Modelos e métodos de e-Science para ciências da vida e agrárias

• Processo: 11/50761-2
• Linha de fomento: Auxílio à Pesquisa - Temático
• Vigência: 01 de fevereiro de 2012 - 30 de setembro de 2016
• Área do conhecimento: Ciências Exatas e da Terra - Ciência da Computação
• Convênio/Acordo: CNPq - Pronex
• Pesquisador responsável: Roberto Marcondes Cesar Junior
• Beneficiário: Roberto Marcondes Cesar Junior
• Instituição-sede: Instituto de Matemática e Estatística (IME). Universidade de São Paulo (USP). São Paulo , SP, Brasil
• Pesquisadores principais: Carlos Alberto Moreira Filho ; Claudia Maria Bauzer Medeiros ; Luciano da Fontoura Costa
• Auxílios(s) vinculado(s): 14/50769-1 - Hand tracking for occupational therapy, AP.R SPRINT; 15/05953-1 - ISMM 2015 - 12th International Symposium on Mathematical Morphology, AR.EXT; 14/50135-2 - Learning salient elements from videos using structural and temporal information, AP.R; + mais auxílios vinculados 13/25918-0 - Visita do prof. Dr. Stéphane Canu ao IME-USP, AV.EXT; 13/03535-2 - 11th International Symposium on Mathematical Morphology (ISMM 2013), AR.EXT; 12/50986-7 - Graph spectra and complex network evolution, AP.R; 12/08637-5 - Visita da Profa. Dr. Florence Tupin ao IME-USP, AV.EXT - menos auxílios vinculados
• Bolsa(s) vinculada(s): 16/13791-4 - Um arcabouço para análise e rastreamento de gestos de mão: casos com formas e movimentos não usuais, BP.DR; 15/13430-9 - Enumerando histórias metabólicas multidimensionais: modelos e métodos, BP.PD; 15/18942-8 - Associando Redes Complexas com Espaços Efetivos de Atributos, BP.PD; + mais bolsas vinculadas 15/18117-7 - Método para amostragem de experiências e intervenção programada (ESPIM), BP.PD; 15/08003-4 - Abordagem de redes complexas em e-Science e dados dinâmicos, BP.PD; 15/07252-0 - Documentos interativos para coleta especializada de experiências do cotidiano: operações para autoria, compartilhamento e análise, BP.DR; 15/11693-2 - Programa de atividades e justificativa para bolsa de treinamento técnico V: gerente dos projetos de software livre ligados ao projeto temático, BP.TT; 14/24918-0 - Deep learning fracamente supervisionado para detecção de faces e atributos de pessoas, BP.DR; 15/03475-5 - Olhando para a cidade: big data e visão computacional para análise de ambientes urbanos, BP.IC; 14/06549-7 - Programa de atividades e justificativa para bolsa de treinamento técnico V: gerente dos projetos de software livre ligados ao projeto temático, BP.TT; 13/00613-2 - Modelos e métodos de e-Science para ciências da vida e agrárias, BP.TT; 12/19164-0 - Proposta de uma metodologia quantitativa de análise do jogo em esportes coletivos de invasão baseada em um modelo formal de estratégia: aplicação ao basquetebol e ao futebol, BP.PD; 12/16072-8 - Gerente dos projetos de software livre ligados ao projeto temático, BP.TT - menos bolsas vinculadas
• Assunto(s): Banco de dados Biologia computacional Mineração de dados Reconhecimento de padrões

Resumo

A ciência moderna é crescentemente interdisciplinar e intensiva em dados. Na área de ciências da vida, por exemplo, com o surgimento de plataformas de alto desempenho para análise de imagens e estudos genômicos, o gargalo não está mais na aquisição de dados, mas sim no seu armazenamento, processamento, análise e visualização. Este cenário levou ao surgimento de um novo campo de pesquisa - eScience - que combina pesquisa avançada em computação e em modelagem matemática para permitir e acelerar pesquisa em outros domínios do conhecimento, desde as ciências exatas até as humanidades e artes. A eScience envolve a chamada "computação centrada em dados" (data-intensive computing), com a busca de soluções para gerenciamento de grandes volumes de dados produzidos por (e para) experimentos científicos, para que a descoberta científica não venha a ser detida pelo "dilúvio de dados". Este projeto visa a criação de uma rede colaborativa de eScience para acelerar pesquisa avançada em ciências da vida (biologia, medicina, oceanografia) e ciências agrárias. Está estruturado em tomo de cinco linhas de pesquisa - biologia de sistemas, planejamento de safras, computação visual, modelagem matemática e bancos de dados. Dentro dessas linhas, serão tratadas questões em aberto associadas às principais componentes de um ambiente de pesquisa em eScience: armazenamento, processamento, análise e visualização de grandes volumes de dados científicos. Os pesquisadores principais têm histórico de cooperação e coordenação de projetos nessas linhas. Questões de interoperalidade permeiam todo o projeto. (AU)

Publicações científicas

(103)

(Referências obtidas automaticamente do Web of Science e do SciELO, por meio da informação sobre o financiamento pela FAPESP e o número do processo correspondente, incluída na publicação pelos autores)

OLIVEIRA, JESSICA S.; FRANCO, FELIPE O.; REVERS, MIRIAN C.; SILVA, ANDREIA F.; PORTOLESE, JOANA; BRENTANI, HELENA; MACHADO-LIMA, ARIANE; NUNES, FATIMA L. S.. Computer-aided autism diagnosis based on visual attention models using eye tracking. SCIENTIFIC REPORTS, v. 11, n. 1, MAY 12 2021. (11/50761-2, 14/50889-7, 20/01992-0)

VEGA-OLIVEROS, DIDIER A.; COSTA, LUCIANO DA FONTOURA; RODRIGUES, FRANCISCO APARECIDO. Influence maximization by rumor spreading on correlated networks through community identification. COMMUNICATIONS IN NONLINEAR SCIENCE AND NUMERICAL SIMULATION, v. 83, APR 2020. (15/22308-2, 11/50761-2, 15/50122-0, 13/07375-0, 16/23698-1, 18/24260-5)

SOUZA, GLAUCIA MENDES; VAN SLUYS, MARIE-ANNE; LEMBKE, CAROLINA GIMILIANI; LEE, HAYAN; MARGARIDO, GABRIEL RODRIGUES ALVES; HOTTA, CARLOS TAKESHI; GAIARSA, JONAS WEISSMANN; DINIZ, AUGUSTO LIMA; OLIVEIRA, MAURO DE MEDEIROS; FERREIRA, SAVIO DE SIQUEIRA; et al. Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop. GIGASCIENCE, v. 8, n. 12, DEC 2019. (11/50761-2, 17/02270-6, 15/15346-5, 16/06917-1, 14/50921-8, 08/52074-0, 17/02842-0, 13/18322-4, 13/23048-9, 15/22993-7, 13/07467-1, 08/52146-0, 16/17545-8, 12/51062-3)

MORIMITSU, HENRIQUE; BLOCH, ISABELLE; CESAR-, JR., ROBERTO M.. Exploring structure for long-term tracking of multiple objects in sports videos. COMPUTER VISION AND IMAGE UNDERSTANDING, v. 159, n. SI, p. 89-104, JUN 2017. (12/09741-0, 14/50135-2, 13/08258-7, 11/50761-2)

MENDEZ-BERMUDEZ, J. A.; FERRAZ DE ARRUDA, GUILHERME; RODRIGUES, FRANCISCO A.; MORENO, YAMIR. Scaling properties of multilayer random networks. Physical Review E, v. 96, n. 1, JUL 7 2017. (13/26416-9, 12/25219-2, 11/50761-2)

AMANCIO, DIEGO R.; SILVA, FILIPI N.; COSTA, LUCIANO DA F.. Concentric network symmetry grasps authors' styles in word adjacency networks. EPL, v. 110, n. 6, JUN 2015. (14/20830-0, 11/50761-2)

CCACYAHUILLCA BEJAR, HANS HARLEY; MIRANDA, PAULO AV. Oriented relative fuzzy connectedness: theory, algorithms, and its applications in hybrid image segmentation methods. EURASIP JOURNAL ON IMAGE AND VIDEO PROCESSING, JUL 23 2015. (11/50761-2)

KOSER, DAVID E.; THOMPSON, AMELIA J.; FOSTER, SARAH K.; DWIVEDY, ASHA; PILLAI, EVA K.; SHERIDAN, GRAHAM K.; SVOBODA, HANNO; VIANA, MATHEUS; COSTA, LUCIANO DA F.; GUCK, JOCHEN; et al. Mechanosensing is critical for axon growth in the developing brain. NATURE NEUROSCIENCE, v. 19, n. 12, p. 1592-1598, DEC 2016. (11/50761-2)

JACOMINI, RICARDO DE SOUZA; MARTINS, JR., DAVID CORREA; DA SILVA, FELIPE LENO; REALI COSTA, ANNA HELENA. GeNICE: A Novel Framework for Gene Network Inference by Clustering, Exhaustive Search, and Multivariate Analysis. JOURNAL OF COMPUTATIONAL BIOLOGY, v. 24, n. 8, p. 809-830, AUG 2017. (16/21047-3, 11/50761-2, 15/16310-4, 15/01587-0)

RODRIGUES, VALQUIRIA DA CRUZ; COMIN, CESAR H.; SOARES, JULIANA COATRINI; SOARES, ANDREY COATRINI; MELENDEZ, MATIAS ELISEO; FREGNANI, JOSE HUMBERTO T. G.; CARVALHO, ANDRE LOPES; COSTA, LUCIANO DA F.; OLIVEIRA, JR., OSVALDO N.. Analysis of Scanning Electron Microscopy Images To Investigate Adsorption Processes Responsible for Detection of Cancer Biomarkers. ACS APPLIED MATERIALS & INTERFACES, v. 9, n. 7, p. 5885-5890, FEB 22 2017. (11/22639-8, 15/18942-8, 13/14262-7, 11/50761-2)

DE ARRUDA, HENRIQUE F.; COMIN, CESAR H.; COSTA, LUCIANO DA F.. How integrated are theoretical and applied physics?. SCIENTOMETRICS, v. 116, n. 2, p. 1113-1121, AUG 2018. (15/18942-8, 15/22308-2, 11/50761-2)

DE ARRUDA, HENRIQUE FERRAZ; COMIN, CESAR HENRIQUE; COSTA, LUCIANO DA FONTOURA. Minimal paths between communities induced by geographical networks. JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, FEB 2016. (11/22639-8, 11/50761-2)

SATO, JOAO RICARDO; BALARDIN, JOANA; VIDAL, MACIEL CALEBE; FUJITA, ANDRE. Identification of segregated regions in the functional brain connectome of autistic patients by a combination of fuzzy spectral clustering and entropy analysis. JOURNAL OF PSYCHIATRY & NEUROSCIENCE, v. 41, n. 2, p. 124-132, MAR 2016. (14/09576-5, 11/50761-2)

DE ARRUDA, HENRIQUE F.; COSTA, LUCIANO DA F.; AMANCIO, DIEGO R.. Using complex networks for text classification: Discriminating informative and imaginative documents. EPL, v. 113, n. 2, JAN 2016. (14/20830-0, 12/50986-7, 11/50761-2)

LIMA, THALES S.; DE ARRUDA, HENRIQUE F.; SILVA, FILIPI N.; COMIN, CESAR H.; AMANCIO, DIEGO R.; COSTA, LUCIANO DA F.. The dynamics of knowledge acquisition via self-learning in complex networks. Chaos, v. 28, n. 8, AUG 2018. (16/19069-9, 17/09280-7, 15/22308-2, 11/50761-2, 17/13464-6, 15/08003-4, 15/18942-8)

DE ARRUDA, HENRIQUE F.; MARINHO, VANESSA Q.; LIMA, THALES S.; AMANCIO, DIEGO R.; COSTA, LUCIANO DA F.. An image analysis approach to text analytics based on complex networks. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, v. 510, p. 110-120, NOV 15 2018. (16/19069-9, 15/22308-2, 15/05676-8, 11/50761-2)

COSTA, LUCIANO DA F.; SILVA, FILIPI N.; COMIN, CESAR H.. Negative feedback, linearity and parameter invariance in linear electronics. ELECTRICAL ENGINEERING, v. 100, n. 2, p. 1159-1181, JUN 2018. (15/08003-4, 15/18942-8, 11/50761-2)

VILLAR COUTO, CYNTHIA MARTINS; COMIN, CESAR HENRIQUE; COSTA, LUCIANO DA FONTOURA. Effects of threshold on the topology of gene co-expression networks. MOLECULAR BIOSYSTEMS, v. 13, n. 10, p. 2024-2035, OCT 2017. (13/19082-7, 15/18942-8, 11/50761-2)

MENDEZ-BERMUDEZ, J. A.; FERRAZ DE ARRUDA, GUILHERME; RODRIGUES, FRANCISCO A.; MORENO, YAMIR. Diluted banded random matrices: scaling behavior of eigenfunction and spectral properties. Journal of Physics A-Mathematical and Theoretical, v. 50, n. 49, DEC 8 2017. (13/26416-9, 15/07463-1, 12/25219-2, 11/50761-2)

AMANCIO, DIEGO R.; OLIVEIRA, JR., OSVALDO N.; COSTA, LUCIANO DA F.. Topological-collaborative approach for disambiguating authors' names in collaborative networks. SCIENTOMETRICS, v. 102, n. 1, p. 465-485, JAN 2015. (13/06717-4, 10/00927-9, 11/50761-2)

JI, PENG; PERON, THOMAS K. D. M.; RODRIGUES, FRANCISCO A.; KURTHS, JUEURGEN. Analysis of cluster explosive synchronization in complex networks. Physical Review E, v. 90, n. 6, DEC 18 2014. (13/26416-9, 12/22160-7, 11/50761-2)

OZAHATA, MINA CINTHO; SABINO, ESTER CERDEIRA; DIAZ, RICARDO SOBHIE; CESAR-, JR., ROBERTO M.; FERREIRA, JOAO EDUARDO. Data-intensive analysis of HIV mutations. BMC Bioinformatics, v. 16, FEB 5 2015. (11/50761-2)

MENDEZ-BERMUDEZ, J. A.; ALCAZAR-LOPEZ, A.; MARTINEZ-MENDOZA, A. J.; RODRIGUES, FRANCISCO A.; PERON, THOMAS K. D. M.. Universality in the spectral and eigenfunction properties of random networks. Physical Review E, v. 91, n. 3, MAR 13 2015. (13/26416-9, 12/22160-7, 11/50761-2)

CRISTINO, A. S.; WILLIAMS, S. M.; HAWI, Z.; AN, J-Y; BELLGROVE, M. A.; SCHWARTZ, C. E.; COSTA, L. DA F.; CLAUDIANOS, C.. Neurodevelopmental and neuropsychiatric disorders represent an interconnected molecular system. MOLECULAR PSYCHIATRY, v. 19, n. 3, p. 294-301, MAR 2014. (11/50761-2)

AMANCIO, DIEGO R.; ALTMANN, EDUARDO G.; RYBSKI, DIEGO; OLIVEIRA, JR., OSVALDO N.; COSTA, LUCIANO DA F.. Probing the Statistical Properties of Unknown Texts: Application to the Voynich Manuscript. PLoS One, v. 8, n. 7, JUL 2 2013. (10/00927-9, 11/50761-2)

DIAS PEDRO, RICARDO WANDRE; NUNES, FATIMA L. S.; MACHADO-LIMA, ARIANE. Using Grammars for Pattern Recognition in Images: A Systematic Review. ACM COMPUTING SURVEYS, v. 46, n. 2, NOV 2013. (10/15691-0, 11/50761-2)

DE ARRUDA, GUILHERME FERRAZ; COSTA, LUCIANO DA FONTOURA; SCHUBERT, DIRK; RODRIGUES, FRANCISCO A.. Structure and dynamics of functional networks in child-onset schizophrenia. CLINICAL NEUROPHYSIOLOGY, v. 125, n. 8, p. 1589-1595, AUG 2014. (10/19440-2, 11/50761-2)

BENATTI, ALEXANDRE; DE ARRUDA, HENRIQUE F.; SILVA, FILIPI NASCIMENTO; COMIN, CESAR HENRIQUE; COSTA, LUCIANO DA FONTOURA. Opinion diversity and social bubbles in adaptive Sznajd networks. JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, v. 2020, n. 2, FEB 2020. (15/22308-2, 11/50761-2, 18/09125-4, 18/10489-0)

FREITAS, ANDERSON M.; TORRES, RICARDO DA S.; MIRANDA, PAULO A. V.. TSS & TSB: Tensor scale descriptors within circular sectors for fast shape retrieval. PATTERN RECOGNITION LETTERS, v. 83, n. 3, p. 303-311, NOV 1 2016. (11/50761-2)

AZEVEDO, HATYLAS; RENESTO, PAULO GUILHERME; CHINEN, ROGERIO; NAKA, ERIKA; CARVALHO DE MATOS, ANA CRISTINA; CENEDEZE, MARCOS ANTONIO; MOREIRA-FILHO, CARLOS ALBERTO; SARAIVA CAMARA, NIELS OLSEN; PACHECO-SILVA, ALVARO. Intragraft transcriptional profiling of renal transplant patients with tubular dysfunction reveals mechanisms underlying graft injury and recovery. HUMAN GENOMICS, v. 10, JAN 7 2016. (12/02270-2, 09/53443-1, 11/50761-2)

SILVA, FILIPI N.; COMIN, CESAR H.; PERON, THOMAS K. D. M.; RODRIGUES, FRANCISCO A.; YE, CHENG; WILSON, RICHARD C.; HANCOCK, EDWIN R.; COSTA, LUCIANO DA F.. Concentric network symmetry. INFORMATION SCIENCES, v. 333, p. 61-80, MAR 10 2016. (11/22639-8, 12/50986-7, 11/50761-2, 12/22160-7, 13/26416-9)

MATUSZEWSKI, DAMIAN J.; CESAR, JR., ROBERTO M.; STRICKLER, J. RUDI; BALDASSO, LUIS F.; LOPES, RUBENS M.. Visual rhythm for particle analysis in sample-in-flow systems: Application for continuous plankton monitoring. LIMNOLOGY AND OCEANOGRAPHY-METHODS, v. 13, n. 12, p. 687-696, DEC 2015. (11/50761-2)

FUJITA, ANDRE; TAKAHASHI, DANIEL Y.; PATRIOTA, ALEXANDRE G.; SATO, JOAO R.. A non-parametric statistical test to compare clusters with applications in functional magnetic resonance imaging data. STATISTICS IN MEDICINE, v. 33, n. 28, p. 4949-4962, DEC 10 2014. (11/50761-2, 12/21788-2, 13/10498-6, 14/09576-5)

AZEVEDO, HATYLAS; FUJITA, ANDRE; BANDO, SILVIA YUMI; IAMASHITA, PRISCILA; MOREIRA-FILHO, CARLOS ALBERTO. Transcriptional Network Analysis Reveals that AT1 and AT2 Angiotensin II Receptors Are Both Involved in the Regulation of Genes Essential for Glioma Progression. PLoS One, v. 9, n. 11, NOV 3 2014. (11/07762-8, 05/56446-0, 09/53443-1, 11/50761-2)

SANTOS, SUZANA DE SIQUEIRA; TAKAHASHI, DANIEL YASUMASA; NAKATA, ASUKA; FUJITA, ANDRE. A comparative study of statistical methods used to identify dependencies between gene expression signals. BRIEFINGS IN BIOINFORMATICS, v. 15, n. 6, p. 906-918, NOV 2014. (11/07762-8, 13/03447-6, 12/25417-9, 11/50761-2)

COMIN, CESAR HENRIQUE; XU, XIAOYIN; WANG, YAMING; COSTA, LUCIANO DA FONTOURA; YANG, ZHONG. An image processing approach to analyze morphological features of microscopic images of muscle fibers. Computerized Medical Imaging and Graphics, v. 38, n. 8, p. 803-814, DEC 2014. (11/22639-8, 11/50761-2)

FONSECA, MONIQUE T.; RODRIGUES, ABNER C.; CEZAR, LUANA C.; FUJITA, ANDRE; SORIANO, FRANCISCO G.; STEINER, ALEXANDRE A.. Spontaneous hypothermia in human sepsis is a transient, self-limiting, and nonterminal response. Journal of Applied Physiology, v. 120, n. 12, p. 1394-1401, JUN 15 2016. (11/50761-2, 09/15530-0, 12/03831-8, 13/00506-1, 14/09576-5)

SILVA, FILIPI N.; AMANCIO, DIEGO R.; BARDOSOVA, MARIA; COSTA, LUCIANO DA F.; OLIVEIRA, JR., OSVALDO N.. Using network science and text analytics to produce surveys in a scientific topic. Journal of Informetrics, v. 10, n. 2, p. 487-502, MAY 2016. (14/20830-0, 15/08003-4, 11/50761-2)

RIBEIRO, ADELE H.; PAVAN SOLER, JULIA MARIA; HIRATA JR, ROBERTO. Variance-Preserving Estimation of Intensity Values Obtained From Omics Experiments. FRONTIERS IN GENETICS, v. 10, SEP 20 2019. (06/03227-2, 11/50761-2, 15/01587-0)

REIS, MARCELO S.; ESTRELA, GUSTAVO; FERREIRA, CARLOS EDUARDO; BARRERA, JUNIOR. Optimal Boolean lattice-based algorithms for the U-curve optimization problem. INFORMATION SCIENCES, v. 471, p. 97-114, JAN 2019. (13/07467-1, 11/50761-2, 14/23564-0)

VEGA-OLIVEROS, DIDIER A.; COSTA, LUCIANO DA F.; RODRIGUES, FRANCISCO A.. Rumor propagation with heterogeneous transmission in social networks. JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, FEB 2017. (13/26416-9, 11/50761-2)

LIMA, WANIA REZENDE; MARTINS, DAVID CORREA; PARREIRA, KLEBER SIMONIO; SCARPELLI, PEDRO; DE MORAES, MIRIAM SANTOS; TOPALIS, PANTELIS; HASHIMOTO, RONALDO FUMIO; GARCIA, CELIA R. S.. Genome-wide analysis of the human malaria parasite Plasmodium falciparum transcription factor PfNF-YB shows interaction with a CCAAT motif. ONCOTARGET, v. 8, n. 69, p. 113987-114001, DEC 26 2017. (15/01587-0, 11/51295-5, 11/50761-2)

DE ARRUDA, HENRIQUE F.; COMIN, CESAR H.; COSTA, LUCIANO DA F.. Problem-solving using complex networks. European Physical Journal B, v. 92, n. 6, JUN 2019. (13/07375-0, 15/22308-2, 11/50761-2, 18/09125-4)

COMIN, CESAR HENRIQUE; COSTA, LUCIANO DA FONTOURA. Shape, connectedness and dynamics in neuronal networks. JOURNAL OF NEUROSCIENCE METHODS, v. 220, n. 2, SI, p. 100-115, NOV 15 2013. (11/22639-8, 11/50761-2)

AMANCIO, DIEGO R.; OLIVEIRA, JR., OSVALDO N.; COSTA, LUCIANO DA F.. A decaying factor accounts for contained activity in neuronal networks with no need of hierarchical or modular organization. JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, NOV 2012. (10/00927-9, 11/50761-2)

DIAS PEDRO, RICARDO WANDRE; MACHADO-LIMA, ARIANE; NUNES, FATIMA L. S.. Towards an approach using grammars for automatic classification of masses in mammograms. COMPUTATIONAL INTELLIGENCE, v. 37, n. 4, SI, p. 1515-1544, NOV 2021. (11/50761-2)

COMIN, CESAR H.; TAYLOR, GAVIN J.; COSTA, LUCIANO DA F.. Quantifying the regularity of a 3D set of points on the surface of an ellipsoidal object. PATTERN RECOGNITION LETTERS, v. 133, p. 1-7, MAY 2020. (15/22308-2, 11/50761-2, 18/09125-4)

RODRIGUEZ, MAYRA Z.; COMIN, CESAR H.; CASANOVA, DALCIMAR; BRUNO, ODEMIR M.; AMANCIO, DIEGO R.; COSTA, LUCIANO DA F.; RODRIGUES, FRANCISCO A.. Clustering algorithms: A comparative approach. PLoS One, v. 14, n. 1, JAN 15 2019. (16/19069-9, 14/20830-0, 15/18942-8, 15/22308-2, 14/08026-1, 18/09125-4, 11/50761-2)

JIMENEZ, RAY DUENAS; MARTINS-JR, DAVID CORREA JR; SANTOS, CARLOS SILVA. One genetic algorithm per gene to infer gene networks from expression data. NETWORK MODELING AND ANALYSIS IN HEALTH INFORMATICS AND BIOINFORMATICS, v. 4, n. 1, DEC 2015. (14/21050-9, 11/50761-2)

MONTOYA CUBAS, CARLOS FERNANDO; MARTINS-JR, DAVID CORREA JR; SANTOS, CARLOS SILVA; BARRERA, JUNIOR. Linear grouping of predictor instances to infer gene networks. NETWORK MODELING AND ANALYSIS IN HEALTH INFORMATICS AND BIOINFORMATICS, v. 4, n. 1, DEC 2015. (11/50761-2)

YE, CHENG; COMIN, CESAR H.; PERON, THOMAS K. D. M.; SILVA, FILIPI N.; RODRIGUES, FRANCISCO A.; COSTA, LUCIANO DA F.; TORSELLO, ANDREA; HANCOCK, EDWIN R.. Thermodynamic characterization of networks using graph polynomials. Physical Review E, v. 92, n. 3, SEP 25 2015. (11/22639-8, 12/50986-7, 11/50761-2, 12/22160-7, 13/26416-9)

COMIN, CESAR H.; SANTOS, JOAO R.; CORRADINI, DARIO; MORRISON, WILL; CURME, CHESTER; ROSENE, DOUGLAS L.; GABRIELLI, ANDREA; COSTA, LUCIANO DA F.; STANLEY, H. EUGENE. Statistical physics approach to quantifying differences in myelinated nerve fibers. SCIENTIFIC REPORTS, v. 4, MAR 28 2014. (11/22639-8, 11/50761-2)

BANDO, SILVIA YUMI; SILVA, FILIPI NASCIMENTO; COSTA, LUCIANO DA FONTOURA; SILVA, ALEXANDRE V.; PIMENTEL-SILVA, LUCIANA R.; CASTRO, LUIZ H. M.; WEN, HUNG-TZU; AMARO, JR., EDSON; MOREIRA-FILHO, CARLOS ALBERTO. Complex Network Analysis of CA3 Transcriptome Reveals Pathogenic and Compensatory Pathways in Refractory Temporal Lobe Epilepsy. PLoS One, v. 8, n. 11, NOV 21 2013. (05/56446-0, 09/53443-1, 05/00587-5, 11/50761-2)

AMANCIO, DIEGO RAPHAEL; OLIVEIRA, JR., OSVALDO N.; COSTA, LUCIANO DA FONTOURA. Identification of literary movements using complex networks to represent texts. NEW JOURNAL OF PHYSICS, v. 14, APR 23 2012. (10/00927-9, 11/50761-2)

AMANCIO, DIEGO R.; ALUISIO, SANDRA M.; OLIVEIRA, JR., OSVALDO N.; COSTA, LUCIANO DA F.. Complex networks analysis of language complexity. EPL, v. 100, n. 5, DEC 2012. (10/00927-9, 11/50761-2)

CERIBELI, CAROLINE; FERRAZ DE ARRUDA, HENRIQUE; DA FONTOURA COSTA, LUCIANO. How coupled are capillary electrophoresis and mass spectrometry?. SCIENTOMETRICS, v. 126, n. 5, p. 3841-3851, MAY 2021. (13/07375-0, 15/22308-2, 19/16223-5, 18/10489-0, 11/50761-2)

OUELLETTE, JULIE; TOUSSAY, XAVIER; COMIN, CESAR H.; COSTA, LUCIANO DA F.; HO, MIRABELLE; LACALLE-AURIOLES, MARIA; FREITAS-ANDRADE, MOISES; LIU, QING YAN; LECLERC, SONIA; PAN, YOULIAN; et al. Vascular contributions to 16p11.2 deletion autism syndrome modeled in mice. NATURE NEUROSCIENCE, v. 23, n. 9, JUL 2020. (15/18942-8, 15/22308-2, 11/50761-2)

OLIVEIRA, MAURO DE MEDEIROS; BONADIO, IGOR; DE MELO, ALICIA LIE; SOUZA, GLAUCIA MENDES; DURHAM, ALAN MITCHELL. TSSFinder-fast and accurate ab initio prediction of the core promoter in eukaryotic genomes. BRIEFINGS IN BIOINFORMATICS, v. 22, n. 6, NOV 2021. (11/50761-2, 14/50921-8)

BANDO, SILVIA Y.; IAMASHITA, PRISCILA; SILVA, FILIPI N.; COSTA, LUCIANO DA F.; ABE, CECILIA M.; BERTONHA, FERNANDA B.; GUTH, BEATRIZ E. C.; FUJITA, ANDRE; MOREIRA-FILHO, CARLOS A.. Dynamic Gene Network Analysis of Caco-2 Cell Response to Shiga Toxin-Producing Escherichia coli-Associated Hemolytic-Uremic Syndrome. MICROORGANISMS, v. 7, n. 7, JUL 2019. (15/22308-2, 11/50761-2)

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DE ARRUDA, HENRIQUE F.; SILVA, FILIPI N.; COMIN, CESAR H.; AMANCIO, DIEGO R.; COSTA, LUCIANO DA F.. Connecting network science and information theory. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, v. 515, p. 641-648, FEB 1 2019. (15/18942-8, 16/19069-9, 14/20830-0, 15/08003-4, 11/50761-2)

BANDO, SILVIA YUMI; IAMASHITA, PRISCILA; GUTH, BEATRIZ E.; DOS SANTOS, LUIS F.; FUJITA, ANDRE; ABE, CECILIA M.; FERREIRA, LEANDRO R.; MOREIRA-FILHO, CARLOS ALBERTO. A hemolytic-uremic syndrome-associated strain O113:H21 Shiga toxin-producing Escherichia coli specifically expresses a transcriptional module containing dicA and is related to gene network dysregulation in Caco-2 cells. PLoS One, v. 12, n. 12, DEC 18 2017. (15/22308-2, 11/50761-2)

SOUZA, PAULO J. P.; COMIN, CESAR H.; COSTA, LUCIANO DA F.. Topology and dynamics in complex networks: The role of edge reciprocity. EPL, v. 122, n. 2, APR 2018. (15/18942-8, 15/22308-2, 11/50761-2)

DE ARRUDA, HENRIQUE F.; MARINHO, VANESSA Q.; COSTA, LUCIANO DA F.; AMANCIO, DIEGO R.. Paragraph-based representation of texts: A complex networks approach. INFORMATION PROCESSING & MANAGEMENT, v. 56, n. 3, p. 479-494, MAY 2019. (16/19069-9, 15/22308-2, 11/50761-2, 17/13464-6, 15/05676-8)

FELTRIN, ARTHUR SANT'ANNA; TAHIRA, ANA CAROLINA; SIMOES, SERGIO NERY; BRENTANI, HELENA; MARTINS, JR., DAVID CORREA. Assessment of complementarity of WGCNA and NERI results for identification of modules associated to schizophrenia spectrum disorders. PLoS One, v. 14, n. 1, JAN 15 2019. (11/04956-6, 11/50761-2, 14/00041-1, 14/10488-3, 15/01587-0)

SWARNKAR, TRIPTI; SIMOES, SERGIO NERY; ANURA, ANJI; BRENTANI, HELENA; CHATTERJEE, JYOTIRMOY; HASHIMOTO, RONALDO FUMIO; MARTINS, DAVID CORREA; MITRA, PABITRA. Identifying dense subgraphs in protein-protein interaction network for gene selection from microarray data. NETWORK MODELING AND ANALYSIS IN HEALTH INFORMATICS AND BIOINFORMATICS, v. 4, n. 1, DEC 2015. (10/52138-8, 11/50761-2)

PINTO, SILVIA C. D.; URBANOVA, PETRA; CESAR, JR., ROBERTO M.. Two-Dimensional Wavelet Analysis of Supraorbital Margins of the Human Skull for Characterizing Sexual Dimorphism. IEEE Transactions on Information Forensics and Security, v. 11, n. 7, p. 1542-1548, JUL 2016. (11/50761-2)

AZEVEDO, HATYLAS; MOREIRA-FILHO, CARLOS ALBERTO. Topological robustness analysis of protein interaction networks reveals key targets for overcoming chemotherapy resistance in glioma. SCIENTIFIC REPORTS, v. 5, NOV 19 2015. (11/50761-2)

DE ARRUDA, GUILHERME FERRAZ; LEBENSZTAYN, ELCIO; RODRIGUES, FRANCISCO A.; RODRIGUEZ, PABLO MARTIN. A process of rumour scotching on finite populations. ROYAL SOCIETY OPEN SCIENCE, v. 2, n. 9, SEP 2015. (11/50761-2, 13/03898-8, 13/26416-9, 12/25219-2, 12/22673-4)

CORREA, DEBORA C.; AP RODRIGUES, FRANCISCO. A survey on symbolic data-based music genre classification. EXPERT SYSTEMS WITH APPLICATIONS, v. 60, p. 190-210, OCT 30 2016. (13/26416-9, 12/17961-0, 11/50761-2)

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LOPES, FABRICIO M.; RAY, SHUBHRA SANKAR; HASHIMOTO, RONALDO F.; CESAR, JR., ROBERTO M.. Entropic Biological Score: a cell cycle investigation for GRNs inference. Gene, v. 541, n. 2, p. 129-137, MAY 15 2014. (10/52138-8, 11/50761-2)

JI, PENG; PERON, THOMAS K. D. M.; RODRIGUES, FRANCISCO A.; KURTHS, JUERGEN. Low-dimensional behavior of Kuramoto model with inertia in complex networks. SCIENTIFIC REPORTS, v. 4, MAY 2 2014. (13/26416-9, 11/50761-2)

AMANCIO, DIEGO R.; OLIVEIRA, JR., OSVALDO N.; COSTA, L. DA F.. Robustness of community structure to node removal. JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, MAR 2015. (14/20830-0, 13/06717-4, 11/50761-2)

DE ARRUDA, HENRIQUE FERRAZ; COMIN, CESAR HENRIQUE; MIAZAKI, MAURO; VIANA, MATHEUS PALHARES; COSTA, LUCIANO DA FONTOURA. A framework for analyzing the relationship between gene expression and morphological, topological, and dynamical patterns in neuronal networks. JOURNAL OF NEUROSCIENCE METHODS, v. 245, p. 1-14, APR 30 2015. (11/22639-8, 07/50988-1, 11/50761-2)

COMIN, CESAR HENRIQUE; SILVA, FILIPI NASCIMENTO; COSTA, LUCIANO DA FONTOURA. A diffusion-based approach to obtaining the borders of urban areas. JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, MAY 2016. (11/22639-8, 11/50761-2)

DE ARRUDA, HENRIQUE F.; COSTA, LUCIANO DA F.; AMANCIO, DIEGO R.. Topic segmentation via community detection in complex networks. Chaos, v. 26, n. 6, JUN 2016. (14/20830-0, 11/50761-2)

SANTOS, SUZANA DE SIQUEIRA; DE ALMEIDA GALATRO, THAIS FERNANDA; WATANABE, RODRIGO AKIRA; OBA-SHINJO, SUELI MIEKO; NAGAHASHI MARIE, SUELY KAZUE; FUJITA, ANDRE. CoGA: An R Package to Identify Differentially Co-Expressed Gene Sets by Analyzing the Graph Spectra. PLoS One, v. 10, n. 8, AUG 27 2015. (13/03447-6, 14/09576-5, 12/25417-9, 11/50761-2)

PERCIANO, T.; TUPIN, F.; HIRATA, JR., R.; CESAR, JR., R. M.. A two-level Markov random field for road network extraction and its application with optical, SAR, and multitemporal data. International Journal of Remote Sensing, v. 37, n. 16, p. 3584-3610, AUG 20 2016. (11/50761-2)

SILVA, FILIPI N.; COMIN, CESAR H.; COSTA, LUCIANO DA F.. Seeking maximum linearity of transfer functions. Review of Scientific Instruments, v. 87, n. 12, DEC 2016. (15/08003-4, 15/18942-8, 11/50761-2)

MACEDO, MAYSA M. G.; GUIMARAES, WELINGSON V. N.; GALON, MICHELI Z.; TAKIMURA, CELSO K.; LEMOS, PEDRO A.; GUTIERREZ, MARCO ANTONIO. A bifurcation identifier for IV-OCT using orthogonal least squares and supervised machine learning. Computerized Medical Imaging and Graphics, v. 46, n. 2, SI, p. 237-248, DEC 2015. (13/09922-8, 11/50761-2)

SIMOES, SERGIO N.; MARTINS, JR., DAVID C.; PEREIRA, CARLOS A. B.; HASHIMOTO, RONALDO F.; BRENTANI, HELENA. NERI: network-medicine based integrative approach for disease gene prioritization by relative importance. BMC Bioinformatics, v. 16, n. 19, DEC 16 2015. (10/52138-8, 11/50761-2)

CORREA, JR., EDILSON A.; SILVA, FILIPI N.; COSTA, LUCIANO DA F.; AMANCIO, DIEGO R.. Patterns of authors contribution in scientific manuscripts. Journal of Informetrics, v. 11, n. 2, p. 498-510, MAY 2017. (14/20830-0, 15/08003-4, 16/19069-9, 11/50761-2)

YE, CHENG; WILSON, RICHARD C.; COMIN, CESAR H.; COSTA, LUCIANO DA F.; HANCOCK, EDWIN R.. Approximate von Neumann entropy for directed graphs. Physical Review E, v. 89, n. 5, MAY 12 2014. (11/22639-8, 12/50986-7, 11/50761-2)

AMANCIO, DIEGO RAPHAEL; COMIN, CESAR HENRIQUE; CASANOVA, DALCIMAR; TRAVIESO, GONZALO; BRUNO, ODEMIR MARTINEZ; RODRIGUES, FRANCISCO APARECIDO; COSTA, LUCIANO DA FONTOURA. A Systematic Comparison of Supervised Classifiers. PLoS One, v. 9, n. 4, APR 24 2014. (13/06717-4, 11/22639-8, 11/50761-2, 14/04930-5, 10/19440-2, 13/14984-2, 10/00927-9)

LOPES, FABRICIO M.; MARTINS, JR., DAVID C.; BARRERA, JUNIOR; CESAR, JR., ROBERTO M.. A feature selection technique for inference of graphs from their known topological properties: Revealing scale-free gene regulatory networks. INFORMATION SCIENCES, v. 272, p. 1-15, JUL 10 2014. (11/50761-2)

MOREIRA-FILHO, CARLOS ALBERTO; BANDO, SILVIA YUMI; BERTONHA, FERNANDA BERNARDI; IAMASHITA, PRISCILA; SILVA, FILIPI NASCIMENTO; COSTA, LUCIANO DA FONTOURA; SILVA, ALEXANDRE VALOTTA; MARTINS CASTRO, LUIZ HENRIQUE; WEN, HUNG-TZU. Community Structure Analysis of Transcriptional Networks Reveals Distinct Molecular Pathways for Early- and Late-Onset Temporal Lobe Epilepsy with Childhood Febrile Seizures. PLoS One, v. 10, n. 5, MAY 26 2015. (05/56446-0, 09/53443-1, 05/00587-5, 11/50761-2)

EROGLU, DENIZ; PERON, THOMAS K. D. M.; MARWAN, NOBERT; RODRIGUES, FRANCISCO A.; COSTA, LUCIANO DA F.; SEBEK, MICHAEL; KISS, ISTVAN Z.; KURTHS, JUERGEN. Entropy of weighted recurrence plots. Physical Review E, v. 90, n. 4, OCT 21 2014. (13/26416-9, 12/22160-7, 11/50761-2)

DE ARRUDA, GUILHERME FERRAZ; BARBIERI, ANDRE LUIZ; RODRIGUEZ, PABLO MARTIN; RODRIGUES, FRANCISCO A.; MORENO, YAMIR; COSTA, LUCIANO DA FONTOURA. Role of centrality for the identification of influential spreaders in complex networks. Physical Review E, v. 90, n. 3, SEP 22 2014. (13/26416-9, 13/03898-8, 11/50761-2)

MOREIRA-FILHO, CARLOS ALBERTO; BANDO, SILVIA YUMI; BERTONHA, FERNANDA BERNARDI; SILVA, FILIPI NASCIMENTO; COSTA, LUCIANO DA FONTOURA; FERREIRA, LEANDRO RODRIGUES; FURLANETTO, GLAUCIO; CHACUR, PAULO; NOGUEIRA ZERBINI, MARIA CLAUDIA; CARNEIRO-SAMPAIO, MAGDA. Modular transcriptional repertoire and MicroRNA target analyses characterize genomic dysregulation in the thymus of Down syndrome infants. ONCOTARGET, v. 7, n. 7, p. 7497-7533, FEB 16 2016. (11/50761-2, 14/50489-9, 05/00587-5, 08/58238-4, 09/53443-1)

COMIN, CESAR H.; SILVA, FILIPI N.; COSTA, LUCIANO DA F.. A framework for evaluating complex networks measurements. EPL, v. 110, n. 6, JUN 2015. (11/22639-8, 11/50761-2)

MIAZAKI, MAURO; VIANA, MATHEUS P.; YANG, ZHONG; COMIN, CESAR H.; WANG, YAMING; COSTA, LUCIANO DA F.; XU, XIAOYIN. Automated high-content morphological analysis of muscle fiber histology. COMPUTERS IN BIOLOGY AND MEDICINE, v. 63, p. 28-35, AUG 1 2015. (11/22639-8, 07/50988-1, 11/50761-2)

LACOSTE, BAPTISTE; COMIN, CESAR H.; BEN-ZVI, AYAL; KAESER, PASCAL S.; XU, XIAOYIN; COSTA, LUCIANO DA F.; GU, CHENGHUA. Sensory-Related Neural Activity Regulates the Structure of Vascular Networks in the Cerebral Cortex. NEURON, v. 83, n. 5, p. 1117-1130, SEP 3 2014. (11/22639-8, 11/50761-2)

DOMINGUES, G. S.; SILVA, F. N.; COMIN, C. H.; COSTA, L. DA F.. Topological characterization of world cities. JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, AUG 2018. (17/09280-7, 15/22308-2, 11/50761-2, 15/08003-4, 15/18942-8)

DE ARRUDA, HENRIQUE F.; SILVA, FILIPI N.; COSTA, LUCIANO DA F.; AMANCIO, DIEGO R.. Knowledge acquisition: A Complex networks approach. INFORMATION SCIENCES, v. 421, p. 154-166, DEC 2017. (14/20830-0, 15/08003-4, 16/19069-9, 11/50761-2)

COSTA, LUCIANO DA F.; SILVA, FILIPI N.; COMIN, CESAR H.. A pattern recognition approach to transistor array parameter variance. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, v. 499, p. 176-185, JUN 1 2018. (15/18942-8, 15/22308-2, 15/08003-4, 11/50761-2)

COSTA, LUCIANO DA F.; SILVA, FILIPI NASCIMENTO; COMIN, CESAR H.. Characterizing BJTs using the Early voltage in the forward active mode. INTERNATIONAL JOURNAL OF CIRCUIT THEORY AND APPLICATIONS, v. 46, n. 4, p. 978-986, APR 2018. (15/18942-8, 15/08003-4, 11/50761-2)

AZEVEDO, HATYLAS; KHALED, NATHALIA AMATO; SANTOS, PAULA; BERTONHA, FERNANDA BERNARDI; MOREIRA-FILHO, CARLOS ALBERTO. Temporal analysis of hippocampal CA3 gene coexpression networks in a rat model of febrile seizures. Disease Models & Mechanisms, v. 11, n. 1, JAN 2018. (11/50761-2)

DAZZI, ESTEPHAN; DE CAMPOS, TEOFILO; HILTON, ADRIAN; CESAR JR, ROBERTO M.. Scalable object instance recognition based on keygraph matching. PATTERN RECOGNITION LETTERS, v. 114, n. SI, p. 53-62, OCT 15 2018. (14/50769-1, 15/22308-2, 11/50761-2)

DE ARRUDA, HENRIQUE FERRAZ; SILVA, FILIPI NASCIMENTO; MARINHO, VANESSA QUEIROZ; AMANCIO, DIEGO RAPHAEL; COSTA, LUCIANO DA FONTOURA. Representation of texts as complex networks: a mesoscopic approach. JOURNAL OF COMPLEX NETWORKS, v. 6, n. 1, p. 125-144, FEB 2018. (16/19069-9, 11/50761-2, 15/08003-4, 14/20830-0, 15/05676-8)

BURKE, PAULO E. P.; COMIN, CESAR H.; SILVA, FILIPI N.; COSTA, LUCIANO DA F.. Biological network border detection. INTEGRATIVE BIOLOGY, v. 9, n. 12, p. 947-955, DEC 2017. (15/08003-4, 15/18942-8, 11/50761-2)

GOUVEIA, AYDEN; SEEGOBIN, MATTHEW; KANNANGARA, TIMAL S.; HE, LING; WONDISFORD, FREDRIC; COMIN, CESAR H.; COSTA, LUCIANO DA F.; BEIQUE, JEAN-CLAUDE; LAGACE, DIANE C.; LACOSTE, BAPTISTE; et al. The aPKC-CBP Pathway Regulates Post-stroke Neurovascular Remodeling and Functional Recovery. STEM CELL REPORTS, v. 9, n. 6, p. 1735-1744, DEC 2017. (15/18942-8, 11/50761-2)

GEWERS, FELIPE L.; FERREIRA, GUSTAVO R.; DE ARRUDA, HENRIQUE F.; SILVA, FILIPI N.; COMIN, CESAR H.; AMANCIO, DIEGO R.; COSTA, LUCIANO DA F.. Principal Component Analysis: A Natural Approach to Data Exploration. ACM COMPUTING SURVEYS, v. 54, n. 4, JUL 2021. (16/19069-9, 15/22308-2, 11/50761-2, 17/13464-6, 18/10489-0, 18/09125-4, 19/16223-5)