Publications

The symbol “$” indicates corresponding author. Authors from our group are marked in bold.

2020

[40] DebRoy, S; Aliaga-Tobar, V; Galvez, G; Arora, S; Liang, X; Horstmann, NM; Maracaja-Coutinho, V; Mauricio Latorre, M; Hook, M; Flores AR; Shelburne, S. Genome-wide analysis of in vivo CcpA binding with and without its key co-factor HPr in the major human pathogen group A Streptococcus. bioRxiv, 2020.

[39] Nakaya, HI$; Thakar, J$; Maracaja-Coutinho, V$. User-friendly tools applied to genetics or systems biology. Frontiers in Genetics, 2020. $ Corresponding Author.

[38] Ramos, TAR; Maracaja-Coutinho, V$; Ortega, JM$; Rêgo, TG$. CORAZON: a web server for data normalization and unsupervised clustering based on expression profiles. BMC Research Notes, 2020. $ Corresponding Author.

[37] Arias-Carrasco, R; Giddaluru, J;  Cardozo, LE; Martins, F; Maracaja-Coutinho, V$; Nakaya, H$. OUTBREAK: A user-friendly georeferencing online tool for disease surveillance. arXive, 2020. $ Corresponding Author.

[36] Gregorio, CD; Contador, D; Díaz, D; Cárcamo, C; Santapau, D; Lobos-Gonzalez, L; Acosta, C; Campero, M; Carpio, D; Gabriele, C; Gaspari, M; Aliaga-Tobar, V; Maracaja-Coutinho, V; Ezquer, M; Ezquer, F. Human adipose-derived mesenchymal stem cell conditioned medium ameliorates polyneuropathy and foot ulceration in diabetic BKS db/db mice. Stem Cell Research & Therapy, 2020.

[35] Sotomayor-Flores, C; Rivera-Mejías, P; Vásquez-Trincado, C; López-Crisosto, C; Morales, PE; Pennanen, C; Polakovicova, I; Aliaga-Tobar V; García, L; Roa, JC; Rothermel, BA; Maracaja-Coutinho, V; Ho-Xuan, H; Meister, G; Chiong, M; Ocaranza, MP; Corvalán, A; Parra, V; Lavandero S. Angiotensin-(1-9) prevents cardiomyocyte hypertrophy by controlling mitochondrial dynamics via miR-129-3p/PKIA pathway. Cell Death & Differentiation, 2020.

[34] Gomez, W; Morales, R; Maracaja-Coutinho, V; Valentina Parra; Nassif, M. Down syndrome and Alzheimer’s disease: Common molecular traits beyond the amyloid precursor protein. Aging, 2020.

[33] Court, AC; Le-Gatt, A; Luz-Crawford, P; Parra-Crisóstomo, E; Aliaga-Tobar, V; Bátiz, LF; Contreras, RA; Ortúzar, MI; Kurte, M; Elizondo-Vega, R; Maracaja-Coutinho, V; Pino-Lagos, K; Figueroa, FE; Khoury, M.Mitochondrial transfer from MSCs to T cells induces Treg differentiation and restricts inflammatory response. EMBO Reports, 2019. 

2019

[32] Gonçalves, ANA; Lever, M; Russo, P; Gomes-Correia, B; Urbanski, AH; Pollara, G; Noursadeghi, M;  Maracaja-Coutinho, V; Nakaya, HI. Assessing the impact of sample heterogeneity on transcriptome analysis of human diseases using MDP webtool. Frontiers in Genetics, 2019. Accepted!

[31] Lima, DS; Cardozo, LE; Maracaja-Coutinho, V; Suhrbier, A; Mane, K; Jeffries, D; Silveira, ELV; Amaral, PP; Rappuoli, R; Silva, TI; Nakaya, HI. Long noncoding RNAs are involved in multiple immunological pathways in response to vaccination. Proceedings of the National Academy of Sciences (PNAS), 2019.

[30] Maracaja-Coutinho, V; Arias-Carrasco, R; Nakaya, HI; Aliaga-Tobar, V. Predicting RNAs families in nucleotide sequences using StructRNAfinder. In: Gene Prediction: Methods and Protocols in Molecular Biology. Springer-Nature, 2019. Book Chapter $

[29] Cardozo, LE; Russo, PST; Gomes-Correia, B; Araujo-Pereira, M; Sepúlveda-Hermosilla, G; Maracaja-Coutinho, V; Nakaya, HI. webCEMiTool: Co-expression modular analysis made easy. Frontiers in Genetics, 2019.

[28] Maracaja-Coutinho, V; Paschoal, AR; Caris-Maldonado, JC; PV Borges, PV; Durham, A. Noncoding RNAs Databases: Current Status and Trends. In: Computational Biology of Non-Coding RNA. Springer-Nature, 2019. Book Chapter.

[27] Serrano-Solis, V; Carlos, AC; Maracaja-Coutinho, V; De Farias, ST. Santander J. Prediction of microRNAs in the Epstein–Barr virus reveals potential targets for the viral self-regulation. Indian Journal of Microbiology, 2019.

2018

[26] Segovia, C; Arias-Carrasco, R; Yáñez, AJ; Maracaja-Coutinho, V; Santander J. Core non-coding RNAs of Piscirickettsia salmonis PLOS One, 2018.

[25] Huanca-Mamani, W $; Arias-Carrasco, R; Cárdenas-Ninasivincha, S; Rojas-Herrera, M; Sepúlveda-Hermosilla, G; Caris-Maldonado, JC; Bastías, E; Maracaja-Coutinho, V $. Long non-coding RNAs responsive to salt and boron stress in the hyper-arid Lluteño maize from Atacama Desert Genes, 2018. $

[24] Amaral, PP; Leonardi, T; Han, N; Vire, E; Gascoigne, DK; Arias-Carrasco, R; Buscher, M; Zhang, A; Pluchino, S; Maracaja-Coutinho, V; Nakaya, HI; Hemberg, M; Shiekhattar, R; Enright, AJ; Kouzarides, T. Genomic positional conservation identifies topological anchor point (tap)RNAs linked to developmental loci. Genome Biology, 2018.

[23] Orell, A; Tripp, V; Aliaga-Tobar, V; Albers, S-V; Maracaja-Coutinho, V; Randau; L. A regulatory RNA is involved in RNA duplex formation and biofilm regulation in Sulfolobus acidocaldarius. Nucleic Acids Research, 2018. 

[22] Russo, PST; Ferreira, GR; Cardozo, LE; Bürger, MC; Arias-Carrasco, R; Maruyama, SR; Hirata, TDC; Lima, DS; Passos, FM; Fukutani, KF; Lever, M; Silva, JS; Maracaja-Coutinho, V; Nakaya, HI. CEMiTool: A Bioconductor package for performing comprehensive modular co-expression analyses. BMC Bioinformatics, 2018. 

[21] Arias-Carrasco, R; Vásquez-Morán, Y; Nakaya, HI; Maracaja-Coutinho, V $. StructRNAfinder: an automated pipeline and web server for RNA families prediction. BMC Bioinformatics, 2018. $

[20] Matamala, JM; Arias-Carrasco, R; Sanchez, C; Uhrig, M; Bargsted, L; Matus, S; Maracaja-Coutinho, V; Abarzua, S; Verdugo R; van Zundert, B; Manque, P; Hertz, C. Genome-wide circulating microRNA expression profiling reveals potential biomarkers for amyotrophic lateral sclerosis. Neurobiology of Aging, 2018.

2017

[19] Nourdin-Galindo, G; Sánchez, P; Molina, CF; Espinoza-Rojas, DA; Oliver, C; Ruiz, P; Vargas-Charcoff, L; Carcamo, JG; Figueroa, JE; Mancilla, M; Maracaja-Coutinho, V $; Yáñez, AJ $. Pan-genome analysis of Piscirickettsia salmonis reveals genomic divergences within genogroups. Frontiers in Cellular and Infection Microbiology, 2017. $

[18] Torres, F; Arias-Carrasco, R; Caris-Maldonado, JC; Barral, A; Maracaja-Coutinho, V $; Queiroz, ATL. LeishDB: a database for coding gene annotation and non-coding RNAs in Leishmania braziliensis. Database, 2017. $

2016

[17] Aguiar, RR; Ambrosio, LA; Sepúlveda-Hermosilla, G; Maracaja-Coutinho, V; Paschoal, AR. miRQuest: integration of tools on a web server for microRNA research. Genetics and Molecular Research, 2016.

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

[15] 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 clustering algorithm. PLOS One, 2016. 

2015

[14] Segovia, C; Vásquez, J; Maracaja-Coutinho, V; Robeson, J; Santander, J. Complete genome sequence of the Salmonella enterica Serovar Enteritidis bacteriophage f18αSE isolated in Chile. Genome Announcements, 2015.

[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 viral-like sequences identified in Aristotelia chilensis (Maqui Berry). Viruses, 2015. $

2014

[12] 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 of Chilean honeybee (Apis mellifera) gut strain Lactobacillus kunkeei MP2. Genome Announcements, 2014.

[11] 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.

2013

[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. 

2012

[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.

2011

[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. 

2010

[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. 

2009

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

2008

[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. 

2005

[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]