Plate VI · News
New papers, tools and news, as posted by @fabian_theis. Replies and reposts are left out.
@HelmholtzMunich townhall meeting - first time semi-virtual again, with fantastic PhD student presentations as well as instructive talk by @UshmaNeill @MSKCancerCenter about how to write a good paper, summarizing important expertise as editor @jclinicalinvest.
Peter Sorger @harvardmed talking at SBMC22 about "Frei independence" and his interesting observation that drugs often seem to act independently in cancer combination therapy, so essentially reflect joint effect on a heterogeneous patient population. Paper: aacrjournals.org/cancerdiscover…
@priscaliberali at SBMC 2022 presenting exciting extension of her organoid setup towards a human colon organoids screen (and differential analysis in cancer setting), with crazy robotics, microscopy + image analysis setup. sbmc2022.de
At one of the first in-person lab meetings: Speaker 'can you see the slides?' - (real life) audience, automatically: 'yes!‘ . . . . everyone burst out laughing.
View on X: post of 12 May 2022How can we extract consistent subcellular structures from multi-condition multiplexed cell imaging? Led by @HannahSpitzer1 & @scottbscience, we find that conditional convolutional VAEs find such representations robustly - thx for great collab @pelkmanslab: biorxiv.org/content/10.110…
Fun comp bio PI aggregation @EMBLHeidelberg advisory board meeting - great to see @dana_peer, @OliverStegle and @wolfgangkhuber again!
Excited to share our finding on quantitive scATAC-seq modeling. Led by @lauradmartens & @gagneurlab, we show that scATAC-seq contains information beyond a binary accessibility state, and that modeling fragment counts via a Poisson model improves analysis. biorxiv.org/content/10.110…
Great @helmholtz_en Incubator meeting - in 3d after so long - at beautiful Spree river location at Berlin. So nice to discuss with colleagues again f2f! helmholtz.de/en/research/ch…
Honored to have been awarded an #ERC Advanced Grant for my project „DeepCell“. With DeepCell, we aim to model drug effects on organoids via mechanism-constrained deep learning and single cell readouts. PhD and postdoc positions available, please apply :) erc.europa.eu/news/erc-2021-…
View on X: post of 26 Apr 2022Celebrating @Eileen_Furlong’s well-deserved Leibniz award w @FGinhoux @schierlab @IdoAmitLab @AlexandervanOu1 at Keystone Florence 🎉
Live report from the Florence Keystone meeting (= one more thing you don’t get in a zoom meeting): @Mo_lotf being overwhelmed by original Italian sometimes too big and sometimes too fried pizza 🍕😅.
Matthias @labs_mann at #Keystone SB meeting showing how proteomics can go from low-input to single cell, referencing recent work @MolSystBiol (embopress.org/doi/full/10.15… with some contributions from us) and his interesting deep visual proteomics with Horvath @hpke1980 lab.
@N_Rajewsky at #Keystone SC Biology meeting just gave a tour de force of recent work from his lab, including a subcellular spatial sequencing idea adapted from Seq-scope, beautiful.
View on X: post of 7 Apr 2022Sarah @teichlab introducing our Computational Biology session at the #Keystone Single Cell Biology meeting. So fun to meet colleagues again and learn about their research f2f. A renaisannce of scientific life in this beautiful renaissance city of Florence!
Happy to announce that @Mo_lotf is now Dr. Mohammad Lotfollahi, congrats for the great and successful PhD defense!
Gave my first non-virtual talk since what felt like ages @sangerinstitute today - felt so good to actually see the people you talk to and then interact in Q&A. Thanks Sarah @teichlab for invite and everyone for fun discussion!
View on X: post of 29 Mar 2022Back on the road again after such long time. Visiting @sangerinstitute and hanging out at beautiful Corpus Christi College with Sam Behjati & @roserventotormo & some anonymous statue. Everything very Harry Potter here.
Hilarious real-world satire demonstrating German bureaucracy - German health insurances @GKV_SV warned that compulsory vaccination cannot be implemented due to lack of sufficient paper for the letters they’d have to send out. 🙈 welt.de/politik/deutsc…
View on X: post of 21 Mar 2022Excited 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! biorxiv.org/content/10.110…
@MDLuecken at #LSC2022 kicking off our integrated Human Lung Cell Atlas - a large community-effort @humancellatlas towards a population-scale atlas. By combining 46 datasets of the human respiratory system, we could map >2.2m cells from 444 individuals across health&disease.
Soroor Zadeh kicking off our #InternationalWomensDay #WomenInScience event today, with fantastic set of speakers talking about their exciting careers. Live broadcast here: youtu.be/zPNa_RdGhc4
Russian war to Ukraine is devastating - easiest but potentially most impactful way for all of us is to donate; here are some international organizations helping 🇺🇦: @Refugees @SaveChildrenDE @MSF unhcr.org savethechildren.net msf.org
View on X: post of 4 Mar 2022War in Europe - why? We all hoped that our children never had to see this.. What can we scientists do? At least show that science and truth are core values, and act as role models for peaceful international collaborations.
View on X: post of 25 Feb 2022Zoom pro-tip I learned from K Kuchenbecker @MPI_IS: during a virtual conference with tight timings, put timer screen with raised hand to make it appear on top of speaker list, and use slide annotation by host to indicate getting close to the end - Katherine was using many ⭐️s.
@davidsebfischer at today’s sfaira data loader workshop, on „the dark matter of single-cell analysis code“, and how to replace it and/or speed up with the sfaira toolbox. theislab.github.io/sfaira-portal/
Coming back from (good!) student seminar today, I started wondering about recommendations for beginners to give great talks - found very useful blogpost by @Pseudomanifold here bastian.rieck.me/blog/posts/201…
View on X: post of 9 Feb 2022Congrats to @LukasHeumos @HelmholtzMunich and team for winning the campusSOURCE Award 2022 for their cookietemple tool 🍪🏛, which provides best-practice programming templates to get your project kickstarted in no time! Try it at github.com/cookiejar/cook… ev.campussource.de/publikationen/…
View on X: post of 9 Feb 2022Excited to share our recent approach for biologically informed reference mapping using 'expiMap'. Led by @Mo_lotf and @Koncopd, we essentially give gene program names to latent space coordinates, thus helping to interpret query perturbation effects. biorxiv.org/content/10.110…
Our review on spatial components of molecular tissue biology is out @NatureBiotech! Together with @g_palla1, @davidsebfischer & Aviv Regev, we describe challenges in spatial tissue analysis & related computational algorithms across length scales. Read at rdcu.be/cGwTC
