Publications

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, S; Pilpel, Y
Molecular Cell.  2016
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 Genetics.  2016
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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 BIOLOGY.  2016
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Rapid evolutionary adaptation to growth on an 'unfamiliar' carbon source.
Tamari, Z; Yona, A H; Pilpel, Y; Barkai, N
BMC genomics.  2016
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Biological causal links on physiological and evolutionary time scales.
Karmon, A; Pilpel, Y
eLife.  2016
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3’UTR Shortening Potentiates MicroRNA-Based Repression of Pro-differentiation Genes in Proliferating Human Cells
Hoffman, Y; Bublik, D R; Ugalde, A P; Elkon, R; Biniashvili, T;Agami, Reuven; Oren, M; Pilpel, Y
PLOS Genetics.  2016
[PDF]
A Relay Race on the Evolutionary Adaptation Spectrum
Yona, AH; Frumkin, I; Pilpel, Y
CELL.  2015
[PDF]
The Lamarckian chicken and the Darwinian egg
Pilpel Y, Rechavi O
BIOLOGY DIRECT.  2015
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MicroRNAs silence the noisy genome
Hoffman, Y; Pilpel, Y
Science.  2015
[PDF]
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
Developmental Neurobiology.  2014
[PDF]
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; Sorensen, KD; Andersen, LD; Andersen, CL; Hulleman, E; Wurdinger, T; Ralfkiaer, E; Helin, K; Gronbaek, K; Omtoft, T; Waszak, SM; Dahan, O; Pedersen, JS; Lund, AH; Pilpel, Y
CELL.  2014
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 GENETICS.  2014
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miR-661 downregulates both Mdm2 and Mdm4 to activate p53
Hoffman, Y; Bublik, DR; Pilpel, Y; Oren, M
Cell Death And Differentiation.  2014
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microRNAs and Alu elements in the p53-Mdm2-Mdm4 regulatory network
Hoffman, Y; Pilpel, Y; Oren, M
Journal Of Molecular Cell Biology.  2014
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mRNA-programmed translation pauses in the targeting of E. coli membrane proteins.
Fluman, N; Navon, S; Bibi, E; Pilpel, Y
Elife.  2014
[PDF]
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
[PDF]
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, QH; Boeke, JD; Dahan, O; Pilpel, Y
Elife.  2013
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 Computational Biology.  2013
[PDF]
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 Computational Biology.  2012
[PDF]
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
Proceedings Of The National Academy Of Sciences Of The United States Of America.  2012
[PDF]
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 Journal.  2012
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Widespread promoter-mediated coordination of transcription and mRNA degradation
Dori-Bachash, M; Shalem, O; Manor, YS; Pilpel, Y; Tirosh, I
Genome Biology.  2012
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Dynamic changes in translational efficiency are deduced from codon usage of the transcriptome
Gingold, H; Dahan, O; Pilpel, Y
Nucleic Acids Research.  2012
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Determinants of translation efficiency and accuracy
Gingold, H; Pilpel, Y
Molecular Systems Biology.  2011
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A mathematical model for adaptive prediction of environmental changes by microorganisms
Mitchell, A; Pilpel, Y
Proceedings Of The National Academy Of Sciences Of The United States Of America.  2011
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The role of codon selection in regulation of translation efficiency deduced from synthetic libraries
Navon, S; Pilpel, Y
Genome Biology.  2011
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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 Genetics.  2011
[PDF]
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 Research.  2011
[PDF]
Noise in Biological Systems: Pros, Cons, and Mechanisms of Control
Pilpel, Y
Yeast Systems Biology: Methods And Protocols.  2011
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Regulatory mechanisms and networks couple the different phases of gene expression
Dahan, O; Gingold, H; Pilpel, Y
Trends In Genetics.  2011
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CpG Islands as a Putative Source for Animal miRNAs: Evolutionary and Functional Implications
Dahary, D; Shalgi, R; Pilpel, Y
Molecular Biology And Evolution.  2011
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Messenger RNA fluctuations and regulatory RNAs shape the dynamics of a negative feedback loop
Martinez, MR; Soriano, J; Tlusty, T; Pilpel, Y; Furman, I
Physical Review E.  2010
[PDF]
Composition and regulation of maternal and zygotic transcriptomes reflects species-specific reproductive mode
Shen-Orr, SS; Pilpel, Y; Hunter, CP
Genome Biology.  2010
[PDF]
An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation
Tuller, T; Carmi, A; Vestsigian, K; Navon, S; Dorfan, Y; Zaborske, J; Pan, T; Dahan, O; Furman, I; Pilpel, Y
Cell.  2010
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; Borresen-Dale, AL; Pilpel, Y; Yakhini, Z; Segal, E; Yarden, Y
Science Signaling.  2010
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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
Science Signaling.  2010
[PDF]
p53-independent upregulation of miR-34a during oncogene-induced senescence represses MYC
Christoffersen, NR; Shalgi, R; Frankel, LB; Leucci, E; Lees, M; Klausen, M; Pilpel, Y; Nielsen, FC; Oren, M; Lund, AH
Cell Death And Differentiation.  2010
[PDF]
Repression of transposable-elements - a microRNA anti-cancer defense mechanism?
Shalgi, R; Pilpel, Y; Oren, M
Trends In Genetics.  2010
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Can Molecular Motors Drive Distance Measurements in Injured Neurons?
Kam, N; Pilpel, Y; Fainzilber, M
Plos Computational Biology.  2009
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Genetic Redundancy: New Tricks for Old Genes
Kafri, R; Springer, M; Pilpel, Y
Cell.  2009
[PDF]
Signaling to Transcription Networks in Nerve Injury Response
Michaelevski, I; Segal-Ruder, Y; Shalem, O; Medzihradszky, KF; Rozenbaum, M; Coppola, G; Geschwind, D; Pilpel, Y; Burlingame, AL; Fainzilber, M
Molecular & Cellular Proteomics.  2009
[PDF]
Adaptive prediction of environmental changes by microorganisms
Mitchell, A; Romano, GH; Groisman, B; Yona, A; Dekel, E; Kupiec, M; Dahan, O; Pilpel, Y
Nature.  2009
Coupling transcriptional and post-transcriptional miRNA regulation in the control of cell fate
Shalgi, R; Brosh, R; Oren, M; Pilpel, Y; Rotter, V
Aging-Us.  2009
[PDF]
Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation
Shalem, O; Dahan, O; Levo, M; Martinez, MR; Furman, I; Segal, E; Pilpel, Y
Molecular Systems Biology.  2008
[PDF]
p53-repressed miRNAs are involved with E2F in a feed-forward loop promoting proliferation
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; Brresen-Dale, AL; Ginsberg, D; Harris, CC; Pilpel, Y; Oren, M; Rotter, V
Molecular Systems Biology.  2008
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Preferential protection of protein interaction network hubs in yeast: Evolved functionality of genetic redundancy
Kafri, R; Dahan, O; Levy, J; Pilpel, Y
Proceedings Of The National Academy Of Sciences Of The United States Of America.  2008
[PDF]
Functional characterization of variations on regulatory motifs
Michal, L; Mizrahi-Man, O; Pilpel, Y
Plos Genetics.  2008
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Global and local architecture of the mammalian microRNA-transcription factor regulatory network
Shalgi, R; Lieber, D; Oren, M; Pilpel, Y
Plos Computational Biology.  2007
[PDF]
Differential translation efficiency of orthologous genes is involved in phenotypic divergence of yeast species
Man, O; Pilpel, Y
Nature Genetics.  2007
Nucleotide variation of regulatory motifs may lead to distinct expression patterns
Segal, L; Lapidot, M; Solan, Z; Ruppin, E; Pilpel, Y; Horn, D
Bioinformatics.  2007
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Characterization of the effects of TF binding site variations on gene expression towards predicting the functional outcomes of regulatory SNPs
Lapidot, M; Pilpel, Y
Systems Biology And Regulatory Genomics.  2007
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Examination of the tRNA adaptation index as a predictor of protein expression levels
Man, O; Sussman, JL; Pilpel, Y
Systems Biology And Regulatory Genomics.  2007
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Amplification of p53 induced "SIGNATURE GENES" in cells transformed in vitro
Varda, R; Milyavsky, M; Tabach, Y; Shats, I; Erez, N; Cohen, Y; Tang, X; Kalis, M; Buganim, Y; Goldfinger, N; Ginsberg, D; Domany, E; Pilpel, Y
Tumor Biology.  2006
Noise in protein expression scales with natural protein abundance
Bar-Even, A; Paulsson, J; Maheshri, N; Carmi, M; O'Shea, E; Pilpel, Y; Barkai, N
Nature Genetics.  2006
The role of LPA(1) in formation of synapses among cultured hippocampal neurons
Pilpel, Y; Segal, M
Journal Of Neurochemistry.  2006
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Promoting human promoters
Furman, I; Pilpel, Y
Molecular Systems Biology.  2006
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The regulatory utilization of genetic redundancy through responsive backup circuits
Kafri, R; Levy, M; Pilpel, Y
Proceedings Of The National Academy Of Sciences Of The United States Of America.  2006
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Genome-wide natural antisense transcription: coupling its regulation to its different regulatory mechanisms
Lapidot, M; Pilpel, Y
Embo Reports.  2006
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Differentially regulated micro-RNAs and actively translated messenger RNA transcripts by tumor suppressor p53 in colon cancer
Xi, YG; Shalgi, R; Fodstad, O; Pilpel, Y; Ju, JF
Clinical Cancer Research.  2006
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Transcription control reprogramming in genetic backup circuits
Kafri, R; Bar-Even, A; Pilpel, Y
Nature Genetics.  2005
Rapid WAVE dynamics in dendritic spines of cultured hippocampal neurons is mediated by actin polymerization
Pilpel, Y; Segal, M
Journal Of Neurochemistry.  2005
[PDF]
3D model of the Escherichia coli multidrug transporter MdfA reveals an essential membrane-embedded positive charge
Sigal, N; Vardy, E; Molshanski-Mor, S; Eitan, A; Pilpel, Y; Schuldiner, S; Bibi, E
Biochemistry.  2005
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Extraction of transcription regulatory signals from genome-wide DNA - protein interaction data
Garten, Y; Kaplan, S; Pilpel, Y
Nucleic Acids Research.  2005
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A catalog of stability-associated sequence elements in 3 ' UTRs of yeast mRNAs
Shalgi, R; Lapidot, M; Shamir, R; Pilpel, Y
Genome Biology.  2005
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The promoters of human cell cycle genes integrate signals from two tumor suppressive pathways during cellular transformation
Tabach, Y; Milyavsky, M; Shats, I; Brosh, R; Zuk, O; Yitzhaky, A; Mantovani, R; Domany, E; Rotter, V; Pilpel, Y
Molecular Systems Biology.  2005
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A catalog of stability associated sequence elements in 3' UTR of yeast mRNA
Shalgi R, Lapidot M, Shamir R, Pilpel Y
Genome Biology.  2005
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Activation of PKC induces rapid morphological plasticity in dendrites of hippocampal neurons via Rac and Rho-dependent mechanisms
Pilpel, Y; Segal, M
European Journal Of Neuroscience.  2004
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Comprehensive quantitative analyses of the effects of promoter sequence elements on mRNA transcription
Lapidot, M; Pilpel, Y
Nucleic Acids Research.  2003
[PDF]
Polyproline type II conformation in the C-terminal domain of the nuclear pore complex protein gp210
Pilpel, Y; Bogin, O; Brumfeld, V; Reich, Z
Biochemistry.  2003
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Genome-wide co-occurrence of promoter elements reveals a cis-regulatory cassette of rRNA transcription motifs in Saccharomyces cerevisiae
Sudarsanam P, Pilpel Y, Church GM
Genome Research.  2002
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Computational identification of transcription factor binding sites via a transcription-factor-centric clustering (TFCC) algorithm
Zhu Z, Pilpel Y, Church GM
Journal of Molecular Biology.  2002
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Discrimination between paralogs using microarray analysis: application to the Yap1p and Yap2p transcriptional networks
Cohen BA, Pilpel Y, Mitra RD, Church GM
Mol. Biol. Cell. .  2002
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Scanning force microscopy in the applied biological sciences
Reich, Z; Kapon, R; Nevo, R; Pilpel, Y; Zmora, S; Scolnik, Y
Biotechnology Advances.  2001
Mouse-human orthology relationships in an olfactory receptor gene cluster
Lapidot, M; Pilpel, Y; Gilad, Y; Falcovitz, A; Sharon, D; Haaf, T; Lancet, D
Genomics.  2001
[PDF]
The human olfactory subgenome: from sequence to structure and evolution
Fuchs, T; Glusman, G; Horn-Saban, S; Lancet, D; Pilpel, Y
Human Genetics.  2001
[PDF]
Identifying regulatory networks by combinatorial analysis of promoter elements
Pilpel Y, Sudarsanam P, Church GM
Nature Genetics.  2001
The olfactory receptor gene superfamily: data mining, classification, and nomenclature
Glusman, G; Bahar, A; Sharon, D; Pilpel, Y; White, J; Lancet, D
Mammalian Genome.  2000
[PDF]
Position-specific codon conservation in hypervariable gene families
Conticello, SG; Pilpel, Y; Glusman, G; Fainzilber, M
Trends In Genetics.  2000
[PDF]
kPROT: A knowledge-based scale for the propensity of residue orientation in transmembrane segments. Application to membrane protein structure prediction
Pilpel, Y; Ben-Tal, N; Lancet, D
Journal Of Molecular Biology.  1999
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Olfaction - Good reception in fruitfly antennae
Pilpel, Y; Lancet, D
Nature.  1999
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The variable and conserved interfaces of modeled olfactory receptor proteins
Pilpel, Y; Lancet, D
Protein Science.  1999
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Molecular biology of olfactory receptors
Pilpel, Y; Sosinsky, A; Lancet, D
Essays In Biochemistry, Vol 33.  1999
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Primate evolution of an olfactory receptor cluster: Diversification by gene conversion and recent emergence of pseudogenes
Sharon, D; Glusman, G; Pilpel, Y; Khen, M; Gruetzner, F; Haaf, T; Lancet, D
Genomics.  1999
[PDF]
GARDobes: Primordial cell nano-precursors with organic catalysis, compositional genome and capacity to evolve
Segre, D; Ben-Eli, D; Pilpel, Y; Kedem, O; Lancet, D
Instruments, Methods, And Missions For Astrobiology Ii.  1999
[PDF]
Graded autocatalysis replication domain (GARD): Kinetic analysis of self-replication in mutually catalytic sets
Segre, D; Lancet, D; Kedem, O; Pilpel, Y
Origins Of Life And Evolution Of The Biosphere.  1998
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Mutual catalysis in sets of prebiotic organic molecules: Evolution through computer simulated chemical kinetics
Segre, D; Pilpel, Y; Lancet, D
Physica A.  1998
[PDF]
Genome dynamics, evolution, and protein modeling in the olfactory receptor gene superfamily
Sharon, D; Glusman, G; Pilpel, Y; Horn-Saban, S; Lancet, D
Olfaction And Taste Xii: An International Symposium.  1998
[PDF]
Molecular biology of olfactory receptors
Pilpel, Y; Sosinsky, A; Lancet, D
Essays In Biochemistry, Vol 33, 1998.  1998
[PDF]
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
Berichte Der Bunsen-Gesellschaft-Physical Chemistry Chemical Physics.  1994
[PDF]
tRNA genes rapidly change in evolution to meet novel translational demands
Avihu H Yona, Zohar Bloom-Ackermann, Idan Frumkin, Victor Hanson-Smith, Yoav Charpak-Amikam, Qinghua Feng, Jef D Boeke, Orna Dahan, Yitzhak Pilpel
Elife. 
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, S; Pilpel, Y
Molecular Cell.  2016
A Relay Race on the Evolutionary Adaptation Spectrum
Yona, AH; Frumkin, I; Pilpel, Y
CELL.  2015
[PDF]
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; Sorensen, KD; Andersen, LD; Andersen, CL; Hulleman, E; Wurdinger, T; Ralfkiaer, E; Helin, K; Gronbaek, K; Omtoft, T; Waszak, SM; Dahan, O; Pedersen, JS; Lund, AH; Pilpel, Y
CELL.  2014
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, QH; Boeke, JD; Dahan, O; Pilpel, Y
Elife.  2013
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
Proceedings Of The National Academy Of Sciences Of The United States Of America.  2012
[PDF]
An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation
Tuller, T; Carmi, A; Vestsigian, K; Navon, S; Dorfan, Y; Zaborske, J; Pan, T; Dahan, O; Furman, I; Pilpel, Y
Cell.  2010
Adaptive prediction of environmental changes by microorganisms
Mitchell, A; Romano, GH; Groisman, B; Yona, A; Dekel, E; Kupiec, M; Dahan, O; Pilpel, Y
Nature.  2009
Differential translation efficiency of orthologous genes is involved in phenotypic divergence of yeast species
Man, O; Pilpel, Y
Nature Genetics.  2007
Noise in protein expression scales with natural protein abundance
Bar-Even, A; Paulsson, J; Maheshri, N; Carmi, M; O'Shea, E; Pilpel, Y; Barkai, N
Nature Genetics.  2006
Transcription control reprogramming in genetic backup circuits
Kafri, R; Bar-Even, A; Pilpel, Y
Nature Genetics.  2005
Identifying regulatory networks by combinatorial analysis of promoter elements
Pilpel Y, Sudarsanam P, Church GM
Nature Genetics.  2001