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Method: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification
- Manuel Tardaguila,
- Lorena de la Fuente,
- Cristina Marti,
- Cécile Pereira,
- Francisco Jose Pardo-Palacios,
- Hector del Risco,
- Marc Ferrell,
- Maravillas Mellado,
- Marissa Macchietto,
- Kenneth Verheggen,
- Mariola Edelmann,
- Iakes Ezkurdia,
- Jesus Vazquez,
- Michael Tress,
- Ali Mortazavi,
- Lennart Martens,
- Susana Rodriguez-Navarro,
- Victoria Moreno-Manzano,
- and Ana Conesa
Genome Res. March 2018 28: 396-411; Published in Advance February 9, 2018, doi:10.1101/gr.222976.117
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Research: Genomic analysis of Rad26 and Rad1–Rad10 reveals differences in their dependence on Mediator and RNA polymerase II
- Diyavarshini Gopaul,
- Cyril Denby Wilkes,
- Arach Goldar,
- Nathalie Giordanengo Aiach,
- Marie-Bénédicte Barrault,
- Elizaveta Novikova,
- and Julie Soutourina
Genome Res. August 2022 32: 1516-1528; Published in Advance June 23, 2022, doi:10.1101/gr.276371.121
...then scraped and diluted in water at 1 OD600. The yeast suspension was serially diluted by 10-fold, and 3 L was spotted on different media (YP medium supplemented with glucose, galactose, ethanol, or glycerol) or UV-irradiated at 5 or 20 J/m2 (UV Stratalinker 1800) and incubated for 3 d or 5 d ...
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Research: Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin
- Hossein Salari,
- Marco Di Stefano,
- and Daniel Jost
Genome Res. January 2022 32: 28-43; Published in Advance December 28, 2021, doi:10.1101/gr.275827.121
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Research: Transposable elements drive the evolution of metazoan zinc finger genes
- Jonathan N. Wells,
- Ni-Chen Chang,
- John McCormick,
- Caitlyn Coleman,
- Nathalie Ramos,
- Bozhou Jin,
- and Cédric Feschotte
Genome Res. August 2023 33: 1325-1339; Published in Advance September 15, 2023, doi:10.1101/gr.277966.123
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Resource: GenomeMUSter mouse genetic variation service enables multitrait, multipopulation data integration and analysis
- Robyn L. Ball,
- Molly A. Bogue,
- Hongping Liang,
- Anuj Srivastava,
- David G. Ashbrook,
- Anna Lamoureux,
- Matthew W. Gerring,
- Alexander S. Hatoum,
- Matthew J. Kim,
- Hao He,
- Jake Emerson,
- Alexander K. Berger,
- David O. Walton,
- Keith Sheppard,
- Baha El Kassaby,
- Francisco Castellanos,
- Govindarajan Kunde-Ramamoorthy,
- Lu Lu,
- John Bluis,
- Sejal Desai,
- Beth A. Sundberg,
- Gary Peltz,
- Zhuoqing Fang,
- Gary A. Churchill,
- Robert W. Williams,
- Arpana Agrawal,
- Carol J. Bult,
- Vivek M. Philip,
- and Elissa J. Chesler
Genome Res. January 2024 34: 145-159; Published in Advance January 30, 2024, doi:10.1101/gr.278157.123
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Mini-Review: The additional diagnostic yield of long-read sequencing in undiagnosed rare diseases
- Giulia F. Del Gobbo and
- Kym M. Boycott
Genome Res. April 2025 35: 559-571; Published in Advance February 3, 2025, doi:10.1101/gr.279970.124
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LETTER: Distinct mechanisms for trans-mediated mobilization of cellular RNAs by the LINE-1 reverse transcriptase
- José L. Garcia-Perez,
- Aurélien J. Doucet,
- Alain Bucheton,
- John V. Moran,
- and Nicolas Gilbert
Genome Res. May 2007 17: 602-611; Published in Advance April 6, 2007, doi:10.1101/gr.5870107
...in its 3-untranslated region (pJM101/ L1.3mneoI ) ( Dombroski et al. 1993 ; Sassaman et al. 1997 ). The retrotransposition cassette consists of a backward copy of the neomycin phosphotransferase gene containing its own promoter and polyadenylation signal ( Jensen and Heidmann 1991 ; Freeman et al. 1994 ...
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Author Index: Author Index, Volume 22, 2012 Genome Res. December 2012 22: 2552-2558

..., N., 837 Ajay, S.S., 1407 Akagi, K., 870 Akalin, A., 486 Akdis, C.A., 1050 Aken, B.L., 1698, 1760 Akey, J.M., 1689 Akimitsu, N., 947 Alani, E., 714 Alba, M.M., 478 Alber, F., 1295 Alekseyenko, A.A., 2188 Alexa, K., 1541 Alexander, R., 1658 Alexis, M.S., 2356 Alisch, R.S., 623, 1395 Alkan, C., 778 ...
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Research: Heritable L1 retrotransposition in the mouse primordial germline and early embryo
- Sandra R. Richardson,
- Patricia Gerdes,
- Daniel J. Gerhardt,
- Francisco J. Sanchez-Luque,
- Gabriela-Oana Bodea,
- Martin Muñoz-Lopez,
- J. Samuel Jesuadian,
- Marie-Jeanne H.C. Kempen,
- Patricia E. Carreira,
- Jeffrey A. Jeddeloh,
- Jose L. Garcia-Perez,
- Haig H. Kazazian, Jr.,
- Adam D. Ewing,
- and Geoffrey J. Faulkner
Genome Res. August 2017 27: 1395-1405; Published in Advance May 8, 2017, doi:10.1101/gr.219022.116
...LaJVM cells for insertion #1 and insertion #7. JM101 is a retrotransposition-competent human L1 (L1.3); JM105 is a negative control, consisting of L1.3 with a reverse transcriptase active site mutation. TGF21 is an active GF subfamily mouse L1; L1spa is an active TF subfamily mouse L1. Colony formation ...
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Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
- Sophia N. Lee,
- Erin C. Banda,
- Lu Qiao,
- Sarah L. Thompson,
- Karan Singh,
- Ryan A. Hagenson,
- Teresa Davoli,
- Stefan F. Pinter,
- and Jason M. Sheltzer
Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125

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