Erich M. Schwarz
@erichmschwarz.bsky.social
Molecular biologist using functional genomics. Started with C. elegans, then diversified.
Thanks!
I was recruited to this project in ~2015. I expected it to be very straightforward -- making a perfect isogenic copy of the N2 genome. I didn't expect to have an extra 2 Mb by 2019, and absolutely didn't expect getting all extra 6 Mb to take until 2025...
I was recruited to this project in ~2015. I expected it to be very straightforward -- making a perfect isogenic copy of the N2 genome. I didn't expect to have an extra 2 Mb by 2019, and absolutely didn't expect getting all extra 6 Mb to take until 2025...
August 3, 2025 at 10:13 PM
Thanks!
I was recruited to this project in ~2015. I expected it to be very straightforward -- making a perfect isogenic copy of the N2 genome. I didn't expect to have an extra 2 Mb by 2019, and absolutely didn't expect getting all extra 6 Mb to take until 2025...
I was recruited to this project in ~2015. I expected it to be very straightforward -- making a perfect isogenic copy of the N2 genome. I didn't expect to have an extra 2 Mb by 2019, and absolutely didn't expect getting all extra 6 Mb to take until 2025...
Good question! We don't know. Generally, my hope is that this new genome will motivate people to look at a lot of phenomena that were harder to study in the N2 genome assembly because it necessarily lacked that extra 6.0 Mb of difficult sequences.
August 3, 2025 at 10:11 PM
Good question! We don't know. Generally, my hope is that this new genome will motivate people to look at a lot of phenomena that were harder to study in the N2 genome assembly because it necessarily lacked that extra 6.0 Mb of difficult sequences.
Protein categories we talk a great deal about in the paper:
1. A complex palette of possible immunomodulators -- some of whose genes transcriptionally upregulate when the worm encounters a functional host immune system.
2. Anticoagulants! Which are unfashionable, but were first seen in 1903.
1. A complex palette of possible immunomodulators -- some of whose genes transcriptionally upregulate when the worm encounters a functional host immune system.
2. Anticoagulants! Which are unfashionable, but were first seen in 1903.
February 5, 2025 at 5:13 PM
Protein categories we talk a great deal about in the paper:
1. A complex palette of possible immunomodulators -- some of whose genes transcriptionally upregulate when the worm encounters a functional host immune system.
2. Anticoagulants! Which are unfashionable, but were first seen in 1903.
1. A complex palette of possible immunomodulators -- some of whose genes transcriptionally upregulate when the worm encounters a functional host immune system.
2. Anticoagulants! Which are unfashionable, but were first seen in 1903.
Thanks!
We do cite extracellular vesicles at one point, to explain a phenomenon that's been known for many years but not discussed much: in our data, and in several other parasitic nematodes, roughly one-third of excreted/secreted proteins lack N-term signals.
We do cite extracellular vesicles at one point, to explain a phenomenon that's been known for many years but not discussed much: in our data, and in several other parasitic nematodes, roughly one-third of excreted/secreted proteins lack N-term signals.
February 5, 2025 at 5:11 PM
Thanks!
We do cite extracellular vesicles at one point, to explain a phenomenon that's been known for many years but not discussed much: in our data, and in several other parasitic nematodes, roughly one-third of excreted/secreted proteins lack N-term signals.
We do cite extracellular vesicles at one point, to explain a phenomenon that's been known for many years but not discussed much: in our data, and in several other parasitic nematodes, roughly one-third of excreted/secreted proteins lack N-term signals.
This is the first time in my life where I wrote a paper, found out that I couldn't preprint or publish that paper until I got a provisional patent application filed, and spent one year fighting in all directions to indeed get it filed. While the paper sat on my desk. Never again, I hope.
February 5, 2025 at 4:50 PM
This is the first time in my life where I wrote a paper, found out that I couldn't preprint or publish that paper until I got a provisional patent application filed, and spent one year fighting in all directions to indeed get it filed. While the paper sat on my desk. Never again, I hope.
Yes. The preprint is an exact copy of what we're submitting to a journal for publication, so, the text you see ("this genome is already available") is what we hope will be in print not *too* many months from now...
We'll definitely make the data files go live before then!
We'll definitely make the data files go live before then!
December 11, 2024 at 2:44 AM
Yes. The preprint is an exact copy of what we're submitting to a journal for publication, so, the text you see ("this genome is already available") is what we hope will be in print not *too* many months from now...
We'll definitely make the data files go live before then!
We'll definitely make the data files go live before then!
That being said, if not having immediate access is going to cost you an R01 application or something, e-mail me at [email protected], and I'll try to get you immediate help!
December 10, 2024 at 6:15 PM
That being said, if not having immediate access is going to cost you an R01 application or something, e-mail me at [email protected], and I'll try to get you immediate help!
WormBase has been given a heads-up on this and they are thinking through their strategy for how to do a migration, which as you can imagine will not be trivial. What they may do is build up CGC1 on their site incrementally, then migrate. OSF.io files will be available ASAP, though.
OSF
OSF.io
December 10, 2024 at 6:14 PM
WormBase has been given a heads-up on this and they are thinking through their strategy for how to do a migration, which as you can imagine will not be trivial. What they may do is build up CGC1 on their site incrementally, then migrate. OSF.io files will be available ASAP, though.
At the request of my coauthors, I've held off on making the assembly publicly available (one of them was burned in the past by sharing data plus Reviewer Number Three feeling no urgency to stop acting out).
But as soon as all authors feel OK, all files will be posted to osf.io for immediate use.
But as soon as all authors feel OK, all files will be posted to osf.io for immediate use.
OSF
osf.io
December 10, 2024 at 6:12 PM
At the request of my coauthors, I've held off on making the assembly publicly available (one of them was burned in the past by sharing data plus Reviewer Number Three feeling no urgency to stop acting out).
But as soon as all authors feel OK, all files will be posted to osf.io for immediate use.
But as soon as all authors feel OK, all files will be posted to osf.io for immediate use.