Man

Alberto Jesus Martin Martin

Assistant professor

Universidad Mayor

Santiago, Chile

Líneas de Investigación


Bioinformatics, Machine Learning, protein structure, biological networks, regulation of gene expression, epigenetics

Educación

  •  Biology mention in Biochemistry and Molecular Biology, Universidad Autonoma de Madrid. España, 2003
  •  Bioinformatics and Computational Biology, Universidad Complutense de Madrid. España, 2005
  •  Computer Science, University College Dublin. Irlanda, 2010
  •  Certificado Adaptacion Pedagogica, Universidad Complutense de Madrid. España, 2004

Experiencia Académica

  •   Postdoc Full Time

    Universita Degli Estudi di Padova

    Faculty of Biology

    Padua, Italia

    2010 - 2013

  •   Associate Researcher Full Time

    Fundacion Ciencia & Vida

    Santiago, Chile

    2013 - 2017

  •   Assistant professor Full Time

    UNIVERSIDAD MAYOR

    Science

    Santiago, Chile

    2017 - A la fecha

Experiencia Profesional

  •   Assistantprofessor Full Time

    Universidad Mayor

    Santiago, Chile

    2017 - A la fecha

Formación de Capital Humano


Finished:
- Supervision of Nicolás Espinoza Wild in the Master degree at Ciencias de la Ingeniera, speciality in Bioengineering at Universidad Adolfo Ibáñez(January 2021 to Janueary 2022, Santiago Chile), title “Neo4GeNet: una base de datos para el estudio de redes de regulación de genes contextualizadas y su aplicación en la infección por sars-cov-2”.
- Supervision of a Sebastian Contreras-Riquelme in the Biotechnology PhD program of the Universidad Nacional Andres Bello (March 2016 to May 2021, Santiago, Chile), title “Búsqueda de genes reguladores maestros del fenotipo patogénico en Linfocitos T CD4+involucrados en enfermedad inflamatoria intestinal: una aproximación desde las herramientas computacionales”.
- Co-supervision Rodrigo A. Santibañez PhD in the Engineering Sciences PhD program of Universidad Catolica (Santiago, Chile) title “Development of rule-based models for regulatory mechanisms of gene expression and bacterial metabolism” (2014-2020).
- Undergraduate thesis co-supervision of Stefania A. Rosso Villanelo for the Biotechnology Degree of the Universidad Mayor (Chile) “Puntaje de Riesgo Poligenico para estimaciön de riesgo de enfermedad de Higado Graso No Alcoholico en una poblacin mestiza chilena”. Six months project (August 2020 to January 2021)
- Undergraduate thesis supervision of Leandro Murgas for the Bioinformatics Engineering Degree of the University of Talca (Chile) “Development of a method for the inference of time and place specific GRNs: application and comparative studies on D. melanogaster”. Six months project (August 2016 to January 2017)
- Several one month practical internships for undergraduate students: Mathematical Engineering University of Chile (3 students), Bioinformatics Engineering Degree University of Talca (2 students), Medicine U. Mayor (3 students) and Biotechnology Universidad Mayor (1 students)

Ongoing:
- Supervision of six PhD candidates in the Integrative Genomics PhD program of Universidad Mayor, Santiago, Chile: Claudia Silva, Camilo Villaman, and Javier Villacreses enrolled in 2019, Veronica Latapiat and Leandro Murgas enrolled in 2018, and Jesus Eduardo Martinez enrolled in 2017. Their PhD work focuses on rational design of bacterial consortia, machine learning determination of structural loops in chromatin, viral DNA elements in plant genomes, machine learning applied to personalized medicine,
epigentic aanalysis and chromatin states determination, and generation of gene regulatory networks in Leishmania and in its host human cells.
- Co-supervisor of a PhD candidate, Sandra Arancibia, supervised by Dr Mauricio Saez and working on epigentic variation in Huntington Disease; and a PhD student, Ivania Valdés, supervised by Dr Erick Riquelme and who will work on the characterization of tumoral microbiomes. Both are enrolled the Integrative Genomics PhD program of Universidad Mayor, respectively in 2018 and 2020.
- Co-supervision of two undergraduate thesis for the Biotechnology degree of Universidad Mayor, Chile.


Difusión y Transferencia


- Co-organizer of the 2021 (First) Annual Meeting of the Chilean Bioinformatics Society, 12 th to 14 th Jan 2022.
- Development committee and treasurer of the Sociedad Chilena de Bioinformática (@scbioinfo).
- Advisor of the Chilean Regional Student Group of the Student Council of the International Society of Computational Biology (2020 to date).
- Co-organizer of the SIBI 2019 - III International Symposium on Integrative Bioinformatics, Universidad de la Frontera Campus Pucón, Chile, December 11 to 13, 2019 (https://es.bioinformaticaintegrativa.cl/)
- Editor of Frontiers Research Topic: “Systems Modeling: Approaches and Applications”, Volumes I and II (https://www.frontiersin.org/research-topics/9750/systems-modeling-approaches-and-applications)
- Starting December 2017, Associated editor for BMC Bioinformatics (https://bmcbioinformatics.biomedcentral.com/)
- One day participation in the course “Introducción práctica a la Bioinformática Genómica” held in Talca and co-organized with the Chilean Regional Student Group of the International Society of Computational Biology (August 2019).
- Three days course, “Introduction to biological Networks”, for the Chilean Regional Student Group of the International Society of Computational Biology (Jan 2018, Jan 2019).
- One day course, “Introduction to biological Networks”, for the Chilean Regional Student Group of the International Society of Computational Biology (Oct 2015).



 

Article (33)

Comparative Genomics of Clostridium baratii Reveals Strain-Level Diversity in Toxin Abundance
Modeling approaches for probing cross-feeding interactions in the human gut microbiome
Automated generation of context-specific Gene Regulatory Networks with a weighted approach in D. melanogaster
Automated generation of context-specific gene regulatory networks with a weighted approach in Drosophila melanogaster
Enforced dimerization between XBP1s and ATF6f enhances the protective effects of the unfolded protein response (UPR) in models of neurodegeneration
Enforced dimerization between XBP1s and ATF6f enhances the protective effects of the UPR in models of neurodegeneration
Filtering of data-driven gene regulatory networks using Drosophila melanogaster as a case study
Network-Based Approaches Reveal Potential Therapeutic Targets for Host-Directed Antileishmanial Therapy Driving Drug Repurposing
Atlas: automatic modeling of regulation of bacterial gene expression and metabolism using rule-based languages
Editorial: Systems Modeling: Approaches and Applications
Pleione: A tool for statistical and multi-objective calibration of Rule-based models
RIP-MD: a tool to study residue interaction networks in protein molecular dynamics
Rule-based models and applications in biology
Stochastic simulation of multiscale complex systems with PISKaS: A rule-based approach
Transcriptional profiling of embryos lacking the lipoprotein receptor SR-B1 reveals a regulatory circuit governing a neurodevelopmental or metabolic decision during neural tube closure
LoTo: a graphlet based method for the comparison of local topology between gene regulatory networks
On Biophysical Properties and Sensitivity to Gap Junction Blockers of Connexin 39 Hemichannels Expressed in HeLa Cells
Graphlet Based Metrics for the Comparison of Gene Regulatory Networks
Multi-drug resistance profile of PR20 HIV-1 protease is attributed to distorted conformational and drug binding landscape: molecular dynamics insights
An integrated molecular dynamics, principal component analysis and residue interaction network approach reveals the impact of M184V mutation on HIV reverse transcriptase resistance to lamivudine.
NeEMO=> A Method Using Residue Interaction Networks to Improve Prediction of Protein Stability upon Mutation
Fly Cryptochrome and the Visual System
PANADA=> Protein Association Network Annotation, Determination and Analysis
ES-pritz=> accurate and fast prediction of protein disorder
MobiDB=> a comprehensive database of intrinsic protein disorder annotations
CSpritz=> accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs
Neural Network Pair-wise Interaction Fields for Protein Model Quality Assessment and Ab Initio Protein Folding
RING=> Networking interacting residues, evolutionary information and energetics in protein structure
MOBI=> a web server to define and visualize structural mobility in NMR protein ensembles
Ab initio and homology based prediction of protein domains by recursive neural networks
Long-range information and physicality constraints improve predicted protein contact maps
Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information
Distill=> A suite of web servers for the prediction of one-, two- and three- dimensional structural features of proteins

BookSection (2)

In Silico Protein Motif Discovery and Structural Analysis
Contact Map Prediction by Machine Learning

ConferencePaper (1)

Neural Network Pairwise Interaction Fields for Protein Model Quality Assessment

Proyecto (8)

DESARROLLO DE CONSORCIOS BACTERIANOS PARA EL TRATAMIENTO DE ENFERMEDADES NEURODEGENERATIVAS
Discovery of neuroprotective bacterial metabolites and their mechanism of action in C. elegans
IDENTIFICATION OF CROSS-FEEDING INTERACTIONS IN THE GUT MICROBIOME FOR DESIGNING MICROBIAL COMMUNITIES
From gene expression data to dynamic simulation of gene regulatory networks: development of inference methods based on local motifs and their biological applications
FROM GENE EXPRESSION DATA TO DYNAMIC SIMULATION OF GENE REGULATORY NETWORKS=> DEVELOPMENT OF INFERENCE METHODS BASED ON LOCAL MOTIFS AND THEIR BIOLOGICAL APPLICATIONS.
FROM GENE EXPRESSION DATA TO DYNAMIC SIMULATION OF GENE REGULATORY NETWORKS=> DEVELOPMENT OF INFERENCE METHODS BASED ON LOCAL MOTIFS AND THEIR BIOLOGICAL APPLICATIONS.
Integracion de la biologia estructural al desarollo de la biotecnologia
Development of Computational Methods for the Determination of Causal-Condition Specific Gene Regulatory Networks
27
Alberto Martin

Assistant professor

Centro de Genómica y Bioinformática

Universidad Mayor

Santiago, Chile

6
Daniel Garrido

Associate Professor

Chemical and Bioprocess Engineering

Pontificia Universidad Católica de Chile

Santiago, Chile

4
Tomas Perez-Acle

Full Professor

Computational Biology Lab

Fundación Ciencia para la Vida

Santiago, Chile

2
Alex Vielma

Postdoctoral researcher

Centro Interdisciplinario de Neurociencias de Valparaíso

Valparaiso, Chile

1
alejandro bernardin

PhD (c)

Fundación Ciencia y Vida

Santiago, Chile

1
Francisca Salas

Asistant Professor

Instituto de Ciencias de la Salud

Universidad de O'Higgins

Rancagua, Chile

1
David Holmes

Head, Laboratory of Bioinformatics and Genome Biology

Center for Bioinformatics and Genome Biology

FUNDACION CIENCIA & VIDA

Santiago, Chile

1
Juan Saez

Professor

Instituto de Neurociencias

Universidad de Valparaiso

Valparaíso, Chile

1
Nicolás Santander

Investigador Postdoctoral

Instituto de Ciencias de la Salud

Universidad de O'Higgins

Rancagua, Chile

1
Claudia Pareja

Postdoc

Departamento de Hematología-Oncología

Pontificia Universidad Católica de Chile

Santiago, Chile

1
José Gárate

Profesor Asistente

Instituto de Neurociencia

Universidad de Valparaíso

Valaparaiso, Chile

1
Dolores Busso

Associate Professor

Centro de Investigación e Innovación Biomédica

Universidad de Los Andes

Santiago, Chile

1
Attilio Rigotti

Full Professor

Nutrition, Diabetes and Metabolism

PONTIFICIA UNIVERSIDAD CATÓLICA DE CHILE - ESCUELA DE MEDICINA - DEPTO DE GASTROENTEROLOGÍA

Santiago, Chile

1
Alejandro Godoy

Associate Professor

Centro de Biología Celular y Biomedicina

Universidad San Sebastián

Santiago, Chile

1
Paulina Troncoso

Inserción PhD

Investigación y Desarrollo

Neurognos SpA

Santiago, Chile

1
Oliver Schmachtenberg

Investigador titular

Instituto de Biología

Universidad de Valparaíso, CINV

Valparaíso, Chile

1
Sebastián Gutiérrez

Investigador postdoctoral

Fundación Ciencia & Vida

Santiago, Chile

1
Pedro Saa

Profesor Asistente

Departmento de Ingenieria Quimica y Bioprocesos

Pontificia Universidad Catolica de Chile

Santiago, Chile