Publications by Marco Pellegrini

  Editorial activities

  1. Emes, R. D., Pirooznia, M., Zou, Q., Pellegrini, M., eds. (2023).
    Insights in computational genomics: 2022.
    Lausanne: Frontiers Media SA. doi: 10.3389/978-2-8325-3173-0
  2. Pellegrini, M., Antoniotti, M., Mishra, B., eds. (2023).
    Network bioscience volume II.
    Lausanne: Frontiers Media SA. doi: 10.3389/978-2-8325-3203-4
  3. Emes RD, Pirooznia M, Zou Q and Pellegrini M (2023)
    Editorial: Insights in computational genomics: 2022.
    Front. Genet. 14:1256011. doi: 10.3389/fgene.2023.1256011
  4. Antoniotti M, Mishra B and Pellegrini M (2023)
    Editorial: Network bioscience Volume II.
    Front. Genet. 14:1256025. doi: 10.3389/fgene.2023.1256025
  5. Pellegrini, M., Antoniotti, M., Mishra, B., eds. (2020).
    Network Bioscience.
    Lausanne: Frontiers Media SA. doi: 10.3389/978-2-88963-289-3
  6. Marco Antoniotti , Bud (Bhubaneswar) Mishra and Marco Pellegrini
    Editorial: Network Bioscience .
    Front. Genet. doi: 10.3389/fgene.2019.00858, 2019.
  7. Marco Pellegrini, Alberto Magi, Costas Iliopoulos (eds.)
    Repetitive Structures in Biological Sequences: Algorithms and Applications .
    Lausanne: Frontiers Media. doi: 10.3389/978-2-88945-018-3, 2016. ISBN: 9782889450183
  8. Marco Pellegrini, Alberto Magi, Costas Iliopoulos Editorial: Repetitive structures in biological sequences: open challenges .
    Front. Bioeng. Biotechnol. 4:66, July 2016. doi: 10.3389/fbioe.2016.00066
  9. Jaroslav Nesetril, Marco Pellegrini (Editors).
    Selected papers of Eurocomb 2013 .
    Special Issue of the European Journal of Combinatorics.
    Volume 48, August 2015, pp 1-234. Elsevier. ISSN 0195-6698. In print
  10. Jiri Matousek, Jaroslav Nesetril, Marco Pellegrini (Editors).
    Geometry, Structure and Randomness in Combinatorics
    Publications of the Scuola Normale Superiore / CRM Series vol 18. 2015. ISBN-13: 9788876425240
  11. Jaroslav Nesetril, Marco Pellegrini (Editors).
    The Seventh European Conference on Combinatorics, Graph Theory and Applications: EuroComb 2013
    Publications of the Scuola Normale Superiore / CRM Series vol 16. 2013. ISBN-13: 978-8876424748.
  12. F. Geraci, R. Marangoni, M. Pellegrini and M. Elena Renda (Editors).
    Proceedings of the 8th Annual Meeting of the Bioinformatics Italian Society, BITS 2011.
    Pisa, Italy. June 2011. Edizioni ETS. ISBN 978-884673069-5.
  13. M. Pellegrini, A. L. N. Fred, J. Filipe and H. Gamboa (Editors).
    BIOINFORMATICS 2011 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms,
    Rome, Italy, 26-29 January, 2011. SciTePress 2011. ISBN 978-989- 8425-36-2.

  Chapters in Books

  1. Marco Pellegrini
    Advances in Network-Based Drug Repositioning
    In: Cantone, D., Pulvirenti, A. (eds) From Computational Logic to Computational Biology.
    Lecture Notes in Computer Science (2024), vol 14070. Springer, Cham. https://doi.org/10.1007/978-3-031-55248-9_5
  2. Fiscon G., Conte F., Farina L., Pellegrini M., Russo F., Paci P.
    Identification of Disease-miRNA Networks Across Different Cancer Types Using SWIM.
    In: Laganà A. (eds) MicroRNA Target Identification. Methods in Molecular Biology.
    vol 1970, (2019), pp 169-181, Humana Press, New York, NY. ISBN 978-1-4939-9206-5.
  3. Francesco Russo, Giulia Fiscon, Federica Conte, Milena Rizzo, Paola Paci, and Marco Pellegrini
    Interplay between long non-coding RNAs and microRNAs in cancer
    In Computational Cell Biology, Methods and Protocols, von Stechow, Louise, Santos Delgado, Alberto (Eds.)
    Humana Press, Springer-Nature, 2018, ISBN 978-1-4939-8617-0.
  4. M. Pellegrini Community Detection in Biological Networks
    In Encyclopedia of Bioinformatics and Computational Biology Elsevier, 2018, DOI: 10.1016/B978-0-12-809633-8.20428-7.
  5. Francesco Russo, Kirstine Belling, Anders Boeck Jensen, Flavia Scoyni, Soren Brunak, Marco Pellegrini
    MicroRNAs, Regulatory Networks, and Comorbidities: Decoding Complex Systems
    In MicroRNA Detection and Target Identification: Methods and Protocols, 2017, Springer New York, ISBN 978-1-4939-6866-4
  6. M. Pellegrini Ray shooting and lines in space
    In Handbook of Discrete and Computational Geometry - third edition Csaba D. Toth, Jacob E. Goodman and Joseph O'Rourke (eds.). Chapman & Hall/CRC Press, Boca Raton, Florida. ISBN 9781498711395. Published Nov. 9th 2017.
  7. Francesco Russo, Flavia Scoyni, Alessandro Fatica, Marco Pellegrini, Alfredo Ferro, Alfredo Pulvirenti and Rosalba Giugno.
    Circulating Non-Coding RNAs as Clinical Biomarkers
    In Epigenetic Biomarkers and Diagnostics , Elsevier, 2015, ISBN 9780128018996
  8. M. Pellegrini Ray shooting and lines in space
    In Handbook of Discrete and Computational Geometry - second edition Jacob E. Goodman and Joseph O'Rourke (eds.). Chapman & Hall/CRC Press, Boca Raton, Florida, pp. 839-856, 2004.
  9. M. Pellegrini Measuring Lines in Space - a Collection of Results
    In Homenatge al professor Lluis Santalo , Carles Barcelo i Vidal (ed). University of Girona, Girona, Spain, pp. 99-111, 2002.
  10. M. Pellegrini Ray-shooting and lines in space.
    In The CRC Handbook of Discrete and Computational Geometry Jacob E. Goodman and Joseph O'Rourke (eds.). CRC Press, Boca Raton, Florida, pp. 599-614, 1997.

  Articles in Professional Journals

  1. Maristella Canovai, Monica Evangelista, Alberto Mercatanti, Romina D'Aurizio, Letizia Pitto, Francesca Marrocolo, Valentina Casieri, Marco Pellegrini, Vincenzo Lionetti, Sergio Bracarda, Milena Rizzo
    Secreted miR-210-3p, miR-183-5p and miR-96-5p reduce sensitivity to docetaxel in prostate cancer cells.
    Cell Death Discov. 9, 445 (2023). https://doi.org/10.1038/s41420-023-01696-4
  2. M. Pellegrini
    Accurate prognosis for localized prostate cancer through coherent voting networks with multi-omic and clinical data
    Sci Rep 13, 7875 (2023). https://doi.org/10.1038/s41598-023-35023-9
    Preprint January 2023. medRxiv 2022.07.28.22278156; doi: https://doi.org/10.1101/2022.07.28.22278156
  3. M. Lucchetta , M. Pellegrini
    Drug Repositioning by Merging Active Subnetworks Validated in Cancer and COVID-19
    Sci Rep 11, 19839 (2021). https://doi.org/10.1038/s41598-021-99399-2
    Preprint May 2021 medRxiv https://doi.org/10.1101/2021.05.13.21257140
  4. M. Pellegrini
    Accurate Prediction of Breast Cancer Survival through Coherent Voting Networks with Gene Expression Profiling
    Sci Rep 11, 14645 (2021). https://doi.org/10.1038/s41598-021-94243-z
    Preprint October 2020. medRxiv 2020.10.28.20221671; doi: https://doi.org/10.1101/2020.10.28.20221671
  5. M. Lucchetta , M. Pellegrini
    Finding disease modules for cancer and COVID-19 in gene co-expression networks with the Core&Peel method
    Sci Rep 10, 17628 (2020). https://doi.org/10.1038/s41598-020-74705-6
  6. Fazio, S.; Berti, G.; Russo, F.; Evangelista, M.; D'Aurizio, R.; Mercatanti, A.; Pellegrini, M.; Rizzo, M.
    The miR-28-5p Targetome Discovery Identified SREBF2 as One of the Mediators of the miR-28-5p Tumor Suppressor Activity in Prostate Cancer Cells.
    Cells 2020, 9, 354. https://doi.org/10.3390/cells9020354, MDPI.
  7. Elena Guzzolino, Mario Pellegrino, Neha Ahuja, Deborah Garrity, Romina D'Aurizio, Marco Groth, Mario Baumgart, Cathy J Hatcher, Alberto Mercatanti, Monica Evangelista, Chiara Ippolito, Elisabetta Tognoni, Ryuichi Fukuda, Vincenzo Lionetti, Marco Pellegrini, Federico Cremisi, Letizia Pitto.
    miR-182-5p is an evolutionarily conserved Tbx5 effector that impacts cardiac development and electrical activity in zebrafish
    Cell. Mol. Life Sci. (2019). https://doi.org/10.1007/s00018-019-03343-7. Springer Verlag.
  8. Andrea Marranci, Romina D'Aurizio, Sebastian Vencken, Serena Mero, Elena Guzzolino, Milena Rizzo, Letizia Pitto, Marco Pellegrini, Giovanna Chiorino, Catherine M. Greene and Laura Poliseno.
    Systematic evaluation of the microRNAome through miR-CATCHv2.0 identifies positive and negative regulators of BRAF-X1 mRNA,
    RNA Biology (2019), doi: 10.1080/15476286.2019.1600934. Taylor & Francis Group.
  9. Guzzardi M., Ait Ali L., D'Aurizio R., Rizzo F., Saggese P., Sanguinetti E., Weisz, A., Pellegrini M., Iozzo P.,
    Fetal cardiac growth is associated with in utero gut colonization,
    Nutrition, Metabolism and Cardiovascular Diseases (2019), 29(2) pp. 170-176. doi: https://doi.org/10.1016/j.numecd.2018.10.005
  10. Loredana M. Genovese, Marco M. Mosca, Marco Pellegrini, Filippo Geraci
    Dot2dot: Accurate Whole-Genome Tandem Repeats Discovery
    Bioinformatics , DOI: https://doi.org/10.1093/bioinformatics/bty747, Oxford University Press, 27 Aug 2018.
  11. Genovese LM, Geraci F, Corrado L, Mangano E, D'Aurizio R, Bordoni R, Severgnini M, Manzini G, De Bellis G, D'Alfonso S and Pellegrini M
    A Census of Tandemly Repeated Polymorphic Loci in Genic Regions Through the Comparative Integration of Human Genome Assemblies
    Front. Genet. (2018) 9:155. doi: 10.3389/fgene.2018.00155
  12. Francesco Russo, Sebastiano Di Bella, Federica Vannini, Gabriele Berti, Flavia Scoyni, Helen V. Cook, Alberto Santos, Giovanni Nigita, Vincenzo Bonnici, Alessandro Lagan�, Filippo Geraci, Alfredo Pulvirenti, Rosalba Giugno, Federico De Masi, Kirstine Belling, Lars J. Jensen, Soren Brunak, Marco Pellegrini, Alfredo Ferro
    miRandola 2017: a curated knowledge base of non-invasive biomarkers.
    Nucleic Acids Research. Database issue 2018. doi.org/10.1093/nar/gkx854
  13. Gabriele Berti, Francesco Russo, Milena Rizzo, Giuseppe Rainaldi, Monica Evangelista, Marco Pellegrini.
    The miRNA pull out assay as a method to validate the miR-28-5p targets identified in other tumor contexts in prostate cancer.
    International Journal of Genomics. Hindawi. 2017. Article ID 5214806.
  14. Milena Rizzo, Gabriele Berti, Francesco Russo, Sofia Fazio, Monica Evangelista, Romina D'Aurizio, Marco Pellegrini, Giuseppe Rainaldi.
    Discovering the miR-26a-5p Targetome in Prostate Cancer Cells.
    Journal of Cancer. 2017; 8(14): 2729-2739. doi: 10.7150/jca.18396
  15. Lorenzo Bascetta, Arianna Oliviero, Romina D'Aurizio, Monica Evangelista, Alberto Mercatanti, Marco Pellegrini, Francesca Marrocolo, Sergio Bracarda, Milena Rizzo.
    The Prostate Cancer Cells Resistant to Docetaxel as in vitro Model for Discovering MicroRNAs Predictive of the Onset of Docetaxel Resistance.
    Int. J. Mol. Sci. 2017, 18(7), 1512; doi:10.3390/ijms18071512.
  16. Marianna Vitiello, Andrea Tuccoli, Romina D�Aurizio, Samanta Sarti, Laura Giannecchini, Simone Lubrano, Andrea Marranci, Monica Evangelista, Silvia Peppicelli, Chiara Ippolito, Ivana Barravecchia, Elena Guzzolino, Valentina Montagnani, Michael Gowen, Elisa Mercoledi, Alberto Mercatanti, Laura Comelli, Salvatore Gurrieri, Lawrence W Wu, Omotayo Ope, Keith Flaherty, Genevieve M Boland, Marc R Hammond, Lawrence Kwong, Mario Chiariello, Barbara Stecca, Gao Zhang, Alessandra Salvetti, Debora Angeloni, Letizia Pitto, Lido Calorini, Giovanna Chiorino, Marco Pellegrini, Meenhard Herlyn, Iman Osman, Laura Poliseno
    Context-dependent miR-204 and miR-211 affect the biological properties of amelanotic and melanotic melanoma cells
    Oncotarget , vol 8, issue 15, pages 25395-25417, 2017. doi: 10.18632/oncotarget.15915
  17. R. D'Aurizio, T. Pippucci, L. Tattini, B. Giusti, M. Pellegrini, A. Magi
    Enhanced copy number variants detection from whole-exome sequencing data using EXCAVATOR2
    Nucleic Acids Research , 2016. doi: 10.1093/nar/gkw695. Aug. 2016.
  18. Romina D'Aurizio, Francesco Russo, Elena Chiavacci, Mario Baumgart, Marco Groth, Mara D'Onofrio, Ivan Arisi, Giuseppe Rainaldi, Letizia Pitto, Marco Pellegrini
    Discovering miRNA regulatory networks in Holt-Oram Syndrome using a Zebrafish model
    Front. Bioeng. Biotechnol, 14 July 2016, 4:60. doi: 10.3389/fbioe.2016.00060
  19. M. Pellegrini, M. Baglioni, F. Geraci.
    Protein complex prediction for large protein protein interaction networks with the Core&Peel Method
    BMC Bioinformatics 17(S-12): 37-58 (2016) .
    Also available on bioRxiv.org doi: http://dx.doi.org/10.1101/053876, 2016.
  20. Monica Evangelista, Mariama El Baroudi, Milena Rizzo, Andrea Tuccoli, Laura Poliseno, Marco Pellegrini, Giuseppe Rainaldi
    Alkaline Phosphatase-Positive Immortal Mouse Embryo Fibroblasts Are Cells in a Transitional Reprogramming State Induced to Face Environmental Stresses.
    In Genetics & epigenetics . Vol 7. pages 33-45, 2015
  21. Elena Chiavacci, Romina D'Aurizio, Elena Guzzolino, Francesco Russo, Mario Baumgart, Marco Groth, Laura Mariani, Mara D�Onofrio, Ivan Arisi, Marco Pellegrini, Alessandro Cellerino, Federico Cremisi, Letizia Pitto
    MicroRNA 19a replacement partially rescues fin and cardiac defects in zebrafish model of Holt Oram syndrome .
    Scientific Reports 5, art. num 18240 (2015). doi:10.1038/srep18240
  22. M. Pellegrini
    Tandem Repeats in Proteins: Prediction Algorithms and Biological Role
    Front Bioeng Biotechnol. 2015; 3: 143. doi: 10.3389/fbioe.2015.00143. Sept 2015.
  23. M Schirripa, F Loupakis, C Cremolini, L Poliseno, L Salvatore, A Tuccoli, C Antoniotti, R D'Aurzio, F Marmorino, B Borelli, D Rossini, A Saettini, S Gini, R Moretto, I Rizzo, E Dell'Aquila, M Pellegrini, A Falcone
    P-198Circulating microRNAs in metastatic colorectal cancer (mCRC) patients (pts) treated with regorafenib .
    Annals of Oncology 26, suppl 4, pages iv57, June 2015
  24. M. Baglioni, F. Russo, F. Geraci, M. Rizzo, G. Rainaldi and M. Pellegrini.
    A new method for finding disease-specific miRNA-target regulatory networks.
    Plos One . 10(4): e0122473. doi:10.1371/journal.pone.0122473 April 2015.
  25. Andrea Marranci, Andrea Tuccoli, Marianna Vitiello, Elisa Mercoledi, Samanta Sarti, Simine Lubrano, Monica Evangelista, Antonella Fogli, Camilo Valdes, Francesco Russo, Massimo Dal Monte, Maria Adelaide Caligo, Marco Pellegrini, Enrico Capobianco, Nicholas Tsinoremas and Laura Poliseno.
    Identification of BRAF 3-UTR isoforms in melanoma .
    Journal of Investigative Dermatology . Epub Feb 2015. doi: 0.1038/jid.2015.47
  26. M. Leoncini, M. Montangero, M. Pellegrini, K. P. Tillan,
    CMStalker: a combinatorial tool for composite motif discovery .
    IEEE/ACM Transactions on Computational Biology and Bioinformatics
    vol.12, no.5, pp.1123-1136, Sept.-Oct. 1 2015, doi: 10.1109/TCBB.2014.2359444
    Supplementary materials
  27. Francesco Russo, Sebastiano Di Bella, Vincenzo Bonnici, Alessandro Laganà, Giuseppe Rainaldi, Marco Pellegrini, Alfredo Pulvirenti, Rosalba Giugno, Alfredo Ferro.
    A knowledge base for the discovery of function, diagnostic potential and drug effects on cellular and extracellular miRNAs .
    BMC Genomics 15(Suppl 3), S4, 2014
  28. M. Baglioni, F. Geraci, M. Pellegrini, E. Lastres.
    Fast exact and approximate computation of betweenness centrality in social networks
    State of the Art Applications of Social Network Analysis.
    In the series Lecture Notes in Social Networks 2014, pages 53-73, Springer International Publishing.
  29. M. Pellegrini, M. Elena Renda and A. Vecchio.
    Tandem Repeats Discovery Service (TReaDS) applied to finding novel Cis-acting factors in Repeat Expansion Diseases .
    BMC Bioinformatics 2012, Vol. 13(Suppl 4):S3, doi:10.1186/1471-2105-13-S4-S3. March 2012.
  30. M. Pellegrini, M. Elena Renda and A. Vecchio.
    Ab Initio Detection of Fuzzy Amino Acid Tandem Repeats in Protein Sequences.
    BMC Bioinformatics 2012, Vol. 13(Suppl 3):S8, doi:10.1186/1471-2105-13-S3-S8. March 2012.
  31. M. Pellegrini, M. Elena Renda and A. Vecchio.
    TRStalker: an Efficient Heuristic for Finding Fuzzy Tandem Repeats
    Bioinformatics 26(12), pp. i358-366, 2010.
    Special issue on Proceedings of the 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2010). Boston, MA, July 11-13, 2010.
  32. M. Furini, F. Geraci, M. Montangero and M. Pellegrini.
    STIMO: STIll and MOving Video Storyboard for the Web Scenario
    Multimedia Tools and Applications , Vol. 46, Num. 1 pp. 47-69, 2010.
  33. Y. Dourisboure, F. Geraci and M. Pellegrini.
    Extraction and Classification of Dense Implicit Communities in the Web Graph
    ACM Transactions on the WEB, Vol 3, Num 2, Art 7, April 2009.
  34. F. Geraci, M. Leoncini, M. Montangero, M. Pellegrini and M. Elena Renda.
    K-boost: A Scalable Algorithm for High Quality Clustering of Microarray Gene Expression Data
    Journal of Computational Biology. Vol. 16, Num. 6 pp. 859-873, June 2009.
  35. L. M. Genovese, F. Geraci, M. Pellegrini.
    SpeedHap: An Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage IEEE/ACM Transactions on Computational Biology and Bioinformatics 5(4), pp. 492-502, 2008. IEEE Computer Society. DOI: http://doi.ieeecomputersociety.org/10.1109/TCBB.2008.67
  36. F. Geraci, M. Pellegrini, E. Renda. AMIC@: All MIcroarray Clusterings @ once.
    Nucleic Acids Research , Vol. 36, Web Server Issue W315~W319, 2008.
  37. M. Pellegrini and G.Fusco. Efficient IP Table Lookup via Adaptive Stratified Trees with Selective Reconstructions .
    The ACM Journal of Experimental Algorithmics , Vol 12, Num 1.4, 2007.
  38. F. Geraci, M. Pellegrini, F. Sebastiani and M. Maggini. Cluster Generation and Cluster Labelling for Web Snippets:A Fast and Accurate Hierarchical Solution.
    Internet Mathematics , 3(4) pp. 413-444, 2007.
  39. L. Galluccio, G. Morabito, S. Palazzo, M. Pellegrini, M. E. Renda and P. Santi. GEOROY: A Location-Aware Enhancement to Viceroy Peer-to-Peer Algorithm .
    Computer Networks , 51(8), pp. 1998-2014, 2007.
  40. G. De Marco, M. Pellegrini and G. Sburlati. Faster Deterministic Wakeup in Multiple Access Channels
    Discrete Applied Mathematics , 155(8), pp. 898-903, 2007.
  41. D. Finocchiaro and M. Pellegrini. On computing the diameter of a point set in high dimensional Euclidean space.
    Theoretical Computer Science , 287(2),pp. 501-514, September 2002
  42. M. Pellegrini. Electrostatic Fields without Singularities: Theory, Algorithms and Error Analysis.
    Journal of the ACM. 45(6), pp. 924-964, November 1998. Also TR IMC B4-97-15.
  43. D. Finocchiaro, M. Pellegrini and P. Bientinesi. On Numerical Approximation of Electrostatic Energy in 3D. Journal of Computational Physics 146/2, pp. 707-725, 1998.
  44. M. Pellegrini. Monte Carlo Approximation of Form Factors with Error Bounded a Priori.
    Discrete & Computational Geometry 17 (3), pp. 319-338, April 1997.
  45. M. Pellegrini. On counting pairs of intersecting segments and off-line triangle range searching. Algorithmica 17 (4), pp. 380-398, April 1997.
  46. M. Pellegrini. On Point Location and Motion Planning in Arrangements of Simplices.
    SIAM J. on Computing, 25 (5), pp. 1061-1081, October 1996.
  47. M. Pellegrini. Repetitive Hidden Surface Removal for Polyhedra.
    Journal of Algorithms, 21, pp. 80-101, 1996.
  48. M. Pellegrini. On Lines Missing Polyhedral Sets in 3-space.
    Discrete & Computational Geometry, 12, pp. 203-221, 1994.
  49. M. Pellegrini. On Collision-Free Placements of Simplices and the Closest Pair of Lines in 3-Space. SIAM J. on Computing, 23 (1), pp. 133-153, 1994.
  50. P.K. Agarwal, M. Pellegrini, and M. Sharir. Counting circular arcs intersections.
    SIAM J. on Computing, 22 (4), 1993.
  51. B. Aronov, M. Pellegrini, and M. Sharir. On the zone of an algebraic surface in a hyperplane arrangement. Discrete & Computational Geometry, 9 (2), pp. 177-188, 1993.
  52. M. Pellegrini. Ray-shooting on triangles in 3-dimensional space.
    Algorithmica, 9, pp. 471-494, 1993.
  53. M. Pellegrini. Lower Bounds for Line Stabbing in 3-Space.
    Computational Geometry: Theory and Applications, 3, pp. 53-58, 1993.
  54. M. Pellegrini and P. Shor. Finding stabbing lines in 3-space.
    Discrete & Computational Geometry, 8, pp. 191-208, 1992.
  55. M. Pellegrini and R. Sepe. Setlog, a tool for experimenting with new semantics.
    Sigplan Notices, 26(2):67-74, February 1991.
  56. M. Pellegrini. Point location and halfspace retrieval.
    AICA-Rivista d'informatica, 20(4), pp. 303-344, Ottobre-Dicembre 1990.

  Refereed Conference Papers

  1. Giacomini G., Ciravegna G., Pellegrini M., D'Aurizio R., Bianchini M.
    A Transcriptional Study of Oncogenes and Tumor Suppressors Altered by Copy Number Variations in Ovarian Cancer.
    In: Chen YW., Tanaka S., Howlett R., Jain L. (eds) Innovation in Medicine and Healthcare. Smart Innovation, Systems and Technologies, vol 192. Springer, Singapore. (2020) https://doi.org/10.1007/978-981-15-5852-8_15
  2. Indrajit Saha, Shib Sankar Bhowmick, Filippo Geraci, Marco Pellegrini, Debotosh Bhattacharjee, Ujjwal Maulik, Dariusz Plewczynski.
    Analysis of Next-Generation Sequencing Data of miRNA for the Prediction of Breast Cancer
    In proceedings of the International Conference on Swarm, Evolutionary, and Memetic Computing (SEMCCO). 2015. pages 116-127.
    Springer International Publishing. LNCS, volume 9873. ISBN 978-3-319-48958-2
  3. E. Bergamini, R. D'Aurizio, M. Leoncini, M. Pellegrini,
    CNVScan: detecting borderline copy number variations in NGS data via scan statistics .
    In Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (BCB 2015)
    pages 335-344, 2015. doi: 10.1145/2808719.2808754, Atlanta, GA, USA, September 9-12, 2015
  4. Pinaki Bhaskar, Marina Buzzi, Filippo Geraci, Marco Pellegrini:
    From Literature to Knowledge: Exploiting PubMed to Answer Biomedical Questions in Natural Language
    In proceedings of Information Technology in Bio- and Medical Informatics - 6th International Conference ITBAM 2015
    pages 3-15, doi: 10.1007/978-3-319-22741-2_1. Valencia, Spain, September 3-4, 2015
  5. M. Leoncini, M. Montangero, M. Pellegrini, K. P. Tillan,
    CMF: a combinatorial tool to find composite motifs .
    In Proceedings of the Learning and Intelligent OptimizatioN Conference, LION 7.
    Lecture Notes in Computer Science, Vol. 7997, pages 196-208. ISBN 978-3-642-44973-4
    Catania - Italy, Jan 7-11, 2013.
  6. M. Baglioni, F. Geraci, M. Pellegrini and E. Lastres,
    Fast exact computation of betweenness centrality in social networks .
    In Proceedings of the 2012 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM 2012),
    Istambul, Turkey, 26-29 August 2012. Pages 450 - 456. ISBN: 978-1-4673-2497-7
  7. M. Pellegrini and M. Elena Renda and A. Vecchio.
    Detecting Fuzzy Amino Acid Tandem Repeats in Protein Sequences
    Proceedings of ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2011 (ACM-BCB), Chicago, IL. August 1-3, 2011.
  8. Felicioli, Claudio, Filippo Geraci, and Marco Pellegrini.
    Medium sized crawling made fast and easy through Lumbricus webis
    In International Conference on Machine Learning and Cybernetics (ICMLC), 2011, vol. 4, pp. 1920-1926. IEEE, 2011.
  9. M. Budinich, B. Codenotti, F. Geraci and M. Pellegrini.
    On the benefits of keyword spreading in sponsored search auctions: an experimental analysis
    Proceedings of the 11th International Conference on Electronic Commerce and Web Technologies (EC-Web 2010)
    Bilbao, Spain, Aug 30 - Sep 3, 2010.
  10. F. Geraci and M. Pellegrini.
    ReHap: an Integrated System for the Haplotype Assembly Problem from Shotgun Sequencing Data
    Proceedings of Bionformatics 2010, INSTICC (Institute for Systems and Technologies of Information, Control and Communication). 2010.
    Valencia, Spain. 20-23 January 2010.
  11. F. Geraci, M. Pellegrini and M. Elena Renda.
    An Efficient Combinatorial Approach for Solving the DNA Motif Finding Problem
    Proceedings of the 9th International Conference on Intelligent Systems Design and Applications (ISDA 09).
    Pisa, Italy, November 30- December 2, 2009. 335-340.
  12. F. Geraci and M. Pellegrini.
    Dynamic User-defined Similarity Searching in Semi-structured Text Retrieval.
    Proceedings of Infoscale 2008, The Third International ICST Conference on Scalable Information Systems.
    Vico Equense, Napoli, June 4-6, 2008. In print.
  13. M. Furini, F. Geraci, M. Montangero and M. Pellegrini.
    On Using Clustering Algorithms to Produce Video Abstracts for the Web Scenario
    In Proceedings of IEEE CCNC2008 Fifth IEEE Consumer Communications & Networking Conference,
    Las Vegas, Nevada, January 10-12, 2008. pages 1112-1116.
  14. L.M. Genovese, F. Geraci and M. Pellegrini.
    A Fast and Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage
    In Proceedings of the 7th Workshop on Algorithms in Bioinformatics (WABI 2007),
    Philadelphia, Pennsylvania, September 8-9, 2007. LNCS 4645, pages 49-60.
  15. M. Furini, F. Geraci, M. Montangero and M. Pellegrini.
    VISTO: VIsual STOryboard for Web Video Browsing
    In Proceedings of ACM CIVR International Conference on Image and Video Retrieval 2007,
    Amsterdam, The Netherlands, July 9-11, 2007.
  16. F. Geraci, M. Leoncini, M. Montangero, M. Pellegrini and M. Elena Renda.
    FPF-SB: A Scalable Algorithm for Microarray Gene Expression Data Clustering
    In Proceedings of HCI International 2007,
    Bejing, China, 22-27 July 2007.
  17. Y. Dourisboure, F. Geraci and M. Pellegrini.
    Extraction and classification of dense communities in the Web
    In Proceedings of the 16th International World Wide Web Conference (WWW2007),
    Banff, Alberta, Canada. May 2007.
  18. F. Geraci, M. Pellegrini, M. Maggini and F. Sebastiani.
    Cluster Generation and Cluster Labelling for Web Snippets: A Fast and Accurate Hierarchical Solution
    In Proceedings of the 13th Symposium on String Processing and Information Retrieval (SPIRE 2006), pages 25-36,
    Glasgow, UK. October 2006.
  19. F. Geraci, M. Pellegrini, F. Sebastiani and P. Pisati. A Scalable Algorithm for High-Quality Clustering of Web Snippets
    In Proceedings of the 21st Annual ACM Symposium on Applied Computing (SAC 2006), pages 1058-1062
    Dijon, France. April 2006.
  20. G. De Marco, M. Pellegrini and G. Sburlati. Faster Deterministic Wakeup in Multiple Access Channels
    In Proceedings of the 9th Italian Conference on Theoretical Computer Science (ICTCS).
    Siena, Italy. October 2005.
  21. F. Geraci, M. Pellegrini, P. Pisati and L. Rizzo. Packet Classification via Improved Space Decomposition Techniques.
    In Proceedings of IEEE Infocom 2005, volume 1, pages 304- 312.
    Also Technical Report IIT TR-10/2004, Istituto di Informatica e Telematica del C.N.R. Pisa, Italy.
    [Data and Code]
  22. M. Pellegrini and G. Fusco. Efficient IP Table Lookup via Adaptive Stratified Trees with Selective Reconstructions.
    In Proceedings of the 12th European Symposium on Algorithms, Lecture Notes in Computer Science 3221, pages 772-783, 2004 .
    [Data and Code]
  23. M. Pellegrini. Randomized Combinatorial Algorithms for Linear Programming when the Dimension is Moderately High.
    In Proceedings of the 12th ACM-SIAM Symposium on Discrete Algorithms, pages 101-108, 2001.
  24. D. Finocchiaro and M. Pellegrini. On computing the diameter of a point set in high dimensional Euclidean space.
    In Proceedings of the Seventh Annual European Symposium on Algorithms. Lecture Notes in Computer Science 1643, pages 366-377, 1999.
  25. M. Pellegrini. A Geometric Approach to Computing Higher Order Form Factors
    In Proceedings of the 15th ACM Symposium on Computational Geometry, pages 69-78, 1999.
  26. M. Pellegrini. Rendering equation revisited: how to avoid explicit visibility computations.
    In Proceedings of the 10th ACM-SIAM Symposium on Discrete Algorithms, pages 725-733, 1999.
  27. M. Pellegrini. Electrostatic Fields without Singularities: Theory and Algorithms.
    In Proceedings of the 7th ACM-SIAM Symposium on Discrete Algorithms, pages 184-191, 1996.
  28. M. Pellegrini. Monte Carlo Approximation of Form Factors with Error Bounded a Priori.
    In Proceedings of the 11th ACM Symposium on Computational Geometry, pages 287-296, 1995.
  29. M. Pellegrini. On Point Location and Motion Planning in Arrangements of Simplices.
    In Proceedings of the 26th ACM Symposium on Theory of Computing, pp. 95-104, 1994.
  30. M. Pellegrini. Repetitive Hidden-Surface-Removal for Polyhedral Scenes
    In Proceedings of the 3rd Workshop on Algorithms and Data Structures,
    Number 709 in Lecture Notes in Computer Science, pages 541-552. Springer Verlag, 1993
  31. M. Pellegrini. On Lines Missing Polyhedral Sets in 3-space.
    In Proceedings of the 9th ACM Symposium on Computational Geometry, pages 19-28, 1993.
  32. M. Pellegrini. Incidence and nearest-neighbor problems for lines in 3-space.
    In Proceedings of the 8th ACM Symposium on Computational Geometry, pages 130-137, 1992.
  33. M. Pellegrini. Ray shooting and isotopy classes of lines in 3-dimensional space.
    In Proceedings of the 2nd Workshop on Algorithms and Data Structures,
    Number 519 in Lecture Notes in Computer Science, pages 20-31. Springer Verlag, 1991.
  34. M. Pellegrini. On the zone of a codimension p surface in a hyperplane arrangement.
    In Proceedings of the Third Canadian Conference on Computational Geometry, pages 233-238, 1991.
  35. M. Pellegrini and P. Shor. Finding stabbing lines in 3-dimensional space.
    In Proceedings of the Second SIAM-ACM Symposium on Discrete Algorithms, pages 24-31, 1991.
  36. M. Pellegrini. Stabbing and ray shooting in 3-dimensional space.
    In Proceedings of the 6th ACM Symposium on Computational Geometry, pages 177-186, 1990.

  Short Articles in Professional Journals

  1. M. Pellegrini. Internet Protocol Table Lookup as a Geometric Problem
    ERCIM News No.50, July 2002.
  2. M. Pellegrini. A High Performance Computing Network for Protein Conformation Simulation
    ERCIM News No.43, October 2000.
  3. M. Pellegrini. From Computational Geometry to Computational Physics
    ERCIM News No.25, April 1996.

  Preprints and Technical Reports

  1. Marco Pellegrini
    Accurate prognosis for localized prostate cancer through coherent voting networks and multi-omic data
    medRxiv 2022.07.28.22278156; doi: https://doi.org/10.1101/2022.07.28.22278156 (July 2022)
  2. M. Pellegrini
    Accurate Prediction of Breast Cancer Survival through Coherent Voting Networks with Gene Expression Profiling
    Preprint October 2020. medRxiv 2020.10.28.20221671; doi: https://doi.org/10.1101/2020.10.28.20221671
  3. M. Lucchetta , M. Pellegrini
    Finding disease modules for cancer and COVID-19 in gene co-expression networks with the Core&Peel method
    Preprint May 2020 bioRxiv 2020.05.27.118414. doi: https://doi.org/10.1101/2020.05.27.118414
  4. F. Geraci, M. Leoncini, M. Montangero, M. Pellegrini and M. Elena Renda.
    K-boost: A Scalable Algorithm for High Quality Clustering of Microarray Gene Expression Data
    TR IIT-2007-015, Istituto di Informatica e Telematica del CNR. Pisa, Italy, December 2007
  5. M. Pellegrini. Fast Internet Packet Filtering on any Number of Attributes via Multi-dimensional Point Stabbing
    TR IMC B4-01-11, Istituto di Matematica Computazionale del CNR, Area della Ricerca, Pisa, Italy. March 2001.
  6. M. Pellegrini. Analysis of Average and Worst case error in Hierarchical Radiosity matrices
    TR IMC B4-99-12, Istituto di Matematica Computazionale del CNR, via Santa Maria 46, Pisa, Italy. June 1999.
  7. P. Bientinesi and M. Pellegrini. Electrostatic fields without singularities: implementation and experiments.
    TR IMC B4-97-16, Istituto di Matematica Computazionale del CNR, via Santa Maria 46, Pisa, Italy. November 1997.
Last update: July 19th, 2021
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