[158] K. Lee, A. Thomas, L. Bolte, J. Bj\"ork, L. Kist de Ruijter, F. Armanini, F. Asnicar, R. Board, N. Calbet-Llopart, ... , T. Spector, R. Weersma, N. Segata: Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma. Nature Medicine, (in press), 2022

[157] F. Meyer, A. Fritz, Z. Deng, D. Koslicki, TR. Lesker, A. Gurevich, G. Robertson, M. Alser, D. Antipov, ... , A. Bremges, A. Sczyrba, AC. McHardy: Critical Assessment of Metagenome Interpretation: the second round of challenges. Nature Methods, 2022

[156] S. Terrisse, A. Goubet, K. Ueda, AM. Thomas, V. Quiniou, C. Thelemaque, G. Dunsmore, E. Clave, M. Gamat-Huber, ... , K. Fizazi, G. Kroemer, L. Zitvogel: Immune system and intestinal microbiota determine efficacy of androgen deprivation therapy against prostate cancer. Journal for ImmunoTherapy of Cancer, 2022

[155] L. Derosa, B. Routy, A. Thomas, V. Iebba, G. Zalcman, S. Friard, J. Mazieres, Audigier-Valette, D. Moro-Sibilot, ... , S. Martinez, J. Soria, B. Besse: Intestinal Akkermansia muciniphila predicts clinical response to PD-1 blockade in patients with advanced non-small-cell lung cancer. Nature Medicine, 2022

[154] S. Bihl, M. de Goffau, D. Podlesny, N. Segata, F. Shanahan, J. Walter, WF. Fricke: When to suspect contamination rather than colonization – lessons from a putative fetal sheep microbiome. Gut Microbes, 2022

[153] L. Bianco, M. Moser, A. Silverj, D. Micheletti, G. Lorenzin, L. Collini, M. Barbareschi, P. Lanzafame, N. Segata, ... , A. Rizzoli, P. Fontana, C. Donati: On the Origin and Propagation of the COVID-19 Outbreak in the Italian Province of Trento, a Tourist Region of Northern Italy. Viruses, 2022

[152] T. Clavel, H. Horz, N. Segata, M. Vehreschild: Next steps after 15 stimulating years of human gut. Microbial Biotechnology, 2022

[151] M. Valles-Colomer, R. Bacigalupe, S. Vieira-Silva, S. Suzuki, Y. Darzi, RY. Tito, T. Yamada, N. Segata, J. Raes, G. Falony: Variation and transmission of the human gut microbiota across multiple familial generations. Nature Microbiology, 2022

[150] N. Tsereteli, R. Vallat, J. Fernandez-tajes, LM. Delahanty, JM. Ordovas, DA. Drew, AM. Valdes, N. Segata, AT. Chan, ... , MP. Walker, TD. Spector, PW. Franks: Impact of insufficient sleep on dysregulated blood glucose control under standardised meal conditions. Diabetologia, 2022


[149] S. Terrisse, L. Derosa, V. Iebba, F. Ghiringhelli, I. Vaz-luis, G. Kroemer, M. Fidelle, S. Christodoulidis, N. Segata, ... , E. Pasolli, S. Delaloge, L. Zitvogel: Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment. Cell Death and Differentiation, 2021

[148] F. Asnicar, ER. Leeming, E. Dimidi, M. Mazidi, PW. Franks, H. Al Khatib, AM. Valdes, R. Davies, E. Bakker, ... , TD. Spector*, N. Segata*, SE. Berry*: Blue Poo: Impact of gut transit time on the gut microbiome using a novel marker. Gut, 2021

[147] MA. Crisci, L. Chen, AE. Devoto, AL. Borges, N. Bordin, R. Sachdeva, A. Tett, AM. Sharrar, N. Segata, ... , S. Lei, JF. Banfield, JM. Santini: Closely related Lak megaphages replicate in the microbiomes of diverse animals. iScience, 2021

[146] AM. Thomas, F. Asnicar, G. Kroemer, N. Segata: Genes Encoding Microbial Acyl Coenzyme A Binding Protein/Diazepam-Binding Inhibitor Orthologs Are Rare in the Human Gut Microbiome and Show No Links to Obesity. Applied and environmental microbiology, 2021

[145] B. Hanson, D. Kits, J. L\"offler, A. Burrichter, A. Fiedler, K. Denger, B. Frommeyer, C. Herbold, T. Rattei, ... , N. Segata, D. Schleheck, A. Loy: Sulfoquinovose is a select nutrient of prominent bacteria and a source of hydrogen sulfide in the human gut. ISME Journal, 2021

[144] N. Karcher, E. Nigro, M. Pun\vcoch\'aĊ™, A. Blanco-Miguez, M. Ciciani, P. Manghi, M. Zolfo, F. Cumbo, S. Manara, ... , M. Valles-Colomer, WM. de Vos, N. Segata: Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly. Genome Biology, 2021

[143] F. Asnicar, SE. Berry, AM. Valdes, LH. Nguyen, G. Piccinno, DA. Drew, E. Leeming, R. Gibson, C. Le Roy, ... , C. Huttenhower, TD. Spector, N. Segata: Microbiome connections with host metabolism and habitual diet from 1098 deeply phenotyped individuals. Nature Medicine, 2021

[142] KM. Kennedy, CJ. Bellissimo, JA. Breznik, J. Barrett, T. Braun, FD. Bushman, MD. Goffau, MA. Elovitz, MM. Heimesaat, ... , MG. Surette, J. Walter, D. Sloboda: Over-celling fetal microbial exposure. Cell, 2021

[141] M. Tomasi, M. Dalsass, F. Beghini, I. Zanella, E. Caproni, L. Fantappi\`e, A. Gagliardi, C. Irene, E. K\"onig, ... , A. Grandi, N. Segata, G. Grandi: Commensal bifidobacterium strains enhance the efficacy of neo-epitope based cancer vaccines. Vaccines, 2021

[140] M. Mazidi, AM. Valdes, JM. Ordovas, WL. Hall, JC. Pujol, J. Wolf, G. Hadjigeorgiou, N. Segata, N. Sattar, ... , TD. Spector, PW. Franks, SE. Berry: Meal-induced inflammation: postprandial insights from the Personalised REsponses to DIetary Composition Trial (PREDICT) study in 1000 participants. The American Journal of Clinical Nutrition, 2021

[139] G. Ferrere, MT. Alou, P. Liu, A. Goubet, M. Fidelle, O. Kepp, S. Durand, V. Iebba, A. Fluckiger, ... , L. Derosa, G. Kroemer, L. Zitvogel: Ketogenic diet and ketone bodies enhance the anticancer effects of PD1 blockade. JCI Insights, 2021

[138] F. Beghini, LJ. McIver, A. Blanco-M\'iguez, L. Dubois, F. Asnicar, S. Maharjan, A. Mailyan, AM. Thomas, P. Manghi, ... , C. Huttenhower, EA. Franzosa, N. Segata: Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. eLife, 2021

[137] A. Bertocchi, S. Carloni, PS. Ravenda, C. Pozzi, G. Penna, A. Bertocchi, S. Carloni, PS. Ravenda, G. Bertalot, ... , C. Pozzi, G. Penna, M. Rescigno: Gut vascular barrier impairment leads to intestinal bacteria dissemination and colorectal cancer metastasis to liver. Cancer Cell, 2021

[136] MC. Wibowo, Z. Yang, M. Borry, A. H\"ubner, KD. Huang, BT. Tierney, S. Zimmerman, F. Barajas-Olmos, C. Contreras-Cubas, ... , M. Snow, S. LeBlanc, AD. Kostic: Reconstruction of ancient microbial genomes from the human gut. Nature, 2021

[135] A. Almeida, S. Nayfach, M. Boland, F. Strozzi, M. Beracochea, ZJ. Shi, KS. Pollard, E. Sakharova, DH. Parks, ... , N. Segata, NC. Kyrpides, RD. Finn: A unified catalog of 204,938 reference genomes from the human gut microbiome. Nature Biotechnology, 2021

[134] D. Serrano, C. Pozzi, S. Guglietta, B. Fosso, M. Suppa, P. Gnagnarella, F. Corso, F. Bellerba, D. Macis, ... , B. Bonanni, M. Rescigno, S. Gandini: Microbiome as mediator of diet on colorectal cancer risk: The role of Vitamin D, markers of inflammation and adipokines. Nutrients, 2021

[133] L. Graneh\"all, KD. Huang, A. Tett, P. Manghi, A. Paladin, NO. Sullivan, O. Rota-stabelli, N. Segata, A. Zink, F. Maixner: Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter. Microbiome, 2021

[132] C. Menni, P. Louca, SE. Berry, A. Vijay, S. Astbury, ER. Leeming, R. Gibson, F. Asnicar, G. Piccinno, ... , N. Segata, TD. Spector, AM. Valdes: High intake of vegetables is linked to lower white blood cell profile and the effect is mediated by the gut microbiome. BMC medicine, 2021

[131] S. Yonekura, S. Terrisse, C. Alves Costa Silva, A. Lafarge, V. Iebba, G. Ferrere, A. Goubet, J. Fahrner, I. Lahmar, ... , E. Pasolli, L. Derosa, L. Zitvogel: Cancer induces a stress ileopathy depending on $\beta$-adrenergic receptors and promoting dysbiosis that contribute to carcinogenesis. Cancer Discovery, 2021

[130] A. Goubet, R. Wheeler, A. Fluckiger, B. Qu, F. Lema\^itre, K. Iribarren, L. Mondrag\'on, M. Tidjani Alou, E. Pizzato, ... , I. Gomperts Boneca, L. Zitvogel, R. Daill\`ere: Multifaceted modes of action of the anticancer probiotic Enterococcus hirae. Cell Death & Differentiation, 2021

[129] C. Mirzayi, A. Renson, C. Furlanello, S. Sansone, F. Zohra, S. Elsafoury, L. Geistlinger, LJ. Kasselman, K. Eckenrode, ... , JB. Dowd, HE. Jones, L. Waldron: Reporting guidelines for human microbiome research: the STORMS checklist. Nature Medicine, 2021

[128] S. Tarallo, G. Ferrero, F. De Filippis, A. Francavilla, E. Pasolli, V. Panero, F. Cordero, N. Segata, S. Grioni, ... , B. Pardini, D. Ercolini, A. Naccarati: Stool microRNA profiles reflect different dietary and gut microbiome patterns in healthy individuals. Gut, 2021

[127] F. Maixner, MS. Sarhan, KD. Huang, A. Tett, A. Schoenafinger, S. Zingale, A. Blanco-M\'iguez, P. Manghi, J. Cemper-Kiesslich, ... , A. Zink, H. Reschreiter, K. Kowarik: Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period. Current Biology, 2021

[126] A. Uzan-Yulzari, O. Turta, A. Belogolovski, O. Ziv, C. Kunz, S. Pershbacher, H. Neuman, E. Pasolli, A. Oz, ... , R. Ensenauer, S. Rautava, O. Koren: Neonatal antibiotic exposure impairs child growth during the first six years of life by perturbing intestinal microbial colonization. Nature Communications, 2021

[125] A. Tett, E. Pasolli, G. Masetti, D. Ercolini, N. Segata: Prevotella diversity, niches and interactions with the human host. Nature Reviews Microbiology, 2021

[124] R. Feuda, M. Goulty, N. Zadra, T. Gasparetti, E. Rosato, D. Pisani, A. Rizzoli, N. Segata, L. Ometto, OR. Stabelli: Phylogenomics of opsin genes in Diptera reveals lineage-specific events and contrasting evolutionary dynamics in Anopheles and Drosophila. Genome Biology and Evolution, 2021

[123] P. Louca, A. Nogal, PM. Wells, F. Asnicar, J. Wolf, CJ. Steves, TD. Spector, N. Segata, SE. Berry, AM. Valdes, C. Menni: Gut microbiome diversity and composition is associated with hypertension in women. Journal of Hypertension, 2021


[122] D. Wylensek, TCA. Hitch, T. Riedel, A. Afrizal, N. Kumar, E. Wortmann, T. Liu, S. Devendran, TR. Lesker, ... , TA. Gulder, J. Overmann, T. Clavel: A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity. Nature Communications, 2020

[121] SE. Berry, AM. Valdes, DA. Drew, F. Asnicar, M. Mazidi, J. Wolf, J. Capdevila, G. Hadjigeorgiou, R. Davies, ... , N. Segata*, PW. Franks*, TD. Spector*: Human postprandial responses to food and potential for precision nutrition. Nature Medicine, 2020

[120] S. Petrini, P. Foladori, F. Beghini, F. Armanini, N. Segata, G. Andreottola: How inoculation affects the development and the performances of microalgal-bacterial consortia treating real municipal wastewater. Journal of Environmental Management, PMID 32174516, 2020

[119] L. Derosa, B. Routy, M. Fidelle, V. Iebba, L. Alla, E. Pasolli, N. Segata, A. Desnoyer, F. Pietrantonio, ... , G. Kroemer, L. Albiges, L. Zitvogel: Gut Bacteria Composition Drives Primary Resistance to Cancer Immunotherapy in Renal Cell Carcinoma Patients. European Urology, 2020

[118] E. Pasolli, F. De Filippis, IE. Mauriello, F. Cumbo, AM. Walsh, J. Leech, PD. Cotter, N. Segata, D. Ercolini: Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome. Nature Communications, 2020

[117] R. Daill\`ere, L. Derosa, M. Bonvalet, N. Segata, B. Routy, C. Chaudonneret, M. Gariboldi, E. Budinsk\'a, L. Heinzerling, ... , J. Fieschi, G. Kroemer, L. Zitvogel: Trial Watch : The gut microbiota as a tool to boost the clinical efficacy of anticancer immunotherapy. OncoImmunology, 2020

[116] P. Ghensi, P. Manghi, M. Zolfo, F. Armanini, E. Pasolli, M. Bolzan, A. Bertelle, F. Dell'Acqua, E. Dellasega, ... , F. Tessarolo, C. Tomasi, N. Segata: Strong oral plaque microbiome signatures for dental implant diseases identified by strain-resolution metagenomics. npj Biofilms and Microbiomes, PMID 25246403, 2020

[115] F. Asnicar, AM. Thomas, F. Beghini, C. Mengoni, S. Manara, P. Manghi, Q. Zhu, M. Bolzan, F. Cumbo, ... , S. Mirarab, C. Huttenhower, N. Segata: Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nature Communications, 2020

[114] A. Fluckiger, R. Daill\`ere, M. Sassi, BS. Sixt, P. Liu, L. Friedemann, R. Corentin, C. Rabu, MT. Alou, ... , V. Cattoir, G. Kroemer, L. Zitvogel: Cross-reactivity between MHC class I-restricted antigens and an enterococcal bacteriophage. Science, 2020

[113] E. Zagato, C. Pozzi, A. Bertocchi, T. Schioppa, F. Saccheri, S. Guglietta, B. Fosso, L. Melocchi, G. Nizzoli, ... , W. Vermi, G. Penna, M. Rescigno: Endogenous murine microbiota member Faecalibaculum rodentium and its human homologue protect from intestinal tumor growth. Nature Microbiology, 2020

[112] G. Caio, L. Lungaro, N. Segata, M. Guarino, G. Zoli, U. Volta, R. De Giorgio: Effect of Gluten-Free Diet on Gut Microbiota Composition in Patients with Celiac Disease and Non-Celiac Gluten/Wheat Sensitivity. Nutrients, 2020

[111] G. Ianiro, E. Rossi, AM. Thomas, G. Schinzari, L. Masucci, G. Quaranta, CR. Settanni, LR. Lopetuso, F. Armanini, ... , A. Gasbarrini, N. Segata*, G. Cammarota*: Faecal microbiota transplantation for the treatment of diarrhoea induced by tyrosine-kinase inhibitors in patients with metastatic renal cell carcinoma. Nature Communications, 2020

[110] G. Bacci, G. Taccetti, D. Dolce, F. Armanini, N. Segata, FD. Cesare, V. Lucidi, E. Fiscarelli, P. Morelli, ... , A. Negroni, A. Mengoni, A. Bevivino: Untargeted Metagenomic Investigation of the Airway Microbiome of Cystic Fibrosis Patients with Moderate-Severe Lung Disease. Microorganisms, 2020

[109] TY. Michaelsen, J. Brandt, C. Singleton, RH. Kirkegaard, N. Segata, M. Albertsen: The signal and the noise - characteristics of antisense RNA in complex microbial communities. mSystems, 2020

[108] MC. Collado, N. Segata: Initial exploration of in utero microbial colonization. Nature Medicine (News&Views commentary), PMID 32242125, 2020

[107] M. Scholz, D. Albanese, K. Tuohy, C. Donati, N. Segata *, O. Rota-Stabelli *: Large scale genome reconstructions illuminate Wolbachia evolution. Nature Communications, 2020

[106] P. Foladori, F. Cutrupi, N. Segata, S. Manara, F. Pinto, F. Malpei, L. Bruni, G. La Rosa: SARS-CoV-2 from faeces to wastewater treatment: what do we know? A review.. Science of the Total Environment, 2020

[105] JR. Swann, M. Rajilic-Stojanovic, A. Salonen, O. Sakwinska, C. Gill, A. Meynier, P. Fan\cca-Berthon, B. Schelkle, N. Segata, C. Shortt, K. Tuohy, O. Hasselwander: Considerations for the design and conduct of human gut microbiota intervention studies relating to foods. European Journal of Nutrition, PMID 32246263, 2020

[104] L. Selbmann, Z. Benko, C. Coleine, S. de Hoog, C. Donati, I. Druzhinina, T. Emri, CL. Ettinger, AS. Gladfelter, ... , P. Zalar, AK. Walker, J. Stajich: Shed Light in the DaRk LineagES of the Fungal Tree of Life — STRES. Life, 2020

[103] N. Karcher, E. Pasolli, F. Asnicar, K. Huang, A. Tett, S. Manara, F. Armanini, D. Bain, SH. Duncan, ... , AW. Walker, C. Huttenhower, N. Segata: Analysis of 1,321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structures and subspecies functional adaptations. Genome Biology, 2020

[102] N. Qin, P. Liang, C. Wu, G. Wang, Q. Xu, X. Xiong, T. Wang, M. Zolfo, N. Segata, ... , R. Knight, JA. Gilbert, TF. Zhu: Longitudinal survey of microbiome associated with particulate matter in a megacity. Genome biology, 2020


[101] AM. Thomas, N. Segata: Multiple levels of the unknown in microbiome research. BMC Biology, 2019

[100] M. Zolfo, F. Pinto, F. Asnicar, A. Tett, FD. Bushman, N. Segata: Detecting contamination in viromes using ViromeQC. Nature Biotechnology, PMID 31748692, 2019

[99] 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 strains of human intestinal Prevotella copri are associated with different habitual diets. Cell Host & Microbe, 2019

[98] LF. Iannone, A. Preda, HM. Blotti\`ere, G. Clarke, D. Albani, V. Belcastro, M. Carotenuto, A. Cattaneo, R. Citraro, ... , F. Zara, E. Russo, P. Striano: Microbiota-gut brain axis involvement in neuropsychiatric disorders. Expert review of neurotherapeutics, 2019

[97] A. McBain, C. O'Neill, A. Am\'ezquita, L. Price, K. Faust, A. Tett, N. Segata, J. Swann, A. Smith, ... , I. Chapple, W. Wade, J. Fernandez-Piquer: Consumer Safety Considerations of Skin and Oral Microbiome Perturbation. Clinical Microbiology Reviews, 2019

[96] E. Pasolli, F. Asnicar, S. Manara, M. Zolfo, N. Karcher, F. Armanini, F. Beghini, P. Manghi, A. Tett, ... , C. Quince, C. Huttenhower, N. Segata: Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle. Cell, PMID 30661755, 2019

[95] H. Fehlner-Peach, C. Magnabosco, V. Raghavan, JU. Scher, A. Tett, LM. Cox, C. Gottsegen, A. Watters, JD. Wiltshire-Gordon, N. Segata, R. Bonneau, DR. Littman: Distinct polysaccharide growth profiles of human intestinal Prevotella copri isolates. Cell host & microbe, 2019

[94] F. Beghini, A. Renson, CP. Zolnik, L. Geistlinger, M. Usyk, TU. Moody, L. Thorpe, JB. Dowd, R. Burk, N. Segata, HE. Jones, L. Waldron: Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study. Annals of Epidemiology, 2019

[93] S. Wuyts, N. Segata: At the forefront of the sequencing revolution - notes from the RNGS19 conference. Genome Biology, 2019

[92] N. Segata: No bacteria found in healthy placentas. Nature (News&Views commentary), 2019

[91] A. Tett, K. Huang, F. Asnicar, H. Fehlner-Peach, E. Pasolli, N. Karcher, F. Armanini, P. Manghi, K. Bonham, ... , C. Huttenhower, F. Maixner, N. Segata: The Prevotella copri complex comprises four distinct clades underrepresented in Westernized populations. Cell Host & Microbe, PMID 31607556, 2019

[90] J. Wirbel, P. Paul Theodor, E. Kartal, K. Zych, A. Kashani, A. Milanese, F. Jonas S, V. Anita Y, A. Palleja, ... , M. Arumugam, P. Bork, G. Zeller: Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. Nature Medicine, 2019

[89] P. Ghensi, E. Bettio, D. Maniglio, E. Bonomi, F. Piccoli, S. Gross, P. Caciagli, N. Segata, G. Nollo, F. Tessarolo: Dental Implants with Anti-Biofilm Properties: A Pilot Study for Developing a New Sericin-Based Coating. Materials, 2019

[88] S. Tarallo, G. Ferrero, G. Gallo, A. Francavilla, G. Clerico, A. Realis Luc, P. Manghi, AM. Thomas, P. Vineis, ... , B. Pardini, A. Naccarati, F. Cordero: Altered fecal small RNA profiles in colorectal cancer reflect gut microbiome composition in stool samples. mSystems, 2019

[87] E. Bolyen, JR. Rideout, MR. Dillon, NA. Bokulich, C. Abnet, GA. Al-Ghalith, H. Alexander, EJ. Alm, M. Arumugam, ... , Y. Zhang, R. Knight, JG. Caporaso: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology, 2019

[86] D. Dolce, S. Neri, L. Grisotto, S. Campana, N. Ravenni, F. Miselli, E. Camera, L. Zavataro, C. Braggion, ... , N. Segata, A. Biggeri, G. Taccetti: Methicillin-resistant Staphylococcus aureus eradication in cystic fibrosis patients: a randomized multicenter study. PLOS ONE, 2019

[85] AM. Thomas, P. Manghi, F. Asnicar, E. Pasolli, F. Armanini, M. Zolfo, F. Beghini, S. Manara, N. Karcher, ... , 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, PMID 30936548, 2019

[84] S. Manara, F. Asnicar, F. Beghini, D. Bazzani, F. Cumbo, M. Zolfo, E. Nigto, N. Karcher, P. Manghi, MI. Metzger, E. Pasolli, N. Segata: Microbial genomes from gut metagenomes of non-human primates expand the tree-of-life with over 1,000 novel species. Genome Biology, PMID 31883524, 2019

[83] Q. Zhu, U. Mai, W. Pfeiffer, S. Janssen, F. Asnicar, JG. Sanders, P. Belda-Ferre, GA. Al-Ghalith, E. Kopylova, ... , L. Smarr, S. Mirarab, R. Knight: Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea. Nature Communications, 2019

[82] L. Waldron, L. Schiffer, R. Azhar, M. Ramos, L. Geistlinger, N. Segata: Waldron et al. Reply to "Commentary on the HMP16SData Bioconductor Package". American journal of epidemiology, 2019

[81] 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, 2019

[80] L. Schiffer, R. Azhar, L. Shepherd, M. Ramos, L. Geistlinger, C. Huttenhower, JB. Dowd, N. Segata, L. Waldron: HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor. American journal of epidemiology, 2019

[79] A. Renson, HE. Jones, F. Beghini, N. Segata, CP. Zolnik, M. Usyk, TU. Moody, L. Thorpe, R. Burk, L. Waldron, JB. Dowd: Sociodemographic variation in the oral microbiome. Annals of Epidemiology, 2019


[78] P. Ferretti, E. Pasolli, A. Tett, F. Asnicar, V. Gorfer, S. Fedi, F. Armanini, DT. Truong, S. Manara, ... , C. Huttenhower, P. Bork, N. Segata: Mother-to-infant microbial transmission from different body sites shapes the developing infant gut microbiome. Cell Host & Microbe, PMID 30001516, 2018

[77] EA. Franzosa, LJ. Mciver, G. Rahnavard, LR. Thompson, M. Schirmer, G. Weingart, K. Schwarzberg Lipson, R. Knight, G. Caporaso, N. Segata, C. Huttenhower: Species-level functional profiling of metagenomes and metatranscriptomes. Nature Methods, PMID 30377376, 2018

[76] AJ. Victoria, E. Cao, N. Salmaso, N. Segata, C. Donati: Draft Genome Sequence of the Cadmium-Resistant Strain JJU2, Belonging to the Family \textlessi\textgreaterHapalosiphonaceae\textless/i\textgreater of the \textlessi\textgreaterCyanobacteria\textless/i\textgreater. Microbiology Resource Announcements, 2018

[75] M. Zolfo, F. Asnicar, P. Manghi, E. Pasolli, A. Tett, N. Segata: Profiling microbial strains in urban environments using metagenomic sequencing data. Biology Direct, 2018

[74] K. Korpela, P. Costea, LP. Coelho, S. Kandels-Lewis, G. Willemsen, DI. Boomsma, N. Segata, P. Bork: Selective maternal seeding and environment shape the human gut microbiome. Genome Research, PMID 29496731, 2018

[73] N. Segata: On the road to strain-resolved comparative metagenomics. mSystems, 2018

[72] D. Kissling, J. Ahumada, A. Bowser, M. Fernandez, N. Fernandez, E. Alonso Garcia, R. Guralnick, N. Isaac, S. Kelling, ... , P. Uhlir, B. Wee, A. Hardisty: Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale. Biological Reviews, PMID 28766908, 2018

[71] H. Shaaban, DA. Westfall, R. Mohammad, D. Danko, D. Bezdan, E. Afshinnekoo, N. Segata, CE. Mason: The Microbe Directory: An annotated, searchable inventory of microbes' characteristics. Gates Open Research, 2018

[70] M. Yassour, L. Hogstrom, E. Jason, H. Siljander, J. Selvenius, S. Oikarinen, H. Hy\"oty, J. Ilonen, S. Virtanen, ... , C. Huttenhower, M. Knip, R. Xavier: Strain-level analysis of mother-to-child bacterial transmission during the first few months of life. Cell Host & Microbe, 2018

[69] 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, 2018

[68] E. Dassi, P. Ferretti, G. Covello, HTM-CMB-2015, R. Bertorelli, MA. Denti, V. De Sanctis, A. Tett, N. Segata: The short-term impact of probiotic consumption on the oral cavity microbiome. Scientific Reports, 2018

[67] S. Manara, E. Pasolli, D. Dolce, N. Ravenni, S. Campana, F. Armanini, F. Asnicar, A. Mengoni, L. Galli, ... , G. Grandi, G. Taccetti, N. Segata: Whole-genome epidemiology, characterization, and phylogenetic reconstruction of Staphylococcus aureus in a paediatric hospital. Genome Medicine, 2018


[66] T. Fedrizzi, CJ. Meehan, A. Grottola, E. Giacobazzi, F. Serpini, S. Tagliazucchi, A. Fabio, C. Bettua, R. Bertorelli, ... , O. Jousson, E. Tortoli, N. Segata: Genomic characterization of Nontuberculous Mycobacteria. Scientific Reports, PMID 28345639, 2017

[65] S. Wuyts, S. Wittouck, I. De Boeck, C. Allonsius, P. Edoardo, N. Segata, S. Lebeer: Large-scale phylogenomics of the Lactobacillus casei group highlights taxonomic inconsistencies and reveals novel clade-associated features. mSystems, PMID 28845461, 2017

[64] DT. Truong, A. Tett, E. Pasolli, C. Huttenhower, N. Segata: Microbial strain-level population structure and genetic diversity from metagenomes. Genome Research, PMID 28167665, 2017

[63] S. Duranti, GA. Lugli, L. Mancabelli, F. Armanini, F. Turroni, K. James, P. Ferretti, V. Gorfer, C. Ferrario, ... , N. Segata, D. van Sinderen, M. Ventura: Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission. Microbiome, PMID 28651630, 2017

[62] A. Tett, E. Pasolli, S. Farina, DT. Truong, F. Asnicar, M. Zolfo, F. Beghini, F. Armanini, O. Jousson, ... , G. Girolomoni, M. Cristofolini, N. Segata: Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis. npj Biofilms and Microbiomes, PMID 28649415, 2017

[61] C. Quince, JT. Simpson, AW. Walker, NJ. Loman, N. Segata: Shotgun metagenomics, from sampling to analysis. Nature Biotechnology, PMID 28898207, 2017

[60] F. Asnicar, S. Manara, M. Zolfo, DT. Truong, M. Scholz, F. Armanini, P. Ferretti, V. Gorfer, A. Pedrotti, A. Tett, N. Segata: Studying vertical microbiome transmission from mothers to infants by strain-level metagenomic profiling. mSystems, PMID 28144631, 2017

[59] G. Bacci, A. Mengoni, E. Fiscarelli, N. Segata, G. Taccetti, D. Dolce, P. Paganin, P. Morelli, V. Tuccio, A. De Alessandri, V. Lucidi, A. Bevivino: A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease. International Journal of Molecular Sciences, PMID 28758937, 2017

[58] E. Tortoli, T. Fedrizzi, CJ. Meehan, A. Grottola, E. Giacobazzi, G. Fregni, S. Tagliazucchi, A. Fabio, C. Bettua, ... , O. Jousson, N. Segata*, DM. Cirillo*: The new phylogeny of the genus Mycobacterium: The old and the news Enrico. Infection, Genetics and Evolution, 2017

[57] 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, 2017

[56] M. Zolfo, A. Tett, O. Jousson, C. Donati, N. Segata: MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples. Nucleic Acid Research, PMID 27651451, 2017

[55] P. Ferretti, S. Farina, M. Cristofoloni, G. Girolomoni, A. Tett, N. Segata: Experimental metagenomics and ribosomal profiling of the human skin microbiome. Experimental Dermatology, PMID 27623553, 2017

[54] E. Pasolli, L. Schiffer, P. Manghi, A. Renson, V. Obenchain, DT. Truong, F. Beghini, F. Malik, M. Ramos, ... , M. Morgan, N. Segata*, L. Waldron*: Accessible, curated metagenomic data through ExperimentHub. Nature Methods, PMID 29088129, 2017

[53] L. Tosi, V. Sridhara, Y. Yang, D. Gua, P. Shpilker, N. Segata, H. Larman, B. Parekkadan: Long-adapter single-stranded oligonucleotide probes for the massively multiplexed cloning of kilobase genome regions. Nature Biomedical Engineering, 2017

[52] LJ. Mciver, G. Abu-ali, EA. Franzosa, R. Schwager, XC. Morgan, L. Waldron, N. Segata, C. Huttenhower: bioBakery: A meta'omic analysis environment. Bioinformatics, PMID 29194469, 2017

[51] F. Beghini, E. Pasolli, DT. Truong, L. Putignani, S. Caccio, N. Segata: Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome. ISME Journal, PMID 28837129, 2017


[50] E. Pasolli, T. Truong, F. Malik, L. Waldron, N. Segata: Machine learning meta-analysis of large metagenomic datasets : tools and biological insights. PLoS Computational Biology, PMID 27400279, 2016

[49] M. Scholz*, D. Ward*, T. Tolio, M. Zolfo, F. Asnicar, DT. Truong, E. Pasolli, A. Tett, A. Morrow, N. Segata: Strain-level microbial epidemiology and population genomics from shotgun metagenomics. Nature Methods, PMID 26999001, 2016

[48] C. Donati, M. Zolfo, D. Albanese, DT. Truong, F. Asnicar, V. Iebba, D. Cavalieri, O. Jousson, C. De Filippo, C. Huttenhower, N. Segata: Uncovering oral Neisseria tropism and persistence using metagenomic sequencing. Nature Microbiology, PMID 27572971, 2016

[47] N. Segata, F. Baldini, J. Pompon, WS. Garrett, DT. Truong, RK. Dabir\'e, A. Diabat\'e, EA. Levashina, F. Catteruccia: The reproductive tracts of two malaria vectors are populated by a core microbiome and by gender- and swarm-enriched microbial biomarkers. Scientific Reports, PMID 27086581, 2016

[46] D. Ward, M. Scholz, M. Zolfo, DH. Taft, KR. Schibler, A. Tett, N. Segata*, AL. Morrow*: Metagenomic sequencing with strain-level resolution implicates uropathogenic E. coli in necrotizing enterocolitis and death in preterm infants. Cell Reports, PMID 26997279, 2016

[45] The MetaSUB International Consortium (including Nicola Segata): The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report. Microbiome, 2016


[44] DT. Truong, E. Franzosa, T. Tickle, M. Scholz, G. Weingart, E. Pasolli, A. Tett, C. Huttenhower, N. Segata: MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nature Methods, PMID 26418763, 2015

[43] AR. Fusco da Costa, T. Fedrizzi, ML. Lopes, M. Pecorari, WL. Oliveira da Costa, E. Giacobazzi, JR. da Costa Bahia, V. De Sanctis, KV. Batista Lima, ... , O. Jousson, N. Segata, E. Tortoli: Characterization of 17 strains belonging to the Mycobacterium simiae complex and description of Mycobacterium paraense sp. nov.. International Journal of Systematic and Evolutionary Microbiology, 2015

[42] F. Asnicar, G. Weingart, TL. Tickle, C. Huttenhower, N. Segata: Compact graphical representation of phylogenetic data and metadata with GraPhlAn. PeerJ, PMID 26157614, 2015

[41] K. Tuohy, F. Fava, N. Segata: Studying the microbiota and microbial ecology of the GI tract in the Omics Era: Tools for stools.. In Probiotics and Prebiotics: Current Research and Future Trends, 2015

[40] C. Milani, L. Mancabelli, GA. Lugli, S. Duranti, F. Turroni, C. Ferrario, M. Mangifesta, A. Viappiani, P. Ferretti, ... , N. Segata, S. van Douwe, M. Ventura: Exploring vertical transmission of bifidobacteria from mother to child. Applied and environmental microbiology, PMID 26231653, 2015

[39] J. Kaminski, MK. Gibson, EA. Franzosa, N. Segata, G. Dantas, C. Huttenhower: High-specificity targeted functional profiling in microbial communities with ShortBRED. PLoS computational biology, PMID 26682918, 2015

[38] C. Milani, GA. Lugli, S. Duranti, F. Turroni, L. Mancabelli, C. Ferrario, M. Mangifesta, A. Gonz\'alez, A. Viappiani, ... , A. Margolles, D. Van Sinderen, M. Ventura: Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut. Scientific Reports, PMID 26506949, 2015

[37] N. Segata: Gut Microbiome: Westernization and the Disappearance of Intestinal Diversity. Current Biology, 2015


[36] MG. Rooks, P. Veiga, L. Wardwell-Scott, TL. Tickle, N. Segata, CA. Gallini, C. Beal, M. Michaud, JE. Van Hylckama-Vlieg, ... , D. Gevers, C. Huttenhower, WS. Garrett: Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission. The ISME journal, PMID 24500617, 2014

[35] K. Huang, A. Brady, A. Mahurkar, O. White, D. Gevers, C. Huttenhower, N. Segata: MetaRef: a pan-genomic database for comparative and community microbial genomics. Nucleic Acid Research, PMID 24203705, 2014

[34] M. Scholz, A. Tett, N. Segata: Computational tools for taxonomic microbiome profiling of shotgun metagenomes. In Metagenomics for Microbiology, 2014

[33] F. Baldini*, N. Segata*, J. Pompon*, R. Dabir\'e, A. Diabat\'e, E. Levashina\^, F. Catteruccia\^: Evidence of natural Wolbachia infections in field populations of Anopheles gambiae. Nature Communications, PMID 24905191, 2014

[32] C. Milani, G. Lugli, F. Turroni, L. Mancabelli, S. Duranti, A. Viappiani, M. Mangifesta, N. Segata, D. van Sinderen, M. Ventura: Evaluation of bifidobacterial community composition in the human gut by means of an ITS-metagenomics protocol. FEMS Microbiology Ecology, 2014

[31] E. Dassi, A. Ballarini, G. Covello, HTM CMB2013, A. Quattrone, O. Jousson, V. De Sanctis, R. Bertorelli, MA. Denti, N. Segata: Enhanced microbial diversity in the saliva microbiome induced by short-term probiotic intake revealed by 16S rRNA sequencing on the IonTorrent PGM platform. Journal of Biotechnology, PMID 24670254, 2014

[30] EA. Franzosa, XC. Morgan, N. Segata, L. Waldron, J. Reyes, AM. Earl, G. Giannoukos, M. Boylan, DM. Ciulla, ... , WS. Garrett, AT. Chan, C. Huttenhower: Relating the metatranscriptome and metagenome of the human gut. Proceedings of the National Academy of Sciences of the United States of America, PMID 24843156, 2014


[29] N. Segata, D. Boernigen, TL. Tickle, X. Morgan, WS. Garrett, C. Huttenhower: Computational meta'omics for microbial community studies. Molecular Systems Biology, PMID 23670539, 2013

[28] A. Ballarini*, N. Segata*, C. Huttenhower\^, O. Jousson\^: Simultaneous quantification of multiple bacteria by the BactoChip microarray designed to target species-specific marker genes. Plos One, 2013

[27] N. Segata, D. B\"ornigen, X. Morgan, C. Huttenhower: PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nature Communications, PMID 23942190, 2013

[26] JU. Scher, A. Sczesnak, RS. Longman, N. Segata, C. Ubeda, C. Bielski, EG. Pamer, S. Abramson, C. Huttenhower, D. Littman: Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. eLIFE, PMID 24192039, 2013

[25] O. Koren, D. Knights, A. Gonzales, L. Waldron, N. Segata, R. Knight, C. Huttenhower, RE. Ley: A Guide to Enterotypes across the Human Body: Meta- Analysis of Microbial Community Structures in Human Microbiome Datasets. PLoS computational biology, PMID 23326225, 2013

[24] TL. Tickle, N. Segata, L. Waldron, C. Huttenhower: Two-stage microbial community experimental design. The ISME Journal, PMID 23949665, 2013

[23] X. Morgan, N. Segata, C. Huttenhower: Biodiversity and Functional Genomics in the Human Microbiome. Trends in Genetics, PMID 23140990, 2013

[22] N. Segata, A. Ballarini, O. Jousson: Genome sequence of Pseudomonas aeruginosa PA45, a highly virulent strain isolated from a patient with bloodstream infection. Genome Announcements, 2013


[21] K. Aagaard, K. Riehle, J. Ma, N. Segata, T. Mistretta, C. Coarfa, S. Raza, S. Rosenbaum, I. Van Den Veyver, ... , C. Huttenhower, J. Petrosino, J. Versalovic: A Metagenomic Approach To Characterization Of The Vaginal Microbiome Signature In Pregnancy. PloS ONE, PMID 22719832, 2012

[20] SJ. Delany, N. Segata, B. Mac Namee: Profiling Instances in Noise Reduction. Knowledge-Based Systems, 2012

[19] N. Segata, SK. Haake, P. Mannon, KP. Lemon, L. Waldron, D. Gevers, C. Huttenhower, J. Izard: Composition of the Adult Digestive Tract Microbiome Based on Seven Mouth Surfaces, Tonsils, Throat and Stool Samples. Genome Biology, PMID 22698087, 2012

[18] N. Segata*, E. Pasolli*, F. Melgani, E. Blanzieri: Local SVM Approaches for Fast and Accurate Classification of Remote Sensing Images. International Journal of Remote Sensing, 2012

[17] L. Waldron, S. Ogino, Y. Hoshida, K. Shima, A. McCart Reed, P. Simpson, Y. Baba, K. Nosho, N. Segata, ... , CS. Fuchs, G. Parmigiani, C. Huttenhower: Expression profiling of archival tissues for long-term health studies. Clinical Cancer Research, 2012

[16] The Human Microbiome Consortium (including Nicola Segata): A Framework for Human Microbiome Research. Nature, PMID 22699610, 2012

[15] K. Faust*, FJ. Sathirapongsasuti*, J. Izard, N. Segata, D. Gevers, J. Raes*, C. Huttenhower*: Microbial co-occurrence relationships in the human microbiome. PLoS Computational Biology, PMID 22807668, 2012

[14] N. Segata, L. Waldron, A. Ballarini, V. Narasimhan, O. Jousson, C. Huttenhower: Metagenomic microbial community profiling using unique clade-specific marker genes. Nature Methods, PMID 22688413, 2012

[13] S. Abubucker, N. Segata, J. Goll, A. Schubert, J. Izard, BL. Cantarel, B. Rodriguez-Mueller, J. Zucker, M. Thiagarajan, ... , D. Gevers, M. Mitreva, C. Huttenhower: Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome. PLoS Computational Biology, PMID 22719234, 2012

[12] The Human Microbiome Consortium (including Nicola Segata): Structure, function and diversity of the healthy human microbiome. Nature, PMID 22699609, 2012

[11] J. Hussnain, N. Segata, P. Bernab\`o, S. Tamburini, A. Ellen, O. Jousson: Clinical populations of Pseudomonas aeruginosa isolated from acute infections show a high virulence range partially correlated with population structure and virulence gene expression. Microbiology, 2012


[10] A. Sczesnak, N. Segata, X. Qin, D. Gevers, JF. Petrosino, C. Huttenhower, D. Littman, I. Ivanov: The genome of Th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment. Cell Host & Microbe, PMID 21925113, 2011

[9] N. Segata, C. Huttenhower: Toward an efficient method of identifying core genes for evolutionary and functional microbial phylogenies. PLoS ONE, PMID 21931822, 2011

[8] SA. Ballal, CA. Gallini, N. Segata, C. Huttenhower, WS. Garrett: Host and gut microbiota symbiotic factors: lessons from inflammatory bowel disease and successful symbionts.. Cellular microbiology, PMID 21314883, 2011

[7] N. Segata, E. Blanzieri: Operators for transforming kernels into quasi-local kernels that improve SVM accuracy. Journal of Intelligent Information Systems, 2011

[6] N. Segata, J. Izard, L. Waldron, D. Gevers, L. Miropolsky, WS. Garrett, C. Huttenhower: Metagenomic Biomarker Discovery and Explanation. Genome Biology, PMID 21702898, 2011


[5] N. Segata, E. Blanzieri: Fast and Scalable Local Kernel Machines. Journal of Machine Learning Research, 2010

[4] N. Segata, E. Blanzieri, SJ. Delany, P. Cunningham: Noise Reduction for Instance-Based Learning with a Local Maximal Margin Approach. Journal of Intelligent Information Systems, 2010

[3] M. Krapivin, A. Autayeu, M. Marchese, E. Blanzieri, N. Segata: Keyphrases Extraction from Scientific Documents: Improving Machine Learning Approaches with Natural Language Processing. In The Role of Digital Libraries in a Time of Global Change, 2010


[2] N. Segata, E. Blanzieri: Stochastic TT-Calculus Modelling of Multisite Phosphorylation Based Signaling: The PHO Pathway in Saccharomyces Cerevisiae. Transactions on Computational Systems Biology, 2008

[1] N. Segata, E. Blanzieri, C. Priami: Towards the integration of computational systems biology and high-throughput data: supporting differential analysis of microarray gene expression data.. Journal of Integrative Bioinformatics, 2008