Falk Hildebrand

Falk Hildebrand

@bioinf.bsky.social

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

305 followers167 following33 posts

Falk Hildebrand reposted

Heng Li
@lh3lh3.bsky.social

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

Falk Hildebrand reposted

Earlham Institute
@earlhaminst.bsky.social

Replying to @earlhaminst.bsky.social

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.comDetecting signatures underlying the composition of biological dataAbstract. Biological compositional data is inherently multidimensional and therefore difficult to visualize and interpret. To allow for the automatic decom

Falk Hildebrand reposted

Aldert Zomer
@aldertzomer.bsky.social

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.comChanges in antimicrobial resistance profiles of Escherichia coli and the metagenome on Dutch pig farms after antimicrobial usage interventions - npj Antimicrobials and Resistancenpj Antimicrobials and Resistance - Changes in antimicrobial resistance profiles of Escherichia coli and the metagenome on Dutch pig farms after antimicrobial usage interventions
Falk Hildebrand
@bioinf.bsky.social

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.comToward ethical human microbiome research: improving health through radical interdisciplinary and intercultural co-laboration - MicrobiomeAs 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.

Falk Hildebrand reposted

Chuen
@chuenlee.bsky.social

Replying to @quadraminstitute.bsky.social

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.orgHost immunogenetic variation and gut microbiome functionality in a wild vertebrate population - MicrobiomeBackground 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...

Falk Hildebrand reposted

Alexandre Almeida
@alexmsalmeida.bsky.social

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.comThe human gut microbiome in enteric infections: from association to translationEnteric 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, ...

Falk Hildebrand reposted

Microbiome
@microbiomej.bsky.social

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

Falk Hildebrand
@bioinf.bsky.social

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.comDetecting signatures underlying the composition of biological dataAbstract. 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

cvaNMF is not only useful for microbiomes, but can also be used to discover e.g. 3 signatures describing tumor stages and progression in single cell sequencing data, while identifying key cell types in each.

Falk Hildebrand
@bioinf.bsky.social

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.comDetecting signatures underlying the composition of biological dataAbstract. Biological compositional data is inherently multidimensional and therefore difficult to visualize and interpret. To allow for the automatic decom
View full thread
Falk Hildebrand
@bioinf.bsky.social

Several other environments were tested, but to mention soil metagenomes, here we described the "Terrasignatures" that can reliable describe different components of soil. The fine grained nature of allows to reconstruct geographic distances between samples (on 5 Terrasignatures):

Falk Hildebrand
@bioinf.bsky.social

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.comDetecting signatures underlying the composition of biological dataAbstract. Biological compositional data is inherently multidimensional and therefore difficult to visualize and interpret. To allow for the automatic decom
Falk Hildebrand
@bioinf.bsky.social

At it's heart, cvaNMF is a pipeline to ease the computing and k-selection of the NMF method used before. We show that the pipeline can - computationally efficient and in stable API - recover signatures from various datasets and propose a new algorithm to discover the optimal signature number.

Falk Hildebrand
@bioinf.bsky.social

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.ukPhD Exploring the genetics of gut microbiomes spatially resolved in IBD patients (HILDEBRAND_Q26MMB) 2026/27 | UEAPhD Exploring the genetics of gut microbiomes spatially resolved in IBD patients (HILDEBRAND_Q26MMB) 2026/27 | UEA
Falk Hildebrand
@bioinf.bsky.social

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.ukPhD PhD Opportunity: Evolutionary and Ecological Impact of the Western Lifestyle on the Gut Microbiome (HILDEBRAND_Q26DTP) 2026/27 | UEAPhD PhD Opportunity: Evolutionary and Ecological Impact of the Western Lifestyle on the Gut Microbiome (HILDEBRAND_Q26DTP) 2026/27 | UEA

Falk Hildebrand reposted

Marcela Hernández
@matehg.bsky.social

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.comLinking antimicrobial resistance, climate warming, and carbon use efficiency in Arctic soils (HERNANDEZ-GARCIA_UEA_ARIES26) at University of East Anglia on FindAPhD.comPhD 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
Falk Hildebrand
@bioinf.bsky.social

Interested in modelling metabolism from food -> gut microbiome -> blood ? 5 days left to apply for a fully funded position to investigate this. 👇👇👇

Falk Hildebrand@bioinf.bsky.social

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?...

Falk Hildebrand reposted

Earlham Institute
@earlhaminst.bsky.social

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.lyNew project explores potential of soil microbes to achieve UK net zero goalsHow does different land uses impact soil microbes and their contribution to carbon storage?

Falk Hildebrand reposted

Quadram Institute
@quadraminstitute.bsky.social

🆕 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.lyNew project explores potential of soil microbes to achieve UK net zero goals - Quadram InstituteResearchers are combining the latest science in climate forecasting and soil science to understand how land use management could enable soil carbon storage

Falk Hildebrand reposted

Microbiome
@microbiomej.bsky.social

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

Falk Hildebrand@bioinf.bsky.social

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...

Falk Hildebrand reposted

Pamela Ferretti
@pamferretti.bsky.social

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.beGenomics of host–microbiome interactions in humansNature 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...