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Editorial: Innovations in computational biology: RECOMB 2024 Special Issue
- Jian Ma and
- Bonnie Berger
Genome Res. September 2024 34: vii-viii; doi:10.1101/gr.280036.124
...proceedings while pursuing journal publication elsewhere. A subset of these papers was invited for further review at Genome Research, ultimately leading to the publication of this Special Issue.RECOMB is the leading international conference on algorithmic computational biology, bridging computational...
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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
...-efficient method for estimating genetic maps from population genotyping data. Our method, FastRecomb, leverages the efficient positional Burrows–Wheeler transform (PBWT) data structure for counting IBD segment boundaries as potential recombination events. We used PBWT blocks to avoid redundant counting of pairwise...
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Method: Secure discovery of genetic relatives across large-scale and distributed genomic data sets
- Matthew M. Hong,
- David Froelicher,
- Ricky Magner,
- Victoria Popic,
- Bonnie Berger,
- and Hyunghoon Cho
Genome Res. September 2024 34: 1312-1323; Published in Advance August 7, 2024, doi:10.1101/gr.279057.124
...results. Removal of duplicate individuals across data sets is a special case of detecting relatives, which our work also addresses.There are several key hurdles to identifying related individuals across data sets. Unlike other analysis tasks that derive aggregate-level insights from the pooled data...
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RECOMB 2022 Special/Methods: Assembler artifacts include misassembly because of unsafe unitigs and underassembly because of bidirected graphs
- Amatur Rahman and
- Paul Medvedev
Genome Res. September 2022 32: 1746-1753; Published in Advance July 27, 2022, doi:10.1101/gr.276601.122
..., then even error-free data result in unsafe unitigs; also, unitigs may unnecessarily split palindromes in half if special care is not taken. To the best of our knowledge, this paper is the first to theoretically predict the existence of these assembler artifacts and confirm and measure the extent...
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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: GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes
- Tomáš Brůna,
- Alexandre Lomsadze,
- and Mark Borodovsky
Genome Res. May 2024 34: 757-768; Published in Advance June 12, 2024, doi:10.1101/gr.278373.123
...specially designed reduced-size databases of the cross-species proteins as the runtime of MAKER2 with our minimal size “order excluded” databases turned out to be prohibitive (see Supplemental Methods, Sec. S5). Change to the smaller databases brought the F1 of GeneMark-ETP down in comparison with its run...
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Method: An efficient genotyper and star-allele caller for pharmacogenomics
- Ananth Hari,
- Qinghui Zhou,
- Nina Gonzaludo,
- John Harting,
- Stuart A. Scott,
- Xiang Qin,
- Steve Scherer,
- S. Cenk Sahinalp,
- and Ibrahim Numanagić
Genome Res. January 2023 33: 61-70; Published in Advance January 19, 2023, doi:10.1101/gr.277075.122
.... 2013). These issues need to be carefully and comprehensively accounted for before the genotyping process in order to obtain accurate results. Lastly, alleles of many pharmacogenes are not defined through a single-nucleotide variant (SNV) but through a complete gene haplotype. Thus, the exact functional...
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RECOMB 2022 Special/Methods: Ultra-high-diversity factorizable libraries for efficient therapeutic discovery
- Zheng Dai,
- Sachit D. Saksena,
- Geraldine Horny,
- Christine Banholzer,
- Stefan Ewert,
- and David K. Gifford
Genome Res. September 2022 32: 1787-1794; Published in Advance June 23, 2022, doi:10.1101/gr.276593.122
...of sequences for our optimization to be useful.A special case in which small feature spaces can be found is when our scoring function can be described with an Ising model or, more generally, a Potts model. Because the only interactions modeled are between pairs of sequence positions, an encoding of size O...
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RECOMB 2022 Special/Methods: Learning probabilistic protein–DNA recognition codes from DNA-binding specificities using structural mappings
- Joshua L. Wetzel,
- Kaiqian Zhang,
- and Mona Singh
Genome Res. September 2022 32: 1776-1786; Published in Advance September 19, 2022, doi:10.1101/gr.276606.122
...specialized experimental protein–DNA interaction assays that position and orient the TF relative to a potential DNA-binding site in a predetermined way (Noyes et al. 2008a,b; Chu et al. 2012; Persikov et al. 2014; Najafabadi et al. 2015); in contrast, our approach does not require a priori knowledge...
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RECOMB 2022 Special/Methods: Unsupervised cell functional annotation for single-cell RNA-seq
- Dongshunyi Li,
- Jun Ding,
- and Ziv Bar-Joseph
Genome Res. September 2022 32: 1765-1775; Published in Advance June 28, 2022, doi:10.1101/gr.276609.122
.... The gene set activity scores are used by an “annotator” to guide the clustering such that cells sharing similar biological processes are more likely to be grouped together. Such a design allows the method to focus on the key processes when clustering cells and so can overcome issues related to noise...

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