- Jul 2023
- The landscape of biomedical research
- Rita González-Márquez,
- Luca Schmidt,
- Benjamin M. Schmidt,
- Philipp Berens
- Dmitry Kobak
- April 11, 2023
- The number of publications in biomedicine and life sciences
- has rapidly grown over the last decades,
- with over 1.5 million papers now published every year.
- This makes it difficult to
- keep track of new scientific works and
- to have an overview of the evolution of the field as a whole.
- Here we
- present a 2D atlas of the entire corpus of biomedical literature, and
- argue that it provides
- a unique and
- useful overview
- of the life sciences research.
- We base our atlas on the abstract texts of
- 21 million English articles from the PubMed database.
- To embed the abstracts into 2D, we use
- a large language model PubMedBERT, combined with
- t-SNE tailored to handle samples of our size.
- We use our atlas to study
- the emergence of the Covid-19 literature,
- the evolution of the neuroscience discipline,
- the uptake of machine learning, and
- the distribution of gender imbalance in academic authorship.
- Furthermore, we present an interactive web version of our atlas that
- allows easy exploration and
- will enable further insights and facilitate future research.
- Oct 2021
Pavord, S., Scully, M., Hunt, B. J., Lester, W., Bagot, C., Craven, B., Rampotas, A., Ambler, G., & Makris, M. (2021). Clinical Features of Vaccine-Induced Immune Thrombocytopenia and Thrombosis. New England Journal of Medicine, NEJMoa2109908. https://doi.org/10.1056/NEJMoa2109908
- University College London Hospitals Biomedical Research Centre
- blood clotting
- Jun 2020
Balloux, F. (2020, May 22) A thread written by @BallouxFrancois. Threader. https://threader.app/thread/1263745877702737920
Zhang, S. (2020, April 8). The Best Hopes for a Coronavirus Drug. The Atlantic. https://www.theatlantic.com/science/archive/2020/04/what-coronavirus-drug-will-look-like/609661/
- May 2020
Ruggeri, K., Linden, S., Wang, C., Papa, F., Riesch, J., & Green, J. (2020, May 7). Standards for evidence in policy decision-making. https://doi.org/10.31234/osf.io/fjwvk
Ferguson, N., Laydon, D., & Nedjati-Gilani, G. (2020). How can we help stop the COVID-19 pandemic? Biomedical Science Journal for Teens. https://www.imperial.ac.uk/media/imperial-college/medicine/mrc-gida/2020-04-28-SJK-Report-9.pdf
- containment measures
- social distancing
- healthcare system
- school closure
Andersen, K.G., Rambaut, A., Lipkin, W.I. et al. The proximal origin of SARS-CoV-2. Nat Med 26, 450–452 (2020). https://doi.org/10.1038/s41591-020-0820-9
Hope, T., Borchardt, J., Portenoy, J., Vasan, K., & West, J. (2020, May 6). Exploring the COVID-19 network of scientific research with SciSight. Medium. https://medium.com/ai2-blog/exploring-the-covid-19-network-of-scientific-research-with-scisight-f75373320a8c
- knowledge sharing
- information sharing
- Apr 2015
his Web portal provides users with a flexible and expandable suite of resources to enable variant-, gene-, and exome-level sequence analysis in a secure, Web-based, and user-friendly fashion. Users can also elect to share data with other MSeqDR Consortium members, or even the general public, either by custom annotation tracks or through the use of a convenient distributed annotation system (DAS) mechanism
Need to look into the DAS and portals like this that are annotating sequences.