Now Siddharth Dey, UCSB
https://deylab.com/

Photo-sensitive barcodes combined with topologically imposed light gradients enable spatially-resolved #SingleCell #transcriptomics and #epigenomics

a new technology: scSTAMP-seq which enables use of light patterning to achieve dynamic spatial resolution

adaptation of STAMP-seq

also applying to DNA methylation
https://www.biorxiv.org/content/10.1101/2023.05.06.539708v1

#CSSingleCells23

First speaker of the session (Cell identity in situ)
is Elana Fertig
of Convergence Institute at Johns Hopkins
https://fertiglab.com/

She has background in weather prediction (!) ⛈️ which has convergence with predictive medicine (such as huge data sets)

Looks at #PancreaticCancer with spatial #proteomics
now #scRNAseq

Developed CoGAPS matrix factorization, can identify cell state transitions

Using PhysiCell to build models
http://physicell.org/

#cancer
#SingleCell
#CSSingleCells23

1/2

Next is Qiong Yang of U Michigan
http://www-personal.umich.edu/~qiongy/

Hashtagged title: Using #SingleCell #SyntheticBiology to Unravel the Mechanisms of Biological Timing and #PatternFormation

Looking at network motifs for biological clocks, working in #Xenopus, building a synthetic cell (cool!)

what makes a tunable biological oscillator?
https://www.biorxiv.org/content/10.1101/2021.05.10.442602v1

can slow down clock (in model system) by knockdown of cyclin B

#ComputationalBiology
@CSSingleCells23

Yogesh Goyal at Northwestern Feinberg
https://www.goyallab.org/

Topic:
Tracing rare cell plasticity and diverse fate decisions in single cancer cells

Begins with reference to (and pic of) Monod's *Chance and Necessity*
#CellFate
#SingleCell
#CSSingleCells23

Emphasizing non-genetic differences between cells, something we can only see at single-cell resolution

Refers to Luria & Delbruck 1943 about bacterial resistance (to phage), relevant to cancer resistance to therapy (selected)

1/2

Now Katie Pollard from UCSF
https://docpollard.org/

Resolving single-cell regulatory elements across species and contexts with CellWalker2

lab builds #statistical models and #ComputationalBiology tools
#neuroscience

did microdissection then single-cell ATAC-seq
developed CellWalker to solve challenges in resolving regulatory elements
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02279-1

#GeneExpression
#genomics
#SingleCell
#CSSingleCells23

1/2

Last speaker of the day is the keynote:
Xiaowei Zhuang
Harvard University
https://zhuang.harvard.edu/pi.html

Spatially resolved #SingleCell genomics and cell atlas of the #brain

Explaining MERFISH, now I get it 🤓

Now have adapted to #epigenome: https://pubmed.ncbi.nlm.nih.gov/36272405/

and to thick tissue:
https://www.biorxiv.org/content/10.1101/2023.07.21.550124v1

Now discussing this epic MERFISH atlas of the whole mouse brain
https://www.biorxiv.org/content/10.1101/2023.03.06.531348v1

use imputation to infer cell-cell interactions (several hundred cell types), cool

#CSSingleCells23

Exciting next talk:

Bosiljka Tasic, Allen Institute for Brain Science
https://alleninstitute.org/person/bosiljka-tasic/

Cell types of adult mouse #brain: definition and experimental access

Giant amazing atlas
https://www.biorxiv.org/content/10.1101/2023.03.06.531121v1

brand new tool:
ABC (Allen Brian Cell) atlas https://community.brain-map.org/t/introducing-the-allen-brain-cell-atlas/2444

Building enhancer virus tools, screening and validating them

and building Brain Knowledge Platform
https://community.brain-map.org/c/how-to/brain-knowledge-platform/16

#SingleCell
#Neuroscience

Now Neda Bagheri at U of Washington
https://www.bagherilab.com/

Emulating emergent spatio-temporal cell population dynamics with #machinelearning algorithms remains challenging

Population dynamics arise from autonomous #SingleCell decisions
e.g. in context of #cancer progression

Created tool called ARCADE = Agent-based Representation of Cells And Dynamic Environments
https://bagherilab.com/resources.php

But model is computationally expensive...
1/2

#ComputationalBiology
#SystemsBiology
#CSSingleCells23

Second half of morning session on Emerging concepts in gene regulation** **kicks off with

Songpeng Zu, UCSD
https://beyondpie.github.io/

Comprehensive single-cell analysis of chromatin accessibility in the adult mouse #brain

117 dissections (!) across whole mouse brain, using SnapATAC2

Putting data on CATlas (catlas.org)

https://www.biorxiv.org/content/10.1101/2023.04.16.536509v1

#SingleCell
#chromatin
#epigenomics
#neuroscience
#CSSingleCells23

Now Aki Minoda, Radboud University, The Netherlands
https://www.ru.nl/en/departments/radboud-institute-for-molecular-life-sciences-fnwi-deel/cell-biology
talking about
the Mukin Mouse Ageing Atlas
(mukin means #germ-free in Japanese)

#SingleCell from tissues sampled at 2 and 19 months in mice, then #omics including #lipidomics

Looking at influence of #microbiota on changes in #aging e.g. expansion of #immune cell types, aka #inflammaging

#CSSingleCells23

Lacramioara Bintu of Stanford
https://bintulab.com/

#SingleCell dynamics of gene silencing, epigenetic memory, and #chromatin organization

silencing & reactivation of expression all-or-none via #histonemethylation

3 states: active, reversible silent, irreversible silent

chromatin regulators move proportion of cells in OFF state

KRAB can "remember" duration of signal, makes heterochromatin, which can spread spatially

Want to see chromatin state in single cells

#CSSinglecells23

1/2

Susanne Rafelski
is Deputy Director of Allen Institute for Cell Science
https://alleninstitute.org/person/susanne-rafelski/

"Integrated intracellular organization and its variations in human iPS cells"

How we can "know" a cell... observables:
molecular census (omics)
environment
organization
behavior

use #human #hiPSC as model

https://alleninstitute.org/news/the-interior-design-of-our-cells-2/

#SingleCell #imaging #CSSingleCells23 #OpenScience

Yannik Severin at ETH Zurich
https://imsb.ethz.ch/research/snijder_group/people/yannik_severin.html
now speaking on
"Multiplexed high-throughput immune cell imaging reveals molecular health-associated phenotypes"

Seeking to be able to screen #immunecells for responses to drugs
#singlecell resolution, to see morphology, subcellular

developed #multiplexed #PBMC characterization, trained #CNN -- as in #NeuralNetwork
https://www.science.org/doi/10.1126/sciadv.abn5631

#CSSingleCells23

Rosalind Xu is up!
From Moffitt lab at Harvard Med and Children's Hospital
https://moffittlab.github.io/people.html

"A single-cell spatial atlas of the mouse gut reveals spatial- and microbiota-dependent sensation"

Using MERFISH which was developed for brain, so she had to develop protocol that works in gut

#SingleCell
#CSSingleCells23
#microbiota
#intestinal
#Transcriptomics

Now Golnaz Vahedi from UPenn
https://vahedilab.com/
speaking on
"Modeling Type 1 #Diabetes progression from single-cell #transcriptomic measurements in #human #islets

Vision is to do #SingleCell profiling of #pancreatic cells and peripheral blood, simultaneously, to identify patients who can benefit from early interventions

https://www.nature.com/articles/s42255-022-00531-x

#CSSingleCells23

Lacramioara Bintu from Stanford introducing the first speaker of the conference! She is Prisca Liberali from FMI in Basel, joining us virtually.

"Decoding the design principles of tissue organization"

Model system is intestinal #organoids
#selforganization

#CSSingleCells23

One #stemcell can generate an entire, organized, organoid

#multiplexed #SingleCell analysis of organoids, using to understand #regeneration after intestinal damage

A screen with 400K organoids and 3000 compounds!

1/2

I'm excited to be at my first conference since I joined @PLOS last year:

The Conceptual Power of Single-Cell Biology

Fun fact: my friend and colleague Quincey Justman and I conceived of this conference when we were both at Cell Press, sometime in 2018.

I'll be tooting as often as I can, at #CSSingleCells23. Hope to attract some others to toot instead of using the MAGA plutocrat's toy.

#SingleCell
#genomics
#Transcriptomics
#CellAtlas
#CSSingleCells23

https://www.cell-symposia.com/conceptual-single-cells-2023/

@pastelbio I guess the HP D100 would fall under FACS, right? Seems like a no brainer for me, but I am definitely partial to cheap things with consumables (side-eye looking at you MS).

(HT @proteomicsnews)

(and is the D300e literally an old ink jet from the 2000s?!)

#SingleCell #Proteomics

Split a #BAM file produced by #CellRanger into one file per #singlecell barcode, using #samtools and #awk:

samtools view in.bam | awk '/CB:Z:/{f=substr($0,match($0,/CB:Z:[ACGT]{16}/)+5,16)".txt"}{print>>f}'

A new study in #PLOSBiology presents a #SingleCell atlas of human neonatal and necrotizing enterocolitis-affected small #intestine, revealing disease-related cellular dysregulation and identifying new therapeutic targets for future studies.
https://plos.io/3Ww8xgc