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Dr. Haley Hallowell

@haleybiont.bsky.social
165 followers 237 following 33 posts

Post-doc in the @SuezLab at Johns Hopkins — Interested in all things Virome (gut and beyond), Viral-Host Co-evolution, and cool computational methods to study them! 🐶 mom 💖💜💙 she/her Views are my own ✨

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Reposted by Dr. Haley Hallowell
Karthik Anantharaman @karthik-a.bsky.social · 17/08/2026
Our latest review paper on deep sea viruses is now live in @annualreviews.bsky.social! This comprehensive review brings together why viruses are essential players not just in ecology, but in evolution and planetary-scale biogeochemistry. www.annualreviews.org/content/jour...
annualreviews.org
Decoding the Deep: The Ecology, Biogeography, and Evolution of Deep-Sea Viruses
Viruses dominate the deep-ocean biosphere (>200-m depth) yet remain profoundly understudied. As the most abundant biological entities on Earth, they govern the geochemistry, evolution, and ecology ...
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Sullivan Lab at OSU @sullivan-lab.bsky.social · 23/07/2026
📢 Applications open! Join us for our upcoming Viromics Workshop! 🧬 Learn cutting-edge metagenomic assembly, viral identification, and annotation pipelines. 🗓️ Dates: Oct 14-16 ⏰ (Extended) Deadline: Aug 20, 2026 🔗 Apply here: forms.gle/pJFLDCNEBvAe... #Viromics #Bioinformatics #AcademicSky
forms.gle
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Steven Robbins @stevenjrobbins.bsky.social · 22/07/2026
It's out! Excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂 www.nature.com/articles/s41...
nature.com
The planktonic microbiome of the Great Barrier Reef - Nature
The Great Barrier Reef Microbial Genomes Database compiles prokaryotic, viral and eukaryotic genomes from seawater collected from the Great Barrier Reef, providing a rich resource for the study of mar...
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Dr. Haley Hallowell @haleybiont.bsky.social · 16/07/2026
Having a ton of ideas for my research statement —> writing them out and thinking they are poop —> feeling overwhelmed and closing the document —> repeat (x10) 🥲🥲 i fee like this is normal tho right??
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Reposted by Dr. Haley Hallowell
Joshua Weitz @joshuasweitz.bsky.social · 15/07/2026
Bacteriophage continue to have so much to teach us. It's in our interest to understand how they work and impact human & environmental health. New joint work led by @mariandm.bsky.social & @rantahan.bsky.social inferring single-cell latent period & burst size heterogeneity from population dynamics.
science.org
Inferring single-cell heterogeneity of bacteriophage lysis-associated life-history traits from population-scale dynamics
Theory-guided experiments reveal single-cell heterogeneity of lysis-associated bacteriophage traits from population scale data.
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Reposted by Dr. Haley Hallowell
Amy D Willis @amydwillis.bsky.social · 25/06/2026
I'm hiring a #postdoc 🥳 and applications are open 🤩 Candidates with interests in EITHER statistical methodology or microbial ecology / microbiome are welcome to apply. The position / projects will be tailored to the candidate 🌟📈🎤 Thank you for sharing widely! apply.interfolio.com/188571
apply.interfolio.com
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
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Reposted by Dr. Haley Hallowell
Annie Hatmaker, Ph.D. @annemakerofhats.bsky.social · 26/05/2026
I shared on LinkedIn already, but I wanted to post here as well since I've got a different audience: I will be joining the Department of Plant Pathology at the @universityofga.bsky.social as an Assistant Professor on Aug 1!! I will keep studying #Aspergillus & #Fusarium that infect plants & humans 🥰
A white woman stands in front of a gray stone sign that says "State Botanical Garden of Georgia" and is wearing a red hat with the letter "G" in black which is the logo for the University of Georgia. Under the "G" is the word "Georgia" in white. She is wearing sunglasses and a black shirt and has brown hair past her shoulders.
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Luisa De Sordi @luisadesordi.bsky.social · 18/05/2026
I had fun writing a short commentary on the importance of integrating prophage biology into microbiome research 🦠 Now out in @cp-cellhostmicrobe.bsky.social #microbiomesky #phagesky www.cell.com/cell-host-mi...
cell.com
Making room for gut prophages in human health
Prophages are pervasive in the human gut yet largely overlooked in microbiome research, despite substantial functional potential. Emerging evidence indicates that prophages regulate bacterial fitness,...
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Reposted by Dr. Haley Hallowell
Ákos T Kovács @evolvedbiofilm.bsky.social · 24/04/2026
Transposable elements are driving rapid adaptation of Enterococcus faecium -in @nature.com from Ami Bhatt www.nature.com/articles/s41...
nature.com
Transposable elements are driving rapid adaptation of Enterococcus faecium - Nature
Over three decades, rapid expansion of the transposable element ISL3 has reshaped Enterococcus faecium, which helps to explain this pathogen’s growing clinical threat.
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c0nc0rdance @c0nc0rdance.bsky.social · 08/04/2026
This tweet is all of us.
2022 Tweet from Caroline Keroack:  "I have a whole PhD I whisper to myself, as I write C1V1 = C2V2 on a paper towel for the 8000th time."
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Eric Topol @erictopol.bsky.social · 26/03/2026
That's good.
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Dr. Haley Hallowell @haleybiont.bsky.social · 26/03/2026
Why why are we still using MDA on viral enrichments? It biases your data so sharply to ssDNA genomes. It's gotten to the point i can look at an abundance graph and guess quite accurately if they used the Genomiphi kit. I get DNA yield is low, but this can't be the best way.
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Reposted by Dr. Haley Hallowell
Jotham Suez (SuezLab@JHU) @suez.bsky.social · 04/02/2026
It's increasingly clear that commensal viruses play important roles in human health, but how do you study them? Our review "Tools and approaches to study the human gut virome: from the bench to bioinformatics" is out today in mSystems! journals.asm.org/doi/10.1128/... @haleybiont.bsky.social
A figure from the paper that provides an overview of available culture-dependent and culture-independent approaches for characterizing the human gut virome. Both culture-dependent and culture-independent approaches should be used to study the gut virome. At the bench, many protocols have been adapted to enrich viruses in a sample and isolate them using a sensitive host. Once a virus is isolated, various assays can be used to characterize how the virus interacts with its bacterial host. On the command line, viral genomes can be predicted and viral taxonomy can be identified within a sample. Once procured, multiple tools can be used to annotate viral genomes for predicted gene content and viral lifestyle and predict bacterial host taxonomy.
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Dr. Haley Hallowell @haleybiont.bsky.social · 04/02/2026
Super excited to share my latest publication with Justin Malogan and @suez.bsky.social , my love letter to viromics! 🦠 Here, we discuss computational and wet lab methods to study the gut virome and how they can be used together But why is this synergy so important? journals.asm.org/doi/10.1128/...
journals.asm.org
Tools and approaches to study the human gut virome: from the bench to bioinformatics | mSystems
The human gut microbiome is a complex community of bacteria, archaea, fungi, protozoa, and viruses that reside within the gastrointestinal (GI) tract (1). Notably, much of the literature regarding the...
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Microbiology Society @microbiologysociety.org · 18/12/2025
Born #OnThisDay in 1922, Esther Lederberg was the first to isolate the lambda phage in 1951. She characterised the lysogenic phase, whereby the phage are able to integrate into the bacterial genome, staying dormant. This discovery made them a model tool of study, leading to many more breakthroughs.
Esther Lederberg in the laboratory in the 1950's. Credit: Estherlederberg.com
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Angie Rasmussen @angierasmussen.bsky.social · 09/12/2025
Acting CDER Director Tracy Beth Høeg is not wasting any time ensuring that babies are as vulnerable as possible to preventable diseases that kill them. Now she's going after preventive RSV meds based on unverified claims from an anti-vax blogger. www.reuters.com/business/hea...
reuters.com
Exclusive: US FDA launches fresh safety scrutiny of approved RSV therapies for infants
U.S. health regulators informed senior executives at Merck, Sanofi and AstraZeneca last week that their approved protective RSV treatments for infants would face fresh safety scrutiny following concer...
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Alex Crits-Christoph @acritschristoph.bsky.social · 08/12/2025
Excited to share new work from @cultivarium.bsky.social on genetic tools (plasmids, inducible promoters, transposases, + more) for Sporosarcina pasteurii. S. pasteurii is used commercially for biocement, controlling road dust, and stabilizing soils, but had no prior published genetics:
Figure 2. Genomic deletion of the S. pasteurii urease pathway. (A) Schematic of the urease cluster deletion construct from pGLU_504 plasmid. (B) Urease activity of wild-type (WT) and urease-knockout (ΔureA-D) strains as measured by change in phenol red pH indicator (A560 nm /A600 nm) from 0 to 2 hours. (C) Biocement-formation assay using S. pasteurii DSM 33 wild-type (WT) and urease-knockout (KO) strain
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Titus Brown @titus.idyll.org · 08/12/2025
Come for the compelling science, stay for the gorgeous pictures of assembly graphs. (COI: I'm a co-author ;)
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Dr. Haley Hallowell @haleybiont.bsky.social · 08/12/2025
What is your favorite gut microbiome paper that started with a simple question but ended with super cool results? Drop them below 🥰
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Dr. Haley Hallowell @haleybiont.bsky.social · 04/12/2025
The tension between me and this chocolate chip sourdough i stress baked is 👀🥵
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Dr. Haley Hallowell @haleybiont.bsky.social · 16/06/2025
and there it is
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Reposted by Dr. Haley Hallowell
Molly Gale (Gale-Hammell Lab) @mollygale.bsky.social · 16/06/2025
🧬🌽 Happy Transposon Day! 🌽🧬 Today we celebrate the birthday of Barbara McClintock - scientist extraordinaire and discoverer of jumping genes. Still the only woman to have an unshared Nobel Prize in the biomedical sciences #TransposonDay2025
Barbara McClintock portrait
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Reposted by Dr. Haley Hallowell
Eloi Littner @eloilittner.bsky.social · 09/05/2025
Habemus paper! Our story on integron-encoded anti-phage defenses is now out in @science.org! 16 new systems, small versions of known ones, and a lot more in this highly-collaborative study. Many thanks to everyone involved, especially my supervisor @epcrocha.bsky.social bsky.app/profile/bapt...
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Dr. Haley Hallowell @haleybiont.bsky.social · 09/05/2025
Needless to say my lab will never allow me to miss a group photo 💚 😂 @suez.bsky.social
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Dr. Haley Hallowell @haleybiont.bsky.social · 04/05/2025
Pls enjoy this little Prothonotary warbler that was showing off this morning 🐤
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Reposted by Dr. Haley Hallowell
Trevor Lithgow @trevor-lithgow.bsky.social · 01/05/2025
"That telomere phages are so prevalent means that they are a selective force, one that we know little about. We now want to understand how the telomere-toxin is secreted and also understand how this ‘telocin’ wheedles its way into unsuspecting bacterial neighbors” www.science.org/doi/10.1126/...
science.org
Telomere bacteriophages are widespread and equip their bacterial hosts with potent interbacterial weapons
Klebsiella host strains infected with telomere phages can grow to be the dominant lineage in mixed populations.
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Reposted by Dr. Haley Hallowell
KaminskiMed @kaminskimed.bsky.social · 30/04/2025
A phage therapy using naturally occurring bacteryophages that not only kill but also selects for less resistant bacteria, shows promise in Cystic Fibrosis patients infected with drug resistant Pseudomonas. Kudos Dr. Chen, Stanley, Turner and Koff!!! #ScienceMatters www.nature.com/articles/s41...
nature.com
Personalized inhaled bacteriophage therapy for treatment of multidrug-resistant Pseudomonas aeruginosa in cystic fibrosis - Nature Medicine
A novel personalized phage therapy strategy that selects phages for a predicted evolutionary trade-off may represent a viable alternative approach for the treatment of antimicrobial-resistant bacteria...
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Reposted by Dr. Haley Hallowell
Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 30/04/2025
www.appropriations.senate.gov/hearings/bio...
appropriations.senate.gov
Biomedical Research: Keeping America’s Edge in Innovation | United States Senate Committee on Appropriations
United States Senate Committee on Appropriations
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Jotham Suez (SuezLab@JHU) @suez.bsky.social · 25/04/2025
Do non-nutritive sweeteners alter the human microbiome? And why is this question important? Check out our new review in Immunometabolism, spearheaded by @kcrakes.bsky.social, Lauren Questell & @subah.bsky.social and quick 🧵👇: journals.lww.com/immunometabo...
AI-generated (ChatGPT) cartoon of different gut bacteria munching on different types of sachets containing "fake sugar" as a reference to non-nutritive sweeteners
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Reposted by Dr. Haley Hallowell
Jotham Suez (SuezLab@JHU) @suez.bsky.social · 24/04/2025
Just signed up to be a mentor for the National Summer Undergraduate Research Project #NSURP2025 #nolabnoproblem www.nsurp.org - if matched, this will be the third year we host a @nsurp.bsky.social scholar in the lab and @haleybiont.bsky.social and I are excited to meet them!
nsurp.org
NSURP.org
National Summer Undergraduate Research Project
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Dr. Haley Hallowell @haleybiont.bsky.social · 26/03/2025
Maybe because I'm still early in my career, but I feel *so honored* when someone i mentor asks me to write a letter for them!
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Dr. Haley Hallowell @haleybiont.bsky.social · 24/03/2025
Had so much presenting at @camri-igs.bsky.social this year! Featuring some phree phage swag!! 🦠
Suez lab and their 3D printed phages! (left to right) Jotham, Haley, Justin, Yingying, Chinmay, Katti, Jason
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Jotham Suez (SuezLab@JHU) @suez.bsky.social · 21/03/2025
Super proud of our postdocs @kcrakes.bsky.social & @haleybiont.bsky.social for their outstanding talks at @camri-igs.bsky.social Mid-Atlantic #Microbiome Meeting, featuring exciting science from all over the region + keynotes by Sue Lynch (UCSF) & @benwolfe.bsky.social (Tufts) + phage swag! 😎 🦠
Dr. Haley Hallowell presenting her research at the Suez Lab, Johns Hopkins University, during the Mid-Atlantic Microbiome meetingDr. Katti Crakes presenting her research at the Suez Lab, Johns Hopkins University, during the Mid-Atlantic Microbiome meetingTwo-thirds of the Suez Lab and one alumnus holding phage swag. From left: Jason, Yingying, Katti, Chinmay, Justin, Haley, Val, JothamHaley (left) and Katti before presenting their talks at the Mid-Atlantic Microbiome Meeting
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Kyle T David @kylethedavid.bsky.social · 17/03/2025
I try to maintain a professional presence on this app and keep personal updates to a minimum, but I'm proud to announce @haleybiont.bsky.social and I became Discus grandparents over the weekend!
a bright blue freshwater discus fish (Symphysodon sp.) guards a clutch of eggs laid on a piece of driftwooda different pair of discus fish also guard a clutch of eggs laid on a piece of driftwood
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Dr. Haley Hallowell @haleybiont.bsky.social · 09/03/2025
Im so proud of you Annie for using your voice! It matters! 🩵
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Cait (spooky edition 🦇) @caitesq.bsky.social · 06/03/2025
Big article about the protests tomorrow, which mentions that they were organized on Bluesky!
nytimes.com
Hit by ‘Gut Punches,’ Scientists Band Together to Protest Trump (Gift Article)
Stand Up for Science aims to revive a movement that started in 2017, but with an all-new team and a more focused vision.
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Dr. Haley Hallowell @haleybiont.bsky.social · 01/03/2025
The way I watched the same men who said a woman was too emotional to be president throw absolute *temper tantrums* in the Oval Office yesterday 🪦 so anyway happy Women’s history month 👩🏻‍🔬
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Prof. Ruth Ley FRS @microbiome.bsky.social · 25/02/2025
So excited to share this latest work by @kelseyhuus.bsky.social !!! She shows that flagellin in the human gut affects whether or not people develop fever in response to vaccine, and the amount of flagellin reflects diet
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Dr. Haley Hallowell @haleybiont.bsky.social · 12/02/2025
any other postdocs feeling existential about science today 🥲 it is so hard to do stuff
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Herman Wong @hermanywong.bsky.social · 11/02/2025
Johns Hopkins officials said the NIH funding cut puts at risk approximately 600 current and ongoing clinical trials at Hopkins, including open clinical trials in cancer, pediatrics and children’s health, heart and vascular studies and the aging brain. www.thebaltimorebanner.com/education/hi...
thebaltimorebanner.com
Johns Hopkins sues federal government over NIH funds
Johns Hopkins University joined several universities in a lawsuit on Monday evening suing the federal government over NIH funding.
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Alt NIH Bluesky 🧪 @altnih4science.bsky.social · 10/02/2025
It should not need to be said that using AI to review grants is utterly stupid and will lead to choosing the most boring and average grants — humans still do way better than AI on expert tasks.
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Julia Van Etten @couchmicroscopy.bsky.social · 06/02/2025
Great reporting in this article! And some of my NSF postdoc cohort bravely speaking out on the record! We cannot let these illegal and unjust attacks on science continue. www.washingtonpost.com/science/2025...
washingtonpost.com
Trump policies sow chaos, confusion across scientific community
U.S. scientists, unaccustomed to shock-and-awe political assaults, are reeling from President Donald Trump’s executive orders on DEI, gender and other subjects.
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Mike Tisza @miketisza.bsky.social · 04/02/2025
We interrupt your regularly-scheduled chaos to bring you some cool microbiome science. 🦠 🖥️ 🧬 "Longitudinal phage–bacteria dynamics in the early life gut microbiome" now out in Nature Microbiology. We wanted a way to measure bacteria and phage in metagenomes 1/ www.nature.com/articles/s41...
nature.com
Longitudinal phage–bacteria dynamics in the early life gut microbiome - Nature Microbiology
Reanalysis of 12,262 longitudinal infant gut microbiome samples using the Marker-MAGu pipeline revealed phage–bacteria dynamics over the first year of life.
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Dr. Haley Hallowell @haleybiont.bsky.social · 05/02/2025
Stress baking the existential dread away (sourdough glazed donuts) 🍩
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Jennifer Goff, PhD @jlgoff.bsky.social · 02/02/2025
I want to expand on the extent to which IDEAA materials have been purged: I wrote an article last year for women’s history month on the history of women in antimicrobial development….DELETED.
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Chelsey Spriggs @drsprggs.bsky.social · 03/02/2025
ASM did a spotlight article on me last February and it has also been taken down as “under review”. Other spotlight articles are still up so not sure how else to interpret this besides the obvious. It feels pretty crappy to have been singled out and I won’t be engaging with them in the future.
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Jennifer Goff, PhD @jlgoff.bsky.social · 02/02/2025
I’m on one of ASMs IDEAA committees and we have received 0 communication from ASM staff on why this is happening. I had to find out via social media. Extremely disappointing.
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Dr. Haley Hallowell @haleybiont.bsky.social · 03/02/2025
ASM … amidst the darkness here goes yet another safe place for American scientists 😓
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WHO @who.int · 28/01/2025
🧵 STATEMENT: WHO expresses deep concern on the implications of the immediate funding pause for #HIV programmes in low- and middle-income countries. These programmes provide access to life-saving HIV therapy to more than 30 million people worldwide. Read more bit.ly/42yxxIz 1/5
WHO statement on potential global threat to people living with HIV
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Michael Baym @baym.lol · 28/01/2025
If you’re at a European institution and are looking to poach American scientists, this would be a very good week to do it
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