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RESOURCE: The International HapMap Project Web site
- Gudmundur A. Thorisson,
- Albert V. Smith,
- Lalitha Krishnan,
- and Lincoln D. Stein
Genome Res. November 2005 15: 1592-1593; doi:10.1101/gr.4413105
...-quality, -wide human genetic data, with an emphasis on the support of tools for facilitating disease association studies. Although the resource is still in development, it currently provides the basic tools for visualizing patterns of common polymorphism among the populations surveyed by the HapMap project...
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RESOURCE: PipMaker—A Web Server for Aligning Two Genomic DNA Sequences
- Scott Schwartz,
- Zheng Zhang,
- Kelly A. Frazer,
- Arian Smit,
- Cathy Riemer,
- John Bouck,
- Richard Gibbs,
- Ross Hardison,
- and Webb Miller
Genome Res. April 1, 2000 10: 577-586; doi:10.1101/gr.10.4.577
..., Berkeley, California USA 94720;3Axys Pharmaceuticals, La Jolla, California USA 92037;4Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas USA 77030 Abstract PipMaker ( http://bio.cse.psu.edu ) is a World-Wide Web site for comparing two long DNA sequences...
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Methods: Global Survey of Chromatin Accessibility Using DNA Microarrays
- M. Ryan Weil,
- Piotr Widlak,
- John D. Minna,
- and Harold R. Garner
Genome Res. July 2004 14: 1374-1381; doi:10.1101/gr.1396104
...of nonhistone proteins in the S1 and P fractions. The DNA gel ( B ) shows the difference in the extent of the digestion between the fractions. The model ( C ) illustrates the basic concept of the chromatin fractionation assay. The isolated S2 fraction, total genomic DNA, and RNA were fluorescently labeled...
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RESOURCE: Versatile Gene-Specific Sequence Tags for Arabidopsis Functional Genomics: Transcript Profiling and Reverse Genetics Applications
- Pierre Hilson,
- Joke Allemeersch,
- Thomas Altmann,
- Sébastien Aubourg,
- Alexandra Avon,
- Jim Beynon,
- Rishikesh P. Bhalerao,
- Frédérique Bitton,
- Michel Caboche,
- Bernard Cannoot,
- Vasil Chardakov,
- Cécile Cognet-Holliger,
- Vincent Colot,
- Mark Crowe,
- Caroline Darimont,
- Steffen Durinck,
- Holger Eickhoff,
- Andéol Falcon de Longevialle,
- Edward E. Farmer,
- Murray Grant,
- Martin T.R. Kuiper,
- Hans Lehrach,
- Céline Léon,
- Antonio Leyva,
- Joakim Lundeberg,
- Claire Lurin,
- Yves Moreau,
- Wilfried Nietfeld,
- Javier Paz-Ares,
- Philippe Reymond,
- Pierre Rouzé,
- Goran Sandberg,
- Maria Dolores Segura,
- Carine Serizet,
- Alexandra Tabrett,
- Ludivine Taconnat,
- Vincent Thareau,
- Paul Van Hummelen,
- Steven Vercruysse,
- Marnik Vuylsteke,
- Magdalena Weingartner,
- Peter J. Weisbeek,
- Valtteri Wirta,
- Floyd R.A. Wittink,
- Marc Zabeau,
- and Ian Small
Genome Res. October 15, 2004 14: 2176-2189; doi:10.1101/gr.2544504
...be available via other Arabidopsis resource Web sites (see Web Site References). The quality of the Arabidopsis annotation improves continuously thanks to the refinement of in silico prediction tools and to the increasing number of experimentally documented transcription units ( Haas et al. 2002 ; Seki et al...
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Research: Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations
- Xiu Fan,
- Qili Qian,
- Wenran Li,
- Tianzi Liu,
- Changqing Zeng,
- Peilin Jia,
- Huandong Lin,
- Xin Gao,
- Li Jin,
- Mingfeng Xia,
- Sijia Wang,
- and Fan Liu
Genome Res. October 2025 35: 2173-2188; Published in Advance August 1, 2025, doi:10.1101/gr.280155.124
...–F). In CD4+ T cells, BASiCS analysis revealed reduced transcriptional noise in aged individuals for genes associated with positive drift-CpGs, suggesting a context-dependent noise-suppressive function. The most pronounced transcriptional perturbations in genes associated with positive epigenetic drift were...
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Perspective: Functional assays in Drosophila facilitate classification of variants of uncertain significance associated with rare diseases
- Jung-Wan Mok,
- Shelley B. Gibson,
- Haley A. Dostalik,
- and Shinya Yamamoto
Genome Res. July 2025 35: 1473-1484; Published in Advance June 4, 2025, doi:10.1101/gr.278291.123
...in the fly ortholog tin (NKX2.5 ortholog), leveraging the fact that both lysine (K) and arginine (R) are basic residues with similar biochemical properties. This approach underscores the potential for cross-species genetic modeling, even when exact amino acid matches are not present.The most straightforward...
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Research: Proteome-wide structural analysis quantifies structural conservation across distant species
- Shijie Zhang,
- Teng Zhang,
- and Yuan Fu
Genome Res. November 2023 33: 1975-1993; Published in Advance November 22, 2023, doi:10.1101/gr.277771.123
...Structural Homolog Finder [SHF]). We have additionally included some structural analog information for Saccharomyces cerevisiae, the unicellular eukaryotic model organism, in the online resource. The webpage can be accessed at http://micc.tmu.edu.cn/shf. On the web interface, the user may enter either...
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Method: Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity
- Mayank Murali,
- Jamie Saquing,
- Senbao Lu,
- Ziyang Gao,
- Emily F. Watts,
- Ben Jordan,
- Zachary Peters Wakefield,
- Ana Fiszbein,
- David R. Cooper,
- Peter J. Castaldi,
- Dmitry Korkin,
- and Gloria M. Sheynkman
Genome Res. April 2025 35: 1012-1024; Published in Advance March 14, 2025, doi:10.1101/gr.279317.124
...with the associated biological mechanism leading to the transcript nucleotide change, e.g., alternative transcriptional start site, splicing event, or polyadenylation. The AS events are then further classified into four basic types: retained intron, alternative donor, alternative exon, or alternative acceptor...
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Resource: Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations
- Wenyu Zhang,
- Anja Guenther,
- Yuanxiao Gao,
- Kristian Ullrich,
- Bruno Huettel,
- Aftab Ahmad,
- Lei Duan,
- Kaizong Wei,
- and Diethard Tautz
Genome Res. November 2024 34: 2118-2132; Published in Advance September 17, 2024, doi:10.1101/gr.279166.124
...Mode Basic ‐‐outFilterMismatchNmax 30 ‐‐scoreDelOpen -1 ‐‐scoreDelBase -1 ‐‐scoreInsOpen -1 ‐‐scoreInsBase -1 ‐‐seedSearchStartLmax 25 ‐‐winAnchorMultimapNmax 100), in order to compensate the sequence divergences of individuals from various populations and species (Zhang et al. 2021). With this optimized...
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Resource: Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis
- Yingshu Li,
- Yongjie Liu,
- Hang Yang,
- Ting Zhang,
- Kiyoshi Naruse,
- and Qiang Tu
Genome Res. June 2020 30: 924-937; Published in Advance June 26, 2020, doi:10.1101/gr.258871.119
...; 2Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; 3University of Chinese Academy of Sciences, Beijing 100049, China; 4Laboratory of Bioresources, National Institute for Basic Biology, Okazaki 444...
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