Helena, PhD
@hexylena.bsky.social
bioinformatician and systems witch. casting the spells that make the servers work 🧙🪄
https://orcid.org/0000-0001-9760-8992
Failure is not an option.
Better living through harm reduction.
Stable like RDX.
she/they/▒▒
https://orcid.org/0000-0001-9760-8992
Failure is not an option.
Better living through harm reduction.
Stable like RDX.
she/they/▒▒
Reposted by Helena, PhD
The new -outfmt 20 in BLAST 😍. No more frustrated googling to remember which column is which.....
September 6, 2025 at 2:54 PM
The new -outfmt 20 in BLAST 😍. No more frustrated googling to remember which column is which.....
Reposted by Helena, PhD
We turn 25 today!
July 7th marks the 25th anniversary of the human genome going online and the start of the UCSC Genome Browser.
Then vs. now, we have 165k monthly visitors, and our codebase is over three million lines of code.
See our news for more: bit.ly/genomeBrowser...
July 7th marks the 25th anniversary of the human genome going online and the start of the UCSC Genome Browser.
Then vs. now, we have 165k monthly visitors, and our codebase is over three million lines of code.
See our news for more: bit.ly/genomeBrowser...
July 7, 2025 at 9:45 PM
We turn 25 today!
July 7th marks the 25th anniversary of the human genome going online and the start of the UCSC Genome Browser.
Then vs. now, we have 165k monthly visitors, and our codebase is over three million lines of code.
See our news for more: bit.ly/genomeBrowser...
July 7th marks the 25th anniversary of the human genome going online and the start of the UCSC Genome Browser.
Then vs. now, we have 165k monthly visitors, and our codebase is over three million lines of code.
See our news for more: bit.ly/genomeBrowser...
Reposted by Helena, PhD
🚨 New paper alert!
How do you pick the right genomes for public health surveillance—when you’ve got 10,000+ E. coli to choose from?
We built an MLST framework to do just that. 🧵👇
🔗 www.mdpi.com/2076-2607/13...
How do you pick the right genomes for public health surveillance—when you’ve got 10,000+ E. coli to choose from?
We built an MLST framework to do just that. 🧵👇
🔗 www.mdpi.com/2076-2607/13...
www.mdpi.com
June 26, 2025 at 3:46 PM
🚨 New paper alert!
How do you pick the right genomes for public health surveillance—when you’ve got 10,000+ E. coli to choose from?
We built an MLST framework to do just that. 🧵👇
🔗 www.mdpi.com/2076-2607/13...
How do you pick the right genomes for public health surveillance—when you’ve got 10,000+ E. coli to choose from?
We built an MLST framework to do just that. 🧵👇
🔗 www.mdpi.com/2076-2607/13...
In many ways, surviving a #PhD and higher education in general, felt like this recent foreign body removal case report.
At least we're both finally free.
doi.org/10.1093/jscr...
At least we're both finally free.
doi.org/10.1093/jscr...
An eight-year asymptomatic retention of a knife blade in the chest: a case report
Abstract. Retained foreign bodies in the thoracic cavity following penetrating trauma are rare and typically identified shortly after injury. However, prol
doi.org
June 13, 2025 at 3:03 PM
In many ways, surviving a #PhD and higher education in general, felt like this recent foreign body removal case report.
At least we're both finally free.
doi.org/10.1093/jscr...
At least we're both finally free.
doi.org/10.1093/jscr...
Reposted by Helena, PhD
New preprint! Deacon is a versatile tool for filtering FASTA/FASTQ files and streams at hundreds of megabases per second using minimizers, built with rapid metagenomic host depletion in mind, but equally useful for search.
github.com/bede/deacon
github.com/bede/deacon
Deacon: fast sequence filtering and contaminant depletion https://www.biorxiv.org/content/10.1101/2025.06.09.658732v1
June 13, 2025 at 1:25 PM
New preprint! Deacon is a versatile tool for filtering FASTA/FASTQ files and streams at hundreds of megabases per second using minimizers, built with rapid metagenomic host depletion in mind, but equally useful for search.
github.com/bede/deacon
github.com/bede/deacon
Reposted by Helena, PhD
NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.
May 22, 2025 at 12:42 PM
NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.
Reposted by Helena, PhD
It pains me to say this, but if you are not a US citizen, you should not attend scientific conferences in the US, visit US institutions, or otherwise travel to our country.
Right now it's not worth the risk.
Hopefully that will change. If it doesn't, science in the US is sunk anyway.
Right now it's not worth the risk.
Hopefully that will change. If it doesn't, science in the US is sunk anyway.
May 26, 2025 at 1:54 AM
It pains me to say this, but if you are not a US citizen, you should not attend scientific conferences in the US, visit US institutions, or otherwise travel to our country.
Right now it's not worth the risk.
Hopefully that will change. If it doesn't, science in the US is sunk anyway.
Right now it's not worth the risk.
Hopefully that will change. If it doesn't, science in the US is sunk anyway.
Reposted by Helena, PhD
🗣️ Quote of #ESHG2025 (so far)
"Who licks bone !?!" 🦴
- Johannes Krause
Anyone have that on your bingo card?
Well apparently archeologists do, to distinguish bone from stones and it causes problems in DNA sequencing. 🤔
"Who licks bone !?!" 🦴
- Johannes Krause
Anyone have that on your bingo card?
Well apparently archeologists do, to distinguish bone from stones and it causes problems in DNA sequencing. 🤔
May 24, 2025 at 1:46 PM
🗣️ Quote of #ESHG2025 (so far)
"Who licks bone !?!" 🦴
- Johannes Krause
Anyone have that on your bingo card?
Well apparently archeologists do, to distinguish bone from stones and it causes problems in DNA sequencing. 🤔
"Who licks bone !?!" 🦴
- Johannes Krause
Anyone have that on your bingo card?
Well apparently archeologists do, to distinguish bone from stones and it causes problems in DNA sequencing. 🤔
Reposted by Helena, PhD
Delighted to see this paper from danderson123.bsky.social 's PhD out. We have been building tools for AMR gene detection for over a decade now, but multicopy genes remain challenging. Dan shows that with a gene-space de Bruijn graph and long reads, you can do well
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
May 19, 2025 at 9:28 AM
Delighted to see this paper from danderson123.bsky.social 's PhD out. We have been building tools for AMR gene detection for over a decade now, but multicopy genes remain challenging. Dan shows that with a gene-space de Bruijn graph and long reads, you can do well
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Helena, PhD
Honestly, same.
People are like "well you *must* be smart with a PhD!". Absolutely not, I am merely obsessively interested in an extremely niche topic and far more stubborn than is good for my health, and otherwise I am content to bumble through my life, occasionally walking into walls.
People are like "well you *must* be smart with a PhD!". Absolutely not, I am merely obsessively interested in an extremely niche topic and far more stubborn than is good for my health, and otherwise I am content to bumble through my life, occasionally walking into walls.
One of the best parts of getting old has been the realization that I am much less smart and competent than I was led to believe when I was younger and accepting that fact has reduced my stress level so much. I think everyone should embrace their stupidity
April 18, 2025 at 5:38 AM
Honestly, same.
People are like "well you *must* be smart with a PhD!". Absolutely not, I am merely obsessively interested in an extremely niche topic and far more stubborn than is good for my health, and otherwise I am content to bumble through my life, occasionally walking into walls.
People are like "well you *must* be smart with a PhD!". Absolutely not, I am merely obsessively interested in an extremely niche topic and far more stubborn than is good for my health, and otherwise I am content to bumble through my life, occasionally walking into walls.
Reposted by Helena, PhD
bioinformatician, computer scientist, and geneticist lead bioinformatic tool development—which one is better? academic.oup.com/bioinformati...
A bioinformatician, computer scientist, and geneticist lead bioinformatic tool development—which one is better?
AbstractMotivation. The development of accurate bioinformatic software tools is crucial for the effective analysis of complex biological data. This study e
academic.oup.com
March 29, 2025 at 7:10 AM
bioinformatician, computer scientist, and geneticist lead bioinformatic tool development—which one is better? academic.oup.com/bioinformati...
Reposted by Helena, PhD
No one should have to choose between care & Covid.
The politicization of masks has led to a reduced infection control in healthcare settings.
Patients are labelled anxious, difficult or worse for asking staff to wear a mask.
We need mandatory masking in healthcare:
The politicization of masks has led to a reduced infection control in healthcare settings.
Patients are labelled anxious, difficult or worse for asking staff to wear a mask.
We need mandatory masking in healthcare:
We Need Mandatory Masking in Healthcare, and We Need it Now
Healthcare facilities should set the tone when it comes to masking. They should help patients protect themselves from Covid and other threats. Instead they push droplet dogma and put lives at risk.
www.disabledginger.com
March 24, 2025 at 5:01 AM
No one should have to choose between care & Covid.
The politicization of masks has led to a reduced infection control in healthcare settings.
Patients are labelled anxious, difficult or worse for asking staff to wear a mask.
We need mandatory masking in healthcare:
The politicization of masks has led to a reduced infection control in healthcare settings.
Patients are labelled anxious, difficult or worse for asking staff to wear a mask.
We need mandatory masking in healthcare:
Reposted by Helena, PhD
I CAN FLY HIGHER THAN AN EAGLE
YOU ARE THE ESCAPE ROUTE OUT MY OFFICE
YOU ARE THE ESCAPE ROUTE OUT MY OFFICE
March 21, 2025 at 4:36 PM
I CAN FLY HIGHER THAN AN EAGLE
YOU ARE THE ESCAPE ROUTE OUT MY OFFICE
YOU ARE THE ESCAPE ROUTE OUT MY OFFICE
Reposted by Helena, PhD
I think "let's learn together" is going to my mission statement for my postdoc. As a senior scientist in my lab group, I'm often asked questions I just don't know the answer to. I think I'm going to approach those interactions with curiosity and learn with trainees. 🧪
March 21, 2025 at 3:30 PM
I think "let's learn together" is going to my mission statement for my postdoc. As a senior scientist in my lab group, I'm often asked questions I just don't know the answer to. I think I'm going to approach those interactions with curiosity and learn with trainees. 🧪
Reposted by Helena, PhD
The summary:
Kiwi, Kiwis: 👫🧑🏾🤝🧑🏾: Homo sapiens
kiwi, kiwi: 🔑🟤: Apteryx spp
kiwifruit, kiwifruit: 🥝: Actinidia cvv
Kiwi, Kiwis: 👫🧑🏾🤝🧑🏾: Homo sapiens
kiwi, kiwi: 🔑🟤: Apteryx spp
kiwifruit, kiwifruit: 🥝: Actinidia cvv
March 16, 2025 at 5:57 AM
The summary:
Kiwi, Kiwis: 👫🧑🏾🤝🧑🏾: Homo sapiens
kiwi, kiwi: 🔑🟤: Apteryx spp
kiwifruit, kiwifruit: 🥝: Actinidia cvv
Kiwi, Kiwis: 👫🧑🏾🤝🧑🏾: Homo sapiens
kiwi, kiwi: 🔑🟤: Apteryx spp
kiwifruit, kiwifruit: 🥝: Actinidia cvv
Reposted by Helena, PhD
🥁 Announcing the Public Domain Image Archive! 🥁
We are v excited to share our new sister-project, the Public Domain Image Archive (PDIA), a curated collection of 10k+ out-of-copyright historical images, all free to explore and reuse: pdimagearchive.org @pdimagearchive
We are v excited to share our new sister-project, the Public Domain Image Archive (PDIA), a curated collection of 10k+ out-of-copyright historical images, all free to explore and reuse: pdimagearchive.org @pdimagearchive
January 8, 2025 at 5:02 PM
🥁 Announcing the Public Domain Image Archive! 🥁
We are v excited to share our new sister-project, the Public Domain Image Archive (PDIA), a curated collection of 10k+ out-of-copyright historical images, all free to explore and reuse: pdimagearchive.org @pdimagearchive
We are v excited to share our new sister-project, the Public Domain Image Archive (PDIA), a curated collection of 10k+ out-of-copyright historical images, all free to explore and reuse: pdimagearchive.org @pdimagearchive
you'd think I died or something 😅
Thank you Bacon Brigade, this was really really lovely of y'all 💜I'm so happy for the positive impact I could have for y'all, and hopefully many more folks on the future.
Thank you Bacon Brigade, this was really really lovely of y'all 💜I'm so happy for the positive impact I could have for y'all, and hopefully many more folks on the future.
An Ode to Helena - from the 🥓Bacon Brigade
Read more at https://training.galaxyproject.org/training-material/news/2025/03/07/ode_to_helena.html
@galaxyproject.bsky.social
Read more at https://training.galaxyproject.org/training-material/news/2025/03/07/ode_to_helena.html
@galaxyproject.bsky.social
March 10, 2025 at 7:45 AM
you'd think I died or something 😅
Thank you Bacon Brigade, this was really really lovely of y'all 💜I'm so happy for the positive impact I could have for y'all, and hopefully many more folks on the future.
Thank you Bacon Brigade, this was really really lovely of y'all 💜I'm so happy for the positive impact I could have for y'all, and hopefully many more folks on the future.
Reposted by Helena, PhD
Such a brilliant cover!
Our 2025 March issue bit.ly/2N9R8Es reviews blood impact on vector-borne diseases, zoonotic Giardia transmission in cattle, parasite subcellular dynamics, Bacillus thuringiensis for nematode management, heptalaminate membrane of intravascular schistosomes, trade-offs in virulence evolution, & more
March 6, 2025 at 3:35 PM
Such a brilliant cover!
So excited for the medical research data privacy Visual Novel.
March 5, 2025 at 11:43 AM
So excited for the medical research data privacy Visual Novel.
Reposted by Helena, PhD
If you own an ebike, scooter, or hoverboard - make sure you charge it safely.
March 4, 2025 at 6:29 PM
If you own an ebike, scooter, or hoverboard - make sure you charge it safely.
March 4, 2025 at 6:34 PM
Reposted by Helena, PhD
Thank you for your patience! Read my latest long-form analysis of how the 2022 Wings Over Dallas air show went tragically wrong. admiralcloudberg.medium.com/passing-the-...
Passing the Buck: The story of the 2022 Wings Over Dallas air show collision
How unsafe practices in the air show industry caused the deaths of six crewmembers and the loss of two iconic aircraft.
admiralcloudberg.medium.com
February 28, 2025 at 6:13 AM
Thank you for your patience! Read my latest long-form analysis of how the 2022 Wings Over Dallas air show went tragically wrong. admiralcloudberg.medium.com/passing-the-...
Reposted by Helena, PhD
We're hiring a postdoc!🚨
Study human-associated microbial communities in health & disease.
🔬Requirements:
- PhD in bioinformatics, microbiology, or related field
- Expertise in omics
- Strong publication record
Apply now!🌟 jobs.vib.be/j/69697/post...
@vibmicrobes.bsky.social
Study human-associated microbial communities in health & disease.
🔬Requirements:
- PhD in bioinformatics, microbiology, or related field
- Expertise in omics
- Strong publication record
Apply now!🌟 jobs.vib.be/j/69697/post...
@vibmicrobes.bsky.social
Postdoctoral position in bioinformatics of the human gut microbiome - VIB
About the Lab
Thelab of JeroenRaes(VIB, KU Leuven) is home to a vibrant, dynamic and international group of researchers in the field of gut microbial ecology and its clinical applications
jobs.vib.be
February 20, 2025 at 7:53 AM
We're hiring a postdoc!🚨
Study human-associated microbial communities in health & disease.
🔬Requirements:
- PhD in bioinformatics, microbiology, or related field
- Expertise in omics
- Strong publication record
Apply now!🌟 jobs.vib.be/j/69697/post...
@vibmicrobes.bsky.social
Study human-associated microbial communities in health & disease.
🔬Requirements:
- PhD in bioinformatics, microbiology, or related field
- Expertise in omics
- Strong publication record
Apply now!🌟 jobs.vib.be/j/69697/post...
@vibmicrobes.bsky.social
Reposted by Helena, PhD
No more stitches? The future of surgery is here! 🚀
Scientists are using lasers to seal wounds—no needles, no scars, just faster healing! 🏥✨
🔗 digitalpatientsafety.com/the-future-o...
🌐 #WomensHealth #DHPSP #MedicalTech #FutureOfSurgery #LaserHealing #CRBIOTECH
Scientists are using lasers to seal wounds—no needles, no scars, just faster healing! 🏥✨
🔗 digitalpatientsafety.com/the-future-o...
🌐 #WomensHealth #DHPSP #MedicalTech #FutureOfSurgery #LaserHealing #CRBIOTECH
February 20, 2025 at 1:19 PM
No more stitches? The future of surgery is here! 🚀
Scientists are using lasers to seal wounds—no needles, no scars, just faster healing! 🏥✨
🔗 digitalpatientsafety.com/the-future-o...
🌐 #WomensHealth #DHPSP #MedicalTech #FutureOfSurgery #LaserHealing #CRBIOTECH
Scientists are using lasers to seal wounds—no needles, no scars, just faster healing! 🏥✨
🔗 digitalpatientsafety.com/the-future-o...
🌐 #WomensHealth #DHPSP #MedicalTech #FutureOfSurgery #LaserHealing #CRBIOTECH
Reposted by Helena, PhD
Some background on the art here: www.bioinf.wits.ac.za/~scott/mbiom... - and some of the folks involved: www.zenzulu.co.za/index.html
AWI-Gen Microbiome Project Art Work
www.bioinf.wits.ac.za
February 20, 2025 at 8:36 PM
Some background on the art here: www.bioinf.wits.ac.za/~scott/mbiom... - and some of the folks involved: www.zenzulu.co.za/index.html