During 2023, the Gerstein lab continued research in several core areas, including cancer genomics, regulatory networks, variant impact, and privacy. We also explored new topics, such as COVID-19. The findings from these studies were published in various high-impact journals, including Cell, Bioinformatics, and PLoS Computational Biology.

A highlight of the year was the publication of the ENTEx project (1). This project involved the generation of a large-scale multi-tissue personal epigenomic resource and a catalog comprising over 1.3 million single-nucleotide variants associated with allele-specific events. We presented several applications of the dataset, including decorating regulatory elements, modeling expression quantitative trait loci in hard-to-obtain tissues, and identifying transcription factor motifs that are "sensitive" to allele-specific events.

One of the new focuses of the lab was COVID-19. We investigated the spatiotemporal flow of SARS-CoV-2 using genetic sequences, providing insights into the development of mitigation strategies (2). In another study, we constructed a model to understand the interactions between the virus and other microbes or human genes (3).

We continued our work in quantum computing and privacy. We incorporated quantum computing into drug design (4) and integrated homomorphic encryption into cancer analysis for privacy protection (5).

Our contributions extended to collaborative efforts in cancer genomics (6, 7, 8), notably resulting in a publication in Nature. Additionally, we engaged in collaborations exploring protein binding (9, 10). An interesting discovery emerged from our research, revealing connections between delayed sleep patterns and social media usage (11, 12).

We systematically summarized the impact of variants on diseases in a review paper (13). Additionally, we reviewed the book "Quantum Supremacy," which deepened our understanding of quantum computing (14), and "Optimal Illusions," a book that discussed society's obsession with optimization (15).

1. Rozowsky, J., et al., The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell, 2023. 186(7): p. 1493-1511 e40.

2. Salichos, L., et al., Genetic determination of regional connectivity in modelling the spread of COVID-19 outbreak for more efficient mitigation strategies. Sci Rep, 2023. 13(1): p. 8470.

3. Lou, S., et al., Constructing a full, multiple-layer interactome for SARS-CoV-2 in the context of lung disease: Linking the virus with human genes and microbes. PLoS Comput Biol, 2023. 19(7): p. e1011222.

4. Lau, B., et al., Insights from incorporating quantum computing into drug design workflows. Bioinformatics, 2023. 39(1).

5. Sarkar, E., et al., Privacy-preserving cancer type prediction with homomorphic encryption. Sci Rep, 2023. 13(1): p. 1661.

6. Erwin, G.S., et al., Recurrent repeat expansions in human cancer genomes. Nature, 2023. 613(7942): p. 96-102.

7. Minteer, C.J., et al., More than bad luck: Cancer and aging are linked to replication-driven changes to the epigenome. Sci Adv, 2023. 9(29): p. eadf4163.

8. Augspach, A., et al., Minor intron splicing is critical for survival of lethal prostate cancer. Mol Cell, 2023. 83(12): p. 1983-2002 e11.

9. Shi, G., et al., Proteome-wide screening for mitogen-activated protein kinase docking motifs and interactors. Sci Signal, 2023. 16(767): p. eabm5518.

10. Chen, Z., et al., Binding peptide generation for MHC Class I proteins with deep reinforcement learning. Bioinformatics, 2023. 39(2).

11. Meyerson, W.U., et al., Estimation of Bedtimes of Reddit Users: Integrated Analysis of Time Stamps and Surveys. JMIR Form Res, 2023. 7: p. e38112.

12. Meyerson, W.U., et al., The association between evening social media use and delayed sleep may be causal: Suggestive evidence from 120 million Reddit timestamps. Sleep Med, 2023. 107: p. 212-218.

13. Kumar, S. and M. Gerstein, Unified views on variant impact across many diseases. Trends Genet, 2023. 39(6): p. 442-450.

14. Greenbaum, D. and M. Gerstein, Calculating the future. Science, 2023. 380(6645): p. 589.

15. Greenbaum, D. and M. Gerstein, Resisting efficiency's overreach. Science, 2023. 381(6663): p. 1162.