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Using genomics & bioinformatics to decipher immunity @SCICambridge @Cambridge_Uni @humancellatlas
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We are excited to announce a new computational tool, drug2cell, published in
@nature
. This tool can provide insights into the precise cellular targets of drugs.
Want to know all about it? Keep reading!
#genomictool
#sangerinnovation
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Welcome on board to the journey through spacetime. In our latest
@Nature
paper we explore the cellular landscape of the gut - one of the most complex organs in the human body with its own immune and nervous systems
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We are pleased to announce Sarah Teichmann has been elected Professor in Stem Cell Medicine at the Cambridge Stem Cell Institute
@SCICambridge
. We will be moving our group to the Biomedical Campus and look forward to working together.
See:
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We are pleased to announce that our paper on CellHint was published today in
@CellCellPress
. Here, we describe this new tool and how it can harmonise single-cell data to help drive biological research.
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You can now check our COVID-19 Cell Atlas online! Great team effort to unravel the cell-specific expression of ACE2 and TMPRSS2 across human tissues
@sangerinstitute
@humancellatlas
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🎉Our Human Developing Limb Cell Atlas is now published in Nature! ✨ We've delved into the intricate world of limb cell states and architecture, uncovering new spatial patterns and regulatory codes. Here's a thread to share the journey! 👇
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Our first COVID-19 paper by the Lung Biological Network is online at Nature Medicine: SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes.
@humancellatlas
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How can single-cell atlases shed light to shared and tissue-specific features of cell types across organs?
Congrats to
@elmentaite
@CDominguezConde
@edenling3
on this review. Great teamwork!
@humancellatlas
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Happy to share our work, a comprehensive single cell & spatial atlas of the human thymus, which uses our newly established common coordinate framework for the thymus, the Cortico-Medullary Axis (CMA), to spatially explore thymic development.
#ThymusCCF
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Please check our CellTypist 2.0!
It incorporates single-cell data harmonisation & integration, aiming to assemble existing annotated single-cell datasets across the community into a uniformly annotated dataset.
#singlecell
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We are delighted to announce our spatial cell atlas of the human heart is now on bioRxiv 🫀:
This work adds new regions, modalities (spRNAseq, snATACseq) and cell types to the heart cell atlas, including the cells of the cardiac conduction system ⚡️
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We are excited to announce our preprint on the spatial cell atlas of the entire human embryonic limb💪🦵
We reveal the orchestral of genes during limb development in space and time, which also yields disease implication and mouse-human evolutionary insight
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Our latest research on genetic variants and immune response has been published in
@NatureGenet
and featured on the cover.
Explore the comprehensive insights into genetic variants on disease susceptibility at
@natsuhiku
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As our lab heads for the new home🏠, Sarah reflects on the pivotal decision she made in 2012 that reshaped our lab’s trajectory. Read the story here🌙💡
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We are delighted to share our work on a new alignment framework for single-cell transcriptomic trajectories (named Genes2Genes -- G2G), now on bioRxiv:
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Our
#LungImmuneAtlas
is online in
@SciImmunology
! We've sky-dived🪂 into the immune land🗺️ of the developing human lung, collaborating with
@drmarkonikolic
's fantastic team at UCL (
@DrJoBarnes
,
@masahiroy15
et al.). Check out the work here
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Our heart cell analysis is now online at AAP
@nature
. Teamwork makes the dream work: an amazing collaborative effort across
@teichlab
,
@HubnerLab
,
@MichelaNoseda
Lab and Seidman Lab (
@harvardmed
).
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22
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Congratulations to the one and only Chenqu Suo on successfully defending her PhD thesis! 🎉🎓
We are honoured to have you as an incredible member of the lab. Wishing you continued success in your clinical & academic journey, looking forward to collaborating with you again soon!
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Happy to share our single-cell map of the developing human intestine and connections to Crohn’s disease led by the rising star
@elmentaite
in collaboration with Alexander Ross, Matt Zilbauer and
@VallierLab
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A toast from TeichGirls to celebrate the International Day of Women and Girls in Science!
@CDominguezConde
@RBartolom
@emmamarydann
@EMadissoon
@elmentaite
@edenling3
@kedlian
@ana_cujba
@AmandaOPhD
@JulianeWeller
& Dinithi, Chenqu
#IDWGS2022
#womeninscience
#WellcomeGenomeWomen
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#MerryChristmas
with lots of love from the lab of Santas 🎅🎄🤶🔔🦌
Wish everyone a prosperous new year! 💪🎆🎓
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Here we are at the TeichLab retreat! It’s great to get together and chat with each other in this beautiful summer day. 🧑🔬👩💻🌳☕️
Sarah and Kerstin emphasised the importance of team work to achieve excellence and go far in science 💞
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Summer lab retreat was a blast! 🎉
Engaging talks, fun self-introductions into personal passions, inspiring breakout discussions, and a fantastic BBQ to wrap it up.
Please check out our new blog post for more details
#ResearchCommunity
#singlecell
#labfun
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Our new method for automated detection of putative cell types, Single-Cell Clustering Assessment Framework (SCAAF), is out! Congratulations to
@chichaumiau
for spearheading this great Sanger-EBI collaboration!
🔎Identifying cell types from single-cell
#RNAsequencing
data is now more efficient than ever, thanks to this new method from
@emblebi
and
@sangerinstitute
researchers
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The lab was celebrating lots of successes together on a sunny afternoon, including
- supportive reviewers’ comments🙌
- job offers🎆
- grants awarded🎉
Thanks to
@emmamarydann
for the delicious Italian tiramisu and Chenqu for the bubbly 🥂🍰
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Many thanks to Dr Kerstin Meyer for the wonderful years of fantastic science & collaborations!
Also a picture of the
#NextGen
of
@teichlab
members
@roserventotormo
@JamesCranley
@AmandaOPhD
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@sangerinstitute
@royalsociety
@humancellatlas
Really honoured by election to the RS that recognises the great teamwork from past & present TeichLab members & collaborators!
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We are expanding our HCA team with several positions open at the moment! Please, RT!
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@sangerinstitute
@imperialcollege
@embl
And also our paper, out in
@nature
:
A big thanks to everyone who made it possible!
@sangerinstitute
@imperial
@thebhf
@dzhk_germany
@humancellatlas
@teichlab
@NosedaLab
@kazukane
@JamesCranley
Krzysztof Polański
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Two positions for Bioinformatician & (Junior) Computational Biologist are now open to anyone with motivation and skill to translate single-cell multiomics data to next-generation therapies! 🥊
Find out more & apply by 26 Sep🗓️
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Pleased to present the preprint of our collaboration w/ the kimber lab which aims to address a vital question in musculoskeletal biology: how faithfully does the development of in vitro chondrocytes recapitulate that of their in vivo counterparts?
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We are pleased to see this go online
@biorxivpreprint
! This is a huge international collaboration exploring the cells in the adult human heart
@sangerinstitute
@MDC_Berlin
@imperialcollege
@harvardmed
@cziscience
@TheBHF
@humancellatlas
@wellcometrust
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Sarah Teichmann and Aviv Regev gave an opening talk yesterday at
#HCA2022GM
with an overview of incredible achievements accomplished by the amazing
@humancellatlas
community and looking into challenges and future opportunities.
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2
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Congrats Krzysztof Polanski
@YayonNadav
@RBartolom
@ioansarr
Chuan Xu, Nick England
@frode_jahnsen
for developping
#Bin2Cell
!!! We hope that this will be useful for the
#SpatialTranscriptomics
community to analyse
#visiumHD
data
@10xGenomics
@sangerinstitute
@czi
@SCICambridge
1/5 Looking to analyse
@10xGenomics
Visium HD datasets in Python? Check out Bin2Cell
@teichlab
! It joins 2μm spots into cells based on morphology images via nuclear segmentation and smart expansion. GitHub and Preprint:
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Congratulations to
@JamesCranley
for passing his viva at
@SCICambridge
@Cambridge_Uni
! We are incredibly proud of your achievements and excited for your future in science. Well done! Thanks to the incredible examiners Prof Ziad Mallat & Prof Nicoletta Bobola!
@sangerinstitute
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We're thrilled to announce that Rasa Elmentaite
@elmentaite
, a former TeichLab PhD student, phenomenal young scientist, has been awarded the prestigious Beddington Medal by
@TheBSDB
for her groundbreaking work in human gut development. 🧬🏅
Read more:
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#throwback
from last Friday's lab retreat.
Punting on a beautiful summer day is the best.
#Cambridge
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🎄✨A glimpse into our festive Christmas lunch 🍽️ - a time for great food, laughter, and shared moments. 🎅 Wishing everyone a rejuvenating break this holiday season. Remember to take proper time off, relax, and soak in the joy of the festivities! 🌟 🎁🥳
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Excited about the spatial transcriptomics session at the UK Conference of Bioinformatics and Computational Biology on 29 Sep.
Sarah will chair the session and
@CataVallejosM
@Mohlotf
@emmamarydann
will present their recent awesome work on new methods for biological data analysis.
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Embarking on a remarkable journey into the human heart! Discover the groundbreaking research and the stories of the dream team.
@JamesCranley
@kazukane
@NosedaMichela
#Science
#Innovation
#HeartHealth
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Excited to have contributed to this impressive integrated human lung cell atlas, such a great resource for the community!
Together with our multi-omic spatial atlas , we are really heading towards a comprehensive map of the human lungs 🫁🗺️
Excited to share our integrated Human Lung Cell Atlas - combining 46 datasets of the human respiratory system, we map >2.2m cells from 444 individuals across health&disease. Led by
@SikkemaLisa
, with
@MC_Nawijn
@Misharin_lab
@MDLuecken
& many others, thx!
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Congrats to Dr Sid Lawrence for completing his PhD viva ⭐️! Well done!!! Thanks to the amazing examiners Professor Sarah Snelling
@Sarah_JB_S
@ndorms
and Professor Stephen McDonnell
@steveskneesCAM
@eoeortho
@CambridgeOrtho1
@sangerinstitute
@SCICambridge
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From School Science Club to Cell Atlasing With Dr. Sarah Teichmann | Technology Networks
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Fantastic experience & amazing illustration!
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Check out the latest episode of the NightScience podcast where Sarah joined
@ItaiYanai
and
@MartinJLercher
to discuss creativity in science
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@sangerinstitute
@imperialcollege
@embl
Where can you learn all about it? Check our technology page on the
@sangerinstitute
website, with additional information on our tool
#academictwitter
#bioinformatics
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Thrilled to be funded and be part of this cohort!
We’re excited to announce 20 new Data Insights grantees addressing challenges in
#SingleCell
biology by:
🔹Integrating data sets to understand cell functions that regulate health + disease
🔹Applying
#ML
methods to the analysis of complex data sets
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Check out this piece by
@roserventotormo
on why CellPhoneDB, a friendly open-source platform, is good for data sharing and collaborations
@WellcomeOpenRes
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9
25
Big congrats to Menna
@ClatworthyLab
🎉🎉🎉
Delighted to announce the appointment of Menna Clatworthy as Director of
#CITIID
Menna is Professor of Translational Immunology based at
@MRC_LMB
. She is also Fellow & Director of Clinical Studies
@pembroke1347
and Faculty Associate
@sangerinstitute
@Cambridge_Uni
|
@MedCambridge
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Preprint alert📣
New method quantifying genome-wide transcription factor binding affinities to investigate how the epigenome influences concentration-dependent TF binding!
Fruitful collab between our
@RLindeboom
and
@HNeikes
at the
@LabVermeulen
.
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Our recent work with
@kevinmbyrd
and
@blakewarner0
shows that salivary gland cells can be infected with SARS-CoV-2. Fantastic kick-start of the Oral & Craniofacial Biological Network from the
@humancellatlas
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Shout out to Luz
@LuzGarAl
and Roser's group
@roserventotormo
for the amazing single-cell and spatial analysis of the human endometrium, which cycles as life blooms through the seasons🌺
Cell types enriched in endometrial cancers and endometriosis also shed light for treatments.
Read our December issue! Single-cell analysis of the endometrium, plasma proteome genetics, rare ALS variants and more!
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4
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We are looking for an enthusiastic and skilled bioinformatician to contribute to cell atlasing research in the lab. Please apply by 16 Jan 🧑💻⏰
Thanks for retweeting!
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New work from the Lung HCA Biological Network: Key nasal cells identified as likely entry points for the new coronavirus.
@humancellatlas
#COVID19
#covid
ー19uk
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It was a pleasure to host Prof Mark Davis from
@StanfordMed
for a lecture
@Cambridge_Uni
@SCICambridge
!
Standing room only this morning to hear Professor Mark Davis' (
@StanfordMed
) talk for the Cambridge Immunology and Medicine Seminar Series in collaboration with Cambridge Stem Cell Institute.
Huge thanks to
@teichlab
for hosting!
@Cambridgeimmuno
|
@SCICambridge
|
@Cambridge_Uni
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1
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First seminar hosted by teichlab
@SCICambridge
@Cambridge_Uni
by Prof Jasmin Fisher
@ucl
on
#DigitalTwins
for
#cancerresearch
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Teichmann Lab members will run in Cambridge’s Chariots of Fire charity race next Sunday on 18th September!
Our runners for this year are Sarah 🏃♀️
James
@JamesCranley
🏃
Kazumasa
@Kazukane
🏃
Veronika
@kedlian
🏃♀️
Bidossessi
@BidossessiH
🏃
(photo from last year's marathon)
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I pledge to oppose racism and hate through active allyship, continuous unlearning, learning, and listening. Join me by nominating 5 others to do the same.
#BlackLivesMatter
👊🏿👊🏽👊🏻and I nominate
@Muzz_Haniffa
@bayraktar_lab
@wikiselev
@MarioniLab
@fabian_theis
I pledge to oppose racism and hate through active allyship, continuous unlearning, learning, and listening. Join me by nominating 5 others to do the same.
#BlackLivesMatter
👊🏿👊🏽👊🏻and I nominate
@marakat
@GosiaTrynka
@teichlab
@roserventotormo
@minouye271
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Great teamwork from Raghd,
@danieljkunz
and Tzachi in our lab in collaboration with
@davisjmcc
,
@YuanhuaHuang
,
@OliverStegle
From
@davisjmcc
,
@YuanhuaHuang
,
@OliverStegle
and Teichmann lab: Cardelino leverages variant information from single-cell RNA-seq data for inferring clonal tree configuration and mapping cells to their clone of origin.
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The HCA white paper v1.0 was first published in 2017
The exciting v2.0 will come out later this year!
Stay tuned 📢
Sarah Teichmann and Aviv Regev gave an opening talk yesterday at
#HCA2022GM
with an overview of incredible achievements accomplished by the amazing
@humancellatlas
community and looking into challenges and future opportunities.
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0
2
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Great turnout at the Hinxton Immunogenomics Day, organised by Wanseon Lee
@WanseonL
,
@AniaLorenc
and our own Lisa Dratva, around all things
#TCR
#MHC
!
@sangerinstitute
@LoKretschmer
@ioansarr
@SCICambridge
0
2
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Delighted about the newest contribution to the Human Cell Atlas of the esophagus, which reveals the origin and developmental pathway of esophageal adenocarcinoma. Great collaboration with
@RFitzgerald_lab
@MarioniLab
We are very excited to share our new paper published in Science today about the origin of pre-cancerous Barrett's esophagus (BE). Here is a story of how we found out that stomach cells can lead to cancer in the esophagus (1/9)
@doctor_kno
@johnlzhuang
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📢📢 Job alert! Cellular Genetics Informatics Team Leader - call open until September 12th
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Delighted to share our latest preprint in which we temporally resolve the immune response to COVID-19 using a unique human challenge model.
Preprint alert! Excited and proud to share our work in which we applied single cell multi-omics on a unique-in-the-world SARS-CoV-2 challenge model to resolve the local and systemic immune response to an exact dose of virions in humans over time. (1/6)
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@sangerinstitute
@imperialcollege
Our tool takes pairs of drugs and their target molecules from drug databases such as
@EMBL
-EBI’s ChEMBL database. It leverages single-cell profiles and the database’s 19 M drug-target interactions.
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We also developed a single-cell analysis tool for drug target analysis called drug2cell () which utilises the ChEMBL database ().
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Congratulations to Cecilia on her PI position at the Human Technopole! The whole TeichLab is delighted and incredibly proud, and wishes her all the best for the next chapter of her scientific adventure! 🌟
📢 📢 It's a great pleasure to announce that I will be opening my lab in June 2022
@HumanTechnopole
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The Teichmann Lab is looking for an enthusiastic (senior) staff scientist who is experienced in NGS experiments. Apply by 10 Jan, 2022 at
Please retweet💪
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Join us at the beautiful Wellcome Genome Campus this summer to meet other single-cell folks, to learn about the incredible advances in the field, and share your science with the community!
📢 Registration open for Single Cell Biology 2022!
#SCB22
Join international
#biologists
to explore the impact of the technological revolution on our understanding of biology at
#SingleCell
resolution.
📩Abstracts due 5 April
🌐
🌍Hinxton or Virtual
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The 25th Human Genome Meeting will take place in Tel Aviv on the May 23-25, 2022 - Save the date!
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By inducing antiviral responses in human fibroblasts, we obtained genetic variations at single-cell resolution and identified 1275 eQTLs, many colocalizing with susceptibility GWAS loci of infectious and autoimmune diseases, e.g. COVID-19 at OAS1.
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If you want to get to know more about the personal and professional life of our very own Sarah Teichmann, check out this great interview by the Sanger Comms Team
#WomenInSTEM
#HumanCellAtlas
From a teenage author 📙 to aiming to map every cell in the human body🧍Sarah Teichmann has had an inspirational career so far.
Read about our Head of Cellular Genetics on our blog ⬇️
#WomenInSTEM
#HumanCellAtlas
@teichlab
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Our study on severe
#COVID19
in end stage kidney disease patients with matched pre-pandemic samples from a broad cohort of 61 individuals is on medRxiv!
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Job Alert! Call for Principal Bioinformatician - application open until the 18th of May
0
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An awesome collaboration with
@teichlab
@mirjana_e
@Muzz_Haniffa
! Single-Cell RNA Sequencing Reveals a Dynamic Stromal Niche That Supports Tumor Growth
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A huge shoutout to our collaborator labs for their invaluable contributions! 🙌 Special thanks to Barbara Wold's lab,
@bayraktar_lab
,
@AlainChedotal
's lab,
@MarioniLab
,
@MekaylaStorer
, and countless others who played a crucial role in this groundbreaking work.
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@Mona_Litvinuk
and
@cartalop
from the lab have led this fantastic effort to fine map 500k cells across heart regions. You can explore the dataset at Great team!
@MDC_Berlin
@Imperial
@harvardmed
@sangerinstitute
@humancellatlas
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The deadline is next week. We are looking forward to meeting you and creating a fruitful 2022 together!
Please help spread the news! 🎉
The Teichmann Lab is looking for an enthusiastic (senior) staff scientist who is experienced in NGS experiments. Apply by 10 Jan, 2022 at
Please retweet💪
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Drug2cell allows us to make mechanistic inferences, including drugs’ side effects such as those impacting heart rate ❤️. It stems from a collaboration from
@Sangerinstitute
@imperialcollege
and others.
1
1
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Please join us at the
@humancellatlas
General Meeting! Register here:
@sangerinstitute
@SCICambridge
@Cambridge_Uni
Join me in Milan on 29-30 September for the 2024 Human Cell Atlas General Meeting! Hear about our scientific progress and help plan future annotation, querying, and spatial omics activities. Early bird registration<> rate runs until the end of June.
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We co-detected these transcripts in specific respiratory, corneal and intestinal epithelial cells, potentially explaining the high efficiency of SARS-CoV-2 transmission. (2/4)
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Thanks to the
@CZI
,
@wellcometrust
@humancellatlas
,
@BHF
we have mapped half a million cardiac cells from six regions and 14 donors, and our study provides better understanding of cardiac function at the single cell level.
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ntroducing GASPACHO: Our novel tool to infer the trajectory of gene expression over a dynamic process, and to model nonlinear dynamic genetic effects in every individual cell.
You can find and apply it at
#Genomics
#SingleCell
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@sangerinstitute
@imperialcollege
@embl
How does it work?
Drugs & target molecules can be queried and filtered based on:
⏺️Activity of drug-target interaction
💊Drug categories
🩺Clinical trial phase
🧫Classes of molecular targets.
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We hope you enjoy your trip and lose track of time browsing the maps at
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Here the link to the HCA and the cited study by Sungnak et al
BBC News - Coronavirus: Why hasn't the UK listed loss of smell as a symptom of Covid-19? . Misses the key point that anosmia suggests nasal infection which the recent Sanger Cell Atlas analysis suggests may be the most infectious stage for transmission!!
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3 senior positions at Transition Bio.
📍Cambridge UK, Cambridge Boston.
🙋♀️Machine Learning Scientist (drug discovery)
🙋Machine Learning Scientist (genomics)
🙋♂️Computational Systems Biologist
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From sleepless nights at a career crossroads during pregnancy to charting new research directions and consolidating the lab culture, this journey defines our group. (For those who missed the earlier news 👉🏻)
We are pleased to announce Sarah Teichmann has been elected Professor in Stem Cell Medicine at the Cambridge Stem Cell Institute
@SCICambridge
. We will be moving our group to the Biomedical Campus and look forward to working together.
See:
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6⃣We would like to thank all those involved in this project from
@sangerinstitute
,
@OfficialUoM
,
@CambridgeOrtho1
,
@Cambridge_Uni
, and
@humancellatlas
.
#Research
#ChondrocyteDevelopment
#RegenerativeMedicine
#ScienceTwitter
#SingleCellRNASeq
#TissueEngineering
#CartilageDevAtlas
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@Muzz_Haniffa
@nat_lebot
@PatrickGoymer
@run_for_heroes
@LCVenema
@josh_brickman
@npariente
@BerginEnda
@GentekRebecca
@SimSci9
@emilyxsx
@gary_d_reynolds
Challenge accepted and done!🏃♀️Nominating
@Zeziliaconzeta
@KylieReneeJames
@PengHeCambridge
Kerstin Meyer & Sarah Aldridge!
@run_for_heroes
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Please support our team in raising money for the Arthur Rank Hospice Charity, which will provide end-of-life support for free to those in need. Please donate at
@ArthurRankHouse
@chariots_fire
@AcademicChatter
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The study offers a useful resource for further lines of inquiry with valuable clinical samples from COVID-19 patients and we provide our data in a comprehensive, open and user-friendly fashion at (4/4)
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@sangerinstitute
@imperialcollege
@embl
Once the drug scores are calculated, you can then find cells which are targeted by drugs of interest or find drugs💊 which target cells of interest, such as heart pacemaker cells in the published paper.
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Toast to
@PengHeCam
, Sid, and Bao and Shuaiyu from
@ZHANGLAB
for this fabulous work!
We also want to acknowledge valuable contributions from labs of Roger Barker,
@MekaylaStorer
, and Barbara Wold, and all other co-authors 👩💻🧑🔬
#singlecell
#ScienceTwitter
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First and foremost, we want to thank our captains
@elmentaite
and
@KylieReneeJames
for steering the ship and brilliant scientists on board
@Muzz_Haniffa
,
@ClatworthyLab
, Matthias Zilbauer, Holm Uhlig,
@KSaebParsy
, Roger Barker,
@bayraktar_lab
,
@MarioniLab
and their amazing teams.
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Sign up to this virtual conference for a bargain price of GBP 50 at .
#UKCBCB
@EarlhamInst
Excited about the spatial transcriptomics session at the UK Conference of Bioinformatics and Computational Biology on 29 Sep.
Sarah will chair the session and
@CataVallejosM
@Mohlotf
@emmamarydann
will present their recent awesome work on new methods for biological data analysis.
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