Group Leader. Helder Takashi Imoto Nakaya

Transcription

1 The Laboratory Our main goal is to solve biological problems through the development and use of computational tools and analysis of high-throughput data. Our research is guided by both hypotheses raised by traditional scientific way, as per hypotheses raised by analyzing big data (data-driven research). Both cases involve systems biology, which is the analysis of the behavior and interaction among components of a biological system, seen as a whole and under different perturbations. In our current scientific projects, we have been applying systems biology approaches to study infectious diseases, vaccine-induced immunity and the regulatory role of non-coding RNAs. These projects are multidisciplinary, including the participation of excellent external collaborators which are vital to the generation of hypotheses and data, to providing important insights and knowledge and to performing experimental validations of our findings.

2 Group Leader Helder Takashi Imoto Nakaya Helder Nakaya is an assistant professor at the University of Sao Paulo, Brazil, in the Department of Clinical Analyses and Toxicology, School of Pharmaceutical Science. He has a PhD in Molecular Biology with extensive training in Bioinformatics. He is an expert in Systems Vaccinology, an interdisciplinary field that combines systems-wide measurements, networks, and predictive modeling in the context of vaccines and infectious disease. Dr. Nakaya has developed systems biology approaches to understand and predict the mechanisms of vaccine induced-immunity for Yellow Fever, seasonal Influenza, Meningococcal, and Tularemia vaccines. His lab is focused on investigating the basis of infectious diseases using computational systems biology. hnakaya@usp.br Lattes:

3 Laboratorie s Members

4 POST-DOCTORAL FELLOWS Melissa Lever Melissa Lever will be joining the lab as a post-doc from February 2016 supervised by Dr Helder Nakaya. Her work will include investigating the gene regulatory networks that modulate metabolic changes during an immune response. She completed a PhD in Systems Biology at the William Dunn School of Pathology, University of Oxford, under the supervision of Dr Omer Dushek. She is excited for the new adventure of leaving native England for sunny Sao Paulo and learning some Python and Portuguese. melissalever@gmail.com Lattes: Flavio Lichtenstein Flavio Lichtenstein is pursuing a pos-doc position at the University of Sao Paulo, Brazil, in the Department of Clinical Analyses and Toxicology, School of Pharmaceutical Science and also in Mathematical and Statistical Institute (Sep to Dec/2015). He has a PhD in Bioinformatics, applying Informational Theory to Molecular Evolution. Still learning different techniques in bioinformatics: bio-statistics, next-generation algorithms, system-biology and now network analyses. Known languages: R, Python, MatLab, C, Java and others. Sql expert in Oracle, SqlServer and MySql. flalix@gmail.com Lattes:

5 PHD STUDENTS Thiago Hirata Bioinformatics PhD student at the Clinical Analysis Programme of the Clinical Analysis and Toxicology Department of the Faculty of Pharmaceutical Sciences of the University of São Paulo. In 2011 I got a bachelor s degree in Pharmacy and Biochemistry at the Faculty of Pharmaceutical Sciences of the University of São Paulo. I have experience in Pharmacy, Molecular Biology, Farmacogenomics, gene expression, cell culture and more recently computational systems biology. I joined CSBL in 2014 and currently work with metabolic syndrome, microarray and RNAseq transcriptomics analysis with R and bash programming. thiagodch@gmail.com Lattes: Mindy Muñoz An bioinformatic engineer from University of Talca. She has worked for the last 3 years in Chile with food improvement research at the Catholic University of Chile, Mayor University and INTA at University of Chile. However now she has found her place in CSBL due to the exciting human cancer researches using system biology. mstephania@gmail.com

6 Diógenes Lima Diogenes Lima, Pharmacy BSc, is a PhD student in the Computational Systems Biology Laboratory. After taking Professor Helder Nakaya s classes during undergrad studies, Diógenes realized that a systems approach to biology is a challenging and awesome way to view biological systems. Thus, he approached professor Helder in the beginning of 2015 and has been a CSBL member ever since. Currently, Diógenes is working in a project about the mechanisms associated with vaccine protection. diogenes.lima@usp.br Lattes: César Prada César is PhD student at University of Sao Paulo, Brazil, in the department of Clinical Analysis, School of Pharmaceutical Sciences. After he got his B.Sc in Biology at Universidad Industrial de Santander, Colombia; and attracted by holism, he began pursuing a Systems Biology career. Merging it with his biomedical experience emerged his encounter with Helder and his further adhesion to the Computational Systems Biology Laboratory in June, Now he is interested in understanding complex inflammatory conditions from an integrative perspective. cesar.prada111@gmail.com Lattes:

7 Pedro Russo Pedro Russo currently is PhD student at the University of São Paulo, Brazil, at the Computational Systems Biology Laboratory. He holds a Bachelor s Degree in Biotechnology from the Federal University of São Carlos (UFSCar) and has done internships in the Biotec industry, where he happened upon the exciting world of computer programming and bioinformatics, and hasn t looked back since. Tells awesome jokes (though sometimes his lab mates disagree). pedro.russo@usp.br Lattes: Patrícia Gonzalez Patricia holds a master s degree in Cellular and Molecular Biology from Instituto Oswaldo Cruz (Fiocruz, Brazil). She studied the immune response induced by different adjuvants and its application in the development of a subunit vaccine against leptospirosis. She is crazy about immunology and vaccinology and moved from the wet to the dry side when she met the Systems Vaccinology, impressed by the possibility of evaluating the response to different disorders as a whole. She sees Systems Biology as a great and exciting challenge. She will develop her PhD project in the Computational Systems Biology Laboratory at the University of São Paulo (USP, Brazil) on integrative analyses of immunomic, transcriptomic and metabolomic data using systems biology approaches to decipher the immune and molecular signatures of the human response elicited in adults and children by a highly protective candidate for Ebola vaccine. patrcgd@gmail.com Lattes:

8 MSC STUDENTS Matheus Carvalho Bürger He has a bachelor s degree in Biomedical Informatics from University of São Paulo (2013) and has involved in bioinformatics since In 2015 he has joined the CSBL in order to get his master degree in bioinformatics from USP. In his project he tries to better understand the modifications in gene expression from blood after the Dengue virus infection as well as the role of long non-coding in the host response. matheus.cburger@gmail.com Lattes: Jaqueline Wang Jaqueline Wang is a MSc Student in Bioinformtics at the University of Sao Paulo, Brazil. She joined the CSBL in August of jaqueline.wang@usp.br Lattes:

9 Lucas Esteves Cardozo Lucas Cardozo is a Master s Student at University of Sao Paulo, Brazil, in the Computational Systems Biology Laboratory, School of Pharmaceutical Sciences. Joined the Computational Systems Biology Laboratory in 2014, when he started to learn computational programming. He worked with expression analysis in different kinds of biological contexts, in particular with the attenuated Schistosoma mansoni cercarie vaccine in mice, which was the focus of his Scientific Initiation project. He is interested in apply computational methods together with graph theory in order to understand biological systems response under different conditions. Has experience with R, Python, Perl and a bit with C. lucas.cardozo@usp.br Lattes: Fernando Marcon Fernando Marcon is currently a Master s Student at the University of São Paulo, Brazil at the Computational Systems Biology Laboratory. He holds a Bachelor s Degree in Health Technology from the Federal University of São Paulo (UNIFESP) and he started his bioinformatics career with Molecular Evolution. Currently he s researching the mechanisms of aging, more specifically about the senescence of our immune system. fmarcon13@gmail.com Lattes:

10 UNDERGRADUATE STUDENTS Gustavo R. Ferreira Gustavo is an undergraduate student at the University of Sao Paulo, currently pursuing a bachelor degree in Molecular Sciences. Interested in Systems Biology, he joined the CSBL early on, in April 2014 so early, he actually had to assemble the lab chairs! gustavo.rodrigues.ferreira@usp.br Lattes: Leonardo dos Reis Gama Leonardo Gama is pursuing his Medical Degree at University of São Paulo, after passing some time at (but not concluding) the Molecular Sciences course in the same university. He s interested in the application of bioinformatics and mathematics in the study of the cancer phenomenon. leonardo.reis.gama@gmail.com Lattes:

11 Fábio Baldívia Pohl An undergraduate student in the Institute of Biosciences at University of São Paulo, Brazil. Joined the Computational Systems Biology Laboratory in He has experience in experimental science, such as Microbiology, Cancer Genetics and Epigenetics. Currently is venturing through the obscure world of Bioinformatics. Lattes: