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2024

Gilda JE, Nahar A, Kasiviswanathan D, Tropp N, Gilinski T, Lahav T, Alexandrovich D, Mandel-Gutfreund Y, Park S, Shemer S (2024). Proteasome gene expression is controlled by coordinated functions of multiple transcription factors. J Cell Biol Aug 5;223(8):e202402046. doi: 10.1083/jcb.202402046 [PDF]
Or Alfi, Mevaseret Cohen, Shikma Bar-On, Tamar Hashimshony, Lorinne Levitt, Yael Raz,
Yair Blecher, M. Zeeshan Chaudhry, Luka Cicin-Sain, Rina Ben-El, Esther Oiknine-Djian, Tamar Lahav,
Olesya Vorontsov, Adiel Cohen, Zichria Zakay-Rones, Leonor Daniel, Michael Berger, Yael Mandel-Gutfreund,
Amos Panet, Dana G. Wolf (2024). Decidual-tissue-resident memory T cells protect against nonprimary human cytomegalovirus infection at the maternal-fetal interface. Cell Reports 43, 113698; doi: https://doi.org/10.1016/j.celrep.2024.113698 [PDF]
 Hadas Biran, Tamar Hashimshony, Tamar Lahav, Or Efrat, Yael Mandel-Gutfreund , Zohar Yakhini (2024).Detecting significant expression patterns in single-cell and spatial transcriptomics with a flexible computational approach  Sci Rep 2024 Oct 30;14:26121. doi: 10.1038/s41598-024-75314-3 [PDF]

2018

Enav H, Kirzner S, Lindell D, Béjà O, Mandel-Gutfreund Y. (2018) Adaptation to sub-optimal hosts is a driver of viral diversification in the ocean. Nat Commun. 9(1):4698. doi: 10.1038/s41467-018-07164-3. [PDF]
Dvir S, Argoetti A, Mandel-Gutfreund Y. (2018) Ribonucleoprotein particles: advances and challenges in computational methods. Curr Opin Struct Biol. 53:124-130. doi: 10.1016/j.sbi.2018.08.002.[PDF]
Budowski-Tal I, Kolodny R, Mandel-Gutfreund Y. (2018) A Novel Geometry-Based Approach to Infer Protein Interface Similarity. Sci Rep. 8(1):8192. doi: 10.1038/s41598-018-26497-z. [PDF]
Polishchuk M*, Paz I*, Yakhini Z, Mandel-Gutfreund Y. (2018) SMARTIV: combined sequence and structure de-novo motif discovery for in-vivo RNA binding data. Nucleic Acids Res. doi: 10.1093/nar/gky453. [Epub ahead of print]. [PDF]

2015

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]
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]

2013

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]

Up to 2005

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]
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, 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.
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]
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