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Items: 1 to 50 of 111

1.

A Ubiquitous Platform for Bacterial Nanotube Biogenesis.

Bhattacharya S, Baidya AK, Pal RR, Mamou G, Gatt YE, Margalit H, Rosenshine I, Ben-Yehuda S.

Cell Rep. 2019 Apr 9;27(2):334-342.e10. doi: 10.1016/j.celrep.2019.02.055. Epub 2019 Mar 28.

2.

In vivo cleavage rules and target repertoire of RNase III in Escherichia coli.

Altuvia Y, Bar A, Reiss N, Karavani E, Argaman L, Margalit H.

Nucleic Acids Res. 2018 Nov 2;46(19):10530-10531. doi: 10.1093/nar/gky816. No abstract available.

3.

In vivo cleavage rules and target repertoire of RNase III in Escherichia coli.

Altuvia Y, Bar A, Reiss N, Karavani E, Argaman L, Margalit H.

Nucleic Acids Res. 2018 Nov 2;46(19):10380-10394. doi: 10.1093/nar/gky684. Erratum in: Nucleic Acids Res. 2018 Nov 2;46(19):10530-10531.

4.

Assessing the functional association of intronic miRNAs with their host genes.

Steiman-Shimony A, Shtrikman O, Margalit H.

RNA. 2018 Aug;24(8):991-1004. doi: 10.1261/rna.064386.117. Epub 2018 May 11.

5.

Post-transcriptional 3´-UTR cleavage of mRNA transcripts generates thousands of stable uncapped autonomous RNA fragments.

Malka Y, Steiman-Shimony A, Rosenthal E, Argaman L, Cohen-Daniel L, Arbib E, Margalit H, Kaplan T, Berger M.

Nat Commun. 2017 Dec 11;8(1):2029. doi: 10.1038/s41467-017-02099-7.

6.

Mapping the small RNA interactome in bacteria using RIL-seq.

Melamed S, Faigenbaum-Romm R, Peer A, Reiss N, Shechter O, Bar A, Altuvia Y, Argaman L, Margalit H.

Nat Protoc. 2018 Jan;13(1):1-33. doi: 10.1038/nprot.2017.115. Epub 2017 Dec 7.

PMID:
29215635
7.

Integration of Bacterial Small RNAs in Regulatory Networks.

Nitzan M, Rehani R, Margalit H.

Annu Rev Biophys. 2017 May 22;46:131-148. doi: 10.1146/annurev-biophys-070816-034058. Review.

PMID:
28532217
8.

Global Mapping of Small RNA-Target Interactions in Bacteria.

Melamed S, Peer A, Faigenbaum-Romm R, Gatt YE, Reiss N, Bar A, Altuvia Y, Argaman L, Margalit H.

Mol Cell. 2016 Sep 1;63(5):884-97. doi: 10.1016/j.molcel.2016.07.026.

9.

Stochastic analysis of bistability in coherent mixed feedback loops combining transcriptional and posttranscriptional regulations.

Nitzan M, Shimoni Y, Rosolio O, Margalit H, Biham O.

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 May;91(5):052706. Epub 2015 May 15.

PMID:
26066198
10.

Degradation of Ndd1 by APC/C(Cdh1) generates a feed forward loop that times mitotic protein accumulation.

Sajman J, Zenvirth D, Nitzan M, Margalit H, Simpson-Lavy KJ, Reiss Y, Cohen I, Ravid T, Brandeis M.

Nat Commun. 2015 May 11;6:7075. doi: 10.1038/ncomms8075.

PMID:
25959309
11.

A defense-offense multi-layered regulatory switch in a pathogenic bacterium.

Nitzan M, Fechter P, Peer A, Altuvia Y, Bronesky D, Vandenesch F, Romby P, Biham O, Margalit H.

Nucleic Acids Res. 2015 Feb 18;43(3):1357-69. doi: 10.1093/nar/gkv001. Epub 2015 Jan 27.

12.

Evolutionary patterns of Escherichia coli small RNAs and their regulatory interactions.

Peer A, Margalit H.

RNA. 2014 Jul;20(7):994-1003. doi: 10.1261/rna.043133.113. Epub 2014 May 27.

13.

Interactions between distant ceRNAs in regulatory networks.

Nitzan M, Steiman-Shimony A, Altuvia Y, Biham O, Margalit H.

Biophys J. 2014 May 20;106(10):2254-66. doi: 10.1016/j.bpj.2014.03.040.

14.

Auxiliary tRNAs: large-scale analysis of tRNA genes reveals patterns of tRNA repertoire dynamics.

Wald N, Margalit H.

Nucleic Acids Res. 2014 Jun;42(10):6552-66. doi: 10.1093/nar/gku245. Epub 2014 Apr 29.

15.

Global regulation of transcription by a small RNA: a quantitative view.

Nitzan M, Wassarman KM, Biham O, Margalit H.

Biophys J. 2014 Mar 4;106(5):1205-14. doi: 10.1016/j.bpj.2014.01.025.

16.

In vivo mapping of RNA-RNA interactions in Staphylococcus aureus using the endoribonuclease III.

Lioliou E, Sharma CM, Altuvia Y, Caldelari I, Romilly C, Helfer AC, Margalit H, Romby P.

Methods. 2013 Sep 15;63(2):135-43. doi: 10.1016/j.ymeth.2013.06.033. Epub 2013 Jul 9.

PMID:
23851283
17.

A functional selection model explains evolutionary robustness despite plasticity in regulatory networks.

Habib N, Wapinski I, Margalit H, Regev A, Friedman N.

Mol Syst Biol. 2012;8:619. doi: 10.1038/msb.2012.50.

18.

Competition between small RNAs: a quantitative view.

Loinger A, Shemla Y, Simon I, Margalit H, Biham O.

Biophys J. 2012 Apr 18;102(8):1712-21. doi: 10.1016/j.bpj.2012.01.058.

19.

Codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids.

Wald N, Alroy M, Botzman M, Margalit H.

Nucleic Acids Res. 2012 Aug;40(15):7074-83. doi: 10.1093/nar/gks348. Epub 2012 May 11.

20.

Reduced polymorphism in domains involved in protein-protein interactions.

Itzhaki Z, Margalit H.

PLoS One. 2012;7(4):e34503. doi: 10.1371/journal.pone.0034503. Epub 2012 Apr 3.

21.

A genome-wide view of the expression and processing patterns of Thermus thermophilus HB8 CRISPR RNAs.

Juranek S, Eban T, Altuvia Y, Brown M, Morozov P, Tuschl T, Margalit H.

RNA. 2012 Apr;18(4):783-94. doi: 10.1261/rna.031468.111. Epub 2012 Feb 21.

22.

A dynamic view of domain-motif interactions.

Akiva E, Friedlander G, Itzhaki Z, Margalit H.

PLoS Comput Biol. 2012 Jan;8(1):e1002341. doi: 10.1371/journal.pcbi.1002341. Epub 2012 Jan 12. Erratum in: PLoS Comput Biol. 2012 Jan;8(1). doi:10.1371/annotation/2e21b1b9-46de-4cbe-a2a4-b4598d90d492.

23.

Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles.

Botzman M, Margalit H.

Genome Biol. 2011 Oct 27;12(10):R109. doi: 10.1186/gb-2011-12-10-r109.

24.

A wide repertoire of miRNA binding sites: prediction and functional implications.

Elefant N, Altuvia Y, Margalit H.

Bioinformatics. 2011 Nov 15;27(22):3093-101. doi: 10.1093/bioinformatics/btr534. Epub 2011 Sep 27.

PMID:
21953484
25.

Comparative functional genomics of the fission yeasts.

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, Robbertse B, Goldberg JM, Aoki K, Bayne EH, Berlin AM, Desjardins CA, Dobbs E, Dukaj L, Fan L, FitzGerald MG, French C, Gujja S, Hansen K, Keifenheim D, Levin JZ, Mosher RA, Müller CA, Pfiffner J, Priest M, Russ C, Smialowska A, Swoboda P, Sykes SM, Vaughn M, Vengrova S, Yoder R, Zeng Q, Allshire R, Baulcombe D, Birren BW, Brown W, Ekwall K, Kellis M, Leatherwood J, Levin H, Margalit H, Martienssen R, Nieduszynski CA, Spatafora JW, Friedman N, Dalgaard JZ, Baumann P, Niki H, Regev A, Nusbaum C.

Science. 2011 May 20;332(6032):930-6. doi: 10.1126/science.1203357. Epub 2011 Apr 21.

26.

Accessibility and evolutionary conservation mark bacterial small-rna target-binding regions.

Peer A, Margalit H.

J Bacteriol. 2011 Apr;193(7):1690-701. doi: 10.1128/JB.01419-10. Epub 2011 Jan 28.

27.

RepTar: a database of predicted cellular targets of host and viral miRNAs.

Elefant N, Berger A, Shein H, Hofree M, Margalit H, Altuvia Y.

Nucleic Acids Res. 2011 Jan;39(Database issue):D188-94. doi: 10.1093/nar/gkq1233. Epub 2010 Dec 10.

28.

Cytomegalovirus microRNAs facilitate persistent virus infection in salivary glands.

Dölken L, Krmpotic A, Kothe S, Tuddenham L, Tanguy M, Marcinowski L, Ruzsics Z, Elefant N, Altuvia Y, Margalit H, Koszinowski UH, Jonjic S, Pfeffer S.

PLoS Pathog. 2010 Oct 14;6(10):e1001150. doi: 10.1371/journal.ppat.1001150.

29.

Preferential use of protein domain pairs as interaction mediators: order and transitivity.

Itzhaki Z, Akiva E, Margalit H.

Bioinformatics. 2010 Oct 15;26(20):2564-70. doi: 10.1093/bioinformatics/btq495. Epub 2010 Aug 27.

PMID:
20802208
30.

Modularity and directionality in genetic interaction maps.

Jaimovich A, Rinott R, Schuldiner M, Margalit H, Friedman N.

Bioinformatics. 2010 Jun 15;26(12):i228-36. doi: 10.1093/bioinformatics/btq197.

31.

Legionella pneumophila 6S RNA optimizes intracellular multiplication.

Faucher SP, Friedlander G, Livny J, Margalit H, Shuman HA.

Proc Natl Acad Sci U S A. 2010 Apr 20;107(16):7533-8. doi: 10.1073/pnas.0911764107. Epub 2010 Apr 5.

32.

Stochastic analysis of the SOS response in Escherichia coli.

Shimoni Y, Altuvia S, Margalit H, Biham O.

PLoS One. 2009;4(5):e5363. doi: 10.1371/journal.pone.0005363. Epub 2009 May 8.

33.

Built-in loops allow versatility in domain-domain interactions: lessons from self-interacting domains.

Akiva E, Itzhaki Z, Margalit H.

Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13292-7. doi: 10.1073/pnas.0801207105. Epub 2008 Aug 29.

34.

A novel Bayesian DNA motif comparison method for clustering and retrieval.

Habib N, Kaplan T, Margalit H, Friedman N.

PLoS Comput Biol. 2008 Feb 29;4(2):e1000010. doi: 10.1371/journal.pcbi.1000010. Erratum in: PLoS Comput Biol. 2011 May;7(5). doiL10.1371/annotation/d876137b-59c5-48cf-8491-c8cf12f26a9b.

35.

A melanoma multiepitope polypeptide induces specific CD8+ T-cell response.

Levy A, Pitcovski J, Frankenburg S, Elias O, Altuvia Y, Margalit H, Peretz T, Golenser J, Lotem M.

Cell Immunol. 2007 Nov-Dec;250(1-2):24-30. doi: 10.1016/j.cellimm.2008.01.001. Epub 2008 Feb 13.

36.

Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence.

Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, Baruch K, Rosenshine I, Margalit H, Altuvia S.

Nucleic Acids Res. 2008 Apr;36(6):1913-27. doi: 10.1093/nar/gkn050. Epub 2008 Feb 11.

37.

Regulation of gene expression by small non-coding RNAs: a quantitative view.

Shimoni Y, Friedlander G, Hetzroni G, Niv G, Altuvia S, Biham O, Margalit H.

Mol Syst Biol. 2007;3:138. Epub 2007 Sep 25.

38.

Host immune system gene targeting by a viral miRNA.

Stern-Ginossar N, Elefant N, Zimmermann A, Wolf DG, Saleh N, Biton M, Horwitz E, Prokocimer Z, Prichard M, Hahn G, Goldman-Wohl D, Greenfield C, Yagel S, Hengel H, Altuvia Y, Margalit H, Mandelboim O.

Science. 2007 Jul 20;317(5836):376-81.

39.

Evolutionary conservation of domain-domain interactions.

Itzhaki Z, Akiva E, Altuvia Y, Margalit H.

Genome Biol. 2006;7(12):R125.

40.

Characterization and prediction of protein-protein interactions within and between complexes.

Sprinzak E, Altuvia Y, Margalit H.

Proc Natl Acad Sci U S A. 2006 Oct 3;103(40):14718-23. Epub 2006 Sep 26.

41.
42.

Towards an integrated protein-protein interaction network: a relational Markov network approach.

Jaimovich A, Elidan G, Margalit H, Friedman N.

J Comput Biol. 2006 Mar;13(2):145-64.

PMID:
16597232
43.

Proteins of the same fold and unrelated sequences have similar amino acid composition.

Ofran Y, Margalit H.

Proteins. 2006 Jul 1;64(1):275-9.

PMID:
16565950
44.

Ab initio prediction of transcription factor targets using structural knowledge.

Kaplan T, Friedman N, Margalit H.

PLoS Comput Biol. 2005 Jun;1(1):e1. Epub 2005 Jun 24.

45.

Assigning functions to genes: identification of S-phase expressed genes in Leishmania major based on post-transcriptional control elements.

Zick A, Onn I, Bezalel R, Margalit H, Shlomai J.

Nucleic Acids Res. 2005 Jul 28;33(13):4235-42. Print 2005.

46.

Clustering and conservation patterns of human microRNAs.

Altuvia Y, Landgraf P, Lithwick G, Elefant N, Pfeffer S, Aravin A, Brownstein MJ, Tuschl T, Margalit H.

Nucleic Acids Res. 2005 May 12;33(8):2697-706. Print 2005.

47.

Chromosomal organization is shaped by the transcription regulatory network.

Hershberg R, Yeger-Lotem E, Margalit H.

Trends Genet. 2005 Mar;21(3):138-42. Review.

PMID:
15734572
48.

Relative predicted protein levels of functionally associated proteins are conserved across organisms.

Lithwick G, Margalit H.

Nucleic Acids Res. 2005 Feb 17;33(3):1051-7. Print 2005.

49.

A structure-based approach for prediction of MHC-binding peptides.

Altuvia Y, Margalit H.

Methods. 2004 Dec;34(4):454-9.

PMID:
15542371
50.

Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction.

Yeger-Lotem E, Sattath S, Kashtan N, Itzkovitz S, Milo R, Pinter RY, Alon U, Margalit H.

Proc Natl Acad Sci U S A. 2004 Apr 20;101(16):5934-9. Epub 2004 Apr 12.

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