Publications

2017

[58] C. Quince, JT. Simpson, AW. Walker, NJ. Loman, N. Segata: Shotgun metagenomic sequencing and analysis. Nature Biotechnology, (in press), 2017

[57] D. Kissling, J. Ahumada, A. Bowser, M. Fernandez, N. Fern{\'{a}}ndez, E. {Alonso Garc{\'{i}}a}, ... , P. Uhlir, B. Wee, A. Hardisty: Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale. Biological Reviews, (in press), 2017

[56] 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, (in press), 2017

[55] 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, (in press), 2017

[54] 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, (in press), 2017

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

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

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

[50] 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

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

[48] 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

[47] 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

2016

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

[45] 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

[44] 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

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

[42] 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

2015

[41] C. Milani, GA. Lugli, S. Duranti, F. Turroni, L. Mancabelli, C. Ferrario, ... , A. Margolles, D. {Van Sinderen}, M. Ventura: Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut. Scientific Reports, PMID 26506949, 2015

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

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

[36] AR. {Fusco da Costa}, T. Fedrizzi, ML. Lopes, M. Pecorari, WL. {Oliveira da Costa}, E. Giacobazzi, ... , 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

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

2014

[34] MG. Rooks, P. Veiga, L. Wardwell-Scott, TL. Tickle, N. Segata, CA. Gallini, ... , 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

[33] E. Dassi, A. Ballarini, G. Covello, {HTM CMB2013}, A. Quattrone, O. Jousson, ... , 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

[32] C. Milani, G. Lugli, F. Turroni, L. Mancabelli, S. Duranti, A. Viappiani, ... , 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] EA. Franzosa, XC. Morgan, N. Segata, L. Waldron, J. Reyes, AM. Earl, ... , 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

[30] 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

[29] 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

2013

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

[27] 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

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

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

[24] 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

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

2012

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

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

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

[17] 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

[16] 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

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

[14] 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

[13] 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

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

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

[10] 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

2011

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

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

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

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

2008

[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