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Method: A framework to score the effects of structural variants in health and disease
- Philip Kleinert and
- Martin Kircher
Genome Res. April 2022 32: 766-777; Published in Advance February 23, 2022, doi:10.1101/gr.275995.121
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Research: Gene essentiality in cancer cell lines is modified by the sex chromosomes
- Shahar Shohat,
- Ethel Vol,
- and Sagiv Shifman
Genome Res. November/December 2022 32: 1993-2002; Published in Advance November 23, 2022, doi:10.1101/gr.276488.121
...in cancer mortality and survival. Cancer Epidemiol Biomarkers Prev 20: 16291637. doi:10.1158/1055-9965.EPI-11-0246 Cyranowski JM, Frank E, Young E, Shear MK. 2000. Adolescent onset of the gender difference in lifetime rates of major depression: a theoretical model. Arch Gen Psychiatry 57: 2127. doi:10 ...
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Research: Chromatin loop dynamics during cellular differentiation are associated with changes to both anchor and internal regulatory features
- Marielle L. Bond,
- Eric S. Davis,
- Ivana Y. Quiroga,
- Anubha Dey,
- Manjari Kiran,
- Michael I. Love,
- Hyejung Won,
- and Douglas H. Phanstiel
Genome Res. August 2023 33: 1258-1268; Published in Advance September 12, 2023, doi:10.1101/gr.277397.122
...chromatin looping and cancer development. Nature 595: 591595. doi:10.1038/s41586-021-03662-5 Alexander JM, Guan J, Li B, Maliskova L, Song M, Shen Y, Huang B, Lomvardas S, Weiner OD. 2019. Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity. eLife 8: e41769 ...
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Research: The rate of de novo structural variation is increased in in vitro–produced offspring and preferentially affects the paternal genome
- Young-Lim Lee,
- Aniek C. Bouwman,
- Chad Harland,
- Mirte Bosse,
- Gabriel Costa Monteiro Moreira,
- Roel F. Veerkamp,
- Erik Mullaart,
- Nadine Cambisano,
- Martien A.M. Groenen,
- Latifa Karim,
- Wouter Coppieters,
- Michel Georges,
- and Carole Charlier
Genome Res. September 2023 33: 1455-1464; Published in Advance October 4, 2023, doi:10.1101/gr.277884.123
...in generating human germline mutations. Proc Natl Acad Sci USA 116: 94919500. doi:10.1073/pnas.1901259116 Goldmann JM, Wong WSW, Pinelli M, Farrah T, Bodian D, Stittrich AB, Glusman G, Vissers LELM, Hoischen A, Roach JC, et al. 2016. Parent-of-origin-specific signatures of de novo mutations. Nat Genet 48: 935 ...
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Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
- Xinghua Li,
- Judith E. Mank,
- and Liping Ban
Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
...convergently retained dosage-sensitive regulators. Nat Genet 49: 387394. doi:10.1038/ng.3778 Belton J-M, McCord RP, Gibcus JH, Naumova N, Zhan Y, Dekker J. 2012. HiC: a comprehensive technique to capture the conformation of s. Methods 58: 268276. doi:10.1016/j.ymeth.2012.05.001 Brashear WA, Bredemeyer KR ...
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Method: A novel approach for in vivo DNA footprinting using short double-stranded cell-free DNA from plasma
- Jan Müller,
- Christina Hartwig,
- Mirko Sonntag,
- Lisa Bitzer,
- Christopher Adelmann,
- Yevhen Vainshtein,
- Karolina Glanz,
- Sebastian O. Decker,
- Thorsten Brenner,
- Georg F. Weber,
- Arndt von Haeseler,
- and Kai Sohn
Genome Res. August 2024 34: 1185-1195; Published in Advance September 13, 2024, doi:10.1101/gr.279326.124
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Method: Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation
- Alexander J. Ritter,
- Jolene M. Draper,
- Christopher Vollmers,
- and Jeremy R. Sanford
Genome Res. November 2024 34: 2000-2011; Published in Advance June 5, 2024, doi:10.1101/gr.279170.124
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Method: Full-resolution HLA and KIR gene annotations for human genome assemblies
- Ying Zhou,
- Li Song,
- and Heng Li
Genome Res. November 2024 34: 1931-1941; Published in Advance June 5, 2024, doi:10.1101/gr.278985.124
...history from 929 diverse s. Science 367: eaay5012. doi:10.1126/science.aay5012 Blanchong CA, Chung EK, Rupert KL, Yang Y, Yang Z, Zhou B, Moulds JM, Yu CY. 2001. Genetic, structural and functional diversities of human complement components C4A and C4B and their mouse homologues, Slp and C4. Int ...
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Research: Estrogen-induced chromatin looping changes identify a subset of functional regulatory elements
- Hosiana Abewe,
- Alexandra Richey,
- Jeffery M. Vahrenkamp,
- Matthew Ginley-Hidinger,
- Craig M. Rush,
- Noel Kitchen,
- Xiaoyang Zhang,
- and Jason Gertz
Genome Res. March 2025 35: 393-403; Published in Advance March 3, 2025, doi:10.1101/gr.279699.124
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Research: Transcriptomic and proteomic effects of gene deletion are not evolutionarily conserved
- Yang Li and
- Jianzhi Zhang
Genome Res. March 2025 35: 512-521; Published in Advance February 18, 2025, doi:10.1101/gr.280008.124
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