Modular modeling improves the predictions of genetic variant effects on splicing

Autor: Jun Cheng, Julien Gagneur, Nguyen Tyd, Žiga Avsec, Muhammed Hasan Çelik, Kamil J. Cygan, William G. Fairbrother

Predicting the effects of genetic variants on splicing is highly relevant for human genetics. We describe the framework MMSplice (modular modeling of splicing) with which we built the winning model of the CAGI 2018 exon skipping prediction challenge.

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9a6ab7f0c7ee2bd6a863be3a2bc7db98

Deep mutational scanning quantifies DNA binding and predicts clinical outcomes of PAX6 variants.

Autor: McDonnell, Alexander F¹ (AUTHOR), Plech, Marcin¹ (AUTHOR), Livesey, Benjamin J¹ (AUTHOR), Gerasimavicius, Lukas¹ (AUTHOR), Owen, Liusaidh J¹ (AUTHOR), Hall, Hildegard Nikki¹ (AUTHOR), FitzPatrick, David R¹ (AUTHOR), Marsh, Joseph A¹ (AUTHOR), Kudla, Grzegorz¹ (AUTHOR) gkudla@gmail.com

Publikováno v: Molecular Systems Biology. Jul2024, Vol. 20 Issue 7, p825-844. 20p.

Assessing predictions of the impact of variants on splicing in CAGI5.

Autor: Mount SM; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland., Avsec Ž; Department of Informatics, Technical University of Munich, Garching, Germany., Carmel L; Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel., Casadio R; Department of Pharmacy and Biotechnology, Biocomputing Group, University of Bologna, Bologna, Italy., Çelik MH; Department of Informatics, Technical University of Munich, Garching, Germany., Chen K; School of Data and Computer Science, Sun Yat-sen University, Guangzhou, China., Cheng J; Department of Informatics, Technical University of Munich, Garching, Germany., Cohen NE; Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.; The integrated program for Computer Science and Computational Biology, School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel., Fairbrother WG; Department of Molecular Biology, Cell Biology, and Biochemistry, Center For Computational Biology, Brown University, Providence, Rhode Island., Fenesh T; The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel., Gagneur J; Department of Informatics, Technical University of Munich, Garching, Germany., Gotea V; National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland., Holzer T; The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel., Lin CF; Translational Informatics, DNAnexus, Mountain View, California., Martelli PL; Department of Pharmacy and Biotechnology, Biocomputing Group, University of Bologna, Bologna, Italy., Naito T; Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan., Nguyen TYD; Department of Informatics, Technical University of Munich, Garching, Germany., Savojardo C; Department of Pharmacy and Biotechnology, Biocomputing Group, University of Bologna, Bologna, Italy., Unger R; The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel., Wang R; Department of Bioengineering, University of California, Berkeley, California.; Department of Plant and Molecular Biology, University of California, Berkeley, California., Yang Y; School of Data and Computer Science, Sun Yat-sen University, Guangzhou, China., Zhao H; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.

Publikováno v: Human mutation [Hum Mutat] 2019 Sep; Vol. 40 (9), pp. 1215-1224. Date of Electronic Publication: 2019 Aug 19.

Analysis of 3760 hematologic malignancies reveals rare transcriptomic aberrations of driver genes.

Autor: Cao, Xueqi^1,2 (AUTHOR), Huber, Sandra³ (AUTHOR), Ahari, Ata Jadid¹ (AUTHOR), Traube, Franziska R.^1,4 (AUTHOR), Seifert, Marc⁵ (AUTHOR), Oakes, Christopher C.⁶ (AUTHOR), Secheyko, Polina^1,7 (AUTHOR), Vilov, Sergey⁸ (AUTHOR), Scheller, Ines F.^1,8 (AUTHOR), Wagner, Nils^1,9 (AUTHOR), Yépez, Vicente A.¹ (AUTHOR), Blombery, Piers^10,11,12 (AUTHOR), Haferlach, Torsten³ (AUTHOR), Heinig, Matthias^1,8 (AUTHOR), Wachutka, Leonhard¹ (AUTHOR) wachutka@cit.tum.de, Hutter, Stephan³ (AUTHOR) stephan.hutter@mll.com, Gagneur, Julien^1,2,8,13 (AUTHOR) gagneur@in.tum.de

Publikováno v: Genome Medicine. 5/20/2024, Vol. 16 Issue 1, p1-21. 21p.

Genetic analysis and molecular basis of G6PD deficiency among malaria patients in Thailand: implications for safe use of 8-aminoquinolines.

Autor: Boonyuen, Usa¹ (AUTHOR) usa.boo@mahidol.ac.th, Jacob, Beatriz Aira C.¹ (AUTHOR), Wongwigkan, Jutamas¹ (AUTHOR), Chamchoy, Kamonwan² (AUTHOR), Singha-art, Natsamon¹ (AUTHOR), Pengsuk, Natnicha¹ (AUTHOR), Songdej, Duantida³ (AUTHOR), Adams, Emily R.⁴ (AUTHOR), Edwards, Thomas⁴ (AUTHOR), Chamnanchanunt, Supat⁵ (AUTHOR), Amran, Syazwani Itri⁶ (AUTHOR), Latif, Nurriza Ab⁶ (AUTHOR), Louis, Naveen Eugene⁶ (AUTHOR), Chandran, Shamini⁶ (AUTHOR)

Publikováno v: Malaria Journal. 2/2/2024, Vol. 23 Issue 1, p1-17. 17p.