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Method: Fast sequence alignment for centromeres with RaMA
- Pinglu Zhang,
- Yanming Wei,
- Qinzhong Tian,
- Quan Zou,
- and Yansu Wang
Genome Res. May 2025 35: 1209-1218; Published in Advance February 12, 2025, doi:10.1101/gr.279763.124
.... 1978. Homology between human and simian repeated DNA. Nature 276: 92–94. https://pubmed.ncbi.nlm.nih.gov/105293. doi:10.1038/276092a0 ↵Marco-Sola S, Moure JC, Moreto M, Espinosa A. 2021. Fast gap-affine pairwise alignment using the wavefront algorithm. Bioinformatics 37: 456–463. doi:10...
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Method: k-mer manifold approximation and projection for visualizing DNA sequences
- Chengbo Fu,
- Einari A. Niskanen,
- Gong-Hong Wei,
- Zhirong Yang,
- Marta Sanvicente-García,
- Marc Güell,
- and Lu Cheng
Genome Res. May 2025 35: 1234-1246; Published in Advance April 10, 2025, doi:10.1101/gr.279458.124
...between ETV6 and FLI1. Moreover, KMAP identifies four prevalent patterns in gene editing data of the AAVS1 locus, aligning with findings reported in the literature. These applications underscore that KMAP can be a valuable tool across various biological contexts.DNA sequence serve as the primary carrier...
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RESOURCE: 28-Way vertebrate alignment and conservation track in the UCSC Genome Browser
- Webb Miller,
- Kate Rosenbloom,
- Ross C. Hardison,
- Minmei Hou,
- James Taylor,
- Brian Raney,
- Richard Burhans,
- David C. King,
- Robert Baertsch,
- Daniel Blankenberg,
- Sergei L. Kosakovsky Pond,
- Anton Nekrutenko,
- Belinda Giardine,
- Robert S. Harris,
- Svitlana Tyekucheva,
- Mark Diekhans,
- Thomas H. Pringle,
- William J. Murphy,
- Arthur Lesk,
- George M. Weinstock,
- Kerstin Lindblad-Toh,
- Richard A. Gibbs,
- Eric S. Lander,
- Adam Siepel,
- David Haussler,
- and W. James Kent
Genome Res. December 2007 17: 1797-1808; Published in Advance November 5, 2007, doi:10.1101/gr.6761107
.... Determining the range of comparison species in which homologs of a DNA sequence are present is fundamental to studying its evolution. We define the alignability of a particular DNA segment (e.g., in human) as the fraction that aligns with a designated comparison species. In the current study, the 28-way...
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Research: Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes
- Ovidiu Popa,
- Einat Hazkani-Covo,
- Giddy Landan,
- William Martin,
- and Tal Dagan
Genome Res. April 2011 21: 599-609; Published in Advance January 26, 2011, doi:10.1101/gr.115592.110
...in the recipient that are found in a perfect match with the donor , providing a proxy for the likelihood of gene acquisition mediated by homologous recombination. The Sgs is similar to the recently suggested average nucleotide identity (ANI) measure that positively correlates with DNA–DNA hybridization...
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METHODS: Detection of Deleted Genomic DNA Using a Semiautomated Computational Analysis of GeneChip Data
- Hugh Salamon,
- Midori Kato-Maeda,
- Peter M. Small,
- Jorg Drenkow,
- and Thomas R. Gingeras
Genome Res. December 1, 2000 10: 2044-2054; Published in Advance November 21, 2000, doi:10.1101/gr.152900
...measured for genomic DNA from a clinical strain and from a vaccine organism. Because individual probe-pair hybridization intensities exhibit limited sensitivity/specificity characteristics to detect deletions, data-analytical methodology to exploit measurements from multiple probes in tandem locations...
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Research: Fusion, fission, and scrambling of the bilaterian genome in Bryozoa
- Thomas D. Lewin,
- Isabel Jiah-Yih Liao,
- Mu-En Chen,
- John D.D. Bishop,
- Peter W.H. Holland,
- and Yi-Jyun Luo
Genome Res. January 2025 35: 78-92; Published in Advance January 6, 2025, doi:10.1101/gr.279636.124
...of rearrangement events (the proximate cause), (2) an increase in the rate of fixation of rearrangement events (the ultimate cause), or (3) both. Loss of DNA repair machinery (Vargas-Chávez et al. 2024), transposable element invasions (Ahola et al. 2014; Höök et al. 2023), or environmental mutagenic agents...
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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
...sequencing (CSS) applied to PacBio's SMRT sequencing (Li et al. 2014). This method obtains the consensus sequence from multiple passes of a circular single molecule made by ligating both ends of the same double-strand DNA to form the circular template. While each pass produces an error-prone read...
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Research: Relationship between histone modifications and transcription factor binding is protein family specific
- Beibei Xin and
- Remo Rohs
Genome Res. March 2018 28: 321-333; Published in Advance January 11, 2018, doi:10.1101/gr.220079.116
...99.8% of putative binding sites in a cellular environment in vivo (Wang et al. 2012). Given the multiple layers that contribute to in vivo binding (Levo and Segal 2014; Slattery et al. 2014; Zentner et al. 2015; Mathelier et al. 2016b), it is clear that DNA sequence and shape at core binding sites...
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Research: A widespread role of the motif environment in transcription factor binding across diverse protein families
- Iris Dror,
- Tamar Golan,
- Carmit Levy,
- Remo Rohs,
- and Yael Mandel-Gutfreund
Genome Res. September 2015 25: 1268-1280; Published in Advance July 9, 2015, doi:10.1101/gr.184671.114
...found that in vivo, TFs sharing homologous DNA binding domains (as defined by Pfam) (Finn et al. 2014) often share the sameGC preferences.We noticed that similar to the in vitro results, TFs from the homeodomain family tend to bindmotifs embeddedwithin higher AT content regions, whereas members of the C...
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Method: Calling amplified haplotypes in next generation tumor sequence data
- Ninad Dewal,
- Yang Hu,
- Matthew L. Freedman,
- Thomas LaFramboise,
- and Itsik Pe'er
Genome Res. February 2012 22: 362-374; Published in Advance November 16, 2011, doi:10.1101/gr.122564.111
...variants.In the pursuit of detecting causal or associated variants, it aids the cancer community to integrate somatic and germline DNA changes. We present a method that helps move toward this end in next generation tumor sequence data. The strong evaluation of HATS provides us confidence to offer...

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