Alistair Forrest

Congratulations Hamid!

Registration is now open for HCA Asia in Fremantle. Come make friends with our nearby neighbours. Many talking slot for EMCRs!
@ozsinglecell.bsky.social @lornegenome.bsky.social #SingleCell #transcriptomics #multiomics #Spatial_transcriptomics

Registration for the HCA Asia Meeting on 2-4 November, 2026 is now open! The #HCA2026Asia meeting will be held in Perth, Australia, and online, and is hosted by @alforrest.bsky.social. Please register at buff.ly/gADDEnC
🖥️ 🧬 #Genomics #SingleCell #Spatial #HumanCellAtlas

A a figure showing comparison of connectomeDB2025 to other ligand-receptor pair databases.

connectomeDB2025: Quality matters!
✅3,579 ligand-receptor pairs supported by 2,803 papers
✅14 vertebrates
❌ >2,900 unsupported pairs from other DBs excluded

connectomedb.org

academic.oup.com/nar/advance-...

@JARamilowski @sakura_maezono @rui_hou_ @weitao_lin @yen_yeow + team

First ride and ocean swim of the year in the big blue antidepressant. There's beauty out there, fish, seaweed and seagrass.. and so far no stingers!

Australia's hyper competitive grant system, and the chronic job insecurity it creates, is harming the very researchers who are working to improve the nation's health. The people striving to fi... Australia's hyper competitive grant system, and the chronic job insecurity it creates, is harming the very researchers who are working to improve the nation's health. The people striving to find cures...

Australia’s hyper-competitive grant system is harming the very researchers working to improve our nation’s health. Chronic stress, relationship breakdowns, depression, burnout, self-medication, and, tragically, suicide are part of our sector's reality.
www.linkedin.com/posts/alforr...

For those outside of Australia this is an anti-gambling advert. I am posting this because funding for science in Australia is at a crisis and for many in the research sector we are gambling with our… ... For those outside of Australia this is an anti-gambling advert. I am posting this because funding for science in Australia is at a crisis and for many in the research sector we are gambling with our f...

Chances are you're about to lose. Science funding in Australia is now a gamble with terrible odds. #NHMRC Ideas success rates have hit 8.1% nationally, <4% in WA. Brilliant colleagues are leaving or quitting. We need change. www.linkedin.com/posts/alforr...

Low success rate in early career grants ‘deeply disappointing’ - Research Professional News “Decay continues” as Australian Research Council’s Decra scheme announces 13.1 per cent success rate

Australia: Low ARC success rates for early career researchers sparks anger (free to read): www.researchprofessionalnews.com/rr-news-aust...

Chelsea Mayoh at #abacbs2025: "If you're not using RNA-seq in your precision medicine program you're probably missing stuff"! Great to see @aliciao.bsky.social lab tools MINTIE, ALLsorts and TALLsorts making an appearance 🎉

Yes they have increased in average awarded amount. $822k in 2019, increasing each year to $1.23m in 2024.

How the war was won: the campaign to stop medical research cuts One day in April, Walter and Eliza Hall Institute of Medical Research director Douglas Hilton called his communications manager, Penny Fannin, into his office. “He said he’d heard significant cuts wer...

It's time... theconversation.com/how-the-war-...

When I took this job as the Head of a department, I never thought my job would involve consoling & moving on some of my most talented researchers at the end of each year - just bc their ARC/NHMRC grant didn’t get up. Having worked in multiple countries, I have never seen this normalised like in Aus.

The success rate for NHMRC Ideas Grants announced yesterday was just over 8%. That means 11 of every 12 people who applied got rejected. This is a culture changing level of rejection and frankly a point of national shame. This is a crisis for research.
I will not rest until we see this resolved.

Be kind to each other.. bad news for most coming in under embargo. We need more funding in the system...

– ConnectomeDB2025

Heading to Radelaide for #ABACBS2025 . Looking forward to catch up with old friends and nerd out on bioinformatics!

Checkout PhD student Peiwen Liu's poster on connectomeDB2025 (Quality matters!) connectomeDB.org

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

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 ...

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...

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...

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...

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. 🌏

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

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.

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. 🔍

A a figure showing comparison of connectomeDB2025 to other ligand-receptor pair databases.

connectomeDB2025: Quality matters!
✅3,579 ligand-receptor pairs supported by 2,803 papers
✅14 vertebrates
❌ >2,900 unsupported pairs from other DBs excluded

connectomedb.org

academic.oup.com/nar/advance-...

@JARamilowski @sakura_maezono @rui_hou_ @weitao_lin @yen_yeow + team

Black text on white background. Screenshot from ARC webpage updating us on changes, in response to community feedback, to their proposed modification to their grants system. This screenshot shows the main changes, listed on that webpage.

The ARC has “announced” an update on the proposed changes to its grant schemes.

Key changes, in response to “nearly 350” submissions” (!) on their proposal, are 👇

More here: www.arc.gov.au/news-publica...

Chicken wings are awesome in the airfryer :) easy and very little mess

Table from page 25 of the proposed restructure of ARC grants. Back text on white background, with the table delineated by a dark blue header row and alternating light and very light blue rows.

The ARC Board has proposed a major shake-up of the National Competitive Grants Program ▶️ www.arc.gov.au/engage-us/co...

I've only skimmed so far, but they propose reducing 13 grant schemes to 6, with intent & scope in the table👇

Submissions are being accepted in response until 13 April. Get to it!

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...

Prohormone cleavage prediction uncovers a non-incretin anti-obesity peptide

.
www.nature.com/articles/s41...

Do you have an exciting story about #enhancers or #enhanceropathies?. Then submit your abstract to the @embo.org workshop on "Enhancer mechanics and Enhanceropathies" in Denmark before is too late: the deadline for abstract submissions is in two weeks (March 17th)!

meetings.embo.org/event/25-enh...

Link to job advert:
external.jobs.uwa.edu.au/en/job/51959...

Heading to #lornegenome25 #LorneCancerConference ? Looking for a computational postdoc to work on spatial and single nuclei transcriptomics of poor prognosis cancers, please DM me or see me at Lorne. We will be advertising soon. @ozsinglecell.bsky.social #LorneCancer2025 #Lorne2025