Vinicius Maracaja-Coutinho

Assistant Professor, Head of the Laboratory of Integrative Bioinformatics (LIB), Bioinformatics Core, Centro de Genómica y Bioinformatica, Universidad Mayor (Mar 2013-Present) - Santiago, Chile

CEO & Founder, Beagle Bioinformatics (Apr 2012-Present) - Santiago, Chile

Researcher, Instituto Vandique (Jan 2008-Present) - João Pessoa, Brazil

Contact

  • E-mail: viniciusmaracaja AT integrativebioinformatics DOT me / maracaja.coutinho AT gmail DOT com
  • Twitter: http://www.twitter.com/vin_maracaja/

Degrees & Positions

  • Expert Mission to Universidad Distrital Francisco José de Caldas, Bogota, Colombia
International Atomic Energy Agency (IAEA), United Nations (UN) - Mar 2016
  • Visiting Researcher
Universidade Federal da Paraíba - UFPB, Joao Pessoa, PB, Brazil -  Nov 2014 ↔ Jan 2014
Fellowship: Becas Santander para Jóvenes Profesores e Investigadores, Santander Universidades
  • Head of the Bioinformatics Core, Facultad de Ciencias, Universidad Mayor
Universidad Mayor, Santiago, Chile -  Mar 2013 ↔ Jan 2015
  • Participant as Entrepreneur at the Start-Up Chile Program

Start-Up Chile Round 9th, Santiago, Chile - Feb 2014 ↔ Nov 2014

  • Participant as Entrepreneur at the Start-Up Chile Program

Start-Up Chile Round 4th, Santiago, Chile - Aug 2012 ↔ Mar 2013 

  • PhD in Bioinformatics

Universidade de São Paulo - USP, Sao Paulo, SP, Brazil - Aug 2007 ↔ Aug 2013 
Thesis: In silico characterization and expression analysis of long non-coding RNAs in Eukaryotes.
Supervisors: Sergio Verjovski-Almeida & João C. Setubal
Fellowship: Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) & Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) 

  • B.Sc. in Biological Sciences

Universidade Federal da Paraíba - UFPB, Joao Pessoa, PB, Brazil -  Oct 2002 ↔ Dec 2006
Monograph: Degenerate primers design targeting NHX1 Antiporter gene in Sorghum bicolor (L.) Moench
Supervisor: Rómulo M. Llamoca-Zárate
 
Fellowship: Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)


Publications

The symbol "$" represents the papers in which I am corresponding author.

[19] Amaral, PP; Leonardi, T; Han, N; Vire, E; Gascoigne, DK; Arias-Carrasco, R;  Buscher, M;  Zhang, A; Pluchino, S; Maracaja-Coutinho, VNakaya, HI; Hemberg, M;  Shiekhattar, R; Enright, AJ; Kouzarides, T. Genomic positional conservation identifies topological anchor point (tap)RNAs linked to developmental loci. bioaRxive, 2016.

[18] Aguiar, RR; Ambrosio, LA; Sepúlveda-Hermosilla, G;  Maracaja-Coutinho, V; Paschoal, ARmiRQuest: Integrating tools in a web server for microRNA investigationGenetics and Molecular Research, 2016.

[17] Vachelard, J; Gambarra-Soares, T; Augustini, G; Riul, P; Maracaja-Coutinho, V. A guide to scientific crowdfundingPLOS Biology,  2016$

[16] De Brito, DM; Maracaja-Coutinho, V;  De Farias, ST; Batista, LV; Do Rêgo, TG. A novel method to predict genomic islands based on mean shift algorithmPLOS One, 2016. 

[15] Segovia, C; Vásquez, J; Maracaja-Coutinho, V;  Robeson, J; Santander, J. Complete genome sequence of the Salmonella enterica serovar enteritidis bacteriophage f18αSE isolated in ChileGenome Announcements, 2015. 

[14] Aguiar, RR; Ambrosio, LA; Sepúlveda-Hermosilla, G; Maracaja-Coutinho, V; Paschoal, AR. Avaliação de Desempenho em Bioinformática: Estudo de caso de sistemas computacionais para a investigação de microRNAs. 14º WPerformance - XIV Workshop em Desempenho de Sistemas Computacionais e de Comunicação, Recife, Brazil, 2015. [Extended Abstract]

[13] Villacreses, J; Rojas-Herrera, M; Sánchez, C; Hewstone, N; Undurraga, SF; Alzate, JF; Manque, P;  Maracaja-Coutinho, V $; Polanco, V $Deep sequencing reveals the complete genome and evidence for transcriptional activity of the first virus like sequences identified in Aristotelia chilensis (Maqui Berry)Viruses, 2015$

[12] Yañez, AJ; Molina, C; Haro, RE; Mendoza, J; Rojas-Herrera, M; Trombert, A; Silva, AX; Cárcamo, JG; Figueroa, J; Polanco, V; Manque, P;  Maracaja-Coutinho, V; Olavarría, VH. Draft genome sequence of the virulent strain AUSTRAL-005 of Piscirickettsia salmonis, the etiological agent of piscirickettsiosis (SPS). Genome Announcements, 2014. 

[11]  Olmos, A; Henríquez-Piskulich, P; Sánchez, C; Rojas-Herrera, M; Moreno, M; Gómez, M; Da Silva, RR; Maracaja-Coutinho, V; Aldea, P; Trombert, A. Draft genome sequence of Lactobacillus kunkeei strain MP2 isolated from Chilean Apis mellifera gutGenome Announcements, 2014.

[10] Fachel, AA; Tahira, AC; Vilella-Arias, SA;  Maracaja-Coutinho, V; Gimba, ERP; Vignal, GM; Campos, FS; Reis, EM; Verjovski-Almeida, S. Expression analysis and in silico characterization of intronic long noncoding RNAs in renal cell carcinoma: emerging functional associations. Molecular Cancer, 2013

[9] *Paschoal, AR; *Maracaja-Coutinho, V; Setubal, JC; Simões, ZLP; Verjovski-Almeida, S; Durham, AM. Non-coding transcription characterization and annotation: a guide and web resource for non-coding RNA databases. RNA Biology, 2012.
* Both authors contributed equally to this work.

[8] Tahira, AC; Kubrusly, MS; Faria, MF; Dazzani, B; Fonseca, RS; Maracaja-Coutinho, V; Verjovski-Almeida, S; Machado, MCC; Reis, EM. Long intronic RNAs are differentially expressed in primary and metastatic pancreatic cancer. Molecular Cancer, 2011

[7] Oliveira, KC; Carvalho, MLP; Maracaja-Coutinho, V; Kitajima, JP; Verjovski-Almeida, S. Non-coding RNAs in Schistosomes: an unexplored world. An. Acad. Bras. Ciênc., 2011.

[6] Queiroz, ATL; Maracaja-Coutinho, V; Jardim, ACG; Rahal, P; Matioli, SR; Mello, IMVGC. Relation of pretreatment sequence diversity in NS5A region of Hepatitis C virus gen 1 with immune response between peg-INF/rib therapy
outcomes. Journal of Viral Hepatitis, 2011.

[5] Dias, AM; Queiroz, ATL;
Maracaja-Coutinho, V. Schizophrenia, brain disease and meta-analyses: integrating the pieces and testing Fusar-Poli's hypothesis. Medical Hypotheses, 2010.

[4] Dias, AM; Maracaja-Coutinho, V; Queiroz, ATL. The role of Neuregulin 1 in schizophrenia: a bioinformatics approach. Nature Precedings, 2009.


[3] Padilha, IQM; Durbano, JP; Martins, AB;
Almeida, RS; Maracaja-Coutinho, V; Araujo, DAM. A Bioinformática como instrumento de inserção digital e de inclusão de Biotecnologia.  Revista Extensão Cidadã, 2008.

[2] Araujo, DAM; Maracaja-Coutinho, V; Rego, TG.; Padilha, IQM. Genômica e Bioinformática: importância e perspectivas para o Nordeste. Ciência & Cotidiano, 2005.

[1] Costa, DA; Ribeiro, ILAC; Amaral CMM. Llamoca-Zarate, RM; Maracaja-Coutinho, V.
Regeneração in vitro de brotos através do ápice caulinar do sorgo (Sorghum bicolor (L.) Moench). XII Congresso Latino Americano de Fisiologia Vegetal & X Congresso Brasileiro de Fisiologia Vegetal, 2005. [Extended Abstract]

Grants


Advisor (PhD, MSc, BSc)

  • Raúl Arias Carrasco, PhD Program on Integrative Genomics, Universidad Mayor (Chile) - Advisor.
  • Victor Aliaga Tobar, PhD Program on Integrative Genomics, Universidad Mayor (Chile) - Advisor.
  • Cristopher Segovia, PhD Program on Integrative Genomics, Universidad Mayor (Chile) - Co-Advisor.
  • Mónica Kurte, PhD Program on Biomedical Sciences, Universidad de Los Andes (Chile) - Co-Advisor.
  • Angelica Cardoso Carlos, MSc Program on Cellular and Molecular Biology, Universidade Federal da Paraíba (Brazil) - Co-Advisor.
  • Felipe Guimarães Torres, MSc Program on Applied Computing, Universidade Estadual de Feira de Santana (Brasil) - Co-Advisor.
  • Guillermo A. Nourdin Galindo, BSc Program on Bioinformatics Engineering, Universidad de Talca (Chile) - Co-Advisor.
  • Javier Villacreses, BSc Program on Biotechnology, Universidad Mayor (Chile) - Co-Advisor.


Reviewer/Editorial Board of Journals


Reviewer of Meetings


Abstracts in Meetings

[55] Nourdin-Galindo, G., Molina, C., Maracaja-Coutinho, V., Yañez, A. C. Análisis comparativo entre cepas aisladas de Piscirickettsia salmonis, 2º Congreso de Bioinformática, Talca, Chile, 2016

[54] Russo, P. S. T., Ferreira, G. R., Medina, C. A. P., Bürger, M. C., Cardozo, L.E., Fonseca, L. S., Hirata, T. D. C., Sepúlveda-Hermosilla, G., Maracaja-Coutinho, V., Nakaya, H. I. CEMiTool: Co-expression Modules Identification Tool. X-Meeting 2016: Annual Meeting from the Brazilian Association forBioinformatics and Computational Biology, Belo Horizonte, Brazil, 2016.

[53] Ramos, T. A. R., De Brito, D. M., Arias-Carrasco, R., Batista, L. V.Gaudencio, T., Maracaja-Coutinho, V. Distinguishing coding and non-coding RNA sequences and improving its functional annotation using machine learning approaches. X-Meeting 2016: Annual Meeting from the Brazilian Association forBioinformatics and Computational Biology, Belo Horizonte, Brazil, 2016.

[52] Castro, F. L., Arias-Carrasco, R., Vásquez-Morán, Y., De Queiroz, A. L.,Nakaya, H. I., Santana, R., Maracaja-Coutinho, V. Impact of genomicRNA structure and non-coding RNAs in Zika virus neuropathogenesis. X-Meeting 2016: Annual Meeting from the Brazilian Association forBioinformatics and Computational Biology, Belo Horizonte, Brazil, 2016.

[51] Lopéz-Quilodrán, N., Caris, C., Slater, A., Muñoz, F., Arias-Carrasco, R.,Maracaja-Coutinho, V., Tevy, F. Mining the aging transcriptome of Drosophila melanogasterChilean Society for Cell Biology XXX Annual Meeting, Puerto Varas, Chile, 2016.

[50] Aliaga-Tobar, V., Arias-Carrasco, R., Tripp, V., Orell, A. Maracaja-Coutinho,V. Landscape of non-coding RNAs in Archaea: diversity,conservation and functional characterization. ISCB Latin America Bioinformatics Conference, Buenos Aires, Argentina, 2016.

[49] Arias-Carrasco, R., Vásquez-Morán, Y., Castro, F. L., De Queiroz, A. L.,Nakaya, H. I., Santana, R., Maracaja-Coutinho, VStructRNAfinder: Predicting RNA families from 3’UTR regions of Zika and related viruses through an automated tool. ISCB Latin America Bioinformatics Conference, Buenos Aires, Argentina, 2016.

[48] Leonardi, T., Amaral, P. P., Han, N., Vire, E., Gascoigne, D. K., Arias-Carrasco, R., Buscher, M., Zhang, A., Pluchino, S., Maracaja-Coutinho, V., Nakaya, H. I., Hemberg, M., Shiekhattar, R., Enright, A. J., Kouzarides, T. Positional conservation identifies topological anchor point(tap)RNAs linked to developmental loci. Quantitative Genomics 2016, London, United Kingdom, 2016.

[47] Villacreses, J; Rojas-Herrera, M; Sánchez, C.; Martinez, C.; Pastor, G.; Hewstone, N; Bastos, A.; Undurraga, SF; Alzate, JF; Manque, PMaracaja-Coutinho, V; Polanco, V. Aristotelia chilensis: el proyecto genoma de una planta nativa chilena. COPE-UC Big Data ConferenceSantiago, Chile, 2015.

[46] Lins, PRB; Souto, MBatista, LV;  Rêgo, TG; Maracaja-Coutinho, V. Predicting Piwi-interacting RNAs by deep learning. X-Meeting 2015 - 8th International Conference of the AB³C (Brazilian Association for Bioinformatics and Computational Biology)Sao Paulo, Brazil, 2015.

[45] Brito, DM; Ramos, TAR; Maracaja-Coutinho, V; Farias, ST;  Batista, LV;  Rêgo, TG. Using the Mean Shift clustering algorithm to predict Genomic Islands in bacteria. X-Meeting 2015 - 8th International Conference of the AB³C (Brazilian Association for Bioinformatics and Computational Biology)Sao Paulo, Brazil, 2015.

[44] Ramos, TAR; Brito, DM; Batista, LV;  Rêgo, TG; Maracaja-Coutinho, V. Predicting non-coding RNA families based on primary sequences and secondary structures analysis using machine learning. X-Meeting 2015 - 8th International Conference of the AB³C (Brazilian Association for Bioinformatics and Computational Biology)Sao Paulo, Brazil, 2015.

[43] Lins, PRB; Machado, KCT; Oliveira, HN; Maracaja-Coutinho, V; Batista, LV;  Rêgo, TG. Detecting bacterial genomic islands using PPM. X-Meeting 2015 - 8th International Conference of the AB³C (Brazilian Association for Bioinformatics and Computational Biology)Sao Paulo, Brazil, 2015.

[42] Machado, K; Ramos, TAR;  Sarmento, R;  Maia, D; Maracaja-Coutinho, V; Rêgo, TG. Bacteria temperature lifestyle classification using machine learning. X-Meeting 2015 - 8th International Conference of the AB³C (Brazilian Association for Bioinformatics and Computational Biology)Sao Paulo, Brazil, 2015.

[41] Verdugo, L; Palominos, F; Sanchez, C; Vásquez-Morán, Y; Maracaja-Coutinho, V; Chavez, F; Calixto, A.  Small RNAs and RNAi machinery mediate transgenerational dauer formation in response to bacterial pathogens in C. elegans. C. elegans 2015 - 20th International MeetingLos Angeles, CA, United States, 2015.

[40] Aliaga-Tobar, V; Arias, R; Albers, S-V; Randau, L; Maracaja-Coutinho, V*; Orell, A*Non-coding RNA repertoire of the archaeal biofilm lifestyle. Gordon Research Conference - Archaea: Ecology, Metabolism & Molecular BiologyNewry, ME, United States, 2015.

[39] Segovia, C; Maracaja-Coutinho, V; Santander, J. Differential expression of non-coding RNAs of Piscirickettsia salmonis in limitation iron conditions). SOMICH - XXXVI Congreso Chileno de MicrobiologíaLa Serena, Chile, 2015.

[38] Haro, RE; Sánchez , P; Oliver, C; Sandoval, R; Valenzuela, K; Molina, C; Isla, A; Rojas-Herrera, M; Manque, P; Maracaja-Coutinho, V; Olavarría, V; Cárcamo, JG; Figueroa , J; Yáñez, AJ. Genomic analysis of a highly virulent strain of Piscirickettsia salmonis isolated from Rainbow Trout (Oncorhynchus mykiss). SOMICH - XXXVI Congreso Chileno de MicrobiologíaLa Serena, Chile, 2015.

[37] Aguiar, RR; Ambrosio, LA; Sepúlveda-Hermosilla, G; Maracaja-Coutinho, V; Paschoal, AR. Avaliação de Desempenho em Bioinformática: Estudo de caso de sistemas computacionais para a investigação de microRNAs. 14º WPerformance - XIV Workshop em Desempenho de Sistemas Computacionais e de Comunicação, Recife, Brazil, 2015.

[36] Borges, PV; Paschoal, AR; Maracaja-Coutinho, V; Setubal JC; Simões ZLP; Verjovski-Almeida, S. Durham AMNRDR 2.0: new database, novel knowledge. ISCB Latin America, Belo Horizonte, Brazil, 2014.

[35] Muñoz, MS; Villacreses, J; Rojas-Herrera, M; Ramírez, I; Manque, P; Maracaja-Coutinho, V*; Polanco, V*Draft genome sequence of the antioxidant-rich plant Maqui Berry (Aristotelia chilensis). ISCB Latin America, Belo Horizonte, Brazil, 2014.

[34] Arias-Carrasco, R; Maracaja-Coutinho, VCGIIS: an automated tool to close gaps inter and intra scaffolds. ISCB Latin American Student Council Symposium, Belo Horizonte, Brazil, 2014.

[33] Segovia, C; Maracaja-Coutinho, V*; Santander, J*Aeromonas salmonicida transcriptomics hunting for loss of virulence mediated by culture temperature. ISCB Latin American Student Council Symposium, Belo Horizonte, Brazil, 2014.

[32] Aliaga-Tobar, V; Maracaja-Coutinho, V*; Orell, A*In silico identification of non-coding RNAs in the Crenarchea Sulfolobus acidocaldarius genome: an RNA secondary structure-based approach. ISCB Latin American Student Council Symposium,Belo Horizonte, Brazil, 2014.

[31] Aliaga-Tobar, V; Arias-Carrasco, R; Maracaja-Coutinho, V*; Orell, A*Non-coding RNAs footprinting of the Thermoacidophilic Crenarchaea Sulfolobus acidocaldarius biofilm lifestyleXXXV Chilean Congress of Microbiology, La Serena, Chile, 2014.

[30] Sepúlveda-Hermosilla, G; Rojas, G; Ferreira, GR; Gonçalves, CE; Maracaja-Coutinho, V*; Nakaya, HI*Crowdnotation: a crowdsourcing annotation game for genomics studies. 1er Congreso en Ingeniaría Bioinformática, Talca, Chile, 2014.

[29] Arias-Carrasco, R; Maracaja-Coutinho, V. CGIIS: an automated tool to Close Gaps Inter and Intra Scaffolds. 1er Congreso en Ingeniaría BioinformáticaTalca, Chile, 2014.

[28] Vásquez-Morán, Y; Arias-Carrasco, R; Manque, P; Maracaja-Coutinho, V. structRNAfinder: an automated toolkit for de novo annotation of non-coding RNAs through secondary structure inference. 1er Congreso en Ingeniaría BioinformáticaTalca, Chile, 2014.

[27] Alamarza, O; Segovia, C; Maracaja-Coutinho, V; Sanchez C; Santander, J. Response of Piscirickettsia salmonis to iron limited conditions. 7th International Symposium on Aquatic Animal Health, Portland, OR, United States, 2014.

[26] Yañez, AC; Molina, C; Raro, RE; Rojas-Herrera, M; Figueroa, J; Manque, P; Maracaja-Coutinho, V; Olavarría, VH; Avendaño, R; Cárcamo, JG. Análisis genómico de Piscirickettsia salmonis y desarrollo de bioproductos para combatir la pirisickettsiosis. XXXIV Congreso de Ciencias del Mar, Osorno, Chile, 2014.

[25] Manque, P; Nassif, M; Vicencio, E; Gheradelli, C; Matamala, JM; Vidal, RL; Arias-Carrasco, R; Rojas-Herrera, M; Maracaja-Coutinho, V; Hetz, C; Woehlbier, U. Bci is a new component of the autophagy pathway. FEBS-EMBO 2014, Paris, France, 2014.

[25] Rojas-Herrera, M; Blanc N; Espinoza, L; Sanchez, C; Ruiz, M; Villacreses, J; Manque, P; Alzate, JF; Undurraga, S; Maracaja-Coutinho, V; Polanco, V. Transcriptome of Maqui Berry (Aristotelia chilensis): towards a molecular understanding of the biosynthesis and regulation of the anthocyanin pathway using extreme colored phenotypes. Plant Biology 2014, Portland, OR, United States, 2014.

[23] Rojas-Herrera, M; Arias-Carrasco, R; Trefault, N; Polanco, V; Maracaja-Coutinho, V. An automated generic pipeline for de novo identification of long and small non-coding transcripts on RNAseq raw data.
X-Meeting 2013 - 9th International Conference of the AB³C (Brazilian Association for Bioinformatics and Computational Biology) & BSB 2013 - Brazilian Symposium on Bioinformatics, Recife, PE, Brazil, 2013.

[22] Matamala, JM; Uhrig, M; Maracaja-Coutinho, V; Arias-Carrasco, R; Sanchez, C; Hetz, C; Manque, P. Small non-coding RNAs as potential biomarkers in Amyotrophic Lateral Sclerosis. 8th Brain Research Conference, San Diego, CA, United States, 2013.

[21] Uhrig, M;
Matamala, JM; Maracaja-Coutinho, V; Sanchez, C; Arias-Carrasco, R; Rojas-Herrera, M.; Valdes, P; Hetz, C; Manque, P. Modulation of small non-coding RNAs in the central nervous system by XBP1 transcription factor. 8th Brain Research Conference, San Diego, CA, United States, 2013.

[20] Fachel, AA; Tahira, AC; VILELLA-ARIAS, SA; Maracaja-Coutinho, V; Gimba, E; Vignal, GM; Reis, EMR; Verjovski-Almeida, S. Long ncRNAs in renal cell carcinoma are correlated to malignancy and survival: functional associations. 72nd Harden Conference - RNA regulators of gene expression, Cambridge, England, 2012.

[19] *Paschoal, AR; *Maracaja-Coutinho, V; Setubal, JC; Simões, ZLP; Verjovski-Almeida, S; Durham, AM. Non-coding transcription characterization and annotation: a guide and web resource for non-coding RNA databases. X-Meeting 2012 - 8
th International Conference of the AB³C (Brazilian Association for Bioinformatics and Computational Biology), Campinas, SP, Brazil, 2012.

[18] Maracaja-Coutinho, V; Beckedorff, FCF; Amaral, MS; Moreira YB; Setubal, JC; Reis, EM; Verjovski-Almeida, S. Expression analysis of the non-coding transcriptome in a prostate cancer cell line revealed novel androgen-regulated intronic ncRNAs. ISMB 2011 - 19th International Conference on Intelligent Systems for Molecular Biology & ECCB 2011 - 10th European Conference on Computational Biology, Vienna, Austria, 2011.

[17] Maracaja-Coutinho, V; Setubal, JC; Verjovski-Almeida, S. Genome-wide in-silico identification of human intronic non-coding RNAs and expression analysis of these transcripts in liver. RECOMB 2010 - 14th International Conference on Research in Computational Biology, Lisboa, Portugal, 2010.

[16] Fachel, AA; Tahira, AC; Maracaja-Coutinho, V; Gimba, ERP; Campos, FS; Louro, R; Reis, EM; Verjovski-Almeida, S. Long intronic noncoding RNA signatures of malignancy and survival outcome in clear cell renal cell carcinoma. System Biology: global regulation of gene expression, Cold Spring Harbor Laboratory, NY, United States, 2010.

[15] Camargo, L; Maracaja-Coutinho, V; Verjovski-Almeida, S; Reis, EM. Effect of DNA methylation on the transcription of intronic noncoding RNAs in cancer cell lines. System Biology: global regulation of gene expression, Cold Spring Harbor Laboratory, NY, United States, 2010.

[14] Fachel, AA; Tahira, AC; Maracaja-Coutinho, V; Gimba, ERP; Vignal, GM; Campos, FS; Louro, R; Reis, EM; Verjovski-Almeida, S. RNAs não-codificadores intrônicos longos correlacionados com carcinogênese e sobrevida em câncer de rim. 56º Congresso Brasileiro de Genética, Guarujá, SP, Brazil. 2010.

[13] Maracaja-Coutinho, V; Setubal, JC; Verjovski-almeida, S. Genome-wide in-silico identification of human intronic non-coding RNAs and expression analysis of these transcripts in liver. X-Meeting 2009 - 5th International Conference of the AB³C
(Brazilian Association for Bioinformatics and Computational Biology), Angra dos Reis, RJ, Brazil, 2009


[12] Grisi, TCSL; Padilha, IQM, Rangel, LTLD; Maracaja-Coutinho, V; Lima, LFA; Araujo, DAM. Diversidade microbiana do solo do Cariri paraibano pela análise da biblioteca metagenômica do gene 16S rDNA. 55º Congresso Brasileiro de Genética, Águas de Lindóia, SP, Brazil, 2009

[11] Maracaja-Coutinho, V; Llamoca-Zarate, RM. Degenerate primers construction for gene identification based on protein sequences. I Simpósio Brasileiro de Genética Molecular de Plantas, Natal, RN, Brazil, 2007.

[10] Padilha, IQM; Martins, AB; Durbano, JP; Almeida RS; Melo, LHM; Maracaja-Coutinho, V; Araujo, DAM. Construção de recursos didáticos como instrumento de apoio para divulgação da Bioinformática. IX Encontro de Extensão e X Encontro de Iniciação à Docência da UFPB, João Pessoa, PB, Brasil, 2007.

[9] Almeida, RS; Maracaja-Coutinho, V; Padilha, IQM; Araujo, DAM; Llamoca-Zarate, RM. Padrões de similaridade entre as enzimas chave para a síntese de Inulina. XXI Reunião Anual da FeSB (Federação de Sociedades de Biologia Experimental), Águas de Lindóia, SP, Brazil, 2006.

[8] *Silva, JC; *Maracaja-Coutinho, V; Nakaya, HI; Louro, R; Amaral, PP; Reis, RM; Verjovski-Almeida, S. Molecular characterization of intronic transcripts regulated by androgen in prostate cancer cell line. XXXIV Reunião Anual da SBBq (Sociedade Brasileira de Bioquímica e Biologia Molecular), Águas de Lindóia, SP, Brazil, 2005.
* Contributed equally to this work.

[7] Maracaja-Coutinho, V; Costa, DA; Ribeiro, ILAC; Amaral, CMM; Araujo, DAM; Llamoca-Zarate, RM. Degenerate primer design targeting the NHX1 Antiporter gene from twenty plant species. X-Meeting 2005 - 1st International Conference of the AB³C (Associação Brasileira de Bioinformática e Biologia Computacional), Caxambu, MG, Brazil, 2005.

[6] Martins, AB; Faucher N; Padilha, IQM; Maracaja-Coutinho, V; Llamoca-Zarate, RM; Araujo, DAM. Degenerate primer design targeting Glyoxylate pathway enzymes: Isocitrate lyase and Malate synthase in Leishmania chagasi. X-Meeting 2005 - 1st International Conference of the AB3C (Brazilian Association for Bioinformatics and Computational Biology), Caxambu, MG, Brazil, 2005.

[5] Costa, DA; Ribeiro, ILAC; Amaral CMM. Llamoca-Zarate, RM; Maracaja-Coutinho, V. Regeneração in vitro de brotos através do ápice caulinar do sorgo (Sorghum bicolor (L.) Moench). XII Congresso Latino Americano de Fisiologia Vegetal & X Congresso Brasileiro de Fisiologia Vegetal, Recife, PE, Brazil, 2005.

[4] Maracaja-Coutinho, V; Araujo, DAM; Llamoca-Zarate, RM. Resistência à salinidade: primers para o gene NHX1 Antiporter de Sorghum sudanense. VI Encontro Unificado de Ensino, Pesquisa e Extensão da UFPB, João Pessoa, PB, Brazil, 2005.

[3] Almeida, RS; Maracaja-Coutinho, V; Padilha, IQM; Araujo, DAM; Llamoca-Zarate, RM. Análise in silico das enzimas chave para a síntese de Inulina. VI Encontro Unificado de Ensino, Pesquisa e Extensão da UFPB, João Pessoa, PB, Brazil, 2005.

[2] Durbano, JP; Padilha, IQM; Maracaja-Coutinho, V; Almeida, RS; Martins, AB; Van Der Linden, MG; Rego, TG; Araujo, DAM. Bioinformática na Extensão Universitária. VI Encontro Unificado de Ensino, Pesquisa e Extensão da UFPB, João Pessoa, PB, Brazil, 2005.

[1] Maracaja-Coutinho, V; Llamoca-Zarate, RM. Patterns of similarity of putative NHX1 Antiporter proteins from twenty plant species. VII Reunião Regional da SBBq (Sociedade Brasileira de Bioquímica e Biologia Molecular) & 2nd International Symposium in Biochemistry of Macromolecules, Recife, PE, Brazil, 2004.

Other Production

  • Created Dodo, a global crowdfunding platform for biotech and life sciences projects (www.dodofunding.com).
  • Co-created the NRDR: Noncoding RNA Databases Resource (www.ncrnadatabases.org)

  • Designed a 244k customized human intronic-exonic-intergenic Agilent oligoarray platform (AMADID: 05248).

  • Designed a 244k customized human intronic-exonic-intergenic Agilent oligoarray platform (AMADID: 028681).


Awards and Fellowships


Awards & Honors 

  • 3rd Place Poster Award
Medical Science & Technology
ISCB Latin America Conference - 2016
Buenos Aires, Argentina, 2016.
Work: StructRNAfinder: Preciting RNA families from 3’UTR regions of Zika andrelated viruses through an automated tool
  • 1st Place Poster Award
Copec-UC "Big Data" Conference
Santiago, Chile, 2015.
Work: Aristotelia chilensis: el proyecto genoma de una planta nativa chilena.
  • Selected to the Parallella University Program - PUP
Adapteva (www.parallella.org)
Lexington, US, 2014.
  • 2nd Austral BIO Challenge
Austral Incuba / Universidad Austral de Chile
Valdivia, Chile, 2014.
  • GBR GapSummit Biotech Leader of Tomorrow
Global Biotech Revolution
Cambridge, England, 2014.
  • Start-Up Chile Recognition Program
Start-Up Chile Program
Santiago, Chile, 2014.
  • Fundacity Entrepreneur of the Week
Fundacity - Latam Startup Ecosystem
Latin America, 2013.
  • Honorable Mention - Databases & Data Integration, Text Mining and Information Extraction
Brazilian Association for Bioinformatics and Computational Biology - AB3C
X-meeting 2012- 8th International Conference of the AB3C. 
Campinas, SP, Brazil, 2012.
Work: NRDR - Non-coding RNA Databases Resource
  • Elo Cidadão Award 2007 for Science Outreach

Universidade Federal da Paraíba
João Pessoa, PB, Brazil, 2007.

  • Fellowship Award - Course: Nucleic Acids Manipulation - PCR, RT-PCR and qPCR  

Universidade Estadual Paulista - UNESP Botucatu
Botucatu, SP, Brazil, 2006.

  • 2nd Place Poster Award  
Brazilian Association for Bioinformatics and Computational Biology - AB3C
X-meeting 2005- 1st International Conference of the AB3C. 
Caxambu, MG, Brazil, 2005.
Work: Degenerate primer design targeting Glyoxylate pathway enzymes: Isocitrate lyase and Malate synthase in Leishmania chagasi
  • Elo Cidadão Award 2005 for Science Outreach

Universidade Federal da Paraíba
João Pessoa, PB, Brazil, 2005.

  • 1st Place Exposciences 2005 - João Pessoa Edition

Paraíba State Scientic Fair
João Pessoa, PB, Brazil, 2005.

Fellowships
  • Santander Universidades

Beca Iberoamérica Santander para Jóvenes Investigadores 2014 - Short-Term Visiting Fellowship for young researchers
Nov 2014 
Jan 2015

  • Fundação de Amparo à Pesquisa do Estado de São Paulo - FAPESP

PhD Fellowship
Mar 2008 
 Feb 2012

  • Programa de Aperfeiçoamento do Ensino USP - PAE/USP

Program for lecturing undergraduate classes at USP
Jul 2010 
 Dec 2010

  • Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES

PhD Fellowship
Sep 2007 
 Feb 2008

  • Brazilian Academy of Sciences - ABC

Programa Aristides Pacheco Leão de Apoio a Vocações Científicas - Short-Term Visiting Fellowship
Jan 2005
Mar 2005

  • National Council for Scientific and Technological Development - CNPq

Undergraduate research
Aug 2004
Dec 2006


Lecturer in Courses & Oral Presentations

PhD Program
  •  Bioinformatics II  - 2016.2 
Integrative Genomics PhD Career
Universidad Mayor, Chile
  •  Bioinformatics I  - 2016.1 
Integrative Genomics PhD Career
Universidad Mayor, Chile
  •  Bioinformatics II  - 2015.2 
Integrative Genomics PhD Career
Universidad Mayor, Chile
  •  Bioinformatics I  - 2015.1 
Integrative Genomics PhD Career
Universidad Mayor, Chile
  •  Research Practices II - 2015.1 
2 Students
Integrative Genomics PhD Career

Universidad Mayor, Chile
  •  Research Practices I  - 2014.2 
3 Students
Integrative Genomics PhD Career

Universidad Mayor, Chile
  •  Bioinformatics II - 2014.2
Integrative Genomics PhD Career
Universidad Mayor, Chile
  •  Bioinformatics I - 2014.1
Integrative Genomics PhD Career
Universidad Mayor, Chile

Undergrad Program
  •  Integrative Workshop on Genomics and Bioinformatics - 2016.2
Biotechnology Undergrad Career
Universidad Mayor, Chile
  •  Genomics, Proteomics and Metabolomics - 2016.2
Biotechnology Undergrad Career
Universidad Mayor, Chile
  •  Genomics, Proteomics and Metabolomics - 2013.2
Biotechnology Undergrad Career
Universidad Mayor, Chile
  • Biochemistry - 2010.2
Biological Sciences Career - Assistant
Universidade de São Paulo, Brazil
 




Events as a Lecturer, Mentor or Organizing Board

  • CBAB Course: Using Bioinformatics for Vaccine Studies - Course Lecturer
Centro Brasileiro-Argentino de Biotecnologia (CBAB), Universidade Federal Paulista, Universidade de São Paulo 
São Paulo, Brazil - May 17-29, 2015 
  • International Course: Bioinformatics Tools Applied to Genomics - Course Lecturer
Universidad Austral de Chile 
Valdivia, Chile - Jan 19-23, 2015 
  • 1st Symposium on Semi-Arid Biotechnology and Bioprocesses Engineering (SENGEBBIO 2014) - Course Lecturer
Universidade Federal de Campina Grande 
Sumé, Brazil - Dec 4-6, 2014 
  • 1st Symposium on Integrative Bioinformatics - Organizer 
Universidad Mayor 
Santiago, Chile - Jul 1, 2014 
  • First Workshop of Massive Parallel Sequencing - Course Lecturer
Universidad Mayor / Universidad de Concepción
Concepción, Chile - Jan 24, 2014 
  • Day for Failure - Organizing Board
Universidad Mayor / Start-Up Chile / GestaMayor
Santiago, Chile - Jan 22, 2014 
  • First Workshop of Massive Parallel Sequencing - Course Lecturer
Universidad Mayor
Santiago, Chile - Dec 16  Dec 17, 2013 
  • Santiago NEXT - Organizing Board
Kauffman Foundation / Google for Entrepreneurs / Universidad Mayor
Santiago, Chile - Nov 09  Dec 08, 2013 
  • Startup Weekend Santiago - Organizing Board
Kauffman Foundation / Universidad de Chile 
Santiago, Chile - Mar 22 ↔ 24, 2013 
  •  Escuela de Verano de la Universidad de Chile - Mentor
Start-Up Chile / Universidad de Chile / Centro Movistar Innova
Santiago, Chile - Jan 10, 2013 
  •  Summer Course on Bioinformatics 2010 - Course Lecturer
Universidade de São Paulo - USP /  Brazilian Association for Bioinformatics and Computational Biology - AB³C
São Paulo, SP, Brazil - Feb 01 Feb 05, 2010 
  •  Summer Course on Bioinformatics 2009 - Course Lecturer

Universidade de São Paulo - USP /  Brazilian Association for Bioinformatics and Computational Biology - AB³C
São Paulo, SP, Brazil - Feb 02 Feb 06, 2009 

  • III Course on Bioinformatics & Molecular Biology: Genomics, Transcriptomics and Proteomics - Course Lecturer and Organizing Board

Universidade Federal da Paraíba - UFPB
João Pessoa
, PB, Brazil - Dec 11 Dec 15, 2006 

  • Introduction to Bioinformatics - Biology Week - Course Lecturer

Universidade Federal da Paraíba - UFPB
João Pessoa
, PB, Brazil - Sep 11 Sep 22, 2006

  • II Course on Bioinformatics & Molecular Biology - Course Lecturer and Organizing Board

Universidade Federal da Paraíba - UFPB
João Pessoa
, PB, Brazil - Mar 27 Apr 11, 2006

  • I Course on Bioinformatics & Molecular Biology - Organizing Board

Universidade Federal da Paraíba - UFPB 
João Pessoa
, PB, Brazi, 2005 


Oral Presentations (Talks)
  • XXXIX Annual Meeting of the Chilean Society for Biochemistry and Molecular Biology
Talk: The landscape of non-coding RNAs in Piscirickettsia salmonis
Chilean Society for Biochemistry and Molecular Biology
Puerto Varas, Chile - Sep 27-30, 2016 
  • 2nd Conference on Bioinformatics Engineering
Talk: Non-coding RNAs - the hidden treasures of the genome
Universidad de Talca
Talca, Chile - Oct 13-14, 2016 
  • 2nd Workshop Research to Business (R2B) Catalyst
Talk: Financiando tu proyecto a través del crowdfunding científico
UC Davis Chile / R2B Catalyst 
Santiago, Chile - Ago 19, 2016
  • Tópicos Selectos en Biologia y Biomedicina - Universidad de Antofagasta
Talk: The hidden treasures behind thegenome trash
PhD Program in Biological Sciences, Universidad de Antofagasta
Antofagasta, Chile - Ago 5, 2016 
  • DIB Talks Santiago - IOT-BIO: El internet de las cosas y las Biociencias
Talk: Cómo el IoT viene cambiando nuestras vidas y la manera de hacer ciencia
Centro de Creación y Comunidad Infante 1415
Santiago, Chile - Jul 27, 2016 
  • Coloquios AUSTRAL-omics 2016
Talk: Non-coding RNAs in fish pathogens
Universidad Austral de Chile
Talca, Chile - May 20, 2016 
    Open Science - Evento de Innovación Abierta
Talk: Raise funds for your research using the power of the crowd
STGO LabSpace, Municipalidad de Providencia
Santiago, Chile - Nov 10-11, 2015 
      EpiCrowd 2015
    Talk: Raise funds for your research using the power of the crowd
    Skoll Global Threats Fund / EpiTrack / ProEpi
    Recife, Brazil - Mar 25-27, 2015 
    • Ideia nas Nuvens
    Talk: The Beagle's Journey
    ClubJob Co-Working
    Joao Pessoa, Brazil - Dec 10, 2014 
    • Campus Festival - Oficina de Startup
    Talk: Business Model Canvas
    Espaço Cultural José Lins do Rêgo
    Joao Pessoa, Brazil - Dec 07, 2014
    • 1st Conference on Bioinformatics Engineering
    Talk: Integrative Bioinformatics: from non-coding RNAs to a digital, collaborative and citizen science
    Universidad de Talca
    Talca, Chile - Oct 10, 2014 
    • Seminars on Entrepreneurship and Innovation
    Talk: The change of paradigm in scientific research and funding: towards digital and collaborative science
    Pontificia Universidad Católica de Valparaiso / Universidad Técnica Federico Santa María
    Valparaiso, Chile - Oct 6, 2014 
    • 1st Symposium on Integrative Bioinformatics
    Talk: Integrative bioinformatics of long non-coding RNAs: insights into function based on expression networks and evolution
    Laboratory of Integrative Bioinformatics, Centro de Genómica y Bioinformática, Universidad Mayor
    Santiago, Chile - July 1, 2014
    •  A new look into Biomedical Engineering
    Talk: Entrepreneurship opportunities in bioinformatics
    Academic Directory, Universidade Federal de Pernambuco 
    Recife, Brazil - April 9, 2014
    •  La BioClínica del Emprendimiento Científico de Todo por La Ciencia
    Talk: Dodo - Biotech Crowdfunding
    Todo por La Ciencia / Redbionova
    Santiago, Chile - Jan 11, 2014
    •  Día de la Biotecnología 2013
    Talk: The hidden treasures in "the trash" of the genome
    Universidad Mayor
    Santiago, Chile - Oct 23 ↔ Oct 24, 2013
    •  Health 2.0 Recife
    Talk: Bioinformatics & Entrepreneurship: The Beagle's Journey
    Health 2.0 Latin America
    Recife, PE, Brazil - Aug 8, 2013
    •  Hackers & Founders Córdoba, Argentina  

    Talk: Bioinformatics needs Tech guys
    ProCórdoba - Agencia para la promoción de las exportaciones.
    Córdoba, Córdoba, Argentina - Nov 23, 2012

    •  SBBq 2005 - XXXIV Reunião Anual da Sociedade Brasileira de Bioquímica e Biologia Molecular

    Talk: Molecular characterisation of intronic transcripts regulated by androgen in prostate cancer cell line
    Sociedade Brasileira de Bioquímica e Biologia Molecular

    Águas de Lindóia, SP, Brazil - Jul 02 ↔ Jul 05, 2005

    •  ENIC 2005 - Encontro Nacional de Iniciação Científica
    Talk: Salt resistance: primers for Na+/H+ Antiporter gene in Sorghum sudanense
    Universidade Federal da Paraíba - UFPB

    João Pessoa, PB, Brazil - Dec 05 Dec 07, 2005
    •  SPB 2005 - Simpósio Paraibano de Bioinformática
    Talk: Salt resistance and the Na+/H+ Antiporter gene
    Universidade Federal da Paraíba - UFPB
    João Pessoa, PB, Brazil - Dec, 2005


    Supplementary Education

    • RNA Structure and Function

    International Centre for Genetic Engineering and Biotechnology - ICGEB
    Trieste, Italy - Mar 30 Apr 02, 2009 
    20 hours

    • RNA Bioinformatics

    1st Brazilian School on Bioinformatics / Brazilian Computer Society
    Santo André, SP, Brazil -  Aug 25 ↔ Aug 28, 2008
    08 hours

    • Comparative Genomics

    1st Brazilian School on Bioinformatics - Brazilian Computer Society
    Santo André, SP, Brazil -  Aug 25 ↔ Aug 28, 2008
    08 hours

    • Nucleic Acids Manipulation: PCR, RT-PCR and qPCR

    Universidade Estadual Paulista – UNESP Botucatu
    Botucatu, SP, Brazil -  July 10 ↔ July 14, 2006
    40 hours

    • Introduction to The Methods for Protein Structural Characterization

    Brazilian Synchrotron Light Laboratory – LNLS
    Campinas, SP, Brazil -  July 06 ↔ July 07, 2006
    16 hours

    • Genome, Proteome and Cellular Universe - PROTEOMICS Course

    Universidade de São Paulo – USP Ribeirão Preto
    Ribeirão Preto, SP, Brazil -  Jan 16 ↔ Jan 28, 2006
    80 hours

    • Extremophiles Biology

    Universidade Federal da Paraíba – UFPB
    João Pessoa
    , PB, Brazil -  Feb 19 ↔ Feb 23, 2004
    10 hours

    • Techniques in Molecular Biology

    5th National Meeting for Biologists – Conselho Federal de Biologia
    Natal
    , RN, Brazil -  Aug 03 ↔ Aug 06, 2003
    04h30 hours

    • Genetic Modified Organisms - GMO

    5th National Meeting for Biologists – Conselho Federal de Biologia
    Natal
    , RN, Brazil -  Aug 03 ↔ Aug 06, 2003
    04h30 hours

    • Introduction to Perl

    Universidade Federal da Paraíba – UFPB
    João Pessoa, PB,
    Brazil -  Mar 31 ↔ Apr 04, 2003
    12 hours

    • Introduction to Bioinformatics

    Universidade Federal da Paraíba – UFPB
    João Pessoa, PB,
    Brazil -  Feb 17 ↔ Feb 22, 2003
    10 hours


    Startups

    Founder
    Advisor


    Judging Committee

    Grants
    • Start-Up Chile Program - Round 12

    Corfo, Chile
    November 2014


    Undergraduate Final Thesis Commission
    • Search and analysis of genomic islands in Mycoplasma genitalium  

    Student: Max Mahyron Guedes Santos
    Universidade Federal da Paraíba, Brazil
    March 2013


    Undergraduate Final Pre-Thesis Commision
    • Identification of transcription factor genes related to Antocianin production in Aristotelia chilensis genome

    Student: Javier Villacreces
    Universidad Mayor, Chile
    June 2013


    Computer Skills

    • Linux 
    • Shell
    • Perl
    • MySQL
    • HTML
    • CGI
    • R
    • WordPress
    • Drupal

    Languages

    • Portuguese (native) 
    • English (advanced)
    • Spanish (intermediary)
    • German (basic)