Personal information

Systems Biology, Computational Biology, Data Science, Metabolic networks, Optimization, Python, R, Javascript, HTML5, CSS3, Metagenomics, Bioinformatics

Biography

Semidán Robaina, PhD is the Principal Systems Modeling Scientist at NewAtlantis Labs (NAL), leading the design and development of computational frameworks to quantify microbial ecosystem services and AI tools to leverage genetic assets from ocean meta-omics samples. He brings over 12 years of experience in computational systems biology and an extensive track record in scientific research and open-source software development. His PhD in Systems Biology, earned through a joint program between the Max Planck Society and the University of Potsdam, focused on designing mathematical frameworks to uncover hidden patterns in microbial and plant metabolism. As Senior Bioinformatician at the University of La Laguna, he led the development of bioinformatics pipelines that revealed groundbreaking discoveries in marine microbial metabolism, including novel sulfur metabolism in deep-sea bacteria and temperature effects on prevalent ocean photosynthesizers. At NAL, he combines his expertise in systems biology and AI to advance a vision where nature's intrinsic worth drives its protection, working with cutting-edge science and technology to protect and restore ocean ecosystems.

Activities

Employment (6)

NewAtlantis Labs: Remote, ES

2023-08-01 to present
Employment
Source: Self-asserted source
Dr. Semidán Robaina Estévez

Universidad de La Laguna: La Laguna, Islas Canarias, ES

2021-03-01 to 2023-07-31 | Bioinformatician (Microbiology)
Employment
Source: Self-asserted source
Dr. Semidán Robaina Estévez

Data Scientist (self-employed): Santa Cruz de Tenerife, ES

2019-05-01 to 2020-12-31 | Data Scientist
Employment
Source: Self-asserted source
Dr. Semidán Robaina Estévez

University of Potsdam: Potsdam, DE

2017-10-01 to 2018-12-31 | Postdoctoral researcher (Bioinformatics)
Employment
Source: Self-asserted source
Dr. Semidán Robaina Estévez

Max Planck Institute of Molecular Plant Physiology: Potsdam, DE

2013-10-01 to 2017-09-15 | IMPRS fellow (Systems Biology and Mathematical Modeling)
Employment
Source: Self-asserted source
Dr. Semidán Robaina Estévez

University of La Laguna: La Laguna, ES

2012-06-01 to 2013-06-01 | Predoctoral researcher (Biochemistry)
Employment
Source: Self-asserted source
Dr. Semidán Robaina Estévez

Education and qualifications (4)

Universidad de La Laguna: La Laguna, Islas Canarias, ES

2020-10-01 to 2021-09-15 | Master's Degree in Teacher Training for Compulsory Secondary Education and Baccalaureate (specialty Biology and Geology)
Qualification
Source: Self-asserted source
Dr. Semidán Robaina Estévez

University of Potsdam: Potsdam, DE

2013-10-01 to 2017-09-15 | Dr. rer. nat. Systems Biology
Education
Source: Self-asserted source
Dr. Semidán Robaina Estévez

University of La Laguna: La Laguna, ES

2012-10-01 to 2013-07-15 | M.Sc. Biotechnology
Qualification
Source: Self-asserted source
Dr. Semidán Robaina Estévez

University of La Laguna: La Laguna, ES

2007-10-01 to 2012-03-15 | Licenciatura in Biology: Focus on Molecular and Cell Biology
Qualification
Source: Self-asserted source
Dr. Semidán Robaina Estévez

Professional activities (2)

Ronin Institute: World, US

2019-09-15 to 2022-07-01 | Research Scholar
Membership
Source: Self-asserted source
Dr. Semidán Robaina Estévez

Max Planck Institute of Molecular Plant Physiology: Potsdam, DE

2017-09-15 to 2019-01-31 | Guest Scientist (Systems Biology and Mathematical Modeling)
Membership
Source: Self-asserted source
Dr. Semidán Robaina Estévez

Works (16)

Applications of marine microbial community models in the nature-based economy

PLOS Sustainability and Transformation
2024-11-27 | Journal article
Contributors: Semidán Robaina-Estévez; Jose Carlos Báez; Jay Gutiérrez
Source: check_circle
Crossref

Gene expression response to temperature acclimation in a model photoheterotrophic marine flavobacterium (Dokdoniasp. MED134)

2023-12-25 | Preprint
Contributors: Semidán Robaina-Estévez; José M. González; Ana María Cabello; Antonio S. Palacio; Ruairí Gallagher; Ángel López-Urrutia; Laura Alonso-Sáez
Source: check_circle
Crossref

Quantifying Microbial Guilds

2023-07-25 | Preprint
Contributors: Juan Rivas-Santisteban; Pablo Yubero; Semidán Robaina-Estévez; José M. González; Javier Tamames; Carlos Pedrós-Alió
Source: check_circle
Crossref

Transcriptional Mechanisms of Thermal Acclimation in Prochlorococcus

mBio
2023-06-27 | Journal article
Contributors: Laura Alonso-Sáez; Antonio S. Palacio; Ana M. Cabello; Semidán Robaina-Estévez; José M. González; Laurence Garczarek; Ángel López-Urrutia; Jennifer B. H. Martiny
Source: check_circle
Crossref

A ubiquitous gammaproteobacterial clade dominates expression of sulfur oxidation genes across the mesopelagic ocean

Nature Microbiology
2023-04-24 | Journal article
Contributors: Federico Baltar; Clara Martínez-Pérez; Chie Amano; Marion Vial; Semidán Robaina-Estévez; Thomas Reinthaler; Gerhard J. Herndl; Zihao Zhao; Ramiro Logares; Sergio E. Morales et al.
Source: check_circle
Crossref

Pynteny: a Python package to perform synteny-aware, profile HMM-based searches in sequence databases

Journal of Open Source Software
2023-03-22 | Journal article
Contributors: Semidán Robaina-Estévez; José M. González
Source: check_circle
Crossref

BRENDApyrser: a Python package to parse and manipulate the BRENDA database

Zenodo
2022-08-26 | Research tool
Contributors: Dr. Semidán Robaina Estévez
Source: Self-asserted source
Dr. Semidán Robaina Estévez

Flux-based hierarchical organization of Escherichia coli’s metabolic network

PLOS Computational Biology
2020-04-20 | Journal article
Contributors: Semidán Robaina-Estévez; Christoph Kaleta; Zoran Nikoloski
Source: check_circle
Crossref

Code and Data of "Flux-based hierarchical organization of Escherichia coli's metabolic network"

2019-09-04 | Software
Source: Self-asserted source
Dr. Semidán Robaina Estévez

Flux-based hierarchical organization of Escherichia coli’s metabolic network

2019-08-10 | Other
Contributors: Semidán Robaina-Estévez; Zoran Nikoloski
Source: check_circle
Crossref

Context-specific metabolic predictions

2017-09 | Dissertation or Thesis
Source: Self-asserted source
Dr. Semidán Robaina Estévez

Resolving the central metabolism of Arabidopsis guard cells

Scientific Reports
2017-08-16 | Journal article
Contributors: Semidán Robaina-Estévez; Danilo M. Daloso; Youjun Zhang; Alisdair R. Fernie; Zoran Nikoloski
Source: check_circle
Crossref

On the effects of alternative optima in context-specific metabolic model predictions

PLOS Computational Biology
2017-05-30 | Journal article
Contributors: Semidán Robaina-Estévez; Christos A. Ouzounis; Zoran Nikoloski
Source: check_circle
Crossref

Metabolic Network Constrains Gene Regulation of C4Photosynthesis: The Case of Maize

Plant Cell Physiol
2016-02 | Journal article
Contributors: Semidán Robaina-Estévez; Zoran Nikoloski
Source: Self-asserted source
Dr. Semidán Robaina Estévez via Crossref Metadata Search

Context-Specific Metabolic Model Extraction Based on Regularized Least Squares Optimization

PLoS ONE
2015-07-09 | Journal article
Contributors: Semidán Robaina Estévez; Zoran Nikoloski; Stephen S. Fong
Source: Self-asserted source
Dr. Semidán Robaina Estévez via Crossref Metadata Search

Generalized framework for context-specific metabolic model extraction methods

Front. Plant Sci.
2014-09 | Journal article
Contributors: Semidán Robaina Estévez; Zoran Nikoloski
Source: Self-asserted source
Dr. Semidán Robaina Estévez via Crossref Metadata Search

Peer review (2 reviews for 2 publications/grants)

Review activity for BMC bioinformatics (1)
Review activity for Plant physiology. (1)