Bioinformatics prediction of gene network and in silico gene perturbation (students in the Computer science major or with strong coding experiences are encouraged to apply)
Guo Huang, Professor
UC San Francisco
Applications for Fall 2024 are closed for this project.
There are emerging AI-trained models that integrate tremendous genomic, genetic and gene expression datasets to successfully predict complex gene networks and functional outcomes after in silico gene perturbation. Now we are exploring these models to understand organ physiology and pathology from developmental and evolutionary perspectives.
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Publications from previous URAP students [name]:
1. Hirose, K.*, Payumo, A. Y.*, Cutie, S., [Hoang, A.], et al., and Huang, G. N. (*, equal contribution) (2019 Apr) Evidence for hormonal control of heart regenerative capacity during endothermy acquisition. Science
2. Cutie, S., [Hoang, A. T.], Payumo, A. Y., and Huang, G. N. (2017 Dec) Unconventional functions of muscles in planarian regeneration. Developmental Cell
3. Hirose, K., [Chang, S.], et al., and Huang, G. N. (Submitted) Loss of a novel striated muscle-enriched mitochondrial protein Coq10a enhances postnatal cardiac hypertrophic growth.
4. [Amram, A.], Cutie, S., and Huang, G. N. (2021 Jan) Hormonal control of cardiac regenerative potential. Endocrine Connections
5. [Khyeam, S.], [Lee, S.], and Huang, G. N. (2021 May) Genetic, epigenetic, and postâtranscriptional basis of divergent tissue regenerative capacities among vertebrates. Advanced Genetics, e10042
6. Payumo, A. Y.*, Chen, X.*, Hirose, K., Chen, X., Hoang, A., [Khyeam, S.], Yu, H., Wang, J., Chen, Q., [Powers, N.], Chen, L., Bigley, R. B., Lovas, J., Hu, G., and Huang, G. N. (*, equal contribution) (2021 Sep) Adrenergic-thyroid hormone interactions drive postnatal thermogenesis and loss of mammalian heart regenerative capacity. Circulation
7. [Amram AV], Cutie S, Huang GN. (2021 Jan) Hormonal control of cardiac regenerative potential. Endocr Connect.
8. [Khyeam S], [Lee S], Huang GN. (2021 Jun) Genetic, Epigenetic, and Post-Transcriptional Basis of Divergent Tissue Regenerative Capacities Among Vertebrates. Adv Genetics.
9. [Powers N], Huang GN. (2022 May) Mending a broken heart with novel cardiogenic small molecules. Cell Regeneration
10. [Powers N], Huang GN. (2022 May) Visualization of regenerating and repairing hearts. Clin Sci.
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Please include in the application
(1) your career plan,
(2) daily schedule of committed hours to perform research in the lab (please exclude the commute time),
(3) prior research experience if any,
(4) a link to your LinkedIn profile (with your head photo),
(5) description of your background in computer science and/or coding.
(6) (optional) a one-sentence description if you are from diverse backgrounds in but not limited to ethnicity, sexual orientation, and geography (including international students with F1 visa).
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Role: Bioinformatics analysis of gene networks using single-cell RNA-seq and ATAC-seq datasets.
Qualifications: This position is open to all who are in the Computer Science major or with strong coding experiences.
Day-to-day supervisor for this project: Xiaoxin Chen, Post-Doc
Hours: 12 or more hours
Off-Campus Research Site: In person training at UCSF Mission Bay campus 555 Mission Bay Blvd South, San Francisco Flexile remote research after trainings is permitted and encouraged.
Related website: https://www.cvri.ucsf.edu/~huang/lab/People.html
Biological & Health Sciences