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Methods: Decoding Randomly Ordered DNA Arrays
- Kevin L. Gunderson,
- Semyon Kruglyak,
- Michael S. Graige,
- Francisco Garcia,
- Bahram G. Kermani,
- Chanfeng Zhao,
- Diping Che,
- Todd Dickinson,
- Eliza Wickham,
- Jim Bierle,
- Dennis Doucet,
- Monika Milewski,
- Robert Yang,
- Chris Siegmund,
- Juergen Haas,
- Lixin Zhou,
- Arnold Oliphant,
- Jian-Bing Fan,
- Steven Barnard,
- and Mark S. Chee
Genome Res. May 2004 14: 870-877; Published in Advance April 12, 2004, doi:10.1101/gr.2255804
...-based assays to large-scale clinical application. We have used decoded arrays to create new assays for largescale genotyping ( Fan et al. 2003 ) and gene expression ( Yeakley et al. 2002 ; Fan et al. 2004 ) using a universal array format. We have also developed gene-specific probe sets for gene expression...
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Review: k-mer approaches for biodiversity genomics
- Katharine M. Jenike,
- Lucía Campos-Domínguez,
- Marilou Boddé,
- José Cerca,
- Christina N. Hodson,
- Michael C. Schatz,
- and Kamil S. Jaron
Genome Res. February 2025 35: 219-230; Published in Advance January 31, 2025, doi:10.1101/gr.279452.124
...Katharine M. Jenike1, Lucía Campos-Domínguez2, Marilou Boddé3, José Cerca4,6, Christina N. Hodson5, Michael C. Schatz1 and Kamil S. Jaron3 1Johns Hopkins University, School of Medicine, Baltimore, Maryland 21205, USA; 2Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus...
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Method: HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
- Sergey Nurk,
- Brian P. Walenz,
- Arang Rhie,
- Mitchell R. Vollger,
- Glennis A. Logsdon,
- Robert Grothe,
- Karen H. Miga,
- Evan E. Eichler,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. September 2020 30: 1291-1305; Published in Advance August 14, 2020, doi:10.1101/gr.263566.120
..., National Institutes of Health, Bethesda, Maryland 20894, USA; 2Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA; 3Pacific Biosciences, Menlo Park, California 94025, USA; 4UC Santa Cruz Genomics Institute, University of California, Santa Cruz...
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LETTER: The genetic code is nearly optimal for allowing additional information within protein-coding sequences
- Shalev Itzkovitz and
- Uri Alon
Genome Res. April 2007 17: 405-412; Published in Advance February 9, 2007, doi:10.1101/gr.5987307
...of codons per each amino acid and the same impact of misread errors as in the real code. We tested the ability of the genetic codes to include arbitrary sequences, denoted n-mers, within protein-coding regions. As an example, consider the 5-mer “UGACA.” This sequence may be a protein-binding site, which...
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Method: taxMaps: comprehensive and highly accurate taxonomic classification of short-read data in reasonable time
- André Corvelo,
- Wayne E. Clarke,
- Nicolas Robine,
- and Michael C. Zody
Genome Res. May 2018 28: 751-758; Published in Advance March 27, 2018, doi:10.1101/gr.225276.117
.... ↵Rosen G, Garbarine E, Caseiro D, Polikar R, Sokhansanj B. 2008. Meta fragment classification using N-mer frequency profiles. Adv Bioinformatics 2008: 205969. ↵Schmieder R, Edwards R. 2011. Quality control and preprocessing of metagenomic datasets. Bioinformatics 27: 863–864. ↵Segata N, Waldron L...
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Research: Overlapping codes within protein-coding sequences
- Shalev Itzkovitz,
- Eran Hodis,
- and Eran Segal
Genome Res. November 2010 20: 1582-1589; Published in Advance September 14, 2010, doi:10.1101/gr.105072.110
...in parentheses. (B) Same asA, for log-ratios ofmononucleotide 6-mers across various phyla. All represents all n-mers in all species. (C ) Same as A, for bacterial restriction enzyme sites. The bacteria encoding recognizing enzyme group (third box plot from left) only displays log-ratios of restriction enzyme...
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METHODS: A System for Specific, High-throughput Genotyping by Allele-specific Primer Extension on Microarrays
- Tomi Pastinen,
- Mirja Raitio,
- Katarina Lindroos,
- Päivi Tainola,
- Leena Peltonen,
- and Ann-Christine Syvänen
Genome Res. July 1, 2000 10: 1031-1042; doi:10.1101/gr.10.7.1031
..., Uppsala University, 75185-Uppsala, Sweden Abstract This study describes a practical system that allows high-throughput genotyping of single nucleotide polymorphisms (SNPs) and detection of mutations by allele-specific extension on primer arrays. The method relies on the sequence...
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REVIEW: Automation for Genomics, Part Two: Sequencers, Microarrays, and Future Trends
- Deirdre Meldrum
Genome Res. September 1, 2000 10: 1288-1303; doi:10.1101/gr.157400
...). In April 2000, Affymetrix introduced the Human Genome U95 Set of GeneChips that includes a single array with &gt;12,000 full-length human sequences and four arrays with 50,000 ESTs. The GeneChip Instrument System includes a GeneChip fluidics station, a GeneArray Scanner by Hewlett-Packard, a Gene...
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REVIEW: Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques
- Laura Elnitski,
- Victor X. Jin,
- Peggy J. Farnham,
- and Steven J.M. Jones
Genome Res. December 2006 16: 1455-1464; Published in Advance October 19, 2006, doi:10.1101/gr.4140006
...Mica, Down and Hubbard 2005 ) and exhaustive enumeration (i.e., detecting the set of all nucleotide n -mers, then reporting the most frequent or overrepresented; e.g., Weeder, Pavesi et al. 2004 ). Alternatively, variations of a pattern can be modeled using information theory ( Schneider 2000 ). Using...
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ARTICLE: A code for transcription initiation in mammalian genomes
- Martin C. Frith,
- Eivind Valen,
- Anders Krogh,
- Yoshihide Hayashizaki,
- Piero Carninci,
- and Albin Sandelin
Genome Res. January 2008 18: 1-12; Published in Advance November 21, 2007, doi:10.1101/gr.6831208
..., but an array of closely located TSSs with different rates of initiation. As a rule, genes have more than one such core promoter; however, defining the boundaries between core promoters is not trivial. These discoveries prompt a re-evaluation of our models for transcription initiation. We describe a new...

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