2022

D. Amgarten, B. Iha, C.M. Piroupo, A.M. da Silva, J.C. Setubal. vHULK, a new tool for bacteriophage host prediction based on annotated genomic features and neural networks. Phage, accepted.

2021

L. Braga, R.V. Pereira, L.F. Martins, L. Moura, F.B. Sanchez, J.S.P. Patané, A.M. da Silva, J.C. Setubal. Genome-resolved metagenome and metatranscriptome analyses of thermophilic composting reveal key bacterial players and their metabolic interactions. BMC Genomics, 22:652, 2021.

2019

P.L. Ramos, S. Santos, S. Vasconcellos, R. Rocha, J.B. Cruz, P. Eugenio, M. Kondo, H. Cabral, M. Juliano, L. Juliano, J.C. Setubal, A.M. da Silva, L. Cappelini. A tropical composting operation unit at São Paulo Zoo as a source of bacterial proteolytic enzymes. Applied Biochemistry and Biotechnology, 187(1), pp. 282-297, 2019.

N. M. Silva, A. M. S. A. de Oliveira, S. Pegorin, C. E. Giustia, V. B. Ferraric, D. Barbosa, L. F. Martins, C. Morais, J. C. Setubal, S. P. Vasconcellos, A. M. da Silva, J. C. F. de Oliveira, R. C. Pascon, C. Viana-Niero. Characterization of novel hydrocarbon-degrading Gordonia paraffinivorans and Gordonia sihwensis strains isolated from composting. PLoS ONE, journal.pone.0215396, April, 2019

2018

A.M. Thomas, F.P. Lima, L.M.S. Moura, A.M. da Silva; E. Dias-Neto, J.C. Setubal. Comparative Metagenomics. Methods in Molecular Biology, v. 1704, pp. 243-260. Springer New York, 2018.

D. Amgarten, L.P.P. Braga, A.M. da Silva, J.C. Setubal. MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins. Frontiers in Genetics, section Bioinformatics and Computational Biology, 304, 2018

2017

L.N. Lemos, R.V. Pereira, R.B. Quaggio, L.F. Martins, L.M.S. Moura, A.R. da Silva, L.P. Antunes, A.M. da Silva, J.C. Setubal. Genome-centric analysis of a thermophilic and cellulolytic bacterial consortium derived from composting. Frontiers in Microbiology, 8 (644), 2017.

D. Amgarten, L.F. Martins, K.C. Lombardi, L.P. Antunes, A.P.S. de Souza, G.G. Nicastro, E.W. Kitajima, R.B. Quaggio, C. Upton, J.C. Setubal, A.M. da Silva. Three novel Pseudomonas phages isolated from composting provide insights into the evolution and diversity of tailed phages. BMC Genomics, 18 (346), 2017.

2016

L.P. Antunes, L.F. Martins, R.V. Pereira, A.M. Thomas, D. Barbosa, L.N. Lemos, G.M.M. Silva, L.M.S. Moura, G.W.C. Epamino, L.A. Digiampietri, K.C. Lombardi, P.L. Ramos, R.B. Quaggio, J.C.F. de Oliveira, R.C. Pascon, J.B. da Cruz, A.M. da Silva, J.C. Setubal. Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics. Scientific Reports, 6:38915, 2016

2014

Trama, B., Fernandes, J.D.S, Labuto, G., Oliveira, J.C.F., Viana-Niero, C., Pascon, R.C. & Vallim, M.A. The evaluation of bioremediation potential of a yeast collection isolated from composting.  Advances in Microbiology 2014 (4), 796-807.

2013

L.F. Martins, L. P. Antunes, R.C. Pascon, J.C. Franco de Oliveira, L.A. Digiampietri, D. Barbosa, B.M. Peixoto, M.A. Vallim, C. Viana-Niero, E.H. Ostroski, G.P. Telles, Z. Dias, J.B. da Cruz, L. Juliano, S. Verjovski-Almeida, A.M. da Silva, J.C. Setubal. Metagenomic analysis of a tropical composting operation at the São Paulo Zoo Park reveals diversity of biomass degradation functions and organisms. PLoS ONE, 8(4):e61928, 2013.

X-Meeting 2015 – 11th International Conference of th AB3C + Brazilian Symposium of Bioinformatics

POSTERS

Gianluca Major – Computational methods for metagenomic data processing in the Metazoo Project

Raquel Riyuzo A. Franco – Analysis of fecal bacterial diversity in howler monkeys (Alouatta) through metagenomics