Samantha Zarate
@szarate.bsky.social
Genome informatics at the Regeneron Genetics Center. All opinions, etc. my own. she/her 🇵🇭🏳️🌈
Pinned
Samantha Zarate
@szarate.bsky.social
· Nov 20
I am one of 100s of scientists in the the World that is Watching the U.S. Deal With Bird Flu, and It’s Scary! Today, my opinion piece on the NY Times. Let's hope we take more serious epidemics and pandemics and deal with them before they emerge. www.nytimes.com/2024/11/19/o...
Opinion | The U.S. Response to Bird Flu is Not Reassuring the World
The U.S. needs to reassure the world it has the outbreak under control.
www.nytimes.com
If you are nervous about a potential bird flu epidemic/pandemic, a very tangible thing you can do is WEAR A MASK. Masking at places like the grocery store, doctor's office, and conferences is an easy way of making our world more accessible. Get masks here: bonafidemasks.com www.planethalohealth.com
Reposted by Samantha Zarate
A bad thing is unfolding at NIH this week: It looks like the Trump administration is trying to replace key civil servant scientific leaders, the Institute Directors, with political hires. These directors control the NIH budget, tens of billions.
A bit of a video explainer here: 1/ 🧪
A bit of a video explainer here: 1/ 🧪
November 13, 2025 at 10:31 PM
A bad thing is unfolding at NIH this week: It looks like the Trump administration is trying to replace key civil servant scientific leaders, the Institute Directors, with political hires. These directors control the NIH budget, tens of billions.
A bit of a video explainer here: 1/ 🧪
A bit of a video explainer here: 1/ 🧪
Reposted by Samantha Zarate
Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
October 9, 2025 at 5:05 PM
Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
Reposted by Samantha Zarate
I've added 7 videos to my Burrows-Wheeler indexing playlist (www.youtube.com/playlist?lis...), rounding out the r-index series and adding a 5-part series on the move structure. Now 27 videos in that playlist. I aim to add videos on prefix-free parsing, PBWT, Wheeler languages/automata in the future.
Burrows-Wheeler Indexing - YouTube
Videos on : (a) the Burrows-Wheeler Transform (BWT), (b) the FM Index, which uses the BWT to construct a full-text index, (c) Wheeler graphs, (d) r-index, an...
www.youtube.com
October 7, 2025 at 2:17 PM
I've added 7 videos to my Burrows-Wheeler indexing playlist (www.youtube.com/playlist?lis...), rounding out the r-index series and adding a 5-part series on the move structure. Now 27 videos in that playlist. I aim to add videos on prefix-free parsing, PBWT, Wheeler languages/automata in the future.
Reposted by Samantha Zarate
🦒Long read giraffe is out!🦒
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2
Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe https://www.biorxiv.org/content/10.1101/2025.09.29.678807v1
October 2, 2025 at 6:28 AM
🦒Long read giraffe is out!🦒
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2
Reposted by Samantha Zarate
Please share with anyone who cares about NSF support for graduate students and take 30 seconds to sign and leave a comment.
The deadline for the 2025 Graduate Research Fellowship Program is about one month away and literally no one can apply. #NSFGRFP
jasonjwilliamsny.github.io/grfp2025/
The deadline for the 2025 Graduate Research Fellowship Program is about one month away and literally no one can apply. #NSFGRFP
jasonjwilliamsny.github.io/grfp2025/
An Open Letter to U.S. STEM Leadership on the NSF Graduate Research Fellowship Program
An Open Letter to U.S. STEM Leadership on the NSF Graduate Research Fellowship Program
jasonjwilliamsny.github.io
September 25, 2025 at 10:09 PM
Please share with anyone who cares about NSF support for graduate students and take 30 seconds to sign and leave a comment.
The deadline for the 2025 Graduate Research Fellowship Program is about one month away and literally no one can apply. #NSFGRFP
jasonjwilliamsny.github.io/grfp2025/
The deadline for the 2025 Graduate Research Fellowship Program is about one month away and literally no one can apply. #NSFGRFP
jasonjwilliamsny.github.io/grfp2025/
Reposted by Samantha Zarate
Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]
A complete diploid human genome benchmark for personalized genomics
Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...
www.biorxiv.org
September 22, 2025 at 5:01 PM
Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]
Reposted by Samantha Zarate
Make no mistake, this remains catastrophic.
It makes it near impossible for people to stay and work in the US, no matter how qualified they are, unless they work for a handful of extremely wealthy companies.
For so many of us, it’s time to make other plans.
It makes it near impossible for people to stay and work in the US, no matter how qualified they are, unless they work for a handful of extremely wealthy companies.
For so many of us, it’s time to make other plans.
September 20, 2025 at 9:12 PM
Make no mistake, this remains catastrophic.
It makes it near impossible for people to stay and work in the US, no matter how qualified they are, unless they work for a handful of extremely wealthy companies.
For so many of us, it’s time to make other plans.
It makes it near impossible for people to stay and work in the US, no matter how qualified they are, unless they work for a handful of extremely wealthy companies.
For so many of us, it’s time to make other plans.
Reposted by Samantha Zarate
The protests yesterday reminded me of this movement. Seeing the recent corruption feels like a repeat of history.
If you are in the Philippines, know that I am thinking of you. If you're taking part in the protests, know I am proud of you and wish for you and your loved ones to be safe. Ingat ka.
If you are in the Philippines, know that I am thinking of you. If you're taking part in the protests, know I am proud of you and wish for you and your loved ones to be safe. Ingat ka.
September 22, 2025 at 11:47 AM
The protests yesterday reminded me of this movement. Seeing the recent corruption feels like a repeat of history.
If you are in the Philippines, know that I am thinking of you. If you're taking part in the protests, know I am proud of you and wish for you and your loved ones to be safe. Ingat ka.
If you are in the Philippines, know that I am thinking of you. If you're taking part in the protests, know I am proud of you and wish for you and your loved ones to be safe. Ingat ka.
Reposted by Samantha Zarate
The protests took place yesterday, which was also the anniversary of declaration of martial law by Ferdinand Marcos, who is the father of the current president. He was known to also take tax payers money to fund his family's lifestyle. He was forced out in 1986 by the People Power Revolution.
September 22, 2025 at 11:47 AM
The protests took place yesterday, which was also the anniversary of declaration of martial law by Ferdinand Marcos, who is the father of the current president. He was known to also take tax payers money to fund his family's lifestyle. He was forced out in 1986 by the People Power Revolution.
Reposted by Samantha Zarate
Over the last day I've seen many videos of Filipinos protesting against corruption (within flooding projects) in the Philippines.
Every time I see these videos, I feel emotional. I am so proud to see Filipinos participating. But also sad because of seeing years of corruption and injustice.
Every time I see these videos, I feel emotional. I am so proud to see Filipinos participating. But also sad because of seeing years of corruption and injustice.
September 22, 2025 at 11:47 AM
Over the last day I've seen many videos of Filipinos protesting against corruption (within flooding projects) in the Philippines.
Every time I see these videos, I feel emotional. I am so proud to see Filipinos participating. But also sad because of seeing years of corruption and injustice.
Every time I see these videos, I feel emotional. I am so proud to see Filipinos participating. But also sad because of seeing years of corruption and injustice.
Reposted by Samantha Zarate
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned
September 15, 2025 at 8:40 AM
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned
Reposted by Samantha Zarate
7/ If you’re under 65 and not high risk, the window to get a Covid-19 vaccine is right now—before the FDA label changes. Once it happens, access will be limited immediately (if it isn’t already). CVS is no longer booking appointments. As far as we know, Walgreens and local pharmacies still are.
August 18, 2025 at 11:37 PM
7/ If you’re under 65 and not high risk, the window to get a Covid-19 vaccine is right now—before the FDA label changes. Once it happens, access will be limited immediately (if it isn’t already). CVS is no longer booking appointments. As far as we know, Walgreens and local pharmacies still are.
Reposted by Samantha Zarate
DHS Chief: ‘We Are A Nation Of Immigrants Who Came Here Between 1776 And 1943’
June 10, 2025 at 2:59 PM
DHS Chief: ‘We Are A Nation Of Immigrants Who Came Here Between 1776 And 1943’
Reposted by Samantha Zarate
Jonathan Joss was murdered in a homophobic hate crime on the first day of Pride Month in the year 2025.
The heartbreaking statement from Jonathan Joss’s husband about his death.
June 2, 2025 at 8:15 PM
Jonathan Joss was murdered in a homophobic hate crime on the first day of Pride Month in the year 2025.
Reposted by Samantha Zarate
Harvard today, your institution tomorrow.
It's all part of the Project 2025 plan to destroy high education in America.
All leading US universities depend on federal funding and tuition dollars from international students. They severely curtailed the former. Now they're eliminating the latter.
It's all part of the Project 2025 plan to destroy high education in America.
All leading US universities depend on federal funding and tuition dollars from international students. They severely curtailed the former. Now they're eliminating the latter.
May 22, 2025 at 6:38 PM
Harvard today, your institution tomorrow.
It's all part of the Project 2025 plan to destroy high education in America.
All leading US universities depend on federal funding and tuition dollars from international students. They severely curtailed the former. Now they're eliminating the latter.
It's all part of the Project 2025 plan to destroy high education in America.
All leading US universities depend on federal funding and tuition dollars from international students. They severely curtailed the former. Now they're eliminating the latter.
Great work from Arun -- who is also looking for a job!
Our pre-print on investigating variation in South Asian genomes is now out!
Thank you to @mikeschatz.bsky.social, @rajivmccoy.bsky.social and @aabiddanda.bsky.social for all their work on this.
🧵 A thread on the key results and takeaways from our work:
Thank you to @mikeschatz.bsky.social, @rajivmccoy.bsky.social and @aabiddanda.bsky.social for all their work on this.
🧵 A thread on the key results and takeaways from our work:
Assembling unmapped reads reveals hidden variation in South Asian genomes https://www.biorxiv.org/content/10.1101/2025.05.14.653340v1
May 15, 2025 at 8:07 PM
Great work from Arun -- who is also looking for a job!
Reposted by Samantha Zarate
📢 HPRC Release 2 is here!
Now with phased genomes from 200+ individuals, a 5x increase from Release 1.
Explore sequencing data, assemblies, annotations & alignments in our interactive data explorer ⬇️:
humanpangenome.org/hprc-data-re...
Now with phased genomes from 200+ individuals, a 5x increase from Release 1.
Explore sequencing data, assemblies, annotations & alignments in our interactive data explorer ⬇️:
humanpangenome.org/hprc-data-re...
May 12, 2025 at 1:15 PM
📢 HPRC Release 2 is here!
Now with phased genomes from 200+ individuals, a 5x increase from Release 1.
Explore sequencing data, assemblies, annotations & alignments in our interactive data explorer ⬇️:
humanpangenome.org/hprc-data-re...
Now with phased genomes from 200+ individuals, a 5x increase from Release 1.
Explore sequencing data, assemblies, annotations & alignments in our interactive data explorer ⬇️:
humanpangenome.org/hprc-data-re...
Reposted by Samantha Zarate
Thank you to everyone who attended, and thank you to everyone who got me to this point - I appreciate you all.
I'm on the job market this summer, so please send any interesting opportunities my way 😃
I'm on the job market this summer, so please send any interesting opportunities my way 😃
May 2, 2025 at 2:25 PM
Thank you to everyone who attended, and thank you to everyone who got me to this point - I appreciate you all.
I'm on the job market this summer, so please send any interesting opportunities my way 😃
I'm on the job market this summer, so please send any interesting opportunities my way 😃
Reposted by Samantha Zarate
Reposted by Samantha Zarate
I'll also be on the job market this summer, so please reach out if you're interested!
You can find out more about me at these links:
LinkedIn: www.linkedin.com/in/arun96/
Personal Website: arundas.org
You can find out more about me at these links:
LinkedIn: www.linkedin.com/in/arun96/
Personal Website: arundas.org
Arun Das
arundas.org
April 21, 2025 at 9:24 PM
I'll also be on the job market this summer, so please reach out if you're interested!
You can find out more about me at these links:
LinkedIn: www.linkedin.com/in/arun96/
Personal Website: arundas.org
You can find out more about me at these links:
LinkedIn: www.linkedin.com/in/arun96/
Personal Website: arundas.org
Reposted by Samantha Zarate
Hello Bluesky 👋🏾
I’m going to be defending my thesis on Wednesday, so I thought this was as good a time as any to introduce myself and my work.
I’m Arun Das, I’m a PhD student in Schatz Lab @ JHU, and my work broadly focuses on algorithms to improve accessibility and representation in genomics.
I’m going to be defending my thesis on Wednesday, so I thought this was as good a time as any to introduce myself and my work.
I’m Arun Das, I’m a PhD student in Schatz Lab @ JHU, and my work broadly focuses on algorithms to improve accessibility and representation in genomics.
April 21, 2025 at 9:24 PM
Hello Bluesky 👋🏾
I’m going to be defending my thesis on Wednesday, so I thought this was as good a time as any to introduce myself and my work.
I’m Arun Das, I’m a PhD student in Schatz Lab @ JHU, and my work broadly focuses on algorithms to improve accessibility and representation in genomics.
I’m going to be defending my thesis on Wednesday, so I thought this was as good a time as any to introduce myself and my work.
I’m Arun Das, I’m a PhD student in Schatz Lab @ JHU, and my work broadly focuses on algorithms to improve accessibility and representation in genomics.
Reposted by Samantha Zarate
“Many academics tell us they’re avoiding US travel entirely due to genuine fears about border detention and visa issues.
"Barnes said many LGBTQ+ researchers, in particular, no longer felt safe travelling to the US for conferences, 'directly impacting their career progression.'"
"Barnes said many LGBTQ+ researchers, in particular, no longer felt safe travelling to the US for conferences, 'directly impacting their career progression.'"
Australian academics refuse to attend US conferences for fear of being detained
‘When academics fear travelling or partnering with US institutions, the impacts ripple through the entire global knowledge ecosystem,’ one says
www.theguardian.com/...
‘When academics fear travelling or partnering with US institutions, the impacts ripple through the entire global knowledge ecosystem,’ one says
www.theguardian.com/...
Australian academics refuse to attend US conferences for fear of being detained
‘When academics fear travelling or partnering with US institutions, the impacts ripple through the entire global knowledge ecosystem,’ one says
www.theguardian.com
April 14, 2025 at 10:51 AM
“Many academics tell us they’re avoiding US travel entirely due to genuine fears about border detention and visa issues.
"Barnes said many LGBTQ+ researchers, in particular, no longer felt safe travelling to the US for conferences, 'directly impacting their career progression.'"
"Barnes said many LGBTQ+ researchers, in particular, no longer felt safe travelling to the US for conferences, 'directly impacting their career progression.'"
I think it is time for the field of genomics to seriously reckon with the idea that our work is NOT apolitical and that bad actors can and will use our work to promote their own agendas. Appearing on Joe Rogan's podcast is a huge red flag and I am dreading where this is going.
the colossal biosciences ceo is saying on the joe rogan podcast that if they had to publish their research they'd never do any research
i desperately need people to recognize this line of thinking as anti-scientific and the mark of a grifter
www.reddit.com/r/biology/co...
i desperately need people to recognize this line of thinking as anti-scientific and the mark of a grifter
www.reddit.com/r/biology/co...
From the biology community on Reddit: Colossal Biosciences CEO Ben Lamm addressing negative feedback on the lack of peer reviewed scientific papers in regard to their re-wilding efforts
Explore this post and more from the biology community
www.reddit.com
April 11, 2025 at 6:59 PM
I think it is time for the field of genomics to seriously reckon with the idea that our work is NOT apolitical and that bad actors can and will use our work to promote their own agendas. Appearing on Joe Rogan's podcast is a huge red flag and I am dreading where this is going.
Reposted by Samantha Zarate
a lesson for every college, law firm, business, etc. — if these chodes demand you do something, your first response should be some form of "make me"
Absolutely incredible: the Feds totally folded on Congestion Pricing, thanks to the MTA just...refusing to abide by their demands
www.cbsnews.com/newyork/news...
www.cbsnews.com/newyork/news...
MTA, feds agree to keep NYC congestion pricing tolls through October
The MTA and the Trump administration have reached an agreement to keep New York City congestion pricing through October.
www.cbsnews.com
April 8, 2025 at 1:16 AM
a lesson for every college, law firm, business, etc. — if these chodes demand you do something, your first response should be some form of "make me"