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Information technology applied to bioenergy genomics: probabilistic annotation using artificial intelligence

Grant number: 09/53161-6
Support type:Program for Research on Bioenergy (BIOEN) - Regular Program Grants
Duration: February 01, 2010 - January 31, 2012
Field of knowledge:Interdisciplinary Subjects
Cooperation agreement: Microsoft Research
Principal Investigator:Ricardo Zorzetto Nicoliello Vêncio
Grantee:Ricardo Zorzetto Nicoliello Vêncio
Home Institution: Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil

Abstract

An alternative to the problem of fossil fuels depletion is the use of renewable energy. In Brazil, sugarcane (Saccharum officinarum) is used for years as alternative energy source and, therefore, Brazil has become a key player in alternative energy development. Our main aim is to develop methods and tools to attack some of the bioinformatics issues raised in sugarcane genomics research. In order to achieve this, we opt for Sifter (Engelhardt et al., 2006), a powerful method based on Bayesian Networks. Our major aim was to establish a local implementation of the Sifter methodology for application in bioenergy related problems and following is to improve the original source code performance, potentially allowing it to be used in a genome-wide scale. (AU)

Articles published in Agência FAPESP Newsletter about the research grant
Ethanol takes off 

Scientific publications
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
JIANG, YUXIANG; ORON, TAL RONNEN; CLARK, WYATT T.; BANKAPUR, ASMA R.; D'ANDREA, DANIEL; LEPORE, ROSALBA; FUNK, CHRISTOPHER S.; KAHANDA, INDIKA; VERSPOOR, KARIN M.; BEN-HUR, ASA; KOO, DA CHEN EMILY; PENFOLD-BROWN, DUNCAN; SHASHA, DENNIS; YOUNGS, NOAH; BONNEAU, RICHARD; LIN, ALEXANDRA; SAHRAEIAN, SAYED M. E.; MARTELLI, PIER LUIGI; PROFITI, GIUSEPPE; CASADIO, RITA; CAO, RENZHI; ZHONG, ZHAOLONG; CHENG, JIANLIN; ALTENHOFF, ADRIAN; SKUNCA, NIVES; DESSIMOZ, CHRISTOPHE; DOGAN, TUNCA; HAKALA, KAI; KAEWPHAN, SUWISA; MEHRYARY, FARROKH; SALAKOSKI, TAPIO; GINTER, FILIP; FANG, HAI; SMITHERS, BEN; OATES, MATT; GOUGH, JULIAN; TORONEN, PETRI; KOSKINEN, PATRIK; HOLM, LIISA; CHEN, CHING-TAI; HSU, WEN-LIAN; BRYSON, KEVIN; COZZETTO, DOMENICO; MINNECI, FEDERICO; JONES, DAVID T.; CHAPMAN, SAMUEL; DUKKA, B. K. C.; KHAN, ISHITA K.; KIHARA, DAISUKE; OFER, DAN; RAPPOPORT, NADAV; STERN, AMOS; CIBRIAN-UHALTE, ELENA; DENNY, PAUL; FOULGER, REBECCA E.; HIETA, REIJA; LEGGE, DUNCAN; LOVERING, RUTH C.; MAGRANE, MICHELE; MELIDONI, ANNA N.; MUTOWO-MEULLENET, PRUDENCE; PICHLER, KLEMENS; SHYPITSYNA, ALEKSANDRA; LI, BIAO; ZAKERI, POOYA; ELSHAL, SARAH; TRANCHEVENT, LEON-CHARLES; DAS, SAYONI; DAWSON, NATALIE L.; LEE, DAVID; LEES, JONATHAN G.; SILLITOE, IAN; BHAT, PRAJWAL; NEPUSZ, TAMAS; ROMERO, ALFONSO E.; SASIDHARAN, RAJKUMAR; YANG, HAIXUAN; PACCANARO, ALBERTO; GILLIS, JESSE; SEDENO-CORTES, ADRIANA E.; PAVLIDIS, PAUL; FENG, SHOU; CEJUELA, JUAN M.; GOLDBERG, TATYANA; HAMP, TOBIAS; RICHTER, LOTHAR; SALAMOV, ASAF; GABALDON, TONI; MARCET-HOUBEN, MARINA; SUPEK, FRAN; GONG, QINGTIAN; NING, WEI; ZHOU, YUANPENG; TIAN, WEIDONG; FALDA, MARCO; FONTANA, PAOLO; LAVEZZO, ENRICO; TOPPO, STEFANO; FERRARI, CARLO; GIOLLO, MANUEL; PIOVESAN, DAMIANO; TOSATTO, SILVIO C. E.; DEL POZO, ANGELA; FERNANDEZ, JOSE M.; MAIETTA, PAOLO; VALENCIA, ALFONSO; TRESS, MICHAEL L.; BENSO, ALFREDO; DI CARLO, STEFANO; POLITANO, GIANFRANCO; SAVINO, ALESSANDRO; REHMAN, HAFEEZ UR; RE, MATTEO; MESITI, MARCO; VALENTINI, GIORGIO; BARGSTEN, JOACHIM W.; VAN DIJK, AALT D. J.; GEMOVIC, BRANISLAVA; GLISIC, SANJA; PEROVIC, VLADMIR; VELJKOVIC, VELJKO; VELJKOVIC, NEVENA; ALMEIDA-E-SILVA, DANILLO C.; VENCIO, RICARDO Z. N.; SHARAN, MALVIKA; VOGEL, JOERG; KANSAKAR, LAKESH; ZHANG, SHANSHAN; VUCETIC, SLOBODAN; WANG, ZHENG; STERNBERG, MICHAEL J. E.; WASS, MARK N.; HUNTLEY, RACHAEL P.; MARTIN, MARIA J.; O'DONOVAN, CLAIRE; ROBINSON, PETER N.; MOREAU, YVES; TRAMONTANO, ANNA; BABBITT, PATRICIA C.; BRENNER, STEVEN E.; LINIAL, MICHAL; ORENGO, CHRISTINE A.; ROST, BURKHARD; GREENE, CASEY S.; MOONEY, SEAN D.; FRIEDBERG, IDDO; RADIVOJAC, PREDRAG. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology, v. 17, SEP 7 2016. Web of Science Citations: 92.
ALMEIDA-E-SILVA, DANILLO C.; VENCIO, RICARDO Z. N. SIFTER-T: A scalable and optimized framework for the SIFTER phylogenomic method of probabilistic protein domain annotation. BIOTECHNIQUES, v. 58, n. 3, p. 140-142, MAR 2015. Web of Science Citations: 1.
SILVA, RICARDO R.; JOURDAN, FABIEN; SALVANHA, DIEGO M.; LETISSE, FABIEN; JAMIN, EMILIEN L.; GUIDETTI-GONZALEZ, SIMONE; LABATE, CARLOS A.; VENCIO, RICARDO Z. N. ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics. Bioinformatics, v. 30, n. 9, p. 1336-1337, MAY 1 2014. Web of Science Citations: 28.

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