Andrea Franceschini

Post Doc
bioinformatician

Research Lines

Genomic Science

Center

CGS@SEMM Milano

Contacts

+39 329 4768198

About

I currently work for IIT (Italian Institute of Technology), SEMM division, at the IIT-IFOM-IEO campus.

I am involved in the R&D of several bioinformatics projects (see below).

Besides, I am constantly engaged in supporting/analyzing experimental data of several biological labs.

 

PREVIOUS

  • 2012-2016 responsible for the bioinformatics analysis of several pathogen Genome Wide siRNA screens performed in Switzerland (UZH, ETH, Novartis Biozentrum), in the context of SystemsX (http://www.systemsx.ch/)
  • 2010-2015 responsible (R&D) for the STRING protein-protein interaction database: http://www.string-db.org  (Swiss Institute of Bioinformatics).
  • 2008-2010 bioinformatician at the SIB (Swiss Institute of Bioinformatics).
  • 2007-2008 java software developer at REPLY s.p.a.

Interests

sailing hiking skiing swimming

Projects

SAMPLE-MANAGER

In order to tackle the increasing needs of our high-throughput facilities we designed and started to develop (July 2019) a new “sample management” application.
Differently from existing LIMS applications, Sample-Manager entails a more general data model that fits with any type of sample (not just NGS) and any facility (e.g. molecular pathology unit, imaging unit, proteomics unit, genomics unit).

 

HTSFLOW

With sequencing data corresponding to hundreds of samples, the ability to monitor the flow of NGS data from their generation to preliminary and higher-level analyses becomes critical. We developed HTS-flow (High-Throughput Sequencing flow) framework to deal with these issue, providing the NGS-users with a system for data management and analysis for NGS data.
Htsflow is a web application that serves our bioinformaticians with the latest bioinformatics tools, ready to be used “out of the box”. 
Analysis are divided in “primary analysis” (i.e. alignments to the genome) and “secondary analysis” (i.e. follow up analysis). The results of both these analysis types can be conveniently searched and visualized in suitable tables, and are stored in Htsflow database for subsequent retrieval.
The tool currently offers the following features:

  • Alignments to the genome of DNA and transcript fragments.
  • Merge and downsample data.
  • Chip-Seq data analyis (peak calling and saturation analysis)
  • RNA-Seq data analysis (differential gene/exons expression)
  • Methylation analysis
  • DNA Seq - Variant calling pipeline for both somatic and germinal analysis.
  • DNA Seq - CNV pipeline (Copy Number Variation) for both somatic and germinal analysis
  • export data to the UCSC genome browser

htsflow image

IIT Publications

  • 2016
  • Franceschini A., Lin J., Von Mering C., Jensen L.J.
    DOI

    SVD-phy: Improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles

    Bioinformatics, vol. 32, (no. 7), pp. 1085-1087
  • Bultet L.A., Aguilar-Rodriguez J., Ahrens C.H., Ahrne E.L., Ai N., Aimo L., Akalin A., Aleksiev T., Alocci D., Altenhoff A., Alves I., Ambrosini G., Pedone P.A., Angelino P., Anisimova M., Appel R., Argoud-Puy G., Arnold K., Arpat B., Artimo P., Ascencao K., Auchincloss A., Axelsen K., Gerritsen V.B., Bairoch A., Bansal P., Baratin D., Barbato A., Barbie V., Barras D., Barreiro M., Barret S., Bastian F., Neto T.B., Baudis M., Beaudoing E., Beckmann J.S., Bekkar A.K., Ben Hamida Cammoun L., Benmohammed S., Bernard M., Bertelli C., Bertoni M., Bienert S., Bignucolo O., Bilbao A., Bilican A., Blank D., Blatter M.-C., Blum L., Bocquet J., Boeckmann B., Bolleman J.T., Bordoli L., Bosshard L., Bouchet G., Bougueleret L., Boutet E., Bovigny C., Bratulic S., Breuza L., Bridge A.J., Britan A., Brito F., Frazao J.B., Bruggmann R., Bucher P., Burdet F., Burger L., Cabello E.M., Gomez R.M.C., Calderon S., Cannarozzi G., Carl S., Casas C.C., Catherinet S., Perier R.C., Charpilloz C., Chaskar P.D., Chen W., Pepe A.C., Chopard B., Chu H.Y., Civic N., Claassen M., Clottu S., Colombo M., Cosandier I., Coudert E., Crespo I., Creus M., Cuche B., Cuendet M.A., Cusin I., Daga N., Daina A., Dauvillier J.O., David F., Davydov I., De Sa Ricca Manadelo Ferreira M., De Beer T., De Castro E., De Santana C., Delafontaine J., Delorenzi M., Delucinge-Vivier C., Demirel O., Derham R., Dermitzakis E.M., Dib L., Diene S., Dilek N., Dilmi J., Domagalski M.J., Dorier J., Dornevil D., Dousse A., Dreos R., Duchen P., Roggli P.D., Duperret I.D., Durinx C., Duvaud S., Engler R., Erkek S., Lopez P.E., Estreicher A., Excoffier L., Fabbretti R., Falcone J.-L., Falquet L., Famiglietti M.L., Ferreira A.-M., Feuermann M., Filliettaz M., Flegel V., Foucal A., Franceschini A., Fucile G., Gaidatzis D., Garcia V., Gasteiger E., Gateau A., Gatti L., Gaudet P., Gaudinat A., Gehant S., Gfeller D., Gharib W.H., Ghraichy M., Gidoin C., Gil M., Gleizes A., Gobeill J., Gonnet G., Gos A., Gotz L., Gouy A., Grbic D., Groux R., Gruaz-Gumowski N., Grun D., Gschwind A., Guex N., Gupta S., Getaz M., Haake D., Haas J., Hatzimanikatis V., Heckel G., Gardiol D.F.H., Hinard V., Hinz U., Homicsko K., Horlacher O., Hosseini S.-R., Hotz H.-R., Hulo C., Hundsrucker C., Ibberson M., Ilmjarv S., Ioannidis V., Ioannidis P., Iseli C., Ivanek R., Iwaszkiewicz J., Jacquet P., Jacquot M., Jagannathan V., Jan M., Jensen J., Johansson M.U., Johner N., Jungo F., Junier T., Kahraman A., Katsantoni M., Keller G., Kerhornou A., Khalid F., Klingbiel D., Komljenovic A., Kriventseva E., Kryuchkova N., Kumar S., Kutalik Z., Kuznetsov D., Kuzyakiv R., Lane L., Lara V., Ledesma L., Leleu M., Lemercier P., Lew D., Lieberherr D., Liechti R., Lisacek F., Lischer H., Litsios G., Liu J., Lombardot T., Mace A., Maffioletti S., Mahi M.-A., Maiolo M., Majjigapu S.R., Malmstrom L., Mangold V., Marek D., Mariethoz J., Marin R., Martin O., Martin X., Martin-Campos T., Mary C., Masclaux F., Masson P., Meier C., Messina A., Lenoir M.M., Meyer X., Michel P.-A., Michielin O., Milanese A., Missiaglia E., Perez J.M., Caria V.M., Moret P., Moretti S., Morgat A., Mottaz A., Mottin L., Mouscaz Y., Mueller M., Murri R., Mylonas R., Neuenschwander S., Nikitin F., Niknejad A., Nouspikel N., Nso L.N., Okoniewski M., Omasits U., Paccaud B., Pachkov M., Paesano S.G., Pagni M., Palagi P.M., Pasche E., Payne J.L., Pedruzzi I., Peischl S., Peitsch M., Perlini S., Pilbout S., Podvinec M., Pohlmann R., Polizzi D., Potter D., Poux S., Pozzato M., Pradervand S., Praz V., Pruess M., Pujadas E., Racle J., Raschi M., Ratib O., Rausell A., De Laval V.R., Redaschi N., Rempfer C., Ren G., Vahdati R.A.R., Rib L., Grognuz O.R., Altimiras E.R., Rivoire C., Robin T., Robinson-Rechavi M., Rodrigues J., Roechert B., Roelli P., Romano V., Rossier G., Roth A., Rougemont J., Roux J., Royo H., Ruch P., Ruinelli M., Sater M.R.A., Rohrig U.F., Rueger S., Salamin N., Sankar M., Sarkar N., Saxenhofer M., Schaeffer M., Schaerli Y., Schaper E., Schmid A., Schmid E., Schmid C., Schmid M., Schmidt S., Schmocker D., Schneider M., Schuepbach T., Schwede T., Schutz F., Sengstag T., Serrano M., Sethi A., Shahmirzadi O., Sigrist C., Silvestro D., Neto F.A.S., Simillion C., Simonovic M., Skunca N., Sluzek K., Soneson C., Sprouffske K., Stadler M., Staehli S., Stevenson B., Stockinger H., Straszewski J., Stricker T., Studer G., Stutz A., Suffiotti M., Sundaram S., Szklarczyk D., Ovenyi P.S., Tegenfeldt F., Teixeira D., Tellenbach S., Smith A.A.T., Tognolli M., Topolsky I., Van Du Tran T., Tsantoulis P., Tzika A.C., Agote A.U., Van Nimwegen E., Von Mering C., Varadarajan A., Veranneman M., Verbregue L., Veuthey A.-L., Vishnyakova D., Vyas R., Wagner A., Walther D., Wan H.W., Wang M., Waterhouse R., Waterhouse A., Wicki A., Wigger L., Wirapati P., Witschi U., Wyder S., Wyler K., Wuthrich D., Xenarios I., Yamada K., Yan Z., Yasrebi H., Zahn M., Zangger N., Zdobnov E., Zerzion D., Zoete V., Zoller S., Abriata L., Aebischer T., Akhmedov M., Filho A.A.M., Andreozzi S., Appel N., Armand F., Arribas A., Asgari S., Ataman M., Audagnotto M., Aydin D., Bady P., Bank C., Barac D., Bargeton B., Barido-Sottani J., Barillari C., Bartha I., Bean A., Becker J., Beerenwinkel N., Bellement G., Benedetti F., Bergmann S., Berneche S., Bevers R., Biasse D., Bichsel M., Bieler J., Piccini A.P.B., Do Amaral M.B., Bolliger C., Boskova V., Brown A., Bryois J., Buil A., Cannavo R., Cardner M., Carelli F.N., Carmona S., Cascione L., Chakrabarti A., Chaturvedi N., Choobdar S., Clivaz C., Constantinescu S., Corre T., Quezada D.C.C., Croce R., Cuendet A., Cui J., Dainese R., Dal Peraro M., Dallavilla T., De Oliveira L., Delaleu N., Delaneau O., Deplancke B., Dharmarajan L., Diekmann M., Dimitrakopoulos C., Dimitriades-Schmutz B., Dimitrova Y., Dirmeier S., Dobay M.P., Dougoud M., Duc J., Dumont G., Du Plessis L., Dorr D., Elfstroem K., Elmer F.-J., Ewing G.B., Fanaswala I., Fellay J., Feller C., Fengos G., Ferrer A., Fiaux S., Field C., Finci I., Fofonjka A., Fonti G., Fried P., Frochaux M., Fuentes J., Galbusera L., Galimberti M., Garcia-Albornoz M., Garcia-Escudero R., Garieri M., Georgieva L., Ghiurcuta C.G., Ghosh S., Gnann A., Gnuegge R., Golumbeanu M., Gomez H., Goudet J.O., Gruber A.J., Gruhl F., Guethe S., Guillot E., Guimaraes J., Gumienny R.W., Gunawan R., Gustafson K., Gypas F., Hadadi N., Hameri T., Hammer C., Heer F., Heller D.M., Hersch M., Hofmann A.L., Howald C., Hutter S., Iber D., Irwin K., Jahn K., Jedlinski D., Jethava V., Jorjani H., Julou T., Kaessmann H., Kalantzi A., Kanitz A., Kapopoulou A., Karamasioti E., Karimaddini Z., Keller I., Kiparissides A., Kohler M., Kousathanas A., Kuipers J., Kupczyk P., Kwee I., Kuhnert D., Lakshmanan L.N., Lamparter D., Lang B., Laurent S., Laurent S., Leigh D., Lin Y., Lindsay H., Link V., Linnik J., Liphardt T., Liu Y., Loetscher A., Luomi A.O., Lykov K., Machlab D., Magnus C., Maillard-Wermelinger A., Malafeev A., Malaspinas A.-S., Parera R.M., Manesso E., Manukyan L., Mapelli S.N., Marbach D., Lopez M.J.M., Wynn M.M., Martin G., Martins A.F., Matthes K., Mazza C., McDaid A., Mermet J.O., Michos O., Milinkovitch M.C., Misios A., Miskovic L., Mitov V., Mitra A., Mittal N., Montazeri H., Moret B., Naef F., Nair N., Nicolas D.L., Nicolet S., Noh H., Nowicka M., Oeyaas O., Omidi S., Ongen H., Ormond L., Ottoz D., Panousis N., Gao N.P., Modarres H.P., Pecerska J., Vieira J.P., Pivkin I., Planet E., Cespedes S.P., Pradhan R., Prados J., Racko D., Radigois M.-F., Rasmussen D., Riba A., Rinn B., Rivoal M., Robinson M., Rossi S., Rudolf F., Rueedi R., Ruscheweyh H.-J., Rybinski M., Rzepiela A.J., Sakoparnig T., San Roman Rincon M.M., Savoglidis G., Scepanovic P., Schaad O., Schleiss R., Schmich F., Schmidt R., Schulthess S., Schwalie P.C., Seifert D., Seijo M., Shao M., Shim H., Singer J., Sobel J., Soh K.C., Flitman R.S., Soto S., Sousa V., Stadler T., Stasiak A., Stefani A., Steger Y., Stelling J., Stopka A., Stevant I., Sunnaker M., Syed A.P., Tamo G., Tanaka S., Theiler G., Thorball C.A.W., Thurnherr T., Ccenhua M.R.T., Tidin O., Tokic M., Riera M.T., Tomasini M., Tymoshenko S., Ud-Dean M., Urchueguia A., Quintero N.V., Vinckenbosch L., Vinuela A., Vollmer J., Voordijk S., Wang J., Wang Z., Warnefors M., Weber L.M., Wegmann D., Whitehead E., Wicky A., Widmer L., Ye M., Yerly F., Yeung J., Yordanov P., Zavolan M., Zehnder T., Zhang C., Zhou X., Zisaki A., Zoller B., Zollinger A.
    DOI

    The SIB Swiss Institute of bioinformatics' resources: Focus on curated databases

    Nucleic Acids Research, vol. 44, (no. D1), pp. D27-D37
  • 2015
  • Szklarczyk D., Franceschini A., Wyder S., Forslund K., Heller D., Huerta-Cepas J., Simonovic M., Roth A., Santos A., Tsafou K.P., Kuhn M., Bork P., Jensen L.J., Von Mering C.
    DOI

    STRING v10: Protein-protein interaction networks, integrated over the tree of life

    Nucleic Acids Research, vol. 43, (no. D1), pp. D447-D452
  • 2014
  • Meier R., Franceschini A., Horvath P., Tetard M., Mancini R., von Mering C., Helenius A., Lozach P.-Y.
    DOI

    Genome-wide small interfering RNA screens reveal VAMP3 as a novel host factor required for uukuniemi virus late penetration

    Journal of Virology, vol. 88, (no. 15), pp. 8565-8578
  • Franceschini A., Meier R., Casanova A., Kreibich S., Daga N., Andritschke D., Dilling S., Ramo P., Emmenlauer M., Kaufmann A., Conde-Alvarez R., Low S.H., Pelkmans L., Helenius A., Hardt W.-D., Dehio C., Von Mering C.
    DOI

    Specific inhibition of diverse pathogens in human cells by synthetic microRNA-like oligonucleotides inferred from RNAi screens

    Proceedings of the National Academy of Sciences of the United States of America, vol. 111, (no. 12), pp. 4548-4553
  • 2013
  • Franceschini A., Szklarczyk D., Frankild S., Kuhn M., Simonovic M., Roth A., Lin J., Minguez P., Bork P., Von Mering C., Jensen L.J.
    DOI

    STRING v9.1: Protein-protein interaction networks, with increased coverage and integration

    Nucleic Acids Research, vol. 41, (no. D1)
  • 2012
  • Kuhn M., Szklarczyk D., Franceschini A., Von Mering C., Jensen L.J., Bork P.
    DOI

    STITCH 3: Zooming in on protein-chemical interactions

    Nucleic Acids Research, vol. 40, (no. D1)
  • 2011
  • Szklarczyk D., Franceschini A., Kuhn M., Simonovic M., Roth A., Minguez P., Doerks T., Stark M., Muller J., Bork P., Jensen L.J., Von Mering C.
    DOI

    The STRING database in 2011: Functional interaction networks of proteins, globally integrated and scored

    Nucleic Acids Research, vol. 39, (no. SUPPL. 1)
  • 2009
  • Kuhn M., Szklarczyk D., Franceschini A., Campillos M., Von Mering C., Jensen L.J., Beyer A., Bork P.
    DOI

    STITCH 2: An interaction network database for small molecules and proteins

    Nucleic Acids Research, vol. 38, (no. SUPPL.1)
  • 2007
  • Masseroli M., Bellistri E., Franceschini A., Pinciroli F.
    DOI

    Statistical analysis of genomic protein family and domain controlled annotations for functional investigation of classified gene lists

    BMC Bioinformatics, vol. 8, (no. SUPPL. 1)
  • 2006
  • Maffezzoli A., Franceschini A., Bellistri E., Pinciroli F., Masseroli M.

    Genomic functional investigation through statistical analysis of protein families and domains.

    AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium