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Editorial: RECOMB 2025 Special Issue
- Sriram Sankararaman and
- Bonnie Berger
Genome Res. December 2025 35: v-vi; doi:10.1101/gr.281664.125
...versions of ∼40% of the accepted papers for further review, ultimately leading to the publication of this Special Issue.RECOMB is the leading international conference on algorithmic computational biology, bridging computational, mathematical, statistical, and biological sciences. It provides a scientific...
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Method: Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories
- Borislav Hrisimirov Hristov,
- William Stafford Noble,
- and Alessandro Bertero
Genome Res. October 2024 34: 1610-1623; Published in Advance September 25, 2024, doi:10.1101/gr.278327.123
.... These, in turn, recruit accessory targets of the same factors. This hypothesis predicts the existence of both transcription factories specialized for certain transcription factors (TFs) and/or chromatin regulators, and other RNA factories specialized for various RNA-binding and regulatory proteins. We...
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Method: Fast inference of genetic recombination rates in biobank scale data
- Ardalan Naseri,
- William Yue,
- Shaojie Zhang,
- and Degui Zhi
Genome Res. July 2023 33: 1015-1022; Published in Advance June 22, 2023, doi:10.1101/gr.277676.123
...avoiding enumerating all possible pairs using PBWT blocks. As a result, the run time of FastRecomb grows linearly with the number of variant sites and the number of individuals. Also, FastRecomb avoids the explicit outputting of IBD segments, a potential I/O bottleneck. These innovations enable FastRecomb...
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Resource: Global networks of functional coupling in eukaryotes from comprehensive data integration
- Andrey Alexeyenko and
- Erik L.L. Sonnhammer
Genome Res. June 2009 19: 1107-1116; Published in Advance February 25, 2009, doi:10.1101/gr.087528.108
...'s neighborhood can be specified by subnetwork size, confidence threshold, network radius, and neighbor-search algorithm. The subnetwork is shown with a specially designed Java applet jSquid ( Klammer et al. 2008 ) that allows flexible user-controlled rendering of the network graph, including node grouping...
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Methods: Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
- Benedict Paten,
- Javier Herrero,
- Kathryn Beal,
- Stephen Fitzgerald,
- and Ewan Birney
Genome Res. November 2008 18: 1814-1828; Published in Advance October 10, 2008, doi:10.1101/gr.076554.108
...that allow the definition of constraints between sequence indices of the form xi ≤ yj (i.e., that position xi must precede or be aligned to position yj in the final alignment), and similarly xi &lt; yj (i.e., that position xi must precede position yj ) can be thought of as specialized types of banded...
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Resource: Breakpoint graphs and ancestral genome reconstructions
- Max A. Alekseyev and
- Pavel A. Pevzner
Genome Res. May 2009 19: 943-957; Published in Advance February 13, 2009, doi:10.1101/gr.082784.108
...these representations are equivalent (i.e., they produce the same final result). Figure 6B illustrates transformation of a simple cycle on six vertices into three complete multi-edges with two 2-breaks. ↵ 8 In the special case x 0 = xm + 1 = ∞, and the flanking edges are of the same -consistent multi...

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