HOME PAGE: Luisa Cutillo's Biography

My research experience started in Computer Science at the time of my graduation in Mathematics. Then I moved to the Applied Statistics pursuing my PhD. During this time I had the opportunity to be visiting student at the Georgia Institute of Technology and to participate to many European schools and conferences. After my PhD, I switched to the field of Bioinformatics visiting the University of Cambridge, within a short term EMBO fellowship. Soon after, I became member of the Bioinformatics Core of the Telethon Institute of Genetics and Medicine in Naples. As last relevant step of my career I gained a position as assistant professor (ricercatore) at the University of Naples Parthenope, at the faculty of Economics. Building on this multidisciplinary background, I was recently awarded a prestigious 2 years Marie S. Curie Individual Fellowship that I carried out in the research group of Professor Neil Lawrence, embedded in a truly multidisciplinary environment at the University of Sheffield at SITraN. I am currently back to my lecturship position in Italy at the Dipartimento di Metodi Quantitativi per le Applicazioni Ecomiche, University Parthenope of Naples. Last July 2017 I was awarded the Abilitazione Scientifica Nazionale in Statistics (SECS S01) that entitles me to be qualified for Professorship in statistics (whenever a call will be opened ;-P so I am like a named knight waiting for his horse or Cavaliere senza Cavallo).

 

 

My Research Interests

My research interests are Network Analysis, time series analysis, count data modelling, clustering methods and multiple hypothesis testing procedures. More in general I use to work in the areas of biostatistics and bioinformatics. In particular I am focusing on analysing and modelling RNA-seq data either from bulk or single cell biological experiments.

Latest Projects

 I developped my international Marie S Curie project CONTESSA: COuNt data TimE SerieS Analysis.

The aim of this project is to develop methods for analysis of time-series based on count data. For example, detecting significant differences between two count data time series would distinguish between two different models: one in which the two time series are interchangeable, and one in which the second sample is a modification of the first, i.e. the two time series are non-interchangeable. The target of my project broadens to general analysis of count time-series data such as clustering, classification, perturbations inference and machine learning over sequential count data. The project focus on count data sets from ribonucleic acid sequencing (RNA-seq) time course experiments. My project potentially has promising applications in biology, recent examples include high- throughput sequencing, such as RNA-seq and chromatin immunoprecipitation sequencing (ChIP-seq) analyses and more recently Single Cell sequencing.

 

My Publications

 

 

Carissimo A., Cutillo L., Defeis I. Validation of community robustness. (2017). Computational Statistics and Data Analysis. (co-first).

 

Carfora F., Cutillo L., Orlando A. A quantitative comparison of stochastic mortality models on Italian population data.(2017) Computational Statistics and Data Analysis. (co-first).

Gambardella G, Carissimo A, Chen A, Cutillo L, Nowakowski, TG, di Bernardo D and Blelloch R. (2016) The impact of microRNAs on transcriptional heterogeneity and gene co-expression across single embryonic stem cells. Nature Communications.

Pinelli, M; Carissimo, A; Cutillo, L; Lai, C-H; Mutarelli, M; Moretti, M; Veer Singh, M; Karali, M; Carrella, D; Pizzo, M; Russo, F; Ferrari, S,; Ponzin, D; Angelini, C; Banfi, S; Di Bernardo, D. (2016) An atlas of gene expression and gene co-regulation in the human retina.Nucleic Acid Research. * (co-first)

Carfora MF, Cutillo L, Orlando A (2014). Modeling the European Central Bank Official Rate: A Stochastic Approach. Journal of Applied Quantitative Methods. V.9, N.3.

Cutillo L, De Feis I, Nikolaidou C, Sapatinas T (2014).Wavelet density estimation for weighted data. Journal of Statistical Planning and Inference 146, 1-19.

Carrella D, Napolitano F, Rispoli R, Miglietta M, Carissimo A, Cutillo L, Sirci F, Gregoretti F, Di Bernardo D (2014). Mantra 2.0: an online collaborative resource for drug mode of action and repurposing by network analysis. Bioinformatics, btu058.

De Cegli R, Iacobacci S, Flore G, Gambardella G, Mao L, Cutillo L, Lauria M, Klose J, Illingworth E, Banfi S, di Bernardo D (2013). Reverse engineering a mouse embryonic stem cell-specific transcriptional network reveals a new modulator of neuronal differentiation. Nucleic Acids Res 41 (2):711-726.

Cutillo L, Carissimo A, Figini S (2012). Network selection: a method for ranked lists selection. PloSone 7 (8):e43678.

Pane LS, Zhang Z, Ferrentino R, Huynh T, Cutillo L, Baldini A (2012). Tbx1 is a negative modulator of Mef2c. Hum Mol Genet 21 (11):2485-2496

Vitiello C, Faraso S, Sorrentino NC, Di Salvo G, Nusco E, Nigro G, Cutillo L, Calabro R, Auricchio A, Nigro V (2009). Disease rescue and increased lifespan in a model of cardiomyopathy and muscular dystrophy by combined AAV treatments.PLoS ONE 4 (3):e5051.

Gennarino VA, Sardiello M, Avellino R, Meola N, Maselli V, Anand S, Cutillo L, Ballabio A, Banfi S (2009). MicroRNA target prediction by expression analysis of host genes. Genome Res 19 (3):481-490.

Cutillo L, Yoon Young J, Ruggieri F, Vidakovic B (2008). Larger Posterior Mode Wavelet Thresholding and Applications.J Stat Plan Inference, 138:3758-3773

Amato U, Antoniadis A, Cuomo V, Cutillo L, Franzese M, Murino L, Serio C (2008). Statistical cloud detection from SEVIRI multispectral images.Remote Sens Environ, 112: 750-766

Angelini C, Cutillo L, De Canditiis D, Mutarelli M, Pensky M (2008). BATS: A Bayesian user friendly Software for analyzing time series microarray experiments. BMC Bioinf 9(415):1-13

Cutillo L, Amato U (2008). Localized empirical discriminant analysis.Comput Stat Data Anal 52:4966-4978

Allocca M, Doria M, Petrillo M, Colella P, Garcia-Hoyos M, Gibbs D, Kim SR, Maguire A, Rex TS, Di Vicino U, Cutillo L, Sparrow JR, Williams DS, Bennett J, Auricchio A (2008). Serotype-dependent packaging of large genes in adeno-associated viral vectors results in effective gene delivery in mice. J Clin Invest 118(5):1955-1964

Lanza A, Cirillo N, Rossiello R, Rienzo M, Cutillo L, Casamassimi A, de Nigris F, Schiano C, Rossiello L, Femiano F, Gombos F, Napoli C (2008). Evidence of key role of Cdk2 over expression in pemphigus vulgaris. J BiolChem 283(13):8736-8745.

 

 BOOK CHAPTERS

 

Angelini C, Cutillo L, De Feis I, van der Wath R, and Lio P (2007).Identifying Regulatory Sites Using Neighborhood Species. In: Lecture Notes in Computer Science. LECTURE NOTES IN COMPUTER SCIENCE, vol. 4447, p. 1-10, Springer

 

 Cutillo L, De Marco G, Donnini C (2012). Networks of Financial Contagion.Advanced Dynamic Modeling of Economic and Social Systems. Studies in Computational Intelligence Volume 448, 2013, pp 31-48.

 

CONFERENCE PAPERS

 

 

Carissimo A, Cutillo L, De Feis I. Validation of Community robustness. In: CIBB 2015: Computational Intelligence Methods for Bioinformatics and biostatistics, CNR Research Area, Naples (Italy) 10-12 September 2015

 

Cutillo L, De Feis I, Nikolaidou C, Sapatinas T (2011). Wavelet Density Estimation for Weighted Data. In: CLADAG 2011 short papers usb pen. Pavia, Sept 7-9, 2011

 

Angelini C., Cutillo L, De Feis I., Liò P., Van Der Wath R. (2008). Combining experimental evidences from replicates and nearby species data for annotating novel genomes . In: AIP Conference Proceedings. Vietrisul Mare, Sept 24-28, 2007.