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The Faculty of Medicine - Microbiology and Molecular Genetics: Margalit Hanah

Researchers

 Last updated June 2021 - School of Pharmacy

List of Publications

(1) Gatt YE, Margalit H. Common Adaptive Strategies Underlie Within-Host Evolution of Bacterial Pathogens. Mol Biol Evol 2021;38(3):1101-1121.

(2) Faigenbaum-Romm R, Reich A, Gatt YE, Barsheshet M, Argaman L, Margalit H. Hierarchy in Hfq Chaperon Occupancy of Small RNA Targets Plays a Major Role in Their Regulation. Cell Rep 2020;30(9):3127-3138.e6.

(3) Bhattacharya S, Baidya AK, Pal RR, Mamou G, Gatt YE, Margalit H, et al. A Ubiquitous Platform for Bacterial Nanotube Biogenesis. Cell Rep 2019;27(2):334-342.e10.

(4) Altuvia Y, Bar A, Reiss N, Karavani E, Argaman L, Margalit H. Corrigendum: In vivo cleavage rules and target repertoire of RNase III in Escherichia coli (Nucleic Acids Research (gky684) DOI: 10.1093/nar/gky684). Nucleic Acids Res 2018;46(19):10530-10531.

(5) Steiman-Shimony A, Shtrikman O, Margalit H. Assessing the functional association of intronic miRNAs with their host genes. RNA 2018;24(8):991-1004.

(6) Altuvia Y, Bar A, Reiss N, Karavani E, Argaman L, Margalit H. In vivo cleavage rules and target repertoire of RNase III in Escherichia coli. Nucleic Acids Res 2018;46(19):10380-10394.

(7) Melamed S, Faigenbaum-Romm R, Peer A, Reiss N, Shechter O, Bar A, et al. Mapping the small RNA interactome in bacteria using RIL-seq. Nat Protoc 2018;13(1):1-33.

(8) Malka Y, Steiman-Shimony A, Rosenthal E, Argaman L, Cohen-Daniel L, Arbib E, et al. Post-transcriptional 3´-UTR cleavage of mRNA transcripts generates thousands of stable uncapped autonomous RNA fragments. Nat Commun 2017;8(1).

(9) Nitzan M, Rehani R, Margalit H. Integration of Bacterial Small RNAs in Regulatory Networks. Annu Rev Biophys 2017;46:131-148.

(10) Melamed S, Peer A, Faigenbaum-Romm R, Gatt YE, Reiss N, Bar A, et al. Global Mapping of Small RNA-Target Interactions in Bacteria. Mol Cell 2016;63(5):884-897.

(11) Nitzan M, Shimoni Y, Rosolio O, Margalit H, Biham O. Stochastic analysis of bistability in coherent mixed feedback loops combining transcriptional and posttranscriptional regulations. Phys Rev E Stat Nonlinear Soft Matter Phys 2015;91(5).

(12) Sajman J, Zenvirth D, Nitzan M, Margalit H, Simpson-Lavy KJ, Reiss Y, et al. Degradation of Ndd1 by APC/CCdh1 generates a feed forward loop that times mitotic protein accumulation. Nat Commun 2015;6.

(13) Nitzan M, Mintzer S, Margalit H. Approaches and developments in studying the human microbiome network. Isr J Ecol Evolution 2015;61(2):90-94.

(14) Nitzan M, Fechter P, Peer A, Altuvia Y, Bronesky D, Vandenesch F, et al. A defense-offense multi-layered regulatory switch in a pathogenic bacterium. Nucleic Acids Res 2015;43(3):1357-1369.

(15) Wald N, Margalit H. Auxiliary tRNAs: Large-scale analysis of tRNA genes reveals patterns of tRNA repertoire dynamics. Nucleic Acids Res 2014;42(10):6552-6566.

(16) Nitzan M, Steiman-Shimony A, Altuvia Y, Biham O, Margalit H. Interactions between distant ceRNAs in regulatory networks. Biophys J 2014;106(10):2254-2266.

(17) Nitzan M, Wassarman KM, Biham O, Margalit H. Global regulation of transcription by a small RNA: A quantitative view. Biophys J 2014;106(5):1205-1214.

(18) Peer A, Margalit H. Evolutionary patterns of Escherichia coli small RNAs and their regulatory interactions. RNA 2014;20(7):994-1003.

(19) Lioliou E, Sharma CM, Altuvia Y, Caldelari I, Romilly C, Helfer A-, et al. In vivo mapping of RNA-RNA interactions in Staphylococcus aureus using the endoribonuclease III. Methods 2013;63(2):135-143.

(20) Habib N, Wapinski I, Margalit H, Regev A, Friedman N. A functional selection model explains evolutionary robustness despite plasticity in regulatory networks. Mol Syst Biol 2012;8.

(21) Loinger A, Shemla Y, Simon I, Margalit H, Biham O. Competition between small RNAs: A quantitative view. Biophys J 2012;102(8):1712-1721.

(22) Itzhaki Z, Margalit H. Reduced polymorphism in domains involved in protein-protein interactions. PLoS ONE 2012;7(4).

(23) Juranek S, Eban T, Altuvia Y, Brown M, Morozov P, Tuschl T, et al. A genome-wide view of the expression and processing patterns of Thermus thermophilus HB8 CRISPR RNAs. RNA 2012;18(4):783-794.

(24) Akiva E, Friedlander G, Itzhaki Z, Margalit H. A dynamic view of domain-motif interactions. PLoS Comput Biol 2012;8(1).

(25) Elefant N, Altuvia Y, Margalit H. A wide repertoire of miRNA binding sites: Prediction and functional implications. Bioinformatics 2011;27(22):3093-3101.

(26) Botzman M, Margalit H. Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles. Genome Biol 2011;12(10).

(27) Rhind N, Chen Z, Yassour M, Thompson DA, Haas BJ, Habib N, et al. Comparative functional genomics of the fission yeasts. Science 2011;332(6032):930-936.

(28) Peer A, Margalit H. Accessibility and evolutionary conservation mark bacterial small-RNA target-binding regions. J Bacteriol 2011;193(7):1690-1701.

(29) Elefant N, Berger A, Shein H, Hofree M, Margalit H, Altuvia Y. RepTar: A database of predicted cellular targets of host and viral miRNAs. Nucleic Acids Res 2011;39(SUPPL. 1):D188-D194.

(30) Dölken L, Krmpotic A, Kothe S, Tuddenham L, Tanguy M, Marcinowski L, et al. Cytomegalovirus microRNAs facilitate persistent virus infection in salivary glands. PLoS Pathog 2010;6(10).

(31) Itzhaki Z, Akiva E, Margalit H. Preferential use of protein domain pairs as interaction mediators: Order and transitivity. Bioinformatics 2010;26(20):2564-2570.

(32) Jaimovich A, Rinott R, Schuldiner M, Margalit H, Friedman N. Modularity and directionality in genetic interaction maps. Bioinformatics 2010;26(12):i228-i236.

(33) Faucher SP, Friedlander G, Livny J, Margalit H, Shuman HA. Legionella pneumophila 6S RNA optimizes intracellular multiplication. Proc Natl Acad Sci U S A 2010;107(16):7533-7538.

(34) Shimoni Y, Altuvia S, Margalit H, Biham O. Stochastic analysis of the SOS response in Escherichia coli. PLoS ONE 2009;4(5).

(35) Akiva E, Itzhaki Z, Margalit H. Built-in loops allow versatility in domain-domain interactions: Lessons from self-interacting domains. Proc Natl Acad Sci U S A 2008;105(36):13292-13297.

(36) Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, Baruch K, Rosenshine I, Margalit H, et al. Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence. Nucleic Acids Res 2008;36(6):1913-1927.

(37) Habib N, Kaplan T, Margalit H, Friedman N. A novel Bayesian DNA motif comparison method for clustering and retrieval. PLoS Comput Biol 2008;4(2).

(38) Levy A, Pitcovski J, Frankenburg S, Elias O, Altuvia Y, Margalit H, et al. A melanoma multiepitope polypeptide induces specific CD8+ T-cell response. Cell Immunol 2007;250(1-2):24-30.

(39) Shimoni Y, Friedlander G, Hetzroni G, Niv G, Altuvia S, Biham O, et al. Regulation of gene expression by small non-coding RNAs: A quantitative view. Mol Syst Biol 2007;3.

(40) Stern-Ginossar N, Elefant N, Zimmermann A, Wolf DG, Saleh N, Biton M, et al. Host immune system gene targeting by a viral miRNA. Science 2007;317(5836):376-381.

(41) Itzhaki Z, Akiva E, Altuvia Y, Margalit H. Evolutionary conservation of domain-domain interactions. Genome Biol 2006;7(12).

(42) Sprinzak E, Altuvia Y, Margalit H. Characterization and prediction of protein-protein interactions within and between complexes. Proc Natl Acad Sci U S A 2006;103(40):14718-14723.

(43) Hershberg R, Margalit H. Co-evolution of transcription factors and their targets depends on mode of regulation. Genome Biol 2006;7(7).

(44) Ofran Y, Margalit H. Proteins of the same fold and unrelated sequences have similar amino acid composition. Proteins Struct Funct Genet 2006;64(1):275-279.

(45) Jaimovich A, Elidan G, Margalit H, Friedman N. Towards an integrated protein-protein interaction network: A relational Markov network approach. J Comput Biol 2006;13(2):145-164.

(46) Altuvia Y, Landgraf P, Lithwick G, Elefant N, Pfeffer S, Aravin A, et al. Clustering and conservation patterns of human microRNAs. Nucleic Acids Res 2005;33(8):2697-2706.

(47) Zick A, Onn I, Bezalel R, Margalit H, Shlomai J. Assigning functions to genes: Identification of S-phase expressed genes in Leishmania major based on post-transcriptional control elements. Nucleic Acids Res 2005;33(13):4235-4242.

(48) Lithwick G, Margalit H. Relative predicted protein levels of functionally associated proteins are conserved across organisms. Nucleic Acids Res 2005;33(3):1051-1057.

(49) Kaplan T, Friedman N, Margalit H. Ab initio prediction of transcription factor targets using structural knowledge. PLoS Comput Biol 2005;1(1):0005-0013.

(50) Predicting transcription factor binding sites using structural knowledge. Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science); 2005.

(51) Hershberg R, Yeger-Lotem E, Margalit H. Chromosomal organization is shaped by the transcription regulatory network. Trends Genet 2005;21(3):138-142.

(52) Towards an integrated protein-protein interaction network. Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science); 2005.

(53) Yeger-Lotem E, Sattath S, Kashtan N, Itzkovitz S, Milo R, Pinter RY, et al. Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proc Natl Acad Sci U S A 2004;101(16):5934-5939.

(54) Altuvia Y, Margalit H. A structure-based approach for prediction of MHC-binding peptides. Methods 2004;34(4):454-459.

(55) Hermjakob H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, et al. IntAct: An open source molecular interaction database. Nucleic Acids Res 2004;32(DATABASE ISS.):D452-D455.

(56) Margalit H, Altuvia Y. Insights from MHC-bound peptides. Novartia Found Symp 2003;254:77-97.

(57) Lithwick G, Margalit H. Hierarchy of sequence-dependent features associated with prokaryotic translation. Genome Res 2003;13(12):2665-2673.

(58) Yeger-Lotem E, Margalit H. Detection of regulatory circuits by integrating the cellular networks of protein-protein interactions and transcription regulation. Nucleic Acids Res 2003;31(20):6053-6061.

(59) Zlotorynski E, Rahat A, Skaug J, Ben-Porat N, Ozeri E, Hershberg R, et al. Molecular basis for expression of common and rare fragile sites. Mol Cell Biol 2003;23(20):7143-7151.

(60) Sprinzak E, Sattath S, Margalit H. How reliable are experimental protein-protein interaction data? J Mol Biol 2003;327(5):919-923.

(61) Miriami E, Margalit H, Sperling R. Conserved sequene elements associated with exon skipping. Nucleic Acids Res 2003;31(7):1974-1983.

(62) Hershberg R, Altuvia S, Margalit H. A survey of small RNA-encoding genes in Escherichia coli. Nucleic Acids Res 2003;31(7):1813-1820.

(63) Friedberg I, Margalit H. Persistently conserved positions in structurally similar, sequence dissimilar proteins: Roles in preserving protein fold and function. Protein Sci 2002;11(2):350-360.

(64) Friedberg I, Margalit H. PeCoP: Automatic determination of persistently conserved positions in protein families. Bioinformatics 2002;18(9):1276-1277.

(65) Altuvia Y, Lithwick G, Margalit H. Harnessing the cellular immune system to the gene-prediction cart. Trends Genet 2001;17(12):732-734.

(66) Schueler-Furman O, Altuvia Y, Margalit H. Differential effects of isomeric incorporation of fluorophenylalanines into PvuII endonuclease. Proteins Struct Funct Genet 2001;45(1):55-61.

(67) Schueler-Furman O, Altuvia Y, Margalit H. Examination of possible structural constraints of MHC-binding peptides by assessment of their native structure within their source proteins. Proteins Struct Funct Genet 2001;45(1):47-54.

(68) Sprinzak E, Margalit H. Correlated sequence-signatures as markers of protein-protein interaction. J Mol Biol 2001;311(4):681-692.

(69) Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EGH, Margalit H, et al. Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr Biol 2001;11(12):941-950.

(70) Schueler-Furman O, Altuvia Y, Margalit H. Comparative modeling of CASP4 target proteins: Combining results of sequence search with three-dimensional structure assessment. Proteins Struct Funct Genet 2001;45:47-54.

(71) Mandel-Gutfreund Y, Baron A, Margalit H. A structure-based approach for prediction of protein binding sites in gene upstream regions. Pac Symp Biocomput 2001:139-150.

(72) Hershberg R, Bejerano G, Santos-Zavaleta A, Margalit H. PromEC: An updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites. Nucleic Acids Res 2001;29(1):277.

(73) Bejerano G, Seldin Y, Margalit H, Tishby N. Markovian domain fingerprinting: Statistical segmentation of protein sequences. Bioinformatics 2001;17(10):927-934.

(74) Altuvia Y, Margalit H. Sequence signals for generation of antigenic peptides by the proteasome: Implications for proteasomal cleavage mechanism. J Mol Biol 2000;295(4):879-890.

(75) Friedberg I, Kaplan T, Margalit H. Glimmers in the midnight zone: characterization of aligned identical residues in sequence-dissimilar proteins sharing a common fold. Proc Int Conf Intell Syst Mol Biol 2000;8:162-170.

(76) Friedberg I, Kaplan T, Margalit H. Evaluation of PSI-BLAST alignment accuracy in comparison to structural alignments. Protein Sci 2000;9(11):2278-2284.

(77) Schueler-Furman O, Altuvia Y, Sette A, Margalit H. Structure-based prediction of binding peptides to MHC class I molecules: Application to a broad range of MHC alleles. Protein Sci 2000;9(9):1838-1846.

(78) Mishmar D, Rahat A, Scherer SW, Nyakatura G, Hinzmann B, Kohwi Y, et al. Molecular characterization of a common fragile site (FRA7H) on human chromosome 7 by the cloning of a simian virus 40 integration site. Proc Natl Acad Sci U S A 1998;95(14):8141-8146.

(79) Mandel-Gutfreund Y, Margalit H. Quantitative parameters for amino acid-base interaction: Implications for prediction of protein-DNA binding sites. Nucleic Acids Res 1998;26(10):2306-2312.

(80) Mandel-Gutfreund Y, Margalit H, Jernigan RL, Zhurkin VB. A role for CH···O interactions in Protein-DNA recognition. J Mol Biol 1998;277(5):1129-1140.

(81) Schueler-Furman O, Elber R, Margalit H. Knowledge-based structure prediction of MHC class I bound peptides: A study of 23 complexes. Fold Design 1998;3(6):549-564.

(82) Altuvia Y, Sette A, Sidney J, Southwood S, Margalit H. A structure-based algorithm to predict potential binding peptides to MHC molecules with hydrophobic binding pockets. Hum Immunol 1997;58(1):1-11.

(83) Nadir E, Margalit H, Gallily T, Ben-Sasson SA. Microsatellite spreading in the human genome: Evolutionary mechanisms and structural implications. Proc Natl Acad Sci U S A 1996;93(13):6470-6475.

(84) Calb R, Davidovitch A, Koby S, Giladi H, Goldenberg D, Margalit H, et al. Structure and function of the Pseudomonas putida integration host factor. J Bacteriol 1996;178(21):6319-6326.

(85) Mandel-Gutfreund Y, Schueler O, Margalit H. Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: In search of common principles. J Mol Biol 1995;253(2):370-382.

(86) Cornette JL, Margalit H, Berzofsky JA, Delisi C. Periodic variation in side-chain polarities of T-cell antigenic peptides correlates with their structure and activity. Proc Natl Acad Sci U S A 1995;92(18):8368-8372.

(87) Fraenkel YM, Mandel Y, Friedberg D, Margalit H. Identification of common motifs in unaligned DNA sequences: Application to Escherichia coli Lrp regulon. Bioinformatics 1995;11(4):379-387.

(88) Schueler O, Margalit H. Conservation of salt bridges in protein families. J Mol Biol 1995;248(1):125-135.

(89) Altuvia Y, Schueler O, Margalit H. Ranking potential binding peptides to MHC molecules by a computational threading approach. J Mol Biol 1995;249(2):244-250.

(90) Margalit H, Nadir E, Ben-Sasson SA. A complete Alu element within the coding sequence of a central gene. Cell 1994;78(2):173-174.

(91) LISSER S, MARGALIT H. Determination of common structural features in Escherichia coli promoters by computer analysis. Eur J Biochem 1994;223(3):823-830.

(92) Altuvia Y, Berzofsky JA, Rosenfeld R, Margalit H. Sequence features that correlate with MHC restriction. Mol Immunol 1994;31(1):1-19.

(93) Schurr T, Nadir E, Margalit H. Identification and characterization of E.coli ribosomal binding sites by free energy computation. Nucleic Acids Res 1993;21(17):4019-4023.

(94) Lisser S, Margalit H. Compilation of E.coli mRNA promoter sequences. Nucleic Acids Res 1993;21(7):1507-1516.

(95) Rosenfeld R, Margalit H. Zinc fingers: Conserved properties that can distinguish between spurious and actual dna-binding motifs. J Biomol Struct Dyn 1993;11(3):557-570.

(96) Margalit H, Fischer N, Ben-Sasson SA. Comparative analysis of structurally defined heparin binding sequences reveals a distinct spatial distribution of basic residues. J Biol Chem 1993;268(26):19228-19231.

(97) Roitberg-Tambur A, Friedmann A, Safirman C, Markitziu A, Ben-Chetrit E, Rubinow A, et al. Molecular analysis of HLA class II genes in primary sjögren's syndrome. A study of Israeli Jewish and Greek Non-Jewish patients. Hum Immunol 1993;36(4):235-242.

(98) Rasmussen OF, Shirvan MH, Margalit H, Christiansen C, Rottem S. Nucleotide sequence, organization and characterization of the atp genes and the encoded subunits of Mycoplasma gallisepticum ATPase. Biochem J 1992;285(3):881-888.

(99) Kotake S, Wiggert B, Redmond TM, Borst DE, Nickerson JM, Margalit H, et al. Repeated determinants within the retinal interphotoreceptor retinoid-binding protein (IRBP): Immunological properties of the repeats of an immunodominant determinant. Cell Immunol 1990;126(2):331-342.

(100) Vajda S, Kataoka R, DeLisi C, Margalit H, Berzofsky JA, Cornette JL. Molecular structure and vaccine design. Annu Rev Biophys Biophys Chem 1990;19:69-82.

(101) Margalit H, Shapiro BA, Oppenheim AB, Maizel JV. Detection of common motifs in RNA secondary structures. Nucleic Acids Res 1989;17(12):4829-4845.

(102) Cornette JL, Margalit H, Delisi C, Berzofsky JA. Identification of T-cell epitopes and use in construction of synthetic vaccines. Methods Enzymol 1989;178(C):611-634.

(103) Redmond TM, Sanui H, Hu L-, Wiggeri B, Margalit H, Berzofsky JA, et al. Immune responses to peptides derived from the retinal protein IRBP: Immunopathogenic determinants are not necessarily immunodominant. Clin Immunol Immunopathol 1989;53(2):212-224.

(104) Sanui H, Redmond TM, Kotake S, Wiggert B, Hu L-, Margalit H, et al. Identification of an immunodominant and highly immunopathogenic determinant in the retinal interphotoreceptor retinoid-binding protein (IRBP). J Exp Med 1989;169(6):1947-1960.

(105) Hale PM, Cease KB, Houghten RA, Ouyang C, Putney S, Javaherian K, et al. T cell multideterminant regions in the human immunodeficiency virus envelope: Toward overcoming the problem of major histocompatibility complex restriction. Int Immunol 1989;1(4):409-415.

(106) Margalit H, Shapiro BA, Nussinov R, Owens J, Jernigan RL. Helix Stability in Prokaryotic Promoter Regions. Biochemistry 1988;27(14):5179-5188.

(107) Sanui H, Redmond TM, Hu L-, Kuwabara T, Margalit H, Cornette JL, et al. Synthetic peptides derived from IRBP induce EAU and EAP in lewis rats. Curr Eye Res 1988;7(7):727-735.

(108) Cease KB, Margalit H, Cornette JL, Putney SD, Robey WG, Ouyang C, et al. Helper T-cell antigenic site identification in the acquired immunodeficiency syndrome virus gp120 envelope protein and induction of immunity in mice to the native protein using a 16-residue synthetic peptide. Proc Natl Acad Sci U S A 1987;84(12):4249-4253.

(109) Cornette JL, Cease KB, Margalit H, Spouge JL, Berzofsky JA, DeLisi C. Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins. J Mol Biol 1987;195(3):659-685.

(110) Margalit H, Spouge JL, Cornette JL, Cease KB, Delisi C, Berzofsky JA. Prediction of immunodominant helper T cell antigenic sites from the primary sequence. J Immunol 1987;138(7):2213-2229.

(111) Spouge JL, Guy HR, Cornette JL, Margalit H, Cease K, Berzofsky JA, et al. Strong conformational propensities enhance T cell antigenicity. J Immunol 1987;138(1):204-212.

(112) Margalit H, Grover NB. Initiation of chromosome replication in bacteria: analysis of an inhibitor control model. J Bacteriol 1987;169(11):5231-5240.

(113) Berzofsky JA, Cease KB, Cornette JL, Spouge JL, Margalit H, Berkower IJ, et al. Protein Antigenic Structures Recognized by T Cells; Potential Applications to Vaccine Design. Immunol Rev 1987;98(1):9-52.

(114) Good MF, Maloy WL, Lunde MN, Margalit H, Cornetre JL, Smith GL, et al. Construction of synthetic immunogen: Use of new T-helper epitope on malaria circumsporozoite protein. Science 1987;235(4792):1059-1062.

(115) Berzofsky JA, Cornette J, Margalit H, Berkower I, Cease K, DeLisi C. Molecular features of class II MHC-restricted T-cell recognition of protein and peptide antigens: the importance of amphipathic structures. Curr Top Microbiol Immunol 1986;130:13-24.

(116) Margalit H, Rosenberger RF, Grover NB. Initiation of DNA replication in bacteria: Analysis of an autorepressor control model. J Theor Biol 1984;111(1):183-199.