Anestis Gkanogiannis, PhD

Anestis Gkanogiannis, PhD

Bioinformatics and Machine/Deep Learning Scientist

Biography

I am an award-winning researcher with a strong background in Bioinformatics, Computational Biology, Artificial Intelligence and Machine Learning and with strong analytical skills and problem-solving capabilities.

I am currently working as a Bioinformatics Scientist at the International Center for Biosaline Agriculture (ICBA) in Dubai, UAE.

I have extensive experience in algorithm construction and prototype software development, with a focus on NGS data analysis/integration/visualization, Computational Biology, Comparative Genomics, Genomic Selection, Artificial Intelligence, Machine Learning, Deep Learning, Big Data Mining, Classification, Clustering, Algorithms and Data Structures, and HPC cluster and systems management. I am proficient in programming languages such as C++, Java, R, and Android development, as well as Nextflow pipeline development and Docker/Singularity container development.

Download my resumé.

Interests
  • Bioinformatics, Computational Biology
  • Machine/Deep Learning
  • Artificial Intelligence
  • Information Retrieval
  • Electronics prototyping (RPi, Arduino)
Education

  • PhD in Machine Learning, 2011

    Athens University of Economics and Business

  • MSc in Machine Learning, 2005

    Athens University of Economics and Business

  • BSc in Physics, 2003

    University of Crete

Recent Posts

Pioneering Biodiversity: Citrullus colocynthis Genome Becomes the First ERGA Community Genome
“Being part of ERGA facilitated collaboration and resource sharing, which were instrumental in achieving the project’s goals.” - says the project leader Anestis Gkanogiannis, PhD. This genome unlocks exciting new research opportunities.
admin
Thursday, 19 Sep 2024 1 min read

Skills

bioinformatics
Bioinformatics

90%

artificial-intelligence
AI

90%

machine-learning
Machine Learning

90%

deep-learning
Deep Learning

80%

rpi
Electronics

80%

hpc
HPC

80%

java
Java

90%

R

80%

c
C/C++

80%

linux
UNIX/Linux

90%

mathematics
Mathematics

80%

physics
Physics

80%

Experience

 
 
 
 
 
International Center for Biosaline Agriculture, ICBA
Bioinformatics Scientist
International Center for Biosaline Agriculture, ICBA
Dec 2022 – Present Dubai, United Arab Emirates
De novo Reference Genome assembly, Reference Genome annotation, Population Genomics
 
 
 
 
 
Gene Regulation, Stem Cells and Cancer, CRG
Bioinformatician
Gene Regulation, Stem Cells and Cancer, CRG
Apr 2022 – Nov 2022 Barcelona, Catalonia, Spain
Cancer metabolism, NGS data analysis (RNA-Seq, ATAC-Seq, Nanopore, WGS, etc.), Nextflow pipeline development, Bioconductor R packages development, CRISPR gene screening, Computational Biology
 
 
 
 
 
Agrobiodiversity Research Area, CIAT/CGIAR
Research Scientist / Bioinformatics Head
Agrobiodiversity Research Area, CIAT/CGIAR
Jan 2017 – Mar 2021 Cali, Valle de Cauca, Colombia
Plant Genomics/Genetics/Bioinformatics (Cassava, Rice, Bean, Forages), NGS data analysis, Computational Biology, Population Genomics, GWAS, Genomic Selection, Machine Learning, Artificial Intelligence, Big Data
 
 
 
 
 
Intégration de données (Equipe ID), CIRAD/BIOS/AGAP
Post-Doctorate Research Fellow
Intégration de données (Equipe ID), CIRAD/BIOS/AGAP
Jun 2015 – Dec 2016 Montpellier, Languedoc-Roussillon-Midi-Pyrénées, France
Research Scientist, Computational Biology, Software Analyst/Developer, Web Developer: RTB (Roots Tubers and Banana).
 
 
 
 
 
Laboratoire de Génomique et Biochimie du Métabolisme(LGBM), CEA/DSV/IG/Genoscope/LGBM
Post-Doctorate Research Fellow
Laboratoire de Génomique et Biochimie du Métabolisme(LGBM), CEA/DSV/IG/Genoscope/LGBM
Jun 2013 – Jun 2015 Evry, Île-de-France, France
Research Scientist, Machine Learning and Computational Biology, Software Analyst/Developer (in cooperation with CEA LIST): MetaTarget
 
 
 
 
 
University of New Brunswick, Faculty of Computer Science
Post-Doctorate Research Fellow
University of New Brunswick, Faculty of Computer Science
Oct 2011 – Mar 2013 Fredericton, NB, Canada
Research Scientist, Machine Learning, Artificial Intelligence, Software Analyst/Developer and Project Manager, I-AID: Intelligent Analysis of Information and Dissemination

Awards

Zindi
First Place Winner (as CGIAR participant)
Syngenta
First Place Winner
ECML
First prize, Spam Detection Task
Greek General Secreteriat for Research and Technology
PENED Scholarship

Publications

Laura Perez-Fons, Tatiana Maria Ovalle, Margit Drapal, Maria Alejandra Ospina, Anestis Gkanogiannis, Adriana Bohorquez-Chaux, Luis Augusto Becerra López-Lavalle, Paul David Fraser (2023). Integrated genetic and metabolic characterization of Latin American cassava (Manihot esculenta) germplasm. Plant Physiology.

PDF Cite DOI

Mauricio Peñuela, Camila Riccio-Rengifo, Jorge Finke, Camilo Rocha, Anestis Gkanogiannis, Rod A. Wing, Mathias Lorieux (2023). Prediction of crossover recombination using parental genomes. PLOS ONE 2023, 18(2), 1-21;.

PDF Cite DOI

Mauricio Peñuela, Jenny Johana Gallo-Franco, Jorge Finke, Camilo Rocha, Anestis Gkanogiannis, Thaura Ghneim-Herrera, Mathias Lorieux (2022). Methylation in the CHH Context Allows to Predict Recombination in Rice. Int. J. Mol. Sci. 2022, 23(20), 12505;.

PDF Cite DOI

Angélica M. Jaramillo, Santiago Sierra, Paul Chavarriaga-Aguirre, Diana Katherine Castillo, Anestis Gkanogiannis, Luis Augusto Becerra López-Lavalle, Juan Pablo Arciniegas, Tianhu Sun, Li Li, Ralf Welsch, Erick Boy, Daniel Álvarez (2022). Characterization of cassava ORANGE proteins and their capability to increase provitamin A carotenoids accumulation. PLoS ONE 17(1): e0262412..

PDF Cite DOI

Anestis Gkanogiannis, Luis Augusto Becerra, et al (2021). The diversity, origin and evolution of wild and landrace varieties of M.esculenta from RADSeq data. In Preparation.

Anestis Gkanogiannis, Luis Augusto Becerra, et al (2021). Two dense genetic maps and WhiteFly infestation QTLs from RADSeq and WGS data of two F1 M.esculenta populations. In Preparation.

See all publications

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