International journal papers with external peer review

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1 International journal papers with external peer review 1. Marini S, Trifoglio E, Barbarini N, Sambo F, Di Camillo B, Malovini A, Manfrini M, Cobelli C, Bellazzi R. A Dynamic Bayesian Network model for long-term simulation of clinical complications in type 1 diabetes. J Biomed Inform Aug 28. pii: S (15) doi: /j.jbi Sanavia T, Finotello F, Di Camillo B. FunPat: function-based pattern analysis on RNA-seq time series. BMC Genomics. 2015, 16(Suppl 6):S2. 3. Pegolo S, Di Camillo B, Montesissa C, Cannizzo FT, Biolatti B, Bargelloni L. Toxicogenomic markers for corticosteroid treatment in beef cattle: integrated analysis of transcriptomic data. Food Chem Toxicol. 2015; 77: Sinigaglia A, Lavezzo E, Trevisan M, Sanavia T, Di Camillo B, Peta E, Scarpa M, Castagliuolo I, Guido M, Sarcognato S, Cappellesso R, Fassina A, Cardin R, Farinati F, Palù G, Barzon L. Changes in microrna expression during disease progression in patients with chronic viral hepatitis. Liver Int. 2015;35(4): Visentin S, Grumolato F, Nardelli GB, Di Camillo B, Grisan E, Cosmi E. Early origins of adult disease: low birth weight and vascular remodeling. Atherosclerosis. 2014;237(2): Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H, Xiao G, Li Y, Allen J, Zhong R, Chen B, Kim M, Wang T, Heiser LM, Realubit R, Mattioli M, Alvarez MJ, Shen Y; NCI-DREAM Community (Di Camillo B. within NCI-DREAM Community), Gallahan D, Singer D, Saez-Rodriguez J, Xie Y, Stolovitzky G, Califano A. A community computational challenge to predict the activity of pairs of compounds. Nat Biotechnol. 2014;32(12): Finotello F, Di Camillo B. Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis. Brief Funct Genomics 2015; 14(2): Fadista J, Vikman P, Ottosson Laakso E, Mollet I, Esguerra J, Taneera J, Storm P, Osmark P, Ladenvall C, Prasad, R, Hansson K, Finotello F, Ofori J, Krus U, Di Camillo B, Hansson O, Eliasson L, Rosengren A, Renström E, Wollheim CB, Groop L. Global genomic and transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism. PNAS 2014; 111(38): Nasso S, Hartler J, Trajanoski Z, Di Camillo B, Mechtlere K, Toffolo G. DSpectra:A 3-Dimensional Quantification Algorithm For LC-MS Labeled Profile Data. Journal of Proteomics 2014;112: Sambo F, Di Camillo B, Toffolo G, Cobelli C. Compression and fast retrieval of SNP data. Bioinformatics 2014, 30(21): Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-Ud-Din M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K; NCI DREAM Community (Di Camillo B. within NCI- DREAM Community), Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G. A community effort to assess and improve drug sensitivity prediction algorithms. Nat Biotechnol doi: /nbt Pag. 1 of 15

2 12. Sambo F, Malovini A, Sandholm N, Stavarachi M, Forsblom C, Mäkinen VP, Harjutsalo V, Lithovius R, Gordin D, Parkkonen M, Saraheimo M, Thorn LM, Tolonen N, Wadén J, He B, Osterholm AM, Tuomilehto J, Lajer M, Salem RM, McKnight AJ; The GENIE Consortium, Tarnow L, Panduru NM, Barbarini N, Di Camillo B, Toffolo GM, Tryggvason K, Bellazzi R, Cobelli C; The FinnDiane Study Group, Groop PH. Novel genetic susceptibility loci for diabetic end-stage renal disease identified through robust naive Bayes classification. Diabetologia Di Camillo B, Eduati F, Nair SK, Avogaro A, Toffolo GM. Leucine modulates dynamic phosphorylation events in insulin signaling pathway and enhances insulindependent glycogen synthesis in human skeletal muscle cells. BMC Cell Biol. 2014, 15(1): Finotello F, Lavezzo E, Bianco L, Barzon L, Mazzon P, Fontana P, Toppo S, Di Camillo B. Reducing bias in RNA sequencing data: a novel approach to compute counts. BMC Bioinformatics, BMC Bioinformatics 2013, 15(Suppl 1):S2014;15 Suppl 1:S7 15. Di Camillo B, Sambo F, Toffolo G, Cobelli C. ABACUS: an entropy based cumulative bivariate statistic robust to rare variants and different direction of genotype effect. Bioinformatics, 2014, 1(30): Online on November Lavezzo E, Toppo S, Franchin E, Di Camillo B, Finotello F, Falda M, Manganelli R, Palù G, Barzon L. Genomic comparative analysis and gene function prediction in infectious diseases: application to the investigation of a meningitis outbreak. BMC Infectious Diseases, 2013, 13(1): Tarca AL, Lauria M, Unger M, Bilal E, Boue S, Kumar Dey K, Hoeng J, Koeppl H, Martin F, Meyer P, Nandy P, Norel R, Peitsch M, Rice JJ, Romero R, Stolovitzky G, Talikka M, Xiang Y, Zechner C; IMPROVER DSC Collaborators (Di Camillo B. within IMPROVER DSC Collaborators). Strengths and limitations of microarraybased phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge. Bioinformatics. 2013, 29(22): Militello V, Lavezzo E, Costanzi G, Franchin E, Di Camillo B, Toppo S, Palù G, Barzon L. Accurate human papillomavirus genotyping by 454 pyrosequencing.clin Microbiol Infect, 2013 Mar 14. doi: / Zycinski G, Barla A, Squillario M, Sanavia T, Di Camillo B, Verri A. Knowledge Driven Variable Selection (KDVS): a new approach to enrichment analysis of gene signatures obtained from high-throughput data. Source Code Biol Med, 2013 ;8(1):2 20. Aghaeepour N, Finak G, FlowCAP Consortium, DREAM Consortium (Di Camillo B. within DREAM Consortium), Hoos H, Mosmann TR, Brinkman R, Gottardo R, Scheuermann RH. Critical assessment of automated flow cytometry data analysis techniques. Nat Methods, 2013; 10(3): Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Törönen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kaßner R, Seemayer S, Vicedo E, Schaefer C,

3 Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Björne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Škunca N, Supek F, Bošnjak M, Panov P, Džeroski S, Šmuc T, Kourmpetis YA, van Dijk AD, ter Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I. A large scale evaluation of computational protein function prediction. Nat Methods, 2013; 10(3): Falda M, Toppo S, Pescarolo A, Lavezzo E, Di Camillo B, Facchinetti A, Cilia E, Velasco R, Fontana P (2012). Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms. BMC Bioinformatics, vol. 13, 13 Suppl 4:S Sambo F, Trifoglio E, Di Camillo B, Toffolo G, Cobelli C. Bag of Naïve Bayes: biomarker selection and classification from Genome-Wide SNP data. BMC Bioinformatics, 2012, 13 Suppl 14:S Sambo F, Montes de Oca M A, Di Camillo B, Toffolo G, Stützle T. MORE: Mixed Optimization for Reverse Engineering. An application to modeling biological networks response via sparse systems of nonlinear differential equations. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2012, 9(5): Eduati F, De Las Rivas J, Di Camillo B, Toffolo G, Saez-Rodriguez J. Integrating literature-constrained and data-driven inference of signalling networks. Bioinformatics, 2012, 28(18): Trojani A, Di Camillo B, Tedeschi A, Lodola M, Montesano S, Ricci F, Vismara E, Greco A, Veronese S, Orlacchio A, Martino S, Colombo C, Mura MA, Nichelatti M, Colosimo A, Scarpati B, Montillo M, Morra E. Gene Expression Profiling Identifies ARSD as a New Marker of Disease Progression in Chronic Lymphocytic Leukemia. Cancer Biomarkers, 2012 vol. 11(1), p Giobbe GG, Zagallo M, Riello M, Serena E, Masi G, Barzon L, Di Camillo B, Elvassore N. Confined 3D microenvironment regulates early differentiation in human pluripotent stem cells. Biotechnol Bioeng, 2012 Jun 4. doi: /bit Di Camillo B, Irving BA, Schimke J, Sanavia T, Toffolo G, Cobelli C, Nair KS. Function-based discovery of significant transcriptional temporal patterns in insulin stimulated muscle cells. PLoS One, 2012;7(3):e Sanavia T, Aiolli F, Da San Martino G, Bisognin A, Di Camillo B. Improving biomarker list stability by integration of biological knowledge in the learning process. BMC Bioinformatics, 2012 Mar 28;13 Suppl 4:S Eduati F, Di Camillo B, Karbiener M, Scheideler M, Corà D, Caselle M, Toffolo G. Dynamic modeling of mirna-mediated feed forward loops. J Comput Biol, 2012 Feb;19(2): Di Camillo B, Sanavia T, Martini M, Jurman G, Sambo F, Barla A, Squillario M, Furlanello C, Toffolo G, Cobelli C. Effect of size and heterogeneity of samples on

4 biomarker discovery: synthetic and real data assessment. PLoS One, 2012;7(3):e Badaloni S, Di Camillo B, Sambo F. Qualitative Reasoning for Biological Network Inference from Systematic Perturbation Experiments. IEEE/ACM Trans Comput Biol Bioinform, 2012, 9(5): Martínez MR, Corradin A, Klein U, Álvareza MJ, Toffolo GM, Di Camillo B, Califano A, Stolovitzky GA. Quantitative modeling of the terminal differentiation of B cells and mechanisms of lymphomagenesis. Proc Natl Acad Sci, 2012, 109(7): Finotello F, Lavezzo E, Fontana P, Peruzzo D, Albiero A, Barzon L, Falda M, Di Camillo B, Toppo S. Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data. Brief Bioinform, (3): De Palo G, Eduati F, Zampieri M, Di Camillo B, Toffolo G, Altafini C. Adaptation as a genome-wide autoregulatory principle in the stress response of yeast. IET Systems Biology, 2011; vol. 5(4); p Di Camillo B., M Falda, G Toffolo, C Cobelli. SimBioNeT: A Simulator of Biological Network Topology. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2012; 9(2): Guerra S, Boscari F, Avogaro A, Di Camillo B., Sparacino G, De Kreutzenberg SV. Haemodynamics Assessed Via Approximate Entropy Analysis Of Impedance Cardiography Time Series: Effect Of Metabolic Syndrome. American Journal of Physiology, 2011, 301(2):H Corradin A, Di Camillo B, Ciminale V, Toffolo G, Cobelli C. Sensitivity analysis of retrovirus HTLV-1 transactivation. J Comput Biol, 2011; 18(2): Di Camillo B, Sanavia T, Iori E, Bronte V, Roncaglia E, Maran A, Avogaro A, Toffolo G, Cobelli C. The transcriptional response in human umbilical vein endothelial cells exposed to insulin: a dynamic gene expression approach. PLoS One, 2010; 5(12):e Eduati F, Corradin A, Di Camillo B, Toffolo G. A Boolean approach to linear prediction for signaling network modeling. PLoS One, 2010; 5(9): e Lavezzo E, Toppo S, Barzon L, Cobelli C, Di Camillo B, Finotello F, Franchin E, Peruzzo D, Toffolo GM, Trevisan M, Palù G. Draft genome sequences of two Neisseria meningitidis serogroup C clinical isolates. Journal of Bacteriology 2010; vol. 192 (19); p Bogner-Strauss Jg, Prokesch A, Sanchez-Cabo F, Rieder D, Hackl H, Duszka K, Krogsdam A, Di Camillo B., Walenta E, Klatzer A, Lass A, Pinent M, Wong Wc, Eisenhaber F, Trajanoski Z. Reconstruction of gene association network reveals a transmembrane protein required for adipogenesis and targeted by PPARgamma. Cellular and Molecular Life Sciences 2010; 67(23): Nasso S, Silvestri F, Tisiot F, Di Camillo B., Pietracaprina A, Toffolo G. An Optimized Data Structure for High Throughput 3D Proteomics Data: mzrtree,. Journal of Proteomics, 2010; 73(6): Di Camillo B, Toffolo G, Cobelli C. A Gene Network Simulator to Assess Reverse Engineering Algorithms. Ann N Y Acad Sci. 2009; 1158:

5 45. Di Camillo B, Toffolo G, S K Nair, Greenlund L J, Cobelli, C Significance analysis of microarray transcript levels in time series experiments. 2007, BMC Bioinformatics, vol. 8(Suppl 1) S1; p Di Camillo B, Sanchez-Cabo F, Toffolo G, Nair Sk, Trajanoski Z, Cobelli C. A quantization method based on threshold optimization for microarray short time series. 2005, BMC Bioinformatics, vol. 6; S Basu R, Di Camillo B., Toffolo G, Basu A, Shah P, Vella A, Rizza R, Cobelli C. Use of a Novel Triple-Tracer Approach to Assess Postprandial Glucose Metabolism. American Journal of Physiology: Endocrinology and Metabolism, 2003 Vol. 284; P. E55-E69 International congress papers with external peer review 1. Sambo F, Di Camillo B, Franzin A, Facchinetti A, Hakaste L, Kravic J, Fico G, Tuomilehto J, Groop L, Gabriel R, Tuomi T, Cobelli C. A Bayesian Network Analysis of the Probabilistic Relations between Risk Factors in the Predisposition to Type 2 Diabetes. In: Proc. of the 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC 2015). 2. Giaretta A, Di Camillo B, Barzon L, Toffolo G. Modeling HPV Early Promoter Regulation. In: Proc. of the 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC 2015). 3. Sambo F, Facchinetti A, Hakaste L, Kravic J, Di Camillo B, Fico G, Tuomilehto J, Groop L, Gabriel R, Tuomi T, Cobelli C. A Bayesian network for probabilistic reasoning and imputation of missing risk factors in type 2 diabetes. In: Proc. of the 15th Conference on Artificial Intelligence in Medicine (AIME 2015), in press. 4. Trojani A, Greco A, Tedeschi A, Lodola M, Di Camillo B, Ricci F, Turrini M, Varettoni M, Rattotti S, Morra E. Microarray demonstrates different gene expression profiling signatures between Waldenström macroglobulinemia and IgM monoclonal gammopathy of undetermined significance. Clin Lymphoma Myeloma Leuk, 2013 Apr;13(2): Zycinski G, Squillario M,, Barla A, Sanavia T, Verri A, Di Camillo B. A prior knowledge based machine learning approach for the identification of discriminant functional groups. European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning, Bruges Belgium, April Sambo F, Di Camillo B. Minimizing Time when Applying Bootstrap to Contingency Tables Analysis of Genome-Wide Data. In: Hamadi, Y., Schoenauer, M. (eds.) Learning and Intelligent Optimization. Lecture Notes in Computer Science. Springer Berlin / Heidelberg, Sambo F, Di Camillo B. Qualitative reasoning on systematic gene perturbation experiments. In: Computational Intelligence Methods for Bioinformatics and Biostatistics. Lecture Notes in Bioinformatics, vol Springer Berlin / Heidelberg, 2011.

6 8. Sambo F, Montes de Oca M A, Di Camillo B and Stützle T. On the difficulty of inferring gene regulatory networks: A study of the fitness landscape generated by relative squared error. In: Collet, P., Monmarché, N., Legrand, P., Schoenauer, M., Lutton, E. (eds.) Artificial Evolution, Lecture Notes in Computer Science, vol. 5975, pp Springer Berlin / Heidelberg, Corradin A, Di Camillo B, Rende F, Ciminale V, Toffolo GM, Cobelli C. Retrovirus HTLV-1 gene circuit: a potential oscillator for eukaryotes. Pac Symp Biocomput. 2010: Sambo F, Di Camillo B, Falda M, Toffolo G, Badaloni S. CNET: an algorithm for the inference of gene regulatory interactions from gene expression time series. In: Proceedings of the 14th Workshop on Intelligent Data Analysis in medicine and Pharmacology IDAMAP09, pp , Sambo F., Di Camillo B, Toffolo G. CNET: an algorithm for Reverse Engineering of Causal Gene Networks. In: Bioinformatics Methods for Biomedical Complex Systems Applications. 8th Workshop on Network Tools and Applications in Biology NETTAB2008. Varenna, Italy. May , pp , Di Camillo B. G.Toffolo, C.Cobelli. Function-Based Discovery Of Temporal Patterns In High-Throughput Genomic Studies. In proceedings of Foundations of Systems Biology and Engineering Stuttgart pg Book Chapters 1. Sambo F, Sanavia T, Di Camillo B. Integration of Genetic Variation as External Perturbation to Reverse Engineer Regulatory Networks from Gene Expression Data. In: de la Fuente A. Gene Network Inference: Verification of Methods for Systems Genetics Data. Springer-Verlag Berlin Heidelberg Di Camillo B, Toffolo G. Reverse Engineering of High-Throughput Genomic and Genetic Data. In: Carson E, Cobelli C. Modeling Methodology for Physiology and Medicine, Elsevier Inc. London Bellazzi R., Bicciato S., Cobelli C., Di Camillo B., Ferrazzi F., Magni P., Sacchi L., Toffolo G. Microarray data analysis: general concepts, gene selection, classification. In: Cerrutti S., Marchesi C. Advanced Methods of Biomedical Signal Processing. IEEE-EMBS, Pàtron (Italy) Bellazzi R., Bicciato S., Cobelli C., Di Camillo B., Ferrazzi F., Magni P., Sacchi L., Toffolo G. Microarray data analysis: gene regulatory networks In: Cerrutti S., Marchesi C. Advanced Methods of Biomedical Signal Processing. IEEE-EMBS, Pàtron (Italy) Di Camillo B, Castiglioni I, Sambo F, Gilardi M C, Toffolo G M. Methods for discovery and integration of genetic and neuroimaging biomarkers. In: Fato M M, Gilardi M C, Schenone A. Neuroinformatica. vol. 30, BOLOGNA: Pàtron (Italy)

7 6. Corradin A, Di Camillo B., Toffolo G (2010). Modelli deterministici e modelli stoocastici per la molecular systems biology. In: Cavalcanti S.. Biologia Sintetica. vol. 29, p , Bologna: Patron (Italy). 7. Di Camillo B., Toffolo G., Cobelli C. (2007). Reverse engineering delle reti di regolazione genica. In: Bellazzi R., Bicciato S., Cavalcanti S., Cobelli C., Toffolo G. Genomica e Proteomica Computazionale. (vol. 26). Bologna: Pàtron (Italy). 8. Toffolo G., Di Camillo B., Cobelli C. (2007). Modelli del turnover e della regolazione proteica. In: Bellazzi R., Bicciato S., Cavalcanti S., Cobelli C., Toffolo G. Genomica e Proteomica Computazionale. (vol. 26). Bologna: Pàtron (Italy). 9. Bellazzi R., Bicciato S., Cobelli C., Di Camillo B., Ferrazzi F., Magni P., Sacchi L., Toffolo G. (2004). Analisi di dati di DNA microarray: fondamenti, selezione di geni, classificazione. In: Cerutti S.,Marchesi C., Metodi avanzati di elaborazione di segnali biomedici. (vol. 23). Bologna: Pàtron (Italy). 10. Bellazzi R., Bicciato S., Cobelli C., Di Camillo B., Ferrazzi F., Magni P., Sacchi L., Toffolo G. (2004) Analisi di dati di DNA microarray: reti di regolazione. In: Cerutti S., Marchesi C. Metodi avanzati di elaborazione di segnali biomedici. (vol. 23). Bologna: Pàtron (Italy). Short congress papers and abstract with external peer review 1. Benguría A, F. Finotello F, Callejas S, Álvarez R, Sánchez-Cabo F, Di Camillo B, Hernández-Chico C, Dopazo A. Analysis of whole blood transcriptome of Spinal Muscular Atrophy patients using RNA-seq. Next Generation Sequencing Conference 2014, June 2-4, 2014, Barcelona, Spain. 2. Finotello F, Lavezzo E, Toppo S, Barzon L, B. Di Camillo B. Reverse engineering the human microbiota. NETTAB from structural bioinformatics to integrative systems biology, October, , Turin, Italy. 3. Baruzzo G, Finotello F, Lavezzo E, Serafini A, Provvedi R, Toppo S, Barzon L, Manganelli R, Di Camillo B. Benchmarking RNA-seq mapping strategies for pairedend reads. NETTAB from structural bioinformatics to integrative systems biology, October, , Turin, Italy. 4. Scarpa M, Barzon L, Costanzi G, Lavezzo E, Finotello F, Erroi F, Dallagnese L, Basato S, Brun P, Toppo S, Di Camillo B, Castoro C, Castagliuolo I. Colonic microbiota and gene methylation in colonic carcinogenesis. In SSAT 55th annual meeting, Digestive Disease Week, May 2-6, 2014, Chicago, Illinois, USA. 5. Sanavia T, Finotello F, Di Camillo B. FunPat: a function-based pattern analysis pipeline for RNA-seq time-series data. Bioinformatics Italyn Society (BITS) annual meeting. February 26-28th 2014, Rome, Italy. 6. Finotello F, Lavezzo E, Zandonà A, Toppo S, Barzon L, Di Camillo B. Modelling differences and interactions in the human microbiota. IV National Congress of Bioengineering, June 25-27, 2014, Pavia, Italy.

8 7. Sanavia T, Finotello F, Di Camillo B. FunPat: a function-based pattern analysis framework for RNA-seq time-series data. IV National Congress of Bioengineering, June 25-27, 2014, Pavia, Italy. 8. A. Giaretta, B. Di Camillo, G.M. Toffolo. Modeling Stochastic Effects in Gene Expression. SSBSS 2014 Book of Abstracts pg June 15-19, 2014 Taormina - Sicily, Italy 9. Sinigaglia A, Lavezzo E, Sanavia T, Di Camillo B, Scarpa M, Castagliuolo I, Farinati F, Palu G, Barzon L. MicroRNA expression signatures in chronic viral hepatitis progression. 5th European Congress of Virology, September 11-14, 2013, Lyon, France 10. Trevisan M, Albonetti C, Lavezzo E, Sanavia T, Sinigaglia A, Di Camillo B, Palu G, Barzon L. Characterization of human cytomegalovirus microrna temporal expression profile and target prediction by dynamic expression analysis. 5th European Congress of Virology, September 11-14, 2013, Lyon, France 11. Di Camillo B, Sambo F, Toffolo G, Cobelli C. A pathway cumulative SNP association analysis robust to rare variants and different direction of genotype effect. RECOMB/ISCB conference on Regulatory and Systems Genomics, with DREAM Challenges. Toronto, Ontario, Canada, November 8-12, Carlon A, Eduati F, Di Camillo B, Toffolo G. Key network motifs of insulin signaling pathway identified by local parametric sensitivity analysis. RECOMB/ISCB conference on Regulatory and Systems Genomics, with DREAM Challenges. Toronto, Ontario, Canada, November 8-12, Di Camillo B, Pasqualetto G,Arrigoni G, Puricelli L, Iori E, Tessari P, Toffolo G. Modeling SILAC data to assess protein turnover in diabetic nephropathy. ITPA, Padova, June 18-21, Carlon A, Eduati F, Di Camillo B, Toffolo G. A comprehensive rule-based model of insulin signaling pathway. Proceedings of Tenth Annual Meeting of the Bioinformatics Italyn Society, May 21-23, 2013, Udine, Italy. 15. Giaretta A, Corradin A, Di Camillo B, Toffolo G. Modeling Stochastic Effects in Gene Expression. Proceedings of Tenth Annual Meeting of the Bioinformatics Italyn Society, May 21-23, 2013, Udine, Italy. 16. Ciccarese F, Grassi A, Agnusdei V, Di Camillo B, Toffolo G, Mitola S, Indraccolo S. IFN-α transcriptional response in endothelial cells reveals new potential modulators of vascular biology. Workshop SIICA "Angiogenesi: basi molecolari ed implicazioni terapeutiche IV", May , Certosa di Pontignano (Siena), Italy 17. Finotello F, Lavezzo E, Barzon L, Mazzon P, Fontana P, Toppo S, Di Camillo B. A strategy to reduce technical variability and bias in RNA sequencing data. EMBnet. journal, 18(B):pp-65, Trifoglio E, Barbarini N, Di Camilo B, Rognoni C, Sambo F, Malovini A, Toffolo G, Bellazzi R, Cobelli C. Predicting diabetes complications through Dynamic Bayesian Networks. In IDAMAP, Intelligent data analysis in biomedicine and pharmacology, November 22,

9 19. Sanavia T, Mina M, Di Camillo B, Guerra C, Toffolo G. Recovering stable biomarker lists using a network-based measure of connectivity from Protein-Protein Interactions. In IDAMAP, Intelligent data analysis in biomedicine and pharmacology, November 22, Finotello F, Lavezzo E, Barzon L, Fontana P, Toppo S, Di Camillo B. Characterization and reduction of biases in RNA sequencing data. In IDAMAP, Intelligent data analysis in biomedicine and pharmacology, November 22, Di Camillo B, Sambo F, Toffolo G, Cobelli C. SPaRa: SNPs and pathways ranking using entropy based methods. RECOMB/ISCB conference on Regulatory and Systems Genomics, with DREAM Challenges November, 2012 San Francisco, USA 22. Corradin A, Di Camillo B, Rende F, Cavallari I, Saccomani MP, Ciminale V, Toffolo G, Cobelli C. HTLV-1 regulatory mechanisms: novel testable hypotheses from modeling HTLV-1 expression data. RECOMB/ISCB conference on Regulatory and Systems Genomics, with DREAM Challenges November, 2012 San Francisco, USA 23. Ciccarese F, Grassi A, Di Camillo B, Toffolo G, Indraccolo S. Transcriptional analysis reveals new candidate modulators of IFN-α response in endothelial cells. Arturo Falaschi Conference Series on Molecular Medicine - Frontiers in Cardiac and Vascular Regeneration, 30 May - 2 June 2012, Trieste, Italy 24. Grassi A, Di Camillo B, Ciccarese F, Finesso L, Indraccolo S, Toffolo G. Reconstruction of gene regulatory modules from RNAi silencing of IFN-α modulators. European Conference on Computational Biology ECCB'12, September , Basil, Switzerland 25. Grassi A, Di Camillo B, Ciccarese F, Indraccolo S, Toffolo G. Inference of gene regulatory modules from RNAi silencing of key regulators. Congresso Nazionale di Bioingegneria 2012 Atti Giugno 2012 Roma. 26. Corradin A, Giaretta A, Di Camillo B, Toffolo G, Cobelli C Finite number effects in stochasticity affecting gene expression. Congresso Nazionale di Bioingegneria 2012 Atti Giugno 2012 Roma. 27. Finotello F, Lavezzo E, Barzon L, Fontana P, Si-Ammour A, Toppo S, Di Camillo B. RNA sequencing data: biases and normalization. EMBnet NEWS, 18(A):p-99, Trifoglio E, Barbarini N, Di Camillo B, Rognoni C, Sambo F, Malovini A, Toffolo G, Bellazzi R and Cobelli C, Dynamic Bayesian Networks for the prediction of Diabetes complications. Terzo Congresso del Gruppo Nazionale di Bioingegneria GNB2012. Rome, Italy, June 26th-29th, Finotello F, Lavezzo E, Barzon L, Fontana P, Si-Ammour A, S Toppo, and Di Camillo B. Comparison of parametric methods for detecting differential expression in RNA sequencing data. Third National Congress of Bioengineering. Rome, Italy. June 26 29, Sambo F, Trifoglio E, Di Camillo B, Toffolo G, Cobelli C. Genome-Wide data analysis with a Bootstrap Ensemble of Naïve Bayes Classifiers. In: Proceedings of

10 the 3rd Congress of the Italyn Group on Bioengineering. Rome, Italy. June 26-29, Trevisan M, Sanavia T, Albonetti C, Lavezzo E, Di Camillo B, Sinigaglia A,Toppo S, Toffolo G, Cobelli C, Palù G, Barzon L Human cytomegalovirus micrornas target prediction by dynamic expression analysis. In: Terzo Congresso Gruppo Nazionale di Bioingegneria (GNB), Rome (Italy), June 26-29, Fontana P, Sanavia T, Facchinetti A, Lavezzo E, Falda M, Cavalieri D, Di Camillo B, Toppo S Can we go beyond sequence similarity to predict protein function? In: Automated Function Prediction SIG 2012: Critical Assessment of Function Annotations (CAFA), Long Beach, California (USA), July 14, (Oral communication) 33. Finotello F, Lavezzo E, Barzon L, Fontana P, Si-Ammour A, S Toppo, and Di Camillo B. RNA sequencing data: biases and normalization. Ninth Annual Meeting of the Bioinformatics Italyn Society, Catania, May 2-4, Eduati F, Di Camillo B, Karbiener M, Scheideler M, Corà D, Caselle M, Toffolo G Dynamic modeling of mirna-mediated Feed-Forward loops. 7th RECOMB Systems biology conference, Oct 16-17, (Oral communication) 35. Sambo F, Trifoglio E, Di Camillo B, Toffolo G, Cobelli C. Bag of Naïve Bayes: biomarker selection and classification from Genome-Wide SNP data. In: Clinical Bioinformatics: Network Tools and Applications in Biology (NETTAB) Workshop, October 2011, Pavia, Italy. (Oral communication) 36. Sanavia T, Crepaldi A, Barla A, Di Camillo B Gene Ontology based classification improves prediction and gene signature interpretability. In: Clinical Bioinformatics: Network Tools and Applications in Biology (NETTAB) Workshop, October 2011, Pavia, Italy. 37. Sanavia T, Aiolli F, Da San Martino G, Bisognin A, Di Camillo B Improving biomarker list stability by integration of biological knowledge in the learning process. In: 19th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 10th European Conference on Computational Biology (ECCB) July 2011, Wien, Austria. 38. Mina M, Sanavia T, Di Camillo B, Toffolo G, Guerra C Functional assessment of topological characterization using graphlet degrees in PPI networks. In: 19th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 10th European Conference on Computational Biology (ECCB) July 2011, Wien, Austria. 39. Sanavia T, Aiolli F, Da San Martino G, Bisognin A, Di Camillo B Stable Feature Selection for Biomarker Discovery: Use of Biological Information. In: BITS Annual Meeting 2011, June 2011, Pisa, Italy. (Oral communication) 40. Facchinetti A, Sanavia T, Di Camillo B, Lavezzo E, Fontana P, Toppo S A Method to Reveal and Handle Heterogeneities and Inconsistencies in Gene Ontology Annotation. In: BITS Annual Meeting 2011, June 2011, Pisa, Italy. (Oral communication) 41. Ciccarese F, Grassi A, Di Camillo B, Toffolo G, Indraccolo S. Identification of new modulators of IFN-α response in endothelial cells: a perturbation-based strategy.

11 ISICR Sponsored Satellite Symposium "Interferon Stimulated Genes and Their Protein Products", October 13-14, 2011, Prato, Italy 42. Sambo F, Di Camillo B, Toffolo G, Vella A, Cobelli C. Potential Role of GLP1R in the Pathogenesis of Type 2 Diabetes Identified Using Bayesian Networks. In: Proceedings of the 4th International Congress on Prediabetes and the Metabolic Syndrome. Madrid, Spain, April 6-9, Sambo F, Di Camillo B, Toffolo G, Vella A, Cobelli C. Type 2 Diabetes: Bayesian Network Modelling of Genetic and Phenotypic Traits. In: Proceedings of the 4th International Conference on Advanced Technologies & Treatments for Diabetes. London, UK, February 16-19, Eduati F, Di Camillo B, Karbiener M, Scheideler M, Corà D, Caselle M, Toffolo G. Selection of active microrna mediated feed-forward loops by dynamical modeling. 9th [BC]2 Basel Computational Biology Conference "Multiscale Modeling", Basel, 2011 Jun Finotello F, Peruzzo D, Lavezzo E, Di Camillo B, Toffolo GM, Cobelli C, Toppo S (2010). Comparative analysis of algorithms for whole genome shotgun assembly. In: BITS 2010 Annual Meeting of the Bioinformatics Italyn Society "Bioinformatics and Computational Biology for Life Sciences" - Conference Proceedings. Bari (Italy), Aprile 2010, BARI: PROGEDIT, vol. 04/2010, p Eduati F, Di Camillo B, Karbiener M, Scheideler M, Corà D, Caselle M, Toffolo G. Identification of active microrna / transcription factor feed-forward loops during adipogenesis. 3rd Annual joint conference on systems biology, regulatory genomics, and reverse engineering challenges. New York, 2010 Nov Sanavia T, Sambo F, Grassi A, Di Camillo B, Toffolo G. Gene Network inference by significance analysis on genotype/phenotype data. In: Proceedings of the 3rd Joint Conference on Systems Biology, Regulatory Genomics, and Reverse Engineering Challenges. New York City, Nov 16 20, Honourable Mention for Best Performer (fourth place) in the DREAM5 challenge: Systems Genetics Challenge. 48. Di Camillo B, Martini M, Sanavia T, Jurman G, Sambo F, Barla A, Squillario M, Furlanello C, Toffolo G, Cobelli C. Effect of size and heterogeneity of samples on biomarker discovery: synthetic and real data assessment. In: Proceedings of the 9th European Conference on Computational Biology ECCB10. Ghent, Belgium. Sep Sanavia T, Barla A, Di Camillo B, Mosci S, Toffolo G. Function-based analysis of microarray data via l1-l2 regularization. In: 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 8th European Conference on Computational Biology (ECCB). 27 Giugno- 2 Luglio 2009, Stoccolma, Svezia. 50. Eduati F, Corradin A, Di Camillo B, Toffolo G. A Boolean approach to linear prediction for signaling network modeling. Joint RECOMB Satellite Conference on Regulatory Genomics, Systems Biology and DREAM4. Boston, 2009 Dec De Palo G, Eduati F, Zampieri M, Di Camillo B, Toffolo G, Altafini C. Autogenous control and genome-wide adaptation in the yeast stress response. ICSB International Conference on Systems Biology. Stanford, 2009 Aug 30 Sep 4.

12 52. Di Camillo B., Martini M, Toffolo G. A simulator of gene regulatory network evolution for validation of biomarker identification methods. In: Bioinformatics Italyn Society. Bioinformatics Italyn Society Meeting Sanavia T, Di Camillo B, Iori E, Maran A, Bronte V, Avogaro A, Toffolo G, Cobelli C. Function-based discovery of characteristic temporal expression profiles in endothelial cells stimulated with insulin. In: 11th International Meeting of Microarray and Gene Expression Data Society (MGED). 1-4 Settembre 2008, Riva del Garda (TN), Italy. 54. Di Camillo B., Toffolo G, Cobelli C. (2008). In silico gene expression microarray experiments. In: 11th International Meeting of Microarray and Gene Expression Data Society (MGED). 1-4 Settembre 2008, Riva del Garda (TN), Italy. 55. Sambo F, Di Camillo B, Falda M,Toffolo G, Badaloni S. Evaluation of local reliability of gene networks inferred from time series expression data. In: RECOMB Satellite on Regulatory Genomics and Systems Biology. Boston, MA. Oct 29 - Nov Abstract Book, p. 121, Sambo F., Di Camillo B, Toffolo G. Role of network structure and experimental design on the performance of two Reverse Engineering methods. In: Proceedings of the 7th European Conference on Computational Biology ECCB2008. Cagliari, Italy. September Di Camillo B., Toffolo G, C.Cobelli. (2008). In silico gene regulatory networks. Primo Congresso Nazionale di Bioingegneria. Pisa, Italy. July, Di Camillo B., Toffolo G, C.Cobelli. (2008). A gene network simulator. BioINF 2008: Teoria dell'informazione in genomica e proteomica. Pisa, Italy. June Sambo F, Di Camillo B., Toffolo G. (2008). Role of network structure and experimental design on the performance of two Reverse Engineering methods. 7TH EUROPEAN CONFERENCE ON COMPUTATIONAL BIOLOGY - ECCB '08. Cagliari, Sardegna, Italy. September Sambo F, Di Camillo B., Toffolo G. (2008). CNET: an algorithm for Reverse Engineering of Causal Gene Networks. NETTAB 2008: Bioinformatics Methods for Biomedical Complex System Applications. Varenna, Como Lake, Italy. May 19-21, Sambo F, Di Camillo B., Falda M, Toffolo G., Badaloni S. (2008) Evaluation of local reliability of gene networks inferred from time series expression data. RECOMB Regulatory Genomics /Systems Biology / DREAM3. Boston MIT 29 October-2 November Corradin A., Di Camillo B., Toffolo G., Cobelli C. In silico assessment of four reverse engineering algorithms: role of network complexity and multi-experiment design in network reconstruction and hub detection. ENFIN DREAM Conference Assessment of Computational Methods in Systems Biology April 28 29, 2008, Madrid 63. Corradin A, Di Camillo B., Toffolo G, Cobelli C. (2008). In silico assessment of four reverse engineering methods: role of system complexity and multi-experiment design on network reconstruction and hub detection. 7TH EUROPEAN

13 CONFERENCE ON COMPUTATIONAL BIOLOGY - ECCB '08. Cagliari, Sardegna, Italy.. September Corradin A, Rende F, Di Camillo B., D'agostino D.M, Toffolo G, Banghman C.R.M, Cobelli C, Ciminale V. (2008). A bistable motif in HTLV-1 retrovirus activation. Primo Congresso Nazionale di Bioingegneria. Pisa, Italy. July, Corradin A., Rende F., Di Camillo B., D Agostino D.M., Toffolo G.M., Bangham C.R.M., Cobelli C., Ciminale V. A bistable motif in HTLV-1 retrovirus activation. Proceedings of the ENFIN Symposium at the Functional Genomics & Disease Conference: Synergy of Experimental and Computational Research in Systems Biology. October 2-4, Innsbruck, Austria 66. Di Camillo B., Toffolo G, Cobelli C. (2007). A Gene Network Simulator to Assess Reverse Engineering Algorithms. DREAM2: second Dialogue for Reverse Engineering Assessments and Methods. December 3-4, 2007, New York Academy of Sciences.New York, NY. 67. Di Camillo B. G.Toffolo, C.Cobelli. A gene network simulator. Sysbiohealth Symposium 2007, October 16-19, 2007, University of Milano-Bicocca, Milan, Italy 68. Di Camillo B. G.Toffolo, C.Cobelli. Annotation Based Discovery of Temporal Patterns in Gene Expression Studies. 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), Wien, July Di Camillo B. G.Toffolo, C.Cobelli A transcription network simulator. in Proceedings of Bioinformatics Italyn Society, Naples April 2007, abstract n Di Camillo B. G.Toffolo, C.Cobelli Bayesian inference of transcriptional networks from gene temporal expression patterns. in Proceedings of Bioinformatics Italyn Society, Naples April 2007, abstract n Di Camillo B. G.Toffolo, C.Cobelli A gene network simulator integrating Boolean regulation in a continuous dynamic model. 5th European Conference on Computational Biology - ECCB '06 Eilat, Israel, September 10-13, Posponed at January 20-24, Di Camillo B. G.Toffolo, C.Cobelli Importance of integration in modeling dynamic data of gene expression. Biobanks for functional genomics: integrating data, integrating models. March 7-8, 2006, ITC-irst Trento. 73. Di Camillo B. G.Toffolo, S.K.Nair, C.Cobelli Significance analysis of microarray transcript levels in time-series experiments. in Proceedings of Bioinformatics Italyn Society, Bologna April 2006, abstract n Jurman G, Di Camillo B, Galea A, Merler S, Toffolo G, Cobelli C, Furlanello C. Subsystem selection from time series microarray data in stimulus-response experiments. MGED 9 meeting, September 7-10, 2006, Seattle, WA, USA 75. Di Camillo B, Jurman G, Merler S, Toffolo G, Cobelli C, Furlanello C. Functionbased discovery of temporal patterns and regulatory modules from high throughput gene expression data. International Conference on Computational Methods in Systems Biology. The Microsoft Research University of Trento, Centre for Computational and Systems Biology. 18 and 19 October 2006 TRENTO ITALY

14 76. Di Camillo B, Toffolo G, Cobelli C. Comparison of three feature selection methods in time series expression studies. Third Bioinformatics Meeting on Machine Learning for Microarray Studies of Disease. Genova, September Di Camillo B., Sanchez-Cabo F., Toffolo G., Nair S.K., Trajanoski Z., Cobelli C. A quantization method based on threshold optimization for microarray short time series. BMC Bioinformatics 2005, 6 (Suppl 4): S F. Sanchez-Cabo, B. Di Camillo, H.Hackl, G.Toffolo, C.Cobelli, Z. Trajanoski. A reverse engineering algorithm to reconstruct gene networks from short time series expression data. in Proceedings of European Mathematical Society Summer School 2005: Statistics in Genetics and Molecular Biology, University of Warwick, UK, September Di Camillo B., F. Sanchez-Cabo, Z. Trajanoski, G.Toffolo, C.Cobelli Optimization of the quantization approach in reverse engineering of microarray data. in Proceedings of European Mathematical Society Summer School 2005: Statistics in Genetics and Molecular Biology, University of Warwick, UK, September Di Camillo B., F. Sanchez-Cabo, S.K.Nair, G.Toffolo, C.Cobelli Identification of gene regulatory modules using entropy and mutual information. in Proceedings of Bioinformatics Italyn Society, Milan March 2005, abstract n Di Camillo B., Sanchez-Cabo F., Toffolo G., Nair S.K.., Cobelli C. Identification of gene regulatory modules using Entropy and Mutual Information. MEDICON and HEALTH TELEMATICS 2004 Conference, Ischia (Na) Italy, July 31/ August 5, Di Camillo B., G.Toffolo, C.Cobelli, S.K.Nair, Selection of insulin regulated gene expression profiles based on intensity-dependent noise distribution of microarray data. In Proceedings of Bioinformatics Italyn Society, Padova March 2004, pg Sanchez-Cabo F., Di Camillo B., Hackl H., Gann G, Thallinger G, Hubbard S., Wolkenhauer O. Trajanoski Z. MICO: Inferring transcriptional networks from microarray data. Molecular medicine beyond differentially expressed genes: Systematic approaches and mathematical modeling. Heidelberg, Germany 5-6 December Di Camillo B., Sreekumar R., Greenlund L.J., Toffolo G., Cobelli C., Nair S.K. Exploiting intensity dependent noise knowledge to select differentially expressed genes in time course experiments. Bioinformatics: From Predictive Models To Inference. Oxford, UK, August 24-29, Di Camillo B., Sreekumar R., Greenlund L.J., Toffolo G., Cobelli C., Nair S.K. Selection of insulin regulated genes based on experimentally derived information on measurement error vs conventional constant-fold change method. In Proceedings of Genomics of Diabetes and Associated Diseases in the Post Genome Era. Lille, France, August , pg PhD Thesis

15 Di Camillo B. Modelling dynamic gene expression profiles: insulin regulation in skeletal muscle, University of Padova, A.A