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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
..., Baltimore, Maryland 21218, USA; 2Howard Hughes Medical Institute, Baltimore, Maryland 21218, USA; 3Biosphere Sciences and Engineering, Carnegie Institution for Science, Baltimore, Maryland 21218, USA; 4Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda...
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Research: Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates
- Étienne Fafard-Couture,
- Pierre-Étienne Jacques,
- and Michelle S. Scott
Genome Res. April 2023 33: 525-540; Published in Advance April 18, 2023, doi:10.1101/gr.277483.122
...dyskerin (Massenet et al. 2017).We recently characterized the abundance patterns of snoRNAs across several healthy human tissues using TGIRT-seq (Fafard-Couture et al. 2021), a high-throughput RNA sequencing approach that accurately quantifies both structured and less structured RNAs in the same sample...
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Research: Kinetic networks identify TWIST2 as a key regulatory node in adipogenesis
- Arun B. Dutta,
- Daniel S. Lank,
- Roza K. Przanowska,
- Piotr Przanowski,
- Lixin Wang,
- Bao Nguyen,
- Ninad M. Walavalkar,
- Fabiana M. Duarte,
- and Michael J. Guertin
Genome Res. March 2023 33: 314-331; Published in Advance February 21, 2023, doi:10.1101/gr.277559.122
...of Pharmacology, University of Virginia, Charlottesville, Virginia 22903, USA; 3Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22903, USA; 4Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA; 5Center for Cell Analysis...
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Method: Accurate typing of short tandem repeats from genome-wide sequencing data and its applications
- Arkarachai Fungtammasan,
- Guruprasad Ananda,
- Suzanne E. Hile,
- Marcia Shu-Wei Su,
- Chen Sun,
- Robert Harris,
- Paul Medvedev,
- Kristin Eckert,
- and Kateryna D. Makova
Genome Res. May 2015 25: 736-749; Published in Advance March 30, 2015, doi:10.1101/gr.185892.114
...repeats long, the PCR+ data had consistently higher STR rates than PCR− data—by ∼4.2- and ∼9.3-fold for monoand dinucleotide STRs, respectively.Our plasmid analysis also confirms that the “1-unit-del” is the most common category of errors (Supplemental Fig. S9). Statistical model for genotyping STRs from...
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Research: Chromatin conformation and transcriptional activity are permissive regulators of DNA replication initiation in Drosophila
- Robin L. Armstrong,
- Taylor J.R. Penke,
- Brian D. Strahl,
- A. Gregory Matera,
- Daniel J. McKay,
- David M. MacAlpine,
- and Robert J. Duronio
Genome Res. November 2018 28: 1688-1700; Published in Advance October 2, 2018, doi:10.1101/gr.239913.118
...of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA; 3Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA; 4Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill...
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Method: Highly efficient gene knockout in mice and zebrafish with RNA-guided endonucleases
- Young Hoon Sung,
- Jong Min Kim,
- Hyun-Taek Kim,
- Jaehoon Lee,
- Jisun Jeon,
- Young Jin,
- Jung-Hwa Choi,
- Young Ho Ban,
- Sang-Jun Ha,
- Cheol-Hee Kim,
- Han-Woong Lee,
- and Jin-Soo Kim
Genome Res. January 2014 24: 125-131; Published in Advance November 19, 2013, doi:10.1101/gr.163394.113
..., Meng X, Paschon DE, Leung E, Hinkley SJ, et al. 2010. A TALE nuclease architecture for efficient editing. Nat Biotechnol 29: 143–148. Nagy A, Gertsenstein M, Vintersten K, Behringer R. 2003. Manipulating the mouse embryo: A laboratory manual, p. 255. Cold Spring Harbor Laboratory Press, Cold Spring...
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Resource: A calibrated human Y-chromosomal phylogeny based on resequencing
- Wei Wei,
- Qasim Ayub,
- Yuan Chen,
- Shane McCarthy,
- Yiping Hou,
- Ignazio Carbone,
- Yali Xue,
- and Chris Tyler-Smith
Genome Res. February 2013 23: 388-395; Published in Advance October 4, 2012, doi:10.1101/gr.143198.112
...–1589. Busby GB, Brisighelli F, Sanchez-Diz P, Ramos-Luis E, Martinez-Cadenas C, Thomas MG, Bradley DG, Gusmao L, Winney B, Bodmer W, et al. 2011. The peopling of Europe and the cautionary tale of Y chromosome lineage R-M269. Proc Biol Sci 279: 884–892. Cann RL, Stoneking M, Wilson AC. 1987. Mitochondrial DNA...
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Method: Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins
- Sojung Kim,
- Daesik Kim,
- Seung Woo Cho,
- Jungeun Kim,
- and Jin-Soo Kim
Genome Res. June 2014 24: 1012-1019; Published in Advance April 2, 2014, doi:10.1101/gr.171322.113
...JC, Tan S, Qiao G, Barlow KA, Wang J, Xia DF, Meng X, Paschon DE, Leung E, Hinkley SJ, et al. 2011. A TALE nuclease architecture for efficient editing. Nat Biotechnol 29: 143–148. Nekrasov V, Staskawicz B, Weigel D, Jones JD, Kamoun S. 2013. Targeted mutagenesis in the model plant...
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Method: Efficient targeted mutagenesis in the monarch butterfly using zinc-finger nucleases
- Christine Merlin,
- Lauren E. Beaver,
- Orley R. Taylor,
- Scot A. Wolfe,
- and Steven M. Reppert
Genome Res. January 2013 23: 159-168; Published in Advance September 25, 2012, doi:10.1101/gr.145599.112
...on a 24-h basis. (B, top) Schematic of monarch cry2 gene and position of the ZFN-targeted site (red star). (Black boxes) Exons. (Bottom) Magnified view illustrating binding sites for the ZFN pair, each consisting of four zinc-finger modules linked to either DD or RR variants of the FokI endonuclease. (C...
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Letter: HBEGF, SRA1, and IK: Three cosegregating genes as determinants of cardiomyopathy
- Frauke Friedrichs,
- Christian Zugck,
- Gerd-Jörg Rauch,
- Boris Ivandic,
- Dieter Weichenhan,
- Margit Müller-Bardorff,
- Benjamin Meder,
- Nour Eddine El Mokhtari,
- Vera Regitz-Zagrosek,
- Roland Hetzer,
- Arne Schäfer,
- Stefan Schreiber,
- Jian Chen,
- Isaac Neuhaus,
- Ruiru Ji,
- Nathan O. Siemers,
- Norbert Frey,
- Wolfgang Rottbauer,
- Hugo A. Katus,
- and Monika Stoll
Genome Res. March 2009 19: 395-403; Published in Advance December 8, 2008, doi:10.1101/gr.076653.108
...of single nucleotide polymorphisms (SNP) and high-throughput genotyping technologies, linkage disequilibrium (LD) mapping approaches are now frequently used to dissect the genetic basis of complex diseases. While LD mapping has proven to be effective in the identification of single genes or risk haplotypes...

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