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Models and methods of e-Science for life and agricultural sciences

Grant number: 11/50761-2
Support Opportunities:Research Projects - Thematic Grants
Duration: February 01, 2012 - September 30, 2016
Field of knowledge:Physical Sciences and Mathematics - Computer Science
Convênio/Acordo: CNPq - Pronex
Principal Investigator:Roberto Marcondes Cesar Junior
Grantee:Roberto Marcondes Cesar Junior
Host Institution: Instituto de Matemática e Estatística (IME). Universidade de São Paulo (USP). São Paulo , SP, Brazil
Pesquisadores principais:
Carlos Alberto Moreira Filho ; Claudia Maria Bauzer Medeiros ; Luciano da Fontoura Costa
Associated grant(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
+ associated grants 13/25918-0 - Professor Dr. Stéphane Canu's visit to 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 - Prof. Dr. Florence Tupin's visit to IME-USP, AV.EXT - associated grants
Associated scholarship(s):16/13791-4 - A framework for hand gesture analysis and tracking: the case for hands with unusual shapes and movements, BP.DR
15/13430-9 - Enumerating multidimensional metabolic stories: models and methods, BP.PD
15/18942-8 - Associating Complex Networks with Effective Feature Spaces, BP.PD
+ associated scholarships 15/18117-7 - Experience Sampling and Programmed Intervention Method (ESPIM), BP.PD
15/08003-4 - Complex network approach to e-Science and dynamic datasets, BP.PD
15/07252-0 - Interactive documents for the specialized data collection of everyday experiences: operations for authoring, sharing and analysis, BP.DR
14/24918-0 - Weakly supervised learning for face and person attributes detection, BP.DR
15/03475-5 - Watching the cities: big data and computer vision for analysis of urban environments, BP.IC
12/19164-0 - Proposal of a quantitative methodology for match analysis in invasion team sports based on a formal model of strategy: application to basketball and soccer, BP.PD - associated scholarships

Abstract

Modern science is increasingly interdisciplinary and data intensive. In the area of life sciences, for example, with the emergence of high-performance platforms for image analysis and genomic studies, the bottleneck is not in data acquisition, but rather in its storage, processing, analysis and visualization. This scenario has led to the emergence of a new field of research-eScience-which combines advanced research in computing and mathematical modelling to enable and accelerate research in other fields of knowledge, from the sciences to the humanities and the arts. The eScience involves the so-called "data-oriented computing" (data-intensive computing), with the search for solutions for managing large volumes of data generated by (and for) scientific experiments, for which the scientific breakthrough will not be owned by the "data deluge". This project aims to create a collaborative network of eScience to accelerate advanced research in life sciences (biology, medicine, oceanography) and agricultural sciences. It is structured in five research lines tomo-systems biology, crop planning, visual computing, mathematical modelling and databanks. Within these lines, it will be dealt with questions related to the main components of a research environment in eScience: storage, processing, analysis and visualization of large volumes of scientific data. The main researchers have history of cooperation and coordination of projects in these lines. Interoperability issues permeate the entire project. (AU)

Articles published in Pesquisa FAPESP Magazine about the research grant:
The Voynich manuscript 
The Voynich manuscript 
El código Voynich 
El código Voynich 
Articles published in Agência FAPESP Newsletter about the research grant:
Articles published in other media outlets (0 total):
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Scientific publications (148)
(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)
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, . (15/18942-8, 15/22308-2, 11/50761-2)
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, . (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, . (11/50761-2, 10/52138-8)
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, . (17/13464-6, 18/09125-4, 15/22308-2, 16/19069-9, 18/10489-0, 11/50761-2, 19/16223-5)
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, . (13/07375-0, 15/22308-2, 19/16223-5, 18/10489-0, 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, . (11/50761-2, 14/50921-8)
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, . (11/50761-2)
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, . (15/22308-2, 11/50761-2)
SILVA, FILIPI N.; COMIN, CESAR H.; COSTA, LUCIANO DA F.. Malleability of complex networks. JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, . (15/22308-2, 15/08003-4, 17/09280-7, 15/18942-8, 13/07375-0, 18/09125-4, 11/50761-2)
MOREIRA TAVARES, ANDERSON CARLOS; CCACYAHUILLCA BEJAR, HANS HARLEY; VECHIATTO MIRANDA, PAULO ANDRE; ANGULO, J; VELASCOFORERO, S; MEYER, F. Seed Robustness of Oriented Image Foresting Transform: Core Computation and the Robustness Coefficient. MATHEMATICAL MORPHOLOGY AND ITS APPLICATIONS TO SIGNAL AND IMAGE PROCESSING (ISMM 2017), v. 10225, p. 12-pg., . (14/12236-1, 11/50761-2)
SIMOES, SERGIO N.; MARTINS, DAVID C., JR.; 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, p. 14-pg., . (10/52138-8, 11/50761-2)
BARBOSA, SAMUEL; COSLEY, DAN; SHARMA, AMIT; CESAR, ROBERTO M., JR.; ACM. Averaging Gone Wrong: Using Time-Aware Analyses to Better Understand Behavior. PROCEEDINGS OF THE 25TH INTERNATIONAL CONFERENCE ON WORLD WIDE WEB (WWW'16), v. N/A, p. 13-pg., . (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, v. N/A, p. 16-pg., . (11/22639-8, 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, v. N/A, p. 12-pg., . (11/22639-8, 11/50761-2)
DAZZI, ESTEPHAN; DE CAMPOS, TEOFILO; HILTON, ADRIAN; CESAR-, ROBERTO M., JR.; IEEE. Efficient object recognition using sampling of keypoint triples and keygraph structure. 2016 29TH SIBGRAPI CONFERENCE ON GRAPHICS, PATTERNS AND IMAGES (SIBGRAPI), v. N/A, p. 8-pg., . (14/50769-1, 11/50761-2)
MORIMITSU, HENRIQUE; BLOCH, ISABELLE; CESAR-, ROBERTO M., JR.. Exploring structure for long-term tracking of multiple objects in sports videos. COMPUTER VISION AND IMAGE UNDERSTANDING, v. 159, p. 16-pg., . (14/50135-2, 11/50761-2, 13/08258-7, 12/09741-0)
CONDORI, MARCOS A. T.; CAPPABIANCO, FABIO A. M.; FALCAO, ALEXANDRE X.; MIRANDA, PAULO A., V. An extension of the differential image foresting transform and its application to superpixel generation. JOURNAL OF VISUAL COMMUNICATION AND IMAGE REPRESENTATION, v. 71, p. 15-pg., . (16/21591-5, 14/12236-1, 11/50761-2, 14/50937-1)
DAZZI, ESTEPHAN; DE CAMPOS, TEOFILO; HILTON, ADRIAN; CESAR JR, ROBERTO M.. Scalable object instance recognition based on keygraph matching. PATTERN RECOGNITION LETTERS, v. 114, p. 10-pg., . (14/50769-1, 11/50761-2, 15/22308-2)
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, p. 9-pg., . (11/50761-2)
CONDORI, MARCOS A. T.; MANSILLA, LUCY A. C.; MIRANDA, PAULO A. V.; ANGULO, J; VELASCOFORERO, S; MEYER, F. Bandeirantes: A Graph-Based Approach for Curve Tracing and Boundary Tracking. MATHEMATICAL MORPHOLOGY AND ITS APPLICATIONS TO SIGNAL AND IMAGE PROCESSING (ISMM 2017), v. 10225, p. 12-pg., . (14/12236-1, 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, v. N/A, p. 18-pg., . (17/09280-7, 15/18942-8, 15/08003-4, 11/50761-2, 15/22308-2)
COMIN, CESAR H.; VIANA, MATHEUS P.; HENNING, BARBARA; DOS SANTOS, THAIS M. P.; LOPES, RICARDO T.; DOS REIS, SERGIO F.; COSTA, LUCIANO DA F.; IEEE. CHARACTERIZING THE TRABECULAR BONE TISSUE OF THE TOCO TOUCAN BILL. 2018 25TH IEEE INTERNATIONAL CONFERENCE ON IMAGE PROCESSING (ICIP), v. N/A, p. 5-pg., . (11/50761-2, 15/18942-8, 15/22308-2)
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, v. N/A, p. 21-pg., . (11/50761-2, 13/26416-9)
COMIN, CESAR HENRIQUE; COSTA, LUCIANO DA FONTOURA. Shape, connectedness and dynamics in neuronal networks. JOURNAL OF NEUROSCIENCE METHODS, v. 220, n. 2, p. 16-pg., . (11/50151-0, 11/50761-2, 11/22639-8)
AMANCIO, DIEGO R.; OLIVEIRA, OSVALDO N., JR.; COSTA, L. DA F.. Robustness of community structure to node removal. JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, v. N/A, p. 18-pg., . (13/06717-4, 14/20830-0, 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, p. 10-pg., . (11/50761-2, 13/26416-9, 12/22160-7)
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, p. 16-pg., . (13/26416-9, 12/50986-7, 11/22639-8, 11/50761-2, 11/50761-2, 12/22160-7)
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, p. 22-pg., . (14/21050-9, 11/50761-2)
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, p. 18-pg., . (11/50761-2, 10/52138-8)
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, p. 12-pg., . (13/09922-8, 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, p. 17-pg., . (13/03898-8, 11/50761-2, 13/26416-9)
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, p. 7-pg., . (11/50761-2, 13/26416-9, 12/22160-7)
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, p. 10-pg., . (11/50761-2, 13/26416-9, 12/22160-7)
CERVANTES, EVELYN PEREZ; COMIN, CESAR HENRIQUE; CESAR JUNIOR, ROBERTO MARCONDES; COSTA, LUCIANO DA FONTOURA; IEEE. Data-oriented neuron classification from their parts. PROCEEDINGS OF THE 2016 IEEE 12TH INTERNATIONAL CONFERENCE ON E-SCIENCE (E-SCIENCE), v. N/A, p. 8-pg., . (11/50761-2, 15/18942-8, 15/01587-0)
TAVARES, ANDERSON C. M.; BEJAR, HANS H. C.; MIRANDA, PAULO A. V.; STYNER, MA; ANGELINI, ED. Seed Robustness of Oriented Relative Fuzzy Connectedness: Core Computation and its Applications. MEDICAL IMAGING 2017: IMAGE PROCESSING, v. 10133, p. 10-pg., . (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, . (14/50769-1, 15/22308-2, 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, . (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, . (14/20830-0, 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, . (11/50761-2, 15/22308-2)
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, . (11/50761-2, 15/22308-2, 15/18942-8)
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, . (17/13464-6, 15/22308-2, 16/19069-9, 11/50761-2, 15/05676-8)
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, . (13/26416-9, 11/22639-8, 12/22160-7, 12/50986-7, 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, . (13/26416-9, 12/25219-2, 13/03898-8, 11/50761-2, 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, . (11/50761-2, 13/26416-9, 12/17961-0)
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, . (16/19069-9, 11/50761-2, 15/05676-8, 14/20830-0, 15/08003-4)
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, . (14/20830-0, 16/19069-9, 11/50761-2, 15/08003-4)
SILVA, FILIPI N.; COMIN, CESAR H.; COSTA, LUCIANO DA F.. Seeking maximum linearity of transfer functions. Review of Scientific Instruments, v. 87, n. 12, . (15/08003-4, 15/18942-8, 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, . (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, . (12/22160-7, 13/26416-9, 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, . (13/26416-9, 13/03898-8, 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, . (14/20830-0, 16/19069-9, 11/50761-2, 15/08003-4)
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, . (07/50988-1, 11/50761-2, 11/22639-8)
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, . (14/09576-5, 12/25417-9, 11/50761-2, 13/03447-6)
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, . (08/58238-4, 14/50489-9, 05/00587-5, 11/50761-2, 09/53443-1)
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, . (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, . (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, . (17/09280-7, 15/22308-2, 11/50761-2, 15/18942-8, 15/08003-4)
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, . (15/18942-8, 16/19069-9, 14/20830-0, 15/08003-4, 11/50761-2)
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, . (15/18942-8, 11/50761-2, 15/08003-4)
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, . (11/50761-2, 15/18942-8)
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, . (15/18942-8, 15/22308-2, 15/08003-4, 11/50761-2)
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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, . (13/26416-9, 11/22639-8, 12/22160-7, 12/50986-7, 11/50761-2)
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, . (11/50761-2)
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, . (13/07467-1, 08/52074-0, 14/50921-8, 15/22993-7, 12/51062-3, 17/02270-6, 11/50761-2, 16/17545-8, 16/06917-1, 13/23048-9, 08/52146-0)
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, . (15/22308-2, 11/50761-2, 15/50122-0, 13/07375-0, 16/23698-1, 18/24260-5)
CERIBELI, CAROLINE; FERRAZ DE ARRUDA, HENRIQUE; DA FONTOURA COSTA, LUCIANO. How coupled are capillary electrophoresis and mass spectrometry?. SCIENTOMETRICS, . (15/22308-2, 13/07375-0, 11/50761-2, 18/10489-0, 19/16223-5)
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, . (15/18942-8, 11/50761-2, 15/08003-4)
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, . (13/26416-9, 11/50761-2, 12/25219-2)
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, . (16/21047-3, 11/50761-2, 15/16310-4, 15/01587-0)
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, . (15/01587-0, 11/51295-5, 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, . (13/19082-7, 11/50761-2, 15/18942-8)
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, . (11/50761-2, 10/00927-9)
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, . (11/22639-8, 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, . (11/50761-2, 10/15691-0)
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, . (11/22639-8, 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, . (11/50761-2, 10/00927-9)
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, . (11/50761-2)

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