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Method: An extended set of yeast-based functional assays accurately identifies human disease mutations
- Song Sun,
- Fan Yang,
- Guihong Tan,
- Michael Costanzo,
- Rose Oughtred,
- Jodi Hirschman,
- Chandra L. Theesfeld,
- Pritpal Bansal,
- Nidhi Sahni,
- Song Yi,
- Analyn Yu,
- Tanya Tyagi,
- Cathy Tie,
- David E. Hill,
- Marc Vidal,
- Brenda J. Andrews,
- Charles Boone,
- Kara Dolinski,
- and Frederick P. Roth
Genome Res. May 2016 26: 670-680; Published in Advance March 14, 2016, doi:10.1101/gr.192526.115
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Research: Histone methyltransferase PRDM9 is not essential for meiosis in male mice
- Ondrej Mihola,
- Florencia Pratto,
- Kevin Brick,
- Eliska Linhartova,
- Tatyana Kobets,
- Petr Flachs,
- Christopher L. Baker,
- Radislav Sedlacek,
- Kenneth Paigen,
- Petko M. Petkov,
- R. Daniel Camerini-Otero,
- and Zdenek Trachtulec
Genome Res. July 2019 29: 1078-1086; Published in Advance June 11, 2019, doi:10.1101/gr.244426.118
...485: 642645. doi:10.1038/nature11089 Brick K, Pratto F, Sun CY, Camerini-Otero RD, Petukhova G. 2018. Analysis of meiotic double-strand break initiation in mammals. Methods Enzymol 601: 391418. doi:10.1016/bs.mie.2017.11.037 Burgoyne PS, Mahadevaiah SK, Turner JM. 2009. The consequences ...
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Research: Diversification and collapse of a telomere elongation mechanism
- Bastien Saint-Leandre,
- Son C. Nguyen,
- and Mia T. Levine
Genome Res. June 2019 29: 920-931; Published in Advance May 28, 2019, doi:10.1101/gr.245001.118
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Method: Methyl-SNP-seq reveals dual readouts of methylome and variome at molecule resolution while enabling target enrichment
- Bo Yan,
- Duan Wang,
- Romualdas Vaisvila,
- Zhiyi Sun,
- and Laurence Ettwiller
Genome Res. November/December 2022 32: 2079-2091; Published in Advance November 4, 2022, doi:10.1101/gr.277080.122
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Method: Phased nanopore assembly with Shasta and modular graph phasing with GFAse
- Ryan Lorig-Roach,
- Melissa Meredith,
- Jean Monlong,
- Miten Jain,
- Hugh E. Olsen,
- Brandy McNulty,
- David Porubsky,
- Tessa G. Montague,
- Julian K. Lucas,
- Chris Condon,
- Jordan M. Eizenga,
- Sissel Juul,
- Sean K. McKenzie,
- Sara E. Simmonds,
- Jimin Park,
- Mobin Asri,
- Sergey Koren,
- Evan E. Eichler,
- Richard Axel,
- Bruce Martin,
- Paolo Carnevali,
- Karen H. Miga,
- and Benedict Paten
Genome Res. March 2024 34: 454-468; Published in Advance April 16, 2024, doi:10.1101/gr.278268.123
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Research: Colibactin leads to a bacteria-specific mutation pattern and self-inflicted DNA damage
- Emily Lowry,
- Yiqing Wang,
- Tal Dagan,
- and Amir Mitchell
Genome Res. August 2024 34: 1154-1164; Published in Advance August 16, 2024, doi:10.1101/gr.279517.124
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Research: Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer
- Yueqiang Song,
- Fuyuan Li,
- Shangzi Wang,
- Yuntong Wang,
- Cong Lai,
- Lian Chen,
- Ning Jiang,
- Jin Li,
- Xingdong Chen,
- Swneke D. Bailey,
- and Xiaoyang Zhang
Genome Res. October 2024 34: 1514-1527; Published in Advance October 18, 2024, doi:10.1101/gr.278418.123
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Method: Unveiling the functional fate of duplicated genes through expression profiling and structural analysis
- Alex Warwick Vesztrocy,
- Natasha Glover,
- Paul D. Thomas,
- Christophe Dessimoz,
- and Irene Julca
Genome Res. October 2025 35: 2273-2284; Published in Advance August 14, 2025, doi:10.1101/gr.280166.124
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Method: MCHelper automatically curates transposable element libraries across eukaryotic species
- Simon Orozco-Arias,
- Pío Sierra,
- Richard Durbin,
- and Josefa González
Genome Res. December 2024 34: 2256-2268; Published in Advance December 9, 2024, doi:10.1101/gr.278821.123
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
.... doi:10.1016/j.cell.2017.09.004 Frankish A, Harrow J. 2014. GENCODE pseudogenes. Methods Mol Biol 1167: 129155. doi:10.1007/978-1-4939-0835-6_10 Frankish A, Uszczynska B, Ritchie GRS, Gonzalez JM, Pervouchine D, Petryszak R, Mudge JM, Fonseca N, Brazma A, Guigo R, et al. 2015. Comparison of GENCODE ...
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