Carly Whyte

Delighted to have the work from my post doc with @LabListon out in @JExpMed today! We show how the cellular context in which IL2 is expressed leads to vastly different outcomes: bit.ly/3MMoM1X

Thrilled to share new work led by @JieYang437 in the lab published today in @Nature. We find that Aspirin prevents metastasis by releasing T cells from immune suppression by platelet TXA2. @Cambridge_Uni @CRUKCamCentre rdcu.be/eci1U

@RoychoudhuriLab @JieYang437 @Nature @Cambridge_Uni @CRUKCamCentre Such a great paper!! Congrats Rahul and @JieYang437

We are excited to recruit a PhD student for 2025 @CCB_Research in Adelaide to tackle immune dysfunction in head and neck cancer. Please share and apply: unisa.edu.au/research/degre…

Following several kind requests, here is a high-level summary of our pre-print in @biorxivpreprint (doi: doi.org/10.1101/2024.1…): STAMP: Single-Cell Transcriptomics Analysis and Multimodal Profiling through Imaging STAMP is a scalable, cost-efficient method for single-cell transcriptomics and multimodal profiling through imaging. It bypasses sequencing, significantly reducing costs while enhancing throughput. #SingleCellRNA #SpatialOmics #STAMP The motivation for this paper comes from the limitations of current scRNA-seq methods, which are costly, inefficient, and struggle to capture low- and high-abundance transcripts. Challenges like droplet instability, cell damage, limited cell capture, cross-contamination, inefficient indexing, and high sequencing costs affect ultra-low and ultra-high cell profiling, hindering accurate analysis of complex cell populations. #Limitations #DropletMicrofluidics STAMP addresses these issues with a scalable, cost-effective, sequencing(costs)-free approach that works efficiently across ultra-low to ultra-high cell numbers, while preserving cellular morphology and enabling multimodal profiling. #SpatialOmics #UltraLow #UltraHigh STAMP uses an imaging-based approach to perform high-throughput RNA and protein profiling by stamping cells onto slides compatible with CosMx and Xenium platforms, allowing multimodal profiling in a single run. #Proteomics STAMP supports single-modal (RNA/protein) and multimodal (RNA + protein) profiling, enhancing experimental flexibility and scalability. This versatility is essential for large-scale atlases and mixed-sample experiments. #SingleCellAtlas #MultiSampleProfiling STAMP scales easily: from less than 100 to millions of cells. It overcomes limitations in droplet-based systems, where throughput is often constrained by sequencing costs. #HighThroughput STAMP handles diverse sample types: PBMCs, dissociated tumors, nuclei, and stem cells. It also excels with fragile or archived tissues, where traditional methods often fail to yield high-quality data. #ArchivedSamples STAMP eliminates sequencing costs, making large-scale single-cell analysis accessible to more labs. #CostEfficiency Here’s a cost comparison between GEM-X and STAMP-X for RNA profiling: GEM-X RNA (20k cells): $0.0764/cell 1M cells = $76,400 (cost/cell = $0.0764) 2M cells = $152.800 (cost/cell = $0.0764) 3M cells = $229,200 (cost/cell = $0.0764) STAMP-X RNA (1M cells): $0.0075/cell 1M cells = $7,500 (cost/cell = $0.0075) 2M cells = $7,500 (cost/cell = $0.00375) 3M cells = $7,500 (cost/cell = $0.0025) In STAMP cells remain intact after imaging, enabling further downstream applications like histological validation or additional molecular assays, adding value to each sample. #NonDestructiveAnalysis We tested STAMP’s sensitivity by identifying, ultra-rare, circulating tumor cells (CTCs) spiked into PBMCs at 1:100,000. Such sensitivity is essential for clinical diagnostics, particularly in rare cell detection. #CTCs #CancerDiagnostics In a high-throughput immuno-phenotyping experiment, STAMP profiled 1.7M PBMCs, capturing a median of 83 transcripts and 49 genes per cell. This resulted in high-resolution immune profiling. #Immunology #HighThroughputProfiling 31 immune cell states were mapped in PBMCs, capturing rare subpopulations (Th1/Th2/Th17 and NK subtypes). Detailed immune phenotyping is critical for understanding immune diversity in health and disease. #ImmuneMapping Whole cells vs. nuclei: STAMP's ability to profile both whole cells and nuclei is crucial for samples with low RNA content (e.g., archived tissues), increasing the platform’s applicability. #NucleiProfiling #SingleCellOmics STAMP integrates RNA and protein profiling. In cancer cell line profiling, RNA and protein data showed strong correlations, confirming the platform’s robustness in multimodal data collection. #MultimodalProfiling STAMP’s multimodal profiling produced high-resolution immune maps, combining RNA and protein data. This approach is essential for dissecting complex immune states and understanding functional responses. STAMP excels in low-input samples. We demonstrated its ability to accurately profile as few as 100 cells, which is critical for studying rare populations in small samples. #LowInput #RareCell In a BMP4-driven stem cell differentiation model, STAMP captured dynamic changes from pluripotency to mesoderm and endoderm progenitors over multiple timepoints, tracking lineage differentiation. #StemCellDifferentiation #LineageTracing Trajectory analysis shows that STAMP’s resolution makes it a powerful tool for developmental biology and perturbation studies. #DevelopmentalBiology #hESC STAMP allows multi-sample profiling on a single slide, reducing batch effects and improving comparative analysis, particularly in drug response and perturbation studies. #MultiSampleAnalysis #PerturbationScreening STAMP represents a significant advance in single-cell research, offering scalable, multimodal RNA/protein profiling at low cost. Its versatility will support a broad range of research, from basic to clinical. #SingleCellTechnology Lots more coming soon... @DrJasPlummer @hoheyn @pascual_reguant @EmanuelePitino1 @helucro @ximbaozao @irepan_salvador @Kellieiswise @m_mohenska @jc_nietos @cnag_eu @StJudeResearch @ACEpigenetics @M_ayco_N @eliseinsing Bill Flynn, Yutian Liu, Hannah Chasteen

Here we go…repurposing spatial imaging techs to achieve ultra-low to ultra-high, multiplexing, nuclei, cells, single (RNA or Protein), multimodal (RNA and Protein), super cheap! NO SEQUENCING! @10xGenomics @nanostringtech @AkoyaBio @bruker

We are recruiting! Come join us in Adelaide to work on cutting-edge translational research and contribute to developing CAR-T cell therapies for brain tumours. Two post-doc positions available, closing soon, details at careers.pageuppeople.com/532/caw/en/job…

Congrats to the team @LabListon @jldvib @olivertburton on this wonderful study 👏 #TissueTregs surprising us on every turn!

@betacellgirl @FlindersHMRI @Flinders @iMOD_lab Congratulations Claire!!

Honoured and completely stoked to be supported by @JDRF for the next 2 years to continue our research on Type 1 diabetes @FlindersHMRI #HMRB @Flinders @iMOD_lab

So great to have this preprint out in the world. My first paper in this new field I love, #StrepA. Thanks to @JoshOsowicki and Andrew Steer @MCRI_for_kids for providing such a cool Strep A challenge model to study, & to all our coauthors, particularly @hrcfrost & @njmoreland

Very excited (& nervous) to share what we've been working on the past many years. Only took 3 first authors (Schreuder the experimentalist, @DawnSLin the analyst, and @syzmath the modeller) & co-senior Weber (computational, modeller, SynBio extraordinaire) biorxiv.org/content/10.110…

Resource: A mega-thread of various #academic #career development projects I have worked on over the years. First up, building career options into your PhD studies, written as part of #ImmunologyFutures for @ImmunolCellBiol with @lydiamakaroff twitter.com/LabListon/stat…

Flow/CyTOF users and leaders: here is an interface that allows you to see exactly where a given cell on a biaxial plot is on a corresponding UMAP. More details:

@DrSarahBoyle @CancerAustralia @CanTooRunSwim Fantastic work Sarah 👏👏 well deserved!

So very thrilled to be awarded funding from @CancerAustralia @CanTooRunSwim! This project will investigate ways to block release of chemicals from breast cancer cells that act on their immediate environment, to tackle breast cancer growth and metastasis.

Seeking experienced senior molecular biologist to lead all single cell/spatial applications running in my lab. Must be willing to learn new stuff all the time & teach students! —>Postdoc Level A or B based on experience. Email CV & Refs to luciano.martelotto@adelaide.edu.au

Excited to be part of this massive international effort, leveraging the power of artificial intelligence in small molecule discovery. @CCB_Research @UniversitySA @AtomwiseInc nature.com/articles/s4159…

Immuno-PhD/Masters/Honours students, it can be hard to decide career direction. Register for our translational immunology conference (14-17 May, Melbourne) & hear from these huge companies! It could decide the next phase of your scientific career! apvic.org

@DrSarahBoyle @UniversitySA @CCB_Research @theTiser This is fantastic Sarah, congratulations!!

Thrilled (and very pleasantly surprised) to be a finalist for the SA Woman of the Year Innovator Award! It is an incredible honour to be recognised in this cohort of amazing inspiring women. #IWD2024 @UniversitySA @CCB_Research @theTiser

@DrSarahBoyle @UniofAdelaide Well done Sarah 👏 very well deserved, congratulations!

Absolutely thrilled and surprised to receive the 2023 @UniofAdelaide Distinguished Alumni James McWha Rising Star Award. I am humbled to receive this recognition amongst many deserving young alumni. Thank you to everyone who has made this possible! adelaide.edu.au/alumni/news/li…

@Anita_Kral @BDBiosciences @ASImmunology 👏👏

Was such a privilege to present in the @BDBiosciences Science Communication Award at the @ASImmunology 2023 meeting. #ASI2023NZ #Auckland #airwaysinadish #airwaydevelopment #mucosal #phdlife

@EmanuelaPasciu1 @CMN_VIB @VIBLifeSciences @UAntwerpen Congrats Manu! So well deserved 👏👏

Thrilled to announce that I am joining @CMN_VIB @VIBLifeSciences @UAntwerpen as new GROUR LEADER!!!! A big Thank you to everyone that helped me along all these years and made possible for me to achieve this important step in my career.