
Alberto Jesus Martin Martin
Associate professor
Universidad San Sebastián
Santiago, Chile
Bioinformatics, Machine Learning, protein structure, biological networks, regulation of gene expression, epigenetics
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Biology mention in Biochemistry and Molecular Biology, Universidad Autonoma de Madrid. España, 2003
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Bioinformatics and Computational Biology, Universidad Complutense de Madrid. España, 2005
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Computer Science, University College Dublin. Irlanda, 2010
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Certificado Adaptacion Pedagogica, Universidad Complutense de Madrid. España, 2004
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Postdoc Full Time
Universita Degli Estudi di Padova
Faculty of Biology
Padua, Italia
2010 - 2013
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Associate Researcher Full Time
Fundacion Ciencia & Vida
Santiago, Chile
2013 - 2017
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Assistant professor Full Time
UNIVERSIDAD MAYOR
Science
Santiago, Chile
2017 - 2022
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Associate professor Full Time
UNIVERSIDAD SAN SEBASTIAN
Facultad de Ingeniería, Arquitectura y Diseño
Santiago, Chile
2022 - At present
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Assistantprofessor Full Time
Universidad Mayor
Santiago, Chile
2017 - 2022
FINISHED:
Postdoc:
- Ana Moya USS grant [USS-FIN-23-PDOC-03] (2023) “Study of the genomic structural and single nucleotide variations of Acidithiobacillia class lineages and their role in the evolution of the taxon”.
- Carolina Gonzalez FONDECYT Postdoc [3190792] (2019-2022) “Unraveling the dynamics and evolutionary mechanisms of polyextremophilic microorganisms by omics approaches”.
PhD:
- Supervision of Claudia Silva in the Integrative Genomics PhD program at Universidad Mayor (March 2019 - December 2024, Santiago, Chile), title: “Design Of Microbial Consortia Based In Cross-Feeding Interaction To The Productions Of Butyrate”.
- Supervision of Veronica Latapiat in the Integrative Genomics PhD program at Universidad Mayor (March 2018 - December 2024, Santiago, Chile), title: “Study of molecular interactions and pathways in individuals with Alzheimer’s disease allows stratification and new therapeutic targets”.
- Supervision of Camilo Villaman in the Integrative Genomics PhD program at Universidad Mayor (March 2019 - November 2024, Santiago, Chile), title: “Prediction of CTCF loop dynamics and its implication in Alzheimer’s Disease”.
- Supervision of Leandro Murgas Saavedra in the Integrative Genomics PhD program at Universidad Mayor (March 2018 - May 2023, Santiago, Chile), title: “Identification of relationships between epigenetic marks with random forest: application to a model of colorectal cancer”.
- Co-supervisor of Sandra Arancibia (supervisor Dr Mauricio Saez) in the Integrative Genomics PhD program at Universidad Mayor (March 2018 - April 2023, Santiago, Chile), title: “Study of the variation in H3K27 acetylation levels and transcriptional changes associated with CRE elements in a model of early stages of Huntington’s disease”.
- Supervision of Jesus Eduardo Martinez in the Integrative Genomics PhD program at Universidad Mayor (March 2017 - August 2022, Santiago, Chile), title: “Determination of changes in the regulation of gene expression caused by pathogen-host interaction using the leishmania-macrophage model”.
- 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”.
MSc:
- Supervision of Alex Cañoles in the Magister in Data Science program at Universidad San Sebastián (November 2023 - November 2024, Chile), title: “Optimización de Merma de Alimento en el Proceso de Alimentación de las Truchas Arco??ris (Oncorhynchus mykiss) Utilizando Modelos Predictivos de Machine Learning”.
- Supervision of Nicolás Espinoza Wild in the Master degree at Ciencias de la Ingenier??a, speciality in Bioengineering at Universidad Adolfo Ibáñez (January 2021 to January 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”.
Undergrduate:
- Undergraduate thesis co-supervision of Sof??a G. Rodr??guez Muñoz for the Biotechnology Degree of the Universidad Mayor (Chile) “Análisis de redes a base de transcriptómica de célula única asociada a S??ndrome de Rett” March 2021 to November 2022.
- Undergraduate thesis co-supervision of Mario Francisco Muñoz Corter for the Biotechnology Degree of the Universidad Mayor (Chile) “Medicina de precisión: Nuevos genes relacionados con el S??ndrome de West de forma in-silico obtenidos mediante la secuenciación de exoma cl??nico aplicado a un trio parental chileno.”. November 2020 to October 2022
- 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 (PhD):
- Supervision of Javier Villacreses, PhD candidate in the Integrative Genomics PhD program of Universidad Mayor, Santiago, Chile. His work focuses on the annotation of viral DNA elements in plant genomes and their association to stress,
- Supervision of PhD candidate of the Computational Biology PhD program of Universidad San Sebastian, Sof??a Rodriguez, who works on the developmetn of automated approaches to determine pseudo-state trajectories in scRNA-seq data.
- Supervision of PhD candidate of the Computational Biology PhD program of Universidad San Sebastián, Mario Maulen, who works on the association between SARS-Cov2 strains and oportunistic pathogens.
- Co-supervisor of a PhD candidate, Solange Gouet, supervisad by Dr Daniela Sauma at the PhD program in Science from University of Chile, mention on Molecular Cell Biology and Neurosciences who work on the characterization of immune cells.
- Supervision of PhD candidate of the Cell Biology and Biomedicine PhD program of Universidad San Sebastian, Ignacio Pezoa, who works on the association of vesicle formation and metastasis in ovary cancer.
- Supervision of PhD candidate of the Computational Biology PhD program of Universidad San Sebastian, Sergio Hernandez, who works on scRNA-seq data imputation and automated developmental trajectory reconstuction.
- 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/)
- Starting August 2024, Associated editor for PLOS Computational Biology
- 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).
In Silico Protein Motif Discovery and Structural Analysis |
Contact Map Prediction by Machine Learning |
Neural Network Pairwise Interaction Fields for Protein Model Quality Assessment |
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 |
Development of Computational Methods for the Determination of Causal-Condition Specific Gene Regulatory Networks |
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 |
Microbial interactions and the homeostasis of the gut microbiome: the role of<i> Bifidobacterium</i> |

Daniel Garrido
Associate Professor
Chemical and Bioprocess Engineering
Pontificia Universidad Católica de Chile
Santiago, Chile

Tomas Perez-Acle
Full Professor
Computational Biology Lab
Fundación Ciencia para la Vida
Santiago, Chile

Alex Vielma
Postdoctoral researcher
Centro Interdisciplinario de Neurociencias de Valparaíso
Valparaiso, Chile

Valentina Castillo
Investigadora Postdoctoral
Instituto de Ingeniería Biológica y Médica
Pontificia Universidad Católica de Chile
Santiago, Chile

Vinicius Ramos Henriques
Associate Professor
Advanced Center for Chronic Diseases - ACCDiS
Univesidad de Chile
Santiago, Chile

Marcelo Garrido
Director
CENTRO DEL CÁNCER, PONTIFICIA UNIVERSIDAD CATÓLICA DE CHILE
Santiago, Chile

Alexis Martinez
Investigador postdoctoral senior
Facultad de medicina
Instituto de Neurcoeincia Biomedica
Santiago, Chile

Guilherme Gischkow
Estudiante doctorado
Doctorado en Neurobiologia
Universidad Mayor de Chile
Santiago, Chile

Rodrigo Pacheco
Associate Investigator; Head of the Laboratory of Neuroimmunology
Fundación Ciencia para la Vida
Santiago, Chile

Francisco Issotta
Investigador Postoctoral
Genética Molecular y Microbiología
Pontificia Universidad Católica de Chile
Santiago, Chile

Paulina Troncoso
Bioquimica PhD
Laboratorio Clínico Banco de Sangre Anatomía Patológica
Clínica Alemana de Santiago
Santiago, Chile

Katherine Rivera
PhD (c) student in Medical Science
Pontificia Universidad Católica de Chile
Santiago, Chile

Claudia Pareja
Investigadora de Postdoctorado
Departamento de Hematología-Oncología
Pontificia Universidad Católica de Chile
Santiago, Chile

Francisca Salas
Asistant Professor
Instituto de Ciencias de la Salud
Universidad de O'Higgins
Rancagua, Chile

David Holmes
Head, Laboratory of Bioinformatics and Genome Biology
Center for Bioinformatics and Genome Biology
FUNDACION CIENCIA & VIDA
Santiago, Chile

Nicolás Santander
Assistant Professor
Instituto de Ciencias de la Salud
Universidad de O'Higgins
Rancagua, Chile

José Gárate
Profesor Asistente
Instituto de Neurociencia
Universidad de Valparaíso
Valaparaiso, Chile

Dolores Busso
Associate Professor
Centro de Investigación e Innovación Biomédica
Universidad de Los Andes
Santiago, Chile

Attilio Rigotti
Full Professor
Nutrition, Diabetes and Metabolism
PONTIFICIA UNIVERSIDAD CATÓLICA DE CHILE - ESCUELA DE MEDICINA - DEPTO DE GASTROENTEROLOGÍA
Santiago, Chile

Alejandro Godoy
Associate Professor
Centro de Biología Celular y Biomedicina
Universidad San Sebastián
Santiago, Chile

Ivan Nancucheo
Profesor Titular
Facultad de Ingeniería, Arquitectura y Diseño
Universidad San Sebastián
Concepción, Chile

Oliver Schmachtenberg
Investigador titular
Instituto de Biología
Universidad de Valparaíso, CINV
Valparaíso, Chile

Claudio Hetz
Deputy Director
INSTITUTO DE CIENCIAS BIOMÉDICAS, FACULTAD DE MEDICINA, UNIVERSIDAD DE CHILE
SANTIAGO, Chile