Vitalii Kleshchevnikov, PhD
@vitaliikl.bsky.social
Researcher @bayraktar_lab @teichlab @steglelab.bsky.social @sangerinstitute.bsky.social | Using models & AI to study cells, cell circuits & brains 🧠 | #SingleCell+spatial | 🌍+🇺🇦
Strongly recommend taking a look!
Are you using any of our factor models, such as MOFA? 🛵
You might’ve found it challenging to tailor them to your specific use cases - not anymore!
Introducing MOFA-FLEX: a flexible, modular factor analysis framework designed for customizable modeling across diverse multi-omics data scenarios. 1/n
You might’ve found it challenging to tailor them to your specific use cases - not anymore!
Introducing MOFA-FLEX: a flexible, modular factor analysis framework designed for customizable modeling across diverse multi-omics data scenarios. 1/n
November 8, 2025 at 8:57 PM
Strongly recommend taking a look!
How many hours per week do you talk to ChatGPT?
I generally do 2-5h in total and several times per day - across coding, science, career, life, health. It’s becoming quite integral. Hard to believe I would say this given what I thought before.
I generally do 2-5h in total and several times per day - across coding, science, career, life, health. It’s becoming quite integral. Hard to believe I would say this given what I thought before.
November 5, 2025 at 10:34 PM
How many hours per week do you talk to ChatGPT?
I generally do 2-5h in total and several times per day - across coding, science, career, life, health. It’s becoming quite integral. Hard to believe I would say this given what I thought before.
I generally do 2-5h in total and several times per day - across coding, science, career, life, health. It’s becoming quite integral. Hard to believe I would say this given what I thought before.
November 5, 2025 at 2:01 AM
Reposted by Vitalii Kleshchevnikov, PhD
Our latest "Dynamic Landscape Analysis of Cell Fate Decisions: Predictive Models of Neural Development From Single-Cell Data"
A rigorous mathematical foundation for Waddington's landscape to study cell fate decision making
Applied to ventral neural tube development
www.biorxiv.org/content/10.1...
A rigorous mathematical foundation for Waddington's landscape to study cell fate decision making
Applied to ventral neural tube development
www.biorxiv.org/content/10.1...
Dynamic Landscape Analysis of Cell Fate Decisions: Predictive Models of Neural Development From Single-Cell Data
Building a mechanistic understanding of cell fate decisions remains a fundamental goal of developmental biology, with implications for stem cell therapies, regenerative medicine and understanding dise...
www.biorxiv.org
May 29, 2025 at 12:08 PM
Our latest "Dynamic Landscape Analysis of Cell Fate Decisions: Predictive Models of Neural Development From Single-Cell Data"
A rigorous mathematical foundation for Waddington's landscape to study cell fate decision making
Applied to ventral neural tube development
www.biorxiv.org/content/10.1...
A rigorous mathematical foundation for Waddington's landscape to study cell fate decision making
Applied to ventral neural tube development
www.biorxiv.org/content/10.1...
Reposted by Vitalii Kleshchevnikov, PhD
Good to see this study from Ribes & co in print: PAX3/PAX7 transcription factors control neural tube patterning by simultaneously repressing ventral fates via H3K27me3 deposition at silencers & activating dorsal fates as pioneer factors at enhancers
@ribes
journals.plos.org/plosbiology/...
@ribes
journals.plos.org/plosbiology/...
Dual transcriptional activities of PAX3 and PAX7 spatially encode spinal cell fates through distinct gene networks
How do transcription factors, with pleotropic functions, generate organized cellular diversity in developing tissues? This study shows that PAX3 and PAX7 orchestrate spinal cord patterning by acting a...
journals.plos.org
October 29, 2025 at 3:21 PM
Good to see this study from Ribes & co in print: PAX3/PAX7 transcription factors control neural tube patterning by simultaneously repressing ventral fates via H3K27me3 deposition at silencers & activating dorsal fates as pioneer factors at enhancers
@ribes
journals.plos.org/plosbiology/...
@ribes
journals.plos.org/plosbiology/...
Very exciting work. Reshaping understanding.
Thrilled to share my main postdoc work with @jamesbriscoe.bsky.social
We used genomic barcoding + scRNAseq in chick & human embryos to reveal a lineage architecture that reshapes how we understand neural tube development & cell fate decisions
🧵👇
www.biorxiv.org/content/10.1...
We used genomic barcoding + scRNAseq in chick & human embryos to reveal a lineage architecture that reshapes how we understand neural tube development & cell fate decisions
🧵👇
www.biorxiv.org/content/10.1...
Hierarchical lineage architecture of human and avian spinal cord revealed by single-cell genomic barcoding
The formation of neural circuits depends on the precise spatial and temporal organisation of neuronal populations during development. In the vertebrate spinal cord, progenitors are patterned into mole...
www.biorxiv.org
November 2, 2025 at 5:27 PM
Very exciting work. Reshaping understanding.
I am wondering what people think about building an AI system to coordinate research. It would be an agent similar to ChatGPT 5. You can talk to it about your research with persistent memory across chats. All chats are used for training without opt-out option.
1/n
1/n
November 2, 2025 at 5:06 PM
I am wondering what people think about building an AI system to coordinate research. It would be an agent similar to ChatGPT 5. You can talk to it about your research with persistent memory across chats. All chats are used for training without opt-out option.
1/n
1/n
Hot take. Excessive benchmarking demands on computational method papers slow down progress. Benchmarks in the paper need to show that your solution works well enough for your goals - not that it is the best solution ever proposed or how exactly it differs from all other existing solutions.
October 24, 2025 at 1:53 AM
Hot take. Excessive benchmarking demands on computational method papers slow down progress. Benchmarks in the paper need to show that your solution works well enough for your goals - not that it is the best solution ever proposed or how exactly it differs from all other existing solutions.
Reposted by Vitalii Kleshchevnikov, PhD
@biorxivpreprint.bsky.social Scalable transcription factor mapping uncovers the regulatory dynamics of natural and synthetic transcription factors in human T cell states
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 12, 2025 at 2:33 AM
@biorxivpreprint.bsky.social Scalable transcription factor mapping uncovers the regulatory dynamics of natural and synthetic transcription factors in human T cell states
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Vitalii Kleshchevnikov, PhD
🚨 new glioblastoma preprint alert!
we present the first spatially resolved single cell atlas comparing radionecrotic changes (RN) and recurrent IDH-wildtype glioblastoma (GB) –– shedding light on a long-standing diagnostic challenge.
🧵 1/
we present the first spatially resolved single cell atlas comparing radionecrotic changes (RN) and recurrent IDH-wildtype glioblastoma (GB) –– shedding light on a long-standing diagnostic challenge.
🧵 1/
October 6, 2025 at 12:41 PM
🚨 new glioblastoma preprint alert!
we present the first spatially resolved single cell atlas comparing radionecrotic changes (RN) and recurrent IDH-wildtype glioblastoma (GB) –– shedding light on a long-standing diagnostic challenge.
🧵 1/
we present the first spatially resolved single cell atlas comparing radionecrotic changes (RN) and recurrent IDH-wildtype glioblastoma (GB) –– shedding light on a long-standing diagnostic challenge.
🧵 1/
How many papers are truly irreproducible and how many show a possible causal path which often isn’t the limiting factor and is conditional on important context (eg mutations, genetics, environment of the experiment)?
Thinking about omnigenic model, “mechanistic bias” in medicine, personalised PRS.
Thinking about omnigenic model, “mechanistic bias” in medicine, personalised PRS.
September 23, 2025 at 6:12 PM
How many papers are truly irreproducible and how many show a possible causal path which often isn’t the limiting factor and is conditional on important context (eg mutations, genetics, environment of the experiment)?
Thinking about omnigenic model, “mechanistic bias” in medicine, personalised PRS.
Thinking about omnigenic model, “mechanistic bias” in medicine, personalised PRS.
Reposted by Vitalii Kleshchevnikov, PhD
Hepatic acetyl-CoA metabolism modulates neuroinflammation and depression susceptibility via acetate @cp-cellmetabolism.bsky.social
www.cell.com/cell-metabol...
www.cell.com/cell-metabol...
September 23, 2025 at 6:02 PM
Hepatic acetyl-CoA metabolism modulates neuroinflammation and depression susceptibility via acetate @cp-cellmetabolism.bsky.social
www.cell.com/cell-metabol...
www.cell.com/cell-metabol...
Very impressive work and interesting modelling ideas 💡:
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
September 23, 2025 at 9:45 AM
Very impressive work and interesting modelling ideas 💡:
Reposted by Vitalii Kleshchevnikov, PhD
By training GPN-Star on vertebrate, mammal, and primate alignments, we reveal task-dependent advantages of modeling deeper versus more recent evolution. These findings offer new biological insights and practical guidance for developing future gLMs and evolutionary models.
(6/n)
(6/n)
September 22, 2025 at 5:29 AM
By training GPN-Star on vertebrate, mammal, and primate alignments, we reveal task-dependent advantages of modeling deeper versus more recent evolution. These findings offer new biological insights and practical guidance for developing future gLMs and evolutionary models.
(6/n)
(6/n)
Reposted by Vitalii Kleshchevnikov, PhD
This is truly an incredible breakthrough IMO. Really exemplifies what you get when deep domain expertise (popgen/evolution/disease genetics in this case) fuses with cleverly crafted ML. What u get r sleek, well thought out architectures that absolutely destroy the behemoths. Wow!! 1/
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
September 22, 2025 at 8:34 AM
This is truly an incredible breakthrough IMO. Really exemplifies what you get when deep domain expertise (popgen/evolution/disease genetics in this case) fuses with cleverly crafted ML. What u get r sleek, well thought out architectures that absolutely destroy the behemoths. Wow!! 1/
If you feel like you need noise canceling headphones 🎧 - you probably actually need to buy them right now. Don’t delay this decision and loose time trying to operate without them.
Noise cancelling headphones are like your work email+slack - you may be able to work without them but it’s pretty hard.
Noise cancelling headphones are like your work email+slack - you may be able to work without them but it’s pretty hard.
September 16, 2025 at 3:48 AM
If you feel like you need noise canceling headphones 🎧 - you probably actually need to buy them right now. Don’t delay this decision and loose time trying to operate without them.
Noise cancelling headphones are like your work email+slack - you may be able to work without them but it’s pretty hard.
Noise cancelling headphones are like your work email+slack - you may be able to work without them but it’s pretty hard.
Has anyone ever seen a house/flat in the UK/Cambridge that had an HRV or ERV system?
If you can’t have windows open at night due to security concerns how are you supposed to ventilate?
I tried closing windows and even with the fan on max CO2 levels never got below 850ppm (bad for sleep quality).
If you can’t have windows open at night due to security concerns how are you supposed to ventilate?
I tried closing windows and even with the fan on max CO2 levels never got below 850ppm (bad for sleep quality).
August 28, 2025 at 7:57 PM
Has anyone ever seen a house/flat in the UK/Cambridge that had an HRV or ERV system?
If you can’t have windows open at night due to security concerns how are you supposed to ventilate?
I tried closing windows and even with the fan on max CO2 levels never got below 850ppm (bad for sleep quality).
If you can’t have windows open at night due to security concerns how are you supposed to ventilate?
I tried closing windows and even with the fan on max CO2 levels never got below 850ppm (bad for sleep quality).
Reposted by Vitalii Kleshchevnikov, PhD
With unprecedented 38× coverage, our atlas resolves single neuron clusters and shows that separate waves of neurogenesis use different modes of molecular identity encoding: discrete in early born and continuous in late born. 3/8
August 21, 2025 at 4:06 PM
With unprecedented 38× coverage, our atlas resolves single neuron clusters and shows that separate waves of neurogenesis use different modes of molecular identity encoding: discrete in early born and continuous in late born. 3/8
Reposted by Vitalii Kleshchevnikov, PhD
Neuronal diversity is written in transcriptional codes 🧬. But what is the logic of these codes that define cell types and wiring patterns?
To find out we built a #scRNAseq developmental atlas of the Drosophila nerve cord and linked it to the #connectome 🪰🧠
#preprint thread ⬇️1/8
To find out we built a #scRNAseq developmental atlas of the Drosophila nerve cord and linked it to the #connectome 🪰🧠
#preprint thread ⬇️1/8
August 21, 2025 at 4:04 PM
Neuronal diversity is written in transcriptional codes 🧬. But what is the logic of these codes that define cell types and wiring patterns?
To find out we built a #scRNAseq developmental atlas of the Drosophila nerve cord and linked it to the #connectome 🪰🧠
#preprint thread ⬇️1/8
To find out we built a #scRNAseq developmental atlas of the Drosophila nerve cord and linked it to the #connectome 🪰🧠
#preprint thread ⬇️1/8
Reposted by Vitalii Kleshchevnikov, PhD
And he made it again!...tour the force from JIa-Wei´s Wang lab using comparative sc-transcriptomes, and developing new analytical tools, to tackle evolutionary trajectories of plant cell types!. Amazing work as usual! www.cell.com/cell/abstrac...
A unified cell atlas of vascular plants reveals cell-type foundational genes and accelerates gene discovery
A cross-species single-cell atlas highlights a core subset of cell-type foundational
genes associated with major vascular plant cell types, enabling the identification
of hidden cell types and the dev...
www.cell.com
August 20, 2025 at 3:50 PM
And he made it again!...tour the force from JIa-Wei´s Wang lab using comparative sc-transcriptomes, and developing new analytical tools, to tackle evolutionary trajectories of plant cell types!. Amazing work as usual! www.cell.com/cell/abstrac...
Ended up coming back to these points to articulate state of the GRN field in the paper/fellowship introduction. Introductions need to be specific about the task specification and model-task mismatch in existing work. Task specification need to match biology terms at the right level of abstraction.
It’s quite hard to systematise where models can go wrong but here is an attempt:
1. Wrong math
2. Wrong mapping of math to code (or vice versa)
3. Correct math and code but wrong interpretation given in text: code solves one task but paper presents it as another task
4. Poorly understood tasks
5. …
1. Wrong math
2. Wrong mapping of math to code (or vice versa)
3. Correct math and code but wrong interpretation given in text: code solves one task but paper presents it as another task
4. Poorly understood tasks
5. …
This phrase was coined in 1976 when the models were a lot simpler than the models published now.
Linear mixed models and PCA can be described this way because as general methods they are wrong in less complex ways.
Specialised models can be wrong in quite misleading ways as well as useless.
Linear mixed models and PCA can be described this way because as general methods they are wrong in less complex ways.
Specialised models can be wrong in quite misleading ways as well as useless.
August 20, 2025 at 10:03 PM
Ended up coming back to these points to articulate state of the GRN field in the paper/fellowship introduction. Introductions need to be specific about the task specification and model-task mismatch in existing work. Task specification need to match biology terms at the right level of abstraction.
Reposted by Vitalii Kleshchevnikov, PhD
👀 we are involved in projects 1 & 6 on the list:
1️⃣ Multicellular molecular characterisation of inflammatory bowel disease
6️⃣ Designing Efficient Single-Cell Perturbation Experiments with Lab-in-the-Loop AI Agents
📅 Application deadline is 30th September ❗
1️⃣ Multicellular molecular characterisation of inflammatory bowel disease
6️⃣ Designing Efficient Single-Cell Perturbation Experiments with Lab-in-the-Loop AI Agents
📅 Application deadline is 30th September ❗
Recruitment is now open for the EMBL-EBI–Sanger Postdoctoral Programme.
ESPOD builds on the collaborative relationship between EMBL-EBI and the @sangerinstitute.bsky.social, offering projects that combine experimental and computational approaches.
www.ebi.ac.uk/research/pos...
🧬🖥️🔬#postdocjob
ESPOD builds on the collaborative relationship between EMBL-EBI and the @sangerinstitute.bsky.social, offering projects that combine experimental and computational approaches.
www.ebi.ac.uk/research/pos...
🧬🖥️🔬#postdocjob
August 14, 2025 at 9:05 AM
👀 we are involved in projects 1 & 6 on the list:
1️⃣ Multicellular molecular characterisation of inflammatory bowel disease
6️⃣ Designing Efficient Single-Cell Perturbation Experiments with Lab-in-the-Loop AI Agents
📅 Application deadline is 30th September ❗
1️⃣ Multicellular molecular characterisation of inflammatory bowel disease
6️⃣ Designing Efficient Single-Cell Perturbation Experiments with Lab-in-the-Loop AI Agents
📅 Application deadline is 30th September ❗
Reposted by Vitalii Kleshchevnikov, PhD
Welcome @timcoorens.bsky.social 🇳🇱, our new Research Group Leader.
Find out how Tim’s group is exploring using large-scale single-cell and spatial data to trace cell lineages, understand cancer origins, and uncover how mutations drive disease.
www.ebi.ac.uk/about/news/p...
🖥️🧬
Find out how Tim’s group is exploring using large-scale single-cell and spatial data to trace cell lineages, understand cancer origins, and uncover how mutations drive disease.
www.ebi.ac.uk/about/news/p...
🖥️🧬
Welcome: Tim Coorens
EMBL-EBI’s newest Research Group Leader is investigating how somatic mutations reveal the hidden histories of human cells.
www.ebi.ac.uk
August 12, 2025 at 9:04 AM
Welcome @timcoorens.bsky.social 🇳🇱, our new Research Group Leader.
Find out how Tim’s group is exploring using large-scale single-cell and spatial data to trace cell lineages, understand cancer origins, and uncover how mutations drive disease.
www.ebi.ac.uk/about/news/p...
🖥️🧬
Find out how Tim’s group is exploring using large-scale single-cell and spatial data to trace cell lineages, understand cancer origins, and uncover how mutations drive disease.
www.ebi.ac.uk/about/news/p...
🖥️🧬
Looks like this platform became almost as unusable as Twitter/X. I rarely open it.
If you want to reach out - you can use slack or email or maybe LinkedIn or for code issues - GitHub Issues.
Please don’t email about the code issues - GitHub Issues is much more useful for managing them.
If you want to reach out - you can use slack or email or maybe LinkedIn or for code issues - GitHub Issues.
Please don’t email about the code issues - GitHub Issues is much more useful for managing them.
August 3, 2025 at 3:00 PM
Looks like this platform became almost as unusable as Twitter/X. I rarely open it.
If you want to reach out - you can use slack or email or maybe LinkedIn or for code issues - GitHub Issues.
Please don’t email about the code issues - GitHub Issues is much more useful for managing them.
If you want to reach out - you can use slack or email or maybe LinkedIn or for code issues - GitHub Issues.
Please don’t email about the code issues - GitHub Issues is much more useful for managing them.