About

This site is under re-constuction

I have been a scientist ever since I remember, spending most of my professional life in academia studying basic biological problems based on genomics and bioinformatics. After many years in academia, I have become increasingly interested in the generation of value from science, of translating knowledge to society, and I am now a full time entrepreneur in the area of med tech.

Professional Activity

Innovation and Companies

• I founded in 2015 a start up dedicated to developing  precision oncology solutions. As CEO, I deal with the everyday management of a company that brings innovation to the clinical market, including managing human resources, budgets, quality, management of an IP portfolio, negotiations with clients and partnerships with industrial players (pharma, devices), etc.
• As scientific director of the business incubator Healthcare City since From 2018 to the end of 2018, I participate in the selection of new start ups from multiple countries evaluating their technical feasibility and business model; I follow and mentor these companies and lecture at the acceleration program “11 Health Market Program”, a program that I co-designed.
• I previously led other innovation projects: i) in pharma, where I took results from my own research in the form of a new antimicrobial compound with application in biodefense, managing an IP portfolio developed around this compound and institucional negotiations about technology transfer ii) in the area of medical software where I deal with issues pertaining licensing and certification. I have been involved in other innovation projects, including in the areas of scientific education, marine resources, among others.

Internacional and in multiple contexts

I was a researcher at multiple and diverse institutions in several countries, which gives me a broad vision of how research an innovation is pursued and the role of basic and applied research in generating innovation and economic and social value.

• 2006-2017 – Principal Investigator – Computational Genomics Laboratory – Instituto Gulbenkian de Ciência (PT)
• 2004-2005 – Career Development Fellow – MRC – Laboratory of Molecular Biology (UK)
• 2004 – Post Doctoral Fellow – MRC – Laboratory of Molecular Biology (UK)
• 2002-2003 – Post Doctoral Fellow – EMBL European Bioinformatics Institute

Beyond my research work, I managed a technological core of a research institution and participated in the development of national and international scientific infrastructures.

• 2013-Present -I was the coordinator of the original proposal and I am the current president of the board of BioData.pt, the Portuguese biological information infrastructure
• 2008-2013 – I represented Portugal in the workgroup that established the ESFRI ELIXIR, a distributed infrastructure for biological information,  and participated in the preparation of its first funding proposal to the Horizon 2020; I was Portugal’s first Head of Node.
• 2006-2014 – Head of the Bioinformatics Core of the Institute Gulbenkian de Ciência

In thesecontexts I participated in multiple funding exercises, with individual and consortia funding resulting millions of Euros that I managed or co-managed. Funding bodies included national and international scientific funding agencies, innovation funding, H2020, EEA program, etc.

Multidisciplinary

My research work and my focus in Bioinformatics and Computational approaches to Biology allowed me to work in several areas of knowledge, including what is currently termed Big Data in Biology, the development of novel computational methods for data analyses, and to help develop a new(wish) research area – Evolutionary Cell Biology. I conducted research in several applied contexts to human health (blindness, cancer, infectious diseases), Biodefense (new drugs), Marine Biotech (micro-organism with biotechnological and/or environmental risk potential), as well as in characterising species of interest for AgroForestry. Finally, during my first foray into research, for about two years I married research in (Eco)Toxicology with optimisation of Nuclear/Analytical Chemistry at the Portuguese Nuclear Reactor. 

 Education & Training

I had the fortune to have been trained at outstanding institutions, by outstanding Professors and Mentors. I have experienced scientific research in basic life sciences domains, as well as within a translational context.

• I was fortunate to participate in the Católica Lisbon  School of Business and Economics – “ADVANCED PROGRAM IN ENTREPRENEURSHIP AND INNOVATION MANAGEMENT  .” I would strongly recommend it to anyone thinking of making the move from Academia to the Business World as it was a real eye opener!
• I was a PhD student under the pioneering Gulbenkian PhD Program in Biology and Medicine(class of 1995), which gave me the opportunity to work under the supervision of Professor Miguel C. Seabra in two outstanding institutions in the UK and USA. I presented my thesis at the University of Porto in 2001, obtaining the title of DOCTOR IN BIOMEDICAL SCIENCES.
• I graduated in BIOCHEMISTRY, still in the older format of the Licenciatura, where we had four years of courses, followed by a one year dissertation. My dissertation work was a mixture of toxicology of heavy metals using animal models, and methodological development, working with Neutron Activation Analysis at the Portuguese Nuclear Reactor.

Supervision and Teaching

Supervision Experience

Supervised 8 PhD students, of which 6 have already graduated*, including MDs, both in academia and in a company setting; I supervised 3 MSc students.

Selected teaching experience – Coordination of modules in Graduate Programs

• 2014 – 2017 – Coordinated the “Hypothesis-driven research” module in the PhD program“Integrative Biosciences” at Instituto Gulbenkian de Ciência.
• 2010 – 2015— Coordinated the “Research in Bioinformatics” module of the MSc in Bioinformatics and Computational Biology program.
• 2012 – 2014 – Coordinated the “Bioinformatics” module of the PhD Program Science for Development  
• 2008 – 2011 – Coordinated the “Genomics and Bioinformatics” module of the Advanced Medical Training Program (a PhD program for MDs)
• 2010 – 2011 – Coordinated the “Structural Biology” module of the Advanced Medical Training Program (a PhD program for MDs)
• 2005-2008 – Coordinated the “Protein interaction networks” module in the PhD Program in Computational Biology

Selected teaching experience – International Summer Schools

• 2015 – Faculty of the Summer Program in Evolutionary Cell Biology, part of the Quantitative Biology Program of the Kavli Institute In Theoretical Physics, in Santa Barbara, USA
• 2013 – Faculty do Physiology Course at the  Marine Biological Laboratory in Woods Hole, USA
• 2011 – Co-organiser of the International summer School in Genome Biology and Evolution at the Instituto Gulbenkian de Ciência, Oeiras, Portugal (VW European Campus of Excellence)

PROJECTS

Current Projects

• I am the CEO, Chairman of the board and Founder of Ophiomics, a precision oncology start up company with the ambition of bringing new solutions based on genomics and bioinformatics to medicine, with a focus on liver cancer. We are located in Lisbon, Portugal, at the “Pólo Tecnológico”.

• I am and have been a member several  of Scientific and Technological Councils/Advisory boards. My areas of intervention include start up strategy, biotechnology of natural resources, science/technology for local/regional development, entrepreneurship, technology readiness, biodefense, among others

Past Projects

• I was the President of the Management Board of the Portuguese Biological Information Infrastructure. This project, entitled BioData.pt, aims to develop a data infrastructure that supports the development of academic research and new business models around available and secure biological data. It is funded under the Portuguese RoadMap of scientific infrastructures.
• I was the Scientific director of Healthcare City since its beginning, a start-up incubator/accelerator focused on the health sector, promoted by Nova Medical School, Janssen, Lusíadas Saúde and Medis – the right place to grow to a global market! My official role was twofold – I developed and actively participate in our 11 Health Market Program acceleration program, and I made sure that from a tech/scientific perspective projects were sound, and were progressing according to realistic paths, establishing any connections that were needed with our scientific system. In addition, I mentored some of our start ups, mostly in the diagnostics area.

• I was the Principal investigator of the Computational Genomics Laboratory at the Instituto Gulbenkian de Ciência in Oeiras, Portugal for the best part of 11 years, until the end of 2017.  We studied evolutionary cell biology (EvoCell) of  intracellular compartmentalisation. Evocell is a scientific area at the intersection of classical evolutionary theory and molecular cell biology, and where the advent of omics technologies allow our bioinformatics approaches to be very relevant. We studied these problems in long evolutionary times, at the million to billion of year scale, as well as  short time frames (few years) using Cancer as a model system. I publish under the scientific name “Jose B. Pereria-Leal or Jose Pereira-Leal”

• My research in the evolution of intracellular parasites led me to the discovery of a novel type of antibiotic. This was accomplished by repositioning a compound that has been used to treat an unrelated condition in humans for many decades, without any side effect.  I have partnered with business developers and a patent attorney to develop this discovery for licensing. We collaboratied with the BioDefense industry in a NATO country to research the use of this drug in Biodefense.
• I was involved in the establishment of the European ESFRI ELIXIR, a proposal to create an European-wide Bioinformatics  research infrastructure. Having participated in the establishment of this infrastructure and finding a niche for Portuguese participation, and having participated in securing ELIXIR’s first main round of funding via a Horizon 2020 Infradev grant, I stepped down to make space for a team with the time and stamina to build the Portuguese node of this network.

• From 2012 to early 2016 I was an Associate Editor of the Journal Genome Biology and Evolution, published by the Society of the Molecular Biology and Evolution. Established in 2010, under the stewardship of Bill Martin it rapidly became a reference journal in its area.

• From 2007 to 2014 I was the Head of the Bioinformatics Unit of the Instituto Gulbenkian de Ciência, a research support facility that supports the work of researchers at the Instituto Gulbenkian de Ciência, and other Institutions in the Oeira Campus, Including ITQB and IBET. The Bioinformatics unit provides support in the areas of biological data analysis, next generation sequencing, data warehousing, etc. In was in this capacity that I was involved in the creation of the Portuguese Bioinformatics Infrastructure BioData.Pt, and our participation in the European Bioinformatics Infrastructure ELIXIR.
• In 2004 to December 2005 I integrated the Computational Genomics Group  group of Sarah Teichmann at the historical MRC Laboratory of Molecular Biology, in Cambridge, UK. My research focused on the evolution of macromolecular assemblies.

• During the years of 2002 and 2003 I was a postdoctoral fellow in the Computational Genomics Group led by Christos Ouzounis at the EMBL outstation European Bioinformatics Institute in Cambridge, UK. There I researched the evolution of bimolecular networks, with a focus on protein-protein interaction networks.

Genealogy

I was born into a family that is scattered in Portugal and internationally. Particularly on my father’s side, the family seems to enjoy crossing oceans and exploring a new life in new lands. Finding about them – who they were, what they did, where and when, is increasingly fascinating for me.

In this process I discovered many interesting things about my father’s family, including that:
– they ALL comes from the “Beiras”, in particular Vale Formoso, Cernache do Bonjardim, Nandufe
– has established itself in Portugal, Brazil, Guiné, USA, UK, at least.
– that it included farmers, traders, railway and telecommunication engineers, haute couture  dressmakers, military, antique dealers, etc. 
– in Beira baixa, my ancestors, like most women were “tecedeiras” or “fiadeiras”.
– many men fought and died in the Great War in France, but some survived.
– I find generation upon generation having really difficult lives, with many children dying very young, poorly payed and hard jobs, German concentration camps, disease, etc… My generation is probably the first to have what one would consider a simpler life. I guess I need to be very thankful for all of them for trying so hard to make it less difficult for all of us that are alive now. 

On my mother’s side, I am finding a family that as far as I can trace has been firmly rooted in the “Bairrada” Region of Beira litoral in Portugal (Bolho, Cantanhede), with a single venture into the promised land of Brazil. A mixture of farmers and traders with more recent generations benefiting from higher levels of education. 

I have been using use Reunion for Mac to organize this research, but while I have grown a bit tired of this.  I need more of a “Lab Note Book for genealogy”, where I can keep track of my own infrequent work and growing to do list, so I am now testing Mac FamilyTree 8 . I also use MyHeritage to share my data with family members. For my father’s family I have this page.

Below is a short genealogical chart, showing only my direct ascendents. It was generated using Mac FamilyTree 8. The image should have enough resolution for enlarging and reading.

If you happened to know of these people below, drop me a line. Also if you have information about the history and/or old media of Nandufe (Tondela), Aldeia do Mato/Vale Formoso (Covilhã) or Pampilhal (Cernache do Bonjardim), I would love to hear about these places.