5 more days to submit abstracts for International Conference on Systems Biology #ICSB2024! Hope to meet you in Dublin!

Thanks @stemcellsystems.bsky.social, I hope #ICSB2024 organisers rewarded you well, your Bluesky coverage was next level! The detail and update frequency were unmatched. Spotted some intriguing systems biology papers, took me back to my postdoc days! Hope you’re loving tour time in Mumbai!

Well that’s a wrap #ICSB2024 🧪- terrific conference! ICSB2025 in Dublin 5-9 October #Ireland

Presented today at #ICSB2024 by @chaitraagrahar.bsky.social - very clear presentation of a complex concept #SystemsBiology #MathematicalBiology

Analyzing signaling activity and function in hematopoietic cells | Journal of Experimental Medicine | Rockefeller University Press

Final plenary of #ICSB2024 from Tim Schroeder @ethzurich.bsky.social making the case for long term live cell measurements doi.org/10.1084/jem....

BioModels BioModels is a repository of freely-available mathematical models of biological and biomedical systems. It hosts a vast selection of physiologically and pharmaceutically relevant mechanistic models in...

Rahuman Sheriff #ICSB2024 @ebi.embl.org asks Are Machine Learning Models of Biology FAIR? www.ebi.ac.uk/biomodels/ thread…spoiler alert, not always FAIR

Patient-specific signaling signatures predict optimal therapeutic combinations for triple negative breast cancer - Molecular Cancer Triple negative breast cancer (TNBC) is a heterogeneous group of tumors which lack estrogen receptor, progesterone receptor, and HER2 expression. Targeted therapies have limited success in treating TN...

1/2 Nataly Kravchenko-Balasha speaks to patient-specific approaches to identify steady-state dynamics and disease-deviation from that steady state. #ICSB2024 #systemsOncology #SystemsBiology doi.org/10.1186/s129...

Scalable and unbiased sequence-informed embedding of single-cell ATAC-seq data with CellSpace - Nature Methods By learning to embed DNA k-mers and cells into a joint space, CellSpace improves single-cell ATAC-seq analysis in multiple tasks such as latent structure discovery, transcription factor activity infer...

#sciencethread Christina Leslie describing Cell Space #ICSB2024 - embedding of DNA peaks (eg ATAC-seq kmers) into a common latent space. #SystemsGenomics doi.org/10.1038/s415...

Cyclin/Forkhead-mediated coordination of cyclin waves: an autonomous oscillator rationalizing the quantitative model of Cdk control for budding yeast - npj Systems Biology and Applications npj Systems Biology and Applications - Cyclin/Forkhead-mediated coordination of cyclin waves: an autonomous oscillator rationalizing the quantitative model of Cdk control for budding yeast

Matteo Barberis describing the minimal gene module for yeast cell cycle #ICSB2024 doi.org/10.1038/s415...

Wow look at that! 🤩
This stage has delivered some complex and fascinating stories the past few days. #ICSB2024

Peter Swain going from #yeast to #drosophila gene regulation and patterning #icsb2024 #iitb #systemsbiology

Great talk @kamatlab.bsky.social and welcome to 🦋! #ICSB2024

Hydrophobic mismatch drives self-organization of designer proteins into synthetic membranes - Nature Communications The organization of membrane proteins is critical to cellular function. Here the authors explore how computational protein design, MD simulation, and cell-free systems can be combined to elucidate how...

2/ can lipid rafts assist the loading of a desired protein into an extracellular vesicles? @kamatlab.bsky.social #ICSB2024 @naturecomms.bsky.social doi.org/10.1038/s414...

Interesting to hear how lipid membrane properties can impact on transmembrane protein assembly and interaction. @kamatlab.bsky.social #ICSB2024 #SyntheticBiology #SystemsBiology #MembraneBiology 🧪

Science 🧪word of the day ‘Umwelt’ courtesy of Madan Rao #ICSB2024
- used here to describe the way a cell senses it’s environment.

Cellular compartmentalisation and receptor promiscuity as a strategy for accurate and robust inference of position during morphogenesis An information theoretic and systems biology approach shows that cellular compartmentalisation and receptor promiscuity can facilitate the accurate and robust inference of position from noisy morphoge...

#ICSB2024 Madan Rao speaking to @elife.bsky.social Cellular compartmentalisation and receptor promiscuity as a strategy for accurate and robust inference of position during morphogenesis doi.org/10.7554/elif...

Who said computational biology is boring? Traditional Indian dance at #icsb2024

@stemcellsystems.bsky.social showing the effort of her lab in unifying and integrating macrophage gene expression data to produce an atlas of human myeloid compartment. Stemformatics.org #icsb2024 #iitbombay

Uppinder "Uppi" Bhalla from #NCBS_Bangalore on modelling neurons, #moose #databases and chemical v/s electrical signalling in #neurons #icsb2024 #iitb

KnotResolver: tracking self-intersecting filaments in microscopy using directed graphs AbstractMotivation. Quantification of microscopy time series of in vitro reconstituted motor-driven microtubule transport in “gliding assays” is typically

3/3 #ICSB2024 Nice image analysis tool available from the team to deconvolute loops that tangle or cross-over themselves doi.org/10.1093/bioi...

Cytoskeleton and Cell Shape (CyCelS) Lab

#ICSB2024 biological variation talks kicked off by Prof Chaitanya Athale looking at microtubule dynamics. www3.iiserpune.ac.in/~cathale/ 1/3

First day just ended with a glorious reception dinner! Excellent organisation and very lively scientific discussion! #icsb2024 #iitbombay

Resolving Crosstalk Between Signaling Pathways Using Mathematical Modeling and Time-Resolved Single Cell Data Crosstalk between signaling pathways can modulate the cellular response to stimuli and is therefore an important part of signal transduction. For a comprehensive understanding of cellular responses, i...

2/2 Jana Wolf Modelling cross talk between NFkB and p53 pathways in radiation induced death to understand patient responses to therapy. #ICSB2024 doi.org/10.1007/978-...

Redirecting

1/2 Jana Wolf models the dynamics of NFkB in cell death/ cell survival, considering multiple scales of time, molecular or cellular responses. #ICSB2024 Reviewed doi.org/10.1016/j.co...

Evolutionary signatures of human cancers revealed via genomic analysis of over 35,000 patients - Nature Communications The identification of cancer type-specific evolutionary signatures could be used for patient stratification. Here, the authors develop a method, ASCETIC, that utilises bulk and single-cell sequencing ...

Alex Graudenzi brings the #ICSB2024 cancer systems session back to cancer evolution- 1 model for each patient to understand history and prognosis. doi.org/10.1038/s414...

drGAT: Attention-Guided Gene Assessment of Drug Response Utilizing a Drug-Cell-Gene Heterogeneous Network - PubMed Drug development is a lengthy process with a high failure rate. Increasingly, machine learning is utilized to facilitate the drug development processes. These models aim to enhance our understanding o...

drGAT is a graph deep learning model that predicts drug sensitivity of cancer cell lines pubmed.ncbi.nlm.nih.gov/38800657/ #Icsb2024 #SystemsBiology

CellMinerCDB: NCATS Is a Web-Based Portal Integrating Public Cancer Cell Line Databases for Pharmacogenomic Explorations - PubMed CellMinerCDB: NCATS provides activity information for 2,675 drugs in 183 cancer cell lines and analysis tools to facilitate pharmacogenomic research and to identify determinants of response.

1/ Augustin Luna @cannin.bsky.social introduces CellMinerCDB pubmed.ncbi.nlm.nih.gov/37140427/ - enabling investigation of cell line to drug interactions #ICSB2024 #SystemsBiology

Integrated genetic and metabolic landscapes predict vulnerabilities of temozolomide resistant glioblastoma cells Metabolic reprogramming and its molecular underpinnings are critical to unravel the duality of cancer cell function and chemo-resistance. Here, we use a constraints-based integrated approach to deline...

Constraint-based modelling is the specialty of Prof Anu Raghunathan #ICSB2024 who predicts metabolic changes in glioblastoma contributes to chemotherapy resistance pmc.ncbi.nlm.nih.gov/articles/PMC...

Context-dependent effects of CDKN2A and other 9p21 gene losses during the evolution of oesophageal cancer CDKN2A is a tumour suppressor located in chromosome 9p21 and frequently lost in Barrett’s oesophagus (BO) and oesophageal adenocarcinoma (OAC). How CDKN2A and other 9p21 gene co-deletions affect OAC e...

5/5 @ciccarellilab.bsky.social shows that tumour suppressor genes such as CDKN2A can select against P53 loss. Context of loss of CDKN2A determines cancer evolution and prognosis @biorxivpreprint.bsky.social www.biorxiv.org/content/10.1... #ICSB2024 #SystemsOncology

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4/5 Tumour suppressor genes are (more commonly?) mutated in somatic precancerous cells than the cancer. Reviewed @cellpress.bsky.social doi.org/10.1016/j.cc... #ICSB2024 #SystemsOncology