Chris Wells

A woman speaks to an audience about the importance of leveraging local experts in global science missions

Day 2 #HCA2025GM day two demonstrates the power of global representation in genome and cell maps. @patriciasevero.bsky.social

Session Details Keynote Day 2 Session Chair: Shyam Prabhakar Speaker:

Virtual attendees can use their registration email to watch the livestream at: buff.ly/Jlsw8X6

A slide describing global representation of the HCA for health benefit for all.

Consortium priorities - integrate the atlases into a whole body view; create 2D/3/D spatially resolved atlases and 3/ build global representation including for disease networks to benefit global health.

It will be interesting to see how researchers use generative AI to explore these data. It will certainly open up equitable access to the data.

AWS Marketplace: Human Cell Atlas

Human Cell Atlas data now hosted on @amazonaws.bsky.social OpenData servers - aws.amazon.com/marketplace/...

The human cell atlas #HCA2025GM really showcases descriptive science at scale - an atlas of human cells that engages globally. It's an exciting grass roots project. Equity and capability building are a core principle - as are coordinated networks focused on tissue specific atlases.

The room is buzzing in Singapore #HCA2025GM

Very happy to be in Singapore for #HCA2025GM

Congratulations Irene!

Thanks!

Graphical summary of our paper. In mice, prior lower airway exposure to diverse inflammatory stimuli, including chronic bacterial infections such as M. tuberculosis, acute bacterial infections such as pulmonary S. aureus, viral infections such as Influenza A, type-II allergic responses such as the OVA-Alum model, activation of pulmonary TLR9 by CpG or pulmonary TLR1/2 by Pam3CSK4 leads to reduced viral burden upon subsequent infection with SARS-CoV-2 (SCV2). (2) This SCV2 restriction occurs prior to induction of SCV2-specific adaptive immune responses and is mediated through innate immune responses, including the induction of IFN-I, TNFα and IL-1 and sustained changes to the TRM (Tissue resident macrophage) cellular compartment and the pulmonary epithelium. (3) Innate cytokine and TLR signaling to both recruited immune cells and the pulmonary epithelium creates a microenvironment in the lung that limits early replication of SCV2. IFN-I signaling to pulmonary ECs (epithelial cells) increases expression of interferon-stimulated genes, that likely cell-intrinsically limit viral replication. TNF- or IL-1 suppress SCV2 independently of IFN-I signaling. TNF acts exclusively through radio-resistant cell types such as the lung epithelium, whereas IL-1 affords control both direct and indirectly, through either stromal and hematopoietic cell types, to restrict overall early SCV2 burden.

Best #Nikolaus 🎅! Our paper on how the 🫁 microenvironment can shape #innate immunity against #viruses is out @sciimmunology.bsky.social This was a herculean effort brilliantly led by @pauljbaker.bsky.social who singlehandedly established the model in the lab during the pandemic. 🧪 #Immunosky 1/9

We’re so pleased to see #HumanCellAtlas 🖥️🧬 on the cover of Nature
illustrating the breadth of the HCA initiative, overlaying a subway-style network of biological systems on a detailed cellular map. Congratulations to Claire Agosti from SayoStudio and Anna Hupalowska

Pyroptotic cell corpses are crowned with F-actin-rich filopodia that engage CLEC9A signaling in incoming dendritic cells - Nature Immunology Pyroptotic cell death results in inflammation. Here the authors find that F-actin-rich structures formed during macrophage pyroptosis persist after cell death to activate dendritic cells.

What a beautiful mechanistic 🧪 insight into the collaboration between macrophages and dendritic cells, even in death. Congratulations @inflammasomelab.bsky.social and team! doi.org/10.1038/s415...

Thanks Andy

Thank you, You’ve taught me something new!

Well that’s a wrap #ICSB2024 🧪- terrific conference! ICSB2025 in Dublin 5-9 October #Ireland

Paywalled - anyone willing to share?

Presented today at #ICSB2024 by @chaitraagrahar.bsky.social - very clear presentation of a complex concept #SystemsBiology #MathematicalBiology

Final plenary of #ICSB2024 from Tim Schroeder @ethzurich.bsky.social making the case for long term live cell measurements doi.org/10.1084/jem....

A bright red poster with a large tree in the bottom right corner. The text “Gulmohar Post-Doc Talk Series” is displayed at the top. Below, it reads “A monthly virtual platform for postdocs to share and connect.” A QR code is provided for sign-up, and contact information is given in the bottom right corner.

InSDB is running a virtual postdoc talk series for postdocs to present their work and share their science! We meet once every month for two fascinating talks.
If you are a postdoc, do sign up to be a speaker now-our slots are filling up
t.co/9j0NsvGSZw
Do share & spread the word among #DevBio folks!

Nice job @chaitraagrahar.bsky.social - interesting #ISCB2024 talk. Will you publish your method? Would love to read further.

Gorgeous work, conceptually and in application- congratulations

a brown puppy with a funny face is being held by someone Alt: a brown puppy with a funny face shaking its head

Machine learning based models are more reproducible right? Right? : doi.org/10.1101/2023...

FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models Genome-scale metabolic models (GEMs) and other constraint-based models (CBMs) play a pivotal role in understanding biological phenotypes and advancing research in areas like metabolic engineering, hum...

What about genome scale models? Can community curation efforts support FAIR models? @biorxivpreprint.bsky.social doi.org/10.1101/2024...

Reproducibility in systems biology modelling | Molecular Systems Biology EMBO Press is an editorially independent publishing platform for the development of EMBO scientific publications.

Reproducibility in systems modelling- does the math lie? - 50% of simple ODE models are not reproducible. doi.org/10.15252/msb...

Rahuman Sheriff #ICSB2024 @ebi.embl.org asks Are Machine Learning Models of Biology FAIR? www.ebi.ac.uk/biomodels/ thread…spoiler alert, not always FAIR

Home - Center for Reproducible Biomedical Modeling Our Center carries out research & technology development; we engage in collaborative research projects with the community; we provide services for biological researchers, and dissemination and educati...

Three cheers from #ISCB2024 audience @ion-moraru.bsky.social ‘reproducibility and replication are not the same thing’ - speaking to the importance of using community standards to support reproducible #systemsBiology #BiologicalModels reproduciblebiomodels.org

Personalized disease signatures through information-theoretic compaction of big cancer data | PNAS Every individual cancer develops and grows in its own specific way, giving rise to a recognized need for the development of personalized cancer dia...

2/2 Underpinning theory @pnas.org 2018 doi.org/10.1073/pnas...

Patient-specific signaling signatures predict optimal therapeutic combinations for triple negative breast cancer - Molecular Cancer Triple negative breast cancer (TNBC) is a heterogeneous group of tumors which lack estrogen receptor, progesterone receptor, and HER2 expression. Targeted therapies have limited success in treating TN...

1/2 Nataly Kravchenko-Balasha speaks to patient-specific approaches to identify steady-state dynamics and disease-deviation from that steady state. #ICSB2024 #systemsOncology #SystemsBiology doi.org/10.1186/s129...

ChromaFold predicts the 3D contact map from single-cell chromatin accessibility - Nature Communications Obtaining a high-resolution contact map using current 3D genomics technologies can be challenging with small input cell numbers. Here, the authors develop ChromaFold, a deep learning model that p...

Very cool to see Christina apply the read based approach to chromatin contact matrix - and borrowing from sc-ATAC to infer this structure @naturecomms.bsky.social #hiC #Chromofold doi.org/10.1038/s414...