Fei Chen Lab
@insitubiology
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Fei Chen's lab at @BroadInstitute and @HSCRB | Spatial and temporal genomics | Tweets by lab members | Where is Fei?
Cambridge, MA
Joined December 2021
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Pinned Tweet
As January wraps up the beginning of the new year, we took time to reflect on Chen Lab highlights from 2023…
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Buy your grad students a 3D printer, they said
It will be useful for science, they said
wondering what's the next big thing after spatial transcriptomics?
3D printed tube holders
@insitubiology
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Started at the bottom (
@broadinstitute
10th floor), now we're here (Broad 11th floor) 🚀
Celebrating the opening of our new lab space with a DIY ribbon cutting ceremony
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Excited to share two new papers, published today in
@Nature
!
Check them out here:
(1) Slide-tags, a new method to unite single-cell and spatial profiling:
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Our spatial transcriptomics DE method, C-SIDE, w/
@rafalab
+ Dylan Cable is now out in Nature Methods! Accounts for spatial mixtures of cell types to find cell type-specific DE as a function of e.g. pathology or other cell types.
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Thanks to
@naturemethods
for writing this fantastic Research Briefing on C-SIDE, our new differential expression method for spatial transcriptomics!
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Put this on your RADARS: our latest work on Reprogrammable ADAR Sensors for cell type targeting
A team effort by Chen lab members Jeremy Koob,
@dawnchenx
, & Yifan Zhang in collaboration with
@idmjky
,
@RohanKrajeski
,
@jgooten
,
@omarabudayyeh
, & AbuGoot lab
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Hello, Twitter! We're so grateful that 2021 was filled with exciting science and lab fun! For our inaugural tweet, we want to appreciate our lab members and collaborators by sharing some of their amazing work from the past 12 months
Presenting the 2021 Chen Lab Year in Review:
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RADARS out in
@NBT
! Fantastic team effort with
@jgooten
@omarabudayyeh
and our lab:
@idmjky
,
@jgkoob
,
@dawnchenx
,
@RohanKrajeski
, and Yifan Zhang with
@VerenaVolf
,
@91_naynay
, Samantha R. Sgrizzi, and
@Lukas
Villiger
. Check out the manuscript here:
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Interested in spatial transcriptomics analyses but don't know where to get started?
Check out this very practical walk-through for analyzing Slide-seqV2 data of kidney tissue by our collaborators Teia Noel,
@qbw_128
,
@AnnaGreka
, and
@JamieLMars
!
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Happy New Year from the Chen lab!
As we all get back to our experiments, we wanted to look back and share some of our lab members' amazing work from 2022:
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Did you bookmark our recent Slide-tags preprint but not get around to reading it? Very relatable
Fortunately for you, you can hear our very own
@jacksonweir4
give a talk about it at Single Cell Genomics Day tomorrow at 1:40 ET!
Interested in single cell genomics but need help getting started? Check out the full agenda for our Single Cell Genomics Day next Friday (4/7). All talks will be live-streamed (no registration required) at
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Fantastic read on single-cell multi-omics featuring
@hattaca
providing insight into inCITE-seq
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"It’s a cool tool, and there’s just a myriad of uses, and we probably haven’t thought of the coolest use of the technology yet" - stock image scientist Fei Chen
Check out the rest of the coverage of RADARS in the Globe!
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A great overview of the latest spatial genomics technologies, featuring Fei's commentary on in situ genome sequencing
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Our new method, C-SIDE, for cell type-specific DE in spatial tx:
Detects DE in diverse contexts such as space, disease, cellular interactions. Controls for cell type effects and mixing. Led by Dylan Cable and colab w/
@rafalab
@macosko
@Vignesh_Shan
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Check out HACE, our new tool for long-range, programmable mutagenesis!
We are happy to share our latest long-range, programmable mutagenesis toolbox - the Helicase-Assisted Continous Editing (HACE) system - to achieve target-specific mutagenesis of the endogenous genome. (1/11)
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(2) A comprehensive spatial atlas of the mouse brain:
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In case you missed it, check out our new method for photoselective sequencing, led by
@s_mangiameli
!
Sharing Photoselective Sequencing (PSS), a new method for genomic and epigenomic measurements within spatial regions of interest.
Thanks to the whole team
@haiqi_chen
,
@H3K4me1
,
@juliedobkin_
,
@DLesman
,
@JD_Buenrostro
, and Fei Chen.
(1/9).
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On the other hand, we're thrilled to have new faces Gio, Julie,
@dawnchenx
,
@VerenaVolf
, Mehdi, Yifan,
@Luyi_T
, Simon, Chen, &
@AndyRusss
!
Looking forward to more exciting science and lab fun in 2022! Happy New Year!
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This wouldn't be possible without two stellar teams of scientists and our ongoing collaborations with
@macosko
's group!
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It was great to be invited to talk about Slide-tags!
Slide-tags: Combining single-nucleus genomics with spatial measurements 🧬🔬
Hear from
@AndyRusss
,
@jacksonweir4
, Naeem Nadaf, and
@insitubiology
as they describe the development and application of this impressive technology
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Send us your technology papers!
Call for papers for our new special issue 'New technology applications in health and disease' guest edited by Francisco De La Vega
@ribozyme
& Fei Chen
@insitubiology
!
Deadline 8/31/22
#SingleCell
#spatialbiology
#artificialintelligence
#MachineLearning
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10. Not a paper, but possibly even more exciting: in December,
@soph_liu
was awarded an
#ImpetusGrant
with Karin Gustafsson from the Scadden lab to study immune cell aging
Thanks to
#ImpetusGrants
@MartinBJensen
@LNuzhna
for funding our project! Grateful for the support from my PI,
@insitubiology
, and excited to work alongside Karin Gustafsson in David Scadden's lab.
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Fast forward to December, we published two Nature papers, both released on the same day!
Congrats to
@AndyRusss
,
@jacksonweir4
, and
@Naeemnadaff
for Slide-tags and to Jonah and Nina for the spatial mouse brain atlas!
Excited to share two new papers, published today in
@Nature
!
Check them out here:
(1) Slide-tags, a new method to unite single-cell and spatial profiling:
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With success comes people moving on, and it was bittersweet to see
@Andrew_C_Payne
(
@E11BIO
),
@PaulReginato
(climate tech), Julia Morriss (Harvard CCB), Bob Stickels (Scale Bio), Evan Murray,
@JamieLMars
(Solid Bio), &
@haiqi_chen
(UTSW) off to new adventures
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6. In October,
@Luyi_T
outlined a vision for the future of tissues genomics in a comprehensive technology review (w/
@macosko
)
Luyi is starting his own group at Guangzhou Lab, be on the lookout for openings!
Our review on Spatial Transcriptomics is out
@NatureBiotech
! With
@insitubiology
and
@macosko
we reviewed the technology advance in sequencing and imaging-based ST and envisioned the future of tissue genomic where dynamics and perturbation measured at spatial levels.
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11. And right before the holidays, Tongtong Zhao and
@z_chiang
adapted Slide-seq beads to measure DNA and used this technique to study clonal heterogeneity in cancer (with
@JD_Buenrostro
)
Just released
@Nature
: slide-DNA-seq, our new method for spatial DNA sequencing in tissues 🧬
Excited to add a genetic dimension to the rapidly expanding spatial toolbox with the tech dev superteam of Tongtong Zhao,
@JD_Buenrostro
&
@insitubiology
(1/6)
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8. In October,
@JamieLMars
shared her work using Slide-seq to map cell neighborhoods in healthy and diseased kidneys
With Teia Noel,
@qbw_128
,
@SilvanaBazua
,
@haiqi_chen
, &
@AnnaGreka
Thrilled to share the Kidney Slide-seq pre-print . HUGE thanks to the amazing kidney slide-seq team Teia Noel,
@qbw_128
, and
@haiqi_chen
. Thanks to Evan Murray for the Slide-seq arrays,
@SilvanaBazua
, and
@AnnaGreka
, Fei Chen, and
@macosko
for mentorship!
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7. In June,
@ehshabibi
and collaborator
@DanielaJDiBella
released a single-cell atlas of mouse corticogenesis (supervised by Aviv Regev &
@ArlottaLab
)
Very excited to share my paper just out in
@NATURE
.
KUDOS to
@DanielaJDiBella
from
@ArlottaLab
, Aviv, Fei, Bob Stickels, Gabriele Scalia, and Tommasso Biancalani for the heroic effort!
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In July,
@Luyi_T
's work alongside
@AbhiSampKumar
and Adriano spatially mapping mouse organogenesis came out in Nature Genetics!
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4. In February, Dylan Cable published RCTD, a computational approach for deconvolving cell type mixtures in spatial transcriptomics data (with
@rafalab
)
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2022 brought so much new energy with our group moving into a new space and welcoming
@HuChenlei
,
@jacksonweir4
,
@sundakao
,
@SandeepKambham2
,
@benno_orr
,
@WollensakDavid
, &
@RuthRaichur
We also celebrated
@juliedobkin_
&
@Luyi_T
taking their next steps!
Started at the bottom (
@broadinstitute
10th floor), now we're here (Broad 11th floor) 🚀
Celebrating the opening of our new lab space with a DIY ribbon cutting ceremony
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In April,
@s_mangiameli
’s new method for genomic and epigenomic measurements within spatial regions of interest, Photoselective Sequencing (PSS), was published in Nature Methods!
Photoselective Sequencing is out in
@naturemethods
! This was a collaborative effort between the
@insitubiology
and
@JD_Buenrostro
labs, and I couldn't have done it without my co-authors
@haiqi_chen
,
@H3K4me1
,
@juliedobkin_
, and
@DLesman
!
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We saw the graduation of our first two Chen lab PhDs.
Dylan is completing a post-doc at Stanford and will be starting his own lab at UMichigan soon!
Sophia is now leading the Liu Lab at the Ragon Institute as an Early Independence Fellow!
The Ragon is proud to welcome our newest Early Independence Fellow, Sophia Liu (
@immunoliugy
), joining Sept 1. Her lab will focus on tools to study cell interactions for enhanced understanding of the immune system.
Welcome, Dr. Liu!
#RagonInstitute
#Immunology
#WomenInSTEM
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6. In April, collaborator Brian Cleary published Composite In Situ Imaging, a compressed sensing method for imaging transcriptomics
With Aviv Regev &
@eric_lander
+ contributions from Evan M,
@sinhanubhav
,
@ehshabibi
, &
@JamieLMars
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8. Lastly, in 2022 we started to really see the results of our work to make spatial tech more broadly accessible -- a true team effort led by Evan Murray and
@Irving_Barrera1
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Throughout the year we said goodbye to lab members as they moved on to exciting new positions:
Sarah took on a new position at Digital Biology and Hattie began as Assistant Professor at Yale to lead her own lab!
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7. A week later,
@soph_liu
brought together spatial tech and immunology with Slide-TCR-seq, a method for spatially mapping T cell receptors and transcriptomes
With Bryan Iorgulescu, Shuqiang Li, and Catherine Wu
Presenting Slide-TCR-seq: our method for measuring the transcriptomes of cells & T cell receptor (TCR) sequences in situ!
This collaboration w/ Bryan Iorgulescu, Shuqiang Li, Catherine Wu, and
@insitubiology
led to some cool findings...
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9. In November,
@haiqi_chen
released the first spatial transcriptomic atlas of mammalian spermatogenesis
Haiqi is starting his own lab
@UTSWNews
and is recruiting at all levels!
Excited to share our work published today
@CellReports
on dissecting spermatogenesis using spatial transcriptomics.
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We are very excited to have you
@jacksonweir4
!
Very excited to share I have joined the Chen Lab
@insitubiology
for my PhD! I will develop new spatial omics tools to answer pressing questions in tissue dynamics and cancer evolution! 🔬🧬
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1. We kicked off 2021 with in situ genome sequencing, a new technique for measuring DNA sequence and structure in intact samples
With
@Andrew_C_Payne
,
@z_chiang
,
@PaulReginato
,
@eboyden3
, &
@JD_Buenrostro
Introducing IN SITU GENOME SEQUENCING, a new technology to resolve DNA sequence🧬 and structure🔬
A team effort with
@Andrew_C_Payne
,
@PaulReginato
,
@eboyden3
,
@JD_Buenrostro
, and Fei Chen
This is how it works: (1/8)
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Do you use computational methods to solve important questions at the intersection of
#biology
,
#informatics
, and
#medicine
? HSCRB and
@HarvardDBMI
are jointly recruiting for a tenure-track faculty. Learn more and apply by 12/1/22.
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@Irving_Barrera1
started medical school at Harvard, Simon started graduate school in New York,
@WollensakDavid
moved to Johns Hopkins to start his PhD, Diane joined the Duke MD-PhD program, and
@anlau19
began a research position at Stanford!
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1. In January, we introduced RADARS, a new programmable way to target cells using RNA sensing
With
@idmjky
,
@jgkoob
,
@dawnchenx
,
@RohanKrajeski
, Yifan Zhang,
@jgooten
, and
@omarabudayyeh
Today we report in
@biorxiv
programmable RNA sensors that express any protein gated on specific RNAs in a cell. Much like gene sequencing necessitated gene editing tools, we answer “What is the Cas9 of single cells?” 🧵👇🏼w
@jgooten
&
@insitubiology
1/17
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3.
@hattaca
dropped inCITE-seq for jointly measuring nuclear proteins and RNA in single cells, which enables quantifying the direct or indirect effects of TFs on gene expression in vivo (supervised by Aviv Regev)
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We were also excited to welcome new scientists to the lab:
@doralidsy
and Yunhao started as post-docs,
@kevin921tw
and Nick joined as PhD students, Mehdi began as a senior computational associate,
@yupines
and DK joined as RAs, and Larissa and Matthew started as undergrads.
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To celebrate one of our most exciting years yet, we held our first lab retreat in New Hampshire. Productive brainstorming sessions were followed by home-cooked meals, team building activities, and The Chen Lab Board Game.
We can't wait to see what 2024 has in store!
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Or if you prefer,
@omarabudayyeh
's:
Today we report in
@biorxiv
programmable RNA sensors that express any protein gated on specific RNAs in a cell. Much like gene sequencing necessitated gene editing tools, we answer “What is the Cas9 of single cells?” 🧵👇🏼w
@jgooten
&
@insitubiology
1/17
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2. ExSeq was published just weeks later, combining in situ transcriptomics and expansion microscopy
With Shahar Alon,
@D_R_Goodwin
,
@sinhanubhav
, Oz Wassie,
@geochurch
,
@AdamMarblestone
, &
@eboyden3
We're excited to share that expansion sequencing (ExSeq) is finally out! ExSeq brings together expansion microscopy and a suite of in situ sequencing technologies, enabling spatially precise in situ sequencing in tissues.
/1
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3. March saw the publication of
@JamieLMars
's work on the spatial organization of kidney disease
With Teia Noel,
@qbw_128
,
@haiqi_chen
, and
@AnnaGreka
🎉 Greka lab paper alert! Our team is excited to share a new story published in
@iScience_CP
led by
@JamieLMars
describing the use of Slide-seqV2 to identify disease-specific cell neighborhoods in human and mouse kidneys.
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5. In March,
@SGRodriques
&
@linlinmc
’s work on RNA timestamps to encode the age of single molecules was released in print (with
@eboyden3
)
New paper out today in
@NatureBiotech
with Linlin Chen, Fei Chen,
@eboyden3
, and many other wonderful coauthors, demonstrating how we can encode the age of an RNA into its sequence to achieve "temporal transcriptomics"
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4. Jumping to August,
@hattaca
shared snFFPE-seq, paving the way for single nucleus RNA-seq of archival clinical samples
With Alexandre Melnikov, Cristin McCabe, and Aviv Regev
Profiling the molecular heterogeneity in diverse patients is key to precision medicine & therapeutics. But single cell methods need fresh/frozen tissues (hard to scale), while FFPE tissues are routinely collected. We share single nucleus RNA-Seq for FFPE:
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5. In September,
@s_mangiameli
introduced photoselective sequencing (PSS), which uses fluorescence imaging to make precise spatial genomic measurements (w/
@JD_Buenrostro
)
Sharing Photoselective Sequencing (PSS), a new method for genomic and epigenomic measurements within spatial regions of interest.
Thanks to the whole team
@haiqi_chen
,
@H3K4me1
,
@juliedobkin_
,
@DLesman
,
@JD_Buenrostro
, and Fei Chen.
(1/9).
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2
@dawnchenx
and
@SandeepKambham2
got exciting news about fellowships:
Dawn was awarded the AHA Predoctoral Fellowship and Sandeep was awarded an NSF GRFP!
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2. In February, Dylan Cable followed up his popular RCTD method with C-SIDE, enabling differential expression for spatial transcriptomics (w/
@rafalab
)
Our new method, C-SIDE, for cell type-specific DE in spatial tx:
Detects DE in diverse contexts such as space, disease, cellular interactions. Controls for cell type effects and mixing. Led by Dylan Cable and colab w/
@rafalab
@macosko
@Vignesh_Shan
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tweetorials on the bioRxiv from
@jgooten
@omarabudayyeh
linked here:
Genome editing owes a huge debt to genome sequencing
With efforts like
@humancellatlas
, we’re sequencing cells like mad. What is the "Cas9" of single cell?
With
@omarabudayyeh
@insitubiology
: RADARS, for programmable cell-specific sensing/expression 🧵👇
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Check out
@jgooten
's tweetorial for more details:
Genome editing owes a huge debt to genome sequencing
With efforts like
@humancellatlas
, we’re sequencing cells like mad. What is the "Cas9" of single cell?
With
@omarabudayyeh
@insitubiology
: RADARS, for programmable cell-specific sensing/expression 🧵👇
8
100
494
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The tweetorial by
@idmjky
describes our updates since our bioRxiv:
Excited to share that our latest RADARS story is finally out in Nature Biotech. Since the last arXiv, we extensively engineered our sensor and now present RADARSv2 with better safety profile and enhanced sensitivity to detect genes as low as 13 TPM.
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Here's hoping for another great year of science and lab fun in 2023!
Still in a reminiscing mood? Check out our 2021 year in review:
Hello, Twitter! We're so grateful that 2021 was filled with exciting science and lab fun! For our inaugural tweet, we want to appreciate our lab members and collaborators by sharing some of their amazing work from the past 12 months
Presenting the 2021 Chen Lab Year in Review:
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