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Items: 29


Current Perspectives on Circulating Tumor DNA, Precision Medicine, and Personalized Clinical Management of Cancer.

Oliveira KCS, Ramos IB, Silva JMC, Barra WF, Riggins GJ, Palande V, Pinho CT, Frenkel-Morgenstern M, Santos SEB, Assumpcao PP, Burbano RR, Calcagno DQ.

Mol Cancer Res. 2020 Jan 29. doi: 10.1158/1541-7786.MCR-19-0768. [Epub ahead of print] Review.


ChiTaRS 5.0: the comprehensive database of chimeric transcripts matched with druggable fusions and 3D chromatin maps.

Balamurali D, Gorohovski A, Detroja R, Palande V, Raviv-Shay D, Frenkel-Morgenstern M.

Nucleic Acids Res. 2020 Jan 8;48(D1):D825-D834. doi: 10.1093/nar/gkz1025.


Identification of Chimeric RNAs Using RNA-Seq Reads and Protein-Protein Interactions of Translated Chimeras.

Frenkel-Morgenstern M.

Methods Mol Biol. 2020;2079:27-40. doi: 10.1007/978-1-4939-9904-0_3.


ProtFus: A Comprehensive Method Characterizing Protein-Protein Interactions of Fusion Proteins.

Tagore S, Gorohovski A, Jensen LJ, Frenkel-Morgenstern M.

PLoS Comput Biol. 2019 Aug 22;15(8):e1007239. doi: 10.1371/journal.pcbi.1007239. eCollection 2019 Aug.


The chromatin remodeler Chd1 regulates cohesin in budding yeast and humans.

Boginya A, Detroja R, Matityahu A, Frenkel-Morgenstern M, Onn I.

Sci Rep. 2019 Jun 20;9(1):8929. doi: 10.1038/s41598-019-45263-3.


Altered Expression and Localization of Tumor Suppressive E3 Ubiquitin Ligase SMURF2 in Human Prostate and Breast Cancer.

Emanuelli A, Manikoth Ayyathan D, Koganti P, Shah PA, Apel-Sarid L, Paolini B, Detroja R, Frenkel-Morgenstern M, Blank M.

Cancers (Basel). 2019 Apr 18;11(4). pii: E556. doi: 10.3390/cancers11040556.


Modulation of Cellular CpG DNA Methylation by Kaposi's Sarcoma-Associated Herpesvirus.

Journo G, Tushinsky C, Shterngas A, Avital N, Eran Y, Karpuj MV, Frenkel-Morgenstern M, Shamay M.

J Virol. 2018 Jul 31;92(16). pii: e00008-18. doi: 10.1128/JVI.00008-18. Print 2018 Aug 15.


Art in Science Competition invites artworks to the annual exhibition on ISMB 2018 in Chicago.

Frenkel-Morgenstern M, Welch L, Gaeta B, Kovats DE.

PLoS Comput Biol. 2018 May 7;14(5):e1006139. doi: 10.1371/journal.pcbi.1006139. eCollection 2018 May. No abstract available.


Art in Science Competition invites artworks to the annual exhibition on ISMB 2018 in Chicago.

Welch L, Gaeta B, Kovats DE, Frenkel Morgenstern M.

F1000Res. 2018 Mar 19;7. pii: ISCB Comm J-337. doi: 10.12688/f1000research.14242.1. eCollection 2018.


Adaptive Transcriptome Profiling of Subterranean Zokor, Myospalax baileyi, to High- Altitude Stresses in Tibet.

Cai Z, Wang L, Song X, Tagore S, Li X, Wang H, Chen J, Li K, Frenkel Z, Gao D, Frenkel-Morgenstern M, Zhang T, Nevo E.

Sci Rep. 2018 Mar 16;8(1):4671. doi: 10.1038/s41598-018-22483-7.


ChiPPI: a novel method for mapping chimeric protein-protein interactions uncovers selection principles of protein fusion events in cancer.

Frenkel-Morgenstern M, Gorohovski A, Tagore S, Sekar V, Vazquez M, Valencia A.

Nucleic Acids Res. 2017 Jul 7;45(12):7094-7105. doi: 10.1093/nar/gkx423.


ChiTaRS-3.1-the enhanced chimeric transcripts and RNA-seq database matched with protein-protein interactions.

Gorohovski A, Tagore S, Palande V, Malka A, Raviv-Shay D, Frenkel-Morgenstern M.

Nucleic Acids Res. 2017 Jan 4;45(D1):D790-D795. doi: 10.1093/nar/gkw1127. Epub 2016 Nov 29.


Transcriptome, genetic editing, and microRNA divergence substantiate sympatric speciation of blind mole rat, Spalax.

Li K, Wang L, Knisbacher BA, Xu Q, Levanon EY, Wang H, Frenkel-Morgenstern M, Tagore S, Fang X, Bazak L, Buchumenski I, Zhao Y, Lövy M, Li X, Han L, Frenkel Z, Beiles A, Cao YB, Wang ZL, Nevo E.

Proc Natl Acad Sci U S A. 2016 Jul 5;113(27):7584-9. doi: 10.1073/pnas.1607497113. Epub 2016 Jun 23.


The UGG Isoacceptor of tRNAPro Is Naturally Prone to Frameshifts.

Gamper HB, Masuda I, Frenkel-Morgenstern M, Hou YM.

Int J Mol Sci. 2015 Jul 1;16(7):14866-83. doi: 10.3390/ijms160714866.


Maintenance of protein synthesis reading frame by EF-P and m(1)G37-tRNA.

Gamper HB, Masuda I, Frenkel-Morgenstern M, Hou YM.

Nat Commun. 2015 May 26;6:7226. doi: 10.1038/ncomms8226.


ChiTaRS 2.1--an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts.

Frenkel-Morgenstern M, Gorohovski A, Vucenovic D, Maestre L, Valencia A.

Nucleic Acids Res. 2015 Jan;43(Database issue):D68-75. doi: 10.1093/nar/gku1199. Epub 2014 Nov 20.


ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data.

Frenkel-Morgenstern M, Gorohovski A, Lacroix V, Rogers M, Ibanez K, Boullosa C, Andres Leon E, Ben-Hur A, Valencia A.

Nucleic Acids Res. 2013 Jan;41(Database issue):D142-51. doi: 10.1093/nar/gks1041. Epub 2012 Nov 9.


Novel domain combinations in proteins encoded by chimeric transcripts.

Frenkel-Morgenstern M, Valencia A.

Bioinformatics. 2012 Jun 15;28(12):i67-74. doi: 10.1093/bioinformatics/bts216.


Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts.

Frenkel-Morgenstern M, Lacroix V, Ezkurdia I, Levin Y, Gabashvili A, Prilusky J, Del Pozo A, Tress M, Johnson R, Guigo R, Valencia A.

Genome Res. 2012 Jul;22(7):1231-42. doi: 10.1101/gr.130062.111. Epub 2012 May 15.


Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels.

Frenkel-Morgenstern M, Danon T, Christian T, Igarashi T, Cohen L, Hou YM, Jensen LJ.

Mol Syst Biol. 2012 Feb 28;8:572. doi: 10.1038/msb.2012.3.


Common peptides study of aminoacyl-tRNA synthetases.

Gottlieb A, Frenkel-Morgenstern M, Safro M, Horn D.

PLoS One. 2011;6(5):e20361. doi: 10.1371/journal.pone.0020361. Epub 2011 May 27.


Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells.

Frenkel-Morgenstern M, Cohen AA, Geva-Zatorsky N, Eden E, Prilusky J, Issaeva I, Sigal A, Cohen-Saidon C, Liron Y, Cohen L, Danon T, Perzov N, Alon U.

Nucleic Acids Res. 2010 Jan;38(Database issue):D508-12. doi: 10.1093/nar/gkp808. Epub 2009 Oct 9.


Intra-protein compensatory mutations analysis highlights the tRNA recognition regions in aminoacyl-tRNA synthetases.

Frenkel-Morgenstern M, Tworowski D, Klipcan L, Safro M.

J Biomol Struct Dyn. 2009 Oct;27(2):115-26.


Dynamic proteomics of individual cancer cells in response to a drug.

Cohen AA, Geva-Zatorsky N, Eden E, Frenkel-Morgenstern M, Issaeva I, Sigal A, Milo R, Cohen-Saidon C, Liron Y, Kam Z, Cohen L, Danon T, Perzov N, Alon U.

Science. 2008 Dec 5;322(5907):1511-6. doi: 10.1126/science.1160165. Epub 2008 Nov 20.


Presence of tRNA-dependent pathways correlates with high cysteine content in methanogenic Archaea.

Klipcan L, Frenkel-Morgenstern M, Safro MG.

Trends Genet. 2008 Feb;24(2):59-63. doi: 10.1016/j.tig.2007.11.007. Epub 2008 Jan 14.


Refining intra-protein contact prediction by graph analysis.

Frenkel-Morgenstern M, Magid R, Eyal E, Pietrokovski S.

BMC Bioinformatics. 2007 May 24;8 Suppl 5:S6.


A pair-to-pair amino acids substitution matrix and its applications for protein structure prediction.

Eyal E, Frenkel-Morgenstern M, Sobolev V, Pietrokovski S.

Proteins. 2007 Apr 1;67(1):142-53.


One-Block CYRCA: an automated procedure for identifying multiple-block alignments from single block queries.

Frenkel-Morgenstern M, Singer A, Bronfeld H, Pietrokovski S.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W281-3.


Enhanced statistics for local alignment of multiple alignments improves prediction of protein function and structure.

Frenkel-Morgenstern M, Voet H, Pietrokovski S.

Bioinformatics. 2005 Jul 1;21(13):2950-6. Epub 2005 May 3.


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