Hanah Margalit - Publications

Affiliations: 
Technion - Israel Institute of Technology, Haifa, Haifa District, Israel 

82 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 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 Reports. 30: 3127-3138.e6. PMID 32130912 DOI: 10.1016/J.Celrep.2020.02.016  0.307
2018 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 Research. PMID 30113670 DOI: 10.1093/Nar/Gky684  0.324
2018 Melamed S, Faigenbaum-Romm R, Peer A, Reiss N, Shechter O, Bar A, Altuvia Y, Argaman L, Margalit H. Mapping the small RNA interactome in bacteria using RIL-seq. Nature Protocols. 13: 1-33. PMID 29215635 DOI: 10.1038/Nprot.2017.115  0.348
2017 Malka Y, Steiman-Shimony A, Rosenthal E, Argaman L, Cohen-Daniel L, Arbib E, Margalit H, Kaplan T, Berger M. Post-transcriptional 3´-UTR cleavage of mRNA transcripts generates thousands of stable uncapped autonomous RNA fragments. Nature Communications. 8: 2029. PMID 29229900 DOI: 10.1038/S41467-017-02099-7  0.346
2017 Nitzan M, Rehani R, Margalit H. Integration of Bacterial Small RNAs in Regulatory Networks. Annual Review of Biophysics. 46: 131-148. PMID 28532217 DOI: 10.1146/Annurev-Biophys-070816-034058  0.353
2016 Melamed S, Peer A, Faigenbaum-Romm R, Gatt YE, Reiss N, Bar A, Altuvia Y, Argaman L, Margalit H. Global Mapping of Small RNA-Target Interactions in Bacteria. Molecular Cell. 63: 884-97. PMID 27588604 DOI: 10.1016/J.Molcel.2016.07.026  0.365
2015 Nitzan M, Shimoni Y, Rosolio O, Margalit H, Biham O. Stochastic analysis of bistability in coherent mixed feedback loops combining transcriptional and posttranscriptional regulations. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 91: 052706. PMID 26066198 DOI: 10.1103/Physreve.91.052706  0.314
2015 Nitzan M, Fechter P, Peer A, Altuvia Y, Bronesky D, Vandenesch F, Romby P, Biham O, Margalit H. A defense-offense multi-layered regulatory switch in a pathogenic bacterium. Nucleic Acids Research. 43: 1357-69. PMID 25628364 DOI: 10.1093/Nar/Gkv001  0.312
2014 Peer A, Margalit H. Evolutionary patterns of Escherichia coli small RNAs and their regulatory interactions. Rna (New York, N.Y.). 20: 994-1003. PMID 24865611 DOI: 10.1261/Rna.043133.113  0.374
2014 Nitzan M, Steiman-Shimony A, Altuvia Y, Biham O, Margalit H. Interactions between distant ceRNAs in regulatory networks. Biophysical Journal. 106: 2254-66. PMID 24853754 DOI: 10.1016/J.Bpj.2014.03.040  0.308
2013 Lioliou E, Sharma CM, Altuvia Y, Caldelari I, Romilly C, Helfer AC, Margalit H, Romby P. In vivo mapping of RNA-RNA interactions in Staphylococcus aureus using the endoribonuclease III. Methods (San Diego, Calif.). 63: 135-43. PMID 23851283 DOI: 10.1016/J.Ymeth.2013.06.033  0.31
2012 Habib N, Wapinski I, Margalit H, Regev A, Friedman N. A functional selection model explains evolutionary robustness despite plasticity in regulatory networks. Molecular Systems Biology. 8: 619. PMID 23089682 DOI: 10.1038/Msb.2012.50  0.348
2012 Wald N, Alroy M, Botzman M, Margalit H. Codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids. Nucleic Acids Research. 40: 7074-83. PMID 22581775 DOI: 10.1093/Nar/Gks348  0.301
2012 Itzhaki Z, Margalit H. Reduced polymorphism in domains involved in protein-protein interactions. Plos One. 7: e34503. PMID 22509312 DOI: 10.1371/Journal.Pone.0034503  0.348
2012 Juranek S, Eban T, Altuvia Y, Brown M, Morozov P, Tuschl T, Margalit H. A genome-wide view of the expression and processing patterns of Thermus thermophilus HB8 CRISPR RNAs. Rna (New York, N.Y.). 18: 783-94. PMID 22355165 DOI: 10.1261/Rna.031468.111  0.344
2012 Akiva E, Friedlander G, Itzhaki Z, Margalit H. A dynamic view of domain-motif interactions. Plos Computational Biology. 8: e1002341. PMID 22253583 DOI: 10.1371/Journal.Pcbi.1002341  0.311
2011 Botzman M, Margalit H. Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles. Genome Biology. 12: R109. PMID 22032172 DOI: 10.1186/Gb-2011-12-10-R109  0.305
2011 Rhind N, Chen Z, Yassour M, Thompson DA, Haas BJ, Habib N, Wapinski I, Roy S, Lin MF, Heiman DI, Young SK, Furuya K, Guo Y, Pidoux A, Chen HM, ... ... Margalit H, et al. Comparative functional genomics of the fission yeasts. Science (New York, N.Y.). 332: 930-6. PMID 21511999 DOI: 10.1126/Science.1203357  0.315
2011 Peer A, Margalit H. Accessibility and evolutionary conservation mark bacterial small-rna target-binding regions. Journal of Bacteriology. 193: 1690-701. PMID 21278294 DOI: 10.1128/Jb.01419-10  0.327
2010 Itzhaki Z, Akiva E, Margalit H. Preferential use of protein domain pairs as interaction mediators: order and transitivity. Bioinformatics (Oxford, England). 26: 2564-70. PMID 20802208 DOI: 10.1093/Bioinformatics/Btq495  0.314
2010 Jaimovich A, Rinott R, Schuldiner M, Margalit H, Friedman N. Modularity and directionality in genetic interaction maps. Bioinformatics (Oxford, England). 26: i228-36. PMID 20529911 DOI: 10.1093/Bioinformatics/Btq197  0.307
2010 Faucher SP, Friedlander G, Livny J, Margalit H, Shuman HA. Legionella pneumophila 6S RNA optimizes intracellular multiplication Proceedings of the National Academy of Sciences of the United States of America. 107: 7533-7538. PMID 20368425 DOI: 10.1073/Pnas.0911764107  0.314
2009 Shimoni Y, Altuvia S, Margalit H, Biham O. Stochastic analysis of the SOS response in Escherichia coli. Plos One. 4: e5363. PMID 19424504 DOI: 10.1371/Journal.Pone.0005363  0.339
2008 Akiva E, Itzhaki Z, Margalit H. Built-in loops allow versatility in domain-domain interactions: lessons from self-interacting domains. Proceedings of the National Academy of Sciences of the United States of America. 105: 13292-7. PMID 18757736 DOI: 10.1073/Pnas.0801207105  0.345
2008 Habib N, Kaplan T, Margalit H, Friedman N. A novel Bayesian DNA motif comparison method for clustering and retrieval. Plos Computational Biology. 4: e1000010. PMID 18463706 DOI: 10.1371/Journal.Pcbi.1000010  0.324
2008 Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, Baruch K, Rosenshine I, Margalit H, Altuvia S. Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence. Nucleic Acids Research. 36: 1913-27. PMID 18267966 DOI: 10.1093/Nar/Gkn050  0.313
2007 Shimoni Y, Friedlander G, Hetzroni G, Niv G, Altuvia S, Biham O, Margalit H. Regulation of gene expression by small non-coding RNAs: a quantitative view. Molecular Systems Biology. 3: 138. PMID 17893699 DOI: 10.1038/Msb4100181  0.392
2007 Margalit H. Regulation Of Gene Expression By Small Non-Coding Rnas Genome Informatics. 19: 195-195. DOI: 10.11234/Gi1990.19.195  0.365
2006 Sprinzak E, Altuvia Y, Margalit H. Characterization and prediction of protein-protein interactions within and between complexes. Proceedings of the National Academy of Sciences of the United States of America. 103: 14718-23. PMID 17003128 DOI: 10.1073/Pnas.0603352103  0.359
2006 Hershberg R, Margalit H. Co-evolution of transcription factors and their targets depends on mode of regulation. Genome Biology. 7: R62. PMID 16859509 DOI: 10.1186/Gb-2006-7-7-R62  0.32
2006 Jaimovich A, Elidan G, Margalit H, Friedman N. Towards an integrated protein-protein interaction network: a relational Markov network approach. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 145-64. PMID 16597232 DOI: 10.1089/Cmb.2006.13.145  0.382
2006 Ofran Y, Margalit H. Proteins of the same fold and unrelated sequences have similar amino acid composition. Proteins. 64: 275-9. PMID 16565950 DOI: 10.1002/Prot.20964  0.33
2005 Kaplan T, Friedman N, Margalit H. Ab initio prediction of transcription factor targets using structural knowledge. Plos Computational Biology. 1: e1. PMID 16103898 DOI: 10.1371/Journal.Pcbi.0010001  0.368
2005 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 Research. 33: 4235-42. PMID 16052032 DOI: 10.1093/Nar/Gki742  0.326
2005 Hershberg R, Yeger-Lotem E, Margalit H. Chromosomal organization is shaped by the transcription regulatory network. Trends in Genetics : Tig. 21: 138-42. PMID 15734572 DOI: 10.1016/J.Tig.2005.01.003  0.666
2005 Lithwick G, Margalit H. Relative predicted protein levels of functionally associated proteins are conserved across organisms. Nucleic Acids Research. 33: 1051-7. PMID 15718304 DOI: 10.1093/Nar/Gki261  0.345
2004 Altuvia Y, Margalit H. A structure-based approach for prediction of MHC-binding peptides. Methods (San Diego, Calif.). 34: 454-9. PMID 15542371 DOI: 10.1016/J.Ymeth.2004.06.008  0.397
2004 Yeger-Lotem E, Sattath S, Kashtan N, Itzkovitz S, Milo R, Pinter RY, Alon U, Margalit H. Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proceedings of the National Academy of Sciences of the United States of America. 101: 5934-9. PMID 15079056 DOI: 10.1073/Pnas.0306752101  0.736
2004 Hermjakob H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, Vingron M, Roechert B, Roepstorff P, Valencia A, Margalit H, Armstrong J, Bairoch A, Cesareni G, Sherman D, et al. IntAct: an open source molecular interaction database. Nucleic Acids Research. 32: D452-5. PMID 14681455 DOI: 10.1093/Nar/Gkh052  0.341
2003 Margalit H, Altuvia Y. Insights from MHC-bound peptides. Novartis Foundation Symposium. 254: 77-90; discussion 91. PMID 14712933 DOI: 10.1002/0470090766.Ch6  0.391
2003 Lithwick G, Margalit H. Hierarchy of sequence-dependent features associated with prokaryotic translation. Genome Research. 13: 2665-73. PMID 14656971 DOI: 10.1101/Gr.1485203  0.358
2003 Yeger-Lotem E, Margalit H. Detection of regulatory circuits by integrating the cellular networks of protein-protein interactions and transcription regulation. Nucleic Acids Research. 31: 6053-61. PMID 14530453 DOI: 10.1093/Nar/Gkg787  0.705
2003 Zlotorynski E, Rahat A, Skaug J, Ben-Porat N, Ozeri E, Hershberg R, Levi A, Scherer SW, Margalit H, Kerem B. Molecular basis for expression of common and rare fragile sites. Molecular and Cellular Biology. 23: 7143-51. PMID 14517285 DOI: 10.1128/Mcb.23.20.7143-7151.2003  0.3
2003 Sprinzak E, Sattath S, Margalit H. How reliable are experimental protein-protein interaction data? Journal of Molecular Biology. 327: 919-23. PMID 12662919 DOI: 10.1016/S0022-2836(03)00239-0  0.372
2003 Miriami E, Margalit H, Sperling R. Conserved sequence elements associated with exon skipping. Nucleic Acids Research. 31: 1974-83. PMID 12655015 DOI: 10.1093/Nar/Gkg279  0.366
2003 Hershberg R, Altuvia S, Margalit H. A survey of small RNA-encoding genes in Escherichia coli. Nucleic Acids Research. 31: 1813-20. PMID 12654996 DOI: 10.1093/Nar/Gkg297  0.32
2002 Friedberg I, Margalit H. PeCoP: Automatic determination of persistently conserved positions in protein families Bioinformatics. 18: 1276-1277. PMID 12217925 DOI: 10.1093/Bioinformatics/18.9.1276  0.302
2002 Friedberg I, Margalit H. Persistently conserved positions in structurally similar, sequence dissimilar proteins: Roles in preserving protein fold and function Protein Science. 11: 350-360. PMID 11790845 DOI: 10.1110/Ps.18602  0.38
2002 Altuvia Y, Lithwick G, Margalit H. Harnessing the cellular immune system to the gene-prediction cart. Trends in Genetics : Tig. 17: 732-4. PMID 11718928 DOI: 10.1016/S0168-9525(01)02496-9  0.381
2001 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. 45: 47-54. PMID 11536359 DOI: 10.1002/Prot.1122  0.374
2001 Sprinzak E, Margalit H. Correlated sequence-signatures as markers of protein-protein interaction. Journal of Molecular Biology. 311: 681-92. PMID 11518523 DOI: 10.1006/Jmbi.2001.4920  0.398
2001 Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H, Altuvia S. Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Current Biology : Cb. 11: 941-50. PMID 11448770 DOI: 10.1016/S0960-9822(01)00270-6  0.315
2001 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 Research. 29: 277. PMID 11125111 DOI: 10.1093/Nar/29.1.277  0.312
2000 Friedberg I, Kaplan T, Margalit H. Evaluation of PSI-BLAST alignment accuracy in comparison to structural alignments Protein Science. 9: 2278-2284. PMID 11152139 DOI: 10.1110/Ps.9.11.2278  0.335
2000 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 Science : a Publication of the Protein Society. 9: 1838-46. PMID 11045629 DOI: 10.1110/Ps.9.9.1838  0.396
2000 Altuvia Y, Margalit H. Sequence signals for generation of antigenic peptides by the proteasome: implications for proteasomal cleavage mechanism. Journal of Molecular Biology. 295: 879-90. PMID 10656797 DOI: 10.1006/Jmbi.1999.3392  0.365
1998 Schueler-Furman O, Elber R, Margalit H. Knowledge-based structure prediction of MHC class I bound peptides: a study of 23 complexes. Folding & Design. 3: 549-64. PMID 9889166 DOI: 10.1016/S1359-0278(98)00070-4  0.376
1998 Mandel-Gutfreund Y, Margalit H. Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites. Nucleic Acids Research. 26: 2306-12. PMID 9580679 DOI: 10.1093/Nar/26.10.2306  0.348
1998 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. Human Immunology. 58: 1-11. PMID 9438204 DOI: 10.1016/S0198-8859(97)00210-3  0.374
1997 Calb R, Davidovitch A, Koby S, Giladi H, Goldenberg D, Margalit H, Holtel A, Timmis K, Sanchez-Romero JM, de Lorenzo V, Oppenheim AB. Structure and function of the Pseudomonas putida integration host factor. Journal of Bacteriology. 178: 6319-26. PMID 8892836 DOI: 10.1128/Jb.178.21.6319-6326.1996  0.322
1996 Nadir E, Margalit H, Gallily T, Ben-Sasson SA. Microsatellite spreading in the human genome: evolutionary mechanisms and structural implications. Proceedings of the National Academy of Sciences of the United States of America. 93: 6470-5. PMID 8692839 DOI: 10.1073/Pnas.93.13.6470  0.316
1996 Fraenkel YM, Mandel Y, Friedberg D, Margalit H. Identification of common motifs in unaligned DNA sequences: application to Escherichia coli Lrp regulon. Computer Applications in the Biosciences : Cabios. 11: 379-87. PMID 8521047 DOI: 10.1093/Bioinformatics/11.4.379  0.371
1995 Schueler O, Margalit H. Conservation of salt bridges in protein families. Journal of Molecular Biology. 248: 125-35. PMID 7731038 DOI: 10.1006/Jmbi.1995.0206  0.357
1995 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 Proceedings of the National Academy of Sciences of the United States of America. 92: 8368-8372. PMID 7667297 DOI: 10.1073/Pnas.92.18.8368  0.568
1995 Mandel-Gutfreund Y, Schueler O, Margalit H. Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: in search of common principles. Journal of Molecular Biology. 253: 370-82. PMID 7563096 DOI: 10.1006/Jmbi.1995.0559  0.302
1995 Altuvia Y, Schueler O, Margalit H. Ranking potential binding peptides to MHC molecules by a computational threading approach. Journal of Molecular Biology. 249: 244-50. PMID 7540211 DOI: 10.1006/Jmbi.1995.0293  0.39
1994 Altuvia Y, Berzofsky JA, Rosenfeld R, Margalit H. Sequence features that correlate with MHC restriction. Molecular Immunology. 31: 1-19. PMID 8302295 DOI: 10.1016/0161-5890(94)90133-3  0.389
1994 Rosenfeld R, Margalit H. Zinc fingers: conserved properties that can distinguish between spurious and actual DNA-binding motifs. Journal of Biomolecular Structure & Dynamics. 11: 557-70. PMID 8129873 DOI: 10.1080/07391102.1993.10508015  0.325
1994 Lisser S, Margalit H. Determination of common structural features in Escherichia coli promoters by computer analysis. European Journal of Biochemistry. 223: 823-30. PMID 8055959 DOI: 10.1111/J.1432-1033.1994.Tb19058.X  0.361
1993 Lisser S, Margalit H. Compilation of E. coli mRNA promoter sequences. Nucleic Acids Research. 21: 1507-16. PMID 8479900 DOI: 10.1093/Nar/21.7.1507  0.309
1993 Schurr T, Nadir E, Margalit H. Identification and characterization of E.coli ribosomal binding sites by free energy computation. Nucleic Acids Research. 21: 4019-23. PMID 7690472 DOI: 10.1093/Nar/21.17.4019  0.312
1990 Vajda S, Kataoka R, DeLisi C, Margalit H, Berzofsky JA, Cornette JL. Molecular structure and vaccine design Annual Review of Biophysics and Biophysical Chemistry. 19: 69-82. PMID 1694668 DOI: 10.1146/annurev.bb.19.060190.000441  0.422
1990 Kotake S, Wiggert B, Redmond TM, Borst DE, Nickerson JM, Margalit H, Berzofsky JA, Chader GJ, Gery I. Repeated determinants within the retinal interphotoreceptor retinoid-binding protein (IRBP): immunological properties of the repeats of an immunodominant determinant. Cellular Immunology. 126: 331-42. PMID 1690082 DOI: 10.1016/0008-8749(90)90325-L  0.365
1989 Hale PM, Cease KB, Houghten RA, Ouyang C, Putney S, Javaherian K, Margalit H, Cornette JL, Spouge JL, Delisi C, Berzofsky1 JA. T cell multideterminant regions in the human immunodeficiency virus envelope: Toward overcoming the problem of major histocompatibility complex restriction International Immunology. 1: 409-415. PMID 2484961 DOI: 10.1093/Intimm/1.4.409  0.691
1989 Cornette JL, Margalit H, DeLisi C, Berzofsky JA. Identification of T-cell epitopes and use in construction of synthetic vaccines Methods in Enzymology. 178: 611-634. PMID 2481216 DOI: 10.1016/0076-6879(89)78042-3  0.556
1989 Redmond TM, Sanui H, Hu LH, Wiggert B, Margalit H, Berzofsky JA, Chader GJ, Gery I. Immune responses to peptides derived from the retinal protein IRBP: immunopathogenic determinants are not necessarily immunodominant. Clinical Immunology and Immunopathology. 53: 212-24. PMID 2477180 DOI: 10.1016/0090-1229(89)90051-2  0.312
1989 Sanui H, Redmond TM, Kotake S, Wiggert B, Hu LH, Margalit H, Berzofsky JA, Chader GJ, Gery I. Identification of an immunodominant and highly immunopathogenic determinant in the retinal interphotoreceptor retinoid-binding protein (IRBP). The Journal of Experimental Medicine. 169: 1947-60. PMID 2471769 DOI: 10.1084/Jem.169.6.1947  0.345
1987 Cornette JL, Cease KB, Margalit H, Spouge JL, Berzofsky JA, DeLisi C. Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins Journal of Molecular Biology. 195: 659-685. PMID 3656427 DOI: 10.1016/0022-2836(87)90189-6  0.659
1987 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. Current Topics in Microbiology and Immunology. 130: 13-24. PMID 3536326 DOI: 10.1007/978-3-642-71440-5_2  0.575
1987 Berzofsky JA, Cease KB, Cornette JL, Spouge JL, Margalit H, Berkower IJ, Good MF, Miller LH, DeLisi C. Protein antigenic structures recognized by T cells: potential applications to vaccine design. Immunological Reviews. 98: 9-52. PMID 2443443 DOI: 10.1111/J.1600-065X.1987.Tb00518.X  0.706
1987 Cease KB, Margalit H, Cornette JL, Putney SD, Robey WG, Ouyang C, Streicher HZ, Fischinger PJ, Gallo RC, DeLisi C. 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 Proceedings of the National Academy of Sciences of the United States of America. 84: 4249-4253. PMID 2438696 DOI: 10.1073/Pnas.84.12.4249  0.575
1987 Good MF, Maloy WL, Lunde MN, Margalit H, Cornette JL, Smith GL, Moss B, Miller LH, Berzofsky JA. Construction of synthetic immunogen: use of new T-helper epitope on malaria circumsporozoite protein. Science (New York, N.Y.). 235: 1059-62. PMID 2434994 DOI: 10.1126/Science.2434994  0.367
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