Jessica Calland
@jesscalland.bsky.social
Microbial genomics post-doc with the Corander lab at Oslo Centre for Biostatistics and Epidemiology, University of Oslo & Oslo University Hospital
Reposted by Jessica Calland
Really pleased to share the first paper to come out of the lab.
We found that hospital patients were frequently colonised with P. aeruginosa and that the same clone was shared between the gut and the lung.
The phylogenies indicate that the clones moved from lung->gut
www.nature.com/articles/s41...
We found that hospital patients were frequently colonised with P. aeruginosa and that the same clone was shared between the gut and the lung.
The phylogenies indicate that the clones moved from lung->gut
www.nature.com/articles/s41...
High frequency body site translocation of nosocomial Pseudomonas aeruginosa - Nature Communications
Here, the authors report within-host diversity and body site translocation dynamics in hospital samples of Pseudomonas aeruginosa and reveal that body site sharing was likely due to within-patient tra...
www.nature.com
November 25, 2025 at 10:40 AM
Really pleased to share the first paper to come out of the lab.
We found that hospital patients were frequently colonised with P. aeruginosa and that the same clone was shared between the gut and the lung.
The phylogenies indicate that the clones moved from lung->gut
www.nature.com/articles/s41...
We found that hospital patients were frequently colonised with P. aeruginosa and that the same clone was shared between the gut and the lung.
The phylogenies indicate that the clones moved from lung->gut
www.nature.com/articles/s41...
Reposted by Jessica Calland
New preprint: we looked into production of the bacterial toxin colibactin and found that MDR E. coli from the global north have co-evolved with endemic colibactin producers, acquiring colibactin resistance genes before undergoing clonal expansions.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Co-evolution between colibactin production and resistance is linked to clonal expansions in Escherichia coli
Specific strains of Escherichia coli employ the polyketide synthase island to produce a metabolite called colibactin that is implicated in colorectal tumorigenesis via its genotoxic effect on human DN...
www.biorxiv.org
November 18, 2025 at 6:41 AM
New preprint: we looked into production of the bacterial toxin colibactin and found that MDR E. coli from the global north have co-evolved with endemic colibactin producers, acquiring colibactin resistance genes before undergoing clonal expansions.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Jessica Calland
New PhD position in my lab at @uniofbath.bsky.social (with both @tweethinking.bsky.social & Dr Bethan Littleford-Colquhoun)!
We're looking for someone keen on bioinformatics and microbiome evolution.
Important info below on eligibility & URSA competition funding👇
www.findaphd.com/phds/project...
We're looking for someone keen on bioinformatics and microbiome evolution.
Important info below on eligibility & URSA competition funding👇
www.findaphd.com/phds/project...
The overlapping microbiome: ecology, function and resilience beyond species boundaries at University of Bath on FindAPhD.com
PhD Project - The overlapping microbiome: ecology, function and resilience beyond species boundaries at University of Bath, listed on FindAPhD.com
www.findaphd.com
November 12, 2025 at 1:20 PM
New PhD position in my lab at @uniofbath.bsky.social (with both @tweethinking.bsky.social & Dr Bethan Littleford-Colquhoun)!
We're looking for someone keen on bioinformatics and microbiome evolution.
Important info below on eligibility & URSA competition funding👇
www.findaphd.com/phds/project...
We're looking for someone keen on bioinformatics and microbiome evolution.
Important info below on eligibility & URSA competition funding👇
www.findaphd.com/phds/project...
Reposted by Jessica Calland
E. coli can spread as quickly as swine flu, new research reveals. 🦠
For the first time, scientists can predict the rate at which gut bacteria pass between people — a major step towards tackling antibiotic-resistant infections.
Read here ⤵️
sanger.ac.uk/news_item/ad...
For the first time, scientists can predict the rate at which gut bacteria pass between people — a major step towards tackling antibiotic-resistant infections.
Read here ⤵️
sanger.ac.uk/news_item/ad...
Advanced disease modelling shows some gut bacteria can spread as rapidly as viruses
Experts can now predict the transmission rate of a bacterial E. coli infection in the same way as they can for viral pandemics, which can help battling treatment-resistant infections in the future.
sanger.ac.uk
November 4, 2025 at 11:55 AM
E. coli can spread as quickly as swine flu, new research reveals. 🦠
For the first time, scientists can predict the rate at which gut bacteria pass between people — a major step towards tackling antibiotic-resistant infections.
Read here ⤵️
sanger.ac.uk/news_item/ad...
For the first time, scientists can predict the rate at which gut bacteria pass between people — a major step towards tackling antibiotic-resistant infections.
Read here ⤵️
sanger.ac.uk/news_item/ad...
Reposted by Jessica Calland
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_...
tuni.rekrytointi.com/paikat/?o=A_...
Doctoral Researcher (simulation-based inference) / Väitöskirjatutkija (simulaatio-pohjainen päättely)
tuni.rekrytointi.com
September 1, 2025 at 6:51 AM
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_...
tuni.rekrytointi.com/paikat/?o=A_...
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...
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
June 11, 2025 at 11:51 AM
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...
www.med.uio.no/imb/om/aktue...
Reposted by Jessica Calland
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...
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
June 11, 2025 at 9:02 AM
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...
www.med.uio.no/imb/om/aktue...
Reposted by Jessica Calland
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...
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
May 26, 2025 at 8:00 AM
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...
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...
Reposted by Jessica Calland
Join us in beautiful Oslo!
Associate Professor @ocbe.bsky.social
@uio.no
Deadline May 18th
www.jobbnorge.no/en/available...
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
May 8, 2025 at 6:55 AM
Join us in beautiful Oslo!
Associate Professor @ocbe.bsky.social
@uio.no
Deadline May 18th
www.jobbnorge.no/en/available...
Associate Professor @ocbe.bsky.social
@uio.no
Deadline May 18th
www.jobbnorge.no/en/available...
Reposted by Jessica Calland
🦠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....
@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
April 30, 2025 at 9:33 AM
🦠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....
@irenlohr.bsky.social @katholt.bsky.social
genomemedicine.biomedcentral.com/articles/10....
Reposted by Jessica Calland
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.
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...
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
April 3, 2025 at 11:34 AM
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.
Reposted by Jessica Calland
🦘✂️ 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...
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
March 4, 2025 at 9:04 AM
🦘✂️ 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...
forms.gle/YJP6WQjsk8KK...
Reposted by Jessica Calland
We have a new preprint out! The title says it all.
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
Surrogate-based ABC matches generalized Bayesian inference under specific discrepancy and kernel choices
https://arxiv.org/abs/2502.11738
February 18, 2025 at 6:33 AM
We have a new preprint out! The title says it all.
Reposted by Jessica Calland
🚨 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
January 27, 2025 at 1:49 PM
🚨 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:
Reposted by Jessica Calland
🚨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🔽
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
January 15, 2025 at 5:52 PM
🚨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🔽
Apply here: tinyurl.com/y57huecd
Please share!!
#MicroSky #PhDSky #AcademicSky Details🔽
Reposted by Jessica Calland
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...
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
December 16, 2024 at 10:40 AM
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...
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...
Reposted by Jessica Calland
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/...
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
November 27, 2024 at 2:44 AM
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/...
medrxiv.org/cgi/content/...
Reposted by Jessica Calland
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
November 21, 2024 at 9:16 AM
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...
Reposted by Jessica Calland
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
November 21, 2024 at 8:22 AM
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
Reposted by Jessica Calland
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
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
November 19, 2024 at 4:09 PM
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
Written fully in Rust and there will be a browser version out later: github.com/tmaklin/kbo 1/3
Reposted by Jessica Calland
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
August 22, 2024 at 9:11 AM
Happy to share the preprint for our strain transmission inference method recently renamed to TRACS! www.biorxiv.org/content/10.1...
Reposted by Jessica Calland
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
June 19, 2024 at 9:28 AM
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...
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...
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
June 12, 2024 at 5:27 PM
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...
www.nature.com/articles/s41...
Reposted by Jessica Calland
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...
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...
April 19, 2024 at 7:28 PM
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...
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...
Reposted by Jessica Calland
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
January 22, 2024 at 4:01 PM
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!