Tessa Pierce Ward, PhD
@bluegenes.bsky.social
Genomics/metagenomics, bioinformatics, open science. Asst Researcher @ UC Davis, remote from San Diego. Budding rustacean.
Formerly: @Scripps_Ocean, @Stanford. Nature lover and book fiend. she/her.
Formerly: @Scripps_Ocean, @Stanford. Nature lover and book fiend. she/her.
Reposted by Tessa Pierce Ward, PhD
There are two recent papers that use sourmash in creative ways - and it gladdens my heart! pubmed.ncbi.nlm.nih.gov/40812187/ by @silask.bsky.social et al looks cleverly at human gut subspecies. www.biorxiv.org/content/10.1... by @rayanchikhi.bsky.social et al counts billions of k-mers. Super neat!
Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research - PubMed
Microbial strains within a single species can exhibit distinct functional characteristics due to variations in gene content and often show individual specificity, which can obscure unbiased associatio...
pubmed.ncbi.nlm.nih.gov
September 8, 2025 at 1:49 PM
There are two recent papers that use sourmash in creative ways - and it gladdens my heart! pubmed.ncbi.nlm.nih.gov/40812187/ by @silask.bsky.social et al looks cleverly at human gut subspecies. www.biorxiv.org/content/10.1... by @rayanchikhi.bsky.social et al counts billions of k-mers. Super neat!
Reposted by Tessa Pierce Ward, PhD
We had a last minute cancellation for STAMPS -- a phenomenal course on microbiome data analysis. Woods Hole, MA, July 14-24 2025.
If you or *anyone* you know is interested to attend, please email Titus &/or me... and we'll do what we can!!!
Thx for sharing widely! 🤞❤️
If you or *anyone* you know is interested to attend, please email Titus &/or me... and we'll do what we can!!!
Thx for sharing widely! 🤞❤️
Hi folks, we had a last minute cancellation at MBL STAMPS, the microbiome data analysis course in Woods Hole that runs from July 14th to July 24th. We can provide housing space for a woman. If you or anyone you know is interested, pls drop me an e-mail at ctbrown@ucdavis.edu. Thx!
June 29, 2025 at 7:00 AM
We had a last minute cancellation for STAMPS -- a phenomenal course on microbiome data analysis. Woods Hole, MA, July 14-24 2025.
If you or *anyone* you know is interested to attend, please email Titus &/or me... and we'll do what we can!!!
Thx for sharing widely! 🤞❤️
If you or *anyone* you know is interested to attend, please email Titus &/or me... and we'll do what we can!!!
Thx for sharing widely! 🤞❤️
Reposted by Tessa Pierce Ward, PhD
The #SCIMaP team announces a major update: an analysis of the economic impacts of the White House's NIH FY26 budget.
Bottom-line, we estimate $46B in total economic loss, 202K lost jobs, and impacts in communities nationwide.
Interactive map and shareable report:
scienceimpacts.org/fy26
a 🧵
Bottom-line, we estimate $46B in total economic loss, 202K lost jobs, and impacts in communities nationwide.
Interactive map and shareable report:
scienceimpacts.org/fy26
a 🧵
June 23, 2025 at 7:10 PM
The #SCIMaP team announces a major update: an analysis of the economic impacts of the White House's NIH FY26 budget.
Bottom-line, we estimate $46B in total economic loss, 202K lost jobs, and impacts in communities nationwide.
Interactive map and shareable report:
scienceimpacts.org/fy26
a 🧵
Bottom-line, we estimate $46B in total economic loss, 202K lost jobs, and impacts in communities nationwide.
Interactive map and shareable report:
scienceimpacts.org/fy26
a 🧵
Reposted by Tessa Pierce Ward, PhD
My HPC team at UC Davis is hiring! Looking for an experienced sysadmin to help build and maintain clusters (hardware and software). HPC experience great, but if you’re an experienced sysadmin and willing to learn, please apply!
careerspub.universityofcalifornia.edu/psc/ucdavis/...
careerspub.universityofcalifornia.edu/psc/ucdavis/...
An error has occurred.
careerspub.universityofcalifornia.edu
June 5, 2025 at 4:49 AM
My HPC team at UC Davis is hiring! Looking for an experienced sysadmin to help build and maintain clusters (hardware and software). HPC experience great, but if you’re an experienced sysadmin and willing to learn, please apply!
careerspub.universityofcalifornia.edu/psc/ucdavis/...
careerspub.universityofcalifornia.edu/psc/ucdavis/...
Reposted by Tessa Pierce Ward, PhD
Another super cool bioinformatics tool (this one using pyani and sourmash) - genomeRxiv, for exploring multiscale taxonomic relationships between genomes. From @borisvinatzer.bsky.social group, by Reza Mazloom, and also with Lenny Heath - all at VT.
GenomeRxiv
A pure CSS toggle switch for form input checkboxes
genomerxiv.cs.vt.edu
May 15, 2025 at 4:25 PM
Another super cool bioinformatics tool (this one using pyani and sourmash) - genomeRxiv, for exploring multiscale taxonomic relationships between genomes. From @borisvinatzer.bsky.social group, by Reza Mazloom, and also with Lenny Heath - all at VT.
Reposted by Tessa Pierce Ward, PhD
For whatever reason, the US government have decided the US should no longer lead in science. Great economic opening for other countries, but really bad for America. This could be stopped by a handful of majority senators. That they aren't doing it tells you they want us to cede 70 years of building
This! 100% this. Funding cuts to basic science will not only fail to save any useful amount of money, they will cost us immeasurably (including in economic terms) --- this is, indeed "economic unilateral disarmament".
www.aei.org/economics/wh...
www.aei.org/economics/wh...
www.aei.org
February 21, 2025 at 1:48 PM
For whatever reason, the US government have decided the US should no longer lead in science. Great economic opening for other countries, but really bad for America. This could be stopped by a handful of majority senators. That they aren't doing it tells you they want us to cede 70 years of building
Reposted by Tessa Pierce Ward, PhD
As we start the new year, I would like to remind everyone that it is now almost 120 years since the US decided consumer protection - by which I mean regulation - mattered. Given the upcoming presidential inauguration, let's talk about how that happened - and why it's so important. (A thread)
January 6, 2025 at 8:42 PM
As we start the new year, I would like to remind everyone that it is now almost 120 years since the US decided consumer protection - by which I mean regulation - mattered. Given the upcoming presidential inauguration, let's talk about how that happened - and why it's so important. (A thread)
Reposted by Tessa Pierce Ward, PhD
Hi all, here's my passion project for December - a Web site for ~realtime DNA sample screening/composition analysis. Let me know what you think!
Announcing: the chill-filter Web site - DNA sample composition at a glance!
what's in my sample, dude?
ivory.idyll.org
December 27, 2024 at 3:28 PM
Hi all, here's my passion project for December - a Web site for ~realtime DNA sample screening/composition analysis. Let me know what you think!
Reposted by Tessa Pierce Ward, PhD
Regularly tempted to write in my NIH grants innovation section: "Funding software that already exists and works well would be highly innovative for the NIH."
(I bet half the panel would break down ROFL, but I'm also highly skeptical that I'd get a good score, or that the PO would be amused.)
(I bet half the panel would break down ROFL, but I'm also highly skeptical that I'd get a good score, or that the PO would be amused.)
December 16, 2024 at 8:13 PM
Regularly tempted to write in my NIH grants innovation section: "Funding software that already exists and works well would be highly innovative for the NIH."
(I bet half the panel would break down ROFL, but I'm also highly skeptical that I'd get a good score, or that the PO would be amused.)
(I bet half the panel would break down ROFL, but I'm also highly skeptical that I'd get a good score, or that the PO would be amused.)
Reposted by Tessa Pierce Ward, PhD
40% of the mass of everything transported by a ship in 2023 was a fossil fuel.
That stat paired with this new study shines a pretty harsh spotlight on how obscenely bad-faith the right-wing concern trolling around offshore wind + whales is
www.seattletimes.com/seattle-news...
That stat paired with this new study shines a pretty harsh spotlight on how obscenely bad-faith the right-wing concern trolling around offshore wind + whales is
www.seattletimes.com/seattle-news...
UW study finds leading cause of whale deaths
New research shows that the top threat to whales around the globe has changed. But it wouldn't take much to reduce the risk, researchers say.
www.seattletimes.com
December 8, 2024 at 8:32 PM
40% of the mass of everything transported by a ship in 2023 was a fossil fuel.
That stat paired with this new study shines a pretty harsh spotlight on how obscenely bad-faith the right-wing concern trolling around offshore wind + whales is
www.seattletimes.com/seattle-news...
That stat paired with this new study shines a pretty harsh spotlight on how obscenely bad-faith the right-wing concern trolling around offshore wind + whales is
www.seattletimes.com/seattle-news...
Reposted by Tessa Pierce Ward, PhD
I've been putting off sending a professional email since July because I've dreaded the response.
I sent it today, and received a reply of "no worries that's fine" in about three minutes.
I will learn nothing from this.
I sent it today, and received a reply of "no worries that's fine" in about three minutes.
I will learn nothing from this.
December 4, 2024 at 8:28 PM
I've been putting off sending a professional email since July because I've dreaded the response.
I sent it today, and received a reply of "no worries that's fine" in about three minutes.
I will learn nothing from this.
I sent it today, and received a reply of "no worries that's fine" in about three minutes.
I will learn nothing from this.
Reposted by Tessa Pierce Ward, PhD
🧬🔍There are 50 petabases of freely-available DNA sequencing data. We introducing Logan Search which allows you to search for any DNA sequence in minutes, bringing Earth’s largest genomic resource to your fingertips.
🏔️ logan-search.org 🏔️
#Genomics #Bioinformatics #OpenScience
🏔️ logan-search.org 🏔️
#Genomics #Bioinformatics #OpenScience
November 11, 2024 at 7:29 PM
🧬🔍There are 50 petabases of freely-available DNA sequencing data. We introducing Logan Search which allows you to search for any DNA sequence in minutes, bringing Earth’s largest genomic resource to your fingertips.
🏔️ logan-search.org 🏔️
#Genomics #Bioinformatics #OpenScience
🏔️ logan-search.org 🏔️
#Genomics #Bioinformatics #OpenScience
This was an interesting take on software dev, and gave me a generalized perspective on some of the challenges we've faced with sourmash over time. www.baldurbjarnason.com/2022/theory-.... Thanks @luizirber.bsky.social for sharing!
Theory-building and why employee churn is lethal to software companies
Web dev at the end of the world, from Hveragerði, Iceland
www.baldurbjarnason.com
December 2, 2024 at 8:25 PM
This was an interesting take on software dev, and gave me a generalized perspective on some of the challenges we've faced with sourmash over time. www.baldurbjarnason.com/2022/theory-.... Thanks @luizirber.bsky.social for sharing!
These grapes were beautiful, inside and out.
November 30, 2024 at 3:38 PM
These grapes were beautiful, inside and out.
Reposted by Tessa Pierce Ward, PhD
Doing good science is 90% finding a science buddy to constantly talk to about the project.
November 9, 2024 at 10:53 PM
Doing good science is 90% finding a science buddy to constantly talk to about the project.
Reposted by Tessa Pierce Ward, PhD
🧪 🍎 📍 🌊 🦑 pathwaystoscience.org
Paid Summer 2025 Undergraduate Research Placements; financial support in graduate school; tips on applications and other resources; opportunities in ocean sciences and engineering
Paid Summer 2025 Undergraduate Research Placements; financial support in graduate school; tips on applications and other resources; opportunities in ocean sciences and engineering
Pathways To Science | Increasing Diversity in STEM
Offering a directory of 1,000+ scholarships, fellowships, internships, and postdoc positions in STEM, with emphasis on supporting underrepresented students.
pathwaystoscience.org
November 20, 2024 at 10:03 PM
🧪 🍎 📍 🌊 🦑 pathwaystoscience.org
Paid Summer 2025 Undergraduate Research Placements; financial support in graduate school; tips on applications and other resources; opportunities in ocean sciences and engineering
Paid Summer 2025 Undergraduate Research Placements; financial support in graduate school; tips on applications and other resources; opportunities in ocean sciences and engineering
Very cool
One of my favourite data discoveries this year: Google's mind-blowing ARCO-ERA5 dataset: hourly data for ~300 climate variables, available globally from 1940! 🤯
Loadable with a single line of Python code from a single cloud-friendly Zarr file! Below: a month of wind waves + swell: 🌊
Loadable with a single line of Python code from a single cloud-friendly Zarr file! Below: a month of wind waves + swell: 🌊
November 27, 2024 at 2:06 PM
Very cool
It’s been a pleasure to co-mentor on this project, excited about the progress!
Really excited about the Ralstonia dashboard that Vienna Elmgreen and Benjamin Ramirez are putting together (co-mentored by @bluegenes.bsky.social )
Eventually it will be a web-hosted shiny app that users can explore by filtering data by country, hosts, or phylogenetic lineages!
Eventually it will be a web-hosted shiny app that users can explore by filtering data by country, hosts, or phylogenetic lineages!
November 26, 2024 at 6:47 PM
It’s been a pleasure to co-mentor on this project, excited about the progress!
Reposted by Tessa Pierce Ward, PhD
Just updated taxid-changelog. Now you can track each NCBI Taxonomy taxon's detailed changes in the past 10 years😮😱😃
This is the proudest work I've done in my past 10+ year academic career, cause it's useful and funny but no one else did this, haha.
github.com/shenwei356/t...
This is the proudest work I've done in my past 10+ year academic career, cause it's useful and funny but no one else did this, haha.
github.com/shenwei356/t...
Release taxid-changelog v2024.11 · shenwei356/taxid-changelog
This version includes taxdump files of "2013-02-21", "2013-05-03", "2014-06-03","2014-07-22"
$ zcat taxid-changelog.csv.gz \
| csvtk grep -f taxid -p 562 \
| csvtk cut -f -lineage-taxids \...
github.com
November 20, 2024 at 1:57 AM
Just updated taxid-changelog. Now you can track each NCBI Taxonomy taxon's detailed changes in the past 10 years😮😱😃
This is the proudest work I've done in my past 10+ year academic career, cause it's useful and funny but no one else did this, haha.
github.com/shenwei356/t...
This is the proudest work I've done in my past 10+ year academic career, cause it's useful and funny but no one else did this, haha.
github.com/shenwei356/t...
Reposted by Tessa Pierce Ward, PhD
This is a very important idea, and worthwhile for those developing bioinformatics software to consider. One massive shortcoming, over which the scientists & devs have quite little control, however, is the huge dearth in funding software dev & maintenance. Software is its own product & requires $!
🧵 Bioinformatics faces a critical challenge: despite its importance, software quality often falls short due to the lack of proper development practices.
In our latest paper, we advocate for improving software quality in bioinformatics through teamwork.
academic.oup.com/bioinformati...
In our latest paper, we advocate for improving software quality in bioinformatics through teamwork.
academic.oup.com/bioinformati...
November 18, 2024 at 2:52 PM
This is a very important idea, and worthwhile for those developing bioinformatics software to consider. One massive shortcoming, over which the scientists & devs have quite little control, however, is the huge dearth in funding software dev & maintenance. Software is its own product & requires $!
Reposted by Tessa Pierce Ward, PhD
Align to AllTheBacteria with low RAM (1-2Gb) and quickly (seconds if just 1000s of hits, 15 mins for a gene present in all 2.4 million genomes) using @shenwei356.bsky.social Lexicmap. So you can basically BLAST AllTheBacteria locally - but need 3-4Tb disk for index
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Latest data from AllTheBacteria described in our updated preprint. All illumina WGS bacterial+archaeal sequence data to Aug 2024 consistently assembled, QC, and now AMR profiling. That's 2.4 million genomes. Gene annotations almost done , coming next. Please use!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
AllTheBacteria - all bacterial genomes assembled, available and searchable
The bacterial sequence data publicly available at the global DNA archives is a vast source of information on the evolution of bacteria and their mobile elements. However, most of it is either unassemb...
www.biorxiv.org
November 15, 2024 at 7:06 PM
Align to AllTheBacteria with low RAM (1-2Gb) and quickly (seconds if just 1000s of hits, 15 mins for a gene present in all 2.4 million genomes) using @shenwei356.bsky.social Lexicmap. So you can basically BLAST AllTheBacteria locally - but need 3-4Tb disk for index
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Tessa Pierce Ward, PhD
A thread with some new starter packs in genomics and bioinformatics 🧵 1/13...
November 15, 2024 at 9:56 AM
A thread with some new starter packs in genomics and bioinformatics 🧵 1/13...
Reposted by Tessa Pierce Ward, PhD
I made a starter pack for algorithmic genomics. It's certainly incomplete, but already has a ton of awesome peeps. Let me know if you know people I should add (with a focus on algorithms and data structures in genomics)
go.bsky.app/TRWCnZs
go.bsky.app/TRWCnZs
November 12, 2024 at 2:03 PM
I made a starter pack for algorithmic genomics. It's certainly incomplete, but already has a ton of awesome peeps. Let me know if you know people I should add (with a focus on algorithms and data structures in genomics)
go.bsky.app/TRWCnZs
go.bsky.app/TRWCnZs