Alistair Forrest
@alforrest.bsky.social
Head of the Systems Biology and Genomics Lab at the Harry Perkins Institute of Medical Research, University of Western Australia
#FANTOM5 #transcriptomics #spatial #cellcommunication #ovariancancer #bioinformatics #singlecell
#FANTOM5 #transcriptomics #spatial #cellcommunication #ovariancancer #bioinformatics #singlecell
Now, with co-first authors Peiwen Liu (Australia) and
@sakura_maezono
(Japan), we’ve released v3 — 10 years on. 🎉
Rigorous QC: >2,900 unsupported pairs excluded.
3,579 validated ligand–receptor pairs across 14 vertebrates.
Check out connectomedb.org
@sakura_maezono
(Japan), we’ve released v3 — 10 years on. 🎉
Rigorous QC: >2,900 unsupported pairs excluded.
3,579 validated ligand–receptor pairs across 14 vertebrates.
Check out connectomedb.org
November 1, 2025 at 12:01 AM
Now, with co-first authors Peiwen Liu (Australia) and
@sakura_maezono
(Japan), we’ve released v3 — 10 years on. 🎉
Rigorous QC: >2,900 unsupported pairs excluded.
3,579 validated ligand–receptor pairs across 14 vertebrates.
Check out connectomedb.org
@sakura_maezono
(Japan), we’ve released v3 — 10 years on. 🎉
Rigorous QC: >2,900 unsupported pairs excluded.
3,579 validated ligand–receptor pairs across 14 vertebrates.
Check out connectomedb.org
In 2020 with then PhD student
@rui_hou_
we released the first update and released NATMI (Network Analysis Toolkit for Multicellular Interactions) for cell-to-cell communication network prediction from single cell and other datasets.
www.nature.com/articles/s41...
@rui_hou_
we released the first update and released NATMI (Network Analysis Toolkit for Multicellular Interactions) for cell-to-cell communication network prediction from single cell and other datasets.
www.nature.com/articles/s41...
Predicting cell-to-cell communication networks using NATMI - Nature Communications
Single cell expression data allows for inferring cell-cell communication between cells expressing ligands and those expressing their cognate receptors. Here the authors present an updated and curated ...
www.nature.com
November 1, 2025 at 12:01 AM
In 2020 with then PhD student
@rui_hou_
we released the first update and released NATMI (Network Analysis Toolkit for Multicellular Interactions) for cell-to-cell communication network prediction from single cell and other datasets.
www.nature.com/articles/s41...
@rui_hou_
we released the first update and released NATMI (Network Analysis Toolkit for Multicellular Interactions) for cell-to-cell communication network prediction from single cell and other datasets.
www.nature.com/articles/s41...
This has been a fun ongoing collaboration with
@JARamilowski
To see if we could build models of cell-to-cell communication based on ligand and receptor expression using the FANTOM5 data we published the first version in 2015 www.nature.com/articles/nco...
@JARamilowski
To see if we could build models of cell-to-cell communication based on ligand and receptor expression using the FANTOM5 data we published the first version in 2015 www.nature.com/articles/nco...
A draft network of ligand–receptor-mediated multicellular signalling in human - Nature Communications
Cell-to-cell communication relies upon interactions between secreted ligands and cell surface receptors. Here, Ramilowski et al.present a draft cell-to-cell communication network based on expression o...
www.nature.com
November 1, 2025 at 12:00 AM
This has been a fun ongoing collaboration with
@JARamilowski
To see if we could build models of cell-to-cell communication based on ligand and receptor expression using the FANTOM5 data we published the first version in 2015 www.nature.com/articles/nco...
@JARamilowski
To see if we could build models of cell-to-cell communication based on ligand and receptor expression using the FANTOM5 data we published the first version in 2015 www.nature.com/articles/nco...
To support broader use, we annotated ligand and receptor reagents by species and expanded via orthology to 14 vertebrates.
connectomeDB2025 enables accurate cell–cell communication analysis across model systems and disease contexts. 🌏
connectomeDB2025 enables accurate cell–cell communication analysis across model systems and disease contexts. 🌏
October 31, 2025 at 11:59 PM
To support broader use, we annotated ligand and receptor reagents by species and expanded via orthology to 14 vertebrates.
connectomeDB2025 enables accurate cell–cell communication analysis across model systems and disease contexts. 🌏
connectomeDB2025 enables accurate cell–cell communication analysis across model systems and disease contexts. 🌏
Literature discovery is a major bottleneck. We used PerplexityAI to speed up identification of candidate papers and potential novel ligands/receptors.
Still manually validated ✅ but it helped us find 800+ new supported pairs. And expand the coverage of major L&R gene families
Still manually validated ✅ but it helped us find 800+ new supported pairs. And expand the coverage of major L&R gene families
October 31, 2025 at 11:59 PM
Literature discovery is a major bottleneck. We used PerplexityAI to speed up identification of candidate papers and potential novel ligands/receptors.
Still manually validated ✅ but it helped us find 800+ new supported pairs. And expand the coverage of major L&R gene families
Still manually validated ✅ but it helped us find 800+ new supported pairs. And expand the coverage of major L&R gene families
For every interaction, we required a publication with primary experimental evidence.
A substantial fraction of pairs in other databases were unsupported or misclassified — we excluded >2,900 low-evidence interactions.
A substantial fraction of pairs in other databases were unsupported or misclassified — we excluded >2,900 low-evidence interactions.
October 31, 2025 at 11:58 PM
For every interaction, we required a publication with primary experimental evidence.
A substantial fraction of pairs in other databases were unsupported or misclassified — we excluded >2,900 low-evidence interactions.
A substantial fraction of pairs in other databases were unsupported or misclassified — we excluded >2,900 low-evidence interactions.
We manually curated thousands of putative ligand–receptor pairs from existing resources (connectomeDB2020, CellChatDB_v2, CellPhoneDB_v5, ICELLNET_v2, CellTalkDB, LIANA).
For many entries we found no primary experimental evidence — rigorous QC really matters. 🔍
For many entries we found no primary experimental evidence — rigorous QC really matters. 🔍
October 31, 2025 at 11:58 PM
We manually curated thousands of putative ligand–receptor pairs from existing resources (connectomeDB2020, CellChatDB_v2, CellPhoneDB_v5, ICELLNET_v2, CellTalkDB, LIANA).
For many entries we found no primary experimental evidence — rigorous QC really matters. 🔍
For many entries we found no primary experimental evidence — rigorous QC really matters. 🔍
Chicken wings are awesome in the airfryer :) easy and very little mess
May 21, 2025 at 4:17 AM
Chicken wings are awesome in the airfryer :) easy and very little mess
Reposted by Alistair Forrest
Prohormone cleavage prediction uncovers a non-incretin anti-obesity peptide
.
www.nature.com/articles/s41...
.
www.nature.com/articles/s41...
Prohormone cleavage prediction uncovers a non-incretin anti-obesity peptide - Nature
Computational drug discovery is used to identify a 12-mer peptide derived from BRINP2 with potent anti-obesity effects that are independent of leptin, glucagon-like peptide 1 receptor and melanocortin...
www.nature.com
March 11, 2025 at 11:14 PM
Prohormone cleavage prediction uncovers a non-incretin anti-obesity peptide
.
www.nature.com/articles/s41...
.
www.nature.com/articles/s41...
Link to job advert:
external.jobs.uwa.edu.au/en/job/51959...
external.jobs.uwa.edu.au/en/job/51959...
February 14, 2025 at 4:46 AM
Link to job advert:
external.jobs.uwa.edu.au/en/job/51959...
external.jobs.uwa.edu.au/en/job/51959...
Reposted by Alistair Forrest
MagLOV!
MagLOV is a fluorescent protein you can "turn off" with a handheld magnet, engineered by @mariaingaramo.bsky.social.
We think/hope we can use it to turn arbitrary proteins (including drugs!) on and off in opaque creatures (including humans!).
bsky.app/profile/addg...
MagLOV is a fluorescent protein you can "turn off" with a handheld magnet, engineered by @mariaingaramo.bsky.social.
We think/hope we can use it to turn arbitrary proteins (including drugs!) on and off in opaque creatures (including humans!).
bsky.app/profile/addg...
November 22, 2024 at 12:06 AM
MagLOV!
MagLOV is a fluorescent protein you can "turn off" with a handheld magnet, engineered by @mariaingaramo.bsky.social.
We think/hope we can use it to turn arbitrary proteins (including drugs!) on and off in opaque creatures (including humans!).
bsky.app/profile/addg...
MagLOV is a fluorescent protein you can "turn off" with a handheld magnet, engineered by @mariaingaramo.bsky.social.
We think/hope we can use it to turn arbitrary proteins (including drugs!) on and off in opaque creatures (including humans!).
bsky.app/profile/addg...