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, 30-31 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 - 2023
• Recommender and reviewer in Peer Community In Neuroscience 2021 - 2023
• Designated trainer for behaviour, surgical prodecures and perfusions, SWC 2019 - 2023
• Tutor assistant in neuromatch academy 2021
• Co-organizer of Emerging Neuroscientists Seminar Series, SWC 2020 - 2023
• Outreach participant in Skype a Scientist program 2021 - 2022
• Active participant in the Research Culture Working Groups, SWC 2020 - 2023
• 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

• Ramón y Cajal Fellowship, € 314.350, 2024 - 2029
• 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

Research Projects

• RYC2022-035145-I: ayudas Ramón y Cajal, convocatoria 2022, to Dr. Hernando Martinez Vergara in Fundació De Recerca Clínic Barcelona-Institut D’investigacions Biomèdiques August Pi I Sunyer. From April 2024 to March 2029. € 314.350,00. Type of participation: principal investigator.
• AEI-Proyectos Generación de Conocimiento, convocatoria 2023: to Dr. Hernando Martinez Vergara in Fundació De Recerca Clínic Barcelona-Institut D’investigacions Biomèdiques August Pi I Sunyer. From December 2024 to December 2027. € 185.000,00. Type of participation: principal investigator.
• 853413: “Elucidating the Basal Ganglia Circuits for Reward Expectation”. European Research Council Starting Grant (LS5), 2019 call, to Marcus Stephenson-Jones in University College London. From January 2020 to December 2024. € 1.498.100,00. Type of participation: postdoctoral researcher.
• GAT3755: Gatsby Foundation Core Grant to Prof Mrsic-Flogel in University College London. From 2020 to 2025. £ 1.426.500,00. Type of participation: postdoctoral researcher.
• 219627/Z/19/Z: Wellcome Trust Core Grant to Prof Mrsic-Flogel in University College London. From 2020 to 2025. £ 792.500,00. Type of participation: postdoctoral researcher.
• GAT3755: Gatsby Foundation Core Grant to Dr. Stephenson-Jones in University College London. From 2020 to 2025. £ 1.162.753,00. Type of participation: postdoctoral researcher.
• 219627/Z/19/Z: Wellcome Trust Core Grant to Dr. Stephenson-Jones in University College London. From 2020 to 2025. £ 645.974,00. Type of participation: postdoctoral researcher.
• 543021: Simons Foundation to Prof. Mrsic-Flogel in University College London, SPI Churchland A. International Brain Laboratory (IBL). From 2018 to 2023. £ 389.363,00. Type of participation: postdoctoral researcher.
• 294810: “A Neuron Type Atlas of the Annelid Brain: Development and Evolution of Chemosensory-Motor Circuits”. European Research Council Advanced Grant (LS3), 2011 call, to Detlev Arendt in European Molecular Biology Laboratory Heidelberg. From March 2012 to February 2017. € 2.489.048,00. Type of participation: graduate researcher and postdoctoral researcher.
• SC3GM081165: “Molecular Mechanisms Underlying Xenopus Somitogenesis”. NIH NIGMS Grant to Carmen Domingo in San Francisco State University. From 2011 to 2013. $ 464.504,00. Type of participation: undergraduate researcher.
• ALTF 827-2018: “Dissociation of cell class-specific roles of cortico-striatal circuits during learning and behavior”. European Molecular Biology Organization Long-Term Fellowship, 2018 call to Dr. Hernando Martinez Vergara in University College London. From January 2019 to December 2020. £ 59.824,00. Type of participation: awarded postdoctoral fellow.