Bioinformatics Group Freiburg group talk

Galaxy pipeline for the identification of non-canonical ORFs and their potential biological function.

References

Babu, M., Kriwacki, R. W., & Pappu, R. V. (2012). Versatility from protein disorder. Science, 337(6101), 1460-1461.

Berlow, R. B., Dyson, H. J., & Wright, P. E. (2018). Expanding the paradigm: intrinsically disordered proteins and allosteric regulation. Journal of molecular biology, 430(16), 2309-2320.

Chakrabarti, P., & Chakravarty, D. (2022). Intrinsically disordered proteins/regions and insight into their biomolecular interactions. Biophysical Chemistry, 283, 106769

Choi, S. W., Kim, H. W., & Nam, J. W. (2019). The small peptide world in long noncoding RNAs. Briefings in bioinformatics, 20(5), 1853-1864.

Erady, Chaitanya, et al. (2021). Pan-cancer analysis of transcripts encoding novel open-reading frames (nORFs) and their potential biological functions." NPJ Genomic Medicine 6.1: 4.

Luo, X., Huang, Y. et al. (2022). SPENCER: a comprehensive database for small peptides encoded by noncoding RNAs in cancer patients. Nucleic Acids Research, 50(D1), D1373-D1381.

Prensner, J. R., Enache, et al. (2021). Noncanonical open reading frames encode functional proteins essential for cancer cell survival. Nature biotechnology, 39(6), 697-704.

Steinberg, R., & Koch, H. G. (2021). The largely unexplored biology of small proteins in pro‐and eukaryotes. The FEBS journal, 288(24), 7002-7024.

Vitting-Seerup, K., & Sandelin, A. (2019). IsoformSwitchAnalyzeR: analysis of changes in genome-wide patterns of alternative splicing and its functional consequences. Bioinformatics, 35(21), 4469-4471.

Wright, B. W., Yi, Z., Weissman, J. S., & Chen, J. (2022). The dark proteome: translation from noncanonical open reading frames. Trends in Cell Biology, 32(3), 243-258.

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