References · USH2A Molecular Research Initiative

References

Last bibliographic review: 2026-10-12. Method papers explain tools; they do not validate this project’s variant-specific predictions. Project results are traced separately in the evidence registry.

1. NCBI RefSeq Homo sapiens usherin (USH2A), transcript variant 2, mRNA — NM_206933.4.

Classical long transcript; sequence facts only. Verified database record.

2. NCBI RefSeq Homo sapiens usherin (USH2A), transcript variant 1, mRNA — NM_007123.6.

Classical short transcript; sequence facts only. Verified database record.

3. UniProt Consortium Usherin — UniProtKB O75445 (USH2A_HUMAN).

Topology/domain annotations; evidence qualifiers must be retained. Verified database record.

4. NCBI Gene USH2A usherin [Homo sapiens] — Gene ID 7399.

General gene/disease annotation; not an individual prognosis. Verified database record.

5. Wang H, Du H, Ren R, et al. (2023). Temporal and spatial assembly of inner ear hair cell ankle link condensate through phase separation. Nature communications. Open-access full text.

General construct-specific experimental background; not G1526R-specific evidence. Verified database record.

6. Jaganathan K, Kyriazopoulou Panagiotopoulou S, McRae JF, et al. (2019). Predicting Splicing from Primary Sequence with Deep Learning. Cell.

Method publication; this paper does not validate the project-specific G1526R prediction. Verified database record. Verified database record. Verified database record. Verified database record. Verified database record. Verified database record. Verified database record. Verified database record.

7. Zeng T, Li YI. (2022). Predicting RNA splicing from DNA sequence using Pangolin. Genome biology. Open-access full text.

8. Avsec Ž, Latysheva N, Cheng J, et al. (2026). Advancing regulatory variant effect prediction with AlphaGenome. Nature. Open-access full text.

9. Jumper J, Evans R, Pritzel A, et al. (2021). Highly accurate protein structure prediction with AlphaFold. Nature. Open-access full text.

10. Mirdita M, Schütze K, Moriwaki Y, et al. (2022). ColabFold: making protein folding accessible to all. Nature methods. Open-access full text.

11. Frenz B, Lewis SM, King I, et al. (2020). Prediction of Protein Mutational Free Energy: Benchmark and Sampling Improvements Increase Classification Accuracy. Frontiers in bioengineering and biotechnology. Open-access full text.

12. Dieckhaus H, Brocidiacono M, Randolph NZ, et al. (2024). Transfer learning to leverage larger datasets for improved prediction of protein stability changes. Proceedings of the National Academy of Sciences of the United States of America. Open-access full text.

13. Eastman P, Galvelis R, Peláez RP, et al. (2024). OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The journal of physical chemistry. B. Open-access full text.