Man

Vinicius Ramos Henriques Maracaja Coutinho

Associate Professor

Univesidad de Chile

Santiago, Chile

Líneas de Investigación


(i) computational systems biology; (ii) RNA bioinformatics; (iii) comparative genomics; (iv) epitranscriptomics of diseases; (v) single-cell transcriptomics; and (vi) development of computational tools/databases

Educación

  •  Bioinformatics, UNIVERSIDADE DE SAO PAULO. Brasil, 2013
  •  Biological Sciences, UNIVERSIDADE FEDERAL DA PARAIBA. Brasil, 2006

Experiencia Académica

  •   Assistant Professor Full Time

    UNIVERSIDAD MAYOR

    Facultad de Ciencias

    Santiago, Chile

    2013 - 2017

  •   Assistant Professor Full Time

    UNIVERSIDAD DE CHILE

    Facultad de Ciencias Químicas y Farmacéuticas

    Santiago, Chile

    2018 - 2022

  •   Associate Professor Full Time

    UNIVERSIDAD DE CHILE

    Facultad de Ciencias Químicas y Farmacéuticas

    Santiago, Chile

    2022 - At present

  •   Visiting Professor Other

    FUNDACAO OSWALDO CRUZ

    Instituto Gonçalo Moniz

    Salvador, Brasil

    2023 - 2023

  •   Visiting Researcher Other

    UNIVERSITY OF CAMBRIDGE

    Gurdon Institute

    Cambridge, Reino Unido

    2018 - 2018

  •   Visiting Researcher Other

    Institut de Recherche pour le Développement - IRD

    Montpellier, Francia

    2022 - 2022

  •   Visiting Researcher Other

    UNIVERSIDADE FEDERAL DE PARAIBA

    Joao Pessoa, Brasil

    2014 - 2015

Experiencia Profesional

  •   Fundador Other

    Beagle Bioinformatics

    Santaigo, Chile

    2013 - At present

Formación de Capital Humano


MSc: 6 graduated students since 2015, 2 in progress.
PhD: 7 graduated students since 2019, 11 in progress.

- Founder and Director of the Graduate Program on Bioinformatics and Computational Biology from the Facultad de Ciencias Químicas y Farmacéuticas de la Universidad de Chile, launched in 2019.

- He coordinado y participado como profesor de cátedra de diversos cursos referentes a Estadística, Programación, Genómica y Bioinformática para distintas carreras de pregrado en la Universidad de Chile y Universidad Mayor.

- He coordinado y participado como profesor de cátedra de diversos cursos referentes a Estadística, Programación, Genómica y Bioinformática para distintos programas de doctorado en la Universidad de Chile, Universidad Mayor y Universidad de La Frontera.


Difusión y Transferencia


- 2014-2015: Founder of the DIB Talks - Disruptive Ideas in Biotech (www.dibtalks.com), a series of talks that aims to disseminate and popularize disjunctive technologies associated with the Biosciences.

- 2014-2016: Founder of a digital platform for collective financing of scientific projects "Dodo Scientific Crowdfunding" (www.dodofunding.com).

- Participation as an exhibitor or organizer in different scientific events, scientific entrepreneurship or scientific dissemination throughout the country.


Premios y Distinciones

  •   Parallella University Program - PUP

    Adapteva

    Estados Unidos, 2014

    Selected to be part of the Parallela University Program, from Adapteva. The goal of the project is to apply computational biology algorithms in the low cost super computer Parallella.

  •   2nd Austral BIO Challenge

    UNIVERSIDAD AUSTRAL DE CHILE

    Chile, 2014

    One of the winners of the 2nd Austral BioChallenge, from Austral Incuba / Universidad Austral de Chile.

  •   GBR GapSummit Biotech Leader of Tomorrow

    Global Biotech Revolution

    Reino Unido, 2014

    Selected one of the Leaders of Tomorrow of Biotechnology, due to my work trying to solve the gaps we current have in funding biotech projects.

  •   3rd Place Poster Award. ISCB Latin America Conference

    ISCB Latin America Conference

    Argentina, 2016

    3rd Place Poster Award. International Society for Computational Biology Latin America Conference, Buenos Aires, Argentina.

  •   1st Place Poster Award. Copec-UC “Big Data” Conference

    FUNDACION COPEC UNIVERSIDAD CATOLICA

    Chile, 2015

    2015 – 1st Place Poster Award. Copec-UC “Big Data” Conference, Santiago, Chile.

  •   Start-Up Chile Recognition Program

    CORPORACION DE FOMENTO DE LA PRODUCCION

    Chile, 2014

    Start-Up Chile Recognition Program, Start-Up Chile, Santiago, Chile.

  •   Fundacity Entrepreneur of the Week

    Fundacity

    Chile, 2013

    Fundacity Entrepreneur of the Week.

  •   Honorable Mention: Databases & Data Integration, Text Mining and Information Extraction

    Associação Brasileira de Bioinformática e Biologia Computacional

    Brasil, 2012

    Honorable Mention: Databases & Data Integration, Text Mining and Information Extraction. X-Meeting 2012, Associação Brasileira de Bioinformática e Biologia Computacional – AB3C, Campinas, Brazil.

  •   Prêmio Elo Cidadão

    Universidade Federal de Paraíba

    Chile, 2007

    Premiación por el trabajo de extensión universitaria asociada a la difusión de la Bioinformática e inserción digital de la comunidad.

  •   Prêmio Elo Cidadão

    Universidade Federal de Paraíba

    Chile, 2005

    Premiación por el trabajo de extensión universitaria asociada a la difusión de la Bioinformática e inserción digital de la comunidad.

  •   2nd Best Place Poster Award. X-Meeting 2005

    Associação Brasileira de Bioinformática e Biologia Computacional

    Chile, 2005

    2nd Best Place Poster Award. X-Meeting 2005, Associação Brasileira de Bioinformática e Biologia Computacional – AB3C, Caxambu, Brazil.


 

Article (62)

<i>Salmo salar</i> Skin and Gill Microbiome during <i>Piscirickettsia salmonis</i> Infection
Administration of Secretome Derived from Human Mesenchymal Stem Cells Induces Hepatoprotective Effects in Models of Idiosyncratic Drug-Induced Liver Injury Caused by Amiodarone or Tamoxifen
Bacterial networks in Atlantic salmon with Piscirickettsiosis
Computational approaches for circRNAs prediction and in silico characterization
Differences in Bacterial Small RNAs in Stool Samples from Hypercholesterolemic and Normocholesterolemic Subjects
Editorial: Applications of biological networks in biomedicine
Effects of Trimetazidine on Right Ventricular Function and Ventricular Remodeling in Patients with Pulmonary Artery Hypertension: A Randomised Controlled Trial
Single-cell transcriptional landscape of long non-coding RNAs orchestrating mouse heart development
Ten quick tips for harnessing the power of ChatGPT in computational biology
Transcriptional Signatures and Network-Based Approaches Identified Master Regulators Transcription Factors Involved in Experimental Periodontitis Pathogenesis
Characterization of microbial communities from gut microbiota of hypercholesterolemic and control subjects
Comparative Profiling of Circulating Exosomal Small RNAs Derived From Peruvian Patients With Tuberculosis and Pulmonary Adenocarcinoma
Insights into agar and secondary metabolite pathways from the genome of the red alga Gracilaria domingensis (Rhodophyta, Gracilariales)
Mitochondrial E3 ubiquitin ligase 1 (MUL1) as a novel therapeutic target for diseases associated with mitochondrial dysfunction
Small RNA Expression Profiling Reveals hsa-miR-181d-5p Downregulation Associated With TNF-alpha Overexpression in Sjogren's Syndrome Patients
Computational Analysis of Transposable Elements and CircRNAs in Plants
Deletion of hippocampal Glucocorticoid receptors unveils sex-biased microRNA expression and neuronal morphology alterations in mice
Development of a Multiplex PCR Assay for Genotyping the Fish Pathogen Piscirickettsia salmonis Through Comparative Genomics
Long non-coding RNAs associated with infection and vaccine-induced immunity
Network-Based Approaches Reveal Potential Therapeutic Targets for Host-Directed Antileishmanial Therapy Driving Drug Repurposing
Novel molecular insights and public omics data in pulmonary hypertension
OUTBREAK: a user-friendly georeferencing online tool for disease surveillance
Sex-Dependent Changes of miRNA Levels in the Hippocampus of Adrenalectomized Rats Following Acute Corticosterone Administration
Angiotensin-(1–9) prevents cardiomyocyte hypertrophy by controlling mitochondrial dynamics via miR-129-3p/PKIA pathway
CORAZON: a web server for data normalization and unsupervised clustering based on expression profiles
Down syndrome and Alzheimer's disease: common molecular traits beyond the amyloid precursor protein
Editorial: User-Friendly Tools Applied to Genetics or Systems Biology
Epigenetic Reader BRD4 (Bromodomain-Containing Protein 4) Governs Nucleus-Encoded Mitochondrial Transcriptome to Regulate Cardiac Function
Genome-wide analysis of in vivo CcpA binding with and without its key co-factor HPr in the major human pathogen group A Streptococcus
Human adipose-derived mesenchymal stem cell-conditioned medium ameliorates polyneuropathy and foot ulceration in diabetic BKS db/db mice
Mitochondrial transfer from MSCs to T cells induces Treg differentiation and restricts inflammatory response
Assessing the Impact of Sample Heterogeneity on Transcriptome Analysis of Human Diseases Using MDP Webtool
Long noncoding RNAs are involved in multiple immunological pathways in response to vaccination
Noncoding RNAs Databases=> Current Status and Trends.
Prediction of MicroRNAs in the Epstein-Barr Virus Reveals Potential Targets for the Viral Self-Regulation.
webCEMiTool=> Co-expression Modular Analysis Made Easy.
A regulatory RNA is involved in RNA duplex formation and biofilm regulation in Sulfolobus acidocaldarius
CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses
Genome-wide circulating microRNA expression profiling reveals potential biomarkers for amyotrophic lateral sclerosis
Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci
Long Non-Coding RNAs Responsive to Salt and Boron Stress in the Hyper-Arid Lluteno Maize from Atacama Desert
StructRNAfinder: an automated pipeline and web server for RNA families prediction
Comparative Pan-Genome Analysis of Piscirickettsia salmonis Reveals Genomic Divergences within Genogroups.
LeishDB=> a database for coding gene annotation and non-coding RNAs in Leishmania braziliensis
A Guide to Scientific Crowdfunding
A Novel Method to Predict Genomic Islands Based on Mean Shift Clustering Algorithm
miRQuest: Integration of tools on a web server for microRNA research
Complete Genome Sequence of Salmonella enterica Serovar Enteritidis Bacteriophage f18SE, Isolated in Chile
Deep Sequencing Reveals the Complete Genome and Evidence for Transcriptional Activity of the First Virus-Like Sequences Identified in Aristotelia chilensis (Maqui Berry)
Draft Genome of Chilean Honeybee (Apis mellifera) Gut Strain Lactobacillus kunkeei MP2
Draft Genome of Chilean Honeybee (Apis mellifera) Gut Strain Lactobacillus kunkeei MP2.
Draft genome sequence of the virulent strain AUSTRAL-005 of Piscirickettsia salmonis, the etiological agent of piscirickettsiosis (SPS)
Draft Genome Sequence of Virulent Strain AUSTRAL-005 of Piscirickettsia salmonis, the Etiological Agent of Piscirickettsiosis.
Expression analysis and in silico characterization of intronic long noncoding RNAs in renal cell carcinoma: emerging functional associations
Non-coding transcription characterization and annotation: A guide and web resource for non-coding RNA databases
Long noncoding intronic RNAs are differentially expressed in primary and metastatic pancreatic cancer
Non-coding RNAs in schistosomes: an unexplored world
Relation of pretreatment sequence diversity in NS5A region of HCV genotype 1 with immune response between pegylated-INF/ribavirin therapy outcomes
Schizophrenia, brain disease and meta-analyses: Integrating the pieces and testing Fusar-Poli's hypothesis
Schizophrenia, brain disease and meta-analyses: Integrating the pieces and testing Fusar-Poli’s hypothesis
The Role of Neuregulin 1 in Schizophrenia: A Bioinformatics Approach
A bioinformática como instrumento de inserção digital e difusão da biotecnologia

BookSection (1)

Transcriptomics at the single cell level and human diseases: opportunities and challenges in data processing and analysis

BookWhole (1)

Predicting RNA Families in Nucleotide Sequences Using StructRNAfinder

ConferencePaper (1)

Avaliação de Desempenho em Bioinformática: Estudo de caso de sistemas computacionais para a investigação de microRNAs

Proyecto (25)

Advanced Center for Chronic Diseases - ACCDiS
Epitranscriptomic regulation of competing endogenous RNA networks in cardiac fibroblasts associated with heart failure with preserved ejection fraction
RCAN1 trisomy and the control of PINK1 levels in the survival of human Down's syndrome induced pluripotent stem cells (iPSC) and iPSC-derived cardiomyocytes
Establecimiento de una línea base de las características genómicas, toxicológicas y ciclos temporales de la marea roja y de las microalgas tóxicas presentes en la costa de la Región de los Ríos para el anticipo de políticas públicas
Instalación y desarrollo del área de investigación y docencia en Bioinformática=> Estudio RNAs no codificantes posicionalmente conservados y su rol en las enfermedades cardiacas a través de la integración de datos multiómicos
BIOINFORMATICS APPROACHES AND ITS APPLICATION ON THE IDENTIFICATION, EVOLUTION AND FUNCTIONAL ASSIGNATION OF NON-CODING RNAS
Dodo Biotech Crowdfunding
Dodo Scientific Crowdfunding - SSAF/CORFO
Generating a reference dataset for non-redundant sequences and for orthologous groups of non-coding RNAs in 50 thousand species
Generating a reference dataset for non-redundant sequences and for orthologous groups of non-coding RNAs in 50 thousand species
A Reciprocal Approach to Promoting Study Abroad in STEM: Montclair State University
A Reciprocal Approach to Promoting Study Abroad in STEM=> Montclair State University, USA and Universidad Mayor, Chile
Computational approaches in RNomics: a data integration study
Computational approaches in RNomics=> a data integration study
Dodo Biotech Crowdfunding
Centro FONDAP de Estudios Avanzados de Enfermedades Crónicas / ACCDiS Advanced Center for Chronic Diseases
Development of cloud solutions for bioinformatics
Systems biology of long non-coding RNAs
Systems Biology of long non-coding RNAs
Beagle Bioinformatics
Beagle Bioinformatics
NimbusGene=> integrating bioinformatics tools on the cloud
In silico characterization and expression analysis of intronic transcripts in human and mouse
Bioinformatics approaches and its application on the identification, evolution and functional assignation of non-coding RNAs
Dodo Scientific Crowdfunding - Start-Up Chile
69
Vinicius Ramos Henriques

Associate Professor

Advanced Center for Chronic Diseases - ACCDiS

Univesidad de Chile

Santiago, Chile

7
Victor Aliaga

Postdoctorante

Universidad de O'Higgins

Santiago, Chile

2
CESAR SAEZ

Associate professor

Chemical and Bioprocess Engineering

PONTIFICIA UNIVERSIDAD CATOLICA DE CHILE

SANTIAGO, Chile

2
Carolina Sanchez

Assistant Professor, Faculty of Science; Principal Investigator of Advanced Genomics Laboratory; Head of DNA Sequencing Core of the Center for Genomics and Bioinformatics

Center for Genomics and Bioinformatics

Universidad Mayor

Santiago, Chile

2
Raúl Arias

Investigador

Universidad Tecnológica Metropolitana

Santiago, Chile

2
Jesus Martinez

Investigador

Centro de Genómica Nutricional Agroacuícola

Temuco, Chile

2
Mario Chiong

Profesor

Departamento de Bioquímica y Biología Molecular

Universidad de Chile

Santiago, Chile

1
Jose Matamala

Assistant Professor of Neurology

Department of Neurological Science

University of Chile

Santiago, Chile

1
Hugo Verdejo

Profesor Asociado

División de Enferemedades Cardiovasculares

Pontificia Universidad Católica de Chile

Santiago, Chile

1
Gabriel Rojas

Academico

Universidad Autónoma de Chile

Talca, Chile

1
Andrew Quest

Full Professor

Biologia Celular y Molecular

FACULTAD DE MEDICINA, UNIVERSIDAD DE CHILE

Santiago, Chile

1
Héctor Levipan

Profesor Asociado

Ciencias y Geografía

Universidad de Playa Ancha de Ciencias de la Educación

VALPARAISO, Chile

1
Jaime Figueroa

Profesor Titular

Bioquimica y Microbiologia

UNIVERSIDAD AUSTRAL DE CHILE

Valdivia, Chile

1
Gonzalo García

Académico

Universidad de La Serena

La Serena, Chile

1
Sara Cuadros

Profesor Titular

Universidad Católica del Maule

Talca, Chile

1
Alberto Martin

Associate professor

Centro Ciencia & Vida

Universidad San Sebastián

Santiago, Chile

1
Macarena Tejos

Trainee (PhD Student)

Pontificia Universidad Católica de Chile

Santiago, Chile

1
Jorge Toledo

Investigador

Departamento de Anatomia y Biologia del Desarrollo

Universidad de Chile; Biomedical Neuroscience Institute (BNI)

Santiago, Chile

1
Mauricio Latorre

Profesor Asociado

INGENIERIA

UNIVERSIDAD DE O'HIGGINS

Rancagua, Chile

1
Pablo Castro

JEFE DIVISION

DIVISION ENFERMEDADES CARDIOVASCULARES

Pontificia Universidad Católica de Chile

SANTIAGO, Chile

1
Mónica Kurte

Investigador

Laboratorio de Inmunologìa

Universidad de los Andes

Santiago, Chile

1
ALEJANDRO CORVALAN

Principal Investigator

Hematology and Oncology

Pontificia Universidad Catolica de Chile

Santiago, Chile

1
Cristian Cortez

Profesor Asociado

Pontificia Universidad Católica de Valparaíso

Valparaíso, Chile

1
Luis Federico Batiz

Full Professor

Center for Biomedical Research and Innovation (CIIB)

Universidad de Los Andes

Santiago, Chile

1
SERGIO LAVANDERO

Director

Advanced Center for Chronic Diseases (ACCDiS)

UNIVERSIDAD DE CHILE, FAC CIENCIAS QUÍMICAS Y FARMACÉUTICAS

Santiago, Chile

1
Maroun Khoury

Professor

Faculty of Medicine

Universidad de Los Andes

santiago, Chile

1
Steffany Cárdenas

Asistente de investigación

Recursos Ambientales

Universidad de Tarapacá

Arica, Chile

1
Karina Pino

Group Leader/Associate Professor

Centro de Investigación Biomédica

Universidad de los Andes

Santiago, Chile

1
Juan Roa

Chair

Pathology

Pontificia Universidad Catolica de Chile

santiago, Chile

1
Fernando Figueroa

Director

Medicina

UNIVERSIDAD DE LOS ANDES

Santiago de Chile, Chile

1
Roberto Elizondo

Profesor Asistente

Departamento de Biología Celular

Universidad de Concepción

CONCEPCION, Chile

1
Angela Court

Asistente de Investigación

Medicina Nanoregenerativa

Universidad de Los Andes

Santiago, Chile

1
Maria Matus

Principal Investigator

Fundacion Ciencia & Vida

Santiago, Chile

1
Patricio Manque

VICE PRESIDENT FOR RESEARCH AND FULL PROFESSOR

UNIVERSIDAD MAYOR

Santiago, Chile

1
Alvaro Elorza

FULL PROFESSOR

INSTITUTE OF BIOMEDICAL SCIENCES

UNIVERSIDAD ANDRES BELLO

Santiago, Chile

1
Wileidy Gómez

Postdoctorado

Medicina

Pontificia Universidad Católica de Chile

Santiago, Chile