Archive for the 'SciLit' Category

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Nature medcine “A minimally invasive dried blood spot biomarker test for the detection of Alzheimer’s dis ease pathology”

January 26, 2026

QT:{{”
The DROP-AD project investigates the potential of dried plasma spot (DPS) and dried blood spot (DBS) analysis, derived from capillary blood, for detecting AD biomarkers, including phosphorylated tau at amino acid 217 (p-tau217), glial fibrillary acidic protein and neurofilament light. …. Similarly, we demonstrated the successful detection of glial fibrillary acidic protein and neurofilament light with strong correlations between DBS and DPS, respectively, using paired venous plasma samples.
“}}

Might find this paper very interesting. Just published this month in Nature Medicine. “A minimally invasive dried blood spot biomarker test for the detection of Alzheimer’s disease pathology.”

A minimally invasive dried blood spot biomarker test for the detection of Alzheimer’s disease pathology – Nature Medicine
https://www.nature.com/articles/s41591-025-04080-0

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Xpresso

January 25, 2026

https://xpresso.gs.washington.edu/

Agarwal V, Shendure J. Predicting mRNA abundance directly from genomic sequence using deep convolutional neural networks. 2020. Cell Reports 31 (7), 107663.

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Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation | Nature Genetics

January 25, 2026

https://github.com/calico/borzoi

N&V – https://www.nature.com/articles/s41588-025-02154-w

https://www.nature.com/articles/s41588-024-02053-6#:~:text=This%20paper%20proposes%20a%20new%20machine%2Dlearning%20model%2C,that%20drive%20RNA%20expression%20and%20post%2Dtranscriptional%20regulation QT:{{” ere, we introduce Borzoi, a model that learns to predict cell-type-specific and tissue-specific RNA-seq coverage from DNA sequence. “}}

Linder, J., Srivastava, D., Yuan, H., Agarwal, V., & Kelley, D. R. (2025). Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation. Nature Genetics, 57(4), 949–961.
https://doi.org/10.1038/s41588-024-02053-6

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Predicting cell type-specific epigenomic profiles accounting for distal genetic effects | Nature Communications

January 25, 2026

https://www.nature.com/articles/s41467-024-54441-5
QT:{{” Enformer Celltyping can predict in new cell types, imputing their epigenetic signal, by embedding global and local chromatin accessibility (ATAC-Seq) signals for the cell type of interest. “}}

Murphy, A. E., Beardall, W., Rei, M., Phuycharoen, M., & Skene, N. G. (2024). Predicting cell type-specific epigenomic profiles accounting for distal genetic effects. Nature Communications, 15(1), 9951. https://doi.org/10.1038/s41467-024-54441-5

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From R.A. Fisher’s 1918 Paper to GWAS a Century Later | Genetics | Oxford Academic

January 1, 2026

https://academic.oup.com/genetics/article/211/4/1125/5931511

Visscher, P. M., & Goddard, M. E. (2019). From R.A. Fisher’s 1918 paper to GWAS a century later. Genetics, 211(4), 1125–1130.
https://doi.org/10.1534/genetics.118.301594

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The human disease network | PNAS

January 1, 2026

https://www.pnas.org/doi/10.1073/pnas.0701361104?url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org&rfr_dat=cr_pub++0pubmed QT:{{” We find that essential human genes are likely to encode hub proteins and are expressed widely in most tissues. This suggests that disease genes also would play a central role in the human interactome. In contrast, we find that the vast majority of disease genes are nonessential and show no tendency to encode hub proteins, and their expression pattern indicates that they are localized in the functional periphery of the network. “}}

Goh, K., Cusick, M. E., Valle, D., Childs, B., Vidal, M., & Barabási, A. (2007). The human disease network. Proceedings of the National Academy of Sciences, 104(21), 8685–8690.
https://doi.org/10.1073/pnas.0701361104

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Creating a functional single-chromosome yeast – PubMed

December 29, 2025

https://pubmed.ncbi.nlm.nih.gov/30069045/
QT:{{” Eukaryotic genomes are generally organized in multiple chromosomes. Here we have created a functional single-chromosome yeast from a Saccharomyces cerevisiae haploid cell containing sixteen linear chromosomes, by successive end-to-end chromosome fusions and centromere deletions. The fusion of sixteen native linear chromosomes into a single chromosome results in marked changes to the global three-dimensional structure of the chromosome due to the loss of all centromere-associated inter-chromosomal interactions, most
telomere-associated inter-chromosomal interactions and 67.4% of intra-chromosomal interactions. However, the single-chromosome and wild-type yeast cells have nearly identical transcriptome and similar phenome profiles. The giant single chromosome can support cell life, although this strain shows reduced growth across environments, competitiveness, gamete production and viability. “}}

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The Mediator complex: a central integrator of transcription | Nature Reviews Molecular Cell Biology

December 29, 2025

https://www.nature.com/articles/nrm3951

Allen, B. L., & Taatjes, D. J. (2015). The Mediator complex: a central integrator of transcription. Nature Reviews Molecular Cell Biology, 16(3), 155–166. https://doi.org/10.1038/nrm3951

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Psychotic symptoms in bipolar disorder and their impact on the illness: A systematic review

December 23, 2025

Chakrabarti, S., & Singh, N. (2022). Psychotic symptoms in bipolar disorder and their impact on the illness: A systematic review. World Journal of Psychiatry, 12(9), 1204–1232.
https://doi.org/10.5498/wjp.v12.i9.1204

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Creation of a bacterial cell controlled by a chemically synthesized genome – PubMed

December 23, 2025

https://pubmed.ncbi.nlm.nih.gov/20488990/

Gibson, D. G., Glass, J. I., Lartigue, C., Noskov, V. N., Chuang, R., Algire, M. A., Benders, G. A., Montague, M. G., Ma, L., Moodie, M. M., Merryman, C., Vashee, S., Krishnakumar, R., Assad-Garcia, N., Andrews-Pfannkoch, C., Denisova, E. A., Young, L., Qi, Z.,
Segall-Shapiro, T. H., . . . Venter, J. C. (2010). Creation of a bacterial cell controlled by a chemically synthesized genome. Science, 329(5987), 52–56. https://doi.org/10.1126/science.1190719

booting up a synthetic genome JCVI-syn1.0

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