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
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
✅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
October 31, 2025 at 11:21 PM
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
✅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
Reposted by Alistair Forrest
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...
Key changes, in response to “nearly 350” submissions” (!) on their proposal, are 👇
More here: www.arc.gov.au/news-publica...
July 14, 2025 at 12:41 AM
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...
Key changes, in response to “nearly 350” submissions” (!) on their proposal, are 👇
More here: www.arc.gov.au/news-publica...
Reposted by Alistair Forrest
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!
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!
February 25, 2025 at 3:46 AM
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!
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!
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...
Reposted by Alistair Forrest
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...
meetings.embo.org/event/25-enh...
March 3, 2025 at 10:02 AM
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...
meetings.embo.org/event/25-enh...
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
bsky.app
February 12, 2025 at 1:28 AM
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
Reposted by Alistair Forrest
@ozsinglecell.bsky.social #OzSingleCell25 has a new website www.ozsinglecell.com See the current list of invited speakers and stay tuned for registration details. Sponsors reach out to [email protected]
January 30, 2025 at 6:31 AM
@ozsinglecell.bsky.social #OzSingleCell25 has a new website www.ozsinglecell.com See the current list of invited speakers and stay tuned for registration details. Sponsors reach out to [email protected]
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...
Reposted by Alistair Forrest
A little video intro into Illumina Single Cell 3' RNA Prep protocols. It has begun!!
#singlecell
#transcriptomics
#PIPSeq
#illumina
#singlecell
#transcriptomics
#PIPSeq
#illumina
🧬Two updated technical videos demonstrating T2 and T20 workflows on newly released #Illumina Single-Cell 3' RNA Prep
T2: www.youtube.com/watch?v=4i5k...
T20: www.youtube.com/watch?featur...
📰 www.prnewswire.com/news-release...
T2: www.youtube.com/watch?v=4i5k...
T20: www.youtube.com/watch?featur...
📰 www.prnewswire.com/news-release...
January 13, 2025 at 7:54 AM
A little video intro into Illumina Single Cell 3' RNA Prep protocols. It has begun!!
#singlecell
#transcriptomics
#PIPSeq
#illumina
#singlecell
#transcriptomics
#PIPSeq
#illumina
Reposted by Alistair Forrest
Out today in @naturegenet.bsky.social -- PERFF-seq! With @tsionabay.bsky.social , @ronanchaligne.bsky.social, Bob Stickels, Meril Takizawa, + Ansu Satpathy, we describe this new assay to study rare populations with programmable nucleic acid cytometry. 1/n
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Transcript-specific enrichment enables profiling of rare cell states via single-cell RNA sequencing - Nature Genetics
Programmable Enrichment via RNA FlowFISH by sequencing (PERFF-seq) isolates rare cells based on RNA marker transcripts for single-cell RNA sequencing profiling of complex tissues, with applicability t...
www.nature.com
January 8, 2025 at 1:30 PM
Out today in @naturegenet.bsky.social -- PERFF-seq! With @tsionabay.bsky.social , @ronanchaligne.bsky.social, Bob Stickels, Meril Takizawa, + Ansu Satpathy, we describe this new assay to study rare populations with programmable nucleic acid cytometry. 1/n
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Alistair Forrest
@nature.com wants to hear from you on the battle of David vs Goliath - aka Twitter 🐥 vs Bluesky 🦋*
And if you’re reading this post I already know your answer to one of the questions 🙂↕️
👉🏼 www.nature.com/articles/d41...
*I’ll let you decide who’s who at this point!
And if you’re reading this post I already know your answer to one of the questions 🙂↕️
👉🏼 www.nature.com/articles/d41...
*I’ll let you decide who’s who at this point!
Has Bluesky replaced X for scientists? Take Nature’s poll
The research community has flocked to the social-media platform Bluesky. Tell us about your experience.
www.nature.com
January 14, 2025 at 8:54 PM
@nature.com wants to hear from you on the battle of David vs Goliath - aka Twitter 🐥 vs Bluesky 🦋*
And if you’re reading this post I already know your answer to one of the questions 🙂↕️
👉🏼 www.nature.com/articles/d41...
*I’ll let you decide who’s who at this point!
And if you’re reading this post I already know your answer to one of the questions 🙂↕️
👉🏼 www.nature.com/articles/d41...
*I’ll let you decide who’s who at this point!
www.cell.com/cell/fulltex...
Perturb-map - focused on receptor/ligands hypothesized to be involved in tumor-macrophage communication
Perturb-map - focused on receptor/ligands hypothesized to be involved in tumor-macrophage communication
Ovarian cancer-derived IL-4 promotes immunotherapy resistance
Cancer-derived paracrine factors create distinct “neighborhoods” in the tumor microenvironment, promoting clonal selection and tumor heterogeneity. In ovarian cancer, IL-4 originating from a minority of cells within the tumor can promote immune suppression and tumor resistance to immune checkpoint blockade therapy.
www.cell.com
January 10, 2025 at 3:36 AM
www.cell.com/cell/fulltex...
Perturb-map - focused on receptor/ligands hypothesized to be involved in tumor-macrophage communication
Perturb-map - focused on receptor/ligands hypothesized to be involved in tumor-macrophage communication
Reposted by Alistair Forrest
I've been catching up on some reading and came across this paper. Ovarian cancers export a cancer-specific #lncRNA, Tu-stroma, to TME via exosomes. Tu-stroma alters spicing of flower gene in stromal cells to reduce cell fitness. Such a cool mechanism.
The battle between cancer and the microenvironment is fierce!
Ovarian cancer cells use lncRNA to weaken healthy tissue.
This was a great project to be a part of.
www.nature.com/articles/s41...
Ovarian cancer cells use lncRNA to weaken healthy tissue.
This was a great project to be a part of.
www.nature.com/articles/s41...
Ovarian tumor cells gain competitive advantage by actively reducing the cellular fitness of microenvironment cells - Nature Biotechnology
Reduced fitness of the tumor microenvironment is mediated by a long non-coding RNA expressed in tumors.
www.nature.com
January 10, 2025 at 2:55 AM
I've been catching up on some reading and came across this paper. Ovarian cancers export a cancer-specific #lncRNA, Tu-stroma, to TME via exosomes. Tu-stroma alters spicing of flower gene in stromal cells to reduce cell fitness. Such a cool mechanism.
Reposted by Alistair Forrest
Sridevi Challa, Lee Kraus et al. discover a druggable PARP14/TARG1-regulated pathway that mediates site-specific mono(ADP-ribosyl)ation of the ribosomal protein RACK1 & modulates the growth of ovarian #cancer cells. https://buff.ly/3DOejo4
January 8, 2025 at 5:48 PM
Sridevi Challa, Lee Kraus et al. discover a druggable PARP14/TARG1-regulated pathway that mediates site-specific mono(ADP-ribosyl)ation of the ribosomal protein RACK1 & modulates the growth of ovarian #cancer cells. https://buff.ly/3DOejo4
Reposted by Alistair Forrest
AI-driven ultrasound detection of ovarian cancer. #NatureMedicine
"AI model ROC curve and human examiner performance"
Open Access
www.nature.com/articles/s41...
"AI model ROC curve and human examiner performance"
Open Access
www.nature.com/articles/s41...
January 4, 2025 at 5:20 PM
AI-driven ultrasound detection of ovarian cancer. #NatureMedicine
"AI model ROC curve and human examiner performance"
Open Access
www.nature.com/articles/s41...
"AI model ROC curve and human examiner performance"
Open Access
www.nature.com/articles/s41...
Reposted by Alistair Forrest
Very excited to announce that the single cell/nuc. RNA/ATAC/multi-ome resource from ENCODE4 is now officially public. This includes raw data, processed data, annotations and pseudobulk products. Covers many human & mouse tissues. 1/
www.encodeproject.org/single-cell/...
www.encodeproject.org/single-cell/...
Single cell – ENCODEHomo sapiens clickable body map
www.encodeproject.org
January 7, 2025 at 9:29 PM
Very excited to announce that the single cell/nuc. RNA/ATAC/multi-ome resource from ENCODE4 is now officially public. This includes raw data, processed data, annotations and pseudobulk products. Covers many human & mouse tissues. 1/
www.encodeproject.org/single-cell/...
www.encodeproject.org/single-cell/...
Reposted by Alistair Forrest
We are here 🦋. Save the date for Oz Single Cell 2025, 23-25 May in Sydney
January 7, 2025 at 3:49 AM
We are here 🦋. Save the date for Oz Single Cell 2025, 23-25 May in Sydney
Wow head-to-head comparison Visium HD FFPE, CosMx 6K, Xenium 5K, Stereo-seq v1.3 and Visium HD FF profiling on HGSOC and HCC. Heads-up @GESTALT_sp hopefully can save community some $$$$
Systematic Benchmarking of High-Throughput Subcellular Spatial Transcriptomics Platforms 🧬🖥️🧪 biorxiv.org/cgi/content/...
Systematic Benchmarking of High-Throughput Subcellular Spatial Transcriptomics Platforms
Recent advancements in spatial transcriptomics technologies have significantly enhanced resolution and throughput, underscoring an urgent need for systematic benchmarking. To address this, we collecte...
biorxiv.org
December 30, 2024 at 9:36 AM
Wow head-to-head comparison Visium HD FFPE, CosMx 6K, Xenium 5K, Stereo-seq v1.3 and Visium HD FF profiling on HGSOC and HCC. Heads-up @GESTALT_sp hopefully can save community some $$$$
Our paper with @NCARD_research is finally out. Finds • Circulating CD8+ TEMs are more abundant in chemoimmunotherapy responders • Stem-like CD8+ TEM expansion links to permissive pre-treatment tumour environment cell.com/cell-reports... #mesothelioma
Coupling of response biomarkers between tumor and peripheral blood in patients undergoing chemoimmunotherapy
Chin et al. analyze tumor and serial blood immune profiles in mesothelioma patients receiving chemoimmunotherapy. They identify stem-like CD8+ T effector memory cells associated with treatment response and demonstrate that combining peripheral blood and tumor data improves prediction of clinical outcome.
cell.com
December 28, 2024 at 7:17 AM
Our paper with @NCARD_research is finally out. Finds • Circulating CD8+ TEMs are more abundant in chemoimmunotherapy responders • Stem-like CD8+ TEM expansion links to permissive pre-treatment tumour environment cell.com/cell-reports... #mesothelioma
Another terrible year for #NHMRC Ideas grants in WA. Only 6 of 127 submissions funded. National rate was 10.1%. If this was an equitable funding scheme WA should have got 12 or 13. Multiple category 6 grants missed out. This means 6 or 7 of the best research groups in WA give up.
December 17, 2024 at 8:16 AM
Another terrible year for #NHMRC Ideas grants in WA. Only 6 of 127 submissions funded. National rate was 10.1%. If this was an equitable funding scheme WA should have got 12 or 13. Multiple category 6 grants missed out. This means 6 or 7 of the best research groups in WA give up.
I need a volunteer..
a desert landscape with trees and bushes in the foreground and mountains in the background
ALT: a desert landscape with trees and bushes in the foreground and mountains in the background
media.tenor.com
December 16, 2024 at 5:45 AM
I need a volunteer..
Is biorxiv down/slow today?
December 9, 2024 at 5:33 AM
Is biorxiv down/slow today?
Reposted by Alistair Forrest
I never tire of seeing these progressively improved pediatric ALL survival curves, which represent one of the most remarkable achievements in all of medicine.
Amazing to see even more improvement with bispecific antibody #immunotherapy presented in the #ASH24 Plenary session. #hematology #leukemia
Amazing to see even more improvement with bispecific antibody #immunotherapy presented in the #ASH24 Plenary session. #hematology #leukemia
December 8, 2024 at 10:16 PM
I never tire of seeing these progressively improved pediatric ALL survival curves, which represent one of the most remarkable achievements in all of medicine.
Amazing to see even more improvement with bispecific antibody #immunotherapy presented in the #ASH24 Plenary session. #hematology #leukemia
Amazing to see even more improvement with bispecific antibody #immunotherapy presented in the #ASH24 Plenary session. #hematology #leukemia
Reposted by Alistair Forrest
Major milestone: Tabula Sapiens 2.0 maps tissue composition & TF expression in 175 cell types, identifying 745 ubiquitous & 890 cell type-specific TFs (many still uncharacterized -> #Codebook) w/ roles in tissue homeostasis, stress response & metabolism. #SingleCell www.biorxiv.org/content/10.1...
Tabula Sapiens reveals transcription factor expression, senescence effects, and sex-specific features in cell types from 28 human organs and tissues
The Tabula Sapiens is a reference human cell atlas containing single cell transcriptomic data from more than two dozen organs and tissues. Here we report Tabula Sapiens 2.0 which includes data from ni...
www.biorxiv.org
December 8, 2024 at 8:55 AM
Major milestone: Tabula Sapiens 2.0 maps tissue composition & TF expression in 175 cell types, identifying 745 ubiquitous & 890 cell type-specific TFs (many still uncharacterized -> #Codebook) w/ roles in tissue homeostasis, stress response & metabolism. #SingleCell www.biorxiv.org/content/10.1...
Reposted by Alistair Forrest
El otro día, un guionista en edad de jubilarse me contó que su mujer le había reñido: “Siempre igual, con mil proyectos a la vez, y diciendo que vas a aflojar cuando no te lo crees ni tú”. Sentí vértigo: ¿serán así mis próximos 25 años? Con suerte. Si alguien encuentra un equilibrio, que avise.
December 5, 2024 at 9:21 AM
El otro día, un guionista en edad de jubilarse me contó que su mujer le había reñido: “Siempre igual, con mil proyectos a la vez, y diciendo que vas a aflojar cuando no te lo crees ni tú”. Sentí vértigo: ¿serán así mis próximos 25 años? Con suerte. Si alguien encuentra un equilibrio, que avise.