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:: Publications

:: Year 2023

  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. 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

:: Year 2022

  1. Roberta Croce, Lucia Corrado, Nadia Barizzone, Alice Di Pierro, Loredana Marialuisa Genovese, Filippo Geraci, Eleonora Mangano, Romina D'Aurizio, Roberta Bordoni, Davide Cora, Francesco Favero, Miriam Zuccala, Cristoforo Comi, Fabiola De Marchi, Luca Magistrelli, Giovanni Manzini, Gianluca De Bellis, Alfredo Brusco, Marco Severgnini, Marco Pellegrini, Letizia Mazzini, Sandra D'Alfonso
    Whole genome sequencing in neurodegenerative diseases: novel variants using different bioinformatics tools.
    In EUROPEAN JOURNAL OF HUMAN GENETICS 2022 Apr 1 (Vol. 30, No. SUPPL 1, pp. 305-305).
    CAMPUS, 4 CRINAN ST, LONDON, N1 9XW, ENGLAND: SPRINGERNATURE.

:: Year 2021

  1. 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
  2. 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
  3. Geraci F, Manzini G.
    EZcount: An all-in-one software for microRNA expression quantification from NGS sequencing data.
    Computers in Biology and Medicine. 2021 Jun 1;133:104352.
  4. Boucher C, Gagie T, Tomohiro I, Köppl D, Langmead B, Manzini G, Navarro G, Pacheco A, Rossi M.
    PHONI: Streamed matching statistics with multi-genome references.
    In 2021 Data Compression Conference (DCC) (pp. 193-202). IEEE.
  5. Travis Gagie, Garance Gourdel, and Giovanni Manzini.
    Compressing and Indexing Aligned Readsets
    In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 13:1-13:21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2021)

:: Year 2020

  1. Pellegrini, M., Antoniotti, M., Mishra, B., eds. (2020).
    Network Bioscience.
    Lausanne: Frontiers Media SA. doi: 10.3389/978-2-88963-289-3
  2. 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
  3. 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.
  4. 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
  5. L Corrado, R Croce, N Barizzone, A Di Pierro, LM Genovese, F Geraci, E Mangano, R D'Aurizio, R Bordoni, D Cora, F Favero, F De Marchi, G De Bellis, G Manzini, M Severgnini, M Pellegrini, L Mazzini, S D'Alfonso
    Identification of new variants in amyotrophic lateral sclerosis patients by whole genome sequencing data.
    In EUROPEAN JOURNAL OF HUMAN GENETICS 2020 Dec 1 (Vol. 28, No. SUPPL 1, pp. 422-423).
    CAMPUS, 4 CRINAN ST, LONDON, N1 9XW, ENGLAND: SPRINGERNATURE.
  6. Mun T, Kuhnle A, Boucher C, Gagie T, Langmead B, Manzini G.
    Matching reads to many genomes with the r-index.
    Journal of Computational Biology. 2020 Apr 1;27(4):514-8.
  7. Kuhnle A, Mun T, Boucher C, Gagie T, Langmead B, Manzini G.
    Efficient construction of a complete index for pan-genomics read alignment.
    Journal of Computational Biology. 2020 Apr 1;27(4):500-13.

:: Year 2019

  1. 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.
  2. Marco Antoniotti , Bud (Bhubaneswar) Mishra and Marco Pellegrini
    Editorial: Network Bioscience .
    Front. Genet. doi: 10.3389/fgene.2019.00858, 2019.
  3. 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.
     
  4. 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
     
  5. 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.
     
  6. Enrico Mini, Andrea Lapucci, Gabriele Perrone, Romina D'Aurizio, Cristina Napoli, Marco Brugia, Ida Landini, Renato Tassi, Lucia Picariello, Lisa Simi, Irene Mancini, Luca Messerini, Alberto Magi, Pamela Pinzani, Teresita Mazzei, Francesco Tonelli, Stefania Nobili,
    RNA sequencing reveals PNN and KCNQ1OT1as predictive biomarkers of clinical outcome in stage III colorectal cancer patients treated with adjuvant chemotherapy.
    International Journal of Cancer, (2019), Volume 145, Issue 9. https://doi.org/10.1002/ijc.32326
     
  7. Marta Schirripa, Beatrice Borelli, Romina D'Aurizio, Simone Lubrano, Chiara Cremolini, Gemma Zucchelli, Carlotta Antoniotti, Federica Marmorino, Alessandra Anna Prete, Sabina Murgioni, Francesca Bergamo, Vittorina Zagonel, Andrea Tuccoli, Andrea Marranci, Milena Rizzo, Lorena Tedeschi, Letizia Magnoni, Alfredo Falcone, Fotios Loupakis, Laura Poliseno.
    Early modifications of circulating microRNAs levels in metastatic colorectal cancer patients treated with regorafenib.
    The Pharmacogenomics Journal, volume 19, pages455-464 (2019). DOI https://doi.org/10.1038/s41397-019-0075-3
     
  8. Kuhnle A., Mun T., Boucher C., Gagie T., Langmead B., Manzini G.
    Efficient Construction of a Complete Index for Pan-Genomics Read Alignment.
    In: Cowen L. (eds) Research in Computational Molecular Biology. RECOMB 2019 . Lecture Notes in Computer Science, vol 11467. Springer.
     
  9. L Egidi, F.A. Louza, G. Manzini, G.P. Telles
    External memory BWT and LCP computation for sequence collections with applications
    Algorithms for Molecular Biology 14 (1), 6 (2019). doi:10.1186/s13015-019-0140-0
     
  10. C. Boucher, T. Gagie, A. Kuhnle, B. Langmead, G. Manzini, T. Mun
    Prefix-free parsing for building big BWTs
    Algorithms for Molecular Biology 14 (1), 13 (2019). https://doi.org/10.1186/s13015-019-0148-5
     
  11. L Corrado, L Genovese, E Mangano, R Croce, A Di Pierro, F Geraci, R Bordoni, R D'Aurizio, N Barizzone, F De Marchi, L Mazzini, G De Bellis, G Manzini, M Severgnini, M Pellegrini, S D'Alfonso
    Analysis of DNA tandem repeats in ALS from Whole Genome Sequencing: Role of FRA10Ac1 gene repeat expansion in ALS.
    In EUROPEAN JOURNAL OF HUMAN GENETICS 2019 Oct 1 (Vol. 27, pp. 1489-1489).
    MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND: NATURE PUBLISHING GROUP.
  12. L Corrado, LM Genovese, E Mangano, A Di Pierro, N Barizzone, R Bordoni, F Geraci, R D'Aurizio, R Croce, F De MArchi, L Mazzini, R Cantello, G De Bellis, G Manzini, M Severgnini, M Pellegrini, S D'Alfonso
    Systematic analysis of the involvement of DNA tandem repeats in Amyotrophic lateral sclerosisfrom Whole Genome Sequencing data.
    In EUROPEAN JOURNAL OF HUMAN GENETICS 2019 Jul 1 (Vol. 27, pp. 313-314).
    MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND: NATURE PUBLISHING GROUP.
  13. L Corrado, F Geraci, M Severgnini, A Di Pierro, V Frontini, E Mangano, LM Genovese, N Barizzone, R D'Aurizio, R Croce, F De Marchi, L Mazzini, A Brusco, G De Bellis, G Manzini, R Bordoni, M Pellegrini, S D'Alfonso
    Disease associated tandem repeat genotyping from NGS target sequencing data.
    In EUROPEAN JOURNAL OF HUMAN GENETICS 2019 Jul 1 (Vol. 27, pp. 532-532).
    MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND: NATURE PUBLISHING GROUP.

:: Year 2018

  1. 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.
     
  2. 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
     
  3. Francesco Russo, Sebastiano Di Bella, Federica Vannini, Gabriele Berti, Flavia Scoyni, Helen V. Cook, Alberto Santos, Giovanni Nigita, Vincenzo Bonnici, Alessandro Laganà, Filippo Geraci, Alfredo Pulvirenti, Rosalba Giugno, Federico De Masi, Kirstine Belling, Lars J. Jensen, Søren 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
     
  4. 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.
     
  5. 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.
     
  6. Milena Rizzo, Pascale Beffy, Renata Del Carratore, Alessandra Falleni, Virginia Pretini, Romina D'Aurizio, Annalisa Botta, Monica Evangelista, Andrea Stoccoro, Fabio Coppedè, Denis Furling, Marcella Simili Activation of the interferon type I response rather than autophagy contributes to myogenesis inhibition in congenital DM1 myoblasts
    Cell Death & Disease (2018) Volume 9 Issue 11 article 1071. doi: https://doi.org/10.1038/s41419-018-1080-1
     
  7. Francesca Forini, Giuseppina Nicolini, Claudia Kusmic, Romina D'Aurizio, Milena Rizzo, Mario Baumgart, Marco Groth, Stefano Doccini, Giorgio Iervasi, Letizia Pitto Integrative analysis of differentially expressed genes and miRNAs predicts complex T3-mediated protective circuits in a rat model of cardiac ischemia reperfusion
    Scientific Reports volume 8, Article number: 13870 (2018). doi: https://doi.org/10.1038/s41598-018-32237-0
     
  8. Vitiello M, D'Aurizio R, Poliseno L. Biological role of miR-204 and miR-211 in melanoma.
    Oncoscience. 2018 Aug 22;5(7-8):248-251. doi: 10.18632/oncoscience.443.
     
  9. Romina D'Aurizio, Roberto Semeraro and Alberto Magi Using XCAVATOR and EXCAVATOR2 to Identify CNVs from WGS, WES, and TS Data
    Current Protocols in Human Genetics Volume 98, Issue 1 (2018). doi: https://doi.org/10.1002/cphg.65
     
  10. Alberto Magi, Roberto Semeraro, Alessandra Mingrino, Betti Giusti, Romina D'Aurizio
    Nanopore sequencing data analysis: state of the art, applications and challenges.
    Briefings in Bioinformatics, Volume 19, Issue 6, November 2018, Pages 1256-1272, https://doi.org/10.1093/bib/bbx062
     
  11. Igor Saggese, Elisa Bona, Max Conway, Francesco Favero, Marco Ladetto, Pietro Liò, Giovanni Manzini, Flavio Mignone
    STAble: a novel approach to de novo assembly of RNA-seq data and its application in a metabolic model network based metatranscriptomic workflow
    BMC Bioinformatics volume 19, Article number: 184 (2018). https://doi.org/10.1186/s12859-018-2174-6
     

:: Year 2017

  1. 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 identi ed in other tumor contexts in prostate cancer.
    International Journal of Genomics. Hindawi. 2017. Article ID 5214806.
     
  2. 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
     
  3. 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.
     
  4. 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
     
  5. Francesco Russo, Kirstine Belling, Anders Boeck Jensen, Flavia Scoyni, Søren 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. Andrew M Hammond, Kyros Kyrou, Marco Bruttini, Ace North, Roberto Galizi, Xenia Karlsson, Nace Kranjc, Francesco M Carpi, Romina D'Aurizio, Andrea Crisanti, Tony Nolan
    The creation and selection of mutations resistant to a gene drive over multiple generations in the malaria mosquito
    PLoS genetics (2017), Volume 13 Issue 10. https://doi.org/10.1371/journal.pgen.1007039
     

:: Year 2016

  1. 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.
     
  2. 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
     
  3. 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.
     
  4. 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
     
  5. Marco Pellegrini, Alberto Magi, Costas Iliopoulos Repetitive structures in biological sequences: open challenges .
    Front. Bioeng. Biotechnol. 4:66, July 2016. doi: 10.3389/fbioe.2016.00066
     
  6. Emilio Siena, Romina D'Aurizio, David Riley, Hervé Tettelin, Silvia Guidotti, Giulia Torricelli, E. Richard Moxon and Duccio Medini
    In-silico prediction and deep-DNA sequencing validation indicate phase variation in 115 Neisseria meningitidis genes
    BMC Genomics volume 17, Article number: 843 (2016). https://doi.org/10.1186/s12864-016-3185-1
     

:: Year 2015

  1. 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
     
  2. 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
     
  3. 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.
     
  4. 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
     
  5. 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.
     
  6. 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
     
  7. 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
     
  8. 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
     
  9. 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
     
  10. 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
     
  11. 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
     
  12. L Tattini, R D'Aurizio, A Magi
    Detection of genomic structural variants from next-generation sequencing data
    Front. Bioeng. Biotechnol. 3: 92 (2015). doi: https://doi.org/10.3389/fbioe.2015.00092
     
  13. Leoncini, Mauro; Montangero, Manuela; Panucia Tillán, Karina
    Investigating Power and Limitations of Ensemble Motif Finders Using Metapredictor CE3
    CURRENT BIOINFORMATICS 10(20 pages 124-138 (2015). http://dx.doi.org/10.2174/157489361002150518122428
     

:: Year 2014

  1. 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
     
  2. Alberto Magi, Romina D'Aurizio, Flavia Palombo, Ingrid Cifola, Lorenzo Tattini, Roberto Semeraro, Tommaso Pippucci, Betti Giusti, Giovanni Romeo, Rosanna Abbate, Gian Franco Gensini
    Characterization and identification of hidden rare variants in the human genome
    BMC Genomics volume 16, Article number: 340 (2015). https://doi.org/10.1186/s12864-015-1481-9
     
  3. Cristina Barsanti, Maria Giovanna Trivella, Romina D'Aurizio, Mariama El Baroudi, Mario Baumgart, Marco Groth, Raffaele Caruso, Alessandro Verde, Luca Botta, Lorena Cozzi, Letizia Pitto
    Differential Regulation of MicroRNAs in End-Stage Failing Hearts Is Associated with Left Ventricular Assist Device Unloading
    BioMed Research International Volume 2015, Article ID 592512, http://dx.doi.org/10.1155/2015/592512
     
  4. Tommaso Pippucci, Laura Licchetta, Sara Baldassari, Flavia Palombo, Veronica Menghi, Romina D'Aurizio, Chiara Leta, Carlotta Stipa, Giovanni Boero, Giuseppe D'Orsi, Alberto Magi, Ingrid Scheffer, Marco Seri, Paolo Tinuper, Francesca Bisulli
    Epilepsy with auditory features
    Neurology: Genetics. 1(1):, JUNE 2015, DOI: 10.1212/NXG.0000000000000005
     

:: Year 2013

  1. Alberto Magi, Lorenzo Tattini, Ingrid Cifola, Romina D'Aurizio, Matteo Benelli, Eleonora Mangano, Cristina Battaglia, Elena Bonora, Ants Kurg, Marco Seri, Pamela Magini, Betti Giusti, Giovanni Romeo, Tommaso Pippucci, Gianluca De Bellis, Rosanna Abbate, Gian Franco Gensini
    EXCAVATOR: detecting copy number variants from whole-exome sequencing data
    Genome Biology volume 14, Article number: R120 (2013).https://doi.org/10.1186/gb-2013-14-10-r120
     

:: Year 2012

  1. Direct vs 2-Stage Approaches to Structured Motif Finding
    M. Federico, M. Leoncini M. Montangero, P. Valente
    Algorithms for Molecular Biology, 2012 Aug;7(1):20. (Epub ahead of print).
     
  2. Composite Motif Finder: a combinatorial tool for finding cis-regulatory modules
    M. Leoncini, M. Montangero, M. Pellegrini, K. Tillan
    Technical report IIT TR-08/2012. July 2012.
     
  3. Tandem Repeats Discovery Service (TReaDS) applied to finding novel Cis-acting factors in Repeat Expansion Diseases
    Marco Pellegrini, M. Elena Renda, Alessio Vecchio
    BMC Bioinformatics 2012, Vol. 13(Suppl 4):S3, doi:10.1186/1471-2105-13-S4-S3. March 2012.
     
  4. Ab initio detection of fuzzy amino acid tandem repeats in protein sequences
    Marco Pellegrini, M. Elena Renda, Alessio Vecchio
    BMC Bioinformatics 2012, Vol. 13(Suppl 3):S8, doi:10.1186/1471-2105-13-S3-S8. March 2012.
     

:: Year 2011

  1. Spaced Seeds Design Using Perfect Rulers
    L. Egidi, G. Manzini
    Proc. 18th International Symposium on String Processing and Information Retrieval, Pisa Italy, October 2011.
     
  2. Detecting Fuzzy Amino Acid Tandem Repeats in Protein Sequences
    Marco Pellegrini, M. Elena Renda, Alessio Vecchio
    ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB). Chicago, USA. August 2011.
     
  3. A High Performing Tool for Residue Solvent Accessibility Prediction using Sequence Homology
    L. Palmieri, M. Federico, M. Leoncini and M. Montangero
    Proc. of the 2nd International Conference on Information Technology in Bio- and Medical Informatics (ITBAM 2011), LNCS 6865, pp. 138-152. August 2011.
     
  4. TReaDS: Tandem Repeats Discovery Service
    M. Elena Renda, Alessio Vecchio, Marco Pellegrini
    VIII Annual Meeting of the Bioinformatics Italian Society (BITS'11), pp 102-104. Pisa, Italy. June 2011.
     
  5. 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.
  6. 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.

:: Year 2010

  1. A comparison of several algorithms for the single individual SNP haplotyping reconstruction problem
    Filippo Geraci
    Bioinformatics, Published by Oxford Journals, Vol. 26, Issue 18, pp 2217-2225, July 2010, doi: 10.1093/bioinformatics/btq411.
     
  2. TRStalker: an Efficient Heuristic for Finding Fuzzy Tandem Repeats
    Marco Pellegrini, M. Elena Renda, Alessio Vecchio
    Bioinformatics. Published by Oxford University Press, Volume 26, Issue 12, pp i358-i366. June 2010. doi: 10.1093/bioinformatics/btq209.
     
  3. ReHap: an Integrated System for the Haplotype Assembly Problem from Shotgun Sequencing Data
    Filippo Geraci, Marco Pellegrini
    Proc. of Bionformatics 2010, INSTICC. Valencia, Spain, 20-23 January 2010.
     

:: Year 2009

  1. An Efficient Combinatorial Approach for Solving the DNA Motif Finding Problem
    Filippo Geraci, Marco Pellegrini, M. Elena Renda
    Proc. of the 9th International Conference on Intelligent Systems Design and Applications (ISDA'09), pp 335-340. Pisa, Italy, Nobember 30 - December 2 2009. doi: http://doi.ieeecomputersociety.org/10.1109/ISDA.2009.41.
     
  2. TRStalker: an Efficient Heuristic for Finding NP-Complete Tandem Repeats
    Marco Pellegrini, M. Elena Renda, Alessio Vecchio
    Tech. Rep. n. 2009-TR-08, Istituto di Informatica e Telematica - CNR, Pisa, October 2009.
     
  3. An efficient algorithm for planted structured motif extraction
    Maria Federico, Paolo Valente, Mauro Leoncini, Manuela Montangero, Roberto Cavicchioli
    Proc. of the 1st ACM Workshop on Breaking Frontiers of Computational Biology (CompBio'09). Ischia, Italy, May 18 - 20 2009. ACM, New York, NY, 1-6, doi: doi.acm.org/10.1145/1531780.1531782.
     
  4. K-Boost: a Scalable Algorithm for High-Quality Clustering of Microarray Gene Expression Data
    Filippo Geraci, Mauro Leoncini, Manuela Montangero, Marco Pellegrini, M. Elena Renda
    Journal of Computational Biology, Published by Mary Ann Liebert, Vol. 16, Issue 6, pp 859-873, June 2009, doi:10.1089/cmb.2008.0201.
    Also Tech. Rep. n. 2007-TR-15, Istituto di Informatica e Telematica - CNR, Pisa, December 2007.
     

:: Year 2008

  1. SpeedHap: An Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage
    Loredana M. Genovese, Filippo Geraci, Marco Pellegrini
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, IEEE Computer Society Digital Library, June 2008, doi.ieeecomputersociety.org/10.1109/TCBB.2008.67
     
  2. AMIC@: All MIcroarray Clusterings @ once
    Filippo Geraci, Marco Pellegrini, M. Elena Renda
    Nucleic Acids Research (NAR), May 2008, Vol. 36, Web Server Issue W315–W319, doi:10.1093/nar/gkn265.
     
  3. TReaDS: Tandem Repeats Discovery Service
    Alessio Vecchio, M. Elena Renda, Marco Pellegrini
    Tech. Rep. n. 2008-TR-06, Istituto di Informatica e Telematica - CNR, Pisa, May 2008.
     

:: Year 2007

  1. Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment
    Paolo Ferragina, Raffaele Giancarlo, Valentina Greco, Giovanni Manzini, Gabriel Valiente
    BMC Bioinformatics, July 2007, doi:10.1186/1471-2105-8-252
     
  2. A Fast and Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage
    Loredana M. Genovese, Filippo Geraci, Marco Pellegrini
    in Proc. 7th Workshop on Algorithms in Bioinformatics (WABI'07), Philadelphia, USA, September 2007.
    Also Tech. Rep. n. 2007-TR-5, Istituto di Informatica e Telematica - CNR, Pisa, May 2007.
     
  3. FPF-SB: a Scalable Algorithm for Microarray Gene Expression Data Clustering
    Filippo Geraci, Mauro Leoncini, Manuela Montangero, Marco Pellegrini, M. Elena Renda
    in Proc. 12th International Conference on Human-Computer Interaction (HCI'07), Beijing, P.R. China, July 2007.
    Also Tech. Rep. n. 2007-TR-1, Istituto di Informatica e Telematica - CNR, Pisa, February 2007.
     
  4. High-Throughput Analysis of Gene Expression Data for Personalized Medicine
    Filippo Geraci, Mauro Leoncini, Manuela Montangero, Marco Pellegrini, M. Elena Renda
    ERCIM News No. 69, April 2007.
     
Styled and mantained by:
M. Elena Renda