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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
..., Computational and Systems Biology, University of California Irvine, Irvine, California 92697, USA; 3Department of Biology, Texas A&M University, College Station, Texas 77843, USA; 4Center for Complex Biological Systems, University of California Irvine, Irvine, California 92697, USA Corresponding authors: mahul...
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Research: Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology
- Abigail L. Lind,
- Nathan A. McDonald,
- Elias R. Gerrick,
- Ami S. Bhatt,
- and Katherine S. Pollard
Genome Res. June 2025 35: 1377-1390; Published in Advance April 22, 2025, doi:10.1101/gr.279080.124
...metabolize compounds that are not digestible by the host, providing access to previously inaccessible nutrients (Yadav et al. 2018). Gut microbes also influence the host's immune system and impact host health through their metabolic byproducts (Sommer and Bäckhed 2013). The microbiome's composition, which...
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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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Method: Factors impacting target-enriched long-read sequencing of resistomes and mobilomes
- Ilya B. Slizovskiy,
- Nathalie Bonin,
- Jonathan E. Bravo,
- Peter M. Ferm,
- Jacob Singer,
- Christina Boucher,
- and Noelle R. Noyes
Genome Res. November 2024 34: 2048-2060; Published in Advance November 5, 2024, doi:10.1101/gr.279226.124
...probes differ from PCR primers in several important ways. First, probe sets can be designed to simultaneously target megabases worth of reference sequences; second, probes are longer than PCR primers, i.e., typically 120 bp; third, probes will hybridize to targets even when the sequences contain many...
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REVIEW: Advanced methods in PCR product detection.
- J G Lazar
Genome Res. August 1994 4: S1-S14
....S. Challberg. 1993. Sensitive and specific detection of PCR products: Application of the Digene SHARP signal system. Presented at the 93rd Annual Meeting of the American Society for Microbiology, May. Atlanta, GA. 24.. Lazar, J.G., J.A. Tropp, A.T. Lorincz, A. Mendoza, and C. Woerle. 1993. Comparison...
ARTICLE: Dealing with contamination: enzymatic control of carryover contamination in PCR.
- J L Hartley and
- A Rashtchian
Genome Res. October 1993 3: S10-S14; doi:10.1101/gr.3.2.S10
..., (24) Lyme disease, (2s) and chlamydia. (26) Com- mercial versions of these tests incorporate the UDG decontamination tech- nology under the trademark AmpErase (Roche Diagnostic Systems). The stability and characteristics of dU-containing PCR products have been studied in detail. Although...
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ARTICLE: Effect of amplicon size on PCR detection of bacteria exposed to chlorine.
- S C McCarty and
- R M Atlas
Genome Res. December 1993 3: 181-185
...- ples using PCR have been developed. (1) Roche Molecular Systems and the Per- kin-Elmer Corporation have developed a commercial PCR kit for the detection of the water-associated pathogen Legionella pneumophila, the EnviroAmp Legionella kit, which allows the semiquantitative detection of the genus...
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Methods: Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines
- Jaswinder Khattra,
- Allen D. Delaney,
- Yongjun Zhao,
- Asim Siddiqui,
- Jennifer Asano,
- Helen McDonald,
- Pawan Pandoh,
- Noreen Dhalla,
- Anna-liisa Prabhu,
- Kevin Ma,
- Stephanie Lee,
- Adrian Ally,
- Angela Tam,
- Danne Sa,
- Sean Rogers,
- David Charest,
- Jeff Stott,
- Scott Zuyderduyn,
- Richard Varhol,
- Connie Eaves,
- Steven Jones,
- Robert Holt,
- Martin Hirst,
- Pamela A. Hoodless,
- and Marco A. Marra
Genome Res. January 2007 17: 108-116; Published in Advance November 29, 2006, doi:10.1101/gr.5488207
...by microdissection. Several RNA isolation methods were used to handle the diversity of samples processed, and various measures were applied to minimize ditag PCR carryover contamination. Modifications in the SAGE protocol resulted in improved cloning and DNA sequencing efficiencies. Bioinformatic measures...
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Method: Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome
- Jakob Skou Pedersen,
- Eivind Valen,
- Amhed M. Vargas Velazquez,
- Brian J. Parker,
- Morten Rasmussen,
- Stinus Lindgreen,
- Berit Lilje,
- Desmond J. Tobin,
- Theresa K. Kelly,
- Søren Vang,
- Robin Andersson,
- Peter A. Jones,
- Cindi A. Hoover,
- Alexei Tikhonov,
- Egor Prokhortchouk,
- Edward M. Rubin,
- Albin Sandelin,
- M. Thomas P. Gilbert,
- Anders Krogh,
- Eske Willerslev,
- and Ludovic Orlando
Genome Res. March 2014 24: 454-466; Published in Advance December 3, 2013, doi:10.1101/gr.163592.113
...the quagga zebra, a species that became extinct in the early 20th century (Higuchi et al. 1984). Soon after, the invention of PCR unlocked access to this fragmented and degraded DNA material (Pa¨a¨bo 1989), making it possible to amplify short gene markers of interest and compare their sequence to that from...
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