Julio Saez-Rodriguez
@JulioSaezRod
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Computational Biologist, Head of research @emblebi , part-time @UniHeidelberg , codirector @DR_E_A_M challenges. Low-activity account, mostly retweets @saezlab
Heidelberg, Germany
Joined March 2011
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first
@ERC_Research
funding after 7 applications and 5 interviews❗ so, if you did not get it, don’t give up! And, if you can, get as awesome partners as
@giacomello_lab
@ejvillablanca
@ZellerGroup
😄 Very thankful to them, many
@saezlab
members & all others that helped us🙏
Thx
@ERC_Research
for funding our
#ERCSyG
project w
@ejvillablanca
@ZellerGroup
@giacomello_lab
🙏. Looking fwd to synergizing our expertise in immunology,
#spatial
techs, microbiome🦠 & computational modeling💻 to study gut host-microbiome interactions in health & disease
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Excited to be (back)
@emblebi
- now as Head of Research. I very much look fwd to helping nurture research (leveraging its trove of resources
#services
+ unique possibilities within
@EMBL
) + support
@emblebi
as a whole as part of its Senior Management Team (congrats
@jomcentyre
!)
Today we announce some changes in EMBL-EBI’s Senior Management Team, which will strengthen the institute’s research efforts and service delivery 👇
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We will be looking for new group leaders, with focus on (AI) methods, and especially young scientists. We evaluate by potential not just your current track record - great place to start a lab (speaking from experience!) - contact if interested, & please RT
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Do you want to pursue your ideas in computational biology independently, running your group in
@embl
‘s uniquely collaborative environment, next to world’s most comprehensive molecular data resources + with top-notch infrastructure
@emblebi
? Apply to join us & pls RT
Apply as a research group leader! Lead an independent research group in computational biology, focusing on AI-biology interfaces. Enjoy core support and outstanding infrastructure. Explore EMBL's Molecules to Ecosystems vision, and more!
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After a great
@ASBMB
meeting
@broadinstitute
and catching with many colleagues, I look forward to going back to
@harvardmed
and present at LSP 👇
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Join us in the European Society for Spatial Biology
@SpatialBio
& its 1st conference in Berlin 12-13 Dec 2024. Thanks to co-founders
@Lab_NieHau
@ChrisSchuerch
@leeat_keren
@HRazaAliLab
@SinemKSaka1
& specially
@DenisSchapiro
for making it happen
European Society for Spatial Biology (ESSB) is here, finally! ESSB is a recently founded scientific society dedicated to advancing research in the emerging interdisciplinary field of spatial biology. This is the perfect spot for spatial enthusiasts! Come join us!
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Happy to join great colleagues in the Advisory Editorial Board of
@MolSystBiol
and support a key journal for
#systemsBiology
A warm welcome to our new Advisory Editorial Board members, we are looking forward to working with you! 🎉
And... a good occasion to thank our entire AEB for their support!
#SysBio
#SystemsBiology
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What a nice surprise to meet
@RongFan8
+ really enjoyed catching up with old colleagues & friends + meeting new
@sangerinstitute
@emblebi
@CRUK_CI
@RArgelaguet
@ReikLab
@MariaPAlcolea
Pau Creixell
@ClatworthyLab
Janet Thornton
@imartincorena
@juan_vizcaino
@Garnettlab
1/2
First day at
@sangerinstitute
in Omer's lab
@bayraktar_lab
. See who I ran into during the coffee time ☺️
@JulioSaezRod
@roserventotormo
. Also, very much enjoyed the impressive talk by
@JulioSaezRod
!
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Thanks
@mo_lotfollahi
for organizing this important and timely hackathon and for having me sharing our experience in benchmarking in
@saezlab
and
@DR_E_A_M
It was pleasure to have
@JulioSaezRod
from
@emblebi
as invited speaker at our foundation model hackathon discussing the importance of benchmarking and community efforts to evaluate models
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Join our faculty: - our 9-year tenure nurtures our group leaders to go on to do great things:
@VirginieUhlmann
@MoritzGerstung
@OliverStegle
@MarioniLab
@teichlab
@pedrobeltrao
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Great to reconnect with the
@OpenTargets
community and discuss how to use single-cell and spatial technologies for target discovery
Thank you to everyone who attended and presented at yesterday's Integration Day — a chance to dive deeper into current and potential future work in single cell sequencing 🧪🧬
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Congrats
@DanielBDimitrov
I am very proud & was great to work with you these years + see you grow - looking forward to the things you will do in the future 🥳
Last week I successfully defended my PhD.
I am super thankful to everyone involved, specifically my kind and welcoming friends/colleagues (
@saezlab
), my family, and
@JulioSaezRod
🙏
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Join us for these exciting projects using Large Language Models and knowledge graphs, building on , within
@OpenTargets
led by
@slobentanzer
Postdoc positions 3 and 4 of our project with Open Targets have opened! If you are passionate for open-source data engineering using Large Language Models, and you like working in a world-leading professional environment, please check them out at
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Look forward to participating in the EMBO|FEBS Lecture Course Cancer systems biology: Promises of artificial intelligence organized by
@institut_curie
September 28- October 2 - application deadline 20 August
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tomorrow finishes my association with
@emblebi
(5 yrs group leader, 3 visiting group leader) - very grateful for the great time, the support, fantastic atmosphere, and all I have learned that I take with me
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I really enjoyed writing with my old friend
@jeriscience
this perspective about
@DR_E_A_M
challenges in the last 10 years, with big thanks to all co-organizers and participants - here 🍾 for what we will learn in the next 10 years
Our
@JulioSaezRod
wrote with
@jeriscience
a summary of the lessons learned in > 10-years of crowdsourcing benchmarks for systems biology as
@DR_E_A_M
challenges and discussed possible future directions
for the 5th anniversary of
@CellSystemsCP
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@slavov_n
We have combined + benchmarked databases of human regulons in DOROTHEA: - There are many other great resources, some listed in this thread, that we keep evaluating/integrating
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If you are interested in microfluidic-based combinatorial screenings, check out this paper from Christoph Merten lab
@EMBL
@EPFL_en
w. contributions from our
@deeeenes
@NadineTuechler
Olga Ivanova - congrats to all involved!
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I retain a part-time position at
@UniHeidelberg
, and
@saezlab
will largely remain there, while developing within
@emblebi
, where I also look forward to reconnecting with colleagues & making new ones
@sangerinstitute
@Cambridge_Uni
& beyond
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Looking forward to participating in this exciting meeting, will discuss our recent & ongoing work comparing cell-cell communication methods for scRNA , and our approaches to analyze spatial transcriptomics
Registrations are now open for the Perth chapter of
#ozSingleCell
2021. Online and in person
Awesome speakers
@JulioSaezRod
@MiriamMerad
@FGinhoux
@dralexswarbrick
@armish1910
@weitao_lin
@rodcarlessi
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Thanks
@EMBL
@emblebi
and selection panel for the trust,
@UniHeidelberg
@uniklinik_hd
for facilitating this step while keeping activities there &
@saezlab
for amazing support🙏
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Come to BioQuant
@UniHeidelberg
(or zoom) 29.10 to hear and talk about using AI in the life sciences and medicine
@ellislifehd
- Great international and local speakers 👇
ELLIS Life Annual Symposium 2021 - only 2 weeks left! Don't miss our keynote talks by Max Welling
@wellingmax
and Barbara Engelhardt
@BeEngelhardt
.
Registration:
About us:
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Additional benchmarking challenges are needed, including both simulations, and experimental data. For the same reason we are happy to openly cooperate with interested groups to find better gold standards for different scenarios (e.g. single-cell data). Feel free to contact us! :D
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@DenisSchapiro
@UniHeidelberg
Welcome
@DenisSchapiro
! We are excited to have you with us in the Institute of Computational Biomedicine
@uniklinik_hd
@UniHeidelberg
and thankful to
@HiGHmed_MI
for the support - we look forward to working together
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Thankful for being invited to help with this initiative to improve Peer Review
Want to find out what
@ReviewCommons
is all about? Then check out these two editorials
@EMBOPress
@ASAPbio_
#peerreview
#scholarlypublishing
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Look forward to presenting
@TheSFPM
a community whose mission fully resonates with me - & especially along
@VPrasadMDMPH
whose great work has been an eye-opener for me
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We particularly welcome groups with a focus on (AI) methods, especially young female scientists. We evaluate by potential not just your current track record - a great place to start a lab - speaking from experience
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Look forward to hosting
@jeanphi_vert
17.11 11AM CET in our
@ellislifehd
seminar - join us to learn about his work on machine learning for single-cells omics 👇
Join the next ELLIS Life / NCT Data Science seminar for an exciting talk by Jean-Philippe Vert on Nov 17 at 11:00 AM CET
@jeanphi_vert
@DataScienceDKFZ
@JulioSaezRod
Meeting link:
ELLIS Life:
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Congrats
@_ms03
and thanks for the hard work you put on building PROGENy's 'footprint' pathway signatures - we keep using it extensively (gives consistently informative signals) + work on extending it, happily with you and other interested
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Very cool work w. nice N&W from
@imartincorena
- congrats to authors specially our new team-member
@eleanorfewings
:)
Beautiful study by
@ShainLab
and colleagues describing the mutational landscape of individual melanocytes. Including the discovery of frequent melanoma driver mutations in normal melanocytes. It was also a pleasure to cover this paper in a News&Views (OA).
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Congrats to
@lena_maierhein
and the rest of BIAS team for this comprehensive study on reporting for biomedical challenges - glad I could help a bit
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saezlab: Welcome
@luchang_lc
as a
@ResearchLifesci
#AI
postdoc who join us to work with
@schirmerlab
@HWardemann
to integrate cellular circuits and immune cell repertoires in spatial and temporal resolution!
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Great news for Heidelberg to become a unit of
@ELLISforEurope
& thankful to be part of it - thanks to
@OliverStegle
@Carsten_Rother
& Anna
@ilastik_team
for organizing it
Heidelberg was selected for an ELLIS Unit
@ELLISforEurope
to advance
#ML
and
#AI
methods . Great collaboration in Heidelberg
@DKFZ
@EMBL
@UniHeidelberg
Co-headed by
@OliverStegle
@Carsten_Rother
and Anna Kreshuk
@ilastik_team
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Today submitted a review in
@PeerRevWeek
- thankful for so many helpful reviews over the years. Peer Review is critical for the academic system and taken for granted, but worth to think about - among other aspects, see e.g. thought-provoking
@450Movement
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We are looking for postdocs and PhD students! 🔍 Join us in beautiful Heidelberg to apply machine learning and dynamic modeling to tackle human diseases
#jobopening
#AcademicTwitter
#PhDposition
#postdocjobs
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@markowetzlab
@bayraktar_lab
@roserventotormo
@e_petsalaki
@ptck72
@isidrolauscher
@constantAmateur
@MarioniLab
Kerstin Meyer + online
@Francesco_i0ri0
@emanuelvgo
+ more - All in 2 days 😅 - thanks to great hosts
@markowetzlab
@mgarnett11
2/2
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We will host next Monday 28.11 at 4pm
@janbaumbach
in
#Bioquant
INF 267 Seminar Room 041 for a seminar on 'Privacy-preserving data science in systems medicine' - come if interested in applying
#AI
&
#Sysbio
to medicine
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Congrats
@jackxuyx
@KuppeChristoph
@rkramann
and rest of the team 👇 glad we could help led by
@PeralesPaton
with the analysis of the scRNA data from kidney organoids using among others progeny and LIANA
We are happy to share our new study out in
@NatureGenetics
today, led by our terrific PhD Student
@jackxuyx
(just graduated last Monday) together with
@KuppeChristoph
, a great collaboration with
@benofreedman
and others 1/n
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Bridge (From law to molecular biology) seminar - Privacy Challenges in the Health Sector Through Emerging Technologies; coorganized w. Fruzsina Molnar-Gabor &
@JanKorbel5
- speakers incl. Yves Moreau,
@jnkath
@MHZawati
- v. important topic as are the others in the
@MKolleg
Jetzt sind auch die Plakate für jedes Brückenseminar fertig und Ihr könnt Euch über den QR-Code direkt im LSF anmelden! 🎉😊
Wir freuen uns auf Euch! 😊
#universit
ätheidelberg
#heidelberg
#uni
#Philosophie
#philosophy
#online
#Psychologie
#Politik
#Politikwissenschaft
#Jura
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Congrats Christian
@FrezzaLab
and well done
@CECAD_
, great catch! Hope this works out + look forward to having you nearby again soon and work further together.
I am honoured to have been awarded the
#AvHProfessorship
. This is testament of the great work of the lab members over the past years. A huge "thank you" to
@CECAD_
for sponsoring and supporting me on this endeavour.
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Look forward the meeting next week, with
@bayraktar_lab
@SinemKSaka1
@slavov_n
@RongFan8
and many others! My talk already available here
Watch here a summary of our methods for single-cell and spatial transcriptomics that will be presented next week at the
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Talks of our international speakers
@bb_610
I Colussi
@MHZawati
@jnkath
Y Moreau in the
@MKolleg
workshop on Privacy Challenges in the Health Sector through Emerging Technologies are open to the public (6th/13th July)👇
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@MendenMichael
@ERC_Research
@ICBmunich
Fantastic news! Very well deserved and look forward to the outcome of this cool project. Congratulations from a proud Doctorvater :-)
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@slavov_n
PS: We arealso investigating different algorithms to estimate TF activities from these regulons and gene expression, BTW, if it is also of interest
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Congrats
@shtriana
@thalexandrov
@BoulantLab
and rest of the team! Very interesting results and amazing data set. Glad that PROGENy was helpful :)
#Singlecell
analyses reveal
#SarsCov2
interference with intrinsic immune response in
#human
#gut
👈
@shtriana
@alexandrovteam
@embl
&
@BoulantLab
applied
#scRNAseq
&
#HiPlex
#RNAscope
to infected organoids, learned about immune responses in
#COVID19
🦠
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@lucaspelkmans
A bit related, this nice piece on 'anthropomorphizing' molecular biology by
@ItaiYanai
& M Lercher
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Congrats Eduardo and team!🥳
Thanks for involving us😄
Happy to share
@FredeAnnika
, Paulo Czarnewski, and
@gamonasterioo
paper showing an unexpected role of B cells during intestinal mucosal healing.
Check the paper, just online in
@ImmunityCP
, here:
and the
@PaperVids
here 👇🏿👇🏽👇🏻👇
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@JulioSaezRod
@mr_netherlands
@wolfgangkhuber
@attila_gbr
@bhaibeka
here is the link for the DREAM challenge capsule, (), the second version is under review. It comes with a generous free plan for academia and it is far simpler to use than I expected.
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Great work
@KSusztak
and team! Interesting both approach and findings.
Back to science ! Happy to introduce our newest preprint from our lab
@XinSheng7
Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments
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Do you wonder what is the best way to estimate Transcription Factor activities from transcriptomics?
Join us in an open benchmarking project to systematically combine and evaluate regulatory networks and algorithms:
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@arneelof
@Alfons_Valencia
@BiolaMJavierre
Hi
@BiolaMJavierre
Very sorry to hear. As someone who went (multiple times) to Brussels and did not succeed, I feel you. As others wrote, you should not take it as a judgment of your great work.
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@fabfrohlich
@fabian_theis
@saezlab
@ben_szalai
@FEBS_Letters
in addition, more expression of B does not mean more activity of B (RNA != protein, + phosphorylation, localization also key but not reflected in GEX)
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@vallens
@emanuelvgo
I also recently bumped into this, I also thin underappreciated, there is also a recent method by
@olafwolkenhauer
- LORAS tat seems to improve SMOTE
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@emanuelvgo
@wellcomegenome
@emblebi
@sangerinstitute
@saezlab
@pedrobeltrao
@Garnettlab
Best of luck
@emanuelvgo
in this new venture! An exciting opportunity and great catch for Ophiomics
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@fabfrohlich
@fabian_theis
@saezlab
@ben_szalai
@FEBS_Letters
i.e. perturb pathway A (e.g. mutation, drug)->TFs->change expression pathway B => what you would get with classic pathway-based enrichment is B
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@fabfrohlich
@gepasi
@saezlab
@Alfons_Valencia
Agreed - what we tried to do in the manuscript is to understand why 'classical' pathway methods are still effective in many cases, which seems to be an indirect downstream effect
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RT
@StrategyCKD
: Daniel Dimitrov, our PhD student (ESR4) at Heidelberg University, Germany 🇩🇪
@UniHeidelberg
PhD project: Integration of the gut microbiome and other different omic data sets by applying bioinformatics and system biology
@DanielD87930940
…
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@Francesco_i0ri0
@humantechnopole
Very exciting to help to shape this very promising center - a great catch for
@humantechnopole
- all the best, I am sure you &
@humantechnopole
will thrive!
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Congrats - very well deserved!
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@fabfrohlich
@fabian_theis
@saezlab
@ben_szalai
@FEBS_Letters
Thanks,
@fabian_theis
- indeed, and as
@fabfrohlich
writes, this is important to keep in mind when interpreting pathway analysis
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@roserventotormo
Congrats
@roserventotormo
@LuzGarAl
@teichlab
@bayraktar_lab
and rest of the team! Impressive data, cool analysis and important insights
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Also, happy and thankful that our review is in the same special issue with those of great colleagues incl.
@HanaScientist
@fabian_theis
@KhammashLab
U. Sauer, B. Berger
@TreyIdeker
D. del Vecchio B. Andrews M. Covert,...
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To automatize the benchmarking process
@jvelezmagic
developed decoupleR (). This flexible R package adapts popular TF activity inference methods and allows you to use them in combination with any regulatory network. (Easily expanda…
0
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@LauraBKleiman
@ecerami
@VBCancerCare
@SAAswim
@TheLynxGroup
@NCODAorg
@Reboot_Rx
Congrats
@LauraBKleiman
! Great recognition for your unique work to provide affordable treatments to cancer patients.
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@RArgelaguet
@MarioniLab
@OliverStegle
@emblebi
Congrats Ricard! Look forward to your future work, surely as cool and useful as what you have done in your amazing PhD
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@arneelof
@Alfons_Valencia
@BiolaMJavierre
I think that the ERC as a very competitive system, but that works generally very well. In ML/stats terms, I see it as a classifier with v very low False Discovery Rate, which comes at the costs of high False Negatives Rates (like you).
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@Al__Forrest
@saezlab
@IdoAmitLab
Thanks
@Al__Forrest
, indeed PIC-seq
@IdoAmitLab
is a great method and we are considering it in this context, Thanks for your other comments too, happy to discuss more and if you like to join the project you are very welcome :)
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@arneelof
@Alfons_Valencia
@BiolaMJavierre
I agree that there should be more support for projects that got close, at EU and/or national level. As
@Alfons_Valencia
says, there is a lot of wasted time/energy (proposals + review). A bit resembles discussions with papers/reviews. The ideas of lotteries are interesting.
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@pedrobeltrao
@embl
@ETH_DBIOL
@IMSB_ETH
Many Congrats
@pedrobeltrao
and great catch
@IMSB_ETH
! A perfect match and an excellent addition to an already outstanding institute
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@emblebi
@MarioniLab
@embl
Congrats John
@MarioniLab
! Also great for
@emblebi
to have a head of research, and fantastic appointee
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@KharchenkoLab
@singlecellomics
@UniHeidelberg
Thanks
@KharchenkoLab
- yes I think it will be recorded and posted on website/youtube. Also happy to share slides, discuss, etc.
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@jnkath
@AIO_Onkologie
@tom_luedde
@lab_pearson
@ReinacherAnke
@NCT_HD
@UniklinikAachen
Congrats
@jnkath
well deserved! keep up the great work
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RT
@sysbiomed
: New Version of CellNOptR 1.2 available in Bioconductor with significant improvements
http://t.co/ZfDtW8VJ
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@ewanbirney
many thanks - indeed great, sp look back at how they developed as scientists (thx great environment @ EBI) Photo is of my copy:)
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@Francesco_i0ri0
@NatureComms
@CancerDataSci
@ClarePacini
@targetvalidate
@DepMapSanger
@CancerDepMap
Congrats
@Francesco_i0ri0
@clarepacini
and rest of the team! A great resource, thanks for putting it together 🙏
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Congrats
@elisabetta1412
and best of luck for launching the lab!
Super excited to join the
@CarrerasIJC
in Barcelona on Jan 2021 as Jr Group Leader of the new Cellular Systems Genomics lab. We will provide new computational tools for the analysis of
#SingleCell
genomics and spatial data in the context of inflammation and inflammatory disorders
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@mr_netherlands
@wolfgangkhuber
yes, christian had good experience with workflowr. Also
@attila_gbr
recently positive impression with codeocean for this paper (
@bhaibeka
uses codeocean a lot). otherwise until now github repos mostly, but also wonder (pros and cons as you say).
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@ixenario
@Janis3_14159
@larsjuhljensen
Thanks - indeed curation is such a huge work - very valuable (& under-appreciated)
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@emanuelvgo
@Garnettlab
@pedrobeltrao
@miguelprocha
Congrats
@emanuelvgo
! Well deserved. Very proud and look forward to seeing the great work coming from your lab.
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Happy to participate in this nice course by
@SysBioCurie
- still open for registrations
Last week to register!! 4th course on Computational Systems Biology of Cancer: Multi-omics and Machine Learning Approaches on Sept. 27th - Oct. 1st, 2021 Application deadline: August 10, 2021
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@lucaspelkmans
Very appealing analogy indeed! We need more of these approaches. As another 'analogy' to some studies in biology, this research is somewhat disputed in terms of reproducibility/underpower.
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