Publications

Journals, 2019

Tagore, S., Gorohovski, A., Jensen, L.J., Frenkel-Morgenstern, M. (2019)
ProtFus: A Comprehensive Method Characterizing Protein-Protein Interactions of Fusion Proteins . PLoS Comput Biol. 2019 Aug 22;15(8):e1007239. doi: 10.1371/journal.pcbi.1007239. eCollection 2019 Aug.
(Impact Factor – 2.776)

Tagore S., Frenkel-Morgenstern M. (2019)
When Mathematics Outsmarts Cancer. In: Rojas I., Valenzuela O., Rojas F., Ortuño F. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2019. Lecture Notes in Computer Science, vol 11465. Springer, Cham. doi.org/10.1007/978-3-030-17938-0_42

Tagore, S., Gorohovski, A., Jensen, L.J., Raviv-Shay, D., Frenkel-Morgenstern, M. (2019).
New Tool Mines Scientific Texts for Fusion Protein Facts. PLOS. “New tool mines scientific texts for fusion protein facts: Computational approach could aid efforts to develop personalized cancer treatments.” ScienceDaily. ScienceDaily, 22 August 2019.

Journals, 2018

Journo, G., Tushinsky, C., Shterngas, A., Avital, N., Eran, Y., Karpuj, M.V., Frenkel-Morgenstern, M., Shamay, M. (2018)
Modulation of Cellular CpG DNA Methylation by Kaposi’s Sarcoma-Associated Herpesvirus. J Virol. 2018 Jul 31;92(16). pii: e00008-18. doi: 10.1128/JVI.00008-18. Print 2018 Aug 15. (Impact Factor – 4.663)

Frenkel-Morgenstern, M., Welch, L., Gaeta, B., Kovats, D.E. (2018)
Art in Science Competition invites artworks to the annual exhibition on ISMB 2018 in Chicago. PLoS Comput Biol. 2018 May 7;14(5):e1006139. doi: 10.1371/journal.pcbi.1006139. eCollection 2018 May.

Welch L., Gaeta, B., Kovats, D.E., Frenkel Morgenstern, M. (2018)
Art in Science Competition invites artworks to the annual exhibition on ISMB 2018 in Chicago. F1000Res. 2018 Mar 19;7. pii: ISCB Comm J-337. doi: 10.12688/f1000research.14242.1. eCollection 2018.

Cai, Z., Wang, L., Li, K., Tagore, S., Li, X., Wang, H., Chen, J., Song, X., Frenkel, Z., Gao, D., Frenkel-Morgenstern, M., Zhang, T., Nevo, E. (2018)
Adaptive Transcriptome Profiling of Subterranean Zokor, Myospalax baileyi, to High- Altitude Stresses in Tibet. Sci Rep. 2018 Mar 16;8(1):4671. doi: 10.1038/s41598-018-22483-7. (Impact Factor – 4.259)

Conferences, 2018

Carmi, G.1, Tagore, S.1, Sivan, A.1, Gorohovski, A.1, Li, K., Nevo, E., Raviv-Shay, D., Frenkel-Morgenstern, M. (2018) 
PASTORAL: Database of Protein-Protein Interactions of the Stress-Response Genes in Subterranean and Fossorial Animals. 7th Translational Research Day, Bar-Ilan University, Safed, Israel, February 26, 2018 (Poster). 1Equal Contribution.

Tagore, S., Frenkel-Morgenstern, M. (2018)
Site-directed percolation of fusion protein-protein interaction networks reveal multi-interface hubs as potential drug targets.
International School and Conference on Network Science (NetSci-X), Hangzhou, China, January 6-8, 2018 (Oral).

Palande, V., Raviv-Shay, D., Frenkel-Morgenstern, M. (2018)
Diagnosis of Glioma Tumors Using Circulating Cell-Free DNA. Next Generation Sequencing (NGS) Conference 2018, April 9–11, 2018, Barcelona, Spain. (Poster)

Tagore, S., Detroja, R., Frenkel-Morgenstern, M. (2018)
Mutated Tumor Suppressors Follow Oncogenes Profile by the Gene Hypermethylation of Partners in the Protein Interaction Networks. Next Generation Sequencing (NGS) Conference 2018, April 9–11, 2018, Barcelona, Spain. (Oral Presentations)

Journals, 2017

Frenkel-Morgenstern, M., Gorohovski, A., Tagore, S., Sekar, V., Vazquez, M., Valencia, A. (2017)
ChiPPI: A Novel Method for Mapping Chimeric Protein-Protein Interactions Uncovers Selection Principles of Protein Fusion Events in Cancer. Nucleic Acids Res. 45(12): 7094-7105. (Impact Factor – 10.12)

Gorohovski, A., Tagore, S., Palande, V., Malka, A., Raviv-Shay, D., Frenkel-Morgenstern, M. (2017)
ChiTaRS-3.1 – the enhanced Chimeric Transcripts and RNA-seq Database matched with Protein-Protein Interactions. Nucleic Acids Res. 45(D1): D790-D795 (Impact Factor – 10.12)

Tagore, S., Frenkel-Morgenstern, M. (2017)
A community-based Naïve Bayes method for classifying oncogenes and tumor suppressors using fusion protein-protein interaction networks. FEBS J, 284: P.3.3.B-006, doi:10.1111/febs.14174 (Abstract) (Impact Factor – 4.2).

Conferences, 2017

Frenkel-Morgenstern, M., Gorohovski, A., Tagore, S., Sekar, V., Vazquez, M., Valencia, A. (2017)
Chimeric Protein-Protein Interaction Networks Reveal Alterations in Cancer-Specific Phenotypes. 15th RECOMB Comparative Genomics Satellite Workshop, Barcelona, Spain, October 4 – 6, 2017 (Poster).

Tagore, S., Frenkel-Morgenstern, M. (2017)
A community-based Naïve Bayes method for classifying oncogenes and tumor suppressors using fusion protein-protein interaction networks. 42nd FEBS Congress, Jerusalem, Israel, September 10 – 14, 2017 (Poster).

Tagore, S., Frenkel-Morgenstern, M. (2017)
Percolation-like phase transitions in protein-protein interactions networks of fusions reveal a discrepancy in cancer phenotypes. ISMB 2017 – Intelligent Systems for Molecular Biology (ISMB), Student Council Symposium, Prague, Czech Republic, July 21, 2017 (Poster).

Tagore, S., Frenkel-Morgenstern, M. (2017)
The communities of party hubs in fusion protein-protein interaction networks increases their robustness against site-directed knockouts. ISMB 2017 – Intelligent Systems for Molecular Biology (ISMB), Net-Biol COSI, Prague, Czech Republic, July 21–25, 2017 (Poster, Talk).

Tagore, S., Frenkel-Morgenstern, M. (2017)
Classifying oncogenes and tumor suppressors in fusion protein-protein interaction networks using a community-based Naïve Bayes approach. ISMB 2017 – Intelligent Systems for Molecular Biology (ISMB), Sys-Mod COSI, Prague, Czech Republic, July 21–25, 2017 (Poster).

Tagore, S., Gorohovski, A., Jensen, L.J., Frenkel-Morgenstern, M. (2017)
A Text Mining Approach Characterizes Fusion Proteins and Their Interactions From PubMed Publications. ISMB 2017 – Intelligent Systems for Molecular Biology (ISMB), Bio-Ontology COSI, Prague, Czech Republic, July 21–25, 2017 (Talk, Flash Update).

Tagore, S., Frenkel-Morgenstern, M. (2017)
The percolation model of fusion protein-protein interaction networks reveals multi-interface hubs as potential drug targets. Great Lakes Bioinformatics Conference (GLBIO-2017), May 15-17, 2017, Univ. of Illinois at Chicago, U.S.A. (Oral).

Frenkel-Morgenstern, M., Tagore, S., Valencia, A. (2017)
The Percolation Analysis of the Chimeric Protein-Protein Interactions in the PanCancer Datasets. Pancancer Teleconference, Pancancer Teleconference, March 22, 2017 (Talk).

Tagore, S., Frenkel-Morgenstern, M. (2017)
The percolation model of the chimeric protein-protein interaction networks reveals central nodes as potential drug targets.
6th Translational Research Day, March 01, 2017, Bar-Ilan University, Safed, Israel (Oral).

Tagore, S., Frenkel-Morgenstern, M. (2017)
Protein-protein Interaction Networks Of Cancer Fusions Display Small World Behavior And Strong Resilience Against Perturbing Lower-Degree Hubs. 8th ILANIT / FISEB Conference, Eilat, Israel, February 20-23, 2017 (E-Poster).

Palande, V., Frenkel-Morgenstern, F., Raviv Shay, D. (2017)
Diagnosis of glioma tumors using circulating cell-free DNA. RSG with DREAM, November 19-21, 2017, New York, (RSG Posters).

Journals, 2016

Li, K., Wang, L., Knisbacher, B.A., Xu, Q., Levanon, E.Y., 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, Y.B., Wang, Z.L., Nevo, E. (2016)
Transcriptome, genetic editing, and microRNA divergence substantiate sympatric speciation of blind mole rat, Spalax. Proc Natl Acad Sci USA. 2016 Jul 5;113(27):7584-9. doi: 10.1073/pnas.1607497113. Epub 2016 Jun 23.

Conferences, 2016

Tagore, S., Gorohovski, A., Jensen, L.J., Frenkel-Morgenstern, M. (2016)
ProtFus: a python repository for tagging fusion proteins and their interactions in text. ISMB 2016 – International Society for Computational Biology (ISCB), 2016, Orlando, Florida, U.S.A., July 8–12, 2016 (Abstract+Poster).

Tagore, S., Gorohovski, A., Jensen, L.J., Frenkel-Morgenstern, M. (2016)
ProtFus: a tool for identifying fusion proteins and their interactions from text. IBS 2016 – Israeli Bioinformatics Symposium, University of Haifa, May 18, 2016, Israel (Abstract+Poster), -pp.17-18.

Tagore, S., Frenkel-Morgenstern, M. (2016)
ProtFus: a python repository for tagging fusion protein instances in PubMed. 5th Translational Research Day, February 15, 2016, Bar-Ilan University, Safed, Israel (Poster).

Journals, 2015

Gamper, H.B., Masuda, I., Frenkel-Morgenstern, M., Hou, Y.M. (2015)
The UGG Isoacceptor of tRNAPro Is Naturally Prone to Frameshifts. International Journal of Molecular Sciences, 16(7):14866-14883.

Gamper, H.B., Masuda, I., Frenkel-Morgenstern, M., Hou, Y.M. (2015)
Maintenance of protein synthesis reading frame by EF-P and m(1)G37-tRNA. Nature Communications 6, Article number:7226.

Journals, 2014

Frenkel-Morgenstern, M., Gorohovski, A., Vucenovic, D., Maestre, L., Valencia, A. (2014)
ChiTaRS 2.1 – an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts. Nucleic Acids Research, 43(1):D68-D75.

Journals, 2013

Milana Frenkel-Morgenstern, Alessandro Gorohovski, Vincent Lacroix, Mark Rogers, Kristina Ibanez, Cesar Boullosa, Eduardo Andres Leon, Asa Ben-Hur and Alfonso Valencia. (2013)
ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data. Nucleic Acids Research, 41(1):D142-151.

Journals, 2012

Frenkel-Morgenstern, M., Valencia, A. (2012)
Novel domain combinations in proteins encoded by chimeric transcripts. Oxford Journals: Bioinformatics, 28(12):i67-74.

Frenkel-Morgenstern, M., Lacroix, V., Ezkurdia, I., Levin, Y., Gabashvili, A., Prilusky, J., Del Pozo, A., Tress, M., Johnson, R., Guigo, R., Valencia, A. (2012)
Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts. Genome Research, 22(7):1231-1242.

Frenkel-Morgenstern, M., Danon, T., Christian, T., Igarashi, T., Cohen, L., Hou, Y.M., Jensen, L.J. (2012)
Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels. Molecular System Biology, 8:572.

Journals, 2011

Gottlieb, A., Frenkel-Morgenstern, M., Safro, M., Horn, D. (2011)
Common peptides study of aminoacyl-tRNA synthetases. PLoS One, 6(5):e20361.

Journals, 2010

Frenkel-Morgenstern, M., Cohen, A.A., Geva-Zatorsky, N., Eden, E., Prilusky, J., Issaeva, I., Sigal, A., Cohen-Saidon, C., Liron, Y., Cohen, L., Danon, T., Perzov, N., Alon, U. (2010)
Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells. Oxford Journals: Nucleic Acids Research, 38(1):D508-D512.

Conferences, 2010

Frenkel-Morgenstern, M., Valencia, A. (2010)
The potential functional role of chimeric transcripts in higher eukaryotes. (Outstanding Poster Award). ISMB2010.
Short Abstract: Chimeric RNAs are produced by trans-splicing of two distinct transcripts, have been reported in different organisms.However, how the trans-splicing machinery can be used to design new functional proteins remains unclear. We found that chimeric RNAs resulting from trans-splicing, if they are translated, might produce the dominant negative effect in cells.

Journals, 2009

Frenkel-Morgenstern, M., Tworowski, D., Klipcan, L., Safro, M. (2009)
Intra-protein compensatory mutations analysis highlights the tRNA recognition regions in aminoacyl-tRNA synthetases. Journal of Biomolecular Structure and Dynamics, 27 Issue 2.

Journals, 2008

Cohen, A.A., 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. (2008)
Dynamic proteomics of individual cancer cells in response to a drug. Science Magazine, 322(5907):1511-6.

Klipcan, L., Frenkel-Morgenstern, M., Safro, M.G. (2008)
Presence of tRNA-dependent pathways correlates with high cysteine content in methanogenic Archaea. Trends in Genetics, 24(2):59-63.

Journals, 2007

Frenkel-Morgenstern, M., Magid, R., Eyal, E., Pietrokovski, S. (2007)
Refining intra-protein contact prediction by graph analysis. BioMed Central Bioinformatics, 8(Suppl 5):S6.

Eyal, E., Frenkel-Morgenstern, M., Sobolev, V., Pietrokovski, S. (2007)
A pair-to-pair amino acids substitution matrix and its applications for protein structure prediction. Proteins: Structure, Function, and Bioinformatics, 67(1):142–153.

Journals, 2005

Frenkel-Morgenstern, M., Singer, A., Bronfeld, H., Pietrokovski, S. (2005)
One-Block CYRCA: an automated procedure for identifying multiple-block alignments from single block queries. Oxford Journals: Nucleic Acids Research, 33(Web Server issue):W281-3.

Frenkel-Morgenstern, M., Voet, H., Pietrokovski, S. (2005)
Enhanced statistics for local alignment of multiple alignments improves prediction of protein function and structure. Oxford Journals: Bioinformatics, 21(13):2950-2956.