After more than 8 years at IBM Research Zurich, it's time for a new chapter:
📢 I am more than thrilled to join the University of Lausanne
@unil
and the Biomedical Data Science Center at
@CHUVLausanne
as a tenure-track Assistant Professor! 🎉
📢 We are hiring! 📢
Are you a MSc/PhD👩🎓👨🎓 passionate about
#AI
#ML
in
#cancer
, looking for your next career step?
Join our newly-founded AI/ML for Biomedicine group part of the Biomedical Data Science Center at
@unil
and
@CHUVLausanne
in beautiful Lausanne!🇨🇭🏔🌈
👇
Black days for Greece. In the country with the worst rail network in Europe, deadly train accident kills dozens. Among the dead many students. Their friends pay their respects - officials don't send psychologists but fully armed riot police. I have no words.
#τεμπη_εγκλημα
Είναι αυτή η πιο ντροπιαστική στιγμή της τετραετίας για την
@hellenicpolice
& τον
@theodorikakosp
?
Οπλισμένα ΜΑΤ με φορεμένες μάσκες αμαυρώνουν τις στιγμές πένθους των φοιτητών που χασαν τους ανθρώπους τους.
Ακόμα και οι κατοχικοι στρατοί το πένθος το σέβονται.
#Τεμπη
I am super excited to share our latest work, out now in
@NAR
Genomics and Bioinformatics!
1. open-access paper:
2. open-sourced code and data:
Buckle up for a Tweetorial 👇
Our amazing colleague Matteo Manica
@drugilsberg
successfully defended his PhD thesis yesterday at ETH Zurich, summarizing 3 years of intense, exceptional research! Congrats from the whole
@IBMResearch
Zurich Lab!
@PrECISE_H2020
I got into CompBio because of the first female researcher I met in my ALL MALE faculty department. And I became a researcher because of a female Professor in my Masters, who became my PhD mentor.
#WomenInSTEM
mentorship is more than career progress, it’s about representation.
After two years in the making, our joint effort on mapping the breast cancer ecosystem at a single cell level is finally out! Big thanks to our collaborators at the
@BodenmillerLab
, it’s been a blast analyzing this tiny dataset :-)
@IBMResearch
194 patient samples, 26 million single cells: our atlas of breast cancer ecosystems reveals links to poor prognosis and immunosuppression . Thanks to all our collaborators, especially
@marianna_raps
,
@MariaRoCompBio
, PATH foundation and
@UniSpitalBasel
Excited to present our team's work on
#spatial
analysis of
#tumorecosystems
in this Cell Press webinar!
Registration is free - check the link 👇 to subscribe!
Doing a Master program at ETH in Computer Science/Bioinformatics and interested in doing your thesis
@IBMResearch
on an exciting topic combining deep learning and biology?
@drugilsberg
and me are excited to meet you! To apply:
Topics of special interest include modeling the tumor
#microenvironment
, and predicting the effects of
#drug
perturbations at a patient level.
Hiring at all career levels - to apply:
- PhD:
- PostDoc:
👇
Excited to share TECH-3D, our humble contribution towards prediction of
#3Dgenome
structure from
#HiC
data, recently accepted to the
@lmrl_bio
#NeurIPS2021
workshop!
Work by super talented master student Tristan Meynier (not on Twitter). Last
#tweetorial
of 2021, 🧵- alert!
I had a lot of fun talking to
@GreekGirlsCode
about my “unconventional” career journey, my passion for Biology and my experiences as mom and
#womeninSTEM
! Thanks for including me and for all the work you do 👍🏻💪🏻
@IBMResearch
@Momademia
📢 The GGC Interview! At
@greekgirlscode
we are featuring interviews with incredible Greek women in
#science
and
#tech
!Meet Marianna Rapsomaniki, a Research scientist at IBM Research, Switzerland.
Read more about Marianna and her research here ⬇️
Check out our computational framework scQUEST, reproducing our
#singlecell
#breastcancer
atlas analysis, now published as a protocol in
@STARProtocols
!
- open-source code:
- original paper:
AI & Pharma – Track spotlight ☄️
Listen to experts sharing their experiences in using AI/ML for Pharma R&D usecases in drug discovery and development!
Join us on March 28 at
#AMLDEPFL22
– organized by
@OwkinScience
More information ➡️
#careeradvice
💥 Thank you
@RealScienceEdu
for this amazing & insightful session 👏🏼
We have still lot time⏰ to go & lots to discuss! JOIN NOW the 💬 over career challenges & paths in
#academia
&
#industry
and ask your ⁉️ directly to the panelists 💪🏻
👉🏼
🎤 We’re pleased to announce that
@dominic_grun
(
@CIBSS_UniFR
), will present his latest research at [BC]2 in the session 'Methods in
#singlecell
#DataAnalysis
: from pre-processing to biological inference'.
👉Interested in participating? Submit an abstract
The call for Posters is now open for AMLD EPFL 2024! Passionate about AI and machine learning? Join a track at AMLD EPFL 2024!
Find out more here. Early Bird rates until 25 January. Register now!
#AMLDEPFL2024
#AI
#MachineLearning
Αυτό το Σάββατο θα συζητήσουμε για τις δυνατότητες που ανοίγει ο προγραμματισμός στη Γενετική και τη Βιολογία - πολλές ενδιαφέρουσες ομιλίες ΚΑΙ hands on workshop σε R! Συνδιοργάνωση
@GreekGirlsCode
και ΣΙΓΕ, η εγγραφή είναι δωρεάν, πληροφορίες εδώ ⬇️
DQBM is delighted to see Johanna Wagner-Albrecht
@bodenmillerlab
win the 2020 Faculty of Science Annual Thesis Award (Jahrespreis), awarded during the UZH Dies academicus. Congratulations, Johanna!
#UZH
#DQBM
In our group we have been using COSIFER for network inference for quite some time, give it a try! Available both as a Python package and web app, and paper just out! Congrats to
@drugilsberg
and all the authors! 🥇👏👇🥳
Willing to infer a network from your data, but not quite sure which method to use 🤔.
COSIFER comes to the rescue:
Application note just published in
@OUPBioinfo
from
@IBMResearch
and funded by
@PrECISE_H2020
and
@iPC_H2020
.
Details in the thread.
Thrilled to be one of the awardees of the CZI 2024 Data Insights grant. Together with
@marianna_raps
and
@ShemaEfrat
. Looking forward to an exciting collaboration made possible by
@cziscience
.
We are committed to building a diverse and inclusive team - candidates of all backgrounds / identities are encouraged to apply!
PS: If you are looking for a master thesis/internship instead, don't hesitate to apply (pick the PhD ad and specify details in your cover letter).
#PaccMann
: A deep learning tool for explainable cancer drug sensitivity from
@IBMResearch
. The paper is finally out in
@Mol_Pharm
.
Paper:
TensorFlow:
PyTorch:
Try it out online:
You will work in a fantastic environment where fundamental and clinical research meet to accelerate new breakthroughs and transform patient care.
Our mission is to develop new AI/ML approaches to elucidate
#cancer
mechanisms using heterogeneous (
#spatial
)
#singlecell
data
👇
Last day tweeting from
@GreekGirlsCode
- the week passed really fast! Today I am talking about mentoring, career choices and pursuing a career in
#STEM
, would love to hear from you as well ☺️
Working with single-cell datasets and struggling with integration? Check out STACAS, an R package for semi-supervised single-cell data integration from the
@carmonation
lab 👇🏻
Happy to share the peer-reviewed version!⛺️
Now including additional analyses of i) impact of celltype composition imbalance across samples, and ii) noise in celltype labels on integration performance. Thanks to reviewers & editor for constructive feedback
An important contribution towards creating a reference T cell atlas from Santiago’s team
@carmonation
Check out the preprint, their code is open on github:
🌟 It is official: the Rapsomaniki lab is opening its doors on March 1st, 2024! 🌟
📢 I will be soon looking for motivated
#PhD
students and
#Postdocs
: if you are passionate about all things
#AI
#ML
for
#singlecellanalysis
and
#spatialbiology
, keep an eye for announcements soon!
Very much looking forward to this event to discuss all things
#cancer
and
#AI
- from understanding cell-cell interactions to modeling drug perturbations.
Join for a series of ✨talks - attendance is free with online registration, deadline today! 👇🏻
Register by March 31st for the Cancer AI Research Workshop. This two-day event will examine the state of
#ArtificialIntelligence
methods, explore how they can be applied to
#CancerResearch
, and discuss how to further advance
#MachineLearning
.
Register:
How can we effectively fight this pandemic? What is the best strategy? What can we learn from other countries? Many questions eloquently answered and many options explored by some of the leading experts in the field. The only way out is science!
I've been mulling over the
@MRC_Outbreak
modeling report on
#COVID19
mitigation and suppression strategies since it was posted on March 16. Although mitigation through social distancing may not solve things I believe we can bring this epidemic under control. 1/19
@jacasiegel
Although I understand where this is coming from, I think what it’s more important to actually demand higher salaries. In many European countries postdocs are not underpaid and can lead a normal life and start a family - parental leave included.
If you have a background in Data Science and are interested in working in one of the most exciting research topics with a great new PI
@hartjackson
, check this out! 👇
The Jackson Lab is opening alongside the re-opening, and building a team focused on multiplexed imaging of cancer
#LTRI
. We are now looking for a Lab Manager and Data Scientist, and recruiting PostDocs and Students in the coming months. Job postings below.
Looking for a highly interdisciplinary Master thesis project? Passionate about designing new solutions for
#drugdiscovery
? We want to meet you!
Join our team at
@IBMResearch
Zurich for an exciting project at the intersection of
#AI
,
#QuantumComputing
and
#singlecell
Biology.
Another great contribution from our colleague
@drugilsberg
- we can't keep up with you anymore 😀
If you are interested in tumor clonal evolution, se sure to check out the paper and try out the tool!
Curious to learn how to estimate tumor clonal composition using WES/WGS from multiple biopsies.
Check out Chimaera: .
Just published in
@Nature_NPJ
from
@IBMResearch
and funded by
@PrECISE_H2020
.
More details in the thread.
Greek neo-Nazi party Golden Dawn was found guilty of running a criminal organization. 60+ members were charged for crimes like attacks on migrants and killing an anti-fascist rapper.
Its leaders face up to 15 years in jail. Thousands rallied in Athens: "Fascism, Never Again"
Organizers of data science and machine learning conferences (NeurIPS, ICML, AISTATS, ICLR, UAI, ...): Allow remote paper & poster presentations at conferences - Sign the Petition! via
@Change
Honored to talk at
@Mila_Quebec
's M2D2 (Molecular Modeling & Drug Discovery) series! 🤩
If you want to hear about Generative Language Models in Molecular Discovery: Regression Transformer, GT4SD and Beyond, tune in *today at 5pm CEST / 11am ET* on Zoom:
A great public resource for anyone working on method development for computational pathology, containing real-world complex H&E stained images - many congrats to the people involved! 👏
I am honored to receive the
#Huber
#Research
#prize
, awarded by the American Society of Civil Engineers
#asce
since 1949. Humbled to join such a distinguished list of colleagues working in the field of
#civil
#engineering
.
SCOOP: I obtained a whistleblower complaint about Stanford's COVID-19 study.
Turns out JetBlue's founder, a critic of the economic shutdowns, helped fund it.
And John Ioannidis and others allegedly ignored internal scientists' concerns about the test.
Ok here we go.
Look at the electoral maps by county for the last few decades of US presidential elections. You’ll notice that the South goes almost uniformly Republican red every time.
Duh.
But if you look closer, there’s something else there ...
11/ If you made it so far, THANK YOU!
TL; DR: In summary, we show through our model that, depending on the level of analysis,
#heterogeneity
and
#robustness
are emerging and non-contradictory characteristics of DNA re-replication.
(5/8) And then focused on computational approaches used to quantify heterogeneity from said measurements. We summarized the most popular computational frameworks, broadly reused across different data modalities ranging from
#molecular
to
#imaging
data:
12/ Many thanks go to all the amazing co-authors: Stella, Patroula, Manuel, Nikos. This study was performed at the Cell Cycle Lab of
@upatras
led by Prof. Zoi Lygerou, (check out their amazing work here: ) funded, among others, by an
@ERC_Research
grant...
All the credit for this work goes to Tristan Meynier, who put all his creativity and enthusiasm in this project. Many thanks to
@_bunnech
for co-supervising and
@AkisPapantonis
and his team for very interesting discussions and invaluable feedback!
My gratitude goes to the numerous mentors, collaborators, friends and family that shared this path with me since my early PhD years!
I can't wait to join such an exceptional research environment, contributing towards the vision of advancing patient care.
2/ But first, why do we even bother studying DNA re-replication? Well, multiple studies have shown that re-replication is a mechanism that can result in local copy number gains and gene amplifications, and is thus linked to genomic
#instability
and
#tumorigenesis
.