Dr. Edoardo Pasolli

I am associate professor at University of Naples Federico II, Department of Agricultural Sciences, Italy. I currently teach the courses "Data science" and "Data science & Computational analysis for metagenomics". In brief, my research interests aim at developing and applying machine learning methodologies and computational tools for complex ecosystems with main focus on the human and food microbiomes. I have also worked on signal and image processing methods.

Previously, I was Marie Sklodowska-Curie individual fellow at University of Trento, Centre for Integrative Biology, Italy (2016-2018). Main results were published in this Cell paper.

I was also postdoctoral fellow at University of Trento, Centre for Integrative Biology, Italy (2014-2016); Purdue University, School of Civil Engineering, United States (2013-2014); NASA Goddard Space Flight Center, Computational and Information Sciences and Technology Office, United States (2012-2013); University of Trento, Department of Information Engineering and Computer Science, Italy (2011-2012).

I received the Ph.D. in Information and Communication Technology (November 2011), Master's degree in Telecommunications Engineering (March 2008, Grade: 110/110 cum laude) and Bachelor's degree in Telecommunications Engineering (January 2006, Grade: 110/110 cum laude) at University of Trento, Italy.

Email: edoardo.pasolli ( at ) unina.it

Last update: March 2024

Current position

Associate professor and Principal investigator, Department of Agricultural Sciences, University of Naples Federico II, Italy

Past positions

2018-2021, Assistant professor (RTDb), Department of Agricultural Sciences, University of Naples Federico II, Italy
2016-2018, Marie Sklodowska-Curie individual fellow, Centre for Integrative Biology, University of Trento, Italy
2014-2016, Postdoctoral fellow, Centre for Integrative Biology, University of Trento, Italy
2013-2014, Postdoctoral fellow, School of Civil Engineering, Purdue University, United States
2012-2013, Scientist, Computational and Information Sciences and Technology Office, NASA Goddard Space Flight Center, United States
2011-2012, Postdoctoral fellow, Department of Information Engineering and Computer Science, University of Trento, Italy

Research visits

2010 (3 months), University of Colorado at Boulder, Department of Aerospace Engineering Sciences, United States

Education

2011 November, Ph.D. in Information and Communication Technology, Department of Information Engineering and Computer Science, University of Trento, Italy
2008 March, Master’s degree in Telecommunications Engineering, Faculty of Engineering, University of Trento, Italy, Grade 110/110 cum laude
2006 January, Bachelor’s degree in Telecommunications Engineering, Faculty of Engineering, University of Trento, Italy, Grade 110/110 cum laude

Grants

2023 - 2025, PNRR PRIN 2022 (Italian Ministry of Education, University and Research)
2023 - 2025, PRIN 2022 (Italian Ministry of Education, University and Research)
2022 - 2025, PNRR Agritech (Italian Ministry of Education, University and Research)
2022 – 2025, Industrial Ph.D. research grant (Campania Region – Italy; Scientific Advisor for the fellowship to Sara Cavaliere)
2021 – 2023, Research grant (University of Naples Federico II – Italy; co-PI)
2019 – 2022, Industrial Ph.D. research grant (Campania Region – Italy; Scientific Advisor for the fellowship to Renato Giliberti)
2019 – 2022, Ph.D. research grant (Italian Ministry of Education, University and Research; Scientific Advisor for the fellowship to Italia Elisa Mauriello)
2016 – 2018, Marie Sklodowska-Curie individual fellowship (EU-H2020; PI)
2014 – 2016, Postdoctoral research grant at the Centre for Integrative Biology, University of Trento, Italy
2013 – 2014, Postdoctoral research grant at the School of Civil Engineering, Purdue University, United States
2012 – 2013, Research grant at the Computational and Information Sciences and Technology Office, NASA Goddard Space Flight Center, United States
2011 – 2012, Postdoctoral research grant at the Department of Information Engineering and Computer Science, University of Trento, Italy
2008 – 2011, PhD research grant at the Department of Information Engineering and Computer Science, University of Trento, Italy

Awards

2023, Inclusion in the list of Highly Cited Researchers 2023 by Clarivate
2021, The publication (Pasolli et al., Nature Communications, 2020) has been included in the “Top 50 life and biological sciences articles” published in Nature Communications in 2020
2020, The publication (Pasolli et al., Cell, 2019) has been included in the “Best of Cell 2019” and in the “Nature Milestones in human microbiota research”
2020, Inclusion in the list of top 2% cited researchers based on the publication 10.1371/journal.pbio.3000918
2020, Best publication in an high IF journal in 2019 for the paper "Distinct genetic and functional traits of human intestinal Prevotella copri strains are associated with different habitual diets", granted by Italian Society of Agro-Food and Environmental Microbiology
2018, "HM Goldman" award co-recipient for the work on "oral microbiome in peri-implantitis", granted by SiDP-Italy
2017, Best Reviewer, IEEE Transactions on Geoscience and Remote Sensing
2017-2026, Qualification as Associate Professor in Italy (ASN, sector 09/F2)
2017, IEEE Senior Member
2017 February, Travel fellowship award by "Simons Center for Data Analysis: The Second Workshop on Challenges in Microbiome Data Analysis" (Boston, United States)
2015 June, Travel fellowship award by "MetaSUB: Metagenomics and Metadesign of Subways and Urban Biomes Conference" (New York, United States)
2015 June, Travel fellowship award by "EMBL Conference on the Human Microbiome" (Heidelberg, Germany)
2013, Best Reviewer, IEEE Transactions on Geoscience and Remote Sensing
2012, Best Reviewer, IEEE Geoscience and Remote Sensing Letters
2012, Best Reviewer, Elsevier Pattern Recognition Letters

Teaching

Since 2021, Lecturer "Data Science and Computational Analysis for Metagenomics" (6 CFU), Master's degree in Agricultural Biotechnologies, Department of Agricultural Sciences, University of Naples Federico II, Italy
Since 2020, Lecturer "Data Science" (6 CFU), Master's degree in Agricultural Biotechnologies, Department of Agricultural Sciences, University of Naples Federico II, Italy
Since 2020, Lecturer "Artificial intelligence/Machine learning/Analytics", 5G Academy (15 hours), Naples, Italy
2018-2020, Lecturer "Data Science" (9 CFU), Master's degree in Agricultural Biotechnologies, Department of Agricultural Sciences, University of Naples Federico II, Italy
2015/2016, Teaching assistant "Digital transmission" (6 CFU), Bachelor's degree in Electronics and Telecommunications Engineering, Department of Information Engineering and Computer Science, University of Trento, Italy
2014/2016, Teaching assistant "Recognition systems" (6 CFU), Master's degree in Telecommunications Engineering, Department of Information Engineering and Computer Science, University of Trento, Italy
2009-2011, Teaching assistant "Remote sensing technologies for archaeology" (3 CFU), Master’s degree in Cultural Heritage, Faculty of Letters and Philosophy, University of Trento, Italy
2009-2010, Teaching assistant "Advanced pattern recognition" (6 CFU), Master’s degree in Telecommunications Engineering, Faculty of Engineering, University of Trento, Italy

Supervision of students

Since 2019, current/previous supervisor of 8 students, Department of Agricultural Sciences, University of Naples Federico II, Italy. Michele Avagliano (Ph.D., 2023 – 2026), Sara Cavaliere (Ph.D., 2022 – 2025), Italia Elisa Mauriello (Ph.D., 2019 – 2023), Renato Giliberti (Ph.D., 2019 – 2023), Gianluca Luongo (Master, 2024), Silvia Palladino (Master, 2023), Adriana Borzacchiello (Master, 2021), Vittoria Borzacchiello (Master, 2021)
2010 – 2018, as postdoc and Ph.D. student, co-supervisor on the research of 30+ Ph.D., Master, and Bachelor students

Institutional responsibilities

Since 2021, Member of the Managing Board of the Task Force on Computational and Quantitative Biology, University of Naples Federico II, Italy
Since 2021, Member of the Board of Professors of the PhD School in Computational and Quantitative Biology, University of Naples Federico II, Italy
Since 2021, Accredited educator for AWS Academy at University of Naples Federico II, Italy
Since 2019, Member of the Task Force on Microbiome Studies, University of Naples Federico II, Italy
Since 2019, Member of the Didactic Coordination Council for the Master’s degree in Agricultural Biotechnologies, Department of Agricultural Sciences, University of Naples Federico II, Italy
Since 2019, Member of the Thesis Committee for the Master’s degree in Agricultural Biotechnologies, Department of Agricultural Sciences, University of Naples Federico II, Italy
Since 2018, Faculty member, Department of Agricultural Sciences, University of Naples Federico II, Italy
2020, Attendance of the F.E.D.E.R.I.C.O. Project (Formation Experiences Didactics Evaluation Innovation Reflexivity Competences Organization), University of Naples Federico II, Italy
Scientific society membership: Institute of Electrical and Electronics Engineers (IEEE), Gruppo Telecomunicazioni e Tecnologie dell'Informazione (Associazione GTTI)

Invited/selected talks & seminars

2024 March, Seminar, EMBL-EBI training (Online)
2023 November, Invited lecture, ECM course, National Congress IG-IBD, Riccione, Italy
2023 October, Invited talk, United European Gastroenterology Week, Copenaghen, Denmark
2023 June, Seminar, We got this Friday@Dept. of Agricultural Sciences, University of Naples Federico II, Naples, Italy
2023 May, Selected talk, Microbiome Applications for Sustainable food systems through Technologies and EnteRprise Workshop, Malaga, Spain
2023 April, Invited talk, European Congress of Clinical Microbiology and Infectious Diseases, Copenaghen, Denmark
2023 April, Seminar, International Faculty Exchange Program Chandigarh University, India (Online)
2022 July, Seminar, NEC Talks, Germany (Online)
2022 May, Seminar, IANUA University of Genova, Italy
2021 November, Seminar, APC Microbiome Institute, Cork, Ireland (Online)
2021 November, Selected talk, Microbiome Virtual International Forum (Online)
2021 November, Invited talk, Human Gut Microbiome Summit 2021, Barcelona, Spain (Online)
2021 October, Invited talk, Targeting Microbiota 2021, Paris, France (Online)
2020 December, Invited lecture, ECM course, IRCCS Burlo Garofolo, Trieste, Italy (Online)
2020 November, Seminar, European Researchers’ Night, Naples, Italy (Online)
2020 February, Invited workshop, Metabarcoding and metagenomic data processing and analysis workshop, Naples, Italy
2019 December, Seminar, Natale in Reggia, Portici, Italy
2019 October, Invited lecture, IEEE International workshop on metrology for agriculture and forestry, Portici, Italy
2019 October, Selected talk, IEEE International workshop on metrology for agriculture and forestry, Portici, Italy
2019 September, Invited talk, Food and nutrition community workshop, The Hague, Netherlands
2019 August, Seminar, IZS Venezie, Padova, Italy
2019 July, Invited talk, Joint statistical meeting, Denver, United States
2019 July, Invited talk, Networking international biometric society regions conference, Naples, Italy
2019 June, Seminar, Caffè scientifico@Dept. of Agricultural Sciences, University of Naples Federico II, Naples, Italy
2019 February, Seminar, Dept. of Electrical Engineering and Information Technology, University of Naples Federico II, Naples, Italy
2018 October, Seminar, University of Southern Denmark, Odense, Denmark
2018 September, Seminar, European Researchers’ Night, Trento, Italy
2018 June, Invited lecture, ECM course, CSS-Mendel Institute, Rome, Italy
2018 May, Seminar, Institut Pasteur, Paris, France
2018 April, Seminar, University of Eastern Piedmont, Novara, Italy
2017 September, Seminar, European Researchers’ Night, Trento, Italy
2017 August, Invited talk, Joint statistical meeting, Baltimore, United States
2017 July, Selected workshop, Bioc 2017: where software and biology connect, Boston, United States
2017 May, Seminar, The Festival of Europe, Trento, Italy
2017 February, Invited talk, Second workshop in statistical and algorithmic challenges in microbiome data analysis, Boston, United States
2015 June, Invited talk, MetaSUB workshop, New York, United States
2015 June, Selected talk, EMBL-The human microbiome conference, Heidelberg, Germany

Organization of scientific meetings

2020, Scientific committee member for the workshop “Metabarcoding and metagenomic data processing and analyses”, Naples, Italy

BookS

Y.Bazi and E. Pasolli. Advanced deep learning strategies for the analysis of remote sensing images. MDPI, 2021.

Book chapters

E. Pasolli, S. Prasad, M. M. Crawford, J. Tilton. Advances in hyperspectral image classification methods for vegetation and agricultural cropland studies. In P. S. Thenkabail et al., editors, Hyperspectral remote sensing of vegetation (second edition). CRC Press, 2019.
N. Meger, E. Pasolli, C. Rigotti, E. Trouve, F. Melgani. Satellite image time series: mathematical models for data mining and missing data restoration. In J. Zerubia and G. Moser, editors, Mathematical models for remote sensing image processing. Springer, 2018.
F. Melgani, G. Mercier, L. Lorenzi, and E. Pasolli. Recent methods for reconstructing missing data in multispectral satellite imagery. In R. S. Anderssen et al., editors, Applications + practical conceptualization + mathematics = fruitul innovation, pages 221-234. Springer, 2016.
F. Melgani and E. Pasolli. Multiobjective PSO for hyperspectral image clustering. In A. Chatterjee and P. Siarry, editors, Modern image processing algorithms employing computational intelligence techniques, pages 265-280. Springer, 2013.

International conference papers

Z. Zhang, E. Pasolli, M. M. Crawford. Crop mapping through an adaptive multiview active learning strategy. In Proceedings of the IEEE International Workshop on Metrology for Agriculture and Forestry 2019, Portici, Italy, 2019.
F. De Filippis, E. Pasolli, A. Tett, M. De Angelis, E. Neviani, S. Turroni, L. Cocolin, M. Gobbetti, N. Segata, D. Ercolini. Habitual diet selects distinct genetic and functional subtypes of intestinal Prevotella copri. In Proceedings of the International Human Microbiome Consortium Meeting 2018, Killarney, Ireland, 2018.
D. Dolce, N. Ravenni, S. Campana, E. Camera, S. Neri, C. Braggion, S. Manara, E. Pasolli, F. Armanini, N. Segata, G. Taccetti. Longitudinal study of methicillin-resistant Staphylococcus aureus genetic background isolated from cystic fibrosis patients. In Proceedings of the European Cystic Fibrosis Conference, Journal of Cystic Fibrosis, 16(S90), Jul. 2017.
D. Dolce, N. Ravenni, S. Campana, E. Camera, T. Orioli, S. Neri, C. Braggion, S. Manara, E. Pasolli, F. Armanini, N. Segata, G. Taccetti. Genetic background of methicillin-resistant Staphylococcus aureus isolates from cystic fibrosis patients: a three-year longitudinal study. In Proceedings of the Annual North American Cystic Fibrosis Conference, Pediatric Pulmonology, 51(S45):318, Oct. 2016.
M. Scholz, D. W. Ward, E. Pasolli, T. Tolio, M. Zolfo, F. Asnicar, D. T. Truong, A. Tett, A. L. Morrow, and N. Segata. Pangenome-based computational metagenomic profiling enables strain-level culture-free epidemiology and population genomic studies. In Proceedings of the ECCB 2016, The Hague, Netherlands, 2016.
E. Pasolli, H. L. Yang, and M. M. Crawford. Combining active and metric learning for hyperspectral image classification. In Proceedings of the IEEE Workshop on Hyperspectral Image and Signal Processing: Evolution in Remote Sensing 2014, Lausanne, Switzerland, 2014.
J. C. Tilton and E. Pasolli. Incorporating edge information into best merge region-growing segmentation. In Proceedings of the IEEE International Geoscience and Remote Sensing Symposium 2014, pages 4891-4894, Quebec, Canada, 2014.
E. Pasolli and F. Melgani. An approach for classifying large scale images. In Proceedings of the IEEE International Geoscience and Remote Sensing Symposium 2012, pages 5410-5413, Munich, Germany, 2012.
F. Douak, F. Melgani, E. Pasolli, and N. Benoudjit. SVR active learning for product quality control. In Proceedings of the International Conference on Information Science, Signal Processing and their Applications 2012, pages 1113-1117, Montreal, Canada, 2012.
E. Pasolli and F. Melgani. Ground-truth assisted design for remote sensing image classification. In Proceedings of the IEEE International Geoscience and Remote Sensing Symposium 2011, pages 609–612, Vancouver, Canada, 2011.
E. Pasolli and F. Melgani. Gaussian process regression within an active learning scheme. In Proceedings of the IEEE International Geoscience and Remote Sensing Symposium 2011, pages 3574–3577, Vancouver, Canada, 2011.
E. Pasolli, F. Melgani, D. Tuia, F. Pacifici, and W. J. Emery. Improving active learning methods using spatial information. In Proceedings of the IEEE International Geoscience and Remote Sensing Symposium 2011, pages 3923–3926, Vancouver, Canada, 2011.
D. Tuia, E. Pasolli, and W. J. Emery. Dataset shift adaptation with active queries. In Proceedings of the Joint Urban Remote Sensing Event 2011, pages 121–124, Munich, German, 2011.
F. Melgani, G. Mahlknecht, E. Pasolli, E. Gottardini, A. Cristofori, F. Cristofolini, and N. La Porta. Exploiting ozone concentration measurements from satellite remote sensors for forest monitoring: a feasibility study. In Proceedings of the IUFRO World Congress 2010, pages 336–336, Seoul, Republic of Korea, 2010.
E. Pasolli and F. Melgani. Model-based active learning for SVM classification of remote sensing images. In Proceedings of the IEEE International Geoscience and Remote Sensing Symposium 2010, pages 820–823, Honolulu, Hawaii, 2010.
A. Paoli, F. Melgani, and E. Pasolli. Swarm intelligence for unsupervised classification of hyperspectral images. In Proceedings of the IEEE International Geoscience and Remote Sensing Symposium 2009, pages V–96–V–99, Cape Town, South Africa, 2009.
E. Pasolli, F. Melgani, and M. Donelli. A pattern recognition system for extracting buried object characteristics in GPR images. In Proceedings of the IEEE International Geoscience and Remote Sensing Symposium 2009, pages IV–430–IV–433, Cape Town, South Africa, 2009.
E. Pasolli, F. Melgani, M. Donelli, R. Attoui, and M. de Vos. A pattern recognition system for archaeological exploration with GPR images. In Proceedings of the Colloque International sur l’Archeologie 2009, Tebessa, Algeria, 2009.
E. Pasolli, F. Melgani, M. Donelli, R. Attoui, and M. de Vos. Automatic detection and classification of buried objects in GPR images using genetic algorithms and support vector machines. In Proceedings of the IEEE International Geoscience and Remote Sensing Symposium 2008, pages II–525–II–528, Boston, USA, 2008.

Editorial, reviewer, and scientific committee activity

Since 2008, Reviewer for 467 papers in 60+ international journals: IEEE: Transactions on Geoscience and Remote Sensing; Geoscience and Remote Sensing Letters; Journal of Selected Topics in Applied Earth Observations and Remote Sensing; Geoscience and Remote Sensing Magazine; Transactions on Image Processing; Transactions on Industrial Electronics; Transactions on Medical Imaging; Transactions on Biomedical Engineering; Transactions on Systems, Man, and Cybernetics, Part B: Cybernetics; Transactions on Systems, Man and Cybernetics: Systems; Transactions on Cybernetics; Electronic Letters; Access. Elsevier: Remote Sensing of Environment; ISPRS Journal of Photogrammetry and Remote Sensing; International Journal of Applied Earth Observation and Geoinformation; Computer & Geosciences; Journal of Applied Geophysics; Journal of the Franklin Institute; Pattern Recognition Letters; Artificial Intelligence in Medicine; Computers in Biology and Medicine; Journal of Chemometrics; Neurocomputing; Chemometrics and Intelligent Laboratory Systems; Biomedical Signal Processing and Control; Computational and Structural Biotechnology Journal; Informatics in Medicine Unlocked; Expert Systems with Applications; Marine Genomics; Journall of Functional Foods; Current Opinion in Microbiology; Microbiological Research; Food Research International; Current Research in Biotechnology. Springer: Journal of Heuristics; Acta Geophysica; Soft Computing; Biomedical Engineering; Signal, Image and Video Processing; Stochastic Environmental Research and Risk Assessment. MDPI: Remote Sensing; ISPRS International Journal of Geo-Information; Sensors; Metabolites. Hindawi: Applied Computational Intelligence and Soft Computing; The Scientific World Journal. BMC: Genome Biology; Genome Medicine; Microbiome; Bioinformatics; Genomics; Medical Informatics and Decision Making; Breast Cancer Research. Nature: Nature Biotechnology; Nature Medicine; Nature Communications; Nature Metabolism; Nature Protocols; Scientific Reports; npj Biofilms and Microbiomes; Scientific Data. Oxford Academic: GigaScience; Bioinformatics; Inflammatory Bowel Diseases; NAR Genomics and Bioinformatics. Taylor & Francis: Annals of Human Biology; International Journal of Remote Sensing; Journal of Spatial Science; Marine Geodesy. SPIE: Journal of Applied Remote Sensing. Others: Cell Host & Microbe; Gut; eLife; Genome Research; mSystems; PLOS Computational Biology; PeerJ; PLOS One; Applied and Environmental Microbiology; Journal of Applied Microbiology; Frontiers in Microbiology; Frontiers in Cellular and Infection Microbiology; Frontiers in Plant Science; Computing Surveys; The Annals of Applied Statistics; Photogrammetric Engineering and Remote Sensing; Progress in Electromagnetics Research; International Journal of Remote Sensing Applications; International Journal on Artificial Intelligence Tools; Journal of Zhejiang University Science C; The Open Civil Engineering Journal
Since 2015, Reviewer for grant proposals: ESCMID (2024), Swiss National Science Foundation (Switzerland, 2023), Fulbright (Luxembourg, 2023), WWTF (Austria, 2023), ESCMID (2023), NSERC (Canada, 2022), National Science Center (Poland, 2023, 2022, 2021, 2020), CORE (Luxembourg, 2021), ANR Agence nationale de la recherche (France, 2021), ESF - Science Connect (2021, 2020, 2019), SIB Swiss Institute of Bioinformatics (2020), European Commission H2020 Marie Sklodowska-Curie individual fellowship (2019), Federal University of Toulouse Midi-Pyrénées (France, 2015)
Since 2019, Ph.D. thesis evaluator: Michela Giulia Clavenna (2023, University of Eastern Piedmont), Maxence Queyrel (2021, Sorbonne University-France), Giorgia Piersigilli (2021, University of Turin-Italy), Camilla Ceccarani (2020, University of Milan-Italy), Mattia Savardi (2019, University of Brescia-Italy)
Since 2019, Editorial board member: BMC Microbiology (since 2023), Frontiers in Microbiology (since 2023), Remote Sensing (2019-2022)
Since 2019, Guest editor for special issues: "Pattern analysis in remote sensing" (Remote Sensing, 2020-2021), "Advanced machine learning approaches for hyperspectral data analysis" (Remote Sensing, 2019-2021), "Computational intelligence and advanced learning techniques in remote sensing" (Remote Sensing, 2019-2020), "Advanced deep learning strategies for the analysis of remote sensing images" (Remote Sensing, 2019-2020), “Transfer learning in remote sensing" (IEEE JSTARS, 2019-2020)
Since 2019, Scientific advisory board member for the company PreBiomics s.r.l. on “machine learning for the oral microbiome”
2021, Referee in the VQR 2015-2019, Ministry of Education, University and Research
2019 October, Organizer of the special session “Remote and proximal sensing metrics for the characterization of agricultural and forestry systems”, IEEE International Workshop on Metrology for Agriculture and Forestry 2019, Portici, Italy
2017, Guest academic editor: PLOS One
2015 June, Technical committee member: Conference "IEEE/ISPRS Workshop: EarthVision 2015”, Boston, United States

International journal papers

* equal contribution, titles are link

D. Bazzani, V. Heidrich, P. Manghi, A. Blanco-Míguez, F. Asnicar, F. Armanini, S. Cavaliere, A. Bertelle, F. Dell'Acqua, E. Dellasega, R. Waldner, D. Vicentini, M. Bolzan, C. Tomasi, N. Segata*, E. Pasolli*, P. Ghensi*. Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases. npj Biofilms and Microbiomes, Feb. 2024 [IF 2022: 9.2].
K.D. Huang, L. Amend, E.J.C. Gálvez, T. Lesker, R. de Oliveira, A. Bielecka, A. Blanco-Míguez, M. Valles-Colomer, I. Ruf, E. Pasolli, J. Buer, N. Segata, S. Esser, T. Strowig, J. Kehrmann. Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices. Cell Reports Medicine, Feb. 2024 [IF 2022: 14.3].
A. Blanco-Míguez, E.J.C. Gálvez*, E. Pasolli*, F. De Filippis*, [20 authors], T. Strowig. Extension of the Segatella copri complex to 13 species with distinct large extrachromosomal elements and associations with host conditions. Cell Host&Microbe, Nov. 2023 [IF 2022: 30.3].
F. De Filippis, M. Bonelli, D. Bruno, G. Sequino, A. Montali, M. Reguzzoni, E. Pasolli, D. Savy, S. Cangemi, V. Cozzolino, G. Tettamanti, D. Ercolini, M. Casartelli, S. Caccia. Plastics shape the black soldier fly larvae gut microbiome and select for biodegrading functions. Microbiome, Sep. 2023 [IF 2022: 15.5].
M. G. Clavenna, M. La Vecchia, M. Sculco, S. Joseph, E. Barberis, E. Amede, M. Mellai, S. Brossa, G. Borgonovi, P. Occhipinti, R. Boldorini, E. Robotti, B. Azzimonti, E. Bona, E. Pasolli, D. Ferrante, M. Manfredi, A. Aspesi, I. Dianzani. Distinct signatures of tumor-associated microbiota and metabolome in low-grade vs. high-grade dysplastic colon polyps: inference of their role in tumor initiation and progression. Cancers, Jun. 2023 [IF 2022: 5.2].
P. Manghi, [18 authors], E. Pasolli, F. Asnicar, T. Strowig, H. Sokol, N. Segata. MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice. Cell Reports, May 2023 [IF 2022: 8.8].
S. Manara, [16 authors], E. Pasolli*, M. C. Collado*, N. Segata*. Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population. Current Biology, Apr. 2023 [IF 2022: 9.2].
A. Aitor, [20 authors], E. Pasolli, F. Asnicar, C. Huttenhower, N. Segata. Extending and improving metagenomic taxonomic profiling with uncharacterized species with MetaPhlAn 4. Nature Biotechnology, Feb. 2023 [IF 2022: 46.9].
M. Valles-Colomer, [37 authors], E. Pasolli, T. D. Spector, E. Domenici, M. C. Collado, N. Segata. The person-to-person transmission landscape of the gut and oral microbiomes. Nature, Jan. 2023 [IF 2022: 64.8].
F. Favero, E. Barberis, M. Gagliardi, S. Espinoza, L. Contu, S. Gustincich, F. Boccafoschi, C. Borsotti, D. Lim, V. Rubino, F. Mignone, E. Pasolli, M. Manfredi, S. Zucchelli, D. Corrà, M. Corazzari. A metabologenomic approach reveals alterations in the gut microbiota of a mouse model of Alzheimer's disease. PLoS ONE, Aug. 2022 [IF 2022: 3.7]
I. Sharon, N. M. Quijada, E. Pasolli, M. Fabbrini, F. Vitali, V. Agamennone, A. Dotsch, E. Selberherr, J. H. Grau, M. Meixner, K. Liere, D. Ercolini, C. De Filippo, G. Caderni, P. Brigidi, S. Turroni. The core human microbiome: does it exist and how can we find it? A critical review of the concept. Nutrients, Jul. 2022 [IF 2022: 5.9].
R. Giliberti, S. Cavaliere, I. E. Mauriello, D. Ercolini, E. Pasolli. Host phenotype classification from human microbiome data is mainly driven by the presence of microbial taxa. PLOS Computational Biology, May 2022 [IF 2022: 4.3].
M. Palladino, N. Romano, E. Pasolli, P. Nasta. Developing pedotransfer functions for predicting soil bulk density in Campania. Geoderma, Apr. 2022 [IF 2022: 6.1].
S. Yonekura, [43 authors], E. Pasolli, L. Derosa, L. Zitvogel. Cancer induces a stress ileopathy depending on B-adrenergic receptors and promoting dysbiosis that contribute to carcinogenesis. Cancer Discovery, Apr. 2022 [IF 2022: 28.2].
C. Mirzayi, [59 authors], E. Pasolli, [44 authors], L. Waldron. Reporting guidelines for human microbiome research: the STORMS checklist. Nature Medicine, Nov. 2021 [IF 2021: 87.241].
F. De Filippis, L. Paparo, R. Nocerino, G. Della Gatta, L. Carucci, R. Russo, E. Pasolli, D. Ercolini, R. Berni Canani. Specific gut microbiome signatures and the associated pro-inflamatory functions are linked to pediatric allergy and acquisition of immune tolerance. Nature Communications, 12, Oct. 2021 [IF 2021: 17.694].
S. Tarallo, G. Ferrero, F. De Filippis, A. Francavilla, E. Pasolli, V. Panero, F. Cordero, N. Segata, S. Grioni, R. G. Pensa, B. Pardini, D. Ercolini, A. Naccarati. Stool microRNA profiles reflect different dietary and gut microbiome patterns in healthy individuals. Gut, Jul. 2021 [IF 2021: 31.793].
A. Tett, E. Pasolli, G. Masetti, D. Ercolini, N. Segata. Prevotella diversity, niches and interactions with the human host. Nature Reviews Microbiology, May 2021 [IF 2021: 78.297].
S. Terrisse, [25 authors], E. Pasolli*, S. Delaloge*, L. Zitvogel*. Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment. Cell Death & Differentiation, May 2021 [IF 2021: 12.067].
A. Uzan-Yulzari, O. Turta, [5 authors], E. Pasolli, [12 authors], S. Rautava, O. Koren. Neonatal antibiotic exposure impairs child growth during the first six years of life by perturbing intestinal microbial colonization. Nature Communications, 12, Jan. 2021 [IF 2021: 17.694].
E. Pasolli, F. De Filippis, I. E. Mauriello, F. Cumbo, A. M. Walsh, J. Leech, P. D. Cotter, N. Segata, D. Ercolini. Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome. Nature Communications, 11, Dec. 2020 [IF 2020: 14.919].
F. De Filippis, E. Pasolli, D. Ercolini. Newly explored Faecalibacterium diversity is connected to age, lifestyle, geography, and disease. Current Biology, 30, Dec. 2020 [IF 2020: 10.834].
F. Asnicar, A. M. Thomas, F. Beghini, C. Mengoni, S. Manara, P. Manghi, Q. Zhu, M. Bolzan, F. Cumbo, U. May, J. G. Sanders, M. Zolfo, E. Kopylova, E. Pasolli, R. Knight, S. Mirarab, C. Huttenhower, N. Segata. Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nature Communications, 11, Dec. 2020 [IF 2020: 14.919].
N. Karcher, E. Pasolli, [19 authors], N. Segata. Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations. Genome Biology, 21:138, Dec. 2020 [IF 2020: 13.583].
P. Ghensi, P. Manghi, M. Zolfo, F. Armanini, E. Pasolli, M. Bolzan, A. Bertelle, F. Dell'Acqua, E. Dellasega, R. Waldner, F. Tessarolo, C. Tomasi, N. Segata. Strong oral plaque microbiome signatures for dental implant diseases identified by strain-resolution metagenomics. npj Biofilms and Microbiomes, Oct. 2020 [IF 2020: 7.290].
A. Fluckiger, [29 authors], E. Pasolli, [20 authors], L. Zitvogel. Cross-reactivity between tumor MHC class I-restricted antigenes and an enterococcal bacteriophage. Science, 369(6506):936-942, Aug. 2020 [IF 2020: 47.728].
F. De Filippis*, E. Pasolli*, D. Ercolini. The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health. FEMS Microbiology Reviews, Jun. 2020 [IF 2020: 16.408].
L. Derosa, B. Routy, M. Fidelle, V. Iebba, L. Alla, E. Pasolli, [27 authors], L. Zitvogel. Gut bacteria composition drives primary resistance to cancer immunotherapy in renal cell carcinoma patients. European Urology, May 2020 [IF 2020: 20.096].
S. Falanga Bolognesi, E. Pasolli, O. R. Belfiore, C. De Michele, G. D'Urso. Harmonized Landsat 8 and Sentinel-2 time series data to detect irrigated areas: an application in southern Italy. Remote Sensing, 12:8, Apr. 2020 [IF 2020: 4.848].
Z. Zhang, E. Pasolli, M. M. Crawford. An adaptive multiview active learning approach for spectral-spatial classification of hyperspectral images. IEEE Transactions on Geoscience and Remote Sensing, 58:4, Apr. 2020 [IF 2020: 5.600].
V. Meslier, M. Laiola, H. M. Roager, F. De Filippis, H. Roume, B. Quinquis, R. Giacco, I. Mennella, R. Ferracane, N. Pons, E. Pasolli, A. Rivellese, L. O. Dragsted, P. Vitaglione, S. D. Ehrlich, D. Ercolini. Mediterranean diet intervention in overweight and obese subjects lowers plasma cholesterol and causes changes in the gut microbiome and metabolome independently of energy intake. Gut, Feb. 2020 [IF 2020: 23.059].
S. Manara, F. Asnicar, F. Beghini, D. Bazzani, F. Cumbo, M. Zolfo, E. Nigro, N. Karcher, P. Manghi, M. I. Metzger, E. Pasolli, N. Segata. Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species. Genome Biology, 20:299, Dec. 2019 [IF 2019: 10.806].
S. Ghaffarian, N. Kerle, E. Pasolli, J.J. Arsanjani. Post-disaster building database updating using automated deep learning: An integration of pre-disaster OpenStreetMap and multi-temporal satellite data. Remote Sensing, 11:20, Oct. 2019 [IF 2019: 4.509].
A. Tett, K. D. Huang, F. Asnicar, H. Fehlner-Peach, E. Pasolli, [26 authors], N. Segata. The Prevotella copri complex comprises four distinct clades underrepresented in Westernised populations. Cell Host&Microbe, 25:10, Oct 2019 [IF 2019: 15.923].
A. Thomas, P. Manghi, F. Asnicar, E. Pasolli, [32 authors], L. Waldron, A. Naccarati, N. Segata. Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. Nature Medicine, 25:667-678, Apr. 2019 [IF 2019: 36.130].
F. De Filippis, E. Pasolli, A. Tett, S. Tarallo, A. Naccarati, M. De Angelis, E. Neviani, L. Cocolin, M. Gobbetti, N. Segata, D. Ercolini. Distinct genetic and functional traits of human intestinal Prevotella copri strains are associated with different habitual diets. Cell Host&Microbe, 25:3, Mar. 2019 [IF 2019: 15.923].
D. Dolce, S. Neri, L. Grisotto, [18 authors], E. Pasolli, [3 authors], G. Taccetti. Methicillin-resistant Staphylococcus aureus eradication in cystic fibrosis patients: A randomized multicenter study. PLOS ONE, Mar. 2019 [IF 2019: 2.740]
E. Pasolli, F. Asnicar, S. Manara, M. Zolfo, N. Karcher, F. Armanini, F. Beghini, P. Manghi, A. Tett, P. Ghensi, M. C. Collado, B. L. Rice, C. DuLong, X. C. Morgan, C. Golden, C. Huttenhower, N. Segata. Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle. Cell, 176:3, Jan. 2019 [IF 2019: 38.637] [ website ].
R. Pedron, A. Esposito, I. Bianconi, E. Pasolli, A. Tett, F. Asnicar, M. Cristofolini, N. Segata, O. Jousson. Genomic and metagenomic insights into the microbial community of a thermal spring. Microbiome, 7:8, Jan. 2019 [IF 2019: 11.607].
S. Manara*, E. Pasolli*, D. Dolce*, N. Ravenni, S. Campana, F. Armanini, F. Asnicar, A. Mengoni, L. Galli, C. Montagnani, E. Venturini, O. Rota-Stabelli, G. Grandi, G. Taccetti, N. Segata. Whole-genome epidemiology, characterisation, and phylogenetic reconstruction of Staphylococcus aureus strains in a paediatric hospital. Genome Medicine, 10:82, Nov. 2018 [IF 2018: 10.886].
P. Ferretti, E. Pasolli*, A. Tett*, F. Asnicar*, [40 authors], N. Segata. Mother-to-infant microbial transmission from different body sites shapes the developing infant gut microbiome. Cell Host&Microbe, 24:1, Jul. 2018 [IF 2018: 15.753] [cover].
M. Yassour, E. Jason, L. J. Hogstrom, T. D. Arthur, S. Tripathi, H. Siljander, J. Selvenius, S. Oikarinen, H. Hyoty, S. M. Virtanen, J. Ilonen, P. Ferretti, E. Pasolli, A. Tett, F. Asnicar, N. Segata, H. Vlamakis, E. S. Lander, C. Huttenhower, M. Knip, R. J. Xavier. Strain-level analysis of mother-to-child bacterial transmission during the first few months of life. Cell Host&Microbe, 24:1, Jul. 2018 [IF 2018: 15.753].
M. Zolfo, F. Asnicar, P. Manghi, E. Pasolli, A. Tett, N. Segata. Profiling microbial strains in urban environments using metagenomic sequencing data. Biology Direct, 13:9, May 2018 [IF 2018: 3.010].
F. Pinto, A. Tett, F. Armanini, F. Asnicar, A. Boscaini, E. Pasolli, M. Zolfo, C. Donati, N. Salmaso, N. Segata. Draft genome sequences of novel Pseudomonas, Flavobacterium, and Sediminibacterium strains from a freshwater ecosystem. Genome Announcements, 6(5):e00009-18, Feb. 2018.
E. Pasolli*, L. Schiffer*, P. Manghi*, A. Renson, V. Obenchain, D. T. Truong, F. Beghini, F. Malik, M. Ramos, J. B. Dowd, C. Huttenhower, M. Morgan, N. Segata, L. Waldron. Accessible, curated metagenomic data through ExperimentHub. Nature Methods, 14(11):1023-1024, Nov. 2017 [IF 2017: 26.919] [ website ].
F. Pinto, A. Tett, F. Armanini, F. Asnicar, A. Boscaini, E. Pasolli, M. Zolfo, C. Donati, N. Salmaso, N. Segata. Draft genome sequence of the planktic cyanobacterium Tychonema bourrellyi, isolated from alpine lentic freshwater. Genome Announcements, 5(47):e01294-17, Nov. 2017.
F. Beghini*, E. Pasolli*, D. T. Truong, L. Putignani, S. Cacciò, N. Segata. Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome. ISME Journal, 11:2848-2863, Aug. 2017 [IF 2017: 9.520].
S. Wuyts, S. Wittouck, I. De Boeck, C. Allonsius, E. Pasolli, N. Segata, S. Lebeer. Large-scale phylogenomics of the Lactobacillus casei group highlights taxonomic inconsistencies and reveals novel clade-associated features. mSystems, 2(4):e00061-17, Aug. 2017 [IF 2017: 5.750].
A. Tett, E. Pasolli*, S. Farina*, D. T. Truong*, F. Asnicar, M. Zolfo, F. Beghini, F. Armanini, O. Jousson, V. De Sanctis, R. Bertorelli, G. Girolomoni, M. Cristofolini, N. Segata. Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis. npj Biofilms and Microbiomes, Jun. 2017 [IF 2017: 4.128].
S. Duranti, [13 authors], E. Pasolli, [17 authors], M. Ventura. Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission. Microbiome, 5:66, Jun. 2017 [IF 2017: 9.133].
D. T. Truong, A. Tett, E. Pasolli, C. Huttenhower, N. Segata. Microbial strain-level population structure and genetic diversity from metagenomes. Genome Research, Feb. 2017 [IF 2017: 10.101] [ code ].
E. Pasolli, D. T. Truong, F. Malik, L. Waldron, N. Segata. Machine learning meta-analysis of large metagenomic datasets: tools and biological insights. PLOS Computational Biology, 12(7):e1004977, Jul. 2016 [IF 2016: 4.542] [ code | Gut check article by Casey S. Greene ].
Z. Zhang, E. Pasolli, H. L. Yang, and M. M. Crawford. Multimetric active learning for classification of remote sensing data. IEEE Geoscience and Remote Sensing Letters, 13(7):1007-1011, Jul. 2016 [IF 2016: 2.761].
The MetaSUB International Consortium. The metagenomics and metadesign of the subways and urban biomes (MetaSUB) international consortium inaugural meeting report. Microbiome, 4(1):1-14, Jun. 2016 [IF 2016: 8.496].
M. Scholz*, D. W. Ward*, E. Pasolli*, T. Tolio, M. Zolfo, F. Asnicar, D. T. Truong, A. Tett, A. L. Morrow, and N. Segata. Strain-level microbial epidemiology and population genomics from shotgun metagenomics. Nature Methods, 13(5):435-438, May 2016 [IF 2016: 25.062] [ code | Strain-level article by Vivien Marx ].
E. Pasolli, H. L. Yang, and M. M. Crawford. Active-metric learning for classification of remotely sensed hyperspectral images. IEEE Transactions on Geoscience and Remote Sensing, 54(4):1925-1939, Apr. 2016 [IF 2016: 4.942].
Z. Zhang, E. Pasolli, M. M. Crawford, and J. C. Tilton. An active learning framework for hyperspectral image classification using hierarchical segmentation. IEEE Journal of Selected Topics in Applied Earth Observation and Remote Sensing, 9(2):640-654, Feb. 2016 [IF 2016: 2.913].
D. T. Truong, E. A. Franzosa, T. T. Tickle, M. Scholz, G. Weingart, E. Pasolli, A. Tett, C. Huttenhower, and N. Segata. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nature Methods, 12(10):902-903, Oct. 2015 [IF 2015: 25.328] [ code ].
E. Pasolli and F. Melgani. Genetic-algorithm based method for mitigating label noise issue in ECG signal classification. Biomedical Signal Processing and Control, 19:130-136, May 2015 [IF 2015: 1.521].
Y. Zhang, H. L. Yang, S. Prasad, E. Pasolli, J. Jung, and M. M. Crawford. Ensemble multiple kernel active learning for classification of multi-source remote sensing data. IEEE Journal of Selected Topics in Applied Earth Observation and Remote Sensing, 8(2):845-858, Feb. 2015 [IF 2015: 2.145].
E. Pasolli, F. Melgani, D. Tuia, F. Pacifici, and W. J. Emery. SVM active learning approach for image classification using spatial information. IEEE Transactions on Geoscience and Remote Sensing, 52(4):2217-2233, Apr. 2014 [IF 2014: 3.514].
J. Jung, E. Pasolli, S. Prasad, J. C. Tilton, and M. M. Crawford. A framework for land cover classification using discrete return LiDAR data: Adopting pseudo-waveform and hierarchical segmentation. IEEE Journal of Selected Topics in Applied Earth Observation and Remote Sensing, 7(2):491-502, Feb. 2014 [IF 2014: 3.026].
N. Alajlan, E. Pasolli, F. Melgani, and A. Franzoso. Large-scale image classification using active learning. IEEE Geoscience and Remote Sensing Letters, 11(1):259-263, Jan. 2014 [IF 2014: 2.095].
E. Pasolli, F. Melgani, N. Alajlan, and N. Conci. Optical image classification: a ground-truth design framework. IEEE Transactions on Geoscience and Remote Sensing, 51(6):3580-3597, Jun. 2013 [IF 2013: 2.933].
E. Pasolli, F. Melgani, N. Alajlan, and Y. Bazi. Active learning methods for biophysical parameter estimation. IEEE Transactions on Geoscience and Remote Sensing, 50(10):4071–4084, Oct. 2012 [IF 2012: 3.467].
N. Segata*, E. Pasolli*, F. Melgani, and E. Blanzieri. Local SVM approaches for fast and accurate classification of remote sensing images. International Journal of Remote Sensing, 33(19):6186–6201, Oct. 2012 [IF 2012: 1.138].
F. Douak, F. Melgani, N. Alajlan, E. Pasolli, Y. Bazi, and N. Benoudjit. Active learning for spectroscopic data regression. Journal of Chemometrics, 26(7):374–383, Jul. 2012 [IF 2012: 1.937].
D. Tuia, E. Pasolli, and W. J. Emery. Using active learning to adapt remote sensing image classifiers. Remote Sensing of Environment, 115(9):2232–2242, Sep. 2011 [IF 2011: 4.574].
E. Pasolli, F. Melgani, and Y. Bazi. Support vector machine active learning through significance space construction. IEEE Geoscience and Remote Sensing Letters, 8(3):431–435, May 2011 [IF 2011: 1.560].
E. Pasolli and F. Melgani. Active learning methods for electrocardiographic signal classification. IEEE Transactions on Information Technology in Biomedicine, 14(6):1405–1416, Nov. 2010 [IF 2010: 1.707].
E. Pasolli, F. Melgani, and M. Donelli. Gaussian process approach to buried object size estimation in GPR images. IEEE Geoscience and Remote Sensing Letters, 7(1):141–145, Jan. 2010 [IF 2010: 1.431].
A. Paoli, F. Melgani, and E. Pasolli. Clustering of hyperspectral images based on multiobjective particle swarm optimization. IEEE Transactions on Geoscience and Remote Sensing, 47(12):4175–4187, Dec. 2009, [IF 2009: 2.234].
E. Pasolli, F. Melgani, and M. Donelli. Automatic analysis of GPR images: a pattern-recognition approach. IEEE Transactions on Geoscience and Remote Sensing, 47(7):2206–2217, Jul. 2009, [IF 2009: 2.234].