Challenges and opportunities for the next generation of computational tumor models
Mathematical models have become essential tools for exploring the complex interplay between cancer cells and their microenvironment, but require multidisciplinary expertise and abundant biological dat...
Mathematical models are essential tools for exploring the complex interplay between #cancer cells and their environment, but require expertise and abundant data to develop. Lance Munn & Rakesh Jain suggest that #AI is leading the way towards the next wave of tumor models ๐งช plos.io/4ofREUk
05.08.2025 16:15 โ ๐ 4 ๐ 4 ๐ฌ 0 ๐ 0
Probabilistic migration events drive transient tissue residency of lymphocytes during homeostasis
Tissue-resident lymphocytes form a phenotypically and functionally distinct analog to the corresponding circulatory lymphocyte populations. Residential CD8 T cells, in particular, are identified as having prolonged residence in the tissues and key functions in recall responses at tissue-environmental interfaces, although the dwell time in individual tissues has yet to be resolved. Residential CD4 T cells, regulatory T cells, B cells, and NK cells have been demonstrated to share phenotypic properties with residential CD8 T cells, but the migratory kinetics are even more poorly defined. Here we used probabilistic modelling on a large parabiosis dataset, covering multiple time-points and tissues, to calculate migration kinetics and dwell times of multiple lymphocyte subsets across a diverse set of tissues. Markov chain modelling identified distinct cell type-specific and tissue-specific residency patterns. The liver and gut were prone to prolonged residency compared to other tissue types, and a hierarchy of residency was observed with CD8 T cells and NK cells demonstrating longer residency than CD4 conventional T cells and regulatory T cells, which in turn resided in tissues longer than B cells. With few exceptions, however, average residency was at least an order of magnitude shorter than the life-span of the mouse, indicating a more dynamic form of steady-state tissue residency than usually assumed. Together these data provide a comprehensive model of a pan-tissue shared program in lymphocyte tissue residence, as well as identifying cell type- and organ-specific modification of the migratory kinetics. ### Competing Interest Statement The authors have declared no competing interest. Wellcome Trust, https://ror.org/029chgv08, 222442/Z/21/Z European Research Council, TissueTreg
I'm excited about a new @biorxivpreprint.bsky.social story that just went live! This one takes a #computational #immunology approach to understanding #tissueresident lymphocytes. The story highlights the extra value mathematical modelling can bring to biology. ๐งต1/10
www.biorxiv.org/content/10.1...
09.07.2025 08:17 โ ๐ 67 ๐ 22 ๐ฌ 1 ๐ 3
Family hubs to open in every council in England
Government says ยฃ500m plan aims to support an extra half a million more children.
Amidst the blizzard of news, this is hardly being reported but will make the biggest difference in peoples' lives www.bbc.co.uk/news/article...
06.07.2025 06:19 โ ๐ 5 ๐ 3 ๐ฌ 0 ๐ 0
From the same team that made vanilla for ice cream using E.coli that digest plastic waste.
24.06.2025 11:42 โ ๐ 18 ๐ 5 ๐ฌ 0 ๐ 0
Polygenic scores (PGS) offer insights into a personโs inherited risk of disease.
GeneticScores.org is a new platform that enables secure, cloud-based calculation of polygenic scores to make genomic risk prediction more accessible.
www.ebi.ac.uk/about/news/u...
๐ฅ๏ธ๐งฌ
09.06.2025 11:20 โ ๐ 19 ๐ 8 ๐ฌ 1 ๐ 1
I've just heard our group of runners for @scotrefugeecouncil.bsky.social have almost raised a collective ยฃ15K!!!
We are just under ยฃ500 off our target!
My JustGiving page closes on Sunday... can we do it before?!!
All shares/donations count!
Thank you!! โค๏ธโค๏ธโค๏ธ
www.justgiving.com/page/amy-mci...
30.05.2025 11:46 โ ๐ 176 ๐ 53 ๐ฌ 7 ๐ 2
๐จ Abstract Deadline - Friday 30th May
There are 10 days left to submit your abstract for EMDS2025. We have >20 selected talk slots - so submit an abstract today!
All details & programme: www.emds2025.com
@britsocimm.bsky.social @societymucosalimm.bsky.social @cytokinesociety.bsky.social
20.05.2025 05:36 โ ๐ 6 ๐ 5 ๐ฌ 0 ๐ 0
Latin-American genetic data available securely to approved researchers worldwide/Datos genรฉticos latinoamericanos disponibles para investigadores de todo el mundo
Big news for health data research and population diversity: The Mexico City Prospective Study data are now available securely to approved researchers worldwide. www.ndph.ox.ac.uk/news/latin-a...
Cohort description: www.ctsu.ox.ac.uk/research/pro...
02.05.2025 09:05 โ ๐ 33 ๐ 17 ๐ฌ 2 ๐ 2
A promotional flyer for the AI@MBL: Machine Learning for Microscopy Image Analysis course at the Marine Biological Laboratory. Course dates are Aug 22 to Sept 6, 2025, with applications due April 30. The image includes a brief paragraph: "This two-week course will familiarize researchers with state-of-the-art deep learning techniques for microscopy image analysis." The image also includes the hashtag #ScienceStartsHere, a logo for the MBL, and an abstract image with different colored blobs.
โ ๏ธ Course deadline extension โ ๏ธ
The last day to apply for the AI@MBL course this summer is now April 30!
๐ฒ Read more and apply: bit.ly/43vIT0u
#ScienceStartsHere
16.04.2025 22:26 โ ๐ 8 ๐ 3 ๐ฌ 0 ๐ 0
Tissue-specific improvements in CD4+ T cell responses after treatment for visceral leishmaniasis. https://www.biorxiv.org/content/10.1101/2025.04.13.648617v1
14.04.2025 04:15 โ ๐ 1 ๐ 2 ๐ฌ 0 ๐ 0
Join us for this @dgz.bsky.social seminar online with very cool talks about the Cell biology of the immune system
There will be of course some #CellMigration of leukocytes ;)
Speakers: @liz-kurtz.bsky.social, #ZahraaA, @labliston.bsky.social and #StefanU
11.04.2025 14:49 โ ๐ 8 ๐ 7 ๐ฌ 0 ๐ 0
A flyer for the MBL Falmouth Forum series. It has the date, time, and location of the event (Friday, April 11, 7:30pm, Cornelia Clapp Auditorium), a photo of speaker Paul Catanzaro with info on him (professor, State Extension Forester, co-director of the Family Forest Research Center, UMass Amherst), a link to the join the talk virtually, a logo for the MBL, and information on how the forum series is supported.
๐ Don't forget to join us TOMORROW, Friday, April 11, for a special MBL Falmouth Forum with Paul Catanzaro!
His talk will begin at 7:30 p.m. in the MBL's Lillie Laboratory. Can't make it in person? That's okay, we'll be streaming live! mbl.edu/falmouth-forum
10.04.2025 19:11 โ ๐ 9 ๐ 4 ๐ฌ 1 ๐ 0
OK here it is, the moment you have all been waiting for! Our advert for 5 posts here at Glasgow: Cognitive neuroscience/psychology. Closing date May 12 - please spread the word
www.nature.com/naturecareer...
28.03.2025 07:06 โ ๐ 121 ๐ 140 ๐ฌ 1 ๐ 3
Do any of my #tbsky friends have interests in T cell responses in people with evidence of prior Mtb infection?
If so, would you have any interest in looking at T cell responses to Mtb-derived peptides that we have detected by mass spectrometry? LMK ๐๐ฝ
28.03.2025 18:04 โ ๐ 7 ๐ 6 ๐ฌ 0 ๐ 0
๐ Update on our preprint about Gene Regulatory Net (GRN) benchmarking ๐
We have included the original and decoupled version of SCENIC+, added a new metric and two more databases. Dictys and SCENIC+ outperformed others, but still performed poorly in causal mechanistic tasks.
doi.org/10.1101/2024... ๐
14.03.2025 10:34 โ ๐ 49 ๐ 18 ๐ฌ 2 ๐ 0
๐ฎ I feel seen.
12.02.2025 10:03 โ ๐ 1 ๐ 0 ๐ฌ 0 ๐ 0
Graphical abstract of BioChatter
Applying LLMs to biomedical research today can go one of two ways: we either use a closed-source web app, or we get coding ourselves. Many researchers lack training for the latter, so their only choice is the former. We want to change that. www.nature.com/articles/s41...
05.02.2025 09:15 โ ๐ 78 ๐ 37 ๐ฌ 2 ๐ 2
Organoids have incredible potential in drug discovery and disease modelling.
In this Scientific Computing World interview, @iguaracy.bsky.social discusses organoid construction, nanobots, and how bioinformatics is transforming biomedical research.
www.scientific-computing.com/article/usin...
04.02.2025 11:09 โ ๐ 22 ๐ 2 ๐ฌ 0 ๐ 1
PhosX: data-driven kinase activity inference from phosphoproteomics experiments
AbstractSummary. The inference of kinase activity from phosphoproteomics data can point to causal mechanisms driving signalling processes and potential dru
Kinases play a role in many diseases, making them prime targets for therapeutic intervention.
Enter PhosX, a new tool transforming the way researchers analyse and interpret kinase activity.
Read the full article: academic.oup.com/bioinformati...
@alussana.bsky.social @epetsalaki.bsky.social
27.01.2025 11:56 โ ๐ 21 ๐ 14 ๐ฌ 1 ๐ 2
๐๐๐จ๐ด
21.01.2025 19:17 โ ๐ 1 ๐ 0 ๐ฌ 0 ๐ 0
Join the Biology of Parasitism (BoP) course at MBL Woods Hole for an unforgetttable summer of science and fun, meet wonderful teachers and make friends for life: www.mbl.edu/education/ad...
09.01.2025 23:24 โ ๐ 11 ๐ 5 ๐ฌ 0 ๐ 0
Flyer for the MBL's 2025 Embryology course
๐Apply now!๐
January 22 is the last day to apply to the MBL's 2025 Embryology course! This comprehensive overview of modern developmental biology is open to graduate students, postdoctoral fellows, and senior researchers.
Learn more: bit.ly/3DKPMjH
#ScienceStartsHere
08.01.2025 13:55 โ ๐ 26 ๐ 20 ๐ฌ 0 ๐ 3
GRETA graphical abstract
We present Gene Regulatory nETwork Analsyis (GRETA), a framework to infer, compare and evaluate gene regulatory networks #GRNs. With it, we have benchmarked multimodal and unimodal GRN inference methods. Check the results here ๐
Paper: doi.org/10.1101/2024.12.20.629764
Code: github.com/saezlab/greta
23.12.2024 08:43 โ ๐ 126 ๐ 46 ๐ฌ 2 ๐ 5
Text reads: Technical Specialist/ARA. ยฃ32,600 - ยฃ39,200 (ARA)
ยฃ40,500 - ยฃ48,600 (Technical Specialist)
Apply by 10 January
Do you have expertise in human-induced pluripotent stem cells, molecular biology (and in vitro infection models)?
Join a collaborative project in the Haniffa/Lotfollahi labs, to optimise protocols to introduce perturbations and evaluate their effects in a skin organoid model derived from hiPSCs. You will
have the opportunity to develop your computational skills and learn concepts about machine learning.
@mhaniffa.bsky.social and Mo Lotfollahi are recruiting!
Do you know your way around hiPSCs, molecular biology, and ideally, in vitro infection models? Are you interested in developing your computational skills?
Apply through the Wellcome Sanger Institute by 10 January
05.12.2024 10:20 โ ๐ 5 ๐ 2 ๐ฌ 0 ๐ 0
NYT columnist. Signal: carlzimmer.31
Newsletter: https://buttondown.com/carlzimmer/
Web: http://carlzimmer.com
[This account includes a tweet archive]
Postdoc at UCL with James Reading. Previously at EMBL working with Wolfgang Huber. Biostats, R, cancer immunology
Resident panhandler, http://trichelab.org/
Posts may contain trace quantities of blood๐ฉธ, chromatin ๐งฌ, and stats ๐งฎ
https://scholar.google.com/citations?user=AOoIO74AAAAJ
physicist, bioinformatics / biostats researcher at University of Heidelberg
Mathematical oncologist working on cancer evolutionary therapy #AndersonLab @mathonco.bsky.social Chair @EvolTherapy.bsky.social Director @smbmathbiology.bsky.social Fellow and former President
The SMB is dedicated to the advancement of research at the interface between the mathematical and biological sciences. smb.org
Associate Professor @ Big Data Institute, University of Oxford
2024 Lister Institute Fellow
genomics | rare disease | gene regulation | genetic therapies
https://rarediseasegenomics.org/
(field) hockey player | cyclist | hiker
PI of @emmersonlab-irr.bsky.social at @edinuni-irr.bsky.social studying regeneration after cancer radiotherapy | Academic Lead for Public Engagement | Stepmum, vegetarian, baker, cyclist
Hola! We are the CRG, a research institute exploring the frontiers of biology in Barcelona. Som un centre CERCA. www.crg.eu
Non-profit research and educational institution at the forefront of molecular biology, cancer, neuroscience, plant biology, and genetics.
https://www.cshl.edu/
Cancer systems biology lab @bsmsmedschool.bsky.social | @UKRI.org Future Leaders Fellow | Director of @SussexCancer.org | Frontiers in Immunology Speciality Chief Editor: Systems Immunology
A British/American group leader at @crg.eu . We study the biology of aging using molecular genetics, engineering, systems biology, and probabilistic machine learning.
Lab page: http://lifespanmachine.crg.eu
The Earth BioGenome Project (EBP), a moonshot for biology, aims to sequence, catalog, and characterize the genomes of all of Earth's eukaryotic biodiversity over a period of ten years.
๐ฒKeep up with all EBP updates: https://linktr.ee/earthbiogenomeproject
Professor of fungal immunology at University of Birmingham. Lister Institute Fellow. Feminist.
www.theradlab.co.uk
โ๐๐ช๐ค๐๐๐๐ค๐ฅ, โ๐๐ค๐๐๐ฃ๐๐ ๐พ๐ฃ๐ ๐ฆ๐ก ๐๐๐๐๐๐ฃ @ ๐๐๐๐ช๐ค๐น๐๐ (โ๐๐โ-๐๐) ๐ค, ๐โ๐ธ/๐ฝ๐ ๐ ๐ ๐๐ ๐ง๐๐ฃ ๐, ๐๐๐ โ๐๐ค๐ฅ๐๐๐๐ฃ๐๐๐!
#BDS
http://www.thesimbiosys.com
Physicist trying to understand the behaviour of living organisms. Group leader at EMBL Barcelona.
Group Leader @EMBLBarcelona | PD @TheCleversLab | PhD @MITBiology (Jacks lab) | B.A. @NewCollegeofFL | She/her | ๐ต๐ท๐บ๐ธ๐ช๐บ| #Organoids, #Neuroendocrine cells
The choreography of multicellular systems, computer simulations, gene regulatory circuits, and swarm robotics.
Head of EMBL Barcelona
Co-chair of the Barcelona Collaboratorium
The Barcelona Collaboratorium for Modelling & Predictive Biology is a joint initiative by @crg.eu & @embl.org, exploring biology's frontiers with computational and theoretical modeling to make systems predictable & controllable.
Nature Aging is a thematic journal from the Nature Portfolio that serves the broad aging research community. Follows & posts โ endorsements.