Writting

About Biology & Healthcare

Toward Ontologies of Biomedical Research (Part 1)One Ontology to Rule Them All? In “weaving the web,” TimBL points out that the web exists to allow the free interchange of knowledge throughout humanity. The spark that he ignited has led to a world where internet search giants like Google have embedded ontologies in the fabric of their search — the

Numbed by NumbersIn these unprecedented times, it's easy to get numbed by numbers. If you're like me, you're checking one of the dashboards where the number of COVID cases are being displayed every day - or maybe even many times a day.

CRISPR for Software EngineersBy now you've heard of CRISPR of course - the technology that will change the world. But you might know it as that thing that biologists use to cut genes but are not really clear about how it works.

Biology is the new technology"Four years learning Biology and this is what you spend your time doing?!" My inner critic says every time I spend more time than I care to admit debugging a piece of code that should just work or preparing data to be used as a machine learning training set, or trying to make an AWS lambda function

What can a knowledge graph do for oncology? About 13 years ago I decided to create a career in oncology - it was not a hard decision. I made that decision soon after starting a PhD in the Department of Bioinformatics at the MD Anderson Cancer Center (MDACC).

Micro-management (of disease) and the 2018 Nobel prize in physiologyOne of my (too many) hobbies is to read and learn about leadership, strategy and effective communication. I developed the habit of reading…

To understand biology understand its constraints – Helena Deus – MediumI have spent the last 12 years working with and around cancer data: visualizing it, integrating it, analyzing it. Until recently, I hadn’t…

Invest in basic biology – Helena Deus – MediumAs a Marine Biologist who has taken a sharp turn after college and ended up graduating with a PhD in Bioinformatics, it’s funny how I keep…

Blogging about events and other stuff

Knowledge Graphs and Machine Learning - ISWC 2018 trip reportLast week I attended the International Semantic Web Conference (ISWC) in Monterey, CA. My role was to speak at the Ada Lovelace Day Celebration about the work that Elsevier is doing with regards to measuring and fixing the gender gap in research (see more here).

AI in healthcare - what works and what doesn'tThanks to Adam Jenkins, who set me up with a free pass, for the past two days I've attended the Global AI Conference in Boston. Overall, the conference missed the energy of other AI and machine learning conferences that I have attended.

INBOUND 2018 - From a data scientist's perspectiveLast week I attended INBOUND 2018, per invitation of the brilliant Saleema Vellani (COO and Co-Founder at Innovazing). As a data scientist and bioinformatician, INBOUND - which is primarily a marketing and sales conference - has not been on my radar (until now!).

Hackathon Projects

MarsElectric

If you landed on Mars and you rover wheel broke, how would you replace it? This was a problem posed by NASA as part of an international competition to build Space Apps. My team's contribution link is below:

https://2022.spaceappschallenge.org/challenges/2022-challenges/mars-habitat/teams/marselectric/project

Onco Twin

There's so much data about cancer that is publicly available that it's like like candy for a computational biologist. But how to make sense of this data? How to create a simulation of a human patient in a way that empowers an oncologist to explore every possible aspect of that cancer, from the morphology, to the chemistry and beyond. In 2020 I was part of a hackathon (MIT Grand Hack) team that addressed this challenge. We won the MIT Grand Hack 2020 - Customized Cancer Care track with our solution:

https://www.slideshare.net/HelenaDeus1/oncotwin-digital-twin-of-a-patient-tumor

Remember Me

How do we explore Venus? How do we store data? Venus high pressure and temperature would cause all our hard drives to melt. This was a problem posed by NASA as part of an international competition to build Space Apps (ISAC). My team tackled this challenge in 2019 and we came up with a solution that won the local prize:

https://2019.spaceappschallenge.org/challenges/planets-near-and-far/memory-maker/teams/remember-me/project

Affordable Haptic Feedback Tool for Surgical TrainingVR’s ability to “touch us back” can be the difference between life and death in surgical training