3. Zviran A., Mor N., Rais Y., Gingold H., Peles S., Chomsky E., Viukov S., Buenrostro J. D., Weinberger L., Manor Y. S., Krupalnik V., Zerbib M., Hezroni H., Jaitin D. A., Larastiaso D., Gilad S., Benjamin S., Mousa A., Ayyash M., Sheban D., Bayerl J., Aguilera Castrejon A., Massarwa R., Maza I., Hanna S., Amit I., Stelzer Y., Ulitsky I., Greenleaf W. J., Pilpel Y., Novershtern N. & Hanna J. H. (2017) BioRxiv.  Abstract
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    Heinemann M. & Pilpel Y. (2017) Current Opinion in Biotechnology. 46, p. IV-V  Abstract
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    Frumkin I., Schirman D., Rotman A., Li F., Zahavi L., Mordret E., Asraf O., Wu S., Levy S. F. & Pilpel Y. (2017) Molecular Cell. 65, 1, p. 142-153  Abstract

2016

  1. application/pdf
    Bar Yaacov Y. 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. (2016) PLoS Biology. 14, 9, e1002557.  Abstract
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    Karmon A. & Pilpel Y. (2016) eLife. 5,  Abstract
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    Hoffman Y., Bublik D. R., Ugalde A. P., Elkon R., Biniashvili T., Agami R., Oren M. & Pilpel Y. (2016) PLoS Genetics. p. 260-262  Abstract
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    Tamari Z., Yona A. H., Pilpel Y. & Barkai N. (2016) BMC Genomics. 17, p. 674  Abstract

2015

  1. application/pdf
    Yona A. H., Frumkin I. & Pilpel Y. (2015) Cell. 163, 3, p. 549-559  Abstract
  2. application/pdf
    Pilpel Y. & Rechavi O. (2015) Biology Direct. 10, 34.  Abstract
  3. Hoffman Y. & Pilpel Y. (2015) Science. 348, 6230, p. 41-42  Abstract

2014

  1. Gingold H., Tehler D., Christoffersen N., Nielsen M., Asmar F., Kooistra S., Christophersen N., Christensen L., Borre M., Sorensen K., Andersen L., Andersen C., Hulleman E., Wurdinger T., Ralfkiaer E., Helin K., Gronbaek K., Omtoft T., Waszak S., Dahan O., Pedersen J., Lund A. & Pilpel Y. (2014) Cell. 158, 6, p. 1281-1292  Abstract
  2. Fluman N., Navon S., Bibi E. & Pilpel Y. (2014) eLife. 3,  Abstract
  3. Hoffman Y., Pilpel Y. & Oren M. (2014) Journal of Molecular Cell Biology. 6, 3, p. 192-197  Abstract
  4. Minis A., Dahary D., Manor O., Leshkowitz D., Pilpel Y. & Yaron A. (2014) Developmental Neurobiology. 74, 3, p. 365-381  Abstract
  5. Hoffman Y., Bublik D. R., Pilpel Y. & Oren M. (2014) Cell Death and Differentiation. 21, 2, p. 302-309  Abstract
  6. Bloom-Ackermann Z., Navon S., Gingold H., Towers R., Pilpel Y. & Dahan O. (2014) PLoS Genetics. 10, 1, e1004084.  Abstract

2013

  1. Yona A. H., Bloom-Ackermann Z., Frumkin I., Hanson-Smith V., Charpak-Amikam Y., Feng Q., Boeke J. D., Dahan O. & Pilpel Y. (2013) eLife. 2,  Abstract
  2. Hoffman Y., Dahary D., Bublik D. R., Oren M. & Pilpel Y. (2013) Bioinformatics. 29, 7, p. 894-902  Abstract
  3. Shalem O., Carey L., Zeevi D., Sharon E., Keren L., Weinberger A., Dahan O., Pilpel Y. & Segal E. (2013) PLoS Computational Biology. 9, 3,  Abstract

2012

  1. Yona A. H., Manor Y. S., Herbst R. H., Romano G. H., Mitchell A., Kupiec M., Pilpel Y. & Dahan O. (2012) Proceedings of the National Academy of Sciences of the United States of America. 109, 51, p. 21010-21015  Abstract
  2. Gingold H., Dahan O. & Pilpel Y. (2012) Nucleic Acids Research. 40, 20, p. 10053-10063  Abstract
  3. Salari R., Wojtowicz D., Zheng J., Levens D., Pilpel Y. & Przytycka T. M. (2012) PLoS Computational Biology. 8, 8,  Abstract
  4. Ben Yaakov Y. K., Dagan S. Y., Segal-Ruder Y., Shalem O., Vuppalanchi D., Willis D. E., Yudin D., Rishal I., Rother F., Bader M., Blesch A., Pilpel Y., Twiss J. L. & Fainzilber M. (2012) EMBO Journal. 31, 6, p. 1350-1363  Abstract
  5. Widespread promoter-mediated coordination of transcription and mRNA degradation
    Dori-Bachash M., Shalem O., Manor Y. S., Pilpel Y. & Tirosh I. (2012) Genome Biology. 13, 12,  Abstract

2011

  1. Shalem O., Groisman B., Choder M., Dahan O. & Pilpel Y. (2011) PLoS Genetics. 7, 9, e1002273.  Abstract
  2. Limor-Waisberg K., Carmi A., Scherz A., Pilpel Y. & Furman I. (2011) Nucleic Acids Research. 39, 14, p. 6016-6028  Abstract
  3. Dahan O., Gingold H. & Pilpel Y. (2011) Trends in Genetics. 27, 8, p. 316-322  Abstract
  4. Pilpel Y. (2011) Yeast Systems Biology. Humana Press, p. 407-425 (Methods in Molecular Biology).  Abstract
  5. Dahary D., Shalgi R. & Pilpel Y. (2011) Molecular Biology and Evolution. 28, 5, p. 1545-1551  Abstract
  6. Gingold H. & Pilpel Y. (2011) Molecular Systems Biology. 7, 481.  Abstract
  7. Mitchell A. & Pilpel Y. (2011) Proceedings of the National Academy of Sciences of the United States of America. 108, 17, p. 7271-7276  Abstract
  8. Navon S. & Pilpel Y. (2011) GENOME BIOLOGY. 12, 2, R12.  Abstract

2010

  1. Michaelevski I., Segal-Ruder Y., Rozenbaum M., Medzihradszky K. F., Shalem O., Coppola G., Horn-Saban S., Ben Yaakov Y. K., Dagan S. Y., Rishal I., Geschwind D. H., Pilpel Y., Burlingame A. L. & Fainzilber M. (2010) Science Signaling. 3, 130, ra53.  Abstract
  2. Avraham R., Sas-Chen A., Manor O., Steinfeld I., Shalgi R., Tarcic G., Bossel N., Zeisel A., Amit I., Zwang Y., Enerly E., Russnes H. G., Biagioni F., Mottolese M., Strano S., Blandino G., Borresen-Dale A., Pilpel Y. & Yakhini Z. (2010) Science Signaling. 3, 124, ra43.  Abstract
  3. Shalgi R., Pilpel Y. & Oren M. (2010) Trends in Genetics. 26, 6, p. 253-259  Abstract
  4. Tuller T., Carmi A., Vestsigian K., Navon S., Dorfan Y., Zaborske J., Pan T., Dahan O., Furman I. & Pilpel Y. (2010) Cell. 141, 2, p. 344-354  Abstract
  5. Martinez M. R., Soriano J., Tlusty T., Pilpel Y. & Furman I. (2010) Physical Review E. 81, 3,  Abstract
  6. Christoffersen N. R., Shalgi R., Frankel L. B., Leucci E., Lees M., Klausen M., Pilpel Y., Nielsen F. C., Oren M. & Lund A. H. (2010) Cell Death and Differentiation. 17, 2, p. 236-245  Abstract
  7. Shen-Orr S. S., Pilpel Y. & Hunter C. P. (2010) Genome Biology. 11, 6,  Abstract

2009

  1. Coupling transcriptional and post-transcriptional miRNA regulation in the control of cell fate
    Shalgi R., Brosh R., Oren M., Pilpel Y. & Rotter V. (2009) AGING-US. 1, 9, p. 762-770  Abstract
  2. Kam N., Pilpel Y. & Fainzilber M. (2009) PLoS Computational Biology. 5, 8,  Abstract
  3. Mitchell A., Romano G. H., Groisman B., Yona A., Dekel E., Kupiec M., Dahan O. & Pilpel Y. (2009) Nature. 460, 7252, p. 220-U80  Abstract

     

    [Highlight]

  4. Kafri R., Springer M. & Pilpel Y. (2009) Cell. 136, 3, p. 389-392  Abstract

2008

  1. Brosh R., Shalgi R., Liran A., Landan G., Korotayev K., Nguyen G. H., Enerly E., Johnsen H., Buganim Y., Solomon H., Goldstein I., Madar S., Goldfinger N., Brresen-Dale A., Ginsberg D., Harris C. C., Pilpel Y., Oren M. & Rotter V. (2008) Molecular Systems Biology. 4,  Abstract
  2. Shalem O., Dahan O., Levo M., Martinez M. R., Furman I., Segal E. & Pilpel Y. (2008) Molecular Systems Biology. 4,  Abstract
  3. Michal L., Mizrahi-Man O. & Pilpel Y. (2008) PLoS Genetics. 4, 3,  Abstract
  4. Kafri R., Dahan O., Levy J. & Pilpel Y. (2008) Proceedings of the National Academy of Sciences of the United States of America. 105, 4, p. 1243-1248  Abstract

2007

  1. Segal L., Lapidot M., Solan Z., Ruppin E., Pilpel Y. & Horn D. (2007) Bioinformatics. 23, 13, p. I440-I449  Abstract
  2. Shalgi R., Lieber D., Oren M. & Pilpel Y. (2007) PLoS Computational Biology. 3, 7, p. 1291-1304  Abstract
  3. Man O. & Pilpel Y. (2007) Nature Genetics. 39, 3, p. 415-421  Abstract
  4. Characterization of the effects of TF binding site variations on gene expression towards predicting the functional outcomes of regulatory SNPs
    Lapidot M. & Pilpel Y. (2007) Systems Biology And Regulatory Genomics. 4023, p. 51-61  Abstract
  5. Examination of the tRNA adaptation index as a predictor of protein expression levels
    Man O., Sussman J. & Pilpel Y. (2007) Systems Biology And Regulatory Genomics. 4023, p. 107-118  Abstract

2006

  1. Lapidot M. & Pilpel Y. (2006) EMBO Reports. 7, 12, p. 1216-1222  Abstract
  2. Kafri R., Levy M. & Pilpel Y. (2006) Proceedings of the National Academy of Sciences of the United States of America. 103, 31, p. 11653-11658  Abstract
  3. Bar-Even A., Paulsson J., Maheshri N., Carmi M., O'Shea E., Pilpel Y. & Barkai N. (2006) Nature Genetics. 38, 6, p. 636-643  Abstract
  4. Xi Y., Shalgi R., Fodstad O., Pilpel Y. & Ju J. (2006) Clinical Cancer Research. 12, 7, p. 2014-2024  Abstract
  5. Furman I. & Pilpel Y. (2006) Molecular Systems Biology. 2,  Abstract
  6. Rotter V., Milyavsky M., Tabach Y., Shats I., Erez N., Cohen Y., Tang X., Kalis M., Buganim Y., Goldfinger N., Ginsberg D., Domany E. & Pilpel Y. (2006) Tumor Biology. 27, suppl. 1, p. 1-1  Abstract

2005

  1. Sigal N., Vardy E., Molshanski-Mor S., Eitan A., Pilpel Y., Schuldiner S. & Bibi E. (2005) Biochemistry. 44, 45, p. 14870-14880  Abstract
  2. Kafri R., Bar-Even A. & Pilpel Y. (2005) Nature Genetics. 37, 3, p. 295-299  Abstract
  3. Tabach Y., Milyavsky M., Shats I., Brosh R., Zuk O., Yitzhaky A., Mantovani R., Domany E., Rotter V. & Pilpel Y. (2005) Molecular Systems Biology. 1,  Abstract
  4. Garten Y., Kaplan S. & Pilpel Y. (2005) Nucleic Acids Research. 33, 2, p. 605-615  Abstract
  5. Shalgi R., Lapidot M., Shamir R. & Pilpel Y. (2005) Genome Biology. 6, 10,  Abstract

2003

  1. Lapidot M. & Pilpel Y. (2003) Nucleic Acids Research. 31, 13, p. 3824-3828  Abstract

2002

  1. Sudarsanam P., Pilpel Y. & Church G. M. (2002) Genome Research. 12, 11, p. 1723-31  Abstract
  2. Cohen B. A., Pilpel Y., Mitra R. D. & Church G. M. (2002) Molecular Biology of the Cell. 13, 5, p. 1608-14  Abstract
  3. Zhu Z., Pilpel Y. & Church G. (2002) Journal of Molecular Biology. 318, 1, p. 71-81  Abstract

2001

  1. Pilpel Y., Sudarsanam P. & Church G. M. (2001) Nature Genetics. 29, 2, p. 153-9  Abstract
  2. Lapidot M., Pilpel Y., Gilad Y., Falcovitz A., Sharon D., Haaf T. & Lancet D. (2001) Genomics. 71, 3, p. 296-306  Abstract
  3. Fuchs T., Glusman G., Horn-Saban S., Lancet D. & Pilpel Y. (2001) Human Genetics. 108, 1, p. 1-13  Abstract

2000

  1. Glusman G., Bahar A., Sharon D., Pilpel Y., White J. & Lancet D. (2000) Mammalian Genome. 11, 11, p. 1016-1023  Abstract
  2. Conticello S., Pilpel Y., Glusman G. & Fainzilber M. (2000) Trends in Genetics. 16, 2, p. 57-59  Abstract

1999

  1. Pilpel Y., Ben-Tal N. & Lancet D. (1999) Journal of Molecular Biology. 294, 4, p. 921-935  Abstract
  2. Sharon D., Glusman G., Pilpel Y., Khen M., Gruetzner F., Haaf T. & Lancet D. (1999) Genomics. 61, 1, p. 24-36  Abstract
  3. The variable and conserved interfaces of modeled olfactory receptor proteins
    Pilpel Y. & Lancet D. (1999) Protein Science. 8, 5, p. 969-977  Abstract
  4. Pilpel Y. & Lancet D. (1999) Nature. 398, 6725, p. 285-+  Abstract
  5. Molecular biology of olfactory receptors
    Pilpel Y., Sosinsky A. & Lancet D. (1999) Essays In Biochemistry, Vol 33. 33, p. 93-104  Abstract
  6. Segre D., Ben-Eli D., Pilpel Y., Kedem O. & Lancet D. (1999) Instruments, Methods, And Missions For Astrobiology Ii. 3755, p. 144-162  Abstract

1998

  1. Segre D., Lancet D., Kedem O. & Pilpel Y. (1998) Origins of Life and Evolution of Biospheres. 28, 6-Apr, p. 501-514  Abstract
  2. Segre D., Pilpel Y. & Lancet D. (1998) Physica A. 249, 4-Jan, p. 558-564  Abstract
  3. Molecular biology of olfactory receptors
    Pilpel Y., Sosinsky A. & Lancet D. (1998) Essays In Biochemistry, Vol 33, 1998. 33, p. 93-104  Abstract
  4. Sharon D., Glusman G., Pilpel Y., Horn-Saban S. & Lancet D. (1998) Olfaction And Taste Xii: An International Symposium. 855, p. 182-193  Abstract

1994

  1. EMERGENCE OF ORDER IN SMALL AUTOCATALYTIC SETS MAINTAINED FAR FROM EQUILIBRIUM - APPLICATION OF A PROBABILISTIC RECEPTOR AFFINITY DISTRIBUTION (RAD) MODEL
    Lancet D., Kedem O. & Pilpel Y. (1994) Berichte Der Bunsen-Gesellschaft-Physical Chemistry Chemical Physics. 98, 9, p. 1166-1169  Abstract