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Cesare Furlanello received his degree in Mathematics at the University of Padua, Italy, in 1986. He is at Fondazione Bruno Kessler (Centre for Scientific and Technological Research of Trento) since 1987, now a Senior Researcher. He is currently leader of the MPBA Project (previously the ITC-IRST Neural Networks for Complex Data Analysis Project, since 1995).
In general terms, he is a data scientist, with main research interests in the interdisciplinary applications of machine learning methods to biomedical and environmental data. He is active in the field of bioinformatics, developing methods and software solutions to find patterns in very high throughput molecular data (such as Next Generation Sequencing and microarrays). He also have years of experience with machine learning and data analysis for geoinformatics, aiming at creating a bridge (geo-bioinformatics) between molecular profiles and spatial data structures. He has designed and managed many collaborative studies with life science researchers, in which math and software infrastructures are integrated to discover patterns in high-throughput datasets. He was first Project manager at IRST for the National Bioelectronics Project (1991-94), and he is currently PI and project manager of research projects in which Predictive Models are applied to Biomedical and Environmental data, for a total of 58 funded projects since 1988. These studies combine statistical machine learning methods with new sw infrastructures for data collection, management and distribution of the resulting models: Predictive Health Platforms and Geoinformatics platforms are thus the final outcome. The most recent research is directed to applications in functional genomics, including the development of computational pipelines and a focus to the problems of scientific reproducibility.
Basic and applied studies have been developed at the MPBA group with colleagues in other institutions on molecular oncology, vector-borne disease mapping, wildlife epidemiology, traffic safety, landscape risk analysis. CF has actively contributed to computational aspects, supporting the development of open source geoinformatics (GIS GRASS, WebGIS) and high performance machine learning (mlpy). Since 2002, he has contributed to the development of predictive classification models and gene selection procedures for molecular diagnostics, in collaboration with national and international centres of excellence in molecular oncology. He is a bioinformatics PI collaborator of international consortia such as the SEQC/MAQC FDA initiative and the FANTOM5 project led by the RIKEN OMICS centre. He has been a PI for AIRC with the IFOM-FIRC institute. He is also a collaborator PI in several projects of the Mach Foundation (FEM) for computational biology (metagenomics) and environmental mapping (climate change and plant genomics)
Several of the systems realized in experimental studies are now data platforms in use as infrastructures by public agencies: IET, MITRIS (Trentino and Friuli-VG), UXB-TN (Trentino), FaunaTN and FaunaBL (Trentino and Belluno) are the largest. The spinoff company MPA Solutions is mantaining these systems and developing WebGIS technologies with predictive modeling functions.
CF was Scientific secretary of the GNCB-CNR school on Neural Networks for Signal Processing (Trento 1989) and organizer of other workshops on Applications of Machine Learning and Neural Networks. In September 2008, he was Local Conference Chair of the MGED11 International Workshop of the MGED Society (in its Advisory Board since 2007) and he is now in the Board of Directors of the FGED society. Lecturer on Neural Network and Statistics at Master School of Advanced Information Science of Salerno University. Chairman of Session Theory 1 at IEEE NNSP-95 Cambridge MA, 1995. Member of the Scientific Board of the Multiple Classifier Systems series of conferences. Invited participant in the Machine Learning and Neural Networks Program of the Newton Institute of Mathematical Science, Cambridge UK, 1998. Member of the Italian Neural Network Society (serving in its Scientific Board 1991-2005), of the International Association for Pattern Recognition.
Invited lectures (a selection): NATO-ASI school Learning with Ensemble models (Vietri 2002), the ECEM/EAML Conference (Bled 2004), at the Int. BCB-Workshop on Machine Learning in Bioinformatics (Oct. 2005, Berlin), Int. School "The analysis of patterns" (Nov. 2005, Erice), "Predictive modeling on spatio-temporal patterns" (April 2007, Univ. Bristol), and "Signature Stability Analysis" (Nov 2007, Silver Springs, FDA).
He has been supervisor of 30 graduate or postgraduate theses for the universities of Trento (Mathematics and Engineering), Milano, Bologna, and Torino, supervisor of Leonardo graduate placements, tutor of 8 ASI-CONAE fellows in 2003-2012. Currently a supervisor of internships for Master thesis in Mathematics, Information and Telecommunication Engineering for the University of Trento, as well as a tutor for post-doc fellowships. Courses held: 1998-2003: Lecturer on COMPUTATIONAL STATISTICS AND PREDICTIVE MODELS, Math MsC, Trento University, and 2004-06: Lecturer on "Statistical Machine Learning", a course for the International Graduate School in ICT, Trento University. He is currently a member of the PhD School in Biomolecular sciences of UniTN.
He is a founder of the WEBVALLEY project, the FBK summer course for dissemination of interdisciplinary scientific research. Since 2001, CF is responsible for the WebValley Scientific program, and a resident tutor for all the 12 editions of this event. Developing the culture of data with open source platforms (web scripting, geodatabases, webGIS, tools for data visualization, statistical analysis decision making) based on a challenging project is the theme of 3 fast-paced weeks, in which about 20 high schools students team up with senior and junior researchers. In 2012, for this activity CF has been listed as "one of the 50 persons that are changing the world" by Wired, Italian edition (at #42, as in the H Guide).
Zhenqiang Su; Paweł P Łabaj; Sheng Li; Jean Thierry-Mieg; Danielle Thierry-Mieg; Wei Shi; Charles Wang; Gary P Schroth; Robert A Setterquist; John F Thompson; Wendell D Jones; Wenzhong Xiao; Weihong Xu; Roderick V Jensen; Reagan Kelly; Joshua Xu; Ana Conesa; Cesare Furlanello; Hanlin Gao; Huixiao Hong; Nadereh Jafari; Stan Letovsky; Yang Liao; Fei Lu; Edward J Oakeley; Zhiyu Peng; Craig A Praul; Javier Santoyo-Lopez; Andreas Scherer; Tieliu Shi; Gordon K Smyth; Frank Staedtler; Peter Sykacek; Xin-Xing Tan; E Aubrey Thompson; Jo Vandesompele; May D Wang; Jian Wang; Russell D Wolfinger; Jiri Zavadil; Scott S Auerbach; Wenjun Bao; Hans Binder; Thomas Blomquist; Murray H Brilliant; Pierre R Bushel; Weimin Cai; Jennifer G Catalano; Ching-Wei Chang; Tao Chen; Geng Chen; Rong Chen; Marco Chierici; Tzu-Ming Chu; Djork-Arné Clevert; Youping Deng; Adnan Derti; Viswanath Devanarayan; Zirui Dong; Joaquin Dopazo; Tingting Du; Hong Fang; Yongxiang Fang; Mario Fasold; Anita Fernandez; Matthias Fischer; Pedro Furió-Tari; James C Fuscoe; Florian Caimet; Stan Gaj; Jorge Gandara; Huan Gao; Weigong Ge; Yoichi Gondo; Binsheng Gong; Meihua Gong; Zhuolin Gong; Bridgett Green; Chao Guo; Lei Guo; Li-Wu Guo; James Hadfield; Jan Hellemans; Sepp Hochreiter; Meiwen Jia; Min Jian; Charles D Johnson; Suzanne Kay; Jos Kleinjans; Samir Lababidi; Shawn Levy; Quan-Zhen Li; Li Li; Li Li; Peng Li; Yan Li; Haiqing Li; Jianying Li; Shiyong Li; Simon M Lin; Francisco J López; Xin Lu; Heng Luo; Xiwen Ma; Joseph Meehan; Dalila B Megherbi; Nan Mei; Bing Mu; Baitang Ning; Akhilesh Pandey; Javier Pérez-Florido; Roger G Perkins; Ryan Peters; John H Phan; Mehdi Pirooznia; Feng Qian; Tao Qing; Lucille Rainbow; Philippe Rocca-Serra; Laure Sambourg; Susanna-Assunta Sansone; Scott Schwartz; Ruchir Shah; Jie Shen; Todd M Smith; Oliver Stegle; Nancy Stralis-Pavese; Elia Stupka; Yutaka Suzuki; Lee T Szkotnicki; Matthew Tinning; Bimeng Tu; Joost van Delft; Alicia Vela-Boza; Elisa Venturini; Stephen J Walker; Liqing Wan; Wei Wang; Jinhui Wang; Jun Wang; Eric D Wieben; James C Willey; Po-Yen Wu; Jiekun Xuan; Yong Yang; Zhan Ye; Ye Yin; Ying Yu; Yate-Ching Yuan; John Zhang; Ke K Zhang; Wenqian Zhang; Wenwei Zhang; Yanyan Zhang; Chen Zhao; Yuanting Zheng; Yiming Zhou; Paul Zumbo; Weida Tong; David P Kreil; Christopher E Mason; Leming Shi,A comprehensive assessment of RNA-Seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium,in «NATURE BIOTECHNOLOGY»,vol. 32,2014, pp. 903 -914
C. Wang; B. Gong; P.R. Bushel; J. Thierry-Mieg; D. Thierry-Mieg; J. Xu; H. Fang; H. Hong; J. Shen; Z. Su; J. Meehan; X. Li; L. Yang; H. Li; P.P. Labaj; D.P. Krell; D. Megherbi; S. Gaj; F. Calment; J. van Delft; J. Kleinjans; A. Sherer; V. Devanarayan; J. Wang; Y. Yang; H.-R. Qian; L.J. Lancashire; M. Bessarabova; Y. Nikolsky; C. Furlanello; M. Chierici; D. Albanese; G. Jurman; S. Riccadonna; M. Filosi; R. Visintainer; K.K. Zhang; J. Li; J.-H. Hsieh; D.L Svoboda; J.C. Fuscoe; Y. Deng; L. Shi; R.S. Paules; S.S. Auerbach; W. Tong,The concordance between RNA-Seq and microarray data depends on chemical treatment and transcript abundance,in «NATURE BIOTECHNOLOGY»,vol. 32,n. 9,2014, pp. 926 -932
Andrea Bizzego;Marco Mina;Calogero Zarbo;Gianluca Esposito;Cesare Furlanello,Physiolyze: A Galaxy-based web service for Heart Rate Variability analysis with online processing2014 8th Conference of the European Study Group on Cardiovascular Oscillations (ESGCO),2014 8th Conference of the European Study Group on Cardiovascular Oscillations (ESGCO),2014, pp. 97-98
D. Albanese; M. Filosi; R. Visintainer; S. Riccadonna; G. Jurman; C. Furlanello,minepy and minerva: a C engine for the MINE suite and its Python, R and MATLAB wrappers,in «BIOINFORMATICS»,vol. 29,n. 3,2013, pp. 407 -408
G. Jurman; S. Riccadonna; C. Furlanello,A comparison of MCC and CEN error measures in multi-class prediction,in «PLOS ONE»,2012
G. Jurman; S. Riccadonna; R. Visintainer; C. Furlanello,Algebraic Comparison of Partial Lists in Bioinformatics,in «PLOS ONE»,vol. 7,n. 5,2012, pp. e36540 -
B. di Camillo; T. Sanavia; M. Martini; G. Jurman; C. Furlanello; F. Sambo; A. Barla; M. Squillario; G. Toffolo; C. Cobelli,Effect of size and heterogeneity of samples on biomarker discovery: synthetic and real data assessment,in «PLOS ONE»,vol. 7,n. 3,2012, pp. e32200 -
M. Chierici; D. Albanese; P. Franceschi; C. Furlanello,TOFwave: Reproducibility in Biomarker Discovery from time-of-flight Mass Spectrometry Data.,in «MOLECULAR BIOSYSTEMS»,2012
R. Sanz-Pamplona; A. Berenguer; D. Cordero; S. Riccadonna; X. Sole'; M. Crous-Bou; E. Guino'; X. Sanjuan; S. Biondo; A. Soriano; G. Jurman; G. Capella; C. Furlanello; V. Moreno,Clinical value of prognosis gene expression signatures in colorectal cancer: a systematic review,in «PLOS ONE»,2012
A. Barla; G. Jurman; R. Visintainer; M. Squillario; M. Filosi; S. Riccadonna; C. Furlanello,A Machine Learning Pipeline for Discriminant Pathways Identification,Springer Handbook of Bio-/Neuroinformatics,Springer,2012