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

Grant number: 11/50761-2
Support type:Research Projects - Thematic Grants
Duration: February 01, 2012 - September 30, 2016
Field of knowledge:Physical Sciences and Mathematics - Computer Science
Cooperation agreement: CNPq - Pronex
Principal Investigator:Roberto Marcondes Cesar Junior
Grantee:Roberto Marcondes Cesar Junior
Home Institution: Instituto de Matemática e Estatística (IME). Universidade de São Paulo (USP). São Paulo , SP, Brazil
Co-Principal Investigators: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
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 Agência FAPESP Newsletter about the research grant
Research furthers understanding of neuron growth regulation 
Study characterize genomic dysregulation in thymus of infants with Down syndrome 
Computer vision systems that can interpret images from street cameras 
The use of bioinformatics in the study of complex diseases 
Brazilian scientists develop a social media simulator  
Search for therapeutic targets leads scientists to map genetic interactions 
"Mother" cells sacrifice themselves for “daughters” 
Articles published in Pesquisa FAPESP Maganize about the research grant:
The Voynich manuscript 
The Voynich manuscript 
Articles published in other midia outlets (2 total):
Resposta imune ajuda a identificar bactéria que causa problema renal 
Resposta imune ajuda a identificar bactéria que causa problema renal 

Scientific publications (93)
(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)
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. Web of Science Citations: 0.
SILVA, FILIPI N.; COMIN, CESAR H.; COSTA, LUCIANO DA F. Malleability of complex networks. JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, AUG 2019. Web of Science Citations: 0.
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. Web of Science Citations: 0.
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. Web of Science Citations: 0.
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. Web of Science Citations: 1.
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. Web of Science Citations: 0.
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. Web of Science Citations: 0.
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. Web of Science Citations: 3.
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. Web of Science Citations: 0.
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. Web of Science Citations: 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. Web of Science Citations: 0.
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. Web of Science Citations: 0.
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. Web of Science Citations: 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. Web of Science Citations: 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. Web of Science Citations: 0.
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. Web of Science Citations: 0.
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. Web of Science Citations: 0.
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. Web of Science Citations: 1.
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. Web of Science Citations: 3.
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. Web of Science Citations: 3.
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. Web of Science Citations: 1.
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. Web of Science Citations: 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. Web of Science Citations: 3.
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. Web of Science Citations: 1.
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. Web of Science Citations: 12.
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; WANG, JING. The aPKC-CBP Pathway Regulates Post-stroke Neurovascular Remodeling and Functional Recovery. STEM CELL REPORTS, v. 9, n. 6, p. 1735-1744, DEC 2017. Web of Science Citations: 8.
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. Web of Science Citations: 1.
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. Web of Science Citations: 0.
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. Web of Science Citations: 6.
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. Web of Science Citations: 3.
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. Web of Science Citations: 5.
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. Web of Science Citations: 4.
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. Web of Science Citations: 9.
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; HOLT, CHRISTINE E.; FRANZE, KRISTIAN. Mechanosensing is critical for axon growth in the developing brain. NATURE NEUROSCIENCE, v. 19, n. 12, p. 1592-1598, DEC 2016. Web of Science Citations: 100.
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. Web of Science Citations: 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, n. 3, p. 303-311, NOV 1 2016. Web of Science Citations: 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. Web of Science Citations: 7.
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. Web of Science Citations: 7.
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. Web of Science Citations: 4.
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. Web of Science Citations: 11.
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. Web of Science Citations: 5.
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. Web of Science Citations: 2.
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. Web of Science Citations: 28.
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. Web of Science Citations: 4.
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. Web of Science Citations: 4.
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. Web of Science Citations: 3.
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. Web of Science Citations: 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. Web of Science Citations: 1.
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. Web of Science Citations: 8.
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. Web of Science Citations: 6.
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. Web of Science Citations: 0.
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. Web of Science Citations: 7.
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. Web of Science Citations: 1.
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. Web of Science Citations: 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. Web of Science Citations: 1.
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. Web of Science Citations: 19.
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. Web of Science Citations: 10.
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. Web of Science Citations: 3.
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. Web of Science Citations: 7.
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. Web of Science Citations: 5.
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. Web of Science Citations: 7.
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. Web of Science Citations: 10.
COMIN, CESAR H.; SILVA, FILIPI N.; COSTA, LUCIANO DA F. A framework for evaluating complex networks measurements. EPL, v. 110, n. 6 JUN 2015. Web of Science Citations: 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. Web of Science Citations: 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, APR 30 2015. Web of Science Citations: 3.
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. Web of Science Citations: 12.
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. Web of Science Citations: 4.
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. Web of Science Citations: 0.
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. Web of Science Citations: 6.
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. Web of Science Citations: 17.
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. Web of Science Citations: 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. Web of Science Citations: 2.
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. Web of Science Citations: 9.
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. Web of Science Citations: 31.
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. Web of Science Citations: 21.
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. Web of Science Citations: 43.
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. Web of Science Citations: 39.
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. Web of Science Citations: 4.
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. Web of Science Citations: 31.
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. Web of Science Citations: 14.
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. Web of Science Citations: 23.
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. Web of Science Citations: 11.
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. Web of Science Citations: 68.
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. Web of Science Citations: 0.
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. Web of Science Citations: 89.
MIRANDA, PAULO A. V.; MANSILLA, LUCY A. C. Oriented Image Foresting Transform Segmentation by Seed Competition. IEEE Transactions on Image Processing, v. 23, n. 1, p. 389-398, JAN 2014. Web of Science Citations: 15.
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. Web of Science Citations: 12.
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. Web of Science Citations: 4.
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. Web of Science Citations: 4.
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. Web of Science Citations: 27.
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. Web of Science Citations: 20.
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. Web of Science Citations: 1.
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. Web of Science Citations: 22.

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