Publications | Yael Mandel Gutfreu

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Yael Mandel-Gutfreund Lab

2025

Efrat Herbst, Yael Mandel-Gutfreund, Zohar Yakhini, Hadas Biran (2025). Inferring single-cell and spatial microRNA activity from transcriptomics data. Commun Biol Jan25 18;8(1):87.doi: 10.1038/s42003-025-07454-9 [PDF]

Amir Argoetti, Dor Shalev, Galia Polyak, Noa Shima, Hadas Biran, Tamar Lahav, Tamar Hashimshony, Yael Mandel-Gutfreund(2025). lncRNA NORAD modulates STAT3/STAT1 balance and innate immune responses in human cells via interaction with STAT3. Nat Commun Jan25 10;16:571. doi: 10.1038/s41467-025-55822-0 [PDF]

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]

2023

Bella M Ben-Oz, Feras E Machour, Marian Nicola, Amir Argoetti, Galia Polyak, Rawad Hanna, Oded Kleifeld, Yael Mandel-Gutfreund, Nabieh Ayoub (2023). A dual role of RBM42 in modulating splicing and translation of CDKN1A/p21 during DNA damage response. Nat Commun 14(1):7628.doi: 10.1038/s41467-023-43495-6 [PDF]

Aditya Kshirsagar, Svetlana Maslov Doroshev, Anna Gorelik, Tsviya Olender, Tamar Sapir, Daisuke Tsuboi, Irit Rosenhek-Goldian, Sergey Malitsky, Maxim Itkin, Amir Argoetti, Yael Mandel-Gutfreund, Sidney R. Cohen, Jacob H. Hanna, Igor Ulitsky, Kozo Kaibuchi , Orly Reiner (2023). LIS1 RNA-binding orchestrates the mechanosensitive properties of embryonic stem cells in AGO2-dependent and independent ways. Nat Commun 14, 3293 (2023); doi.org/10.1038/s41467-023-38797-8 [PDF]

2022

Paz I, Argoetti A, Cohen N, Even N, Mandel-Gutfreund Y. (2022) RBPmap: A Tool for Mapping and Predicting the Binding Sites of RNA-Binding Proteins Considering the Motif Environment. Methods Mol Biol.2022;2404:53-65. doi: 10.1007/978-1-0716-1851-6_3. PMID: 34694603 [PDF]

2021

Dvir S, Argoetti A, Lesnik C, Roytblat M, Shriki K, Amit M, Hashimshony T, Mandel-Gutfreund Y. (2021) Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells. Cell Rep. 35(9):109198. doi: 10.1016/j.celrep.2021.109198.PMID: 34077720. [PDF]

2020

Yelin I, Aharony N, Tamar ES, Argoetti A, Messer E, Berenbaum D, Shafran E, Kuzli A, Gandali N, Shkedi O, Hashimshony T, Mandel-Gutfreund Y, Halberthal M, Geffen Y, Szwarcwort-Cohen M, Kishony R. (2020) Evaluation of COVID-19 RT-qPCR Test in Multi sample Pools. Clin Infect Dis. 71(16):2073-2078. doi: 10.1093/cid/ciaa531.PMID: 32358960. [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]

2017

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.

2016

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]

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]

2014

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]

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]

2012

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]

Kligun E, Mandel-Gutfreund Y. (2013) Conformational readout of RNA by small ligands. Nucleic Acids Res. 10(6):982-9. [PDF]

2011

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]

2010

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]

2009

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]

2008

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]

2007

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]

2006

Akerman M, Mandel-Gutfreund Y. (2006) Alternative splicing regulation at tandem 3' splice sites. Nucleic Acids Res. 34(1):23-31. [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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