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Falk Hildebrand

@bioinf.bsky.social
304 followers 167 following 33 posts

Bioinformatician, Quadram & Earlham Institute, Norwich, loves when programs break .. not

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Reposted by Falk Hildebrand
Evelien Adriaenssens @evelienadri.bsky.social · 25/09/2026
Here are my first thoughts as a phage person about the @anthropic.com announcement about a novel enzyme on a phage: www.linkedin.com/pulse/my-tho...
linkedin.com
My thoughts on the Anthropic phage enzyme discovery
* Disclaimer: This is not a scientific review, just a few thoughts I had while reading..
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Jacobo de la Cuesta-Zuluaga @jdlcz.bsky.social · 14/09/2026
Just out! @kiranrpatil.bsky.social @lisamaierlab.bsky.social and I wrote about how compounds not considered antibiotics (pharmaceutical, dietary, industrial, agricultural) can still impact the #microbiome 🦠 and human #health nature.com/articles/s41575-026-01258-w @natrevgastrohep.nature.com
Diagram of how non-antibiotic chemicals (from food, drugs, industry, and farming) interact with gut bacteria. Left side lists each source with an example compound and its structure: carboxymethyl cellulose from diet, metformin from pharmaceuticals, perfluorooctanoic acid from industry, chlorpyrifos from agriculture. In the center, arrows connect host and microbiome in both directions, labeled "Pharmacoecology" and "Pharmacomicrobiomics." The right side shows six effects on bacteria: bioaccumulation, direct killing, growth inhibition, horizontal gene transfer, cross-sensitization, and cross-protection. Boxes along the bottom flag the variables that shape these outcomes: exposure timing and dose, host diet and physiology, and the microbiome's existing structure.
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NFDI4Microbiota @nfdi4microbiota.bsky.social · 17/08/2026
📢 Flex Funds Call for 2027 is now open! Contribute to advancing #FAIRData, #OpenScience, infrastructure, workflows, or training in #microbiology! 💶 Funding: €10,000–€40,000/project 📅 Funding period: Apr–Dec 2027 📆 Application deadline: Oct 11 👉️ More details: nfdi4microbiota.de/newsroom/fle...
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Heng Li @lh3lh3.bsky.social · 16/06/2026
Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357
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Falk Hildebrand @bioinf.bsky.social · 07/08/2026
After a very long time, I'm very proud that we have now Joachim "magnus opum" on www.biorxiv.org/content/10.6... Protal is a ultra fast metagenomic species profiler. More precise than other profiled software, faster than most (not sylph though), but generates strain resolution instead.
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Quadram Institute @quadraminstitute.bsky.social · 03/05/2026
We’re looking for a Research Scientist (Metagenomics) to join Professor @bioinf.bsky.social 's group to investigate how bacterial genomes evolve in closely related family members 🧬 💷 £37,500 to £43,350 🗓️ Apply by 17 May 2026 ➡️ buff.ly/r50zlA9
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Earlham Institute @earlhaminst.bsky.social · 21/04/2026
At 14.45 BST Anthony Duncan will present a new tool developed to uncover biologically meaningful patterns in biological datasets. The Python tool - cvaNMF - aims to describe samples from complex biological communities as a mixture of a small number of underlying signatures. @bioinf.bsky.social
academic.oup.com
Detecting signatures underlying the composition of biological data
Abstract. Biological compositional data is inherently multidimensional and therefore difficult to visualize and interpret. To allow for the automatic decom
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Reposted by Falk Hildebrand
Aldert Zomer @aldertzomer.bsky.social · 17/04/2026
Just out in npj Antimicrobials & Resistance @natureportfolio.nature.com www.nature.com/articles/s44... We looked at what actually happens to AMR on pig farms when you reduce antimicrobial use through real-world, coaching-based interventions.
nature.com
Changes in antimicrobial resistance profiles of Escherichia coli and the metagenome on Dutch pig farms after antimicrobial usage interventions - npj Antimicrobials and Resistance
npj Antimicrobials and Resistance - Changes in antimicrobial resistance profiles of Escherichia coli and the metagenome on Dutch pig farms after antimicrobial usage interventions
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Quadram Institute @quadraminstitute.bsky.social · 16/04/2026
🆕 We are seeking an established scientific leader, with proven experience and capabilities to serve as Chair of the QIB Board of Trustees. 🗓️ Apply by 11 May 2026 ➡️ buff.ly/rlL2jAU
A social card with a photo of the Quadram Institute with pink blossom in the foreground. There is the text "Chair of the QIB Board of Trustees, an established scientific leader, with proven experience and capabilities to serve as Chair of our Board of Trustees. Apply by 11 May 2026"
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Quadram Institute @quadraminstitute.bsky.social · 14/04/2026
🆕 Vacancy! We’re looking for a Research Scientist (Data Science) to join Professor @bioinf.bsky.social 's group to investigate how novel fermented plant-based foods influence the human gut microbiome 📊 💷 £37,500 to £43,350 🗓️ Apply by 17 May 2026 ➡️ buff.ly/X88I01N
A social media card with a photo of fermented food and the text "Research Scientist (Data Science) to investigate how novel fermented plant-based foods influence the human gut microbiome, Salary: £37.500 to £43,350, Contract length: 2 years, Apply by 17 May 2026"
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Quadram Institute @quadraminstitute.bsky.social · 15/04/2026
🆕 Vacancy! We’re looking for a Research Scientist (Metagenomics) to join Professor @bioinf.bsky.social 's group to investigate how bacterial genomes evolve in closely related family members 🧬 💷 £37,500 to £43,350 🗓️ Apply by 17 May 2026 ➡️ buff.ly/HggGS1j
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Falk Hildebrand @bioinf.bsky.social · 10/04/2026
The importance of sharing data and equivalizing sampling efforts of microbiome research across continents by @raeslab.org and colleagues: link.springer.com/article/10.1... Well spoken, let's all put this into action now!
link.springer.com
Toward ethical human microbiome research: improving health through radical interdisciplinary and intercultural co-laboration - Microbiome
As human microbiome research is globalizing, it raises ethical concerns regarding the European and North American dominance in the field, which may reproduce a colonial bias and perpetuate inequities in global health research and outcomes. We suggest disentangling this ethical quandary into three main concerns: 1) scientific bias toward European and North American populations; 2) limited meaningful community inclusion, participation, and ownership, and 3) scant significant inclusion of diverse global researchers. We then formulate three recommendations for their resolution, deploying co-laboration—joint labor of diverse partners in generating synergies between diverse disciplines, cultures, and knowledges around shared concerns—and co-laborative science—a form of citizen science based on such synergies between diverse partners—to guide meaningful inclusive, participatory, and ethical human microbiome research. To conclude, we promote a programmatic list for putting co-laborative ethical science into practice, benefiting global communities, individuals, and researchers alike and decolonizing and improving health worldwide.
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Reposted by Falk Hildebrand
Chuen @chuenlee.bsky.social · 12/03/2026
Thank you for sharing! It was a pleasure to work with @bioinf.bsky.social on this project. Read the full paper here: doi.org/10.1186/s401...
doi.org
Host immunogenetic variation and gut microbiome functionality in a wild vertebrate population - Microbiome
Background The gut microbiome (GM) –important for host health and survival– is partially shaped by host immunogenetics. However, to date, no study has investigated the influence of host Major Histocom...
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Alexandre Almeida @alexmsalmeida.bsky.social · 12/01/2026
Our team wrote a review for Gut Microbes on the role of the gut #microbiome in modulating enteric infections. Great team effort by Qi Yin, @samriddhigupta.bsky.social and Efrat Muller: www.tandfonline.com/doi/full/10....
tandfonline.com
The human gut microbiome in enteric infections: from association to translation
Enteric infections remain a leading global cause of morbidity, mortality and economic loss, increasingly compounded by the rise of antimicrobial resistance. The gut microbiome — spanning bacteria, ...
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Reposted by Falk Hildebrand
Microbiome @microbiomej.bsky.social · 12/01/2026
In #Microbiome 🚨Introducing MicroPhrophet: a personalized, temporal‑aware framework that accurately forecasts microbial abundance trajectories from incomplete longitudinal data, without the need for data imputation Read more 👉 doi.org/qk8x #OpenAccess
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Falk Hildebrand @bioinf.bsky.social · 09/01/2026
Led by Anthony Duncan, and after much hard work, we have now published an Enterosignature follow-up paper: cvaNMF academic.oup.com/nar/article/... This work represents a generalization of the Enterosignature (ES) framework e.g. discovering ES disease associations, and describe "Terrasignatures" 👇👇👇
academic.oup.com
Detecting signatures underlying the composition of biological data
Abstract. Biological compositional data is inherently multidimensional and therefore difficult to visualize and interpret. To allow for the automatic decom
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Falk Hildebrand @bioinf.bsky.social · 11/12/2025
That's a well-prepared journalist, well done: www.youtube.com/watch?v=ufkt...
youtube.com
British Reporter DISMANTLES Trump Bootlicker With ONE Simple Question!
YouTube video by Brit With a Mic
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Falk Hildebrand @bioinf.bsky.social · 14/11/2025
PhD opportunity at the @quadraminstitute.bsky.social in my group: using population genetics we will explore bacterial evolution in IBD patients in a so far unprecedented spatiotemporal resolution: www.uea.ac.uk/course/phd-d... Deadline: 6th Jan
uea.ac.uk
PhD Exploring the genetics of gut microbiomes spatially resolved in IBD patients (HILDEBRAND_Q26MMB) 2026/27 | UEA
PhD Exploring the genetics of gut microbiomes spatially resolved in IBD patients (HILDEBRAND_Q26MMB) 2026/27 | UEA
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Falk Hildebrand @bioinf.bsky.social · 31/10/2025
PhD opportunity: Exploring the western gut microbiome and how these transfer between family members (2nd Dec 25 deadline). www.uea.ac.uk/course/phd-d... This bioinformatic-project will teach high-resolution metagenomics, population genetics, mobile DNA and about bacterial species theory. Please RT
uea.ac.uk
PhD PhD Opportunity: Evolutionary and Ecological Impact of the Western Lifestyle on the Gut Microbiome (HILDEBRAND_Q26DTP) 2026/27 | UEA
PhD PhD Opportunity: Evolutionary and Ecological Impact of the Western Lifestyle on the Gut Microbiome (HILDEBRAND_Q26DTP) 2026/27 | UEA
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Quadram Institute @quadraminstitute.bsky.social · 27/10/2025
🆕We’re looking for a motivated candidate to explore the evolution of the gut microbiome in patients with Inflammatory Bowel Disease, working on cutting-edge metagenomics with clinical translation 🧬 🗓️ Apply by 6 January 2026 ➡️ buff.ly/dFWnLv7 @bioinf.bsky.social
PhD position advertisement that reads "Funded PhD. Exploring the genetics of gut microbiomes spatially resolved in IBD patients. With Professor Falk Hildebrand. Apply by 6 January 2026."
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Quadram Institute @quadraminstitute.bsky.social · 14/10/2025
🎓 #PhDPosition ! 🍔 Evolutionary and Ecological Impact of the Western Lifestyle on the Gut Microbiome with Dr Falk Hildebrand @bioinf.bsky.social 📅Apply by 2 December ➡️ buff.ly/nZfTKMR
A digital illustration of the gut microbiome with the text "Funded PhD, Evolutionary and Ecological Impact of the Western Lifestyle on the Gut Microbiome, with Dr Falk Hildebrand, Apply by 2 December 2025"
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Marcela Hernández @matehg.bsky.social · 07/10/2025
PhD opportunity to work in my lab at UEA, together with @drbradbrad.bsky.social and Marc Dumont “Linking AMR, global warming and CUE in deglaciated soils” www.findaphd.com/phds/project...
findaphd.com
Linking antimicrobial resistance, climate warming, and carbon use efficiency in Arctic soils (HERNANDEZ-GARCIA_UEA_ARIES26) at University of East Anglia on FindAPhD.com
PhD Project - Linking antimicrobial resistance, climate warming, and carbon use efficiency in Arctic soils (HERNANDEZ-GARCIA_UEA_ARIES26) at University of East Anglia, listed on FindAPhD.com
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Mark Hamill @markhamillofficial.bsky.social · 06/10/2025
Same. #AlsoTiredOfWaitingForTheEPSTEIN_Files
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Falk Hildebrand @bioinf.bsky.social · 25/09/2025
Interested in modelling metabolism from food -> gut microbiome -> blood ? 5 days left to apply for a fully funded position to investigate this. 👇👇👇
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Earlham Institute @earlhaminst.bsky.social · 15/09/2025
Applications close soon for a postdoctoral researcher to join Dr Falk Hildebrand and Dr Chris Quince at the Earlham Institute, looking at microbial perspectives into land use & climate scenarios. buff.ly/wR1Ym1z #SoilHealth #Microbial #SciJobs @bioinf.bsky.social
buff.ly
Postdoctoral Research Scientist - Soil Microbiomes
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Falk Hildebrand @bioinf.bsky.social · 13/09/2025
We want to explore the metabolic interactions among gut bacteria, when the human host eats different foods - maybe this explain partly the Enterosignature structure? Please do apply for our bioinformatic post to explore this question in metagenomes: jobs.quadram.ac.uk/Details.asp?...
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Falk Hildebrand @bioinf.bsky.social · 12/09/2025
Only 5 days left to apply for our Soil metagenomics position: estimating the impact microbiomes in restored agricultural sites can have on climate change (closing 19th Sep): jobs.earlham.ac.uk/Details.asp?...
jobs.earlham.ac.uk
Earlham Institute
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Falk Hildebrand @bioinf.bsky.social · 09/09/2025
How do you long-read sequence metagenomes? I would argue it starts with the right sample storage & DNA extraction, to enable efficient @nanoporetech.com /@pacbio.bsky.social sequencing, which we investigated in our new paper: www.biorxiv.org/content/10.1... Massive thanks to Klara for driving this
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Earlham Institute @earlhaminst.bsky.social · 26/08/2025
Researchers at the Earlham Institute and @quadraminstitute.bsky.social are studying the role of #soil #microbes in carbon storage, and how different land uses impact these communities. 🦠💻🌱🧬 👉 buff.ly/5f1Eo64 @bioinf.bsky.social @tyndallcentre.bsky.social
buff.ly
New project explores potential of soil microbes to achieve UK net zero goals
How does different land uses impact soil microbes and their contribution to carbon storage?
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Quadram Institute @quadraminstitute.bsky.social · 29/08/2025
🆕 New project explores potential of soil microbes to achieve UK net zero goals Providing expertise in cutting edge methodologies for studying microbes, @bioinf.bsky.social and Dr Chris Quince, Group Leaders at the Quadram Institute & Earlham Institute, will together explore key research questions.
buff.ly
New project explores potential of soil microbes to achieve UK net zero goals - Quadram Institute
Researchers are combining the latest science in climate forecasting and soil science to understand how land use management could enable soil carbon storage
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Quadram Institute @quadraminstitute.bsky.social · 03/09/2025
🆕 Vacancy! We’re looking for a #Metagenomics Research Scientist to join the Laboratory of Dr Falk Hildebrand @bioinf.bsky.social to study diet impact on the gastrointestinal microbiome. 💷 £37,500 - £42,000 🗓️ Apply by 30 September 2025 ➡️ buff.ly/uwqGQQm
An illustration of a network with the text "Metagenomics Research Scientist, to join Falk Hildebrand's group to study the diet impact on the gastrointestinal microbiome. Salary: £37,500 to £42,000, Contract length: 2.5 years, Apply by 30 September 2025"
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Falk Hildebrand @bioinf.bsky.social · 23/07/2025
Last two days to apply for postdoc in my lab, a bioinformatic post to model metabolite fluxes in the gut microbiome during different diets: jobs.quadram.ac.uk/Details.asp?...
jobs.quadram.ac.uk
Quadram Institute
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Nandita Garud @nanditagarud.bsky.social · 22/07/2025
I am seeking a postdoc for my group at UCLA. We work at the intersection of population genetics x microbiome (garud.eeb.ucla.edu). If interested, please message me!
garud.eeb.ucla.edu
Garud Lab
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Tami Lieberman @contaminatedsci.bsky.social · 22/07/2025
We are on the lookout for postdocs for two different projects at the intersection of ecology, evolution, and the human microbiome. See thread for more information and reach out!
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Microbiome @microbiomej.bsky.social · 27/06/2025
A vacancy in @bioinf.bsky.social team -2.5 year post on food-associated changes in gut microbiomes.... please see original post for more details
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Falk Hildebrand @bioinf.bsky.social · 27/06/2025
Happy to announce that we have a new 2.5 year post on food-associated changes in gut microbiomes. We are looking for a strong bioinformatician with experience in metagenomics, metabolic modelling, functional genomics, system biology. (application deadline 20.7.25) quadram.ac.uk/vacancies/me...
Fig from https://www.nature.com/articles/s41531-025-00885-5
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Quadram Institute @quadraminstitute.bsky.social · 26/06/2025
🆕 Researchers find new way to detect early signs of pancreatic cancer 📰 Dr Falk Hildebrand @bioinf.bsky.social‬ and Daisuke Suzuki's Conversation article featured in @the-independent.com‬ ⤵️ buff.ly/lWOmRn5
the-independent.com
Researchers find new way to detect early signs of pancreatic cancer
The discovery could transform outcomes for thousands of patients
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Falk Hildebrand @bioinf.bsky.social · 26/06/2025
2.5 year postdoctoral vacancy in my group: buff.ly/NGi1dUn Deadline: 11th July This position is mostly about understanding gut microbial interactions with diet & the body through tracing/modelling metabolic processes. Will rely on metagenomics & machine learning, including other *omics approaches.
buff.ly
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Quadram Institute @quadraminstitute.bsky.social · 17/06/2025
🆕 Vacancy! We are looking for a Metagenomics Research Scientist to join the laboratory of Dr @bioinf.bsky.social‬ to study the exchange of metabolites between gut microbes and their host 💷 £36,720 to £42,000 🗓️ Apply by 11 July 2025 ➡️ buff.ly/NGi1dUn
A digital illustration of globules in the gut and the text "Metagenomics Research Scientist, to join Falk Hildebrand's group to study the exchange of metabolites between gut microbes and their host. Salary: £36,720 to £42,000, Contract length: 2.5 years, Apply by 11 July 2025"
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Falk Hildebrand @bioinf.bsky.social · 06/06/2025
Happy to announce that we have an open PDRA position in my lab, that will be about a) soil metagenomics b) green house gases c) Archaea d) combine metaGenomics with metaTranscriptomics. Apply by 8th July 25 jobs.quadram.ac.uk/Details.asp?... @quadraminstitute.bsky.social @earlhaminst.bsky.social
jobs.quadram.ac.uk
Quadram Institute
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Pamela Ferretti @pamferretti.bsky.social · 04/06/2025
Interested in microbiome GWAS and heritability studies? Check out our new Review in Nature Reviews Genetics! We explore key findings, challenges, and future directions of the field. rdcu.be/epoRR @blekhman.bsky.social @sambhawa.bsky.social and Dr. Kelsey Johnson.
rdcu.be
Genomics of host–microbiome interactions in humans
Nature Reviews Genetics - In this Review, Ferretti et al. discuss advances in our understanding of interactions between the human genome and the microbiome, including the effects of the microbiome...
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Falk Hildebrand @bioinf.bsky.social · 04/06/2025
After much work, we have finally published our KSGP 16S reference database paper: academic.oup.com/ismecommun/a... KSGP is GTDB taxonomy compliant, has >= 4x more Archaea/Bacteria assignments than SILVA or Greengenes2, and allows better filtering of mitochondrial mis-amplicons.
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Quadram Institute @quadraminstitute.bsky.social · 08/05/2025
🆕 Vacancy! We are looking for a Group Leader in Functional Microbiome Research to join the laboratory of Professor @dfigeys.bsky.social 💷 Competitive 🗓️ Apply by 28 May 2025 ➡️ buff.ly/Kef1N76
A digital illustration of the gut microbiome with the text "Group Leader in Functional Microbiome Research to help deliver world-class research on precision microbiome ex vivo assays and precision microbiome intervention trials. Salary: Competitive, Contract length: Permanent, Apply by 28 May 2025"
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Earlham Institute @earlhaminst.bsky.social · 08/05/2025
🆕 Applications are open for a #postdoc to join @bioinf.bsky.social at the Earlham Institute and @quadraminstitute.bsky.social. The role will study how #soil #microbes establish and maintain healthy #biodiverse communities, and how are these impacted by different land use scenarios. #metagenomics
buff.ly
Postdoctoral Research Scientist in Metagenomics
This post is part of the OpenCLIM_LANDS project, that aims at providing the insights needed to put the UK on a path to achieving net-zero emissions by 2050.
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Falk Hildebrand @bioinf.bsky.social · 07/05/2025
Open postdoc position in my lab @earlhaminst.bsky.social @quadraminstitute.bsky.social We will generate large-scale soil metagenomes to research the impact of agriculture on healthy soil microbiomes, developing strategies to increase carbon retention: jobs.earlham.ac.uk/Details.asp?... Please RT
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Falk Hildebrand @bioinf.bsky.social · 11/04/2025
Only a few days left to apply for our PhD position
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Laure Bindels @laurebindels.bsky.social · 08/04/2025
New editorial at Microbiome 🦠 ! Co-authored by the Senior Editors, it aims to highlight current challenges in the field of environmental and host-associated microbiome research and provides a blueprint for contemporary studies of the microbiomes. microbiomejournal.biomedcentral.com/articles/10....
microbiomejournal.biomedcentral.com
A blueprint for contemporary studies of microbiomes - Microbiome
This editorial piece co-authored by the Senior Editors at Microbiome aims to highlight current challenges in the field of environmental and host-associated microbiome research. We also take the opport...
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Thomas Clavel @tclavel.bsky.social · 08/04/2025
Here the Senior Editors at Microbiome share their thoughts on current challenges and misconceptions in microbiome research 🤗 doi.org/10.1186/s401...
doi.org
A blueprint for contemporary studies of microbiomes - Microbiome
This editorial piece co-authored by the Senior Editors at Microbiome aims to highlight current challenges in the field of environmental and host-associated microbiome research. We also take the opport...
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Raes Lab @raeslab.org · 08/04/2025
🚨PhD position in AI in Microbiology! We’re looking for a PhD researcher passionate about developing automated systems for microbiological research. 🌍 More info & apply: jobs.vib.be/j/109363/phd... @vibmicrobes.bsky.social @vibai.bsky.social
jobs.vib.be
PhD Position in AI in Microbiology - VIB
About the labThe lab of Jeroen Raes (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. In additi...
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Falk Hildebrand @bioinf.bsky.social · 07/04/2025
We have an open PhD position (deadline 14th March) in my group at QIB, Norwich, UK: buff.ly/1zRakR6 This might be of interest for researchers who want to understand gut microbial evolution, and how this changes when the human host is sick. Please RT.
buff.ly
PhD Gut bacterial adaptation to disease and inflammation (HILDEBRAND_Q25MMB) 2025/26 | UEA
PhD Gut bacterial adaptation to disease and inflammation (HILDEBRAND_Q25MMB) 2025/26 | UEA
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