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. “}}
Archive for the 'SciLit' Category
Creating a functional single-chromosome yeast – PubMed
December 29, 2025The Mediator complex: a central integrator of transcription | Nature Reviews Molecular Cell Biology
December 29, 2025https://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
Psychotic symptoms in bipolar disorder and their impact on the illness: A systematic review
December 23, 2025Chakrabarti, 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
Creation of a bacterial cell controlled by a chemically synthesized genome – PubMed
December 23, 2025https://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
How to use likelihood ratios to interpret evidence from randomized trials – ScienceDirect
November 30, 2025Rare genetic variants confer a high risk of ADHD and implicate neuronal biology | Nature
November 23, 2025https://www.nature.com/articles/s41586-025-09702-8
Demontis, D., Duan, J., Hsu, Y. H., Pintacuda, G., Grove, J., Nielsen, T. T., Thirstrup, J., Martorana, M., Botts, T., Satterstrom, F. K., Bybjerg-Grauholm, J., Tsai, J. H. Y., Glerup, S., Hoogman, M., Buitelaar, J., Klein, M., Ziegler, G. C., Jacob, C., Grimm, O., . . . Børglum, A. D. (2025). Rare genetic variants confer a high risk of ADHD and implicate neuronal biology. Nature.
https://doi.org/10.1038/s41586-025-09702-8
QT:{{”
Common genetic variants associated with the disorder have been identified12,13, but the role of rare variants in ADHD is mostly unknown. Here, by analysing rare coding variants in exome-sequencing data from 8,895 individuals with ADHD and 53,780 control individuals, we identify three genes (MAP1A, ANO8 and ANK2; P < 3.07 × 10−6; odds ratios 5.55–15.13) that are implicated in ADHD.
“}}
Follow-up on error-controlled hypothesis generation
November 22, 2025Chen, W., Jiang, Y., Noble, W. S., & Lu, Y. Y. (2025).
Error-controlled non-additive interaction discovery in machine learning models. Nature Machine Intelligence, 7(9), 1541–1554. https://doi.org/10.1038/s42256-025-01086-8
Crystal structure of globular domain of histone H5 and its implications for nucleosome binding – PubMed
October 19, 2025The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery: Cell
October 18, 2025Capstone reviews/perspectives for reference
**IHEC**
The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery
Hendrik G. Stunnenberg ∙ The International Human Epigenome Consortium4 ∙ Martin Hirst
Stunnenberg, H. G., Hirst, M., Abrignani, S., Adams, D., De Almeida, M., Altucci, L., Amin, V., Amit, I., Antonarakis, S. E., Aparicio, S., Arima, T., Arrigoni, L., Arts, R., Asnafi, V., Esteller, M., Bae, J., Bassler, K., Beck, S., Berkman, B., . . . Zipprich, G. (2016). The International Human Epigenome Consortium: a blueprint for Scientific collaboration and Discovery. Cell, 167(5), 1145–1149.
https://doi.org/10.1016/j.cell.2016.11.007
** EXRNA**
The Extracellular RNA Communication Consortium: Establishing Foundational Knowledge and Technologies for Extracellular RNA Research
Das, S., Ansel, K. M., Bitzer, M., Breakefield, X. O., Charest, A., Galas, D. J., Gerstein, M. B., Gupta, M., Milosavljevic, A., McManus, M. T., Patel, T., Raffai, R. L., Rozowsky, J., Roth, M. E., Saugstad, J. A., Van Keuren-Jensen, K., Weaver, A. M., Laurent, L. C., Abdel-Mageed, A. B., . . . Zhang, H. (2019). The Extracellular RNA Communication Consortium: Establishing foundational knowledge and technologies for extracellular RNA research. Cell, 177(2), 231–242. https://doi.org/10.1016/j.cell.2019.03.023
**ENCODE3**
Perspectives on ENCODE
The ENCODE Project Consortium, Michael P Snyder 1,2,✉, Thomas R Gingeras 3, Jill E Moore 4, Zhiping Weng 4,5,6, Mark B Gerstein 7, Bing Ren 8,9, Ross C Hardison 10, John A Stamatoyannopoulos 11,12,13, Brenton R Graveley 14, Elise A Feingold 15, Michael J Pazin 15, Michael Pagan 15, Daniel A Gilchrist 15, Benjamin C Hitz 1, J Michael Cherry 1, Bradley E Bernstein 16, Eric M Mendenhall 17,18, Daniel R Zerbino 19, Adam Frankish 19, Paul Flicek 19, Richard M Myers 18
Abascal, F., Acosta, R., Addleman, N. J., Adrian, J., Afzal, V., Aken, B., Ai, R., Akiyama, J. A., Jammal, O. A., Amrhein, H., Anderson, S. M., Andrews, G. R., Antoshechkin, I., Ardlie, K. G., Armstrong, J., Astley, M., Banerjee, B., Barkal, A. A., Barnes, I. H. A., . . . Myers, R. M. (2020).
Perspectives on ENCODE. Nature, 583(7818), 693–698.
https://doi.org/10.1038/s41586-020-2449-8
A computational pipeline for spatial mechano-transcriptomics | Nature Methods
September 7, 2025https://www.nature.com/articles/s41592-025-02618-1
Hallou, A., He, R., Simons, B. D., & Dumitrascu, B. (2025). A computational pipeline for spatial mechano-transcriptomics. Nature Methods. https://doi.org/10.1038/s41592-025-02618-1
Reviews:
https://www.nature.com/articles/s41580-023-00583-1#Sec35
(difficult to follow)
Combining with Spatial transcriptomics:
https://www.nature.com/articles/s41592-025-02618-1
(new thing)
linkstream2 microblog 