Bioinformatics Sannio

Publications

Relevant Publications

Mauriello, Angela, Roberta Zeuli, Beatrice Cavalluzzo, Annacarmen Petrizzo, Maria Lina Tornesello, Franco M. Buonaguro, Michele Ceccarelli, Maria Tagliamonte, and Luigi Buonaguro. “High Somatic Mutation and Neoantigen Burden Do Not Correlate with Decreased Progression-Free Survival in HCC Patients Not Undergoing Immunotherapy.” Cancers 11, no. 12 (November 20, 2019). https://doi.org/10.3390/cancers11121824. Download
Roelands, Jessica, Wouter Hendrickx, Peter J.K. Kuppen, Raghvendra Mall, Gabriele Zoppoli, Mohamad Saad, Kyle Halliwill, et al. “Genomic Landscape of Tumor-Host Interactions with Differential Prognostic and Predictive Connotations.” Preprint. Cancer Biology, February 12, 2019. https://doi.org/10.1101/546069. Download
Caruso, Francesca Pia, Luciano Garofano, Fulvio D’Angelo, Kai Yu, Fuchou Tang, Jinzhou Yuan, Jing Zhang, et al. “A MAP of Tumor-Host Interactions in Glioma at Single Cell Resolution.” Preprint. Bioinformatics, November 1, 2019. https://doi.org/10.1101/827758.
Noviello, Teresa M. R., Antonella Di Liddo, Giovanna M. Ventola, Antonietta Spagnuolo, Salvatore D’Aniello, Michele Ceccarelli, and Luigi Cerulo. “Detection of Long Non-Coding RNA Homology, a Comparative Study on Alignment and Alignment-Free Metrics.” BMC Bioinformatics 19, no. 1 (November 6, 2018): 407. https://doi.org/10.1186/s12859-018-2441-6. Download
Bedognetti, Davide, Michele Ceccarelli, Lorenzo Galluzzi, Rongze Lu, Karolina Palucka, Josue Samayoa, Stefani Spranger, et al. “Toward a Comprehensive View of Cancer Immune Responsiveness: A Synopsis from the SITC Workshop.” Journal for Immunotherapy of Cancer 7, no. 1 (May 22, 2019): 131. https://doi.org/10.1186/s40425-019-0602-4. Download
Di Iorio, Biagio R., Antonio Bellasi, Kalani L. Raphael, Domenico Santoro, Filippo Aucella, Luciano Garofano, Michele Ceccarelli, et al. “Treatment of Metabolic Acidosis with Sodium Bicarbonate Delays Progression of Chronic Kidney Disease: The UBI Study.” Journal of Nephrology, October 9, 2019. https://doi.org/10.1007/s40620-019-00656-5.
Guerriero, Ilaria, Maria Teresa De Angelis, Fulvio D’Angelo, Rita Leveque, Eleonora Savignano, Luca Roberto, Valeria Lucci, et al. “Exploring the Molecular Crosstalk between Pancreatic Bud and Mesenchyme in Embryogenesis: Novel Signals Involved.” International Journal of Molecular Sciences 20, no. 19 (October 3, 2019). https://doi.org/10.3390/ijms20194900. Download
Cuomo, Danila, Immacolata Porreca, Michele Ceccarelli, David W. Threadgill, William T. Barrington, Annacristina Petriella, Fulvio D’Angelo, et al. “Transcriptional Landscape of Mouse-Aged Ovaries Reveals a Unique Set of Non-Coding RNAs Associated with Physiological and Environmental Ovarian Dysfunctions.” Cell Death Discovery 4, no. 1 (2018). https://doi.org/10.1038/s41420-018-0121-y. Download
Monaco, Gianni, Bernett Lee, Weili Xu, Seri Mustafah, You Yi Hwang, Christophe Carré, Nicolas Burdin, et al. “RNA-Seq Signatures Normalized by MRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types.” Cell Reports 26, no. 6 (2019): 1627-1640.e7. https://doi.org/10.1016/j.celrep.2019.01.041. Download
Zhang, Jing, Francesca P. Caruso, Jason K. Sa, Sune Justesen, Do-Hyun Nam, Peter Sims, Michele Ceccarelli, Anna Lasorella, and Antonio Iavarone. “The Combination of Neoantigen Quality and T Lymphocyte Infiltrates Identifies Glioblastomas with the Longest Survival.” Communications Biology 2, no. 1 (2019). https://doi.org/10.1038/s42003-019-0369-7. Download
Silvestri, Elena, Rosalba Senese, Federica Cioffi, Rita De Matteis, Davide Lattanzi, Assunta Lombardi, Antonia Giacco, et al. “3,5-Diiodo-L-Thyronine Exerts Metabolically Favorable Effects on Visceral Adipose Tissue of Rats Receiving a High-Fat Diet.” Nutrients 11, no. 2 (January 27, 2019): 278. https://doi.org/10.3390/nu11020278. Download
Giordano, Guido, Pietro Parcesepe, Mario Rosario D’Andrea, Luigi Coppola, Tania Di Raimo, Andrea Remo, Erminia Manfrin, et al. “JAK/Stat5-Mediated Subtype-Specific Lymphocyte Antigen 6 Complex, Locus G6D (LY6G6D) Expression Drives Mismatch Repair Proficient Colorectal Cancer.” Journal of Experimental & Clinical Cancer Research 38, no. 1 (2019). https://doi.org/10.1186/s13046-018-1019-5. Download
D’Angelo, Fulvio, Michele Ceccarelli, Tala, Luciano Garofano, Jing Zhang, Véronique Frattini, Francesca P. Caruso, et al. “The Molecular Landscape of Glioma in Patients with Neurofibromatosis 1.” Nature Medicine 25, no. 1 (2019): 176–87. https://doi.org/10.1038/s41591-018-0263-8.
D’Angelo, Fulvio, Michele Ceccarelli, Tala, Luciano Garofano, Jing Zhang, Véronique Frattini, Francesca P. Caruso, et al. “The Molecular Landscape of Glioma in Patients with Neurofibromatosis 1.” Nature Medicine, December 10, 2018. https://doi.org/10.1038/s41591-018-0263-8.
Cuomo, Danila, Immacolata Porreca, Michele Ceccarelli, David W. Threadgill, William T. Barrington, Annacristina Petriella, Fulvio D’Angelo, et al. “Transcriptional Landscape of Mouse-Aged Ovaries Reveals a Unique Set of Non-Coding RNAs Associated with Physiological and Environmental Ovarian Dysfunctions.” Cell Death Discovery 4, no. 1 (2018). https://doi.org/10.1038/s41420-018-0121-y.
Remo, Andrea, Erminia Manfrin, Pietro Parcesepe, Alberto Ferrarini, Hye Seung Han, Ugnius Mickys, Carmelo Laudanna, et al. “Centrosome Linker–Induced Tetraploid Segregation Errors Link Rhabdoid Phenotypes and Lethal Colorectal Cancers.” Molecular Cancer Research 16, no. 9 (2018): 1385–1395. https://doi.org/10.1158/1541-7786.MCR-18-0062.
Noviello, Teresa M. R., Antonella Di Liddo, Giovanna M. Ventola, Antonietta Spagnuolo, Salvatore D’Aniello, Michele Ceccarelli, and Luigi Cerulo. “Detection of Long Non–Coding RNA Homology, a Comparative Study on Alignment and Alignment–Free Metrics.” BMC Bioinformatics 19, no. 1 (2018). https://doi.org/10.1186/s12859-018-2441-6.
Bertucci, François, Pascal Finetti, Ines Simeone, Wouter Hendrickx, Ena Wang, Francesco M. Marincola, Patrice Viens, et al. “The Immunologic Constant of Rejection Classification Refines the Prognostic Value of Conventional Prognostic Signatures in Breast Cancer.” British Journal of Cancer, October 24, 2018. https://doi.org/10.1038/s41416-018-0309-1.
Angelova, Mihaela, Bernhard Mlecnik, Angela Vasaturo, Gabriela Bindea, Tessa Fredriksen, Lucie Lafontaine, Bénédicte Buttard, et al. “Evolution of Metastases in Space and Time under Immune Selection.” Cell, 2018. https://doi.org/10.1016/j.cell.2018.09.018.
Ferreira, Letícia Antunes Muniz, Juliana Capannacci, Newton Key Hokama, Célia Regina Nogueira, Michele Ceccarelli, Luigi Cerulo, Fulvio D’Angelo, and Paula de Oliveira Montandon Hokama. “Circulating MicroRNAs Expression Profile in Newly Diagnosed and Imatinib Treated Chronic Phase – Chronic Myeloid Leukemia.” Leukemia & Lymphoma, September 6, 2018, 1–7. https://doi.org/10.1080/10428194.2018.1499905.
Yuan, Jinzhou, Hanna Mendes Levitin, Veronique Frattini, Erin C. Bush, Deborah M. Boyett, Jorge Samanamud, Michele Ceccarelli, et al. “Single-Cell Transcriptome Analysis of Lineage Diversity in High-Grade Glioma.” Genome Medicine 10, no. 1 (2018). https://doi.org/10.1186/s13073-018-0567-9.
Rosenberg, Shai, Iva Simeonova, Franck Bielle, Maite Verreault, Bertille Bance, Isabelle Le Roux, Mailys Daniau, et al. “A Recurrent Point Mutation in PRKCA Is a Hallmark of Chordoid Gliomas.” Nature Communications 9, no. 1 (2018). https://doi.org/10.1038/s41467-018-04622-w.
Remo, Andrea, Erminia Manfrin, Pietro Parcesepe, Alberto Ferrarini, Hye Seung Han, Mickys Ugnius, Carmelo Laudanna, et al. “Centrosome Linker-Induced Tetraploid Segregation Errors Link Rhabdoid Phenotypes and Lethal Colorectal Cancers.” Molecular Cancer Research, May 21, 2018, molcanres.0062.2018. https://doi.org/10.1158/1541-7786.MCR-18-0062.
Pascarella, A., G. Ferrandino, S. C. Credendino, C. Moccia, F. D’Angelo, B. Miranda, C. D’Ambrosio, et al. “DNAJC17 Is Localized in Nuclear Speckles and Interacts with Splicing Machinery Components.” Scientific Reports 8, no. 1 (2018). https://doi.org/10.1038/s41598-018-26093-1.
Silvestri, Elena, Federica Cioffi, Rita De Matteis, Rosalba Senese, Pieter de Lange, Maria Coppola, Anna M. Salzano, et al. “3,5-Diiodo-L-Thyronine Affects Structural and Metabolic Features of Skeletal Muscle Mitochondria in High-Fat-Diet Fed Rats Producing a Co-Adaptation to the Glycolytic Fiber Phenotype.” Frontiers in Physiology 9 (March 9, 2018). https://doi.org/10.3389/fphys.2018.00194.
Silva, Tiago Chedraoui, Antonio Colaprico, Catharina Olsen, Tathiane M Malta, Gianluca Bontempi, Michele Ceccarelli, Benjamin P Berman, and Houtan Noushmehr. “TCGAbiolinksGUI: A Graphical User Interface to Analyze Cancer Molecular and Clinical Data.” F1000Research 7 (April 10, 2018): 439. https://doi.org/10.12688/f1000research.14197.1.
Mall, Raghvendra, Ehsan Ullah, Khalid Kunji, Michele Ceccarelli, and Halima Bensmail. “An Unsupervised Disease Module Identification Technique in Biological Networks Using Novel Quality Metric Based on Connectivity, Conductance and Modularity.” F1000Research 7 (March 26, 2018): 378. https://doi.org/10.12688/f1000research.14258.1.
Mall, Raghvendra, Luigi Cerulo, Luciano Garofano, Veronique Frattini, Khalid Kunji, Halima Bensmail, Thais S Sabedot, et al. “RGBM: Regularized Gradient Boosting Machines for Identification of the Transcriptional Regulators of Discrete Glioma Subtypes.” Nucleic Acids Research, January 19, 2018. https://doi.org/10.1093/nar/gky015.
Frattini, Véronique, Stefano M. Pagnotta, Tala, Jerry J. Fan, Marco V. Russo, Sang Bae Lee, Luciano Garofano, et al. “A Metabolic Function of FGFR3-TACC3 Gene Fusions in Cancer.” Nature 553, no. 7687 (January 3, 2018): 222–27. https://doi.org/10.1038/nature25171.
Guerriero, Ilaria, Daniela D’Angelo, Pierlorenzo Pallante, Mafalda Santos, Marianna Scrima, Donatella Malanga, Carmela De Marco, et al. “Analysis of MiRNA Profiles Identified MiR-196a as a Crucial Mediator of Aberrant PI3K/AKT Signaling in Lung Cancer Cells.” Oncotarget 8, no. 12 (March 21, 2017): 19172–91. https://doi.org/10.18632/oncotarget.13432.
De Marco, Carmela, Carmelo Laudanna, Nicola Rinaldo, Duarte Mendes Oliveira, Maria Ravo, Alessandro Weisz, Michele Ceccarelli, et al. “Specific Gene Expression Signatures Induced by the Multiple Oncogenic Alterations That Occur within the PTEN/PI3K/AKT Pathway in Lung Cancer.” Edited by Francisco X. Real. PLOS ONE 12, no. 6 (June 29, 2017): e0178865. https://doi.org/10.1371/journal.pone.0178865.
Silva, Tiago C., Antonio Colaprico, Catharina Olsen, Gianluca Bontempi, Michele Ceccarelli, Benjamin P. Berman, and Houtan Noushmehr. “TCGAbiolinksGUI: A Graphical User Interface to Analyze Cancer Molecular and Clinical Data,” June 8, 2017. https://doi.org/10.1101/147496.
Mall, Raghvendra, Ehsan Ullah, Khalid Kunji, Fulvio D’Angelo, Halima Bensmail, and Michele Ceccarelli. “Differential Community Detection in Paired Biological Networks,” June 8, 2017. https://doi.org/10.1101/147538.
Mall, Raghvendra, Luigi Cerulo, Khalid Kunji, Halima Bensmail, Thais Sabedot, Houtan Noushmehr, Antonio Iavarone, and Michele Ceccarelli. “RGBM: Regularized Gradient Boosting Machines For The Identification of Transcriptional Regulators Of Discrete Glioma Subtypes.” BioRxiv, 2017. https://doi.org/10.1101/132670.
Ventola, Giovanna M. M., Teresa M. R. Noviello, Salvatore D’Aniello, Antonietta Spagnuolo, Michele Ceccarelli, and Luigi Cerulo. “Identification of Long Non-Coding Transcripts with Feature Selection: A Comparative Study.” BMC Bioinformatics 18, no. 1 (2017). https://doi.org/10.1186/s12859-017-1594-z.
Roelands, Jessica, Julie Decock, Sabri Boughorbel, Darawan Rinchai, Cristina Maccalli, Michele Ceccarelli, Michael Black, et al. “A Collection of Annotated and Harmonized Human Breast Cancer Transcriptome Datasets, Including Immunologic Classification.” F1000Research 6 (March 20, 2017): 296. https://doi.org/10.12688/f1000research.10960.1.
Porreca, Immacolata, Fulvio D’Angelo, Daniela Gentilcore, Emanuele Carchia, Angela Amoresano, Andrea Affuso, Michele Ceccarelli, et al. “Cross-Species Toxicogenomic Analyses and Phenotypic Anchoring in Response to Groundwater Low-Level Pollution.” BMC Genomics 15 (December 5, 2014): 1067. https://doi.org/10.1186/1471-2164-15-1067.
Pancione, Massimo, Guido Giordano, Pietro Parcesepe, Luigi Cerulo, Luigi Coppola, Anais Del Curatolo, Fabiana Conciatori, Michele Milella, and Almudena Porras. “Emerging Insight into MAPK Inhibitors and Immunotherapy in Colorectal Cancer.” Current Medicinal Chemistry, February 27, 2017. https://doi.org/10.2174/0929867324666170227114356.
Mall, Raghvendra, Luigi Cerulo, Halima Bensmail, Antonio Iavarone, and Michele Ceccarelli. “Detection of Statistically Significant Network Changes in Complex Biological Networks.” BMC Systems Biology 11, no. 1 (2017). https://doi.org/10.1186/s12918-017-0412-6.
Hendrickx, Wouter, Ines Simeone, Samreen Anjum, Younes Mokrab, François Bertucci, Pascal Finetti, Giuseppe Curigliano, et al. “Identification of Genetic Determinants of Breast Cancer Immune Phenotypes by Integrative Genome-Scale Analysis.” OncoImmunology, February 6, 2017, e1253654. https://doi.org/10.1080/2162402X.2016.1253654.
Guerriero, Ilaria, Daniela D’Angelo, Pierlorenzo Pallante, Mafalda Santos, Marianna Scrima, Donatella Malanga, Carmela De Marco, et al. “Analysis of MiRNA Profiles Identified MiR-196a as a Crucial Mediator of Aberrant PI3K/AKT Signaling in Lung Cancer Cells.” Oncotarget, November 17, 2016. https://doi.org/10.18632/oncotarget.13432.
Porreca, Immacolata, Fulvio D’Angelo, Lucia De Franceschi, Alessandro Mattè, Michele Ceccarelli, Achille Iolascon, Alberto Zamò, et al. “Pesticide Toxicogenomics across Scales: In Vitro Transcriptome Predicts Mechanisms and Outcomes of Exposure in Vivo.” Scientific Reports 6 (December 1, 2016): 38131. https://doi.org/10.1038/srep38131.
Silva, Tiago C., Antonio Colaprico, Catharina Olsen, Fulvio D’Angelo, Gianluca Bontempi, Michele Ceccarelli, and Houtan Noushmehr. “TCGA Workflow: Analyze Cancer Genomics and Epigenomics Data Using Bioconductor Packages.” F1000Research 5 (June 29, 2016): 1542. https://doi.org/10.12688/f1000research.8923.1.
Frezzetti, D., M. De Menna, P. Zoppoli, C. Guerra, A. Ferraro, A. M. Bello, P. De Luca, et al. “Upregulation of MiR-21 by Ras in Vivo and Its Role in Tumor Growth.” Oncogene 30, no. 3 (January 20, 2011): 275–86. https://doi.org/10.1038/onc.2010.416.
Sabatino, L., A. Fucci, M. Pancione, V. Carafa, A. Nebbioso, C. Pistore, F. Babbio, et al. “UHRF1 Coordinates Peroxisome Proliferator Activated Receptor Gamma (PPARG) Epigenetic Silencing and Mediates Colorectal Cancer Progression.” Oncogene 31, no. 49 (December 6, 2012): 5061–72. https://doi.org/10.1038/onc.2012.3.
Agnihotri, Sameer, Shahrzad Jalali, Mark R. Wilson, Arnavaz Danesh, Mira Li, George Klironomos, Jonathan R. Krieger, et al. “The Genomic Landscape of Schwannoma.” Nature Genetics 48, no. 11 (November 2016): 1339–48. https://doi.org/10.1038/ng.3688.
Ciccarelli, M., R. Finelli, N. Rivera, G. Santulli, R. Izzo, N. De Luca, F. Rozza, et al. “The Possible Role of Chromosome X Variability in Hypertensive Familiarity.” Journal of Human Hypertension, February 25, 2016. https://doi.org/10.1038/jhh.2016.9.
Colaprico, Antonio, Tiago C. Silva, Catharina Olsen, Luciano Garofano, Claudia Cava, Davide Garolini, Thais S. Sabedot, et al. “TCGAbiolinks: An R/Bioconductor Package for Integrative Analysis of TCGA Data.” Nucleic Acids Research 44, no. 8 (May 5, 2016): e71. https://doi.org/10.1093/nar/gkv1507.
Ceccarelli, Michele, Floris P. Barthel, Tathiane M. Malta, Thais S. Sabedot, Sofie R. Salama, Bradley A. Murray, Olena Morozova, et al. “Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma.” Cell 164, no. 3 (January 28, 2016): 550–63. https://doi.org/10.1016/j.cell.2015.12.028.
Tagliaferri, Daniela, Maria Teresa De Angelis, Nicola Antonino Russo, Maria Marotta, Michele Ceccarelli, Luigi Del Vecchio, Mario De Felice, and Geppino Falco. “Retinoic Acid Specifically Enhances Embryonic Stem Cell Metastate Marked by Zscan4.” PloS One 11, no. 2 (2016): e0147683. https://doi.org/10.1371/journal.pone.0147683.