Roberta Bosotti
Socio Ordinario
Ricercatore
Contact Information
RESEARCH AREA
biological data integration,comparative genomics,machine learning,sequence analysis,system biology
RESEARCH ACTIVITY
Bioinformatics, Molecular Biology, NGS and microarray data analysis, Pathway Analysis, Data Mining, Comparative and functional genomics, System Biology, Drug Discovery, Oncology
SELECTED PUBLICATIONS
A single-cell analysis of breast cancer cell lines to study tumour heterogeneity and drug response.
Gambardella G, Viscido G, Tumaini B, Isacchi A, Bosotti R, di Bernardo D.
Nat Commun. 2022 Mar 31;13(1):1714. doi: 10.1038/s41467-022-29358-6.
Mining potentially actionable kinase gene fusions in cancer cell lines with the KuNG FU database.
Somaschini A, Di Bella S, Cusi C, Raddrizzani L, Leone A, Carapezza G, Mazza T, Isacchi A, Bosotti R.
Sci Data. (2020)
A benchmarking of pipelines for detecting ncRNAs from RNA-Seq data.
Di Bella S, La Ferlita A, Carapezza G, Alaimo S, Isacchi A, Ferro A, Pulvirenti A, Bosotti R.
Brief Bioinform. (2020)
Carapezza G, Cusi C, Rizzo E, Raddrizzani L, Di Bella S, Somaschini A, Leone A, Lupi R, Mutarelli M, Nigro V, di Bernardo D, Magni P, Isacchi A, Bosotti R.
Comprehensive kinome NGS targeted expression profiling by KING-REX.
BMC Genomics. (2019)
Ukmar G, Melloni GEM, Raddrizzani L, Rossi P, Di Bella S, Pirchio MR, Vescovi M, Leone A, Callari M, Cesarini M, Somaschini A, Della Vedova G, Daidone MG, Pettenella M, Isacchi A, Bosotti R.
PATRI, a Genomics Data Integration Tool for Biomarker Discovery.
Biomed Res Int. (2018)
Magnaghi P, Salom B, Cozzi L, Amboldi N, Ballinari D, Tamborini E, Gasparri F, Montagnoli A, Raddrizzani L, Somaschini A, Bosotti R, Orrenius C, Bozzi F, Pilotti S, Galvani A, Sommer J, Stacchiotti S, Isacchi A.
Afatinib is a new therapeutic approach in chordoma with a unique ability to target EGFR and Brachyury.
Mol Cancer Ther. (2017)
Milione M, Ardini E, Christiansen J, Valtorta E, Veronese S, Bosotti R, Pellegrinelli A, Testi A, Pietrantonio F, Fucà G, Wei G, Murphy D, Siena S, Isacchi A, De Braud F.
Identification and characterization of a novel SCYL3-NTRK1 rearrangement in a colorectal cancer patient.
Oncotarget (2017)
Bosotti Roberta, Magnaghi Paola, Di Bella Sebastiano, Cozzi Liviana, Cusi Carlo, Bozzi Fabio, Beltrami Nicola, Carapezza Giovanni, Ballinari Dario, Amboldi Nadia, Lupi Rosita, Somaschini Alessio, Raddrizzani Laura, Salom Barbara, Galvani Arturo, Stacchiotti Silvia, Tamborini Elena, Isacchi Antonella.
Establishment and genomic characterization of the new chordoma cell line Chor-IN-1.
Sci Rep. (2017)
Angelo Nuzzo, Giovanni Carapezza, Sebastiano Di Bella, Alfredo Pulvirenti, Antonella Isacchi and Roberta Bosotti
KAOS: a new automated computational method for the identification of overexpressed genes
BMC Bioinformatics (2016)
Carrella D, Manni I, Tumaini B, Dattilo R, Papaccio F, Mutarelli M, Sirci F, Amoreo CA, Mottolese M, Iezzi M, Ciolli L, Aria V, Bosotti R, Isacchi A, Loreni F, Bardelli A, Avvedimento VE, di Bernardo D, Cardone L
Computational drugs repositioning identifies inhibitors of oncogenic PI3K/AKT/P70S6K-dependent pathways among FDA-approved compounds
Oncotarget (2016)
Ardini E, Menichincheri M, Banfi P, Bosotti R, De Ponti C, Pulci R, Ballinari D, Ciomei M, Texido G, Degrassi A, Avanzi N, Amboldi N, Saccardo MB, Casero D, Orsini P, Bandiera T, Mologni L, Anderson D, Wei G, Harris J, Vernier JM, Li G, Felder E, Donati D, Isacchi A, Pesenti E, Magnaghi P and Galvani A
Entrectinib, a Pan-TRK, ROS1 and ALK Inhibitor with Activity in Multiple Molecularly Defined Cancer Indications
Mol Cancer Ther, Published OnlineFirst March 3, 2016 (2016)
doi:10.1158/1535-7163.MCT-15-0758
Amatu A, Somaschini A, Cerea G, Bosotti R, Valtorta E, Buonandi P, Marrapese G, Veronese S, Luo D, Hornby Z, Multani P, Murphy D, Shoemaker R, Lauricella C, Giannetta L, Maiolani M, Vanzulli A, Ardini E, Galvani A, Isacchi A, Sartore-Bianchi A, Siena S.
Novel CAD-ALK gene rearrangement is drugable by entrectinib in colorectal cancer
Br J Cancer 113(12):1730-4 (2015)
doi: 10.1038/bjc.2015.401
Sartore-Bianchi A, Ardini E, Bosotti R, Amatu A, Valtorta E, Somaschini A, Raddrizzani L, Palmeri L, Banfi P, Bonazzina E, Misale S, Marrapese G, Leone A, Alzani R, Luo D, Hornby Z, Lim J, Veronese S, Vanzulli A, Bardelli A, Martignoni M, Davite C, Galvani A, Isacchi A, Siena S.
Sensitivity to Entrectinib Associated With a Novel LMNA-NTRK1 Gene Fusion in Metastatic Colorectal Cancer
J Natl Cancer Inst. 108(1) (2015)
doi: 10.1093/jnci/djv306
Facchiano A, Angelini C, Bosotti R, Guffanti A, Marabotti A, Marangoni R, Pascarella S, Romano P, Zanzoni A and Helmer-Citterich M
Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics
BMC Bioinformatics, 16(Suppl 9):51 (2015)
ISSN: 1471-2105
Ardini E, Bosotti R, Borgia AL, De Ponti C, Somaschini A, Cammarota R, Amboldi N, Raddrizzani L, Milani A, Magnaghi P, Ballinari D, Casero D, Gasparri F, Banfi P, Avanzi N, Saccardo MB, Alzani R, Bandiera T*, Felder E, Donati D, Pesenti E, Sartore-Bianchi A, Gambacorta M, Pierotti MA, Siena S, Veronese S, Galvani A and Isacchi A
The TPM3-NTRK1 rearrangement is a recurring event in colorectal carcinoma and is associated with tumor sensitivity to TRKA kinase inhibition
Mol Oncol. 8(8):1495-507 (2014)
Cell line identity finding by fingerprinting, an optimized resource for short tandem repeat profile authentication.
Somaschini A, Amboldi N, Nuzzo A, Scacheri E, Ukmar G, Ballinari D, Malyszko J, Raddrizzani L, Landonio A, Gasparri F, Galvani A, Isacchi A and Bosotti R.
Genet Test Mol Biomarkers 17(3):254-9 (2013)
Transcriptional analysis of the Aurora inhibitor Danusertib leading to biomarker identification in TP53 wild type cells.
Bosotti R, Carpinelli P, Healy S, Locatelli G, Cappella P, Lanfrancone L, Calogero R, Moll J and Isacchi. A.
Gene, 494(2):202-8 (2012)
GDF15 as a Novel Biomarker for Monitoring Danusertib Activity.
Carpinelli P, Cappella P, Losa M, Croci V, Bosotti R, Lanfrancone L, Isacchi A and Moll J.
J Mol Biomark Diagn, S2:001 (2011)
Identification of candidate substrates for Poly(ADP-ribose) polymerase-2 (PARP2) in the absence of DNA damage using high-density protein microarrays. Troiani S, Lupi R, Perego R, Re Depaolini S, Thieffine S, Bosotti R, Rusconi L.
FEBS J, 278(19):3676-87 (2011)
Summarizing Probe Intensities of Affymetrix GeneChip 3' Expression Arrays Taking into Account Day-to-Day Variability.
Magni P, Simeone A, Healy S, Isacchi A, Bosotti R.
IEEE/ACM Trans Comput Biol Bioinform, 8(5):1425-30 (2011)
Abcg2 overexpression represents a novel mechanism for acquired resistance to the multi-kinase inhibitor Danusertib in BCR-ABL-positive cells in vitro.
Balabanov S, Gontarewicz A, Keller G, Raddrizzani L, Braig M, Bosotti R, Moll J, Jost E, Rhoe I, Bokemeyer C, Holyoake TL and Brümmendorf TH.
PLoS One 6(4):e19164 (2011)
Discovery of drug mode of action and drug repositioning from transcriptional responses
Iorio F, Bosotti R, Scacheri E, Belcastro V, Mthbaokar P, Ferriero R, Murino L, Tagliaferri R, Brunetti-Pierri N, Isacchi A and di Bernardo D. Proc Natl Acad Sci U S A. 107(33):14621-6 (2010)
Summarizing Probe Intensities of Affymetrix GeneChip 3' Expression Arrays Taking into Account Day-to-Day Variability.
Magni P, Simeone A, Healy S, Isacchi A and Bosotti R.
IEEE/ACM Transactions on Computational Biology and Bioinformatics (2010)
Transcriptional analysis of an E2F-dependent gene signature as a biomarker of activity of the Cdk inhibitor PHA-793887 in tumor and skin biopsies from a Phase I clinical study
Locatelli § G, Bosotti § R, Ciomei M, Brasca MG, Calogero R, Mercurio C, Fiorentini F, Bertolotti M, Scacheri E, Scaburri A, Galvani A, Pesenti E, De Baere T, Soria JC, Lazar V and Isacchi A
Mol Cancer Ther; 9(5); 1265-73 (2010)
§ The authors equally contributed to the work
First Cdc7 Kinase Inhibitors: Pyrrolopyridinones as Antitumor Agents. 1. Synthesis and Structure-Activity Relationships
Vanotti E, Amici R, Bargiotti A, Berthelsen J, Bosotti R, Ciavolella A, Cirla A, Cristiani C, D’Alessio R, Forte B, Martina K, Menichincheri M, Molinari A, Montagnoli A, Orsini P, Pillan A, Roletto F, Scolaro A, Tibolla M, Valsasina B, Volpi D, Santocanale C
Journal of medicinal chemistry: 51(3):487-501 (2008)
Cross platform microarray analysis for robust identification of differentially expressed genes
Bosotti R, Locatelli G, Healy S, Scacheri E, Sartori L, Mercurio C, Calogero R, Isacchi A
BMC Bioinformatics; 8(Suppl 1): (2007)
PoInTree: a polar and interactive phylogenetic tree
Carreras M, Gianti E, Sartori L, Plyte S, Isacchi A and Bosotti R
Genomics, Proteomics & Bioinformatics:3(1):58-60 (2005)
Sequence and structural analysis of kinase ATP pocket residues
Vulpetti A and Bosotti R
Farmaco;59(10):759-65 (2004)
Drf1, a novel regulatory subunit for human Cdc7 kinase
Montagnoli A, Bosotti R, Villa F, Rialland M, Brotherton D, Mercurio C, Berthelsen J, Santocanale C.
EMBO J.;21(12):3171-81(2002).
Detection of a polymorphism in exon 8 of the human CD86 gene
Delneste Y., Bosotti R., Magistrelli G., Bonnefoy J.Y. and Gauchat J.F.
Immunogenetics 51 (8-9): 762-3 (2000)
A novel domain in PIK-related kinases: the FAT domain
Bosotti R., Isacchi A. and Sonnhammer E.L.
Trends Biochem Sci. 25(5), 225-7 (2000)
Activation of ZAP-70 tyrosine kinase activity due to a structural rearrangement induced by tyrosine phosphorylation and/or ITAM binding
Visco C., Magistrelli G., Bosotti R., Perego R., Rusconi L., Toma S., Zamai M., Acuto O. and Isacchi A.
Biochemistry 39, 2784-2791 (2000)
Role of the Src homology 2 domains and interdomain regions in ZAP-70 phosphorylation and enzymatic activity
Magistrelli G., Bosotti R., Valsasina B., Visco C., Perego R., Toma S., Acuto O. and Isacchi A.
Eur. J. Biochem. 266, 1166-1173 (1999)
Gambardella G, Viscido G, Tumaini B, Isacchi A, Bosotti R, di Bernardo D.
Nat Commun. 2022 Mar 31;13(1):1714. doi: 10.1038/s41467-022-29358-6.
Mining potentially actionable kinase gene fusions in cancer cell lines with the KuNG FU database.
Somaschini A, Di Bella S, Cusi C, Raddrizzani L, Leone A, Carapezza G, Mazza T, Isacchi A, Bosotti R.
Sci Data. (2020)
A benchmarking of pipelines for detecting ncRNAs from RNA-Seq data.
Di Bella S, La Ferlita A, Carapezza G, Alaimo S, Isacchi A, Ferro A, Pulvirenti A, Bosotti R.
Brief Bioinform. (2020)
Carapezza G, Cusi C, Rizzo E, Raddrizzani L, Di Bella S, Somaschini A, Leone A, Lupi R, Mutarelli M, Nigro V, di Bernardo D, Magni P, Isacchi A, Bosotti R.
Comprehensive kinome NGS targeted expression profiling by KING-REX.
BMC Genomics. (2019)
Ukmar G, Melloni GEM, Raddrizzani L, Rossi P, Di Bella S, Pirchio MR, Vescovi M, Leone A, Callari M, Cesarini M, Somaschini A, Della Vedova G, Daidone MG, Pettenella M, Isacchi A, Bosotti R.
PATRI, a Genomics Data Integration Tool for Biomarker Discovery.
Biomed Res Int. (2018)
Magnaghi P, Salom B, Cozzi L, Amboldi N, Ballinari D, Tamborini E, Gasparri F, Montagnoli A, Raddrizzani L, Somaschini A, Bosotti R, Orrenius C, Bozzi F, Pilotti S, Galvani A, Sommer J, Stacchiotti S, Isacchi A.
Afatinib is a new therapeutic approach in chordoma with a unique ability to target EGFR and Brachyury.
Mol Cancer Ther. (2017)
Milione M, Ardini E, Christiansen J, Valtorta E, Veronese S, Bosotti R, Pellegrinelli A, Testi A, Pietrantonio F, Fucà G, Wei G, Murphy D, Siena S, Isacchi A, De Braud F.
Identification and characterization of a novel SCYL3-NTRK1 rearrangement in a colorectal cancer patient.
Oncotarget (2017)
Bosotti Roberta, Magnaghi Paola, Di Bella Sebastiano, Cozzi Liviana, Cusi Carlo, Bozzi Fabio, Beltrami Nicola, Carapezza Giovanni, Ballinari Dario, Amboldi Nadia, Lupi Rosita, Somaschini Alessio, Raddrizzani Laura, Salom Barbara, Galvani Arturo, Stacchiotti Silvia, Tamborini Elena, Isacchi Antonella.
Establishment and genomic characterization of the new chordoma cell line Chor-IN-1.
Sci Rep. (2017)
Angelo Nuzzo, Giovanni Carapezza, Sebastiano Di Bella, Alfredo Pulvirenti, Antonella Isacchi and Roberta Bosotti
KAOS: a new automated computational method for the identification of overexpressed genes
BMC Bioinformatics (2016)
Carrella D, Manni I, Tumaini B, Dattilo R, Papaccio F, Mutarelli M, Sirci F, Amoreo CA, Mottolese M, Iezzi M, Ciolli L, Aria V, Bosotti R, Isacchi A, Loreni F, Bardelli A, Avvedimento VE, di Bernardo D, Cardone L
Computational drugs repositioning identifies inhibitors of oncogenic PI3K/AKT/P70S6K-dependent pathways among FDA-approved compounds
Oncotarget (2016)
Ardini E, Menichincheri M, Banfi P, Bosotti R, De Ponti C, Pulci R, Ballinari D, Ciomei M, Texido G, Degrassi A, Avanzi N, Amboldi N, Saccardo MB, Casero D, Orsini P, Bandiera T, Mologni L, Anderson D, Wei G, Harris J, Vernier JM, Li G, Felder E, Donati D, Isacchi A, Pesenti E, Magnaghi P and Galvani A
Entrectinib, a Pan-TRK, ROS1 and ALK Inhibitor with Activity in Multiple Molecularly Defined Cancer Indications
Mol Cancer Ther, Published OnlineFirst March 3, 2016 (2016)
doi:10.1158/1535-7163.MCT-15-0758
Amatu A, Somaschini A, Cerea G, Bosotti R, Valtorta E, Buonandi P, Marrapese G, Veronese S, Luo D, Hornby Z, Multani P, Murphy D, Shoemaker R, Lauricella C, Giannetta L, Maiolani M, Vanzulli A, Ardini E, Galvani A, Isacchi A, Sartore-Bianchi A, Siena S.
Novel CAD-ALK gene rearrangement is drugable by entrectinib in colorectal cancer
Br J Cancer 113(12):1730-4 (2015)
doi: 10.1038/bjc.2015.401
Sartore-Bianchi A, Ardini E, Bosotti R, Amatu A, Valtorta E, Somaschini A, Raddrizzani L, Palmeri L, Banfi P, Bonazzina E, Misale S, Marrapese G, Leone A, Alzani R, Luo D, Hornby Z, Lim J, Veronese S, Vanzulli A, Bardelli A, Martignoni M, Davite C, Galvani A, Isacchi A, Siena S.
Sensitivity to Entrectinib Associated With a Novel LMNA-NTRK1 Gene Fusion in Metastatic Colorectal Cancer
J Natl Cancer Inst. 108(1) (2015)
doi: 10.1093/jnci/djv306
Facchiano A, Angelini C, Bosotti R, Guffanti A, Marabotti A, Marangoni R, Pascarella S, Romano P, Zanzoni A and Helmer-Citterich M
Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics
BMC Bioinformatics, 16(Suppl 9):51 (2015)
ISSN: 1471-2105
Ardini E, Bosotti R, Borgia AL, De Ponti C, Somaschini A, Cammarota R, Amboldi N, Raddrizzani L, Milani A, Magnaghi P, Ballinari D, Casero D, Gasparri F, Banfi P, Avanzi N, Saccardo MB, Alzani R, Bandiera T*, Felder E, Donati D, Pesenti E, Sartore-Bianchi A, Gambacorta M, Pierotti MA, Siena S, Veronese S, Galvani A and Isacchi A
The TPM3-NTRK1 rearrangement is a recurring event in colorectal carcinoma and is associated with tumor sensitivity to TRKA kinase inhibition
Mol Oncol. 8(8):1495-507 (2014)
Cell line identity finding by fingerprinting, an optimized resource for short tandem repeat profile authentication.
Somaschini A, Amboldi N, Nuzzo A, Scacheri E, Ukmar G, Ballinari D, Malyszko J, Raddrizzani L, Landonio A, Gasparri F, Galvani A, Isacchi A and Bosotti R.
Genet Test Mol Biomarkers 17(3):254-9 (2013)
Transcriptional analysis of the Aurora inhibitor Danusertib leading to biomarker identification in TP53 wild type cells.
Bosotti R, Carpinelli P, Healy S, Locatelli G, Cappella P, Lanfrancone L, Calogero R, Moll J and Isacchi. A.
Gene, 494(2):202-8 (2012)
GDF15 as a Novel Biomarker for Monitoring Danusertib Activity.
Carpinelli P, Cappella P, Losa M, Croci V, Bosotti R, Lanfrancone L, Isacchi A and Moll J.
J Mol Biomark Diagn, S2:001 (2011)
Identification of candidate substrates for Poly(ADP-ribose) polymerase-2 (PARP2) in the absence of DNA damage using high-density protein microarrays. Troiani S, Lupi R, Perego R, Re Depaolini S, Thieffine S, Bosotti R, Rusconi L.
FEBS J, 278(19):3676-87 (2011)
Summarizing Probe Intensities of Affymetrix GeneChip 3' Expression Arrays Taking into Account Day-to-Day Variability.
Magni P, Simeone A, Healy S, Isacchi A, Bosotti R.
IEEE/ACM Trans Comput Biol Bioinform, 8(5):1425-30 (2011)
Abcg2 overexpression represents a novel mechanism for acquired resistance to the multi-kinase inhibitor Danusertib in BCR-ABL-positive cells in vitro.
Balabanov S, Gontarewicz A, Keller G, Raddrizzani L, Braig M, Bosotti R, Moll J, Jost E, Rhoe I, Bokemeyer C, Holyoake TL and Brümmendorf TH.
PLoS One 6(4):e19164 (2011)
Discovery of drug mode of action and drug repositioning from transcriptional responses
Iorio F, Bosotti R, Scacheri E, Belcastro V, Mthbaokar P, Ferriero R, Murino L, Tagliaferri R, Brunetti-Pierri N, Isacchi A and di Bernardo D. Proc Natl Acad Sci U S A. 107(33):14621-6 (2010)
Summarizing Probe Intensities of Affymetrix GeneChip 3' Expression Arrays Taking into Account Day-to-Day Variability.
Magni P, Simeone A, Healy S, Isacchi A and Bosotti R.
IEEE/ACM Transactions on Computational Biology and Bioinformatics (2010)
Transcriptional analysis of an E2F-dependent gene signature as a biomarker of activity of the Cdk inhibitor PHA-793887 in tumor and skin biopsies from a Phase I clinical study
Locatelli § G, Bosotti § R, Ciomei M, Brasca MG, Calogero R, Mercurio C, Fiorentini F, Bertolotti M, Scacheri E, Scaburri A, Galvani A, Pesenti E, De Baere T, Soria JC, Lazar V and Isacchi A
Mol Cancer Ther; 9(5); 1265-73 (2010)
§ The authors equally contributed to the work
First Cdc7 Kinase Inhibitors: Pyrrolopyridinones as Antitumor Agents. 1. Synthesis and Structure-Activity Relationships
Vanotti E, Amici R, Bargiotti A, Berthelsen J, Bosotti R, Ciavolella A, Cirla A, Cristiani C, D’Alessio R, Forte B, Martina K, Menichincheri M, Molinari A, Montagnoli A, Orsini P, Pillan A, Roletto F, Scolaro A, Tibolla M, Valsasina B, Volpi D, Santocanale C
Journal of medicinal chemistry: 51(3):487-501 (2008)
Cross platform microarray analysis for robust identification of differentially expressed genes
Bosotti R, Locatelli G, Healy S, Scacheri E, Sartori L, Mercurio C, Calogero R, Isacchi A
BMC Bioinformatics; 8(Suppl 1): (2007)
PoInTree: a polar and interactive phylogenetic tree
Carreras M, Gianti E, Sartori L, Plyte S, Isacchi A and Bosotti R
Genomics, Proteomics & Bioinformatics:3(1):58-60 (2005)
Sequence and structural analysis of kinase ATP pocket residues
Vulpetti A and Bosotti R
Farmaco;59(10):759-65 (2004)
Drf1, a novel regulatory subunit for human Cdc7 kinase
Montagnoli A, Bosotti R, Villa F, Rialland M, Brotherton D, Mercurio C, Berthelsen J, Santocanale C.
EMBO J.;21(12):3171-81(2002).
Detection of a polymorphism in exon 8 of the human CD86 gene
Delneste Y., Bosotti R., Magistrelli G., Bonnefoy J.Y. and Gauchat J.F.
Immunogenetics 51 (8-9): 762-3 (2000)
A novel domain in PIK-related kinases: the FAT domain
Bosotti R., Isacchi A. and Sonnhammer E.L.
Trends Biochem Sci. 25(5), 225-7 (2000)
Activation of ZAP-70 tyrosine kinase activity due to a structural rearrangement induced by tyrosine phosphorylation and/or ITAM binding
Visco C., Magistrelli G., Bosotti R., Perego R., Rusconi L., Toma S., Zamai M., Acuto O. and Isacchi A.
Biochemistry 39, 2784-2791 (2000)
Role of the Src homology 2 domains and interdomain regions in ZAP-70 phosphorylation and enzymatic activity
Magistrelli G., Bosotti R., Valsasina B., Visco C., Perego R., Toma S., Acuto O. and Isacchi A.
Eur. J. Biochem. 266, 1166-1173 (1999)
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