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A widespread role of the motif environment in transcription factor binding across diverse protein families.

Dror I, Golan T, Levy C, Rohs R, Mandel-Gutfreund Y.

Genome Res. 2015 Sep;25(9):1268-80. doi: 10.1101/gr.184671.114. Epub 2015 Jul 9.


The role of RNA conformation in RNA-protein recognition.

Kligun E, Mandel-Gutfreund Y.

RNA Biol. 2015;12(7):720-7. doi: 10.1080/15476286.2015.1040977.


PfSR1 controls alternative splicing and steady-state RNA levels in Plasmodium falciparum through preferential recognition of specific RNA motifs.

Eshar S, Altenhofen L, Rabner A, Ross P, Fastman Y, Mandel-Gutfreund Y, Karni R, Llinás M, Dzikowski R.

Mol Microbiol. 2015 Jun;96(6):1283-97. doi: 10.1111/mmi.13007. Epub 2015 Apr 16.


A diverse epigenetic landscape at human exons with implication for expression.

Singer M, Kosti I, Pachter L, Mandel-Gutfreund Y.

Nucleic Acids Res. 2015 Apr 20;43(7):3498-508. doi: 10.1093/nar/gkv153. Epub 2015 Mar 12.


ORF57 overcomes the detrimental sequence bias of Kaposi's sarcoma-associated herpesvirus lytic genes.

Vogt C, Hackmann C, Rabner A, Koste L, Santag S, Kati S, Mandel-Gutfreund Y, Schulz TF, Bohne J.

J Virol. 2015 May;89(9):5097-109. doi: 10.1128/JVI.03264-14. Epub 2015 Feb 18.


RNA-dependent chromatin localization of KDM4D lysine demethylase promotes H3K9me3 demethylation.

Zoabi M, Nadar-Ponniah PT, Khoury-Haddad H, Usaj M, Budowski-Tal I, Haran T, Henn A, Mandel-Gutfreund Y, Ayoub N.

Nucleic Acids Res. 2014 Dec 1;42(21):13026-38. doi: 10.1093/nar/gku1021. Epub 2014 Nov 5.


RBPmap: a web server for mapping binding sites of RNA-binding proteins.

Paz I, Kosti I, Ares M Jr, Cline M, Mandel-Gutfreund Y.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W361-7. doi: 10.1093/nar/gku406. Epub 2014 May 14.


Comparative metagenomic analyses reveal viral-induced shifts of host metabolism towards nucleotide biosynthesis.

Enav H, Mandel-Gutfreund Y, Béjà O.

Microbiome. 2014 Mar 26;2(1):9. doi: 10.1186/2049-2618-2-9.


Covariation between homeodomain transcription factors and the shape of their DNA binding sites.

Dror I, Zhou T, Mandel-Gutfreund Y, Rohs R.

Nucleic Acids Res. 2014 Jan;42(1):430-41. doi: 10.1093/nar/gkt862. Epub 2013 Sep 27.


DRIMust: a web server for discovering rank imbalanced motifs using suffix trees.

Leibovich L, Paz I, Yakhini Z, Mandel-Gutfreund Y.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W174-9. doi: 10.1093/nar/gkt407. Epub 2013 May 17.


The hnRNP F/H homologue of Trypanosoma brucei is differentially expressed in the two life cycle stages of the parasite and regulates splicing and mRNA stability.

Gupta SK, Kosti I, Plaut G, Pivko A, Tkacz ID, Cohen-Chalamish S, Biswas DK, Wachtel C, Waldman Ben-Asher H, Carmi S, Glaser F, Mandel-Gutfreund Y, Michaeli S.

Nucleic Acids Res. 2013 Jul;41(13):6577-94. doi: 10.1093/nar/gkt369. Epub 2013 May 10.


Conformational readout of RNA by small ligands.

Kligun E, Mandel-Gutfreund Y.

RNA Biol. 2013 Jun;10(6):982-9. doi: 10.4161/rna.24682. Epub 2013 Apr 16.


Searching for protein signatures using a multilevel alphabet.

Hod R, Kohen R, Mandel-Gutfreund Y.

Proteins. 2013 Jun;81(6):1058-68. doi: 10.1002/prot.24261. Epub 2013 Feb 27.


A complex immunodeficiency is based on U1 snRNP-mediated poly(A) site suppression.

Langemeier J, Schrom EM, Rabner A, Radtke M, Zychlinski D, Saborowski A, Bohn G, Mandel-Gutfreund Y, Bodem J, Klein C, Bohne J.

EMBO J. 2012 Oct 17;31(20):4035-44. doi: 10.1038/emboj.2012.252. Epub 2012 Sep 11.


A novel Plasmodium falciparum SR protein is an alternative splicing factor required for the parasites' proliferation in human erythrocytes.

Eshar S, Allemand E, Sebag A, Glaser F, Muchardt C, Mandel-Gutfreund Y, Karni R, Dzikowski R.

Nucleic Acids Res. 2012 Oct;40(19):9903-16. doi: 10.1093/nar/gks735. Epub 2012 Aug 9.


An integrated regulatory network reveals pervasive cross-regulation among transcription and splicing factors.

Kosti I, Radivojac P, Mandel-Gutfreund Y.

PLoS Comput Biol. 2012;8(7):e1002603. doi: 10.1371/journal.pcbi.1002603. Epub 2012 Jul 26.


Characterization of coding synonymous and non-synonymous variants in ADAMTS13 using ex vivo and in silico approaches.

Edwards NC, Hing ZA, Perry A, Blaisdell A, Kopelman DB, Fathke R, Plum W, Newell J, Allen CE, S G, Shapiro A, Okunji C, Kosti I, Shomron N, Grigoryan V, Przytycka TM, Sauna ZE, Salari R, Mandel-Gutfreund Y, Komar AA, Kimchi-Sarfaty C.

PLoS One. 2012;7(6):e38864. doi: 10.1371/journal.pone.0038864. Epub 2012 Jun 29.


Predicting nucleic acid binding interfaces from structural models of proteins.

Dror I, Shazman S, Mukherjee S, Zhang Y, Glaser F, Mandel-Gutfreund Y.

Proteins. 2012 Feb;80(2):482-9. doi: 10.1002/prot.23214. Epub 2011 Nov 16.


Cyanophage tRNAs may have a role in cross-infectivity of oceanic Prochlorococcus and Synechococcus hosts.

Enav H, Béjà O, Mandel-Gutfreund Y.

ISME J. 2012 Mar;6(3):619-28. doi: 10.1038/ismej.2011.146. Epub 2011 Oct 20.


Ancient diversity of splicing motifs and protein surfaces in the wild emmer wheat (Triticum dicoccoides) LR10 coiled coil (CC) and leucine-rich repeat (LRR) domains.

Sela H, Spiridon LN, Petrescu AJ, Akerman M, Mandel-Gutfreund Y, Nevo E, Loutre C, Keller B, Schulman AH, Fahima T.

Mol Plant Pathol. 2012 Apr;13(3):276-87. doi: 10.1111/j.1364-3703.2011.00744.x. Epub 2011 Sep 23.

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