ohai.social

Stephen Matheson🌵🌲Last talk of the <a href="https://fediscience.org/tags/CSSingleCells23" class="mention hashtag" rel="nofollow noopener" target="_blank">#CSSingleCells23</a> conference: Karin Pelka, Gladstone/UCSF <a href="https://pelkalab.org/" rel="nofollow noopener" target="_blank">https://pelkalab.org/</a>Spatially organized <a href="https://fediscience.org/tags/immune" class="mention hashtag" rel="nofollow noopener" target="_blank">#immune</a> hubs in <a href="https://fediscience.org/tags/colon" class="mention hashtag" rel="nofollow noopener" target="_blank">#colon</a> <a href="https://fediscience.org/tags/cancer" class="mention hashtag" rel="nofollow noopener" target="_blank">#cancer</a> <a href="https://fediscience.org/tags/ColonCancer" class="mention hashtag" rel="nofollow noopener" target="_blank">#ColonCancer</a> <a href="https://fediscience.org/tags/scRNAseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scRNAseq</a><a href="https://pubmed.ncbi.nlm.nih.gov/34450029/" rel="nofollow noopener" target="_blank">https://pubmed.ncbi.nlm.nih.gov/34450029/</a>Then: predict cellular interaction networks via correlations of gene program activities across <a href="https://fediscience.org/tags/tumors" class="mention hashtag" rel="nofollow noopener" target="_blank">#tumors</a>anti-tumor hubs in tumors, ISGs including CXCR3 ligands, differs between tumor types (MMR+ or -)have data from clinical trial (biopsies before and after treatment) <a href="https://pubmed.ncbi.nlm.nih.gov/36702949/" rel="nofollow noopener" target="_blank">https://pubmed.ncbi.nlm.nih.gov/36702949/</a>1/2

Stephen Matheson🌵🌲Last session of the conference! Continuing theme of "Cell identity in situ"Parker Côté, DFCI in Li Lab <a href="https://ki.mit.edu/people/clinical-investigators-research-fellows/hojun-li" rel="nofollow noopener" target="_blank">https://ki.mit.edu/people/clinical-investigators-research-fellows/hojun-li</a>The <a href="https://fediscience.org/tags/transcriptional" class="mention hashtag" rel="nofollow noopener" target="_blank">#transcriptional</a> dynamics of human <a href="https://fediscience.org/tags/hematopoiesis" class="mention hashtag" rel="nofollow noopener" target="_blank">#hematopoiesis</a> at <a href="https://fediscience.org/tags/SingleCell" class="mention hashtag" rel="nofollow noopener" target="_blank">#SingleCell</a> resolutiondo <a href="https://fediscience.org/tags/StemCells" class="mention hashtag" rel="nofollow noopener" target="_blank">#StemCells</a> and <a href="https://fediscience.org/tags/ProgenitorCells" class="mention hashtag" rel="nofollow noopener" target="_blank">#ProgenitorCells</a> in <a href="https://fediscience.org/tags/hematopoietic" class="mention hashtag" rel="nofollow noopener" target="_blank">#hematopoietic</a> system (<a href="https://fediscience.org/tags/HSPC" class="mention hashtag" rel="nofollow noopener" target="_blank">#HSPC</a>) change with age?HSPCs exist on a continuum of cell typesThey identified <a href="https://fediscience.org/tags/GeneExpression" class="mention hashtag" rel="nofollow noopener" target="_blank">#GeneExpression</a> programs active in uncommitted cells, looking across human development (fetal to aged)<a href="https://www.biorxiv.org/content/10.1101/2021.08.25.457678v1" rel="nofollow noopener" target="_blank">https://www.biorxiv.org/content/10.1101/2021.08.25.457678v1</a><a href="https://fediscience.org/tags/CSSingleCells23" class="mention hashtag" rel="nofollow noopener" target="_blank">#CSSingleCells23</a>

Stephen Matheson🌵🌲Now Siddharth Dey, UCSB <a href="https://deylab.com/" rel="nofollow noopener" target="_blank">https://deylab.com/</a>Photo-sensitive barcodes combined with topologically imposed light gradients enable spatially-resolved <a href="https://fediscience.org/tags/SingleCell" class="mention hashtag" rel="nofollow noopener" target="_blank">#SingleCell</a> <a href="https://fediscience.org/tags/transcriptomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#transcriptomics</a> and <a href="https://fediscience.org/tags/epigenomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#epigenomics</a>a new technology: scSTAMP-seq which enables use of light patterning to achieve dynamic spatial resolutionadaptation of STAMP-seqalso applying to DNA methylation <a href="https://www.biorxiv.org/content/10.1101/2023.05.06.539708v1" rel="nofollow noopener" target="_blank">https://www.biorxiv.org/content/10.1101/2023.05.06.539708v1</a><a href="https://fediscience.org/tags/CSSingleCells23" class="mention hashtag" rel="nofollow noopener" target="_blank">#CSSingleCells23</a>

Stephen Matheson🌵🌲Next is Melanie Samuel from BCM <a href="https://thesamuellab.org/" rel="nofollow noopener" target="_blank">https://thesamuellab.org/</a>Molecular regulation of <a href="https://fediscience.org/tags/immune" class="mention hashtag" rel="nofollow noopener" target="_blank">#immune</a> cell <a href="https://fediscience.org/tags/plasticity" class="mention hashtag" rel="nofollow noopener" target="_blank">#plasticity</a> and function in the <a href="https://fediscience.org/tags/brain" class="mention hashtag" rel="nofollow noopener" target="_blank">#brain</a>"Our brain is the ultimate time machine" 🙂How to target <a href="https://fediscience.org/tags/synapses" class="mention hashtag" rel="nofollow noopener" target="_blank">#synapses</a> (for intervention) while preserving them (to avoid "turning back the clock"Possibility that <a href="https://fediscience.org/tags/microglia" class="mention hashtag" rel="nofollow noopener" target="_blank">#microglia</a> could be harnessedpartnered with IMPC (impc.org) to find microglia regulators in retina one cool hit: SIRPα it's NOT involved in <a href="https://fediscience.org/tags/phagocytosis" class="mention hashtag" rel="nofollow noopener" target="_blank">#phagocytosis</a>... surprise<a href="https://fediscience.org/tags/CSSingleCells23" class="mention hashtag" rel="nofollow noopener" target="_blank">#CSSingleCells23</a>1/2

Stephen Matheson🌵🌲First speaker of the session (Cell identity in situ) is Elana Fertig of Convergence Institute at Johns Hopkins <a href="https://fertiglab.com/" rel="nofollow noopener" target="_blank">https://fertiglab.com/</a>She has background in weather prediction (!) ⛈️ which has convergence with predictive medicine (such as huge data sets)Looks at <a href="https://fediscience.org/tags/PancreaticCancer" class="mention hashtag" rel="nofollow noopener" target="_blank">#PancreaticCancer</a> with spatial <a href="https://fediscience.org/tags/proteomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#proteomics</a> now <a href="https://fediscience.org/tags/scRNAseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scRNAseq</a> Developed CoGAPS matrix factorization, can identify cell state transitionsUsing PhysiCell to build models <a href="http://physicell.org/" rel="nofollow noopener" target="_blank">http://physicell.org/</a><a href="https://fediscience.org/tags/cancer" class="mention hashtag" rel="nofollow noopener" target="_blank">#cancer</a> <a href="https://fediscience.org/tags/SingleCell" class="mention hashtag" rel="nofollow noopener" target="_blank">#SingleCell</a> <a href="https://fediscience.org/tags/CSSingleCells23" class="mention hashtag" rel="nofollow noopener" target="_blank">#CSSingleCells23</a>1/2

Stephen Matheson🌵🌲Final session of the great conference isCell identity in situ<a href="https://fediscience.org/tags/CSSingleCells23" class="mention hashtag" rel="nofollow noopener" target="_blank">#CSSingleCells23</a>

Stephen Matheson🌵🌲Judith Zaugg from EMBL <a href="https://www.embl.org/groups/zaugg/" rel="nofollow noopener" target="_blank">https://www.embl.org/groups/zaugg/</a>How do cells integrate extrinsic signals and intrinsic state? A systems <a href="https://fediscience.org/tags/epigenetics" class="mention hashtag" rel="nofollow noopener" target="_blank">#epigenetics</a> approachIndividual uniqueness (of people) -- molecular basis of <a href="https://fediscience.org/tags/variation" class="mention hashtag" rel="nofollow noopener" target="_blank">#variation</a> Needed: systems epigenetics framework signaling -- TFs -- regulatory elements -- genestools for inference & evaluation of enhancer-mediated gene regulatory networks called GRaNIE and GRaNPA 😃 <a href="https://www.embopress.org/doi/full/10.15252/msb.202311627" rel="nofollow noopener" target="_blank">https://www.embopress.org/doi/full/10.15252/msb.202311627</a>example of problem: <a href="https://www.embopress.org/doi/full/10.15252/msb.20209539" rel="nofollow noopener" target="_blank">https://www.embopress.org/doi/full/10.15252/msb.20209539</a><a href="https://fediscience.org/tags/CSSingleCells23" class="mention hashtag" rel="nofollow noopener" target="_blank">#CSSingleCells23</a> 1/2

Stephen Matheson🌵🌲Second half of the "variation and information" session <a href="https://fediscience.org/tags/CSSingleCells23" class="mention hashtag" rel="nofollow noopener" target="_blank">#CSSingleCells23</a> led off by Sam Morris of WashU <a href="http://morrislab.wustl.edu/" rel="nofollow noopener" target="_blank">http://morrislab.wustl.edu/</a>Multi-omic lineage tracing: insights into reprogramming cell identityher piece in *Development*, "The evolving concept of cell identity in the single cell era"working on "induced hepatocytes", start with fibroblasts, via "induced endoderm progenitors"new work on <a href="https://fediscience.org/tags/adipocytes" class="mention hashtag" rel="nofollow noopener" target="_blank">#adipocytes</a> <a href="https://www.biorxiv.org/content/10.1101/2023.06.01.543318v1" rel="nofollow noopener" target="_blank">https://www.biorxiv.org/content/10.1101/2023.06.01.543318v1</a><a href="https://fediscience.org/tags/reprogramming" class="mention hashtag" rel="nofollow noopener" target="_blank">#reprogramming</a> <a href="https://fediscience.org/tags/StemCells" class="mention hashtag" rel="nofollow noopener" target="_blank">#StemCells</a> <a href="https://fediscience.org/tags/CellIdentity" class="mention hashtag" rel="nofollow noopener" target="_blank">#CellIdentity</a> <a href="https://fediscience.org/tags/CellFate" class="mention hashtag" rel="nofollow noopener" target="_blank">#CellFate</a> 1/2

Stephen Matheson🌵🌲Yogesh Goyal at Northwestern Feinberg <a href="https://www.goyallab.org/" rel="nofollow noopener" target="_blank">https://www.goyallab.org/</a>Topic: Tracing rare cell plasticity and diverse fate decisions in single cancer cellsBegins with reference to (and pic of) Monod's *Chance and Necessity* <a href="https://fediscience.org/tags/CellFate" class="mention hashtag" rel="nofollow noopener" target="_blank">#CellFate</a> <a href="https://fediscience.org/tags/SingleCell" class="mention hashtag" rel="nofollow noopener" target="_blank">#SingleCell</a> <a href="https://fediscience.org/tags/CSSingleCells23" class="mention hashtag" rel="nofollow noopener" target="_blank">#CSSingleCells23</a>Emphasizing non-genetic differences between cells, something we can only see at single-cell resolutionRefers to Luria & Delbruck 1943 about bacterial resistance (to phage), relevant to cancer resistance to therapy (selected)1/2

Stephen Matheson🌵🌲Now Katie Pollard from UCSF <a href="https://docpollard.org/" rel="nofollow noopener" target="_blank">https://docpollard.org/</a>Resolving single-cell regulatory elements across species and contexts with CellWalker2lab builds <a href="https://fediscience.org/tags/statistical" class="mention hashtag" rel="nofollow noopener" target="_blank">#statistical</a> models and <a href="https://fediscience.org/tags/ComputationalBiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#ComputationalBiology</a> tools <a href="https://fediscience.org/tags/neuroscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#neuroscience</a>did microdissection then single-cell ATAC-seq developed CellWalker to solve challenges in resolving regulatory elements <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02279-1" rel="nofollow noopener" target="_blank">https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02279-1</a><a href="https://fediscience.org/tags/GeneExpression" class="mention hashtag" rel="nofollow noopener" target="_blank">#GeneExpression</a> <a href="https://fediscience.org/tags/genomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#genomics</a> <a href="https://fediscience.org/tags/SingleCell" class="mention hashtag" rel="nofollow noopener" target="_blank">#SingleCell</a> <a href="https://fediscience.org/tags/CSSingleCells23" class="mention hashtag" rel="nofollow noopener" target="_blank">#CSSingleCells23</a>1/2

Stephen Matheson🌵🌲First speaker: Jingyi Jessica Li, UCLA <a href="http://jsb.ucla.edu/" rel="nofollow noopener" target="_blank">http://jsb.ucla.edu/</a>Enhancing <a href="https://fediscience.org/tags/statistical" class="mention hashtag" rel="nofollow noopener" target="_blank">#statistical</a> rigor in single-cell data analysis using synthetic negative controls"In <a href="https://fediscience.org/tags/genomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#genomics</a>, the negative control is often not so obvious"How to choose null hypothesis? question is often "too abstract for biologists" 🤓Now discussing (infamous) problems with dubious use of t-SNEdeveloped tool called scDEED <a href="https://www.biorxiv.org/content/10.1101/2023.04.21.537839v1" rel="nofollow noopener" target="_blank">https://www.biorxiv.org/content/10.1101/2023.04.21.537839v1</a><a href="https://fediscience.org/tags/CSSingleCells23" class="mention hashtag" rel="nofollow noopener" target="_blank">#CSSingleCells23</a> <a href="https://fediscience.org/tags/ComputationalBiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#ComputationalBiology</a> <a href="https://fediscience.org/tags/statistics" class="mention hashtag" rel="nofollow noopener" target="_blank">#statistics</a>1/2

Stephen Matheson🌵🌲First session of the last day at this great conference, Conceptual power of single cell biology <a href="https://www.cell-symposia.com/conceptual-single-cells-2023/" rel="nofollow noopener" target="_blank">https://www.cell-symposia.com/conceptual-single-cells-2023/</a>The session is "Variation and information" <a href="https://fediscience.org/tags/CSSingleCells23" class="mention hashtag" rel="nofollow noopener" target="_blank">#CSSingleCells23</a><a href="https://fediscience.org/tags/BiologicalInformation" class="mention hashtag" rel="nofollow noopener" target="_blank">#BiologicalInformation</a>

Stephen Matheson🌵🌲Last speaker of the day is the keynote: Xiaowei Zhuang Harvard University <a href="https://zhuang.harvard.edu/pi.html" rel="nofollow noopener" target="_blank">https://zhuang.harvard.edu/pi.html</a>Spatially resolved <a href="https://fediscience.org/tags/SingleCell" class="mention hashtag" rel="nofollow noopener" target="_blank">#SingleCell</a> genomics and cell atlas of the <a href="https://fediscience.org/tags/brain" class="mention hashtag" rel="nofollow noopener" target="_blank">#brain</a>Explaining MERFISH, now I get it 🤓Now have adapted to <a href="https://fediscience.org/tags/epigenome" class="mention hashtag" rel="nofollow noopener" target="_blank">#epigenome</a>: <a href="https://pubmed.ncbi.nlm.nih.gov/36272405/" rel="nofollow noopener" target="_blank">https://pubmed.ncbi.nlm.nih.gov/36272405/</a>and to thick tissue: <a href="https://www.biorxiv.org/content/10.1101/2023.07.21.550124v1" rel="nofollow noopener" target="_blank">https://www.biorxiv.org/content/10.1101/2023.07.21.550124v1</a>Now discussing this epic MERFISH atlas of the whole mouse brain <a href="https://www.biorxiv.org/content/10.1101/2023.03.06.531348v1" rel="nofollow noopener" target="_blank">https://www.biorxiv.org/content/10.1101/2023.03.06.531348v1</a>use imputation to infer cell-cell interactions (several hundred cell types), cool<a href="https://fediscience.org/tags/CSSingleCells23" class="mention hashtag" rel="nofollow noopener" target="_blank">#CSSingleCells23</a>

Stephen Matheson🌵🌲Now Neda Bagheri at U of Washington <a href="https://www.bagherilab.com/" rel="nofollow noopener" target="_blank">https://www.bagherilab.com/</a>Emulating emergent spatio-temporal cell population dynamics with <a href="https://fediscience.org/tags/machinelearning" class="mention hashtag" rel="nofollow noopener" target="_blank">#machinelearning</a> algorithms remains challengingPopulation dynamics arise from autonomous <a href="https://fediscience.org/tags/SingleCell" class="mention hashtag" rel="nofollow noopener" target="_blank">#SingleCell</a> decisions e.g. in context of <a href="https://fediscience.org/tags/cancer" class="mention hashtag" rel="nofollow noopener" target="_blank">#cancer</a> progressionCreated tool called ARCADE = Agent-based Representation of Cells And Dynamic Environments <a href="https://bagherilab.com/resources.php" rel="nofollow noopener" target="_blank">https://bagherilab.com/resources.php</a>But model is computationally expensive... 1/2<a href="https://fediscience.org/tags/ComputationalBiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#ComputationalBiology</a> <a href="https://fediscience.org/tags/SystemsBiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#SystemsBiology</a> <a href="https://fediscience.org/tags/CSSingleCells23" class="mention hashtag" rel="nofollow noopener" target="_blank">#CSSingleCells23</a>

Stephen Matheson🌵🌲Rong Fan at Yale <a href="https://www.fan-lab.org/" rel="nofollow noopener" target="_blank">https://www.fan-lab.org/</a>Spatial Multi-Omics Sequencing at Cellular Level via Deterministic Barcoding in Tissuefirst slide called "2006--the ice age of single-cell biology," referring to review article by Johanna JoyceRecent great technical advance: spatial CITE-seq <a href="https://www.nature.com/articles/s41587-023-01676-0" rel="nofollow noopener" target="_blank">https://www.nature.com/articles/s41587-023-01676-0</a>and spatial ATAC-seq<a href="https://fediscience.org/tags/Transcriptomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Transcriptomics</a> <a href="https://fediscience.org/tags/Epigenetics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Epigenetics</a> <a href="https://fediscience.org/tags/CSSingleCells23" class="mention hashtag" rel="nofollow noopener" target="_blank">#CSSingleCells23</a>

Stephen Matheson🌵🌲Aviv Regev (Genentech) <a href="https://www.gene.com/scientists/our-scientists/aviv-regev" rel="nofollow noopener" target="_blank">https://www.gene.com/scientists/our-scientists/aviv-regev</a>From cell to perturbation atlasesDeciphering causal intra- and intercellular circuitsUsing Perturb-seq <a href="https://www.biorxiv.org/content/10.1101/2023.01.23.525198v1" rel="nofollow noopener" target="_blank">https://www.biorxiv.org/content/10.1101/2023.01.23.525198v1</a><a href="https://fediscience.org/tags/SystemsBiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#SystemsBiology</a> <a href="https://fediscience.org/tags/CSSingleCells23" class="mention hashtag" rel="nofollow noopener" target="_blank">#CSSingleCells23</a> <a href="https://fediscience.org/tags/GeneExpression" class="mention hashtag" rel="nofollow noopener" target="_blank">#GeneExpression</a> Now want to do multiple perturbations in one cell... do effects combine? Can do this with orig Perturb-seq, then categorize interactionsBut the space of interactions is far bigger than the number of cells (in universe)1/2

Stephen Matheson🌵🌲first speaker of this session: Leeat Keren, Weizmann Institute of Science Escalating high-dimensional imaging using combinatorial multiplexing and <a href="https://fediscience.org/tags/deeplearning" class="mention hashtag" rel="nofollow noopener" target="_blank">#deeplearning</a>Why can't combinatorial staining approaches (used with <a href="https://fediscience.org/tags/RNA" class="mention hashtag" rel="nofollow noopener" target="_blank">#RNA</a>) work with proteins? overlapping signals cause big math problemsAnd... <a href="https://fediscience.org/tags/proteins" class="mention hashtag" rel="nofollow noopener" target="_blank">#proteins</a> about 10,000X more abundant than RNAidea: use structure of biological images to constrain math solutions after combinatorial staining of proteins<a href="https://fediscience.org/tags/CSSingleCells23" class="mention hashtag" rel="nofollow noopener" target="_blank">#CSSingleCells23</a>1/2

Stephen Matheson🌵🌲Third major session at Conceptual Power of Single-Cell Biology is "Cells in context" chaired by Melanie Samuel (BCM) and Karin Pelka (Gladstone/UCSF)Very cool topics incoming<a href="https://fediscience.org/tags/CSSingleCells23" class="mention hashtag" rel="nofollow noopener" target="_blank">#CSSingleCells23</a>

Stephen Matheson🌵🌲Sophie Dumont at UCSF <a href="http://www.dumontlab.ucsf.edu/" rel="nofollow noopener" target="_blank">http://www.dumontlab.ucsf.edu/</a><a href="https://fediscience.org/tags/Chromosome" class="mention hashtag" rel="nofollow noopener" target="_blank">#Chromosome</a> size alters <a href="https://fediscience.org/tags/kinetochore" class="mention hashtag" rel="nofollow noopener" target="_blank">#kinetochore</a> attachment stability and alignment order in mammalian <a href="https://fediscience.org/tags/mitosis" class="mention hashtag" rel="nofollow noopener" target="_blank">#mitosis</a>Lab interested in <a href="https://fediscience.org/tags/SelfOrganization" class="mention hashtag" rel="nofollow noopener" target="_blank">#SelfOrganization</a> and emergent mechanics across scales.... "biological structures build themselves" using only local cues they get global information. mitotic spindle a great examplekinetochores attach, sense tension, can make mistakes which are corrected. how does this work when chromosomes vary in size?<a href="https://fediscience.org/tags/CSSingleCells23" class="mention hashtag" rel="nofollow noopener" target="_blank">#CSSingleCells23</a> 1/2

Stephen Matheson🌵🌲Polly Fordyce at Stanford <a href="http://www.fordycelab.com/" rel="nofollow noopener" target="_blank">http://www.fordycelab.com/</a>Question: How do <a href="https://fediscience.org/tags/transcription" class="mention hashtag" rel="nofollow noopener" target="_blank">#transcription</a> factors activate transcription? Outside the DNA binding domain of a TF, there are numerous disordered domains, including activation domains that interact with co-activators-- very little known about thatactivation domains are disordered, poorly conserved, and binding to co-activators is very low affinitydeveloped a <a href="https://fediscience.org/tags/microfluidic" class="mention hashtag" rel="nofollow noopener" target="_blank">#microfluidic</a> platform to measure, tech called STAMMP<a href="https://fediscience.org/tags/CSSingleCells23" class="mention hashtag" rel="nofollow noopener" target="_blank">#CSSingleCells23</a>1/2

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