Publications

2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 Up to 2005
Polishchuk M, Paz I, Kohen R, Mesika R, Yakhini Z, Mandel-Gutfreund Y. (2017) A Combined Sequence and Structure Based Method for Discovering Enriched Motifs in RNA from in-vivo Binding Data. Methods pii: S1046-2023(17)30100-7. doi: 10.1016/j.ymeth.2017.03.003. [PDF]
Cohn-Alperovich D, Rabner A, Kifer I, Mandel-Gutfreund Y, Yakhini Z. (2016) Mutual enrichment in aggregated ranked lists with applications to gene expression regulation. Bioinformatics 32(17):i464-i472. [PDF]
Paz I, Kligun E, Bengad B, Mandel-Gutfreund Y. (2016) BindUP: a web server for non-homology-based prediction of DNA and RNA binding proteins. Nucleic Acids Res. 44(W1):W568-74. [PDF]
Dror I, Rohs R, Mandel-Gutfreund Y. (2016) How motif environment influences transcription factor search dynamics: Finding a needle in a haystack. Bioessays doi: 10.1002/bies.201600005 [Epub ahead of print]. [PDF]
Dror I, Golan T, Levy C, Rohs R, Mandel-Gutfreund Y. (2015) A widespread role of the motif environment on transcription factor binding across diverse protein families. Genome Res. 25(9):1268-80. [PDF]
Kligun E, Mandel-Gutfreund Y. (2015) The role of RNA conformation in RNA-protein recognition. RNA Biol. 12(7):720-7. [PDF]
Eshar S, Altenhofen L, Rabner A, Ross P, Fastman Y, Mandel-Gutfreund Y, Karni R, Llinás M, Dzikowski R. (2015) PfSR1 controls alternative splicing and steady-state RNA levels in Plasmodium falciparum through preferential recognition of specific RNA motifs. Mol Microbiol. 96(6):1283-97. [PDF]
Singer M*, Kosti I*, Pachter L, Mandel-Gutfreund Y. (2015) A diverse epigenetic landscape at human exons with implication for expression. Nucleic Acids Res. 43(7):3498-508. [PDF]
Vogt C, Hackmann C, Rabner A, Koste L, Santag S, Kati S, Mandel-Gutfreund Y, Schulz TF, Bohne J. (2015) ORF57 Overcomes the Detrimental Sequence Bias of Kaposi's Sarcoma-Associated Herpesvirus Lytic Genes. J Virol. 89(9):5097-109. [PDF]
Zoabi M, Nadar-Ponniah PT, Khoury-Haddad H, Usaj M, Budowski-Tal I, Haran T, Henn A, Mandel-Gutfreund Y, Ayoub N. (2014) RNA-dependent chromatin localization of KDM4D lysine demethylase promotes H3K9me3 demethylation. Nucleic Acids Res. 42(21):13026-38. [PDF]
Paz I, Kosti I, Ares M Jr, Cline M, Mandel-Gutfreund Y. (2014) RBPmap: a web server for mapping binding sites of RNA-binding proteins. Nucleic Acids Res. 42(Web Server issue):W361-7. [PDF]
Enav H, Mandel-Gutfreund Y, Beja O. (2014) Comparative metagenomic analyses reveal viral induced shifts of host metabolism towards nucleotide biosynthesis. Microbiome 2, 9. [PDF]
Dror I, Zhou T, Mandel-Gutfreund Y, Rohs R. (2013) Covariation between homeodomain transcription factors and the shape of their DNA binding sites. Nucleic Acids Res. 42(1):430-41. [PDF]
Leibovich L*, Paz I*, Yakhini Z, Mandel-Gutfreund Y. (2013) DRIMust: a web server for Discovering Rank Imbalanced Motifs Using Suffix Trees. Nucleic Acids Res. 41(Web Server issue):W174-9. [PDF]
Gupta S*, Kosti I*, Plaut G*, Pivko A, Biswas D, Wachtel C, Waldman Ben-Asher H, Carmi S, Glaser F, Mandel-Gutfreund Y, Michaeli S. (2013) The hnRNP F/H homologue of Trypanosoma bruceiis differentially expressed in the two life cycle stages of the parasite and regulates splicing and mRNA stability. Nucleic Acids Res. 41(13):6577-94. [PDF]
Kligun E, Mandel-Gutfreund Y. (2013) Conformational readout of RNA by small ligands. Nucleic Acids Res. 10(6):982-9. [PDF]
Hod R, Kohen R, Mandel-Gutfreund Y. (2013) Searching for protein signatures using a multilevel alphabet. Proteins 81(6):1058-68. [PDF]
Langemeier J, Schrom EM, Rabner A, Radtke M, Zychlinski D, Saborowski A, Bohn G, Mandel-Gutfreund Y, Bodem J, Klein C, Bohne J (2012) A complex immunodeficiency is based on U1 snRNP-mediated poly(A) site suppression. EMBO J. 31(20):4035-44. [PDF]
Kosti I, Radivojac P, Mandel-Gutfreund Y. (2012) An Integrated Regulatory Network Reveals Pervasive Cross-Regulation among Transcription and Splicing Factors. PLoS Comput. Biol. 8(7): e1002603. [PDF]
Enav H, Be´ja` O, Mandel-Gutfreund Y. (2012) Cyanophage tRNAs may have a role in cross-infectivity of oceanic Prochlorococcus and Synechococcus hosts. ISME J. 6, 619-628. [PDF]
Dror I, Shazman S, Mukherjee S, Zhang Y, Glaser F, Mandel-Gutfreund Y. (2011) Predicting nucleic acid binding interfaces from structural models of proteins. Proteins 80(2), 482–489. [PDF]
Yosefzon Y, Koh YY, Chritton JJ, Lande A, Leibovich L, Barziv L, Petzold C, Yakhini Z, Mandel-Gutfreund Y, Wickens M, Arava Y. (2011) Divergent RNA binding specificity of yeast Puf2p. RNA 17(8):1479-88. [PDF]
Shazman S, Elber G, Mandel-Gutfreund Y. (2011) From face to interface recognition: a differential geometric approach to distinguish DNA from RNA binding surfaces. Nucleic Acids Res. 39(17):7390-9. [PDF]
Leibovich L, Mandel-Gutfreund Y, Yakhini Z. (2010) A structural-based statistical approach suggests a cooperative activity of PUM1 and miR-410 in human 3'-untranslated regions. Silence, 22;1(1):17. [PDF]
Paz I*, Akerman M*, Dror I, Kosti I, Mandel-Gutfreund Y. (2010) SFmap: a web server for motif analysis and prediction of splicing factor binding sites. Nucleic Acids Res., 38:W281-W285. [PDF]
David-Eden H, Mankin A.S, Mandel-Gutfreund Y. (2010) Structural signatures of antibiotic binding sites on the ribosome. Nucleic Acids Res. 38(18):5982-94. [PDF]
Kosti I, Mandel-Gutfreund Y, Glaser F, Horwitz B.A. (2010) Comparative analysis of fungal protein kinases and associated domains. BMC Genomics 11:133. [PDF]
Tzahor S, Man-Aharonovich D, Kirkup B.C, Yogev T, Berman-Frank I, Polz M.F, Be´ja` O, Mandel-Gutfreund Y. (2009) A supervised learning approach for taxonomic classification of core-photosystem-II genes and transcripts in the marine environment. BMC Genomics 10(1):229. [PDF]
Oved K, Eden E, Akerman M, Noy R, Wolchinsky R, Izhaki O, Schallmach E, Kubi A, Zabari N, Schachter J, Alon U, Mandel-Gutfreund Y, Besser MJ, Reiter Y. (2009) Predicting and controlling the reactivity of immune cell populations against cancer. Mol Syst Biol. 5:265. [PDF]
Akerman M, David-Eden H, Pinter R.Y, Mandel-Gutfreund Y. (2009) A computational approach for genome-wide mapping of splicing factor binding sites. Genome Biol., 10(3):R30. [PDF]
David-Eden H, Mandel-Gutfreund Y. (2008) Revealing Unique Properties of the Ribosome using a Network Based Analysis. Nucleic Acids Res. 36(14):4641-52 [PDF]
Shazman S, Mandel-Gutfreund Y. (2008) Classifying RNA-Binding Proteins Based on Electrostatic Properties. PLoS CB. 4(8):e1000146 [PDF]
Akerman M, Mandel-Gutfreund Y. (2007) Does Distance matter? Variation in alternative splicing regulation. Nucleic Acids Res. 35:5487-98 [PDF]
Sharon I, Tzahor S, Williamson S, Shmoish M, Man-Aharonovich D, Rusch DB, Yooseph S, Zeidner G, Golden SS, Mackey SR, Adir N, Weingart U, Horn D, Venter JC, Mandel-Gutfreund Y, Oded Be´ja` (2007) Viral photosynthetic reaction centre genes and transcripts in the marine environment. ISME 1:492-501
Shazman S, Celniker G, Haber O, Glaser F, Mandel-Gutfreund Y. (2007) Patch Finder Plus (PFplus): A web server for extracting and displaying positive electrostatic patches on protein surfaces. Nucleic Acids Res. 35:526-30 [PDF]
Akerman M, Mandel-Gutfreund Y. (2006) Alternative splicing regulation at tandem 3' splice sites. Nucleic Acids Res. 34(1):23-31. [PDF]
Srinivasan K, Shiue L, Hayes JD, Centers R, Fitzwater S, Loewen R, Edmondson LR, Bryant J, Smith M, Rommelfanger C, Welch V, Clark TA, Sugnet CW, Howe KJ, Mandel-Gutfreund Y, Ares M Jr. (2005) Detection and measurement of alternative splicing using splicing-sensitive microarrays. Methods 37:345-59 [PDF]
Burckin T, Nagel R, Mandel-Gutfreund Y, Shiue L, Clark TA, Chong J-L, Chang T-H, Squazzo S, Hartzog G, Ares M Jr. (2004) Exploring function relationships between components of the gene expression machinery. Nature Struct. Mol. Biol. 12:175-82 [PDF]
Karplus K, Karchin R, Draper J, Casper J, Mandel-Gutfreund Y, Diekans M, Hughey R. (2003) Combining local-structure, fold-recognition and new fold methods for protein-structure prediction. Proteins 53:491-96 [PDF]
Karchin R, Cline M, Mandel-Gutfreund Y, Karplus K. (2003) Hidden Markov Models that use predicted local structure for fold recognition: alphabets of backbone geometry. Proteins 51:504-14 [PDF]
Stawiski EW, Gregoret LM, Mandel-Gutfreund Y. (2003) Annotating nucleic acid binding function based on protein structure. J. Mol. Biol. 326(4):1065-79 [PDF]
Mandel-Gutfreund Y, Gregoret LM. (2002) On the significance of alternating patterns of polar and non-polar residues in beta-strands. J. Mol. Biol. 323(3):453-61 [PDF]
Stawiski EW, Mandel-Gutfreund Y, Gregoret LM. (2002) Progress in predicting protein function from structure: Unique features of O-glycosidases. Pac. Symp. Biocomput. 323(3):453-61 [PDF]
Mandel-Gutfreund Y, Baron A, Margalit H. (2001) A structure-based approach for prediction of protein binding sites in gene upstream regions. Pac. Symp. Biocomput. 6:139-50 [PDF]
Mandel-Gutfreund Y, Zaremba SM, Gregoret LM. (2001) Contributions of residue pairing to beta-sheet formation: conservation and covariation of amino acid residue pairs on antiparallel beta-strands. J. Mol. Biol. 305:1145-59 [PDF]
Mandel-Gutfreund Y, Margalit H, Jernigan RL, Zhurkin VB. (1998) A role for CH...O interactions in protein-DNA recognition. J. Mol. Biol. 277:1129-40 [PDF]
Mandel-Gutfreund Y, Margalit H. (1998) Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites. Nucleic. Acids Res. 26:2306-12 [PDF]
Mandel-Gutfreund Y., Schueler O., Margalit H. (1995) Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: in search of common principles. J. Mol. Biol. 253:370-82 [PDF]