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ababaian

436 karma · joined November 20, 2022

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ababaian··on 'Obelisks': New class of life has been found in human digestive system
Largely we don't know. That's what makes them cool. This opens up a fairly large debate about where you draw the boundary of "life", "organisms", and "entities". It's a fun debate to have over a few beers since there is no objective correct answer.

My view is that Obelisks are more like Viruses or Viroids, or some kind of mobile genetic element. The key detail is that they appear to be strictly RNA elements (they don't have a DNA counterpart). So they're most likely using host RNA transcription machinery to make more copies of themselves, this is what viroids and satellite viruses like "Hepatitis Delta Virus" do.

What do they do? Well that's the right question. My guess is the kinds of things that bacteriophages do, Obelisks do too. Exploit cells to make more copies of themselves as selfish replicators.

ababaian··on 'Obelisks': New class of life has been found in human digestive system
Cool :) I'm a co-author on this. AMA.

This is now a peer-reviewed paper, published last month in Cell [https://www.cell.com/cell/fulltext/S0092-8674(24)01091-2].

Obelisks are part of a larger research program we're developing at the University of Toronto + collaborators, see also: Virus-Viroid Hybrids paper [https://www.nature.com/articles/s41467-023-38301-2] and the Zeta-Elements [https://www.nature.com/articles/s41586-021-04332-2].

Computational biology is driving a revolutionary expansion of our understanding of Earth's biodiversity. I believe Zeta-elements, Ambiviruses, and Obelisks are just the beginning. If you're interested, our "Laboratory for RNA-Based Lifeforms" (University of Toronto) is hiring passionate developers/post-docs/graduate students [https://www.rnalab.ca].

Edit: OK going to call it for now. I'll check in later today if there's any outstanding questions.

ababaian··on Ask HN: Who is hiring? (August 2024)
The Laboratory for RNA-Based Lifeforms | UI/UX Science Developer | Toronto, ONSITE | ~1-2mo Contract | RNAlab.ca

We're an academic research lab focused on Exploring Earth's Virome, and identifying which viruses could be human disease-causing agents. We are building, Open Virome, an open-source platform to provide scientists with the ability to derive actionable insights from a massive DNA/RNA sequencing database, the Sequence Read Archive (SRA). The SRA houses billions of dollars of data from over 27 million datasets (~100 petabytes raw data) collected over 16 years. By querying, aggregating and displaying relationships between sequencing datasets (and meta-data) and the viruses they contain, we hope to illuminate the hidden universe of viruses all around us.

Project Overview: https://www.youtube.com/watch?v=mPUM-adhXd8&t=5875s

Project Paper: https://www.nature.com/articles/s41586-021-04332-2

We're seeking a talented and innovative designer to assist the team with designing a user-friendly, intuitive, and visually compelling web interface for this research project and help further biomedical discovery. Looking for the right balance of design, data-scientist, and data visualization. Expertise in network analysis / virology is an asset. Send an email, introduce yourself, and please include your portfolio (examples of your previous work).

ababaian··on Ask HN: Who is hiring? (May 2023)
The Laboratory for RNA-Based Lifeforms | University of Toronto | Full-Time | ONSITE

We're a research computational biology lab at the forefront of RNA virus discovery. Our goal is to help prevent the next pandemic by building the technical infrastructure to assist global virology research and public-health responses.

Seeking a Computational Virology / Microbiologist / Bioinformatician who is creative, passionate, and willing to learn. Key assets: Python/R, AWS/HPC, postgres, javascript. See full job posting: http://rrna.ca/id0001

Learn more about our work in this CBC News article (https://www.cbc.ca/news/health/supercomputer-virus-study-dis...).

See Also:

* Serratus Website (https://serratus.io)

* Nature Paper: https://www.nature.com/articles/s41586-021-04332-2

* GitHub Repo: https://github.com/ababaian/serratus

ababaian··on Ask HN: Who is hiring? (March 2023)
I'll consider anyone if it's the right person.
ababaian··on Ask HN: Who is hiring? (March 2023)
Thanks fixed :)
ababaian··on Ask HN: Who is hiring? (March 2023)
The Laboratory for RNA-Based Lifeforms | University of Toronto | Full-Time | ONSITE

We're a research computational biology lab at the forefront of RNA virus discovery. Our goal is to help prevent the next pandemic by building the technical infrastructure to assist global virology research and public-health responses.

Seeking a full-stack developer who is creative, passionate, and willing to learn. No biology experience is necessary, but it is a plus. Key assets: Python/R, AWS/HPC, postgres, javascript. See full job posting: http://rrna.ca/id0002 or if you're a biologist http://rrna.ca/id0001

Learn more about our work in this CBC News article (https://www.cbc.ca/news/health/supercomputer-virus-study-dis...).

See Also:

* Serratus Website (https://serratus.io)

* Nature Paper: https://www.nature.com/articles/s41586-021-04332-2

* GitHub Repo: https://github.com/ababaian/serratus

ababaian··on Ask HN: Who is hiring? (February 2023)
The Laboratory for RNA-Based Lifeforms | University of Toronto | Full-Time | ONSITE

We're a research computational biology lab at the forefront of RNA virus discovery. Our goal is to help prevent the next pandemic by building the technical infrastructure to assist global virology research and public-health responses.

Seeking a full-stack developer who is creative, passionate, and willing to learn. No biology experience is necessary, but it is a plus. Key assets: Python/R, AWS/HPC, postgres, javascript. See full job posting: http://rrna.ca/id0002 or if you're a biologist http://rrna.ca/id0001

Learn more about our work in this CBC News article (https://www.cbc.ca/news/health/supercomputer-virus-study-dis...).

See Also:

* Serratus Website (https://serratus.io)

* Nature Paper: https://www.nature.com/articles/s41586-021-04332-2

* GitHub Repo: https://github.com/ababaian/serratus

ababaian··on Ask HN: What are you working on this year?
I'm a developer for the OSS Serratus project, https://www.serrartus.io where we have a web-portal used to explore where RNA viruses show up in public sequencing datasets (we've analyzed ~21 petabytes of sequencing data to make this dataset). There's lots of rich meta-data associated with these RNA sequencing datasets, so what I'm trying to do is create meaningful meta-data aggregation and associate them with different types of viruses to make a sort of procedural generated encyclopedia of RNA viruses. Be less biased by what scientists expect to see, and focus more on what is actually observed for virus biology and epidemiology. I've built a little proof of concept called `palmID` (www.serratus.io/palmid) but I think there's lots more to be done to make this really shine.
ababaian··on Ask HN: Who is hiring? (January 2023)
The Laboratory for RNA-Based Lifeforms | University of Toronto | Full-Time | ONSITE

We're a research computational biology lab at the forefront of RNA virus and virus-like agent discovery. Our goal is to help prevent the next pandemic by building the technical infrastructure to assist global virology research and public-health responses.

Seeking a full-stack developer who is creative, passionate, and willing to learn. No biology experience neccesary, but are a plus. Key assets: Python/R, AWS/HPC, postgres, javascript. See full job posting: http://rrna.ca/id0002

See: Serratus (https://serratus.io) - paper: https://www.nature.com/articles/s41586-021-04332-2 - github: https://github.com/ababaian/serratus

ababaian··on Consider working on genomics
Serratus (https://github.com/ababaian/serratus) is an OSS bioinformatics project created by a passionate group of volunteers. Short story is we're re-analyzing all of the world's DNA/RNA sequencing data to find new viruses that other people have missed. It works surprisingly well, but there's a ton left to do.
ababaian··on Consider working on genomics
Genomics today is the internet of the early 90s or programming of the late 70s. There is going to be an enormous boom in genomics-derived technologies in the coming decade which has been driven by the exponential decay in data generation costs. You're absolutely right that places with a "startup" mentality are where to be right now.

On that note :) I'm starting a forward-looking research lab at UofT to advance massive-scale (think petabytes) genetic analyses and am looking to find the right few individuals who have a similar vision. It's difficult to find passionate engineers with a solid CS and HPC background who are willing to meet halfway and work _together_ with biologists in getting the analysis right. Robert does this _very_ well, and that's why we recently co-wrote a landmark Nature paper: https://www.nature.com/articles/s41586-021-04332-2.

Job post: https://jobrxiv.org/job/university-of-toronto-27778-full-sta...

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