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Resource: Spatial transcriptomics reveals asymmetric cellular responses to injury in the regenerating spiny mouse (Acomys) ear
- Henriëtte van Beijnum,
- Tim Koopmans,
- Antonio Tomasso,
- Vanessa Disela,
- Severin te Lindert,
- Jeroen Bakkers,
- Anna Alemany,
- Eugene Berezikov,
- and Kerstin Bartscherer
Genome Res. August 2023 33: 1424-1437; Published in Advance September 19, 2023, doi:10.1101/gr.277538.122
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Research: Rtt109 promotes nucleosome replacement ahead of the replication fork
- Felix Jonas,
- Gilad Yaakov,
- and Naama Barkai
Genome Res. June 2022 32: 1089-1098; Published in Advance May 24, 2022, doi:10.1101/gr.276674.122
...structural changes due to acetylation. J Mol Biol 236: 685690. doi:10.1006/jmbi.1994.1180 Bechhoefer J, Rhind N. 2012. Replication timing and its emergence from stochastic processes. Trends Genet 28: 374381. doi:10.1016/j.tig.2012.03.011 Berndsen CE, Tsubota T, Lindner SE, Lee S, Holton JM, Kaufman PD ...
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Method: Enhancing CRISPR deletion via pharmacological delay of DNA-PKcs
- Núria Bosch-Guiteras,
- Tina Uroda,
- Hugo A. Guillen-Ramirez,
- Rahel Riedo,
- Amiq Gazdhar,
- Roberta Esposito,
- Carlos Pulido-Quetglas,
- Yitzhak Zimmer,
- Michaela Medová,
- and Rory Johnson
Genome Res. March 2021 31: 461-471; Published in Advance February 11, 2021, doi:10.1101/gr.265736.120
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Research: Cellular age explains variation in age-related cell-to-cell transcriptome variability
- Ming Yang,
- Benjamin R. Harrison,
- and Daniel E.L. Promislow
Genome Res. November 2023 33: 1906-1916; Published in Advance November 16, 2023, doi:10.1101/gr.278144.123
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Perspective: Ribosome decision graphs for the representation of eukaryotic RNA translation complexity
- Jack A.S. Tierney,
- Michał Świrski,
- Håkon Tjeldnes,
- Jonathan M. Mudge,
- Joanna Kufel,
- Nicola Whiffin,
- Eivind Valen,
- and Pavel V. Baranov
Genome Res. April 2024 34: 530-538; Published in Advance May 7, 2024, doi:10.1101/gr.278810.123
...ER, Weissman JS. 2013. Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster. eLife 2: e01179. doi:10.7554/eLife.01179 Fedorova AD, Kiniry SJ, Andreev DE, Mudge JM, Baranov PV. 2022. Thousands of human non-AUG extended proteoforms lack evidence ...
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Method: Haplotype-aware sequence alignment to pangenome graphs
- Ghanshyam Chandra,
- Daniel Gibney,
- and Chirag Jain
Genome Res. September 2024 34: 1265-1275; Published in Advance July 16, 2024, doi:10.1101/gr.279143.124
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Method: Genetics-driven risk predictions leveraging the Mendelian randomization framework
- Daniel Sens,
- Liubov Shilova,
- Ludwig Gräf,
- Maria Grebenshchikova,
- Bjoern M. Eskofier,
- and Francesco Paolo Casale
Genome Res. September 2024 34: 1276-1285; Published in Advance September 27, 2024, doi:10.1101/gr.279252.124
...Health Econ 70: 102300. doi:10.1016/j.jhealeco.2020.102300 Edlitz Y, Segal E. 2022. Prediction of type 2 diabetes mellitus onset using logistic regression-based scorecards. eLife 11: e71862. doi:10.7554/eLife.71862 Engelmann JP, Palma A, Tomczak JM, Theis FJ, Casale FP. 2024. Mixed models with multiple ...
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Method: Simultaneous assessment of human genome and methylome data in a single experiment using limited deamination of methylated cytosine
- Bo Yan,
- Duan Wang,
- and Laurence Ettwiller
Genome Res. June 2024 34: 904-913; Published in Advance June 10, 2024, doi:10.1101/gr.278294.123
..., molecular cloning, and enzymatic amplification. Proc Natl Acad Sci 86: 19391943. doi:10.1073/pnas.86.6.1939 Rand AC, Jain M, Eizenga JM, Musselman-Brown A, Olsen HE, Akeson M, Paten B. 2017. Mapping DNA methylation with high-throughput nanopore sequencing. Nat Methods 14: 411413. doi:10.1038/nmeth.4189 ...
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Research: Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps
- Kristine Bilgrav Saether,
- Jesper Eisfeldt,
- Jesse D. Bengtsson,
- Ming Yin Lun,
- Christopher M. Grochowski,
- Medhat Mahmoud,
- Hsiao-Tuan Chao,
- Jill A. Rosenfeld,
- Pengfei Liu,
- Marlene Ek,
- Jakob Schuy,
- Adam Ameur,
- Hongzheng Dai,
- Undiagnosed Diseases Network,
- James Paul Hwang,
- Fritz J. Sedlazeck,
- Weimin Bi,
- Ronit Marom,
- Josephine Wincent,
- Ann Nordgren,
- Claudia M.B. Carvalho,
- and Anna Lindstrand
Genome Res. November 2024 34: 1785-1797; Published in Advance November 1, 2024, doi:10.1101/gr.279346.124
...This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.References Abergel C, Monchois V, Byrne D, Chenivesse S, Lembo F, Lazzaroni JC, Claverie JM. 2007. Structure and evolution ...
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Method: Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT and otter
- Niccoló Tesi,
- Alex Salazar,
- Yaran Zhang,
- Sven van der Lee,
- Marc Hulsman,
- Lydian Knoop,
- Sanduni Wijesekera,
- Jana Krizova,
- Anne-Fleur Schneider,
- Maartje Pennings,
- Kristel Sleegers,
- Erik-Jan Kamsteeg,
- Marcel Reinders,
- and Henne Holstege
Genome Res. November 2024 34: 1942-1953; Published in Advance October 15, 2024, doi:10.1101/gr.279351.124
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