Kieran Campbell
@kieranrcampbell.bsky.social
https://www.camlab.ca | ML for cancer genomics + single-cell and spatial computational methods | Toronto Canada 🖥️🧬
Pinned
Segmentation aware probabilistic phenotyping of single-cell spatial protein expression data - Nature Communications
Spatial expression assays are affected by segmentation errors leading to difficulty interpreting cell types. Here, the authors introduce a machine learning model to infer cell types accounting for suc...
www.nature.com
How can we quantify single cell expression from multiplexed imaging datasets given segmentation errors?
To help tackle this, we introduce evaluation metrics, a gold-standard dataset, and STARLING—a new probabilistic machine learning method (1/4)
www.nature.com/articles/s41...
To help tackle this, we introduce evaluation metrics, a gold-standard dataset, and STARLING—a new probabilistic machine learning method (1/4)
www.nature.com/articles/s41...
Congratulations to @michaelgeuenich.bsky.social selected as the Canadian representative at the Young Investigator Symposium at SITC 2025.
He's presenting our work on tertiary lymphoid structures in pancreatic cancer tomorrow at 8.15am at SITC
Abstract ➡️ www.immunotherapycancer.ca/2025-michael...
He's presenting our work on tertiary lymphoid structures in pancreatic cancer tomorrow at 8.15am at SITC
Abstract ➡️ www.immunotherapycancer.ca/2025-michael...
November 4, 2025 at 11:05 PM
Congratulations to @michaelgeuenich.bsky.social selected as the Canadian representative at the Young Investigator Symposium at SITC 2025.
He's presenting our work on tertiary lymphoid structures in pancreatic cancer tomorrow at 8.15am at SITC
Abstract ➡️ www.immunotherapycancer.ca/2025-michael...
He's presenting our work on tertiary lymphoid structures in pancreatic cancer tomorrow at 8.15am at SITC
Abstract ➡️ www.immunotherapycancer.ca/2025-michael...
Reposted by Kieran Campbell
"The advent of large language models have made this type of content relatively easy to churn out on demand, and the majority of the review articles we receive are little more than annotated bibliographies, with no substantial discussion of open research issues."
November 2, 2025 at 5:00 AM
"The advent of large language models have made this type of content relatively easy to churn out on demand, and the majority of the review articles we receive are little more than annotated bibliographies, with no substantial discussion of open research issues."
Fix Canada’s Primary R&D Program - excellent article on issues with federal support for R&D in Canada
www.buildcanada.com/en/memos/fix...
www.buildcanada.com/en/memos/fix...
Fix Canada’s Primary R&D Program
SR&ED credits are the largest federal support for R&D. But the process is complex, often rewards the wrong companies, and doesn’t support business value.
www.buildcanada.com
October 28, 2025 at 7:24 PM
Fix Canada’s Primary R&D Program - excellent article on issues with federal support for R&D in Canada
www.buildcanada.com/en/memos/fix...
www.buildcanada.com/en/memos/fix...
Reposted by Kieran Campbell
Cooperative and antagonistic interactions between sub-clones favour the co-existence of multiple resistance mechanisms in melanoma https://www.biorxiv.org/content/10.1101/2025.10.23.684170v1
October 24, 2025 at 10:48 PM
Cooperative and antagonistic interactions between sub-clones favour the co-existence of multiple resistance mechanisms in melanoma https://www.biorxiv.org/content/10.1101/2025.10.23.684170v1
How can we scale subcellular spatial proteomics across many experiments and conditions?
Our new paper presents a genetic algorithm and evaluation framework that optimizes bait subsets for proximity proteomics platforms like BioID enabling context-specific proteome mapping.
Our new paper presents a genetic algorithm and evaluation framework that optimizes bait subsets for proximity proteomics platforms like BioID enabling context-specific proteome mapping.
October 23, 2025 at 1:40 PM
How can we scale subcellular spatial proteomics across many experiments and conditions?
Our new paper presents a genetic algorithm and evaluation framework that optimizes bait subsets for proximity proteomics platforms like BioID enabling context-specific proteome mapping.
Our new paper presents a genetic algorithm and evaluation framework that optimizes bait subsets for proximity proteomics platforms like BioID enabling context-specific proteome mapping.
Reposted by Kieran Campbell
Guaranteed funding for five years and a 20% increase in a $39K base stipend if you haul in a fellowship. World class facilities and faculty in metabolism, structural biology, epigenetics, and beyond. Grand Rapids is half the cost of living of California or Boston. Apply by December 1st if interested
October 22, 2025 at 3:55 PM
Guaranteed funding for five years and a 20% increase in a $39K base stipend if you haul in a fellowship. World class facilities and faculty in metabolism, structural biology, epigenetics, and beyond. Grand Rapids is half the cost of living of California or Boston. Apply by December 1st if interested
Reposted by Kieran Campbell
Applications are now open for entry in academic year 2026/27 for the Centre for Doctoral Training in Fundamentals of AI @ox.ac.uk with @eitoxford.bsky.social: www.ox.ac.uk/admissions/g...
Fundamentals of AI (EIT CDT) | University of Oxford
About the courseFundamentals of AI (EIT CDT) is a research-based DPhil course focused on foundational AI, machine learning, and computational statistics. Students will help shape the future of AI and
www.ox.ac.uk
October 19, 2025 at 9:17 PM
Applications are now open for entry in academic year 2026/27 for the Centre for Doctoral Training in Fundamentals of AI @ox.ac.uk with @eitoxford.bsky.social: www.ox.ac.uk/admissions/g...
Reposted by Kieran Campbell
The journal version of our Multi-omic Pathway Analysis of Cells (MPAC) software is now out: doi.org/10.1093/bioi...
MPAC uses biological pathway graphs to model DNA copy number and gene expression changes and infer activity states of all pathway members.
MPAC uses biological pathway graphs to model DNA copy number and gene expression changes and infer activity states of all pathway members.
October 10, 2025 at 2:56 PM
The journal version of our Multi-omic Pathway Analysis of Cells (MPAC) software is now out: doi.org/10.1093/bioi...
MPAC uses biological pathway graphs to model DNA copy number and gene expression changes and infer activity states of all pathway members.
MPAC uses biological pathway graphs to model DNA copy number and gene expression changes and infer activity states of all pathway members.
Reposted by Kieran Campbell
⏰Reminder: There's still time to apply!
LTRI is hiring two outstanding Principal Investigators in Population Health Data Science.
Find out more and apply by October 20th, 2025 ➡️ apply.interfolio.com/172529
LTRI is hiring two outstanding Principal Investigators in Population Health Data Science.
Find out more and apply by October 20th, 2025 ➡️ apply.interfolio.com/172529
September 23, 2025 at 8:01 PM
⏰Reminder: There's still time to apply!
LTRI is hiring two outstanding Principal Investigators in Population Health Data Science.
Find out more and apply by October 20th, 2025 ➡️ apply.interfolio.com/172529
LTRI is hiring two outstanding Principal Investigators in Population Health Data Science.
Find out more and apply by October 20th, 2025 ➡️ apply.interfolio.com/172529
Reposted by Kieran Campbell
Studying cancer evolution needs multi-region or single cell seq for phylogenetics, right? Amazingly (I think!) we found single-sample bulk methylation suffices, via analysis of "fluctuating methylation". In @nature.com today led by brilliant @calumgabbutt.bsky.social www.nature.com/articles/s41...
Fluctuating DNA methylation tracks cancer evolution at clinical scale - Nature
Cancer evolutionary dynamics are quantitatively inferred using a method, EVOFLUx, applied to fluctuating DNA methylation.
www.nature.com
September 10, 2025 at 3:21 PM
Studying cancer evolution needs multi-region or single cell seq for phylogenetics, right? Amazingly (I think!) we found single-sample bulk methylation suffices, via analysis of "fluctuating methylation". In @nature.com today led by brilliant @calumgabbutt.bsky.social www.nature.com/articles/s41...
Reposted by Kieran Campbell
Full professor complaining to an assistant professor on how hard it is to get funding nowadays
September 10, 2025 at 2:11 PM
Full professor complaining to an assistant professor on how hard it is to get funding nowadays
Fantastic hosting @alexr.bsky.social in Toronto today discussing the hype of AI in cancer biology and a realistic route to leverage it for personalized immunotherapy
September 3, 2025 at 7:43 PM
Fantastic hosting @alexr.bsky.social in Toronto today discussing the hype of AI in cancer biology and a realistic route to leverage it for personalized immunotherapy
Reposted by Kieran Campbell
Cancer cells are notoriously plastic, but what triggers the changes in cell state? In our new Nature (@nature.com) paper, Miranda Hunter (@mrndhntr.bsky.social) found that mechanical pressure is a key to this switch. Check it out here: go.nature.com/47iwDm2
August 28, 2025 at 3:15 PM
Cancer cells are notoriously plastic, but what triggers the changes in cell state? In our new Nature (@nature.com) paper, Miranda Hunter (@mrndhntr.bsky.social) found that mechanical pressure is a key to this switch. Check it out here: go.nature.com/47iwDm2
Reposted by Kieran Campbell
JOB ALERT 🚨 We are hiring TWO principal investigators in cell, molecular, systems, or chemical biology in Toronto, Canada at @sinaihealth.bsky.social. We provide a generous startup, fully funded salary and academic appointment at U of Toronto.
www.nature.com/naturecareer...
Please repost!
www.nature.com/naturecareer...
Please repost!
August 28, 2025 at 6:34 AM
JOB ALERT 🚨 We are hiring TWO principal investigators in cell, molecular, systems, or chemical biology in Toronto, Canada at @sinaihealth.bsky.social. We provide a generous startup, fully funded salary and academic appointment at U of Toronto.
www.nature.com/naturecareer...
Please repost!
www.nature.com/naturecareer...
Please repost!
Reposted by Kieran Campbell
August 18, 2025 at 2:09 PM
Reposted by Kieran Campbell
Online now! Tumor dynamics & spatial proteomics-informed personalized predictions of growth & response
Beyond RECIST: mathematical modeling and Bayesian inference reveal the importance of immune parameters in metastatic breast cancer
www.biorxiv.org/content/10.1...
Beyond RECIST: mathematical modeling and Bayesian inference reveal the importance of immune parameters in metastatic breast cancer
www.biorxiv.org/content/10.1...
August 12, 2025 at 11:34 PM
Online now! Tumor dynamics & spatial proteomics-informed personalized predictions of growth & response
Beyond RECIST: mathematical modeling and Bayesian inference reveal the importance of immune parameters in metastatic breast cancer
www.biorxiv.org/content/10.1...
Beyond RECIST: mathematical modeling and Bayesian inference reveal the importance of immune parameters in metastatic breast cancer
www.biorxiv.org/content/10.1...
Reposted by Kieran Campbell
Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
August 4, 2025 at 1:52 PM
Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
Reposted by Kieran Campbell
The grand vision of the AI university. Professors design curricula, lecture notes and exam questions using genAI. Students read the notes and submit essays and exam answers using LLMs. Massive efficiency and speed gains ensue. Students can go play pool, professors write grants in the saved time.
July 29, 2025 at 11:17 AM
The grand vision of the AI university. Professors design curricula, lecture notes and exam questions using genAI. Students read the notes and submit essays and exam answers using LLMs. Massive efficiency and speed gains ensue. Students can go play pool, professors write grants in the saved time.
Reposted by Kieran Campbell
Check out how we tackled one of the fundamental challenges in immunology, out today @cp-cellsystems.bsky.social: www.cell.com/cell-systems.... Our major innovations are BATCAVE and BATMAN, two new players to get us closer to solving TCR-pMHC predictions!
T cell receptor cross-reactivity prediction improved by a comprehensive mutational scan database
Banerjee et al. present a comprehensive T cell receptor cross-reactivity database
and a hierarchical Bayesian framework to predict T cell receptor targets. Together,
they reveal structural and biochem...
www.cell.com
July 25, 2025 at 3:00 PM
Check out how we tackled one of the fundamental challenges in immunology, out today @cp-cellsystems.bsky.social: www.cell.com/cell-systems.... Our major innovations are BATCAVE and BATMAN, two new players to get us closer to solving TCR-pMHC predictions!
Reposted by Kieran Campbell
The DNA of pure DCIS. We look at prognosis (invasive & in situ local recurrence) & benefit to radiotherapy in a unique cohort of Ontarians. A manuscript with my long term collaborators Eileen Rakovitch (Sunnybrook) & @vdumeaux.bsky.social breast-cancer-research.biomedcentral.com/articles/10....
Mutational landscape of pure ductal carcinoma in situ and associations with disease prognosis and response to radiotherapy - Breast Cancer Research
Background Managing Ductal Carcinoma in Situ (DCIS) remains challenging due to the lack of reliable biomarkers to predict radiotherapy (RT) response, leading to both overtreatment of indolent disease ...
breast-cancer-research.biomedcentral.com
July 8, 2025 at 2:28 PM
The DNA of pure DCIS. We look at prognosis (invasive & in situ local recurrence) & benefit to radiotherapy in a unique cohort of Ontarians. A manuscript with my long term collaborators Eileen Rakovitch (Sunnybrook) & @vdumeaux.bsky.social breast-cancer-research.biomedcentral.com/articles/10....
Reposted by Kieran Campbell
I am thrilled to share with the world a new preprint, spearheaded by the truly amazing Jose Reyes in partnership with the Lowe lab. The paper sheds light on benign to malignant transition in PDAC, uncovering roles of plasticity, tissue remodeling and P53. -> www.biorxiv.org/content/10.1...
Oncogenic and tumor-suppressive forces converge on a progenitor-orchestrated niche to shape early tumorigenesis
The transition from benign to malignant growth is a pivotal yet poorly understood step in cancer progression that marks the shift from a pathologically inert condition to a clinically lethal disease. ...
www.biorxiv.org
July 3, 2025 at 1:12 PM
I am thrilled to share with the world a new preprint, spearheaded by the truly amazing Jose Reyes in partnership with the Lowe lab. The paper sheds light on benign to malignant transition in PDAC, uncovering roles of plasticity, tissue remodeling and P53. -> www.biorxiv.org/content/10.1...
Reposted by Kieran Campbell
@saramostafavi.bsky.social (@Genentech) & I (@Stanford) r excited to announce co-advised postdoc positions for candidates with deep expertise in ML for bio (especially sequence to function models, causal perturbational models & single cell models). See details below. Pls RT 1/
June 19, 2025 at 8:55 PM
@saramostafavi.bsky.social (@Genentech) & I (@Stanford) r excited to announce co-advised postdoc positions for candidates with deep expertise in ML for bio (especially sequence to function models, causal perturbational models & single cell models). See details below. Pls RT 1/
Six days left to apply!
🧬 We're hiring - join our lab in Toronto, Canada! 🇨🇦
Exciting postdoc joint with @hartjackson.bsky.social developing machine learning methods for the next generation of spatial histopathology technologies joint with industry partners in the Bay Area.
👉 apply.interfolio.com/168307
Exciting postdoc joint with @hartjackson.bsky.social developing machine learning methods for the next generation of spatial histopathology technologies joint with industry partners in the Bay Area.
👉 apply.interfolio.com/168307
Apply - Interfolio
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apply.interfolio.com
June 16, 2025 at 5:23 PM
Six days left to apply!
Reposted by Kieran Campbell
Please check out our new approach to modeling somatic mutation signatures.
DAMUTA has independent Damage and Misrepair signatures whose activities are more interpretable and more predictive of DNA repair defects, than COSMIC SBS signatures 🧬🖥️🧪
www.biorxiv.org/content/10.1...
DAMUTA has independent Damage and Misrepair signatures whose activities are more interpretable and more predictive of DNA repair defects, than COSMIC SBS signatures 🧬🖥️🧪
www.biorxiv.org/content/10.1...
Damage and Misrepair Signatures: Compact Representations of Pan-cancer Mutational Processes
Mutational signatures of single-base substitutions (SBSs) characterize somatic mutation processes which contribute to cancer development and progression. However, current mutational signatures do not ...
www.biorxiv.org
June 3, 2025 at 12:34 AM
Please check out our new approach to modeling somatic mutation signatures.
DAMUTA has independent Damage and Misrepair signatures whose activities are more interpretable and more predictive of DNA repair defects, than COSMIC SBS signatures 🧬🖥️🧪
www.biorxiv.org/content/10.1...
DAMUTA has independent Damage and Misrepair signatures whose activities are more interpretable and more predictive of DNA repair defects, than COSMIC SBS signatures 🧬🖥️🧪
www.biorxiv.org/content/10.1...
Reposted by Kieran Campbell
Spatial Biology and Organoid Technologies Reveal a Potential Therapy-Resistant Cancer Stem Cell Population in Pancreatic Ductal Adenocarcinoma 🧪 www.biorxiv.org/content/10.1...
Spatial Biology and Organoid Technologies Reveal a Potential Therapy-Resistant Cancer Stem Cell Population in Pancreatic Ductal Adenocarcinoma
Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest malignancies with a 5-year survival rate of less than 10%. Chemotherapy is the current standard-of-care (SOC) for advanced PDAC; ho...
www.biorxiv.org
May 27, 2025 at 4:50 PM
Spatial Biology and Organoid Technologies Reveal a Potential Therapy-Resistant Cancer Stem Cell Population in Pancreatic Ductal Adenocarcinoma 🧪 www.biorxiv.org/content/10.1...