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Page 1
Temporal modelling using single-cell transcriptomics.
Ding J, Sharon N, Bar-Joseph Z. Ding J, et al. Nat Rev Genet. 2022 Jun;23(6):355-368. doi: 10.1038/s41576-021-00444-7. Epub 2022 Jan 31. Nat Rev Genet. 2022. PMID: 35102309 Free PMC article. Review.
Complete genomic and epigenetic maps of human centromeres.
Altemose N, Logsdon GA, Bzikadze AV, Sidhwani P, Langley SA, Caldas GV, Hoyt SJ, Uralsky L, Ryabov FD, Shew CJ, Sauria MEG, Borchers M, Gershman A, Mikheenko A, Shepelev VA, Dvorkina T, Kunyavskaya O, Vollger MR, Rhie A, McCartney AM, Asri M, Lorig-Roach R, Shafin K, Lucas JK, Aganezov S, Olson D, de Lima LG, Potapova T, Hartley GA, Haukness M, Kerpedjiev P, Gusev F, Tigyi K, Brooks S, Young A, Nurk S, Koren S, Salama SR, Paten B, Rogaev EI, Streets A, Karpen GH, Dernburg AF, Sullivan BA, Straight AF, Wheeler TJ, Gerton JL, Eichler EE, Phillippy AM, Timp W, Dennis MY, O'Neill RJ, Zook JM, Schatz MC, Pevzner PA, Diekhans M, Langley CH, Alexandrov IA, Miga KH. Altemose N, et al. Science. 2022 Apr;376(6588):eabl4178. doi: 10.1126/science.abl4178. Epub 2022 Apr 1. Science. 2022. PMID: 35357911 Free PMC article.
A complete reference genome improves analysis of human genetic variation.
Aganezov S, Yan SM, Soto DC, Kirsche M, Zarate S, Avdeyev P, Taylor DJ, Shafin K, Shumate A, Xiao C, Wagner J, McDaniel J, Olson ND, Sauria MEG, Vollger MR, Rhie A, Meredith M, Martin S, Lee J, Koren S, Rosenfeld JA, Paten B, Layer R, Chin CS, Sedlazeck FJ, Hansen NF, Miller DE, Phillippy AM, Miga KH, McCoy RC, Dennis MY, Zook JM, Schatz MC. Aganezov S, et al. Science. 2022 Apr;376(6588):eabl3533. doi: 10.1126/science.abl3533. Epub 2022 Apr 1. Science. 2022. PMID: 35357935 Free PMC article.
Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation.
Kolmogorov M, Billingsley KJ, Mastoras M, Meredith M, Monlong J, Lorig-Roach R, Asri M, Alvarez Jerez P, Malik L, Dewan R, Reed X, Genner RM, Daida K, Behera S, Shafin K, Pesout T, Prabakaran J, Carnevali P, Yang J, Rhie A, Scholz SW, Traynor BJ, Miga KH, Jain M, Timp W, Phillippy AM, Chaisson M, Sedlazeck FJ, Blauwendraat C, Paten B. Kolmogorov M, et al. Nat Methods. 2023 Oct;20(10):1483-1492. doi: 10.1038/s41592-023-01993-x. Epub 2023 Sep 14. Nat Methods. 2023. PMID: 37710018 Free PMC article.
Modelling post-implantation human development to yolk sac blood emergence.
Hislop J, Song Q, Keshavarz F K, Alavi A, Schoenberger R, LeGraw R, Velazquez JJ, Mokhtari T, Taheri MN, Rytel M, Chuva de Sousa Lopes SM, Watkins S, Stolz D, Kiani S, Sozen B, Bar-Joseph Z, Ebrahimkhani MR. Hislop J, et al. Nature. 2024 Feb;626(7998):367-376. doi: 10.1038/s41586-023-06914-8. Epub 2023 Dec 13. Nature. 2024. PMID: 38092041 Free PMC article.
Cell type ontologies of the Human Cell Atlas.
Osumi-Sutherland D, Xu C, Keays M, Levine AP, Kharchenko PV, Regev A, Lein E, Teichmann SA. Osumi-Sutherland D, et al. Nat Cell Biol. 2021 Nov;23(11):1129-1135. doi: 10.1038/s41556-021-00787-7. Epub 2021 Nov 8. Nat Cell Biol. 2021. PMID: 34750578 Review.
Interactive single-cell data analysis using Cellar.
Hasanaj E, Wang J, Sarathi A, Ding J, Bar-Joseph Z. Hasanaj E, et al. Nat Commun. 2022 Apr 14;13(1):1998. doi: 10.1038/s41467-022-29744-0. Nat Commun. 2022. PMID: 35422041 Free PMC article.
GBZ file format for pangenome graphs.
Sirén J, Paten B. Sirén J, et al. Bioinformatics. 2022 Nov 15;38(22):5012-5018. doi: 10.1093/bioinformatics/btac656. Bioinformatics. 2022. PMID: 36179091 Free PMC article.
Optimal gap-affine alignment in O(s) space.
Marco-Sola S, Eizenga JM, Guarracino A, Paten B, Garrison E, Moreto M. Marco-Sola S, et al. Bioinformatics. 2023 Feb 3;39(2):btad074. doi: 10.1093/bioinformatics/btad074. Bioinformatics. 2023. PMID: 36749013 Free PMC article.
50 results