An interview was given to BioInform upon their request on SIMAP and
Compugen & Aureus role in the project. An article was published in
the same journal afterwards.
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the article
Functional analyses and Molecular modeling of two c-Kit mutations
responsible for Imatinib secondary resistance in GIST patients.
Tamborini E, Pricl S, Negri T, Lagonigro ML, Miselli F, Greco A,
Gronchi A, Casali PG, Ferrone M, Fermeglia M, Pierotti MA,
Pilotti S.
Oncogene, 2006, 25: 6140-6 (INT)
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the article
c-Kit/PDGFRA Gene Status Alterations Possibly Related to Primary
Imatinib Resistance in Gastrointestinal Stromal Tumors.
Francesca Miselli, Paola Casieri, Tiziana Negri, Marta Orsenigo, M.
Stefania Lagonigro, Alessandro Gronchi, Marco Fiore, Paolo G. Casali,
Rossella Bertulli, Antonino Carbone, Marco A. Pierotti, Elena Tamborini
and Silvana Pilotti
Clin Cancer Res. 13 2369 (2007).
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the article
A sporadic multiple GIST with unusual pathological, molecular and
genetic features
Miselli F, Conca E, Casieri P, Grosso F, Schiavo M, Tamborini E,
Pilotti S.
Am J Surg Pathol. 32, 340 (2008).
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the article
Transcriptomal profiling of site-specific Ras signals
Agudo-Ibanez L., Nunez F., Calvo F., Berenjeno I.M, Bustelo X.R.,
and Crespo P. "Transcriptomal profiling of site-specific Ras
signals". Cell. Signal.., 19, 2264-2276. (2007).
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the article
Regulation of MAPKs by growth factors and receptor tyrosine kinase.
Katz M, Amit I and Yarden Y. (2007)
Biochim. Biophys. Acta: (Epub ahead of publication)
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the article
Role of Non-phosphorylated Activation Loop Residues in Determining
ERK2 Dephosphorylation Activity, and Subcellular Localization
Bendetz-Nezer, S., and R Seger, R. (2007)
Role of non-phosphorylated activation loop residues in determining
ERK2 dephosphorylation, activity, and subcellular localization.
J. Biol. Chem. (2007), 282, 25114-25122.
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the article
Calcium-mediated interactions regulate the subcellular localization of
extracellular signal-regulated kinases (ERKs)
Chuderland, D., Marmor, G., Shainskaya, A., and Seger, R. (2007).
J. Biol. Chem. (2008)
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Compugen Profile- As appeared in "Future Magazine":
Compugen's mission is to be the world leader in the discovery and
licensing of product candidates to the drug and diagnostic industry. The
Company's powerful discovery engines enable the predictive discovery
of numerous potential therapeutics and diagnostic biomarkers.
Read the article
Role of Non-phosphorylated
Activation Loop Residues in Determining ERK2 Dephosphorylation,
Activity, and Subcellular Localization
Sarit
Bendetz-Nezer and Rony Seger
From the
Department of Biological Regulation, Weizmann institute of Science
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space
SH2B1b
adaptor is a key enhancer of RET tyrosine kinase signaling
S Donatello, A
Fiorino, D Degl?fInnocenti, L Alberti, C Miranda, L Gorla,
I Bongarzone, MG
Rizzetti, MA Pierotti and MG Borrello
Department of
Experimental Oncology, Research Unit no. 3, Milan, Italy; Department of
Experimental Oncology, Research Unit no. 4, Milan, Italy; Scientific
Direction, IRCCS Istituto Nazionale Tumori Foundation, Milan, Italy and
FIRC Institute of Molecular Oncology Foundation, Milan, Italy
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@
Presentation of conference paper: David Gilbert and Monika Heiner,
From Petri Nets to Differential Equations -
An Integrative Approach for Biochemical Network Analysis, 27th
International Conference on Application and Theory of Petri Nets and
other models of concurrency (ATPN06), Turku, Finland, June 26-30, 2006.
Proceedings; Editors: Susanna Donatelli, P. S. Thiagarajan; LNCS 4024 /
2006, pp. 181-200, ISBN: 3-540-34699-6 (GU)
http//www.brc.dcs.gla.ac.uk/~drg/publications/conferences/icatpn2006_17.pdf
https://commerce.metapress.com/content/l85l6147038t012j/resource-secured/?target=fulltext.pdf&sid=2wmxvl45ndbfsq45va0nc045&sh=www.springerlink.com
A global analysis of cross-talk in a mammalian cellular signalling network
Nature Cell Biology Published online: 14 May 2006; | doi:10.1038/ncb1418
Madhusudan Natarajan, Keng-Mean Lin, Robert C. Hsueh, Paul C. Sternweis & Rama
Ranganathan.
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Targeting tyrosine kinases in cancer: the second wave.
Oncology Program, Vall d'Hebron University Hospital and Vall d'Hebron Research Institute, Universidad Autonoma de Barcelona, Barcelona 08035, Spain.
Baselga J.
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---------------
WIS - Amit, I., Citri, A., Shay, T., Lu, Y., Katz, M.,
Zhang, F., Tarcic, G., Siwak, D., Lahad, J., Jacob-Hirsch, J., et al.
(2007). A module of negative feedback regulators defines growth
factor signaling. Nat Genet 39, 503-512.
www.nature.com/ng/journal/v39/n4/full/ng1987.html
WIS - Amit, I., Wides, R., and Yarden, Y. (2007). Evolvable signaling
networks of receptor tyrosine kinases: relevance of robustness to
malignancy and to cancer therapy. Mol Syst Biol 3, 151
http://www.nature.com/msb/journal/v3/n1/full/msb4100195.html
WIS - Katz, M., Amit, I., Citri, A., Shay, T., Carvalho, S., Lavi, S.,
Milanezi, F., Lyass, L., Amariglio, N., Jacob-Hirsch, J., et al. (2007).
A reciprocal tensin-3-cten switch mediates EGF-driven mammary cell
migration. Nat Cell Biol 9, 961-969.
http://www.nature.com/ncb/journal/v9/n8/abs/ncb1622.html
WIS - Shaul Y.D., and Seger, R. (2007) The MEK/ERK cascade: from
signaling specificity to diverse functions. Biochim Biophys Acta. 1773, 1213-1226.
http://www.ncbi.nlm.nih.gov/pubmed/17112607?ordinalpos=3....
WIS
- Chuderland,
D.,
Marmor, G., Shainskaya, A., and Seger,
R.
(2008) Calcium-mediated interactions regulate the subcellular
localization of extracellular signal-regulated kinases (ERKs). J.
Biol. Chem. 283, 11176-11188.
http://www.jbc.org/cgi/content/full/283/17/11176
WIS - Identification of a novel general nuclear translocation signal (NTS), Chuderland,
D., and Seger, R. (2007),). Mol Cell 31,
850-861.
http://linkinghub.elsevier.com/retrieve/pii/S1097276508005431
CSIC - Casar B., Pinto A., and Crespo P. "Essential
role of ERK dimers for the activation of cytoplasmic but not nuclear
substrates by ERK-scaffold complexes" Mol. Cell. Under final
revision
http://www.sciencedirect.com/science?_ob=M....
INT -.Negri T, Bozzi F, Conca E, Brich S, Gronchi A, Bertulli R, Fumagalli
E, Pierotti MA, Tamborini E, Pilotti S. "Oncogenic and
ligand-dependent activation of KIT/PDGFRA in surgical samples of
imatinib-treated gastrointestinal stromal tumours (GISTs)".
Accepted with revision in Journal of Pathology
http://www3.interscience.wiley.com/user/accessdenied....
INT - Borrello MG, Degl'innocenti D, Pierotti MA. Inflammation
and cancer: "The oncogene-driven connection". Cancer Lett.
2008 in press
http://www.ncbi.nlm.nih.gov/pubmed/18502035
GU - Richard Orton, Oliver Sturm, Amelie Gormand, Walter Kolch and David
Gilbert (2008). "Computational modelling reveals feedback
redundancy within the EGFR/ERK signalling pathway". IET
Systems Biology Vol. 2, No. 4, pp. 173 - 183.
(RJ)
http://ieeexplore.ieee.org/Xplore/login.jsp?url=http%3A%2F%..
GU - Xuan Liu, Jipu Jiang, Oluwafemi Ajayi, Xu Gu, David
Gilbert, Richard Sinnott (2008). BioNessieG – "A Grid
Enabled Biochemical Networks Simulation Environment". Accepted for
HealthGrid 2008. In Studies
in Health Technology and Informatics IOS Press, 2008, 138: 147-157. Global
Healthgrid: e-Science Meets Biomedical Informatics - Proceedings of
HealthGrid 2008. Edited by Tony Solomonides, Jonathan C.
Silverstein, Joel Saltz, Yannick Legre, Mary Kratz, Ian Foster, Vincent
Breton, J. Robert Beck (Refereed Conference)
http://www.dcs.gla.ac.uk/~drg/publications/conferences/BioNessieG.pdf
WIS
- Paper: Chuderland, D., Konson, A., and Seger, R. (2008)
"Identification and characterization of a general nuclear
translocation signal in signaling proteins" Mol Cell.
31,
850-861.
http://www.ncbi.nlm.nih.gov/pubmed/18760948
WIS - Zehorai E, Yao Z, Plotnikov A, Seger R. (2009). Subcellular
localization of MEK and ERK-A novel nuclear translocation signal (NTS)
paves a way to the nucleus. Mol
Cell Endocrinol. In press.
http://www.sciencedirect.com/science?_ob=ArticleURL&...
INT - Cassinelli G, Favini E, Degl'Innocenti D, Salvi A, De Petro G, Pierotti
MA, Zunino F, Borrello MG, Lanzi C.RET/PTC1. gDriven neoplastic transformation and
proinvasive phenotype of human thyrocytes involve Met induction and
beta-catenin nuclear translocation". Neoplasia. 2009 Jan;11(1):10-21.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2606114
GU - B. He, C. Macdonald, I. Ounis, J. Peng, and R.L.T.
Santos. University of Glasgow at TREC 2008: "Experiments in Blog,
Enterprise, and Relevance Feedback Tracks with Terrier". In
Proceedings of the Text Retrieval Conference (TREC) 2008. (Refereed
Conference)
http://trec.nist.gov/pubs/trec17/papers/uglasgow.blog.ent.rf.rev.pdf
GU - Rainer Breitling, David Gilbert, Monika Heiner, Richard
Orton (2008). "A structured approach for the engineering of
biochemical network models, illustrated for signalling pathways".
Briefings in Bioinformatics, 2008 9(5):404-42
http://bib.oxfordjournals.org/cgi/content/..
GU / UBRUN - Robin Donaldson and David Gilbert (2008). "A Model
Checking Approach to the Parameter Estimation of Biochemical Pathways".
In proceedings CMSB 2008 (Computational Methods in Systems Biology).
Heiner, Monika; Uhrmacher, Adelinde M. (Eds.) LNCS 5307/2008, pp269-287.
https://commerce.metapress.com/content/..
CSIC - Casar B., Pinto A., and Crespo P. "Essential role
of ERK dimers in the activation of cytoplasmic but not nuclear
substrates by ERK-scaffold complexes".
Mol. Cell, 31, 708-721. (2008).
http://linkinghub.elsevier.com/retrieve/pii/S1097276508005741
CSIC - González J.M., Navarro A., Casar B., Crespo P., and Andrés
V. "Fast regulation of
AP-1 activity through interaction of lamin A/C, ERK 1/2 and c-Fos at the
nuclear envelope". J.
Cell Biol. 183, 653-666. (2008).
http://digital.csic.es/bitstream/10261/12626/..
CSIC - Casar B., Arozarena I., Sanz-Moreno V., Pinto A., Agudo-Ibáñez
L., Marais R., Lewis R.E., Berciano M.T. and Crespo P. "Ras
subcellular localization defines ERKs substrate specificity though
distinct utilization of scaffold proteins". Mol. Cell. Biol., 29,
1338-1353. (2009).
http://mcb.asm.org/cgi/content/abstract/MCB.01359-08v1
CSIC - Casar B., Pinto A., and Crespo P. "ERK dimers
and scaffold proteins: unexpected partners for a forgotten (cytoplasmic)
task". Cell Cycle, 8,
1007-1013. (2009).
http://www.labmeeting.com/paper/28811025/.......
CSIC - Calvo F., and Crespo P. "Structural
and spatial determinants regulating TC-21 activation by RasGRF family
Nucleotide Exchange Factors". Mol. Biol. Cell, In press
http://www.molbiolcell.org/cgi/content/abstract/E09-03-0212v1
WIS - Amit, I., Citri, A., Shay, T., Lu, Y., Katz, M.,
Zhang, F., Tarcic, G., Siwak, D., Lahad, J., Jacob-Hirsch, J., et al.
(2007). A module of negative feedback regulators defines growth
factor signaling. Nat Genet 39, 503-512.
www.nature.com/ng/journal/v39/n4/full/ng1987.html
WIS - Amit, I., Wides, R., and Yarden, Y. (2007). Evolvable signaling
networks of receptor tyrosine kinases: relevance of robustness to
malignancy and to cancer therapy. Mol Syst Biol 3, 151
http://www.nature.com/msb/journal/v3/n1/full/msb4100195.html
WIS - Katz, M., Amit, I., Citri, A., Shay, T., Carvalho, S., Lavi, S.,
Milanezi, F., Lyass, L., Amariglio, N., Jacob-Hirsch, J., et al. (2007).
A reciprocal tensin-3-cten switch mediates EGF-driven mammary cell
migration. Nat Cell Biol 9, 961-969.
http://www.nature.com/ncb/journal/v9/n8/abs/ncb1622.html
WIS - Shaul Y.D., and Seger, R. (2007) The MEK/ERK cascade: from
signaling specificity to diverse functions. Biochim Biophys Acta. 1773, 1213-1226.
http://www.ncbi.nlm.nih.gov/pubmed/.........
WIS - Chuderland,
D.,
Marmor, G., Shainskaya, A., and Seger,
R.
(2008) Calcium-mediated interactions regulate the subcellular
localization of extracellular signal-regulated kinases (ERKs). J.
Biol. Chem. 283, 11176-11188.
http://www.jbc.org/cgi/content/full/283/17/11176
WIS - Identification of a novel general nuclear translocation signal (NTS), Chuderland,
D., and Seger, R. (2007),). Mol Cell 31,
850-861.
http://linkinghub.elsevier.com/retrieve/pii/S1097276508005431
CSIC - Casar B., Pinto A., and Crespo P. "Essential
role of ERK dimers for the activation of cytoplasmic but not nuclear
substrates by ERK-scaffold complexes". Mol. Cell. Under final
revision
http://www.sciencedirect.com/science?_ob=M
INT -.Negri T, Bozzi F, Conca E, Brich S, Gronchi A, Bertulli R, Fumagalli
E, Pierotti MA, Tamborini E, Pilotti S. "Oncogenic and
ligand-dependent activation of KIT/PDGFRA in surgical samples of
imatinib-treated gastrointestinal stromal tumours (GISTs)".
Accepted with revision in Journal of Pathology
http://www3.interscience.wiley.com/user/........
INT - Borrello MG, Degl'innocenti D, Pierotti MA. Inflammation
and cancer: "The oncogene-driven connection". Cancer Lett.
2008 in press
http://www.ncbi.nlm.nih.gov/pubmed/18502035
GU - Richard Orton, Oliver Sturm, Amelie Gormand, Walter Kolch and David
Gilbert (2008). "Computational modelling reveals feedback
redundancy within the EGFR/ERK signalling pathway". IET
Systems Biology Vol. 2, No. 4, pp. 173 - 183.
(RJ)
http://ieeexplore.ieee.org/Xplore/..........
GU - Xuan Liu, Jipu Jiang, Oluwafemi Ajayi, Xu Gu, David
Gilbert, Richard Sinnott (2008). BioNessieG – "A Grid
Enabled Biochemical Networks Simulation Environment". Accepted for
HealthGrid 2008. In Studies
in Health Technology and Informatics IOS Press, 2008, 138: 147-157. Global
Healthgrid: e-Science Meets Biomedical Informatics - Proceedings of
HealthGrid 2008. Edited by Tony Solomonides, Jonathan C.
Silverstein, Joel Saltz, Yannick Legre, Mary Kratz, Ian Foster, Vincent
Breton, J. Robert Beck (Refereed Conference)
http://www.dcs.gla.ac.uk/~drg/publications/conferences/BioNessieG.pdf
WIS
- Paper: Chuderland, D., Konson, A., and Seger, R. (2008) "Identification and characterization of a general nuclear
translocation signal in signaling proteins". Mol Cell.
31,
850-861.
http://www.ncbi.nlm.nih.gov/pubmed/18760948
WIS - Zehorai E, Yao Z, Plotnikov A, Seger R. (2009). Subcellular
localization of MEK and ERK-A novel nuclear translocation signal (NTS)
paves a way to the nucleus. Mol
Cell Endocrinol. In press.
http://www.sciencedirect.com/science?_ob=A......
INT - Cassinelli G, Favini E, Degl'Innocenti D, Salvi A, De Petro G, Pierotti
MA, Zunino F, Borrello MG, Lanzi C.RET/PTC1. "Driven neoplastic transformation and
proinvasive phenotype of human thyrocytes involve Met induction and
beta-catenin nuclear translocation". Neoplasia. 2009 Jan;11(1):10-21.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2606114
GU - B. He, C. Macdonald, I. Ounis, J. Peng, and R.L.T.
Santos. University of Glasgow at TREC 2008: "Experiments in Blog,
Enterprise, and Relevance Feedback Tracks with Terrier". In
Proceedings of the Text Retrieval Conference (TREC) 2008. (Refereed
Conference)
http://trec.nist.gov/pubs/trec17/papers/uglasgow.blog.ent.rf.rev.pdf
GU - Rainer Breitling, David Gilbert, Monika Heiner, Richard
Orton (2008). "A structured approach for the engineering of
biochemical network models, illustrated for signalling pathways".
Briefings in Bioinformatics, 2008 9(5):404-42
http://bib.oxfordjournals.org/cgi/content....
GU / UBRUN - Robin Donaldson and David Gilbert (2008). "A Model
Checking Approach to the Parameter Estimation of Biochemical Pathways".
In proceedings CMSB 2008 (Computational Methods in Systems Biology).
Heiner, Monika; Uhrmacher, Adelinde M. (Eds.) LNCS 5307/2008, pp269-287.
https://commerce.metapress.com.......
CSIC - Casar B., Pinto A., and Crespo P. "Essential role
of ERK dimers in the activation of cytoplasmic but not nuclear
substrates by ERK-scaffold complexes".
Mol. Cell, 31, 708-721. (2008).
http://linkinghub.elsevier.com/retrieve/pii/S1097276508005741
CSIC - González J.M., Navarro A., Casar B., Crespo P., and Andrés
V. "Fast regulation of
AP-1 activity through interaction of lamin A/C, ERK 1/2 and c-Fos at the
nuclear envelope". J.
Cell Biol. 183, 653-666. (2008).
http://digital.csic.es/bitstream/10261/1262....
CSIC - Casar B., Arozarena I., Sanz-Moreno V., Pinto A., Agudo-Ibáñez
L., Marais R., Lewis R.E., Berciano M.T. and Crespo P. "Ras
subcellular localization defines ERKs substrate specificity though
distinct utilization of scaffold proteins". Mol. Cell. Biol., 29,
1338-1353. (2009).
http://mcb.asm.org/cgi/content/abstract/MCB.01359-08v1
CSIC - Casar B., Pinto A., and Crespo P. "ERK dimers
and scaffold proteins: unexpected partners for a forgotten (cytoplasmic)
task". Cell Cycle, 8,
1007-1013. (2009).
http://www.labmeeting.com/paper/28811025..
CSIC - Calvo F., and Crespo P. "Structural
and spatial determinants regulating TC-21 activation by RasGRF family
Nucleotide Exchange Factors". Mol. Biol. Cell, In press
http://www.molbiolcell.org/cgi/content/abstract/E09-03-0212v1
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