IFOM Publications Francesco Ferrari

Publications Francesco Ferrari

Publications by the research group

  1. Salviato E*, Djordjilovi? V, Hariprakash JM, Tagliaferri I, Pal K, Ferrari F*.
    Leveraging three-dimensional chromatin architecture for effective reconstruction of enhancer-target gene regulatory interactions.
    Nucleic Acids Research 2021(ACCEPTED - IN PRESS)
    (* co-corresponding authors)

  2. Sebestyén E, Marullo F, Lucini F, Petrini C, Bianchi A, Valsoni S, Olivieri I, Antonelli L, Gregoretti F, Oliva G, Ferrari F*, Lanzuolo C*.
    SAMMY-seq reveals early alteration of heterochromatin and deregulation of bivalent genes in Hutchinson-Gilford Progeria Syndrome.
    Nature Communications 2020 Dec 8;11(1):6274.
    (* co-corresponding/co-last authors)

  3. Pal K, Forcato M, Jost D, Sexton T, Vaillant C, Salviato E, Mazza EMC, Lugli E, Cavalli G, Ferrari F.
    Global chromatin conformation differences in the Drosophila dosage compensated chromosome X.
    Nature Communications 2019 Nov 25;10(1):5355.

  4. Pal K, Tagliaferri I, Livi CM,Ferrari F..
    HiCBricks: building blocks for efficient handling of large Hi-C datasets.
    Bioinformatics. 2019 Nov 7. pii: btz808.

  5. Forcato M, Nicoletti C, Pal K, Livi CM, Ferrari F.*, Bicciato S*.
    Comparison of computational methods for the analysis of Hi-C data.
    Nature Methods, 2017 Jul; 14(7):679-685. (* co-corresponding/co-last authors)

  6. Puccio S, Grillo G, Liciulli F, Severgnini M, Liuni S, Bicciato S, De Bellis G, Ferrari F.*, Peano C*.
    WoPPER: Webserver for Position Related data analysis of gene Expression in Prokaryotes.
    Nucleic Acids Res., 2017 July 3; 45(W1):W109-115. Epub 2017 Apr 29 (* co-corresponding/co-last authors)

Review material

  1. Pal K* and Ferrari F*.
    Visualising and annotating Hi-C data. Book chapter for "Hi-C data analysis: methods and protocols" volume of the Methods in Molecular Biology book series by Springer. 2021 IN PRESS
    2021 IN PRESS
    (* co-corresponding authors)

  2. Hariprakash JM, Ferrari F.
    Computational biology solutions to identify enhancers-target gene pairs.
    Comput Struct Biotechnol J. 2019 Jun 14;17:821-831.

  3. Pal K, Forcato M*, Ferrari F.*.
    Hi-C analysis: from data generation to integration
    (Review article) Biophysical Reviews, 2018 Dec 20 [Epub ahead of print]. doi: 10.1007/s12551-018-0489-1. (* co-corresponding/co-last authors)

Other publications arising from collaborations of the research group

  1. Morello G, Cancila V, La Rosa M, Germano G, Lecis D, Amodio V, Zanardi F, Iannelli F, Greco D, La Paglia L, Fiannaca A, Urso AM, Graziano G, Ferrari F, Pupa SM, Sangaletti S, Chiodoni C, Pruneri G, Bardelli A, Colombo MP, Tripodo C.
    T Cells Expressing Receptor Recombination/Revision Machinery Are Detected in the Tumor Microenvironment and Expanded in Genomically Over-unstable Models.
    Cancer Immunol Res. 2021 May 3. PMID: 33941587

  2. Arnone CM, Polito VA, Mastronuzzi A, Carai A, Diomedi FC, Antonucci L, Petrelli LL, Vinci M, Ferrari F, Salviato E, Scarsella M, De Stefanis C, Weber G, Quintarelli C, De Angelis B, Brenner MK, Gottschalk S, Hoyos V, Locatelli F, Caruana I, Del Bufalo F.
    Oncolytic adenovirus and gene therapy with EphA?2-BiTE? for the treatment of pediatric high-grade gliomas.
    J Immunother Cancer. 2021 May;9(5):e001930. PMID: 33963009

  3. Atashpaz S, Samadi Shams S, Martin Gonzalez J, Sebestyén E, Minardi S, Allievi E, Arghavanifard N, Gnocchi A, Albers E, Falco G, Fernandez-Capetillo O, Ferrari F., López-Contreras AJ, Costanzo V.
    ATR expands embryonic stem cell fate potential in response to replication stress.
    Elife. 2020 Mar 12;9:e54756

  4. Bianchi A, Mozzetta C, Pegoli G, Lucini F, Valsoni S, Rosti V, Petrini C, Cortesi A, Gregoretti F, Antonelli L, Oliva G, De Bardi M, Rizzi R, Bodega B, Pasini D, Ferrari F., Bearzi C, Lanzuolo C.
    Dysfunctional polycomb transcriptional repression contributes to Lamin A/C dependent muscular dystrophy.
    J Clin Invest. 2020 May 1;130(5):2408-2421.

  5. De Simone G, Mazza EMC, Cassotta A, Davydov AN, Kuka M, Zanon V, De Paoli F, Scamardella E, Metsger M, Roberto A, Pilipow K, Colombo FS, Tenedini E, Tagliafico E, Gattinoni L, Mavilio D, Peano C, Price DA, Singh SP, Farber JM, Serra V, Cucca F, Ferrari F., Orrù V, Fiorillo E, Iannacone M, Chudakov DM, Sallusto F, Lugli E.
    CXCR3 Identifies Human Naive CD8(+) T Cells with Enhanced Effector Differentiation Potential.
    J Immunol. 2019 Dec 15;203(12):3179-3189.

  6. Brummelman J, Mazza EMC, Alvisi G, Colombo FS, Grilli A, Mikulak J, Mavilio D, Alloisio M, Ferrari F., Lopci E, Novellis P, Veronesi G, Lugli E.
    High-dimensional single cell analysis identifies stem-like cytotoxic CD8(+) T cells infiltrating human tumors.
    J Exp Med. 2018 Oct 1;215(10):2520-2535.

PI's postdoctoral and graduate work - selected publications

  1. De Los Angeles A*, Ferrari F.*, Fujiwara Y, Mathieu R, Lee S, Lee S, Tu H, Ross S, Chou S, Nguyen M, Wu Z, Theunissen TW, Powell BE, Imsoonnthornruksa S, Chen J, Borkent M, Krupalnik V, Lujan E, Wernig M, Hanna JH, Hochedlinger K, Pei D, Jaenisch R, Deng H, Orkin SH, Park PJ, Daley GQ.
    Failure to Replicate the STAP Cell Phenomenon.
    Nature, 2015 Sep 24;525(7570):E6-9. (* equal contribution)

  2. De Los Angeles A, Ferrari F., Xi R, Fujiwara Y, Benvenisty N, Deng H, Hochedlinger K, Jaenisch R, Lee S, Leitch HG, Lensch MW, Lujan E, Pei D, Rossant J, Wernig M, Park PJ, Daley GQ.
    Hallmarks of Pluripotency.
    (Review article) Nature 2015 Sep 23;525(7570):469-78.

  3. Biagioli M*, Ferrari F.*, Mendenhall EM, Zhang Y, Erdin S, Vijayvargia R, Vallabh SM, Solomos N, Manavalan P, Ragavendran A, Ozsolak F, Lee JM, Talkowski ME, Gusella JF, MacDonald ME, Park PJ, Seong IS.
    Htt CAG repeat expansion confers pleiotropic gains of mutant huntingtin function in chromatin regulation.
    Hum Mol Genet., 2015 May 1;24(9):2442-57. Epub 2015 Jan 8. (* equal contribution)

  4. Cheloufi S, Elling U, Hopfgartner B, Jung YL, Murn J, Ninova M, Hubmann M, Badeaux AI, Euong Ang C, Tenen D, Wesche DJ, Abazova N, Hogue M, Tasdemir N, Brumbaugh J, Rathert P, Jude J, Ferrari F., Blanco A, Fellner M, Wenzel D, Zinner M, Vidal SE, Bell O, Stadtfeld M, Chang HY, Almouzni G, Lowe SW, Rinn J, Wernig M, Aravin A, Shi Y, Park PJ, Penninger JM, Zuber J, Hochedlinger K.
    The histone chaperone CAF-1 safeguards somatic cell identity.
    Nature 2015 Dec 10;528(7581):218-24.

  5. Choi J, Lee S, Mallard W, Clement K, Malagoli-Tagliazucchi G, Lim H, Choi IY, Ferrari F., Tsankov AM, Pop R, Lee G, Rinn JL, Meissner A, Park PJ, Hochedlinger K.
    A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs.
    Nature Biotechnology 2015 Nov;33(11):1173-81.

  6. Ferrari F., Alekseyenko AA, Park PJ, Kuroda MI.
    Transcriptional control of a whole chromosome: emerging models for the molecular basis of dosage compensation.
    (Review article) Nature Structural and Molecular Biology, 2014 Feb;21(2):118-25.

  7. Ferrari F.*, Apostolou E*, Park PJ, Hochedlinger K.
    Rearranging the chromatin for pluripotency.
    Cell Cycle, 2014 January 15; 13(2):167-168 Epub 2013, Nov 15 (editorial commentary) (* equal contribution)

  8. Ho J, Jung Y, Liu T, Alver B, Lee S, Ikegami K, Sohn K, Minoda A, Tolstorukov M, Appert A, Parker S, Gu T, Kundaje A, Riddle N, Bishop E, Egelhofer T, Hu S, Alekseyenko A, Rechtsteiner A, Asker D, Belsky J, Bowman S, Chen Q, Chen R, Day D, Dong Y, Dos´ A, Duan X, Epstein C, Ercan S, Feingold E, Ferrari F., Garrigues J, Gehlenborg N, Good P, Haseley P, He D, Herrmann M, Hoffman M, Jeffers T, Kharchenko P, Kolasinska-Zwierz P, Kotwaliwale C, Kumar N, Langley S, Larschan E, Latorre I, Libbrecht M, Lin X, Park R, Pazin M, Pham H, Plachetka A, Qin B, Schwartz Y, Shoresh N, Stempor P, Vielle A, Wang C, Whittle C, Xue H, Kingston R, Kim J, Bernstein B, Dernburg A, Pirrotta V, Kuroda M, Noble W, Tullius T, Kellis M, MacAlpine D, Strome S, Elgin S, Liu X, Lieb J, Ahringer J, Karpen G, Park PJ.
    Comparative analysis of metazoan chromatin organization.
    Nature 2014, Aug 28;512(7515):449-52.

  9. Ferrari F.*, Plachetka A*, Alekseyenko AA*, Jung YL, Ozsolak F, Kharchenko PV, Park PJ, Kuroda MI.
    "Jumpstart and gain" model for dosage compensation in Drosophila based on direct sequencing of nascent transcripts.
    Cell Reports, 2013 Nov 14;5(3):629-636 (* equal contribution)

  10. Apostolou E*, Ferrari F.*, Walsh RM, Bar-Nur O, Stadtfeld M, Cheloufi S, Stuart HT, Polo JM, Ohsumi TK, Borowsky ML, Kharchenko PV, Park PJ, Hochedlinger K.
    Genome-wide interactions of the Nanog locus in pluripotency, differentiation and cellular reprogramming.
    Cell Stem Cell, 2013 Jun 6;12(6):699-712. (* equal contribution).

  11. Ferrari F.*, Jung YL*, Kharchenko PV, Plachetka A, Alekseyenko AA, Kuroda MI, Park PJ.
    Comment on 'Drosophila dosage compensation involves enhanced Pol II recruitment to male X-linked promoters'.
    Science, 2013 Apr 19;340(6130):273. (* equal contribution) (technical comment article: i.e. reanalysis challenging previous publication)

  12. Stadtfeld M*, Apostolou E*, Ferrari F., Choi J, Walsh RM, Chen T, Ooi SS, Kim SY, Bestor TH, Shioda T, Park PJ, Hochedlinger K.
    Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all-iPS cell mice from terminally differentiated B cells.
    Nature Genetics 2012 Mar 4;44(4):398-405, S1-2.

  13. Ferrari F., Solari A, Battaglia C, Bicciato S.
    PREDA: an R-package to identify regional variations in genomic data.
    Bioinformatics. 2011 Sep 1;27(17):2446-7.

  14. Gurumurthy S, Xie S.Z., Alagesan B, Kim J, Yusuf R.Z., Saez B, Tzatsos A, Oszolak F, Milos P, Ferrari F., Park P.J., Shirihai O, Scadden D.T., and Bardeesy N.
    Lkb1 regulates stem cell quiescence, energy metabolism, and cell survival in the hematopoietic system.
    Nature. 2010 Dec 2;468(7324):659-63.

  15. Martello G, Rosato A, Ferrari F., Manfrin A, Cordenonsi M, Dupont S, Enzo E, Guzzardo V, Rondina M, Spruce T, Parenti AR, Daidone MG, Bicciato S and Piccolo S.
    A microRNA targeting Dicer for metastasis control.
    Cell 2010 Jun 25; 141(7):1195-207.

  16. Coppe A*, Ferrari F.*, Bisognin A, Danieli GA, Ferrari S, Bicciato S, Bortoluzzi S.
    Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.
    Nucleic Acids Res. 2009; 37(2):533-49. Epub 2008 Dec 5. (*equal contribution).

  17. Ferrari F., Bortoluzzi S, Coppe A, Sirota A, Safran M, Shmoish M, Ferrari S, Lancet D, Danieli GA, Bicciato S.
    Novel definition files for human GeneChips based on GeneAnnot.
    BMC Bioinformatics. 2007 Nov 15;8:446

  18. Ferrari F., Bortoluzzi S, Coppe A, Basso D, Bicciato S, Zini R, Gemelli C, Danieli GA, Ferrari S.
    Genomic expression during human myelopoiesis.
    BMC Genomics. 2007 Aug 3;8(1):264

Uptade: Jun 2021