CV

Education

PhD in Natural Sciences, Heidelberg University, 2016
MSc in Cell and Developmental Biology, San Francisco State University, 2012
MSc in Bioinformatics, King’s College London, 2010
BSc in Biotechnology, Universitat Autonoma de Barcelona, 2009

Professional experience

Ramon y Cajal Fellow, FCRB-IDIBAPS, 2024 - Currently employed
- Leading a research group.
- Investigating the neural circuits involved in learning.
Head of Neuroanalytics and Multiomics, EsyaLabs, 2023 - 2024
- Developed automatic high-throughput image analysis methods, speeding the analysis of complex datasets by a factor of 1000x.
- Combined multi-omics (transcriptomics, proteomics) and multi-modal data using modeling and machine learning for the detection and classification of neurodegenerative diseases.
- Stablished CI/CD practices in the team.
- Developed the ability to communicate with multiple stakeholders.
- Developed the ability to work in a fast-paced environment.
- Experience in distinct medical regulatory environments (e.g. FDA).
- Acquisition of >1M GBP in funding through grants and competitions.
Senior Research Fellow, Sainsbury Wellcome Center, UCL, 2018 - 2023
- Led research on the neural basis of learning in mice resulting in one high-impact publication. //: <> (in a time-efficient manner for the standards of the field.)
- Supervised the scientific work of four researchers.
- Implemented and automated over ten statistical workflows for the analysis of complex time-series datasets involving machine learning toolkits (e.g. scikit-learn) in Python.
- Designed two histological quantification and visualization software packages for the high-throughput analysis of biomarkers in Python and Java, increasing efficiency twenty-fold.
- Designed and performed over fifty in vivo experiments involving behavioral training of rodents, electrophysiological recordings of neurons, optogenetic and pharmacological manipulations or neuronal activity, and anatomical tracing of neuronal processes.
- Processed hundreds of histological samples, optimised protocols to label RNA and protein biomarkers, and imaged animal tissue samples using confocal and two-photon microscopy.
- Accomplished over a hundred complex stereotactical brain surgeries in mice successfully.
- Worked extensively with AAVs and other viruses to label and manipulate neurons specifically.
- Engineered and designed hardware components for the control of experimental variables in close loop, involving electronics and robotics, and programming in Matlab and Python.
- Completed three international courses for leadership and laboratory management.
- Prepared and delivered over twenty scientific presentations and presented two posters in international meetings.
- Organized scientific dissemination events and participated in public outreach.
- Secured personal funding (>70K GBP) by achieving a highly competitive international grant.
- Led the implementation of several policies at the institutional level.
- Trained multiple researchers in experimental competencies for handling and working with animals.
- Teached two courses on behavioural experiments.
Postdoctoral and Graduate Researcher, European Molecular Biology Laboratory, 2012 - 2017
- Led research on the evolution of the nervous system, resulting in seven scientific articles in high-impact journals.
- Designed and implemented a high-throughput transcriptomics method, and developed the current state-of-the-art software to automatically analyze gene expression data to generate spatial transcriptome atlases using image analysis in ImageJ and R.
- Managed an international collaboration project involving multidisciplinary research groups, dealing with single-cell and spatial omics, resulting in a breakthrough publication in the journal Cell.
- Completed ten courses on machine learning, artificial intelligence, mathematical modeling, software development, and biomedical entrepreneurship.
- Performed multiple experiments involving plasmid design and cloning, Crispr-Cas9 gene editing, sequencing and phylogenetics, DNA and RNA purification, blotting, cell culture, microinjection, histology and staining, and imaging using confocal and electron microscopy.
- Collaborated in a project to spatially map single-cell sequencing data.
- Designed a software for motion tracking on freely moving animals in Matlab.
- Teached four introductory courses on image analysis.
- Prepared and delivered multiple scientific reports and oral presentations for effective dissemination of scientific data.
- Supervised the scientific work of two researchers.
Additional experience, KCL, SFSU, 2009 - 2012
- Led research in muscle development using gene expression interference.
- Secured personal funding (>120K USD) by achieving a highly competitive grant.
- Performed bioinformatics analysis of genetic interaccions using graph theory.

Skills

Project management
Team management
Statistics and data analysis
Multi-omics
Biomarkers
Image analysis
Microscopy and histology
Software development
Data visualisation
Scientific communication
Cell and molecular biology
Neurobiology
Animal biology (in vivo)
Python
ImageJ
R Bioconductor
Matlab
HPC clusters
Adobe Illustrator
Office

Publications

The Role of Sdf-1α signaling in Xenopus laevis somite morphogenesis

Marisa Leal, Sarah Fickel, Armbien Sabillo, Julio Ramirez, Hernando Vergara, Ceazar Nave, Daniel Saw, Carmen Domingo, "The Role of Sdf-1α signaling in Xenopus laevis somite morphogenesis." Developmental Dynamics, 2014.

Descriptive and functional approaches for a system-level understanding of Platynereis dumerilii and the evolution of locomotor circuits in Bilateria

Hernando Martinez, "Descriptive and functional approaches for a system-level understanding of Platynereis dumerilii and the evolution of locomotor circuits in Bilateria." Heidelberg University Library, 2016.

Whole-organism cellular gene-expression atlas reveals conserved cell types in the ventral nerve cord of Platynereis dumerilii

Hernando Vergara, Paola Bertucci, Peter Hantz, Maria Tosches, Kaia Achim, Pavel Vopalensky, Detlev Arendt, "Whole-organism cellular gene-expression atlas reveals conserved cell types in the ventral nerve cord of Platynereis dumerilii." Proceedings of the National Academy of Sciences of the United States of America, 2017.

Spatial Transcriptomics: Constructing a Single-Cell Resolution Transcriptome-Wide Expression Atlas

Kaia Achim, Hernando Vergara, Jean-Baptiste Pettit, "Spatial Transcriptomics: Constructing a Single-Cell Resolution Transcriptome-Wide Expression Atlas." RNA Detection: Methods and Protocols, 2018.

Whole-Body Single-Cell Sequencing Reveals Transcriptional Domains in the Annelid Larval Body

Kaia Achim, Nils Eling, Hernando Vergara, Paola Bertucci, Jacob Musser, Pavel Vopalensky, Thibaut Brunet, Paul Collier, Vladimir Benes, John Marioni, Detlev Arendt, "Whole-Body Single-Cell Sequencing Reveals Transcriptional Domains in the Annelid Larval Body." Molecular Biology and Evolution, 2018.

miR-206 is required for changes in cell adhesion that drive muscle cell morphogenesis in Xenopus laevis

Hernando Vergara, Julio Ramirez, Trista Rosing, Ceazar Nave, Rebecca Blandino, Daniel Saw, Parag Saraf, Gabriel Piexoto, Coohleen Coombes, Melissa Adams, Carmen Domingo, "miR-206 is required for changes in cell adhesion that drive muscle cell morphogenesis in Xenopus laevis." Developmental Biology, 2018.

Whole-body integration of gene expression and single-cell morphology

Hernando Vergara, Constantin Pape, Kimberly Meechan, Valentyna Zinchenko, Christel Genoud, Adrian Wanner, Kevin Mutemi, Benjamin Titze, Rachel Templin, Paola Bertucci, Oleg Simakov, Wiebke Dürichen, Pedro Machado, Emily Savage, Lothar Schermelleh, Yannick Schwab, Rainer Friedrich, Anna Kreshuk, Christian Tischer, Detlev Arendt, "Whole-body integration of gene expression and single-cell morphology." Cell, 2021.

Standardized and reproducible measurement of decision-making in mice

The Laboratory, Valeria Aguillon-Rodriguez, Dora Angelaki, Hannah Bayer, Niccolo Bonacchi, Matteo Carandini, Fanny Cazettes, Gaelle Chapuis, Anne Churchland, Yang Dan, Eric Dewitt, Mayo Faulkner, Hamish Forrest, Laura Haetzel, Michael Häusser, Sonja Hofer, Fei Hu, Anup Khanal, Christopher Krasniak, Ines Laranjeira, Zachary Mainen, Guido Meijer, Nathaniel Miska, Thomas Mrsic-Flogel, Masayoshi Murakami, Jean-Paul Noel, Alejandro Pan-Vazquez, Cyrille Rossant, Joshua Sanders, Karolina Socha, Rebecca Terry, Anne Urai, Hernando Vergara, Miles Wells, Christian Wilson, Ilana Witten, Lauren Wool, Anthony Zador, "Standardized and reproducible measurement of decision-making in mice." eLife, 2021.

The Nereid on the rise: Platynereis as a model system

B. Özpolat, Nadine Randel, Elizabeth Williams, Luis Bezares-Calderon, Gabriele Andreatta, Guillaume Balavoine, Paola Bertucci, David Ferrier, Maria Gambi, Eve Gazave, Mette Handberg-Thorsager, Jörg Hardege, Cameron Hird, Yu-Wen Hsieh, Jerome Hui, Kevin Mutemi, Stephan Schneider, Oleg Simakov, Hernando Vergara, Michel Vervoort, Gaspar Jekely, Kristin Tessmar-Raible, Florian Raible, Detlev Arendt, "The Nereid on the rise: Platynereis as a model system." EvoDevo, 2021.

The conserved core of the nereid brain: Circular CNS, apical nervous system and lhx6-arx-dlx neurons

Detlev Arendt, Idoia Urzainqui, Hernando Vergara, "The conserved core of the nereid brain: Circular CNS, apical nervous system and lhx6-arx-dlx neurons." Current Opinion in Neurobiology, 2021.

Action prediction error: a value-free dopaminergic teaching signal that drives stable learning

Francesca Greenstreet, Hernando Vergara, Sthitapranjya Pati, Laura Schwarz, Matthew Wisdom, Fred Marbach, Yvonne Johansson, Lars Rollik, Theodore Moskovitz, Claudia Clopath, Marcus Stephenson-Jones, "Action prediction error: a value-free dopaminergic teaching signal that drives stable learning." bioRxiv, 2022.

MoBIE: a Fiji plugin for sharing and exploration of multi-modal cloud-hosted big image data

Constantin Pape, Kimberly Meechan, Ekaterina Moreva, Martin Schorb, Nicolas Chiaruttini, Valentyna Zinchenko, Hernando Vergara, Giulia Mizzon, Josh Moore, Detlev Arendt, Anna Kreshuk, Yannick Schwab, Christian Tischer, "MoBIE: a Fiji plugin for sharing and exploration of multi-modal cloud-hosted big image data." Nature Methods, 2023.

Relevant presentations

Selected talk at the BARCCSYN meeting, Barcelona, 29-30 May 2024
Poster presentation in BioTechX conference, Basel, 4-6 October, 2023
Poster presentation in AAIC conference, Ambsterdam, 16-20 July, 2023
Selected talk at Instituto de Neurociencias Christmas meeting, Alicante, 21-22 December 2022
Invited speaker at IDIBAPS SysNeuro JC, Barcelona, 21 October 2022
Poster presentation in Federation of European Neuroscience Societies (FENS), Paris, 9-13 July 2022
Invited speaker at UCL Bioimage Analysis series, London, 24 September 2021
Seminar at the Interdisciplinary Center for Neurosciences, Heidelberg University, 9 November 2018
Invited speaker in series of talks: seminars in Evo-Devo, Cambridge University, 17 January 2018
Poster presentation in conference Neuro-Evo II, Janelia Farm, 6-9 May 2018
Talk at the workshop “Advances in molecular biology by young researchers”, CNB Madrid, 20 December 2017
Invited speaker at Conference “De la mer à l’image”, Banyuls sur Mer, 11-12 July 2017
Short talk at Neptune EvoDevo Symposium, Lisbon, 9-11 November 2016
Poster presentation in conference Neuro-Evo I, Janelia Farm, May 15-18 2016
Short talk at COS Symposium “Darwin 2.0 - New tools to go through time”, Heidelberg 17 June 2015
Poster presentation in conference Hypothatlamic circuits, Janelia Farm, 27-30 September 2015
Poster presentation in congress Neurobiology of action, ESF-FENS, Stresa 20-24 October 2013
Poster presentation at BaMBa, Stanford, 9 November 2010.

Teaching

Teacher in the Behavioural Module at the SWC PhD course, 2018 - 2021
Teacher in the Developmental Biology Module at the EMBL PhD course, 2013 - 2016
Teacher in the MAMED course for marine biology, 2015

Supervision

Co-supervisor of Quentin Pajot-Moric, rotation PhD student in Stephenson-Jones lab, 2021
Co-supervisor of Matthew Wisdom, research assistant in Stephenson-Jones lab, 2020
Co-supervisor of Yasmin Meyer, research assistant in Stephenson-Jones lab, 2020
Co-supervisor of Laura Schwarz, research assistant in Stephenson-Jones lab, 2019 - 2020
Co-supervisor of Ryan Prestil, international summer student in Arendt lab, 2014
Co-supervisor of David Puga, master student in Arendt lab, 2013

Relevant additional training

EMBO laboratory leadership course, virtual 2021
Cajal course in computational neuroscience, Lisbon 2017
Advanced R programming, Heidelberg 2017
Artificial intelligence nanodegree Udacity program, online 2017
Biotech entrepreneurship training program, Heidelberg 2016
EMBL advanced course in software carpentry, Heidelberg 2014
Leadership training SWC pilot program, virtual 2020
Leading collaborative projects, online UCL program 2021
R debugging & robust programming, Heidelberg 2016
Writing and publishing scientific papers EMBL course, Cambridge 2016

Service and leadership

Postdoc representative in the SWC 2022 - present
Recommender and reviewer in Peer Community In Neuroscience 2021 - present
Designated trainer for behaviour, surgical prodecures and perfusions, SWC 2019 - present
Tutor assistant in neuromatch academy 2021
Co-organizer of Emerging Neuroscientists Seminar Series, SWC 2020 - present
Outreach participant in Skype a Scientist program 2021 - present
Active participant in the Research Culture Working Groups, SWC 2020 - present
Speaker to Santarder Bank high-school student awardees 2016
Science Slam speaker, outreach activity, Heidelberg 2015
Main co-organizer of the EMBL PhD Symposium 2013

Grants and awards

EMBO Long-Term Fellowship, £ 60.000, 2018 - 2020
EMBO Long-Term Fellowship, Rejected, 2017
EMBL International PhD Programme, € 48.000, 2012 - 2016
La Caixa Scholarship for post-graduate studies in the USA, $ 120.000, 2010 - 2012
Janelia Conference full travel grant, HHMI, € 1.700, 2018/16/15
Deep Mind / FENS grant for Computational Neuroscience, € 1.150, 2017
IRA Research Grant, San Francisco State University, $ 750, 2010
Collaboration Scholarship, Spanish Goverment, € 2.700, 2008 - 2009
JAE CSIC “Introduction to Research” Scholarship, € 1.000, 2008
Menendez Pelayo International University conference grant, € 500, 2007

Hernando M. Vergara

CV