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ChromaFold predicts the 3D contact map from single-cell chromatin accessibility.
Gao VR, Yang R, Das A, Luo R, Luo H, McNally DR, Karagiannidis I, Rivas MA, Wang ZM, Barisic D, Karbalayghareh A, Wong W, Zhan YA, Chin CR, Noble W, Bilmes JA, Apostolou E, Kharas MG, Béguelin W, Viny AD, Huangfu D, Rudensky AY, Melnick AM, Leslie CS. Gao VR, et al. Among authors: bilmes ja. bioRxiv [Preprint]. 2023 Jul 28:2023.07.27.550836. doi: 10.1101/2023.07.27.550836. bioRxiv. 2023. PMID: 37546906 Free PMC article. Preprint.
Epiphany: predicting Hi-C contact maps from 1D epigenomic signals.
Yang R, Das A, Gao VR, Karbalayghareh A, Noble WS, Bilmes JA, Leslie CS. Yang R, et al. Among authors: bilmes ja. Genome Biol. 2023 Jun 6;24(1):134. doi: 10.1186/s13059-023-02934-9. Genome Biol. 2023. PMID: 37280678 Free PMC article.
MS1Connect: a mass spectrometry run similarity measure.
Lin A, Deatherage Kaiser BL, Hutchison JR, Bilmes JA, Noble WS. Lin A, et al. Among authors: bilmes ja. Bioinformatics. 2023 Feb 3;39(2):btad058. doi: 10.1093/bioinformatics/btad058. Bioinformatics. 2023. PMID: 36702456 Free PMC article.
Segway 2.0: Gaussian mixture models and minibatch training.
Chan RCW, Libbrecht MW, Roberts EG, Bilmes JA, Noble WS, Hoffman MM. Chan RCW, et al. Among authors: bilmes ja. Bioinformatics. 2018 Feb 15;34(4):669-671. doi: 10.1093/bioinformatics/btx603. Bioinformatics. 2018. PMID: 29028889 Free PMC article.
23 results