Senior Bioinformatician & Scientific Data Curator

• Feb 2022 - Present

ITTM is a member organisation of the i2b2 tranSMART Foundation and is one of the first SMEs which received training and was certified as EHDEN Certified SME. ITTM offers hands-on Data Management and Data Science services including cleansing of pre-clinical and clinical data, validation, harmonization, and standardization. Data Curation combines multiple processing steps including data cataloguing, data quality control, data cleansing, definition of a data model, design and implementation… Show more ITTM is a member organisation of the i2b2 tranSMART Foundation and is one of the first SMEs which received training and was certified as EHDEN Certified SME. ITTM offers hands-on Data Management and Data Science services including cleansing of pre-clinical and clinical data, validation, harmonization, and standardization. Data Curation combines multiple processing steps including data cataloguing, data quality control, data cleansing, definition of a data model, design and implementation of ETLs, as well as data storage. ITTM supports the design and implementation of secure knowledge platforms (like i2b2, tranSMART, ARACHNE, etc) with a strong focus on data interoperability, re-usage, and analysis. ITTM also offers Data Science support starting from collection of data, in-depth data analysis towards data visualisation (reporting).

Cofounder

• Apr 2015 - Present

ITTM provides data integration and knowledge management solutions and services to all bio-medical research areas. It focuses especially on translational medicine studies and clinical trials, in which heterogeneous data need to be curated, linked and integrated. http://www.ittm-solutions.com

Visiting Researcher

• Sep 2022 - Present

Visiting Researcher (External) at the Luxembourg Centre for Systems Biomedicine (LCSB) collaborating with the project IMI BioMap (https://biomap-imi.eu/). Visiting Researcher (External) at the Luxembourg Centre for Systems Biomedicine (LCSB) collaborating with the project IMI BioMap (https://biomap-imi.eu/).

Tutor of Bioinformatics, Computational Biology and Data Science

• Feb 2022 - Present

Learn Computational Biology, Bioinformatics and Data Science with my workshops held on Zoom! Topics are: Introduction to Bioinformatics; Biological Databases; Introduction to Sequence Alignment and Database Search; Protein Function Prediction; Text-mining for the reconstruction of biological interactions; Prime of Systems Biology; Introduction to Machine Learning for Health Data Science; Practical Machine Learning for Health Data… Show more Learn Computational Biology, Bioinformatics and Data Science with my workshops held on Zoom! Topics are: Introduction to Bioinformatics; Biological Databases; Introduction to Sequence Alignment and Database Search; Protein Function Prediction; Text-mining for the reconstruction of biological interactions; Prime of Systems Biology; Introduction to Machine Learning for Health Data Science; Practical Machine Learning for Health Data Science using R; Practical Machine Learning for Health Data Science using Python; Exploratory Data Analysis using Python. In order to take part in these classes, you have to register AND purchase a ticket on EventBrite. We use Zoom for our workshops! Show less Learn Computational Biology, Bioinformatics and Data Science with my workshops held on Zoom! Topics are: Introduction to Bioinformatics; Biological Databases; Introduction to Sequence Alignment and Database Search; Protein Function Prediction; Text-mining for the reconstruction of biological interactions; Prime of Systems Biology; Introduction to Machine Learning for Health Data Science; Practical Machine Learning for Health Data… Show more Learn Computational Biology, Bioinformatics and Data Science with my workshops held on Zoom! Topics are: Introduction to Bioinformatics; Biological Databases; Introduction to Sequence Alignment and Database Search; Protein Function Prediction; Text-mining for the reconstruction of biological interactions; Prime of Systems Biology; Introduction to Machine Learning for Health Data Science; Practical Machine Learning for Health Data Science using R; Practical Machine Learning for Health Data Science using Python; Exploratory Data Analysis using Python. In order to take part in these classes, you have to register AND purchase a ticket on EventBrite. We use Zoom for our workshops! Show less

Senior Postdoctoral Researcher

• May 2021 - Dec 2021

Research of the Section for Artificial Intelligence and Decision Support (AID) in the application of Artificial Intelligence (AI) and computer-based decision support technologies in the medical domain. This includes the development and application of advanced machine learning methods, knowledge-based systems technology for decision support and therapy planning, and natural language processing which deals with automatic processing of text and speech. I am particularly interested in the… Show more Research of the Section for Artificial Intelligence and Decision Support (AID) in the application of Artificial Intelligence (AI) and computer-based decision support technologies in the medical domain. This includes the development and application of advanced machine learning methods, knowledge-based systems technology for decision support and therapy planning, and natural language processing which deals with automatic processing of text and speech. I am particularly interested in the application of machine learning (ML) methods for the stratification of patients on diseases sub-groups based on multi-modal data, analysis of diseases trajectories, discovery of biomarkers for disease severity using OMICs data (e.g. RNASeq, scRNASeq, ChIP-Seq), analysis of imaging data (MRI) for biomarkers extraction in neurodegenerative and cardiovascular diseases, and last but not least, data integration and mining of population-based healthcare (primary and secondary) data. Show less Research of the Section for Artificial Intelligence and Decision Support (AID) in the application of Artificial Intelligence (AI) and computer-based decision support technologies in the medical domain. This includes the development and application of advanced machine learning methods, knowledge-based systems technology for decision support and therapy planning, and natural language processing which deals with automatic processing of text and speech. I am particularly interested in the… Show more Research of the Section for Artificial Intelligence and Decision Support (AID) in the application of Artificial Intelligence (AI) and computer-based decision support technologies in the medical domain. This includes the development and application of advanced machine learning methods, knowledge-based systems technology for decision support and therapy planning, and natural language processing which deals with automatic processing of text and speech. I am particularly interested in the application of machine learning (ML) methods for the stratification of patients on diseases sub-groups based on multi-modal data, analysis of diseases trajectories, discovery of biomarkers for disease severity using OMICs data (e.g. RNASeq, scRNASeq, ChIP-Seq), analysis of imaging data (MRI) for biomarkers extraction in neurodegenerative and cardiovascular diseases, and last but not least, data integration and mining of population-based healthcare (primary and secondary) data. Show less

Founder and Director

• Mar 2019 - Jun 2021

The London Academy of Life Data Science aims to bring the elite scientists on Data Science applied to various aspect of Life Sciences Research on open events aimed to the citizen scientists. We believe that Data Science should be democratized, allowing a broader range of people to have the opportunity to have access to high quality training using real-world examples in Life Sciences. The London Academy of Life Data Science aims to bring the elite scientists on Data Science applied to various aspect of Life Sciences Research on open events aimed to the citizen scientists. We believe that Data Science should be democratized, allowing a broader range of people to have the opportunity to have access to high quality training using real-world examples in Life Sciences.

Honorary Health Data Scientist

• Sep 2020 - Apr 2021

UKRI Rutherford Fund Innovation Fellow / Lecturer

• Mar 2018 - Apr 2021

Health Data Research UK Fellow for cardiovascular translational research. My aim is to integrate the UK Biobank and The Barts Bioresource collections of clinical, omics and imaging cardiovascular data. Barts and The London School of Medicine and Dentistry - Lecturer; William Harvey Research Institute - Researcher; Institute of Applied Data Science - Academic Member; Centre for Computational Biology - Core Academic Member; NIHR Barts Biomedical Research Centre - Researcher; Health Data Research UK Fellow for cardiovascular translational research. My aim is to integrate the UK Biobank and The Barts Bioresource collections of clinical, omics and imaging cardiovascular data. Barts and The London School of Medicine and Dentistry - Lecturer; William Harvey Research Institute - Researcher; Institute of Applied Data Science - Academic Member; Centre for Computational Biology - Core Academic Member; NIHR Barts Biomedical Research Centre - Researcher;

UKRI Rutherford Innovation Fellow

• Mar 2018 - Apr 2021

Subject Matter Expert in Data Science

• Nov 2020 - Jan 2021

Subject matter expert in data science. On-line exploratory data analysis tutor of Python. Subject matter expert in data science. On-line exploratory data analysis tutor of Python.

Guest Tutor of Machine Learning

• Nov 2020 - Nov 2020

Guest tutor of Machine Learning for epigenomics analysis (6h). Guest tutor of Machine Learning for epigenomics analysis (6h).

Guest Tutor of Machine Learning

• Sep 2019 - Sep 2019

Tutor at the Autumn School in Data Science: Machine Learning Applications for Life Sciences Tutor at the Autumn School in Data Science: Machine Learning Applications for Life Sciences

Guest Tutor of Machine Learning

• Aug 2019 - Aug 2019

The first four days will include a mix of plenary lectures, short courses and discussion meetings on topics suggested by participants. These will be run as a sequence of parallel sessions, allowing each participant to pick their own programme to match their interests and requirements. The fifth day will be a Schools Engagement Event with senior pupils from two local secondary schools. The first four days will include a mix of plenary lectures, short courses and discussion meetings on topics suggested by participants. These will be run as a sequence of parallel sessions, allowing each participant to pick their own programme to match their interests and requirements. The fifth day will be a Schools Engagement Event with senior pupils from two local secondary schools.

Research Associate

• Apr 2013 - Mar 2018

Luxembourg Centre for Systems Biomedicine Bioinformatics Core (Reinhard Schneider Group) Data Integration, Clinical Data Management, Text-mining and Translational Bioinformatics Funding: European Union (EU), IMI, EFPIA Luxembourg Centre for Systems Biomedicine Bioinformatics Core (Reinhard Schneider Group) Data Integration, Clinical Data Management, Text-mining and Translational Bioinformatics Funding: European Union (EU), IMI, EFPIA

Guest Lecturer of Systems Biology

• Feb 2017 - Feb 2017

Guest Lecturer at the M.Sc. in Translational Medicine Module: Bioinformatics and data analysis for high-troughput data Lectures: a) Principles of biological systems design using SBML; b) Oscillatory MAPK pathway simulation using CellDesigner. Guest Lecturer at the M.Sc. in Translational Medicine Module: Bioinformatics and data analysis for high-troughput data Lectures: a) Principles of biological systems design using SBML; b) Oscillatory MAPK pathway simulation using CellDesigner.

Guest Lecturer of Systems Biology

• Sep 2016 - Sep 2016

Guest Lecturer at the Genetics Post-graduate Programme. Course: Computational biology for the analysis of biological networks Guest Lecturer at the Genetics Post-graduate Programme. Course: Computational biology for the analysis of biological networks

Guest Lecturer of Systems Biology

• Nov 2014 - Nov 2014

Scientific Consultant

• Sep 2013 - Nov 2014

Scientific consultant for text-mining in the project SysmedIBD. Scientific consultant for text-mining in the project SysmedIBD.

Associate Professor of Bioinformatics

• Feb 2011 - Jan 2013

Note: This position in Brazil in defined as "Professor Adjunto", a tenured position. --Bioinformatics Lectures: 1) Introduction to Bioinformatics; 2) Biological Databases; 3) Structural and Functional Genomics, regulatory sequences, and structural/functional motifs in protein sequences; 4) RNA-Seq analysis using Bioconductor/DESeq; 5) Text-mining approaches for biological networks reconstruction; 6) Web resources applied to Biological Systems… Show more Note: This position in Brazil in defined as "Professor Adjunto", a tenured position. --Bioinformatics Lectures: 1) Introduction to Bioinformatics; 2) Biological Databases; 3) Structural and Functional Genomics, regulatory sequences, and structural/functional motifs in protein sequences; 4) RNA-Seq analysis using Bioconductor/DESeq; 5) Text-mining approaches for biological networks reconstruction; 6) Web resources applied to Biological Systems Studies; --Molecular Biology Lectures: 7) PCR Applications; 8) Recombinant DNA Technology. --Bioinformatics Master's Supervisor. Show less Note: This position in Brazil in defined as "Professor Adjunto", a tenured position. --Bioinformatics Lectures: 1) Introduction to Bioinformatics; 2) Biological Databases; 3) Structural and Functional Genomics, regulatory sequences, and structural/functional motifs in protein sequences; 4) RNA-Seq analysis using Bioconductor/DESeq; 5) Text-mining approaches for biological networks reconstruction; 6) Web resources applied to Biological Systems… Show more Note: This position in Brazil in defined as "Professor Adjunto", a tenured position. --Bioinformatics Lectures: 1) Introduction to Bioinformatics; 2) Biological Databases; 3) Structural and Functional Genomics, regulatory sequences, and structural/functional motifs in protein sequences; 4) RNA-Seq analysis using Bioconductor/DESeq; 5) Text-mining approaches for biological networks reconstruction; 6) Web resources applied to Biological Systems Studies; --Molecular Biology Lectures: 7) PCR Applications; 8) Recombinant DNA Technology. --Bioinformatics Master's Supervisor. Show less

Postdoctoral Research Associate

• Aug 2008 - Jan 2011

Computational Biology and Data Mining (Andrade) Group. Fields: Systems Biology, Text-mining and Data Integration Funding: BMBF Computational Biology and Data Mining (Andrade) Group. Fields: Systems Biology, Text-mining and Data Integration Funding: BMBF

Ph.D Scholar

• 2004 - 2008

Laboratory of Biodados (Supervisor: Dr. J. Miguel Ortega) Fields: Genomics, Bioinformatics and Computational Biology Funding: CAPES/Brazil Laboratory of Biodados (Supervisor: Dr. J. Miguel Ortega) Fields: Genomics, Bioinformatics and Computational Biology Funding: CAPES/Brazil

Visiting Predoctoral Fellow

• May 2006 - Jan 2007

Data Integration and Knowledge Management (Reinhard Schneider's) Group Fields: Text-mining and Data Integration Funding: CAPES/Brazil Data Integration and Knowledge Management (Reinhard Schneider's) Group Fields: Text-mining and Data Integration Funding: CAPES/Brazil

Scientific Initiation Fellow

• 2000 - 2004

Laboratory of Plant Genetics and Biotechnology (Supervisor: Dr. Ana. Maria Benko-Iseppon) Field of research: Genomics, Data Mining and Bioinformatics Funding: FACEPE/Brazil Laboratory of Plant Genetics and Biotechnology (Supervisor: Dr. Ana. Maria Benko-Iseppon) Field of research: Genomics, Data Mining and Bioinformatics Funding: FACEPE/Brazil