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

• 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

• 2024 – 2027, Industrial Ph.D. research grant (Italian Ministry of Education, University and Research; Scientific Advisor for the fellowship to Francesco Fagnano)

• 2023 - 2025, PNRR PRIN 2022 (Italian Ministry of Education, University and Research)

• 2023 – 2026, Ph.D. research grant (Italian Ministry of Education, University and Research; Scientific Advisor for the fellowship to Michele Avagliano)

• 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

• 2024, Inclusion in the list of Highly Cited Researchers 2024 by Clarivate

• 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” 

• Since 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, 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

• 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

• 2024, Lecturer "Microbiome data science and biostatistics" (5 CFU), CRESCENDO Transdisciplinary Doctoral Programme, University of Naples Federico II, Italy

• 2024, Lecturer "Shotgun metagenomic processing and analysis" (24 hours), Physalia courses (Online)

• 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

• 2024 October, Invited lecture, Inserm Symposium on Microbiota, Paris, France

• 2024 October, Seminar, Workshop Task Force on Computational and Quantitative Biology, Naples, Italy

• 2024 June, Seminar, Caffè scientifico@Dept. of Agricultural Sciences, University of Naples Federico II, Naples, Italy

• 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

• Since 2008, Reviewer for 472 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; Cell Reports Methods; 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; Phytochemical Analysis; 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, 2024, 2023), Fulbright (Luxembourg, 2023), WWTF (Austria, 2023), ESCMID (2023, 2024), 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 

• 2015 June, Technical committee member: Conference "IEEE/ISPRS Workshop: EarthVision 2015”, Boston, United States

• Since 2022, Scientific committee member for the Microbiome Virtual International Forum

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

* equal contribution, titles are link

1. C. Fruggiero, G. Aufiero, D. D'Angelo, E. Pasolli, N. D'Agostino.  Refining dual RNA-seq mapping: sequential and combined approaches in host-parasitic plant dynamics. Frontiers in Plant Science, Nov. 2024 [IF 2023: 4.1].

2. N. Carlino, [34 authors], D. Ercolini*, P. Cotter*, N. Segata*, E. Pasolli*. Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome. Cell, Aug. 2024 [IF 2023: 45.5].

3. B. Medrouh, A. Abdelli, S. Belkessa, Y. Ouinten, M. Brahimi, A. Hakem, T. Kernif, S. M. Singer, H. Ziam, A. D. Tsaousis, P. Jokelainen, G. Savini, E. Pasolli. Seroprevalence and risk factors of bluetongue virus in domestic cattle, sheep, goats and camels in Africa: a systematic review and meta-analysis. Veterinary Quarterly, Aug. 2024 [IF 2023: 7.9].

4. F. De Filippis, V. Valentino, M. Yap, R. Cabrera-Rubio, C. Barcenilla, N. Carlino, J. F. Cobo-Diaz, N. M. Quijada, I. Calvete-Torre, P. Ruas-Madiedo, C. Sabater, G. Sequino, E. Pasolli, M. Wagner, A. Margolles, N. Segata, A. Alvarez-Ordonez, P. D. Cotter, D. Ercolini. Microbiome mapping in dairy industry reveals new species and genes for probiotic and bioprotective activities. npj Biofilms and Microbiomes, Aug. 2024 [IF 2023: 7.8].

5. E. Piperni, L. H. Nguyen, P. Manghi, H. Kim, E. Pasolli, [30 authors], F. Asnicar. Intestinal Blastocystis is linked to healthier diets and more favorable cardiometabolic outcomes in 56,989 individuals from 32 countries. Cell, Jul. 2024 [IF 2023: 45.5]. 

6. I. Giordano, E. Pasolli, G. Mauriello. Transcriptomic analysis reveals differential gene expression patterns of Lacticaseibacillus casei ATCC 393 in response to ultrasound stress. Ultrasonics Sonochemistry, May 2024 [IF 2023: 8.7]. 

7. F. De Filippis, V. Valentino, G. Sequino, G. Borriello, M. G. Riccardi, B. Pierri, P. Cerino, A. Pizzolante, E. Pasolli, M. Esposito, A. Limone, D. Ercolini. Exposure to environmental pollutants selects for xenobiotic-degrading functions in the human gut microbiome. Nature Communications, May 2024 [IF 2023: 14.7].

8. 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 2023: 7.8].

9. 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 2023: 11.7].

10. 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 2023: 20.6].

11. 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 2023: 13.8].

12. 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 2023: 4.5].

13. 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 2023: 7.5].

14. 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 2023: 8.1].

15. 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 2023: 33.1].

16. 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 2023: 50.5].

17. 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]

18. 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].

19. 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].

20. 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].

21. 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].

22. 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].

23. 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].

24. 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].

25. 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].

26. 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].

27. 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].

28. 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].

29. 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].

30. 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].

31. 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].

32. 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].

33. 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].

34. 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].

35. 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].

36. 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].

37. 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].

38. 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].

39. 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].

40. 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].

41. 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].

42. 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].

43. 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].

44. 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] 

45. 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 ]. 

46. 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]. 

47. 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].

48. 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].

49. 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].

50. 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].

51. 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.

52. 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 ].

53. 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.

54. 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].

55. 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].

56. 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].

57. 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].

58. 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 ].

59. 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 ].

60. 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].

61. 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].

62. 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 ].

63. 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].

64. 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].

65. 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 ].

66. 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].

67. 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].

68. 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].

69. 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].

70. 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].

71. 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].

72. 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].

73. 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].

74. 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].

75. 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].

76. 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].

77. 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].

78. 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].

79. 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].

80. 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].

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

2. 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.

3. 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.

4. 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.

5. 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.

1. 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.

2. 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.

3. 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.

4. 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.

5. 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.

6. 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.

7. 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.

8. 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.

9. 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.

10. 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.

11. 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.

12. 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.

13. 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.

14. 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.

15. 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.

16. 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.

17. 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.

18. 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.

19. 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.