Helena Deus, PhD
Cambridge, Massachusetts, United States
6K followers
500+ connections
About
I work at the edge between what medicine thinks is possible with data and what actually…
Articles by Helena
Activity
-
Organizations are already superhuman intelligences. The University of Pennsylvania or Walmart or whatever is far more capable than any human af a…
Organizations are already superhuman intelligences. The University of Pennsylvania or Walmart or whatever is far more capable than any human af a…
Liked by Helena Deus, PhD
-
Gemini now can create documents, and it is a nice start, but not up to the frontier yet, as you can see from my "evil buyout of Hogwarts" test, where…
Gemini now can create documents, and it is a nice start, but not up to the frontier yet, as you can see from my "evil buyout of Hogwarts" test, where…
Liked by Helena Deus, PhD
Experience
Education
-
Universidade Nova de Lisboa
-
-
Thesis - Improving Discovery in the Life Sciences using Semantic Web Technologies and Linked Data: Design Principles for Life Sciences Knowledge Organization Systems
-
-
-
-
Licenses & Certifications
Volunteer Experience
-
Mentor
Science Club for Girls
- Present 3 months
Science and Technology
help the girls fall in love with science and math
-
Student Mentor
IMFAHE
- Present 7 years 5 months
Science and Technology
I meet with my mentees once a month, guide them through their PhDs, grant applications, and celebrate their achievement with them.
-
Mentor
RELX
- 1 year 6 months
Education
I mentor women in tech across the organization, help them pursue careers aligned with their interests and skills, advise them on creating a mindset of networking and of relationship building and help them overcome frustration.
-
Meeting coordinator and facilitator
Quercus Portugal
- 3 years 1 month
Environment
Align and lead groups from multiple environmental agencies around causes such as prevention of unnecessary forest destruction due to dam-related flooding and use of renewable energies. Partially due to my efforts, Portugal has one of the best clean energy strategies in europe.
-
Mentor at the Cockrell Butterfly Center
Houston Museum of Natural Science
Children
Help children learn about and walk around live butterflies.
Publications
-
S3QL: A distributed domain specific language for controlled
BMC Bioinformatics
See publicationThe value and usefulness of data increases when it is explicitly interlinked with related data. This is the core principle of Linked Data. For life sciences researchers, harnessing the power of Linked Data to improve biological discovery is still challenged by a need to keep pace with rapidly evolving domains and requirements for collaboration and control as well as with the reference semantic web ontologies and standards. Knowledge organization systems (KOSs) can provide an abstraction for…
The value and usefulness of data increases when it is explicitly interlinked with related data. This is the core principle of Linked Data. For life sciences researchers, harnessing the power of Linked Data to improve biological discovery is still challenged by a need to keep pace with rapidly evolving domains and requirements for collaboration and control as well as with the reference semantic web ontologies and standards. Knowledge organization systems (KOSs) can provide an abstraction for publishing biological discoveries as Linked Data without complicating transactions with contextual minutia such as provenance and access control. We have previously described the Simple Sloppy Semantic Database (S3DB) as an efficient model for creating knowledge organization systems using Linked Data best practices with explicit distinction between domain and instantiation and support for a permission control mechanism that automatically migrates between the two. In this report we present a domain specific language, the S3DB query language (S3QL), to operate on its underlying core model and facilitate management of Linked Data.
-
AGUIA: autonomous graphical user interface assembly for clinical trials semantic data services
BMC Medical Informatics and Decision Making
-
Exposing the cancer genome atlas as a SPARQL endpoint
Journal of Biomedical Informatics
-
RIMS: an information management system for Reverse Phase Protein Arrays
BMC Bioinformatics
-
Exposing the cancer genome atlas as a SPARQL endpoint.
Journal of Biomedical Informatics
-
Provenance of Microarray Experiments for a Better Understanding of Experiment Results
Proceeding of the second International Workshop on the role of Semantic Web in Provenance Management
Patents
-
SYSTEM AND METHOD FOR MANAGING GENOMIC INFORMATION
Issued US
Various embodiments provide interfaces to access genomic testing information and incorporate it into daily physician practice. According to one aspect, a graph-based data model is used that may be used to organizes and revise precision medicine knowledge. In one example structure, gene states are abstracted into alteration groups, where alteration groups are built using reverse engineering actionable information and storing that information within the graph-based data structure. Volumes of…
Various embodiments provide interfaces to access genomic testing information and incorporate it into daily physician practice. According to one aspect, a graph-based data model is used that may be used to organizes and revise precision medicine knowledge. In one example structure, gene states are abstracted into alteration groups, where alteration groups are built using reverse engineering actionable information and storing that information within the graph-based data structure. Volumes of genomic alterations and associated information (e.g., journal articles, clinical trial information, therapies, etc.) are analyzed and synthesized into actionable information items viewable on an alteration system in a graph-based data format. According to one embodiment, the system can be configured to focus practitioners on discrete portions of the alteration information on which they can act. According to other aspects, curated information is provided on the system to enable practitioners to make informed decisions regarding the implications of the presence of specific genomic alterations.
Other inventorsSee patent
Projects
-
GRANATUM project enhances the global collaboration of researchers, driving forward the discovery of innovative cancer prevention methods and ultimately contributing to improved health outcomes.
-
The GRANATUM project, funded by the EU, has developed an innovative web portal that fosters collaboration among biomedical researchers in cancer drug research, enhancing access to crucial data and resources.
🌍 The GRANATUM IT platform integrates data from 83 global sources for cancer research and pharmaceutical agents.
🤝 Researchers can collaborate, share hypotheses, and conduct in-silico experiments directly on the platform.
📅 The project began in 2011, aimed at…The GRANATUM project, funded by the EU, has developed an innovative web portal that fosters collaboration among biomedical researchers in cancer drug research, enhancing access to crucial data and resources.
🌍 The GRANATUM IT platform integrates data from 83 global sources for cancer research and pharmaceutical agents.
🤝 Researchers can collaborate, share hypotheses, and conduct in-silico experiments directly on the platform.
📅 The project began in 2011, aimed at simplifying complex experimental preparations for cancer prevention.
⚙️ Scientists can use a Scientific Workflow Management System to create, share, and manage modeling experiments.
🛠️ The platform is designed for interaction among universities, research institutes, and pharmaceutical companies to expedite research.
🔗 Utilizing the GRANATUM Biomedical Semantic Model, it allows semantic annotation and management of biomedical resources.
🌐 The project includes seven partners from various European institutions and is coordinated by Fraunhofer FIT.Other creatorsSee project -
Simple Sloppy Semantic Database (S3DB)
-
The Simple Sloppy Semantic Database (S3DB) is an open-source distributed data management system designed for the management of heterogeneous data using Semantic Web principles. It has evolved through various versions, enhancing its capabilities and applications in the life sciences.
🌍 S3DB was proposed in 2006 to manage omics datasets as RDF triples.
📅 The first version (1.0) focused on indexing for triplestore management, with subsequent versions adding distributed…The Simple Sloppy Semantic Database (S3DB) is an open-source distributed data management system designed for the management of heterogeneous data using Semantic Web principles. It has evolved through various versions, enhancing its capabilities and applications in the life sciences.
🌍 S3DB was proposed in 2006 to manage omics datasets as RDF triples.
📅 The first version (1.0) focused on indexing for triplestore management, with subsequent versions adding distributed infrastructure and a specialized query language (S3QL).
🔗 A 2011 application of S3DB's API was utilized in managing a clinical trial at MD Anderson Cancer Center.
📄 Research publications highlight S3DB's use in NIH/NCI SPORE awards and its capacity for context-based permission control and access.
🔒 S3QL supports a detailed permission control mechanism to manage data access and provenance metadata.
🧬 The technology is geared towards integrative biomedical informatics, illustrating varied use cases in genomic characterization and infectious disease epidemiology.
🎓 S3DB has the potential to influence standards in the Semantic Web community, especially regarding data integration and access control.
Honors & Awards
-
First place on the Catalyst Leadership Business Simulation Program
BMS
The Catalyst Program is a prestigious, nomination-based leadership development experience designed for high-potential Directors and above. With limited cohort sİzes and a rigorous selection process, it focuses on accelerating enterprise leadership capabilities through immersive modules, executive coaching, and strategic exposure. Participants develop skills in leading self, teams, and the broader organization-building executive presence, inclusive leadership, and enterprise acumen to prepare…
The Catalyst Program is a prestigious, nomination-based leadership development experience designed for high-potential Directors and above. With limited cohort sİzes and a rigorous selection process, it focuses on accelerating enterprise leadership capabilities through immersive modules, executive coaching, and strategic exposure. Participants develop skills in leading self, teams, and the broader organization-building executive presence, inclusive leadership, and enterprise acumen to prepare for critical future roles. My team won the business simulation at the end of the program which was designed by BTS to mimic BMS realistic executive decision making.
-
First place in the MIT Grand Hack 2020 - Customized Cancer Care track
MIT
The MIT Grand Hack is a highly competitive hackathon that happens every year, organized by MIT, with the intent of advancing healthcare by ideating on innovative solutions to pressing problems in healthcare. In 2020, the competition was run entirely virtually, which meant that multiple international participants were also invited to join, bringing together ~900 participants. I led the team that built Onco Twin - the project that won the first place in the "Customized Cancer Care" track. We…
The MIT Grand Hack is a highly competitive hackathon that happens every year, organized by MIT, with the intent of advancing healthcare by ideating on innovative solutions to pressing problems in healthcare. In 2020, the competition was run entirely virtually, which meant that multiple international participants were also invited to join, bringing together ~900 participants. I led the team that built Onco Twin - the project that won the first place in the "Customized Cancer Care" track. We competed against ~20 other teams.
https://grandhack.mit.edu/boston/ -
SILVER RECOGNITION AWARD
Elsevier
The SILVER award is given quarterly to individuals that are selected by Elsevier management team that demonstrate one or more of the key behaviors we are driving within the organization. I won one of these in 2020
-
Global Finalist in the NASA SpaceApps Challenge 2019
-
Space Apps is an international hackathon for coders, scientists, designers, storytellers, makers, builders, technologists, and others in cities around the world, where teams engage with the National Aeronautics and Space Administration’s free and open data to address real-world problems on Earth and in space. Space Apps 2019 included over 29,000 participants at 225 events in 71 countries. Space Apps is a NASA-led initiative organized in collaboration with Booz Allen Hamilton, Mindgrub and…
Space Apps is an international hackathon for coders, scientists, designers, storytellers, makers, builders, technologists, and others in cities around the world, where teams engage with the National Aeronautics and Space Administration’s free and open data to address real-world problems on Earth and in space. Space Apps 2019 included over 29,000 participants at 225 events in 71 countries. Space Apps is a NASA-led initiative organized in collaboration with Booz Allen Hamilton, Mindgrub and SecondMuse. My team won the Boston event and was one of 36 Global Finalists and one of the top 3 finalists for the Memory-Maker challenge.
https://www.spaceappschallenge.org/ -
1st place in the NASA Space Apps Challenge 2019 - Boston
Binnovative
The International Space Apps Challenge (ISAC) is an international mass collaborative hackathon focused on space exploration that takes place over 48-hours in cities around the world. The event embraces collaborative problem solving with a goal of producing relevant open-source solutions to address global needs applicable to both life on Earth and life in space. NASA is leading this global collaboration along with a number of additional government collaborators and 100+ local partner…
The International Space Apps Challenge (ISAC) is an international mass collaborative hackathon focused on space exploration that takes place over 48-hours in cities around the world. The event embraces collaborative problem solving with a goal of producing relevant open-source solutions to address global needs applicable to both life on Earth and life in space. NASA is leading this global collaboration along with a number of additional government collaborators and 100+ local partner organizations.
http://www.binnovative.org/isac2019 -
Finalist in the 2017 MIT GrandHack - Smart robotics and Intelligent Technologies
-
The MIT GrandHack is a flagship event of MIT Hacking Medicine. It’s the world’s largest healthcare hackathon, with participants from across the country and around the globe.
The event brings together people with backgrounds in medicine, technology, and business to find solutions to today’s most pressing health issues. In 2017, there were over 400 participants - my team won a finalist award in the Smart Robotics and Intelligent Technologist track with our project…The MIT GrandHack is a flagship event of MIT Hacking Medicine. It’s the world’s largest healthcare hackathon, with participants from across the country and around the globe.
The event brings together people with backgrounds in medicine, technology, and business to find solutions to today’s most pressing health issues. In 2017, there were over 400 participants - my team won a finalist award in the Smart Robotics and Intelligent Technologist track with our project "Shadow".
https://www.bostonglobe.com/business/2017/05/11/mit-grand-hackathon/AXC7mtqao3JCddp84ZsfAL/story.html -
Winner 2013 Semantic Web Challenge - Big Data Prize
Elsevier
The Challenge serves several purposes:
Helps us illustrate to society what the Semantic Web can provide;
Gives researchers an opportunity to showcase their work and compare it to others;
Stimulates current research to a higher final goal by showing the state-of-the-art every year
There were 17 submissions in 2013, my team won first place for category "Big Data…The Challenge serves several purposes:
Helps us illustrate to society what the Semantic Web can provide;
Gives researchers an opportunity to showcase their work and compare it to others;
Stimulates current research to a higher final goal by showing the state-of-the-art every year
There were 17 submissions in 2013, my team won first place for category "Big Data Prize"
https://www.journals.elsevier.com/journal-of-web-semantics/news/semantic-web-challenge-2013-submissions-announced -
4 year PhD Studentship awardee
FCT
This is a PhD studentship award that the Portuguese foundation for science and technology (FCT) sponsors with the aim of supporting the best graduates who wish to pursue research leading to a PhD degree, and the most creative post-doctoral researchers in pursuing cutting-edge projects, in Portuguese or foreign research centres, in all fields of research.
The success rate of these scholarships is 18% - I won one of these scholarships in 2008 -
Trainee Excellence Award @ MDAnderson Cancer Center
MD Anderson Cancer Center
The UT MDAnderson trainee Excellence Award Program grants 12 awards annually in the amount of $500 each for abstracts presented at scientific or medical society meetings
I won one of these awards in 2007 -
2003/2004 Prodep III – Portuguese Program of Educational Development
Portuguese Program of Educational Development
This program was designed to achieve a more effective integration of portugal with the european community. I won one of these awards in 2003
-
Winner Linked Data Cup 2013
LOD2/iSemantics
The Linked Data Cup awards prizes to the most promising innovation involving linked data. The Linked Data Cup invites scientists and practitioners to submit novel and innovative linked data sets and applications built on linked data technology, but also new insights that can be discovered throug using linked data. My team won first place in 2013
Languages
-
English
Native or bilingual proficiency
-
Portuguese
Native or bilingual proficiency
Other similar profiles
Explore top content on LinkedIn
Find curated posts and insights for relevant topics all in one place.
View top content