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Reposted by Jessica Calland

Henri Pesonen @hpesonen.bsky.social · Sep 1

I'm looking for a Doctoral Researcher (PhD student) to work with me on simulation-based inference at Data Science Research Centre, Tampere University Check the link for details and send an application before October 10th.

tuni.rekrytointi.com/paikat/?o=A_...

Doctoral Researcher (simulation-based inference) / Väitöskirjatutkija (simulaatio-pohjainen päättely)

tuni.rekrytointi.com

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Jessica Calland @jesscalland.bsky.social · Jun 11

Overjoyed to have received one of the FRIPRO Young Talent grants from the Norwegian research council to investigate the effects of hospitalisation on Klebsiella colonisation! 🎉🥳
www.med.uio.no/imb/om/aktue...

Tildelt ti millioner for å forske på Klebsiella - Institutt for medisinske basalfag

Bakterien Klebsiella kan gi lungebetennelse og blodforgiftning, og mange får den mens de er innlagt på sykehus. Nå får Jessica Calland ti millioner fra NFRs FRIPRO for å forske på den lumske bakterien...

www.med.uio.no

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Reposted by Jessica Calland

Manuela Zucknick @manuelazucknick.bsky.social · Jun 11

Congratulations to our own fantastic Jessica Calland @ocbe.bsky.social for receiving the prestigious FRIPRO Young Talents grant from the Norwegian Research Council! 🎉 She will continue her work identifying drivers of Klebsiella colonisation in critically ill patients.

www.med.uio.no/imb/om/aktue...

Tildelt ti millioner for å forske på Klebsiella - Institutt for medisinske basalfag

Bakterien Klebsiella kan gi lungebetennelse og blodforgiftning, og mange får den mens de er innlagt på sykehus. Nå får Jessica Calland ti millioner fra NFRs FRIPRO for å forske på den lumske bakterien...

www.med.uio.no

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Reposted by Jessica Calland

Tommi Mäklin @themaklin.bsky.social · May 26

New preprint: we used k-mer matching with suffix match length information to create an assembly-to-assembly alignment algorithm + software, kbo.

We wanted to create a reference-based aligner and variant caller that scales to at least 10-100k bacterial queries.

www.biorxiv.org/content/10.1...

Sequence alignment with k-bounded matching statistics

Finding high-quality local alignments between a query sequence and sequences contained in a large genomic database is a fundamental problem in computational genomics, at the core of thousands of biolo...

www.biorxiv.org

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Reposted by Jessica Calland

Marit B. Veierød @maritbveierod.bsky.social · May 8

Join us in beautiful Oslo!
Associate Professor @ocbe.bsky.social
@uio.no
Deadline May 18th
www.jobbnorge.no/en/available...

Associate Professor at the Oslo Centre for Biostatistics and Epidemiology (276924) | University of Oslo

Job title: Associate Professor at the Oslo Centre for Biostatistics and Epidemiology (276924), Employer: University of Oslo, Deadline: Sunday, May 18, 2025

www.jobbnorge.no

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Reposted by Jessica Calland

Marit Hetland @genomarit.bsky.social · Apr 30

🦠Happy to share that our paper studying >3000 Klebsiella pneumoniae genomes in a #OneHealth perspective is now published in Genome Medicine! #MicroSky 🎉

@irenlohr.bsky.social @katholt.bsky.social

genomemedicine.biomedcentral.com/articles/10....

A genome-wide One Health study of Klebsiella pneumoniae in Norway reveals overlapping populations but few recent transmission events across reservoirs - Genome Medicine

Background Members of the Klebsiella pneumoniae species complex (KpSC) are opportunistic pathogens that cause severe and difficult-to-treat infections. KpSC are common in non-human niches, but the cli...

genomemedicine.biomedcentral.com

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Reposted by Jessica Calland

Rebecca Gladstone @becctococcus.bsky.social · Apr 3

Being able to data plasmid acquisition, and to see the diversity of plasmids being gained and lost from lineages, was really eye opening! It was a pleasure to contribute my tiny bit to this huge paper and the data has so much more to give! @arredondo.bsky.social @gerrythill.bsky.social et al.

Wellcome Sanger Institute @sangerinstitute.bsky.social · Apr 3

Read ‘Plasmid-driven strategies for clone success in Escherichia coli.’ From @sangerinstitute.bsky.social @uitnorgesarktiske.bsky.social, the University of Oslo, and others, in @naturecomms.bsky.social, here ⤵️

www.nature.com/articles/s41...

Plasmid-driven strategies for clone success in Escherichia coli - Nature Communications

Plasmids can encode multiple traits that contribute to the emergence and dissemination of their bacterial hosts. Here the authors use Nanopore long-read technology to sequence the complete genomes of ...

www.nature.com

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Reposted by Jessica Calland

Torsten Seemann @torstenseemann.bsky.social · Mar 4

🦘✂️ Thanks to @cziscience.bsky.social , @wytamma.bsky.social and I are writing the next version of the Snippy bacterial variant calling pipeline. We want your input on what features s it will have. Please fill out this (longish) survey to help make Snippy great again!
forms.gle/YJP6WQjsk8KK...

Snippy: Microbial Variant Calling Community Survey

Help us drive the next wave of innovation in Single-Nucleotide Polymorphism (SNP) discovery and genome analysis by sharing your valuable experiences and insights. This in-depth survey aims at understa...

forms.gle

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Reposted by Jessica Calland

Henri Pesonen @hpesonen.bsky.social · Feb 18

We have a new preprint out! The title says it all.

arxiv.stat.ME @arxiv-stat-me.bsky.social · Feb 18

Marko J\"arvenp\"a\"a, Jukka Corander, Henri Pesonen
Surrogate-based ABC matches generalized Bayesian inference under specific discrepancy and kernel choices
https://arxiv.org/abs/2502.11738

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Reposted by Jessica Calland

Fiona J Whelan @whelanfj.bsky.social · Jan 27

🚨 We are hiring for a 3-yr PDRA 🚨 The Whelan lab is seeking a microbiologist interested in microbe-pathogen competition and use of a Drosophila melanogaster chronic infection model to investigate the cystic fibrosis lung microbiome. For more info check out whelanlab.co.uk & apply at the link below:

Research Associate in Microbe-Microbe Interactions :Manchester

www.jobs.manchester.ac.uk

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Reposted by Jessica Calland

Jai Mehat @jaimehat.bsky.social · Jan 15

🚨An exciting #PhD opportunity in my group🧫 @UniSurreyBioSci with Linda Oyama @QUB to work on #phage modulation of the poultry #microbiome and suppressing AMR. Closing date for applications is 3rd Feb

Apply here: tinyurl.com/y57huecd

Please share!!
#MicroSky #PhDSky #AcademicSky Details🔽

PhD Opportunities - FoodBioSystems

Four-year funded PhD projects are available in areas that span the food chain from farm to fork. Closing date: 3 February 2024 (10:00 GMT)

tinyurl.com

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Reposted by Jessica Calland

Jon Michael Gran @jmgran.bsky.social · Dec 16

Want to do a postdoc in Oslo? We're seeking candidates for a four year postdoc position in causal inference/time-to-event analysis.

Application deadline is January 31. See below for more information and feel free to take contact if you have any questions! www.jobbnorge.no/en/available...

Four year postdoc position at the Oslo Centre for Biostatistics and Epidemiology (OCBE) (272144) | University of Oslo

Job title: Four year postdoc position at the Oslo Centre for Biostatistics and Epidemiology (OCBE) (272144), Employer: University of Oslo, Deadline: Friday, January 31, 2025

www.jobbnorge.no

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Reposted by Jessica Calland

Rebecca Gladstone @becctococcus.bsky.social · Nov 27

How invasive are different E .coli capsules and how many are there? Find out here and use the group 2 and 3 database to type your own!
medrxiv.org/cgi/content/...

Group 2 and 3 ABC-transporter dependant capsular K-loci contribute significantly to variation in the invasive potential of Escherichia coli

The major opportunistic pathogen Escherichia coli is the largest cause of antimicrobial resistance (AMR) associated infections and deaths globally. Considerable antigenic diversity has been documented...

medrxiv.org

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Reposted by Jessica Calland

Dr. Amy Lee @minisciencegirl.bsky.social · Nov 21

Every year, >200K newborns die from sepsis.
Our team used machine learning to develop a set of genes that can predict neonatal sepsis risk using at birth blood samples.
www.thelancet.com/journals/ebi...

Predictive gene expression signature diagnoses neonatal sepsis before clinical presentation

Despite appearing healthy at birth, neonates who later developed EOS already had distinct whole blood gene expression changes at birth, which enabled the development of a 4-gene predictive signature f...

www.thelancet.com

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Reposted by Jessica Calland

Oslo Centre for Biostatistics and Epidemiology @ocbe.bsky.social · Nov 21

OCBE is preparing to leave the dark social media. To help you connect with our community here 🦋, me made a starter pack with present and past OCBE members, a list that will probably will grow soon 😊 go.bsky.app/6bqMnLQ

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Reposted by Jessica Calland

Tommi Mäklin @themaklin.bsky.social · Nov 19

New tool from me: I wrote a local aligner that can do approximate reference-based alignment and find genes in a query microbial genome, without a separate indexing step or any temporary disk space usage.

Written fully in Rust and there will be a browser version out later: github.com/tmaklin/kbo 1/3

GitHub - tmaklin/kbo: Spectral Burrows-Wheeler transform accelerated local alignment search.

Spectral Burrows-Wheeler transform accelerated local alignment search. - tmaklin/kbo

github.com

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Jessica Calland @jesscalland.bsky.social · Nov 18

Me please!

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Reposted by Jessica Calland

Gerry Tonkin-Hill @gerrythill.bsky.social · Aug 22

Happy to share the preprint for our strain transmission inference method recently renamed to TRACS! www.biorxiv.org/content/10.1...

Enhanced metagenomics-enabled transmission inference with TRACS

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

www.biorxiv.org

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Reposted by Jessica Calland

Tommi Mäklin @themaklin.bsky.social · Jun 19

New paper: we deep sequenced E. coli within-host diversity in ~900 people in Pakistan, and found massive diversity in E. coli from lineages that are somewhat uncommon in Europe 1/5 www.nature.com/articles/s41...

Deep sequencing of Escherichia coli exposes colonisation diversity and impact of antibiotics in Punjab, Pakistan - Nature Communications

E coli is an important cause of infection globally but there is limited understanding of the genetic diversity of strains circulating in South Asia. Here, the authors characterise strains in Punjab pr...

www.nature.com

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Jessica Calland @jesscalland.bsky.social · Jun 12

Our study on combining genomics with autogenous vaccine design to control Campylobacter in poultry is out today in npj Vaccines!
www.nature.com/articles/s41...

Genomic tailoring of autogenous poultry vaccines to reduce Campylobacter from farm to fork - npj Vaccines

npj Vaccines - Genomic tailoring of autogenous poultry vaccines to reduce Campylobacter from farm to fork

www.nature.com

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Reposted by Jessica Calland

Jesse Shapiro @bjesseshapiro.bsky.social · Apr 19

Now published: "Phage predation, disease severity, and pathogen genetic diversity in cholera patients"

www.science.org/doi/10.1126/...

Check out the podcast to hear co-senior author Eric Nelson talk about the twists and turns of our study (around 18:25):
www.science.org/content/podc...

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Reposted by Jessica Calland

John Lees @bacpop.org · Jan 22

We are happy to have been selected by SMBE to host a satellite meeting on Pathogen Pangenome Evolution Between and Within their Hosts: smbepangenomes.bacpop.org We are expecting the meeting to be in Tokyo on 26-28th November 2024, save the date!

SMBE Satellite Workshop on Pathogen Pangenome Evolution

Academic conference held in Tokyo, Japan 2024

smbepangenomes.bacpop.org

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Reposted by Jessica Calland

Fiona J Whelan @whelanfj.bsky.social · Nov 28

📣 PhD opportunity 📣
Come discover how longterm antibiotic use shapes the lung microbiome of people with COPD and how it contributes to antimicrobial resistance transmission between microbes!

"Transmissible Antimicrobial Resistance in the Respiratory Microbiome" (1/n)

#PhDSky 🦠 🧪

PhD Opportunities – MRC AIM

more.bham.ac.uk

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Jessica Calland @jesscalland.bsky.social · Nov 23

For those who missed it, this is our latest preprint on using genomics to develop autogenous vaccines to reduce Campylobacter ending up on our plates!
www.biorxiv.org/content/10.1...

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