HudsonAlpha Research Report 2023-2024

CONTRIBUTORS

REFERENCES

CITATIONS: References

IMAGES: Adobe Stock Unsplash

p. 8-11 Moyers BA, et al. Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells. Genome Res. (2023) 33(11):1879-1892. DOI: 10.1101/ gr.278205.123. Loupe JM, et al. Multiomic profiling of tran- scription factor binding and function in human brain. Nat Neurosci. (2024) 27(7):1387-1399. DOI: 10.1038/s41593-024-01658-8.

p. 46-47 Roberts BS, et al. Probabilistic association of differentially expressed genes with cis-regulatory elements. Genome Res. 2024 May 15;34(4):620-632. Doi: 10.1101/gr.278598.123. Anderson AG, et al. Allele-specific transcription factor binding across human brain regions offers mechanistic insight into eQTLs. Genome Res. 2024 Sep 20;34(8):1224-1234. doi: 10.1101/gr.278601.123.

HudsonAlpha Archives Jeff White Photography National Agricultural Advisory Services Elizabeth City CVB Charlie Scutt

WRITER/PRODUCER: Sarah Sharman, PhD

p. 12-13 Carey, S.B., et al. ZW sex chromosome

structure in Amborella trichopoda. Nat. Plants 10, 1944–1954 (2024). DOI: 10.1038/s41477- 024-01858-x. p. 18-19 Hiatt, S.M., et al. Long-read genome sequenc- ing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders. Ge- nome Research (2024) 34 (12) DOI: 10.1101/ gr.279227.124. p. 22-25 Rogers, B., et al., Neuronal MAPT expression is mediated by long-range interactions with cis-regulatory elements. The American Jour- nal of Human Genetics (2024) 111, 259–279, DOI: 10.1016/j.ajhg.2023.12.015. p. 26-27 Gordon, E.R., et al. Transcriptomic and func- tional analysis of ANGPTL4 overexpression in pancreatic cancer nominates targets that reverse chemoresistance. BMC Cancer (2023) 23, 524 DOI: 10.1186/s12885-023-11010-1. p. 34-37 Trieu, A., et al., Transformation and gene editing in the bioenergy grass Miscanthus. Biotechnology for Biofuels and Bioproducts 15, 148 (2022). DOI: 10.1186/s13068-022-02241-8. Fu J, et al. Cell-type-specific transcriptom- ics uncovers spatial regulatory networks in bioenergy sorghum stems. Plant J. 2024 Jun;118(5):1668-1688. doi: 10.1111/tpj.16690. Epub 2024 Feb 26. p. 38-39 Reed J, et al. Elucidation of the pathway for biosynthesis of saponin adjuvants from the soapbark tree. Science. (2023) 379(6638):1252- 1264. DOI: 10.1126/science.adf3727. Jo, S., et al. Unlocking saponin biosynthesis in soapwort. Nat Chem Biol (2024). DOI: 10.1038/ s41589-024-01681-7. p. 42-43 Sreedasyam, A., et al. Genome resources for three modern cotton lines guide future breed- ing efforts. Nat. Plants (2024) 10, 1039–1051. DOI: 10.1038/s41477-024-01713-z Healey, A.L., et al. The complex polyploid genome architecture of sugarcane. Nature (2024) 628, 804–810. DOI: 10.1038/s41586- 024-07231-4

FUNDING SOURCES

DESIGNER: Cathleen Shaw

HUDSONALPHA RESEARCH AFFAIRS TEAM:

Research at HudsonAlpha is made possible by generous philanthropic donations, private foundations, the State of Alabama, and federal grants. The work cited in this report was supported as follows: p. 8-11: National Institutes of Health (NIH) grant UM- 1HG009411; National Institutes of Health grant 5R01MH110472 ; the Memory and Mobility Fund from HudsonAlpha Institute for Biotechnology; and support from the Pritzker Neuropsychiatric Research Consortium p. 12-13: National Science Foundation (NSF) IOS-PGRP CA- REER no. 2239530; US Department of Energy (DOE) Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, was supported under contract no. DE-AC02-05CH11231

Flo Behn, PhD Nancy Westfall

LaShawn Jackson Aida Starling, PhD Alissa Mackiewicz

Special thanks to Lillie Mermoud for editorial contributions

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