miR-6850 Drives Phenotypic Changes and Signaling in High Grade Serous Ovarian Cancer https://www.biorxiv.org/content/10.1101/2025.07.30.667620v1
02.08.2025 10:51 β π 0 π 1 π¬ 0 π 0
Loss of tumour suppressor p53 rewires enhancer landscape and governs oncogenic progression https://www.biorxiv.org/content/10.1101/2025.07.28.667341v1
02.08.2025 19:33 β π 3 π 1 π¬ 0 π 0
Breast cancer identity is defined by specialized enhancer sets via lysine deacetylation https://www.biorxiv.org/content/10.1101/2025.07.31.668008v1
02.08.2025 19:48 β π 0 π 1 π¬ 0 π 0
Umap and Bismap: quantifying genome and methylome mappability
Abstract. Short-read sequencing enables assessment of genetic and biochemical traits of individual genomic regions, such as the location of genetic variati
We are creating new software to quantify genome mappability, a successor to Umap, our previous work described in the linked paper. What standard read lengths should we provide in BED/Wiggle format? Previous was 24/36/50/100 bp. academic.oup.com/nar/article/...
01.08.2025 18:51 β π 26 π 4 π¬ 5 π 0
Histone Acetylation Differentially Modulates CTCF-CTCF Loops and Intra-TAD Interactions https://www.biorxiv.org/content/10.1101/2025.07.29.667515v1
01.08.2025 20:33 β π 6 π 3 π¬ 0 π 0
PEANUT: Pathway Enrichment Analysis through Network Utilization. #PathwayEnrichment #Bioinformatics 𧬠π₯οΈ
academic.oup.com/bioinformati...
25.07.2025 09:15 β π 3 π 1 π¬ 0 π 0
Excited to share one of the first papers to link #lncRNA #structure to its function in #cancer!
We mapped the structure of a tumor-suppressive DRAIC lncRNA and identified a 36-nucleotide hairpin as necessary and sufficient for its #anti-oncogenic function.
www.sciencedirect.com/science/arti...
25.07.2025 19:52 β π 7 π 2 π¬ 0 π 0
Quite an optimistic viewpoint here....we have a long way to go to reduce the toll of cancer
www.economist.com/leaders/2025...
17.07.2025 14:28 β π 107 π 13 π¬ 11 π 4
Neutrophils drive vascular occlusion, tumour necrosis and metastasis - Nature
Neutrophils actively induce tumour necrosis, driving vascular occlusion, pleomorphic necrosis and metastasis.
As a new postdoc in my lab (@cshlnews.bsky.social β @jhu.edu) @adrover.bsky.social (now @crick.ac.uk) saw NETs in tumorsβI shrugged. But he looked closer in 3D: NETs block tumor vessels, driving necrosis, hypoxia, EMT & metastasis.
π www.nature.com/articles/s41...
@jhu-bdps.bsky.social @nature.com
17.07.2025 19:26 β π 36 π 10 π¬ 0 π 1
#Perplexity is a helpful resource in science. I ask my question, look at the response, and then always ask "show me the publications" that I then read. If we don't use these tools we will be like ostriches with heads in the sand. If we use them without checks & balances; however, we are fools. #AI
15.07.2025 03:53 β π 2 π 1 π¬ 1 π 0
5-hydroxymethylcytosine deposition mediates Polycomb Repressive Complex 2 function in MYCN-amplified neuroblastoma https://www.biorxiv.org/content/10.1101/2025.07.05.663256v1
10.07.2025 04:48 β π 0 π 1 π¬ 0 π 0
OpenAI's o3 tops new AI league table for answering scientific questions
SciArena uses votes by researchers to evaluate large language modelsβ responses on technical topics.
o3, an AI model developed by the creators of ChatGPT, has been ranked the best AI tool for answering science questions in multiple fields, according to a benchmarking platform launched last week by the Allen Institute for Artificial Intelligence
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www.nature.com/articles/d41...
11.07.2025 07:00 β π 6 π 3 π¬ 2 π 1
An expanded reference catalog of translated open reading frames for biomedical research
Non-canonical (i.e., unannotated) open reading frames (ncORFs) have until recently been omitted from reference genome annotations, despite evidence of their translation, limiting their incorporation into biomedical research. To address this, in 2022, we initiated the TransCODE consortium and built the first community-driven consensus catalog of human ncORFs, which was openly distributed to the research community via Ensembl-GENCODE. While this catalog represented a starting point for reference ncORF annotation, major technical and scientific issues remained. In particular, this initial catalogue had no standardized framework to judge the evidence of translation for individual ncORFs. Here, we present an expanded and refined catalog of the human reference annotation of ncORFs. By incorporating more datasets and by lifting constraints on ORF length and start-codon, we define a comprehensive set of 28,359 ncORFs that is nearly four times the size of the previous catalog. Furthermore, to aid users who wish to work with ncORFs with the strongest and most reproducible signals of translation, we utilized a data-driven framework (i.e. translation signature scores) to assess the accumulated evidence for any individual ncORF. Using this approach, we derive a subset of 7,888 ncORFs with translation evidence on par with canonical protein-coding genes, which we refer to as the Primary set. This set can serve as a reliable reference for downstream analyses and validation, with a particular emphasis on high quality. Overall, this update reflects continual community-driven efforts to make ncORFs accessible and actionable to the broader research public and further iterations of the catalog will continue to expand and refine this resource. ### Competing Interest Statement J.R.P. has received research honoraria from Novartis Biosciences and Quantum-Si, and is a paid consultant for ProFound Therapeutics. J.L.A. is an advisor to Microneedle Solutions. G.M. is co-founder and CSO of OHMX.bio. P.F. is a member of the scientific advisory board of Infinitopes. A.-R. C. is a member of the advisory board of ProFound Therapeutics. P.V.B. is a cofounder and shareholder of Eirnabio Ltd.
Are you looking to study the #darkproteome but don't know where to start?
Never fear, we've got your back.
Here, we share the latest catalog for #RiboSeq #ORFs.
Thanks to Sonia Chothani and @jruizorera.bsky.social for leading!
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#GENESky
#bioinformatics
www.biorxiv.org/content/10.1...
07.07.2025 13:24 β π 22 π 8 π¬ 1 π 0
Cancer type-specific association of p53 deficiency with aneuploidy and chromosome losses https://www.biorxiv.org/content/10.1101/2025.07.04.663162v1
07.07.2025 17:48 β π 1 π 1 π¬ 0 π 0
Review: Structural variants in the 3D genome as drivers of disease www.nature.com/articles/s41... (read free: rdcu.be/eu0KR) π§¬π₯οΈπ§ͺ
07.07.2025 18:31 β π 9 π 1 π¬ 0 π 0
An optimised computational approach for the identification of somatic structural variants in cancer. #SomaticStructuralVariants #CancerGenetics #Genomics #Bioinformatics #ToolsBenchmarking @biorxiv-bioinfo.bsky.social 𧬠π₯οΈ
www.biorxiv.org/content/10.1...
06.07.2025 18:05 β π 6 π 1 π¬ 0 π 0
Gain of Function p53 mutant R273H confers distinct methylation profiles and consequent partial or full EMT states to colon tumour https://www.biorxiv.org/content/10.1101/2025.07.03.662954v1
06.07.2025 05:47 β π 1 π 1 π¬ 0 π 0
The Somatic Mosaicism across Human Tissues Network - Nature
The Somatic Mosaicism across Human Tissues Network aims to create a reference catalogue of somatic mosaicism across different tissues and cells within individuals.
We are all somatic mutation mosaics.
"There are trillions of cells in a human body and so the total number of somatic mutations acquired in a single individual may well exceed quadrillions, millions of times the size of the human genome."
@nature.com
nature.com/articles/s41...
02.07.2025 16:21 β π 113 π 33 π¬ 1 π 1
Studying cellular #stress responses, particularly #senescence and its impact on #immune response, #ageing and #cancer, #tumorigenesis at Cancer Research UK CI βͺ@cruk-ci.bsky.socialβ¬, University of Cambridge βͺ@cam.ac.ukβ¬
Website: naritalab.com
Incoming Group Leader of Cancer Immunology
University of Oxford
We are a free biomedical research literature discovery platform that uses machine learning and expert curation. Find out more https://biomed.news
β¨ Tools for caregiving, built with compassion and conscience. We stand for LGBTQIA+ rights, health equity, racial equality, sustainability, and economic justice.β¨
#Health #Healthcare #ElderCare #News
π·πβ₯οΈπ°
linktr.ee/ceceliacares
Pronounced: CHEE-DEM
Postdoc at Cancer Early Detection Advanced Research (CEDAR) Center, @ohsuknight.bsky.social | Interpretable ML| Computational and Systems Biology
Interested in DNA damage, mutations, adaptation and evolution.
Postdoctoral bioinformatician at the University of Edinburgh Institute of Genetics and Cancer.
Currently working on chromosomal instability and mutational landscapes in tumours.
Happiest when out in nature!
Prof (CS @Stanford), Co-Director @StanfordHAI, Cofounder/CEO @theworldlabs, CoFounder @ai4allorg #AI #computervision #robotics #AI-healthcare
Meet new people
Computational Biologist in Singapore. Nocturnal baker and maker of caffeinated beverages.
A platform for life sciences. Publications, research protocols, news, events, jobs and more. Sign up at https://www.lifescience.net.
Research Group Leader at the University of Cologne - Enthusiastic about mitochondrial dynamics and cell division
Kadance provides DNA insights for genetic cancer risk, personalized medication guidance, and expert cancer support. www.kadance.com
Cancer researcher, Oncolytic Viruses - @boehringer Ingelheim, @GlasgowECMC, @UniversityofGlasgow, @DKFZ, @DKTK, @DKTK- Essen, @US Department of State.
Oxford University's Medical Sciences Division is an internationally recognised centre of excellence for biomedical and clinical research and teaching, comprised of 16 core departments and the School of Medicine and Biomedical Sciences. www.medsci.ox.ac.uk
Previvor | Lynch Syndrome (MSH6) & CHEK2
Podcast Host π | Keynote Speaker π€
Advocating for hereditary cancer awareness & prevention
Host of The Positive Gene Podcast
Building personalized Bluesky feeds for academics! Pin Paper Skygest, which serves posts about papers from accounts you're following: https://bsky.app/profile/paper-feed.bsky.social/feed/preprintdigest. By @sjgreenwood.bsky.social and @nkgarg.bsky.social
Thriving with polyposis. Patient advocate and PPI rep Lynch Syndrome Ireland Group. Hereditary cancer awareness & support. Passionate about cancer research and PPI. Tries a bit of gardening π±πΊπ
