Ibai Irastorza Azcarate - Data Scientist 🔬💻📚

Email / Email2 / LinkedIn / GitHub / Google Scholar

Ph.D. in Bioinformatics with Computer Engineering background. 10 years of experience in research and data science, and more than 4 in software development. With a diverse professional journey, I’ve served as a High-Performance Computer Administrator and contributed to the development of various applications in the private sector and academia. Proficient in Python, Pandas and Pyplot, I am confident in handling large genomic data. I am also committed to continuous learning, evident in my recent participation in Deep Learning workshops or courses in Machine learning in weather and climate. I excel in synthesizing information into compelling theses and research articles, showcasing strong written communication skills. My international academic experience has cultivated cultural awareness, adaptability, and resilience, enabling effective collaboration in diverse teams. Proficient in English, I have attended numerous international conferences to showcase my work, fostering confidence in my English communication and presentation abilities. Additionally, I have provided supervision to colleagues and successfully managed substantial projects, affirming my proficiency in leadership and systematic skills.

🎓 Education

Ph.D., Bioinformatics Complutense University of Madrid (Oct 2013 - May 2018)
M.Sc., Bioinformatics National Health Institute Carlos III, Madrid (Oct 2012 - Oct 2013)
B.Sc., Computer Engineering Complutense University of Madrid (Sep 2009 - Sep 2011)
B.Sc., Technical Computer Engineering in Computer Systems University of Mondragon, Spain (Jul 2003 - Jul 2009)

💼 Work experience

Post-Doctoral Researcher @ MDC-BIMSB (Berlin) Supervisor: Dr. Ana Pombo (Jun 2018 - Present)

Integration of spatial genomics data with epigenetic data
Python, Pandas, Numpy, Scikit, Bash, Git, Inkscape, Docker…
Data science, data visualization, software engineering, ML algorithms
Grant acquisition: FEBS long-term fellowship: 100.000 €

Ph.D. Candidate @ CABD (Seville) / Complutense University of Madrid Supervisor: Dr. Damien Devos (Oct 2013 - May 2018)

3D Modeling and Integration of spatial proteomics and genomics data
Python, R, Pandas, Scikit, Bash, Git, Inkscape, Docker…
Software engineering, data science, data visualization, ML algorithms
HPC administration and R teacher in masters degree.

M.Sc. Internship @ University of Heidelberg and the Center for Organismal studies, Heidelberg, Germany (May 2013 - Sep 2013)

Integrative 3D modeling of protein complexes
Analysis, interpretation and integration of spatial proteomic data

Android Applications Developer (Oct 2011 - May 2013)

Game and application development as a freelancer

Software Developer @ Accenture / BBVA (Madrid) (Oct 2011 - Aug 2012)

Development of software applications. Maintenance and support of bank applications.
Developing, testing, debugging and deploying in Java

Software Developer @ Mon Digital (IT company, Madrid) (May 2011 - Oct 2011)

Design, development, testing and deploying of web sites and web crawlers using Python, Django, Javascript and CSS.

Software Developer @ Embedded Technologies Innovation Centre / Microsoft (Arrasate, Spain) (Sep 2008 - Jul 2009)

Developed software for a medicine dispenser in .Net Micro Framework
Designing, developing, testing, debugging and deploying in C#.

💻 ML projects

ML project: Satellite image classification ( Tensorflow, keras, Docker, flask): My Code

Deep Learning project: Rain prediction (Scikit-learn, Docker, AWS, Elastic BeanStalk, Flask): My Code

MLOps project: Drought prediction (Mlflow, Prefect, Prometheus, Grafana, Docker, Flask, Scikit-learn): My Code

✍️ Courses/Activities

AI & Data Engineer Online Training @ International University (June 2024 - October 2024)

Machine Learning operations (MLOps) course @ DataTalksClub (May 2024 - Aug 2024) My Code

Machine learning in Weather and Climate, Massive Open Online Course @ ECMWF (Dec 2023 - Present) My Code

Machine Learning course @ DataTalksClub (Sep 2023 - Dec 2023) My Code

Applied Deep Learning in Bioinformatics, Summer School @ Copenhagen University (Aug 2023)

Review Editor in “Frontiers in Cell and Developmental Biology” (Aug 2023 - Present)

Master Thesis reviewer of Altair Hernández Chichilla, Pompeu Fabra University, Barcelona (Jul 2020)

Master degree Teacher in Bioinformatic Analysis. Universidad Pablo de Olavide (UPO), Sevilla. (Jan 2016 - Mar 2018) R and Perl programming languages

Integration of MultiOmic Data in Genetic Association Studies. Universidad de Sevilla. (Sep 2017)

High Performance Computer Administrator @ CABD (Seville) (Dec 2015 - Dec 2017)

Secondment @ University California San Francisco (Sep 2014 - Oct 2014)

3D genome modeling workshop, Strasbourg (Sep 2014)

💻 Technical Skills:

Profficient with Python (Pandas, Numpy, Pyplot, Seaborn, Scikit-learn …), Bash, Git, Inkscape, Docker
ML experience: Tensorflow, Keras, AWS, Kubernetes
MLOps experience: Mlflow, Prefect, Prometheus, Grafana
Also worked with Java, C, C#, Javascript, CSS, Html, PHP, Corba, Jinja, Django, Werkzeug, MySQL, SQLite, PostgreSQL.
Experience with embedded systems and -NET micro Framework
Software engineering, UML and different development states of informatic projects.
Experience in development environments like NetBeans, Eclipse, Visual Studio and Visual Code.
Functionality and structure of Operatives systems based on Linux.
Creation and management of Network protocols.
Web positioning (SEO) knowledge.

🦾 Other Skills

Working in an independent manner and also in big collaborations
Gathering, evaluating and synthesizing of information into articles
Project management and mentoring
Good communication and presentation skills
Good at problem solving and adaptability

🎤 Communication in International meetings

Climate Career week (25/03/2024)
CABD 20th scientific anniversary, Sevilla (Oral Communication) (06/06/2023)
SPP2202 monthly meeting (Oral Communication, Online) (10/05/2023)
Joint Meeting in Neuroepigenetics, Alicante (Organization and Oral Communication) (31/03/2023)
4DN monthly meeting (Oral Communication, Online) (06/03/2023)
Annual lab retreat, Berlin (Oral Communication) (21/11/2022)
Till Bartke Lab retreat, Berlin (Oral Communication, invited speaker) (21/09/2022)
Bioinformatics Social Meetings, Berlin (Oral Communication, Online) (27/01/2021)
4D Epigenome conference, Venice (02/10/2019)
4DN-ASCB Satellite Meeting, San Diego (Oral Communication) (06/12/2018)
4DN Annual Meeting, San Diego (04/12/2018)
Annual lab retreat, Berlin (Oral Communication) (21/11/2018)
3D/4D organization of chromatin, BioMed Conference, Barcelona. (13/11/2017)
ZENCODE/DevCom Conference, Carmona (27/03/2017)
4D Genome ERC Workshop. Dynamics of Genome Structure, Barcelona. (22/09/2016)
XIII Symposium on Bioinformatics. Valencia, Spain. (Oral Communication, Highlight Talk) (10/05/2016)
HPC admin tech 2016 conference, Madrid. (02/03/2016)
IX meeting of the Protein Structure and Function Network, Sevilla (Oral Communication) (11/11/2015)
ISMB/ECCB 2015, Dublin (10/07/2015)
13th European Conference on Computational Biology, Strasburg (07/09/2014)
V IMMPC Annual Conference and 4DCellFate Workshop, Barcelona (Oral Communication) (27/03/2014)

🏆 Accomplishments

FEBS long term fellowship 100.000 € https://www.febs.org/funding/fellowships/ (Jun 2018 - Dec 2020)

💬 Languages

🇵🇲 Euskara/Basque: Native
🇪🇸 Spanish: Native
🇬🇧 English: C1 Proficient User
🇩🇪 German: A2 Basic User

🔬 Research Publications

Ibai Irastorza-Azcarate,#, Alexander Kukalev,#, Rieke Kempfer,#, Christoph Thieme, Guido Mastrobuoni, Julia Markowski, Gesa Loof, Thomas M. Sparks, Emily Brookes, Kedar Natarajan, Mario Nicodemi, Bing Ren, Roland Schwarz, Stefan Kempa, and Ana Pombo. “Extensive folding variability between homologous chromosomes in mammalian cells” Sent to Molecuar Systems Biology
RD Acemel, JJ Tena, I Irastorza-Azcarate, F Marlétaz, C Gómez-Marín, …
“A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation”
Nature genetics, 48 (3), 336-341, 2016
DOI: https://doi.org/10.1038/ng.3497
W Winick-Ng, A Kukalev, I Harabula, L Zea-Redondo, D Szabó, M Meijer, …
“Cell-type specialization is encoded by specific chromatin topologies”
Nature, 599 (7886), 684-691, 2021
DOI: https://doi.org/10.1038/s41586-021-04081-2
A Picco, I Irastorza-Azcarate, T Specht, D Böke, I Pazos, AS Rivier-Cordey, …
“The in vivo architecture of the exocyst provides structural basis for exocytosis”
Cell, 168 (3), 400-412. e18, 2017
DOI: https://doi.org/10.1016/j.cell.2017.01.004
L Fiorillo, F Musella, M Conte, R Kempfer, AM Chiariello, S Bianco, …
“Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin”
Nature methods, 18 (5), 482-490, 2021
DOI: https://doi.org/10.1038/s41592-021-01135-1
M Franke, E De la Calle-Mustienes, A Neto, M Almuedo-Castillo, …
“CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression”
Nature communications, 12 (1), 5415, 2021
DOI: https://doi.org/10.1038/s41467-021-25604-5
C Vicente-Garcia, B Villarejo-Balcells, I Irastorza-Azcarate, S Naranjo, …
“Regulatory landscape fusion in rhabdomyosarcoma through interactions between the PAX3 promoter and FOXO1 regulatory elements”
Genome Biology, 18, 1-18, 2017
DOI: https://doi.org/10.1186/s13059-017-1225-z
R Alcalá-Vida, J Seguin, C Lotz, AM Molitor, I Irastorza-Azcarate, A Awada, …
“Age-related and disease locus-specific mechanisms contribute to early remodelling of chromatin structure in Huntington’s disease mice”
Nature communications, 12 (1), 364, 2021
DOI: https://doi.org/10.1038/s41467-020-20605-2
I Irastorza-Azcarate, RD Acemel, JJ Tena, I Maeso, JL Gómez-Skarmeta, …
“4Cin: A computational pipeline for 3D genome modeling and virtual Hi-C analyses from 4C data”
PLoS Computational Biology, 14 (3), e1006030, 2018
DOI: https://doi.org/10.1371/journal.pcbi.1006030
J Markowski, R Kempfer, A Kukalev, I Irastorza-Azcarate, G Loof, B Kehr, …
“GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data”
Bioinformatics, 37 (19), 3128-3135, 2021
DOI: https://10.1093/bioinformatics/btab238
I Irastorza-Azcarate, D Castaño-Díez, DP Devos, O Gallego
“Live-cell structural biology to solve biological mechanisms: The case of the exocyst”
Structure, 27 (6), 886-892, 2019
DOI: https://doi.org/10.1016/j.str.2019.04.010