Alejandro Brenes
@ajbrenes.com
PostDoc @walmsley-lab.bsky.social @edinuni-irr.bsky.social @edinburgh-uni.bsky.social
| neutrophils single cell proteomics | road cyclist and aero bike enthusiast 🇨🇷🏴
Creator of the Immunological Proteome Resource @immpres.bsky.social
| neutrophils single cell proteomics | road cyclist and aero bike enthusiast 🇨🇷🏴
Creator of the Immunological Proteome Resource @immpres.bsky.social
Pinned
Alejandro Brenes
@ajbrenes.com
· Jul 27
Single cell proteomic analysis defines discrete neutrophil functional states in human glioblastoma
Neutrophils are vital innate immune cells shown to infiltrate glioblastomas, however we currently lack the molecular understanding of their functional states within the tumour niche. Neutrophils are k...
www.biorxiv.org
Happy to share our latest preprint doing low cell number (mini-bulk) and single cell #proteomics on tumour associated neutrophils from human glioblastoma where we find multiple functional states that would be invisible to scRNAseq, some showing pro-tumoural states with potential therapeutic value
Reposted by Alejandro Brenes
New preprint! More landing soon!
New preprint: Viral protease-mediated polyprotein processing in human astroviruses
Great collaboration with Lulla lab. And the first of @leandroxneves.bsky.social proteolysis stories. More coming soon!
www.biorxiv.org/content/10.1...
Great collaboration with Lulla lab. And the first of @leandroxneves.bsky.social proteolysis stories. More coming soon!
www.biorxiv.org/content/10.1...
Viral protease-mediated polyprotein processing in human astroviruses
Positive-sense RNA viruses often encode large polyproteins that are proteolytically processed by viral and host proteases into functional replication proteins. Astroviruses infect intestinal and neuro...
www.biorxiv.org
November 25, 2025 at 7:34 AM
New preprint! More landing soon!
Reposted by Alejandro Brenes
I tried the updated Gemini image generator on scientific related image prompts that have failed in the past and I am really impressed by the quality of the outputs. The first is drawing a diagram for a pocket prediction algorithm using Voronoi diagram, Delaunay triangulation and alpha shapes
November 21, 2025 at 1:14 PM
I tried the updated Gemini image generator on scientific related image prompts that have failed in the past and I am really impressed by the quality of the outputs. The first is drawing a diagram for a pocket prediction algorithm using Voronoi diagram, Delaunay triangulation and alpha shapes
Reposted by Alejandro Brenes
A very nice highlight of our recent paper!
Researchers have identified gene-regulatory variants that might have contributed to Neanderthals’ beefy jaws — offering a window on how the human face developed
go.nature.com/3Ke6StJ
go.nature.com/3Ke6StJ
Neanderthal DNA reveals how human faces form
Subtle genomic variations between humans and Neanderthals provide clues to how DNA shapes our facial features.
go.nature.com
November 22, 2025 at 8:06 AM
A very nice highlight of our recent paper!
Reposted by Alejandro Brenes
Solving the computational challenge of phosphoproteomics with 𝐏𝐡𝐨-𝐓𝐢𝐩: dephosphorylation on-tip identifies the sequences of phosphorylated peptides.
This serves as a basis for predicted spectral libraries, reducing the search space 10x-20x. www.biorxiv.org/content/10.1...
This serves as a basis for predicted spectral libraries, reducing the search space 10x-20x. www.biorxiv.org/content/10.1...
November 19, 2025 at 10:07 AM
Solving the computational challenge of phosphoproteomics with 𝐏𝐡𝐨-𝐓𝐢𝐩: dephosphorylation on-tip identifies the sequences of phosphorylated peptides.
This serves as a basis for predicted spectral libraries, reducing the search space 10x-20x. www.biorxiv.org/content/10.1...
This serves as a basis for predicted spectral libraries, reducing the search space 10x-20x. www.biorxiv.org/content/10.1...
Great lab and great opportunity, take a look and get in touch with luke if you want more details
Quick heads up - there will soon be a job posting for a Staff Scientist / Senior Staff Scientist in our lab in Copenhagen to support all our mass spec proteomics adventures!
Great colleagues, lots of cool projects… and you’ll get to work with me 😅
Please DM if you’re interested!
Great colleagues, lots of cool projects… and you’ll get to work with me 😅
Please DM if you’re interested!
November 21, 2025 at 1:08 AM
Great lab and great opportunity, take a look and get in touch with luke if you want more details
Reposted by Alejandro Brenes
Affinity has been my favorite design software for awhile now. Now that its free is even better!
I'm a longtime fan of Affinity Designer as an affordable Illustrator-killer for figures, and... it's now free?! www.canva.com/newsroom/new...
Highly recommended if you're sick of paying Adobe $. Maybe Canva can buy NPG too and get rid of the OA fees.
Highly recommended if you're sick of paying Adobe $. Maybe Canva can buy NPG too and get rid of the OA fees.
Why we made Affinity free, and how we’ll keep it that way
We’ve made Affinity completely free, empowering professional designers with studio-grade creative software, supported by Canva’s sustainable ecosystem.
www.canva.com
November 19, 2025 at 2:49 AM
Affinity has been my favorite design software for awhile now. Now that its free is even better!
excellent webinar that will be 100% worth it. there's still to register so dont miss out
One week to go for our November webinar on Proteomic approaches to investigate proteolytic ECM remodeling with Dr Salvo Santamaria ft. short talks by PhD students Tina and Alex
Register here: forms.gle/7fXirr7kskVy...
Register here: forms.gle/7fXirr7kskVy...
Our November #TheMeshwork seminar dives into proteomics & proteolytic ECM remodeling in cardiovascular pathologies 🫀Featuring Dr. Salvatore Santamaria and PhD students Tina Burkhard & Alex Minns @uniofsurrey.bsky.social
📅 Nov 25 | ⏰ 1 PM UK 🔗 Register: forms.gle/EY6aiWgsS3Rb...
📅 Nov 25 | ⏰ 1 PM UK 🔗 Register: forms.gle/EY6aiWgsS3Rb...
November 17, 2025 at 1:37 PM
excellent webinar that will be 100% worth it. there's still to register so dont miss out
Reposted by Alejandro Brenes
Reposted by Alejandro Brenes
www.gla.ac.uk/colleges/mvl...
Fantastic PhD opportunity with us! 'Can gut stem cells remember?' Apply below. Grateful for a share!
#PhD #stemcells #epigenetics
Fantastic PhD opportunity with us! 'Can gut stem cells remember?' Apply below. Grateful for a share!
#PhD #stemcells #epigenetics
November 14, 2025 at 5:44 PM
www.gla.ac.uk/colleges/mvl...
Fantastic PhD opportunity with us! 'Can gut stem cells remember?' Apply below. Grateful for a share!
#PhD #stemcells #epigenetics
Fantastic PhD opportunity with us! 'Can gut stem cells remember?' Apply below. Grateful for a share!
#PhD #stemcells #epigenetics
Reposted by Alejandro Brenes
Congratulations to Bill Noble on receiving the 2026 Gil Omenn Computational Proteomics Award from US HUPO!
us-hupo.org/Computationa...
us-hupo.org/Computationa...
US HUPO - Computational Proteomics Award
us-hupo.org
November 12, 2025 at 5:14 PM
Congratulations to Bill Noble on receiving the 2026 Gil Omenn Computational Proteomics Award from US HUPO!
us-hupo.org/Computationa...
us-hupo.org/Computationa...
Reposted by Alejandro Brenes
Exited to share our latest work! Out now in @natcomms.nature.com
Koina aims to transform how #proteomics uses machine learning. You no longer need to be a tech wizard to use ML and now can easily run #ML models. Integrated with FragPipe, Skyline and EncyclopeDIA!
www.nature.com/articles/s41...
Koina aims to transform how #proteomics uses machine learning. You no longer need to be a tech wizard to use ML and now can easily run #ML models. Integrated with FragPipe, Skyline and EncyclopeDIA!
www.nature.com/articles/s41...
Koina: Democratizing machine learning for proteomics research - Nature Communications
Koina is an open-source, online platform that simplifies access to machine learning models in proteomics, enabling easier integration into analysis tools and helping researchers adopt and reuse ML mod...
www.nature.com
November 11, 2025 at 8:06 PM
Exited to share our latest work! Out now in @natcomms.nature.com
Koina aims to transform how #proteomics uses machine learning. You no longer need to be a tech wizard to use ML and now can easily run #ML models. Integrated with FragPipe, Skyline and EncyclopeDIA!
www.nature.com/articles/s41...
Koina aims to transform how #proteomics uses machine learning. You no longer need to be a tech wizard to use ML and now can easily run #ML models. Integrated with FragPipe, Skyline and EncyclopeDIA!
www.nature.com/articles/s41...
Reposted by Alejandro Brenes
by Aglaia Skolariki & @eileenparkes.bsky.social
Single-cell proteomics sheds light on neutrophil diversity in glioblastoma - Nature Reviews Immunology
A preprint by Sadiku et al. characterizes neutrophil diversity in glioblastoma using a new workflow for single-cell proteomic profiling.
www.nature.com
November 11, 2025 at 4:39 PM
by Aglaia Skolariki & @eileenparkes.bsky.social
Reposted by Alejandro Brenes
Neanderthal DNA enhances our understanding of face development
This Research Highlight showcases the work from Hannah Long @hannahlong.bsky.social, Kirsty Uttley @kirstyuttley.bsky.social, Hannah Jüllig @hannahjuellig.bsky.social and colleagues: journals.biologists.com/dev/article/...
This Research Highlight showcases the work from Hannah Long @hannahlong.bsky.social, Kirsty Uttley @kirstyuttley.bsky.social, Hannah Jüllig @hannahjuellig.bsky.social and colleagues: journals.biologists.com/dev/article/...
November 10, 2025 at 1:04 PM
Neanderthal DNA enhances our understanding of face development
This Research Highlight showcases the work from Hannah Long @hannahlong.bsky.social, Kirsty Uttley @kirstyuttley.bsky.social, Hannah Jüllig @hannahjuellig.bsky.social and colleagues: journals.biologists.com/dev/article/...
This Research Highlight showcases the work from Hannah Long @hannahlong.bsky.social, Kirsty Uttley @kirstyuttley.bsky.social, Hannah Jüllig @hannahjuellig.bsky.social and colleagues: journals.biologists.com/dev/article/...
We (@walmsley-lab.bsky.social) are thrilled to have our pre-print highlighted by the Journal Club from @natrevimmunol.nature.com
We think single cell proteomics has the capacity to revolutionise our understanding of neutrophil functional heterogeneity, shown here in glioblastoma.
We think single cell proteomics has the capacity to revolutionise our understanding of neutrophil functional heterogeneity, shown here in glioblastoma.
Single-cell proteomics sheds light on neutrophil diversity in glioblastoma - Nature Reviews Immunology
A preprint by Sadiku et al. characterizes neutrophil diversity in glioblastoma using a new workflow for single-cell proteomic profiling.
www.nature.com
November 11, 2025 at 2:25 PM
We (@walmsley-lab.bsky.social) are thrilled to have our pre-print highlighted by the Journal Club from @natrevimmunol.nature.com
We think single cell proteomics has the capacity to revolutionise our understanding of neutrophil functional heterogeneity, shown here in glioblastoma.
We think single cell proteomics has the capacity to revolutionise our understanding of neutrophil functional heterogeneity, shown here in glioblastoma.
Reposted by Alejandro Brenes
May Institute on Computation & Statistics for MS and Proteomics is taking great shape. Fantastic new and repeat instructors and lots of new content. We are grateful to our sponsors Fragmatics and Biognosys. Keep an eye on the website computationalproteomics.khoury.northeastern.edu
November 10, 2025 at 4:39 PM
May Institute on Computation & Statistics for MS and Proteomics is taking great shape. Fantastic new and repeat instructors and lots of new content. We are grateful to our sponsors Fragmatics and Biognosys. Keep an eye on the website computationalproteomics.khoury.northeastern.edu
Reposted by Alejandro Brenes
📣 Paper alert!
I am delighted that our paper exploring the impact of Neanderthal-derived variants on the activity of a disease-associated craniofacial enhancer has been published in Development today!
journals.biologists.com/dev/article/...
I am delighted that our paper exploring the impact of Neanderthal-derived variants on the activity of a disease-associated craniofacial enhancer has been published in Development today!
journals.biologists.com/dev/article/...
November 10, 2025 at 11:11 AM
📣 Paper alert!
I am delighted that our paper exploring the impact of Neanderthal-derived variants on the activity of a disease-associated craniofacial enhancer has been published in Development today!
journals.biologists.com/dev/article/...
I am delighted that our paper exploring the impact of Neanderthal-derived variants on the activity of a disease-associated craniofacial enhancer has been published in Development today!
journals.biologists.com/dev/article/...
Reposted by Alejandro Brenes
Proteoforms matter:
Protein functions change due to sequence variants and diverse modifications regulating their activities.
𝐓𝐨 𝐬𝐞𝐞 𝐛𝐢𝐨𝐥𝐨𝐠𝐲 (𝐚𝐧𝐝 𝐝𝐢𝐬𝐞𝐚𝐬𝐞) 𝐜𝐥𝐞𝐚𝐫𝐥𝐲, 𝐰𝐞 𝐧𝐞𝐞𝐝 𝐩𝐫𝐨𝐭𝐞𝐨𝐟𝐨𝐫𝐦-𝐥𝐞𝐯𝐞𝐥 𝐪𝐮𝐚𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐚𝐭 𝐬𝐜𝐚𝐥𝐞.
1/2
Protein functions change due to sequence variants and diverse modifications regulating their activities.
𝐓𝐨 𝐬𝐞𝐞 𝐛𝐢𝐨𝐥𝐨𝐠𝐲 (𝐚𝐧𝐝 𝐝𝐢𝐬𝐞𝐚𝐬𝐞) 𝐜𝐥𝐞𝐚𝐫𝐥𝐲, 𝐰𝐞 𝐧𝐞𝐞𝐝 𝐩𝐫𝐨𝐭𝐞𝐨𝐟𝐨𝐫𝐦-𝐥𝐞𝐯𝐞𝐥 𝐪𝐮𝐚𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐚𝐭 𝐬𝐜𝐚𝐥𝐞.
1/2
A beautiful example illustrating a difference between plasma protein analysis by different technologies.
Peptides from some proteoforms correlate better to epitope-based measurements (Olink) than others.
The measurements differ because they reflect different proteoforms !
Peptides from some proteoforms correlate better to epitope-based measurements (Olink) than others.
The measurements differ because they reflect different proteoforms !
November 8, 2025 at 3:02 PM
Proteoforms matter:
Protein functions change due to sequence variants and diverse modifications regulating their activities.
𝐓𝐨 𝐬𝐞𝐞 𝐛𝐢𝐨𝐥𝐨𝐠𝐲 (𝐚𝐧𝐝 𝐝𝐢𝐬𝐞𝐚𝐬𝐞) 𝐜𝐥𝐞𝐚𝐫𝐥𝐲, 𝐰𝐞 𝐧𝐞𝐞𝐝 𝐩𝐫𝐨𝐭𝐞𝐨𝐟𝐨𝐫𝐦-𝐥𝐞𝐯𝐞𝐥 𝐪𝐮𝐚𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐚𝐭 𝐬𝐜𝐚𝐥𝐞.
1/2
Protein functions change due to sequence variants and diverse modifications regulating their activities.
𝐓𝐨 𝐬𝐞𝐞 𝐛𝐢𝐨𝐥𝐨𝐠𝐲 (𝐚𝐧𝐝 𝐝𝐢𝐬𝐞𝐚𝐬𝐞) 𝐜𝐥𝐞𝐚𝐫𝐥𝐲, 𝐰𝐞 𝐧𝐞𝐞𝐝 𝐩𝐫𝐨𝐭𝐞𝐨𝐟𝐨𝐫𝐦-𝐥𝐞𝐯𝐞𝐥 𝐪𝐮𝐚𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐚𝐭 𝐬𝐜𝐚𝐥𝐞.
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Reposted by Alejandro Brenes
Well done to all our CIR PhD students for their brilliant presentations at last week's Annual Poster Day 🎉! Congratulations to our award winners:
Best Presentation: Marcin Maniak (left)
Best Science: Broc Drury (middle)
Best Poster: Saule Zubyte (right)
@cmvm-edinburghuni.bsky.social
Best Presentation: Marcin Maniak (left)
Best Science: Broc Drury (middle)
Best Poster: Saule Zubyte (right)
@cmvm-edinburghuni.bsky.social
November 7, 2025 at 8:43 AM
Well done to all our CIR PhD students for their brilliant presentations at last week's Annual Poster Day 🎉! Congratulations to our award winners:
Best Presentation: Marcin Maniak (left)
Best Science: Broc Drury (middle)
Best Poster: Saule Zubyte (right)
@cmvm-edinburghuni.bsky.social
Best Presentation: Marcin Maniak (left)
Best Science: Broc Drury (middle)
Best Poster: Saule Zubyte (right)
@cmvm-edinburghuni.bsky.social
🎉Thrilled to share that my Wellcome ECA has been funded.🎉 I'll be using ultra-sensitive proteomics—mini-bulk and single-cell—to map neutrophil functional states in COPD.
Hugely grateful to @wellcometrust.bsky.social, my host @walmsley-lab.bsky.social and @edinuni-irr.bsky.social colleagues 🙏.
Hugely grateful to @wellcometrust.bsky.social, my host @walmsley-lab.bsky.social and @edinuni-irr.bsky.social colleagues 🙏.
November 6, 2025 at 7:05 PM
🎉Thrilled to share that my Wellcome ECA has been funded.🎉 I'll be using ultra-sensitive proteomics—mini-bulk and single-cell—to map neutrophil functional states in COPD.
Hugely grateful to @wellcometrust.bsky.social, my host @walmsley-lab.bsky.social and @edinuni-irr.bsky.social colleagues 🙏.
Hugely grateful to @wellcometrust.bsky.social, my host @walmsley-lab.bsky.social and @edinuni-irr.bsky.social colleagues 🙏.
Reposted by Alejandro Brenes
Looking forward to the BMSS Single cell SIG today!
November 5, 2025 at 9:25 AM
Looking forward to the BMSS Single cell SIG today!
Reposted by Alejandro Brenes
Highlight of @natimmunol.nature.com paper by @mas-g.bsky.social @walmsley-lab.bsky.social showing epigenetic reprogramming of neutrophils in response to hypoxia to reduce lung tissue damage
#immunosky
#immunosky
Hypoxia-induced epigenetic reprogramming of neutrophil progenitors - Nature Reviews Immunology
Sanchez-Garcia et al. report that systemic hypoxia-induced epigenetic reprogramming of neutrophil progenitors in the bone marrow reduces their effector function to limit lung tissue damage.
www.nature.com
November 5, 2025 at 11:43 AM
Highlight of @natimmunol.nature.com paper by @mas-g.bsky.social @walmsley-lab.bsky.social showing epigenetic reprogramming of neutrophils in response to hypoxia to reduce lung tissue damage
#immunosky
#immunosky
Reposted by Alejandro Brenes
Ecstatic to share out latest research looking at the role of mitochondrial ABHD11 in controlling T-cell responses. We think this may be a viable target for autoimmunity. Please do give it a read, we would love to hear your thoughts.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Mitochondrial ABHD11 inhibition drives sterol metabolism to modulate T-cell effector function - Nature Communications
α/β-hydrolase domain-containing protein 11 (ABHD11) is a mitochondrial hydrolase, and its expression in CD4 + T-cells has been linked to remission status in rheumatoid arthritis. Here the authors repo...
www.nature.com
November 3, 2025 at 10:20 AM
Ecstatic to share out latest research looking at the role of mitochondrial ABHD11 in controlling T-cell responses. We think this may be a viable target for autoimmunity. Please do give it a read, we would love to hear your thoughts.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Alejandro Brenes
#Proteomics Tutorial drop!
Had fun writing this, ping me if interested in other search engines. #TeamMassSpec
www.parallelsq.org/blog/fantast...
Had fun writing this, ping me if interested in other search engines. #TeamMassSpec
www.parallelsq.org/blog/fantast...
Fantastic Proteins and Where to Find Them - PTI - Parallel Squared Technology Institute
Here, we will offer a tutorial for how to build instrument-specific spectral library predictions for PSMtag modified peptides using DIA-NN 2.3.0. This will allow users to do more accurate proteome-wid...
www.parallelsq.org
November 4, 2025 at 4:47 PM
#Proteomics Tutorial drop!
Had fun writing this, ping me if interested in other search engines. #TeamMassSpec
www.parallelsq.org/blog/fantast...
Had fun writing this, ping me if interested in other search engines. #TeamMassSpec
www.parallelsq.org/blog/fantast...
Reposted by Alejandro Brenes
November 4, 2025 at 5:20 PM
Reposted by Alejandro Brenes
pmultiqc: An open-source, lightweight, and metadata-oriented QC reporting library for MS proteomics www.biorxiv.org/cont...
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#proteomics #prot-preprint
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#proteomics #prot-preprint
November 4, 2025 at 3:40 PM
pmultiqc: An open-source, lightweight, and metadata-oriented QC reporting library for MS proteomics www.biorxiv.org/cont...
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#proteomics #prot-preprint
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#proteomics #prot-preprint