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Resource: Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise
- Aliza B. Rubenstein,
- Gregory R. Smith,
- Zidong Zhang,
- Xi Chen,
- Toby L. Chambers,
- Frederique Ruf-Zamojski,
- Natalia Mendelev,
- Wan Sze Cheng,
- Michel Zamojski,
- Mary Anne S. Amper,
- Venugopalan D. Nair,
- Andrew R. Marderstein,
- Stephen B. Montgomery,
- Olga G. Troyanskaya,
- Elena Zaslavsky,
- Todd Trappe,
- Scott Trappe,
- and Stuart C. Sealfon
Genome Res. July 2025 35: 1664-1677; Published in Advance May 20, 2025, doi:10.1101/gr.280051.124
...(self-reported).Participants arrived at about 06:00 to the laboratory after an ∼10 h overnight fast on the morning of their trial and rested in the supine position for at least 30 min prior to sample collection. The average oxygen uptake during the trial was 2.41 ± 0.26 L/min, which was 71 ± 1% of VO2...
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Method: Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR
- Artem Mikelov,
- George Nefediev,
- Alexander Tashkeev,
- Oscar L. Rodriguez,
- Diego Aguilar Ortmans,
- Valeriia Skatova,
- Mark Izraelson,
- Alexey N. Davydov,
- Stanislav Poslavsky,
- Souad Rahmouni,
- Corey T. Watson,
- Dmitriy Chudakov,
- Scott D. Boyd,
- and Dmitry Bolotin
Genome Res. December 2024 34: 2293-2303; Published in Advance October 21, 2024, doi:10.1101/gr.278775.123
...by the total number of haplotypes for this gene in the population. For the IGH data, we also were able to calculate allele frequencies for four major ethnic groups—African, Asian, European, Hispanic/Latino (self-reported by participants, where missing assigned to “unknown”).To evaluate pairwise similarity...
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Research: Genomic context sensitivity of insulator function
- André M. Ribeiro-dos-Santos,
- Megan S. Hogan,
- Raven D. Luther,
- Ran Brosh,
- and Matthew T. Maurano
Genome Res. March 2022 32: 425-436; Published in Advance January 26, 2022, doi:10.1101/gr.276449.121
...of sequencing libraries (Fig. 2A; Supplemental Fig. S4): an inverse PCR (iPCR) library to map reporter genomic insertion sites, a DNA library to determine their representation, and an RNA library to measure their expression. Sequencing libraries were constructed using a two-stage nested polymerase chain...
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Research: Genomic environments scale the activities of diverse core promoters
- Clarice K.Y. Hong and
- Barak A. Cohen
Genome Res. January 2022 32: 85-96; Published in Advance December 27, 2021, doi:10.1101/gr.276025.121
...) with primers specific to our reporter gene (CPL4-5) (Supplemental Table S4). We performed 32 PCR reactions per cDNA biological replicate and 48 PCR reactions per gDNA biological replicate, then pooled the PCRs of each replicate for PCR purification. Four nanograms from each replicate were then further...
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Research: MYT1L is required for suppressing earlier neuronal development programs in the adult mouse brain
- Jiayang Chen,
- Nicole A. Fuhler,
- Kevin K. Noguchi,
- and Joseph D. Dougherty
Genome Res. April 2023 33: 541-556; Published in Advance April 26, 2023, doi:10.1101/gr.277413.122
...difference. CUT&RUN on more homogenous cell populations or single-cell TF-DNA interaction profiling assays (Cammack et al. 2020; Moudgil et al. 2020) will be needed to differentiate these two possibilities in the future. Likewise, how MYT1L influences histones and chromatin accessibility at its bound sites...
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Research: Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time
- David T. Pride,
- Christine L. Sun,
- Julia Salzman,
- Nitya Rao,
- Peter Loomer,
- Gary C. Armitage,
- Jillian F. Banfield,
- and David A. Relman
Genome Res. January 2011 21: 126-136; Published in Advance December 13, 2010, doi:10.1101/gr.111732.110
...with significant immunosuppression. All subjects self-reported their health status. Each subject was subjected to a full baseline periodontal examination consisting of measurements of probing depths, clinical attachment loss, Gingival Index, Plaque Index, and gingival irritation (Loe 1967). Each subject was found...

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