Publications

[14.]. Asnicar F, Thomas AM, Beghini F, Mengoni C, Manara S, Manghi P, Zhu Q, Bolzan M, Cumbo F, May U, Sanders JG, Zolfo M, Kopylova E, Pasolli E, Knight R, Mirarab S, Huttenhower C, Segata N. (2020). Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nature Communications 11, 2500.

[13.]. Al Assal K, Prifti E, Belda E, Sala P, Clément K, Dao MC, Doré J, Levenez F, Taddei CR, Fonseca DC, Rocha IM, Balmant BD, Thomas AM, Santo MA, Dias-Neto E, Setubal JC, Zucker JD, Belarmino G, Torrinhas RS, Waitzberg D. (2020). Gut Microbiota Profile of Obese Diabetic Women Submitted to Roux-en-Y Gastric Bypass and Its Association with Food Intake and Postoperative Diabetes Remission. Nutrients 12(2), 278.

[12.]. Tarallo S, Ferrero G, Gallo G, Francavilla A, Clerico G, Luc AR, Manghi P, Thomas AM, Vineis P, Segata N, Pardini B, Naccarati A, Cordero F. (2019). Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples. Msystems 4(5) e00289-19.

[11.]. Fukumori C, Casaro MB, Thomas AM, Mendes E, Ribeiro WR, Crisma AR, Murata GM, Bizzarro B, Dias-Neto E, Setubal JC, Oliveira MA, Tavares-de-Lima W, Curi R, Bordin S, Sartorelli P, Ferreira CM. (2019). Maternal supplementation with a synbiotic has distinct outcomes on offspring gut microbiota formation in A/J and C57BL/6 mice, differentially affecting airway inflammatory cell infiltration and mucus production. Journal of Functional Foods. 61(103496).

[10.] Thomas AM & Segata N. (2019). Multiple levels of the unknown in microbiome research. BMC Biology. 17(48).

[9.] Fachi JL, Felipe JS, Pral LP, da Silva BK, Corrêa RO, de Andrade MCP, da Fonseca DM, Basso PJ, Câmara NOS, de Sales E Souza ÉL, Dos Santos Martins F, Guima SES, Thomas AM, Setubal JC, Magalhães YT, Forti FL, Candreva T, Rodrigues HG, de Jesus MB, Consonni SR, Farias ADS, Varga-Weisz P, Vinolo MAR. (2019). Butyrate Protects Mice from Clostridium difficile-Induced Colitis through an HIF-1-Dependent Mechanism. Cell Reports. 27(3):750-761.

[8.] Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A, Segata N. (2019). Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. Nature Medicine. 25;667–678. 

[7.] Wirbel J, Pyl PT, Kartal E, Zych K, Kashani A, Milanese A, Fleck JS, Voigt AY, Palleja A, Ponnudurai RP, Sunagawa S, Coelho LP, Schrotz-King P, Vogtmann E, Habermann N, Niméus E, Thomas AM, Manghi P, Gandini S, Serrano D, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Waldron L, Naccarati A, Segata N, Sinha R, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G. (2019). Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. Nature Medicine. 25;679-689. 

[6.] Mendes E, Acetturi BG, Thomas AM, Martins FS, Crisma AR, Murata G, Braga TT, Camâra NOS, Franco ALS, Setubal JC, Ribeiro WR, Valduga CJ, Curi R, Dias-Neto E, Tavares-de-Lima W, Ferreira CM. (2017). Prophylactic Supplementation of Bifidobacterium longum 51A Protects Mice from Ovariectomy-Induced Exacerbated Allergic Airway Inflammation and Airway Hyperresponsiveness. Front. Microbiol. 8:1732.

[5.] GE4GAC group. (2017). Genomics and epidemiology for gastric adenocarcinomasApplied Cancer Research 37:7.

[4.] Antunes LP, Martins LF, Pereira RV, Thomas AM, Barbosa D, Lemos LN, Silva GMM, Moura LMS, Epamino GWC, Digiampietri LA, Lombardi KC, Ramos PL, Quaggio RB, Oliveira JCF, Pascon RC, Cruz JB, Silva AM, Setubal JC. (2016). Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomicsScientific Reports 6:38915.

[3.] Thomas AM,  Jesus EC, Lopes A, Aguiar S Jr., Begnami MD, Rocha RM, Carpinetti PA, Camargo AA, Hoffmann C,  Freitas HC,  Silva IT, Nunes DN,  Setubal JC, Dias-Neto E. (2016). Tissue-Associated Bacterial Alterations in Rectal Carcinoma Patients Revealed by 16S rRNA Community Profiling. Front. Cell. Infect. Microbiol. 6:179.

[2.] Kinker GS, Thomas AM, Carvalho VJ, Lima FP, Fujita A. (2016). Deletion and low expression of NFKBIA are associated with poor prognosis in lower-grade glioma patients. Scientific Reports 6:24160.

[1.] Thomas AM, Gleber-Netto F, Fernandes GR, Amorim M, Barbosa LF, Francisco ALN, Guerra de Andrade A, Setubal JC, Kowalski LP, Nunes DN, Dias-Neto E. (2014). Alcohol and tobacco consumption affects bacterial richness in oral cavity mucosa biofilmsBMC Microbiology 14:250.

Book chapters:

[1.] Thomas AM, Lima FP, Moura LMS, Silva AM, Dias-Neto E, Setubal JC. (2016). Comparative MetagenomicsMethods Mol Biol 1704:243-260. 

Prizes:

2019 – Best PhD thesis, Prêmio CAPES de teses (área de Biológicas I), Brazil.

2019 – Best research in oncology, X Prêmio Octávio Frias de Oliveira, São Paulo, Brazil.  

2017 – Best experimental work poster, 19th Research Forum on Clinical and Experimental Nutrition, Brazil. 

2012 – Best Graduate Oral Presentation – Microorganism Genetics, Brazilian Genetics Society.

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