Group Leader:
Mariana Boroni, Ph.D. Mariana Boroni, Ph.D., is an associated researcher at the Brazilian National Cancer Institute (INCA), where she directs the Bioinformatics and Computational Biology Lab and serves as the coordinator of the Computational platform. She has a bachelor's degree in biochemistry and an M.Sc. in biochemistry from Universidade Federal de Viçosa, a Ph.D. in bioinformatics from Universidade Federal de Minas Gerais (visiting student at the NIH - National Institute of Health, Bethesda, US), and did her PostDoc in bioinformatics at the Ludwig Maximilians Universität München, Germany. Her group is interested in data analysis and the development of workflows/tools for the immuno-oncology interface, with a focus on high throughput sequencing approaches such as genomics, epigenomics, and transcriptomics in cellular and spatial resolution.
Lattes curriculum: http://lattes.cnpq.br/2407012834433865
email: mariana.boroni@inca.gov.br
phone: +55 21 3207-6550
Technologist:
Nicole Scherer, PhD. Dr. Nicole Scherer finished undergraduate studies in biological sciences (Universidade Federal do Rio Grande do Sul – UFRGS – Porto Alegre, Brazil), and began a master’s degree in genetics in the same institution with a project in plant evolution to be performed totally in silico. Being the only student working with bioinformatics in the genetics institute at that time, she decided to deepen her knowledge in the field and applied to do a PhD in Germany. During her graduate studies in bioinformatics (Faculty of Mathematics and Natural Sciences - Heinrich Heine University, Düsseldorf), she learned programming in Perl and R, and acquired the necessary skills in GNU/Linux for the use of bioinformatics software. In 2011 she joined LBBC as a technologist in bioinformatics at the Brazilian National Cancer Institute (INCA – Rio de Janeiro). The research center of INCA was planning to start a bioinformatics multi-user platform to serve all research groups of the institute. Since the acquisition of our first cluster, in 2013, she is the manager of the bioinformatics platform, offering technical and scientific support for over 40 users. She is engaged in education and outreach of bioinformatics and is a member of the directory board of the Brazilian Association of Bioinformatics and Computational Biology (AB3C), being on the organizing committee of the X-Meeting, the largest conference for bioinformatics in Brazil.
Lattes curriculum: http://lattes.cnpq.br/3555370764574908
email: nscherer@inca.gov.br
phone: +55 21 3207-6546
Current members:
Postdoctoral researchers:
Caroline P. Poubel, PhD. Postdoctoral fellow at the Brazilian National Cancer Institute (INCA), working in the Molecular Onco-Hematology Group as well as the Bioinformatics and Computational Biology Laboratory. She has a Bachelor's degree in Biomedicine from Fluminense Federal University (UFF), in addition to a Master and Doctorate in Oncology from INCA. She has worked in the field of Molecular Biology, primarily on studies of genetic and epigenetic alterations in the etiology of acute leukemias. She has become an expert in bioinformatics over the last five years, working with omics data using R and Bash programming. Her current research focuses on the role of enhancer RNAs (eRNAs) in gene transcription regulation using ChIP-seq and RNA-seq data.
Lattes curriculum: http://lattes.cnpq.br/6857179921103991
Linkedin: www.linkedin.com/in/caroline-poubel
Cristóvão Antunes de Lanna, PhD. Postdoctoral fellow at the Brazilian National Cancer Institute (INCA), working at LBBC as well as the Molecular Carcinogenesis Program (PCM). Bachelor in Biomedicine at the Rio de Janeiro State Federal University (2013), with a Masters degree in Biological Sciences (Biophysics) at the Carlos Chagas Filho Institute (IBCCF), from the Rio de Janeiro Federal University (2016), and a PhD in Oncology with an emphasis in Data Analysis at INCA (2023). Expertises include clinical analyses applied to laboratory animals, molecular biology, genomics, and transcriptomics. He is currently developing in silico analysis workflows including multi-omics data (genomics, transcriptomics, epigenomics) for the identification of novel therapeutic targets in a variety of tumors and tumor-derived cell lines.
Lattes curriculum: http://lattes.cnpq.br/0341173575404468
Elvismary Molina de Armas, PhD at Computer Science at PUC-Rio (2019). Master in Applied Informatics at the University of Informatics Sciences of Cuba (UCI) and graduated as Engineer in Computer Science from the same university. She is currently linked to the Laboratory of Bioinformatics and Databases (BioBD) at PUC-Rio and is a postdoctoral student at the Laboratory of Bioinformatics and Computational Biology (LBBC) at the National Cancer Institute (INCA). She has experience in software development for bioinformatics and biomedical information management. Her current focus is the development of scientific workflows, specifically for calling genetic variants following the best practices of the state-of-the-art, as well as the development of algorithms and data structures to support bioinformatics tasks such as de novo assembly.
Lattes curriculum: https://lattes.cnpq.br/8882801043033251
Leandro Santos, PhD. Ph.D. and Masters in Biological Sciences (Biophysics) by the Biophysics Institute Carlos Chagas Filho (IBCCF) at the Federal University of Rio de Janeiro (UFRJ). Specialization in Forensic Biology from Castelo Branco University (UCB) / Bioforense and Graduated in Biomedicine from Severino Sombra University (USS / RJ). Post-doctorate by the Virus Molecular Biology Laboratory (IBCCF / UFRJ) and by the Laboratoire de Pharmacologie Cellulaire (IBMM - Montpellier / France). He has experience in omics data analysis using bioinformatics tools, phylogeny, comparative genomics, as well as modeling and molecular dynamics. Experience also in techniques of genetic manipulation of microorganisms, molecular biology and biochemistry, especially Sanger and NGS sequencing. Currently, postdoctoral fellow at the Laboratory of Bioinformatics and Computational Biology (LBBC) of the National Cancer Institute (INCA) where he has been developing a project to characterize and determine the function of different subpopulations of macrophages in relation to pro-inflammatory diseases, especially cancer. This project uses public single-cell sequencing (scRNA-seq) data in order to create an atlas of macrophages associated with solid tumors.
Lattes curriculum: http://lattes.cnpq.br/5119748444791109
Nayara Toledo, PhD. Ph.D. and Masters in Bioinformatics at the Universidade Federal de Minas Gerais (UFMG). Biologist graduated from the UFMG (Bachelor with emphasis in biotechnology and health). She has experience in Molecular Biology and transcriptomic analysis, with emphasis on alternative splicing. Currently, postdoctoral fellow at the Laboratory of Bioinformatics and Computational Biology (LBBC) of the National Cancer Institute (INCA), working mainly to investigate the mechanism underlying the ZNF429-mediated regulation in ovarian tumors, their targets and how this regulation affects the pathways involved in tumor biology and progression.
Lattes curriculum: http://lattes.cnpq.br/5054763686499204
Nayara Tessarollo, PhD. PhD in Biotechnology from the Federal University of Espírito Santo (2017) (sandwich period at Johns Hopkins University, Baltimore, USA). Master in Health Sciences with emphasis in Cellular and Molecular Biology from the René Rachou Research Center-FIOCRUZ/MG (2013). Bachelor in Biochemistry from the Federal University of Viçosa (2010). Post-doctorate in Oncology from the Cancer Institute of the State of São Paulo (ICESP). Currently, she is a postdoctoral student at the Laboratory of Bioinformatics and Computational Biology (LBBC) of the National Cancer Institute (INCA), developing the project high resolution characterization of the transcriptome of subpopulations of the tumor microenvironment of ovarian cancer and its impact on clinical outcome and therapy resistance. She has experience in the field of gene therapy, biochemistry, molecular and cell biology, immunology.
Lattes curriculum: http://lattes.cnpq.br/8607496356516938
Alessandra Serain PhD. PhD in Sciences from the Universidade Estadual de Campinas (2020) (internship period at the Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy). Bachelor in Pharmacy from the Universidade Estadual de Campinas (2014). Postdoctoral degree in Biochemistry and Bioluminescent Technologies from the Universidade Federal de São Carlos (Ufscar). She has experience in chemistry of natural products, studies of bioprospecting with culture of tumor cells, development of analytical methods for quantification of chemotherapy in plasma and solid tumor samples using mass spectrometry, application of bioluminescence in new technological systems of biosensors. She is currently a Postdoctoral student at the Laboratory of Bioinformatics and Computational Biology (LBBC) of the Instituto Nacional do Câncer (INCA), developing a research project with ovarian tumor and resistance to therapies through knowledge of subpopulations of the tumor microenvironment and analysis of snRNA-Seq and spatial transcriptomics .
Lattes curriculum: http://lattes.cnpq.br/0430250077903286
PhD. Students:
Masters Students:
Gabriela Rapozo Guimarães. Graduated in Biomedicine with emphasis in Clinical Analysis at the Federal Fluminense University (UFF), where she acquired experience in virology and HPV during three years of Scientific Initiation in the Laboratory of Virological Diagnosis of UFF. She was a student at the Laboratory of Bionformatics and Computational Biology (LBBC), where she is currently a Master's student under the supervision of Mariana Boroni and co-supervision of Marcelo Mori (UNICAMP). The project aims to correlate the clinical impact of macrophage aging in triple negative breast cancer through spatial and single cell transcriptomics.
Lattes curriculum: http://lattes.cnpq.br/4915949596150748
Under Improvement Student I:
Gabriel Fonseca, BSc. Bachelor in Biological Sciences from Universidade Federal Fluminense (UFF), with an emphasis on health and oncology. He was a Scientific Initiation (CI) student at the UFF Neurobiology laboratories studying the structure and function of endocannabinoid receptors and their modulation by their endogenous and exogenous neurotransmitters and was also a CI student at the Laboratory of Bioinformatics and Computational Biology (LBBC-INCA/RJ) , where he is currently an improvement student I participating in a project whose objective is to investigate the role of the transcription factor ZNF429 in the regulation of cellular pathways in pancreatic cancer.
Lattes curriculum: http://lattes.cnpq.br/2132058819644177
Linkedin: Gabriel (Gabriel Fonseca) Fernando Costa Da Fonseca | LinkedIn
Glenerson Batista. Bachelor in Biological Sciences, with emphasis on Cellular Biology and Health, from Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF). Conducted Scientific Initiation with a FAPERJ/UENF grant from 2018-2022 at the Laboratory of Cellular and Tissue Biology, aiming to identify patterns of expression and activity of Ionic Pumps in human tumors associated with HPV infections, evaluating the potential of such pumps as biomarkers, through approaches with cell line assays, immunofluorescence and bioinformatics. He is currently a student of Improvement I at the Laboratory of Bioinformatics and Computational Biology at the National Cancer Institute - INCA / RJ, aiming to understand the mechanism of gene regulation by the transcription factor ZNF429 in ovarian tumor pathways.
Lattes curriculum: https://lattes.cnpq.br/1257237863199012
Under Improvement Student II:
Cristiane Esteves Teixeira. Biologist, graduated from the Federal University of the State of Rio de Janeiro (UNIRIO). I have experience in genomic assembly and analysis. She has an advanced degree in bioinformatics from the Bioinformatics and Computational Biology Laboratory of the National Cancer Institute (LBBC-INCA/RJ), and a master's degree in Oncology with an emphasis on Data Analysis (LBBC-INCA/RJ). He is now working on improvement II in collaboration with the Big Data and Predictive Analysis Laboratory at the University of São Paulo (LABDAPS - USP). Her master's project involves predicting prognosis and identifying biomarkers in ovarian tumors using machine learning techniques based on multi-omics data (RNA-seq, miRNA-seq, mutations and epigenetics).
Lattes curriculum: http://lattes.cnpq.br/4723769716945310
Jéssica Gonçalves Vieira da Cruz, MSc. Improvement Student II at the Laboratory of Bioinformatics and Computational Biology at the National Cancer Institute. Graduation in Biomedicine with emphasis in Scientific Research from the Fluminense Federal University (UFF - Brazil) with a sandwich period at the University of Hull, United Kingdom. Has laboratory experience in general and applied microbiology, use of the PCR technique (polymerase chain reaction), Western Blotting, Ca ++ uptake assays, bacterial transformation and transfection of cells in culture for expression of mutated proteins. He did Improvement I and Master in our laboratory, aggregating omics (RNA-seq, ChIP-seq, methylation, proteomics) and clinical data in order to understand how the function of ZNF429 and the regulation of its potential targets impacts the survival of patients with adenocarcinoma high-grade serous ovary.
Lattes curriculum: http://lattes.cnpq.br/7271057089770480
Scientific Initiation Student:
Andressa Fagundes. Undergraduate student in Biophysics with emphasis in Bioinformatics and Molecular Biophysics at the Federal University of Rio de Janeiro (UFRJ). Currently at LBBC, she is learning experimental benchtop and bioinformatics methods for her project on the role of macrophages and their differentially expressed genes in the evolution of ovarian cancer, arising from the work of the scRNA-seq group.
Lattes curriculum: http://lattes.cnpq.br/6083058381657677
Linkedin: https://www.linkedin.com/in/andressa-fagundes-6592b7141/
Lucas Aleixo Leal. Underdegree student in Biomedicine from the Federal University of Pernambuco (UFPE), where he developed research using C.elegans as an experimental model for toxicological studies and worked with structural bioinformatics to prospect new drugs aimed at the therapy of neurodegenerative diseases. He is currently a scientific initiation student at LBBC and conducts studies using single-cell data in order to elucidate the role of tumour-associated macrophages in the clinical outcome of patients with melanoma.
Lattes curriculum: http://lattes.cnpq.br/1045077074450512
Linkedin: https://www.linkedin.com/in/lucas-aleixo-b1a3141b4/
Email: lucas.aleixoleal17@gmail.com
Pedro Videira. Underdegree student in biology with emphasis in biotechnology from the State University of Rio de Janeiro (UERJ). Currently at LBBC learning about spatial transcriptomics technology for his project under the guidance of Dr. Mariana Boroni and co-supervision of Cristóvão Antunes de Lanna on the spatial context of macrophage interactions with immune cells. With this, verify changes between data from different staging and resistance to therapies.
Lattes curriculum: http://lattes.cnpq.br/6424380990004157
Email: pedrovp161@gmail.com
Layse Gomes. Undergraduate student in Biological Sciences at Universidade Federal Fluminense with emphasis on health. During her graduation she has been part of extension projects and scientific initiations involving structural biology. She is currently a scientific initiation student at LBBC and has been developing her skills in bioinformatics tools for analysis with scRNA-seq (single-cell RNA-seq) data and studies the diversity of phenotypes of resident tissue macrophages (RTMs) through the association of gene expression patterns of coding genes and lncRNAs under the orientation of Dr. Leandro Santos and co-supervision of Dr. Mariana Boroni.
Email: laysegomes1600@gmail.com
Alumni:
Marco Antônio Pretti, MSc. Technician in biotechnology from the Federal Institute of Rio de Janeiro (IFRJ - Brazil) and graduated in Pharmacy from the Federal University of Rio de Janeiro (UFRJ - Brazil) with a sandwich degree at the Université de Bordeaux, France. He has experience in molecular biology, cell culture, gene therapy and cell transfection and transduction system. Developed an in silico immunological analysis on next-generation sequencing data as part of her master's project at the National Cancer Institute (INCA - Brazil). He spent one year doing a sandwich doctorate in France collaborating with the Gustave Roussy Institute and the Curie Institute in the framework of his PhD project and during this period he described the cross-reactivities of T lymphocytes using the electrostatic charge of the HLA molecule that interacts with CD8 T lymphocytes, and thus defended his PhD thesis entitled "Evaluation of the patential cross-reactivity of T cell receptors to tumor epitopes".
Lattes curriculum: http://lattes.cnpq.br/3857079614636425
Giovanna R. Maklouf. Biotechnology graduate from the Federal University of Amazonas (UFAM). As her master's project, developed the characterization of the ovarian cancer tumor microenvironment, integrating single-cell and bulk transcriptomics to investigate the impact of different subpopulations on patient outcomes. At present, is a PhD student at the Laboratory of Genomics and bioEnergy (LGE) at the State University of Campinas (Unicamp), where she works with high-throughput prospection of industrial phenotypes in collections of yeast isolates and engineering of strains of bioenergy interest. The prospection includes analysis of a variety of data (genomics, transcriptomics, QTL), part of these skills due to the knowledge acquired during the M.Sc. at LBBC.
Lattes curriculum: http://lattes.cnpq.br/9038517267899194
Brena Duraes Rangel dos Santos. Undergraduate Biomedicine student at the Brazilian Institute of Rehabilitation Medicine, she was a Scientific Initiation student at the LBBC-INCA.
Natasha Andressa Nogueira Jorge, PhD. Postdoc at LBBC-INCA. She has a PhD and a Master's degree in Systems and Computational Biology from the Oswaldo Cruz Foundation (FIOCRUZ-RJ) and a bachelor's degree in Biomedicine from the Rio de Janeiro State Federal University. In the last three years, she was in a 9-month internship at Cambridge University, working with microRNA RNA-Seq in a variety of blood cell types, has published two papers and co-supervised a Scientific Initiation student. Her main research areas are: noncoding RNAs, high-throughput sequencing, bioinformatics, riboswitches and transcriptomics.
Lattes curriculum: http://lattes.cnpq.br/2674218363518596
NatDaniel Andrade Moreira, PhD. He holds a degree in Biological Sciences from the Federal University of Rio Grande do Norte (2008), a Master's degree in Science (Biophysics) from the Federal University of Rio de Janeiro (2012) and a Ph. Oswaldo Cruz - FIOCRUZ. He has practice with various molecular biology techniques. He has experience in genetics, molecular biology, transcriptomics, genomics, bioinformatics and programming (R, Perl and Shell script). He has worked on assembly and annotation projects for transcriptomes and mitochondrial genomes, with emphasis on evolution and molecular systematics (phylogenetic analyses). He was a postdoctoral fellow at the Laboratory of Bioinformatics and Computational Biology (National Cancer Institute), working on analyzing data from high-performance sequencers in order to comprehensively characterize the molecular events in various tumor types. He is currently working on the Bioinformatics Platform (RPT04A), part of the Fiocruz Technological Platforms Network.
Lattes curriculum: http://lattes.cnpq.br/5022535003622760
Guilherme Duarte de Moraes. Technician in Programming by the ORT technology institute and graduating in Biological Sciences Bachelor's degree with an emphasis on ecology at Veiga de Almeida University (UVA). He is currently doing an intership at the Laboratory of Bioinformatics and Computational Biology of the Brazilian National Cancer Institute, developing machine learning techniques to identify lncRNAs with the potential to be prognostic biomarkers in metastatic melanoma.
Lattes curriculum: http://lattes.cnpq.br/7180272245037507
Palloma Porto Almeida, MSc. Bachelor in Biotechnology from the Federal University of Bahia (UFBA) and a Master's degree in Cellular and Structural Biology from the Federal University of Viçosa (UFV). She has experience in theoretical and experimental cell biology, bioterism and animal bioethics, flow cytometry, histopathology, purification of native and recombinant proteins, and scientific communication. Currently develops postgraduate research at the National Cancer Institute at the Laboratory of Bioinformatics and Computational Biology, working with analysis of single-cell RNA-sequencing data to identify subpopulations of macrophages in the melanoma tumor microenvironment and the association of these subpopulations with progressive disease, response to therapy and prognosis.
Lattes curriculum: http://lattes.cnpq.br/7725181602733235
External collaborators:
Romulo Galvani, PhD. Biomedical from the Federal University of Rio de Janeiro. He holds a Master's Degree in Cancer Care (INCA-RJ) and a PhD in Immunology (UFRJ). He did Postdoctoral work in a project on Oral Tolerance mediated by B Lymphocytes at the Thymus Research Laboratory at Fiocruz. He has experience in Bioinformatics and is a collaborator of the Laboratory of Bioinformatics and Computational Biology at INCA-RJ. He went on a mission for 3 months at the Karolinska Institute where he worked in the Laboratory of researcher Lisa Westerberg with Bioinformatics and Immunology.
Lattes curriculum: http://lattes.cnpq.br/4019471385460431