Searching journal content for articles similar to Borozan et al. 35 (12): 2770.

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  1. Editorial: RECOMB 2025 Special Issue
    • Sriram Sankararaman and
    • Bonnie Berger
    Genome Res. December 2025 35: v-vi; doi:10.1101/gr.281664.125
    ...in this issue. Wang et al. (2025) introduce geneCover, a combinatorial, label-free, method to select an optimal panel of minimally correlated marker genes, whereas SepSolve from Borozan et al. (2025) seeks to find a small set of marker genes that lead to “c-separated cell types.” The last paper in this issue...
  2. Research: Variation in the fitness impact of translationally optimal codons among animals
    • Florian Bénitière,
    • Tristan Lefébure,
    • and Laurent Duret
    Genome Res. March 2025 35: 446-458; Published in Advance February 10, 2025, doi:10.1101/gr.279837.124
    ....duret@univ-lyon1.frAbstractEarly studies in invertebrate model organisms (fruit flies, nematodes) showed that their synonymous codon usage is under selective pressure to optimize translation efficiency in highly expressed genes (a process called translational selection). In contrast, mammals show little evidence...
  3. Corrigendum: Corrigendum: Human auditory ossicles as an alternative optimal source of ancient DNA
    • Kendra Sirak,
    • Daniel Fernandes,
    • Olivia Cheronet,
    • Eadaoin Harney,
    • Matthew Mah,
    • Swapan Mallick,
    • Nadin Rohland,
    • Nicole Adamski,
    • Nasreen Broomandkhoshbacht,
    • Kimberly Callan,
    • Francesca Candilio,
    • Ann Marie Lawson,
    • Kirsten Mandl,
    • Jonas Oppenheimer,
    • Kristin Stewardson,
    • Fatma Zalzala,
    • Alexandra Anders,
    • Juraj Bartík,
    • Alfredo Coppa,
    • Tumen Dashtseveg,
    • Sándor Évinger,
    • Zdeněk Farkaš,
    • Tamás Hajdu,
    • Jamsranjav Bayarsaikhan,
    • Lauren McIntyre,
    • Vyacheslav Moiseyev,
    • Mercedes Okumura,
    • Ildikó Pap,
    • Michael Pietrusewsky,
    • Pál Raczky,
    • Alena Šefčáková,
    • Andrei Soficaru,
    • Tamás Szeniczey,
    • Béla Miklós Szőke,
    • Dennis Van Gerven,
    • Sergey Vasilyev,
    • Lynne Bell,
    • David Reich,
    • and Ron Pinhasi
    Genome Res. June 2020 30: 938_1; doi:10.1101/gr.266098.120
    OPEN ACCESS ARTICLE
  4. Method: Human auditory ossicles as an alternative optimal source of ancient DNA
    • Kendra Sirak,
    • Daniel Fernandes,
    • Olivia Cheronet,
    • Eadaoin Harney,
    • Matthew Mah,
    • Swapan Mallick,
    • Nadin Rohland,
    • Nicole Adamski,
    • Nasreen Broomandkhoshbacht,
    • Kimberly Callan,
    • Francesca Candilio,
    • Ann Marie Lawson,
    • Kirsten Mandl,
    • Jonas Oppenheimer,
    • Kristin Stewardson,
    • Fatma Zalzala,
    • Alexandra Anders,
    • Juraj Bartík,
    • Alfredo Coppa,
    • Tumen Dashtseveg,
    • Sándor Évinger,
    • Zdeněk Farkaš,
    • Tamás Hajdu,
    • Jamsranjav Bayarsaikhan,
    • Lauren McIntyre,
    • Vyacheslav Moiseyev,
    • Mercedes Okumura,
    • Ildikó Pap,
    • Michael Pietrusewsky,
    • Pál Raczky,
    • Alena Šefčáková,
    • Andrei Soficaru,
    • Tamás Szeniczey,
    • Béla Miklós Szőke,
    • Dennis Van Gerven,
    • Sergey Vasilyev,
    • Lynne Bell,
    • David Reich,
    • and Ron Pinhasi
    Genome Res. March 2020 30: 427-436; Published in Advance February 25, 2020, doi:10.1101/gr.260141.119
    ...the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provides optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of morphological information caused by its sampling. Motivated...
  5. Method: HINGE: long-read assembly achieves optimal repeat resolution
    • Govinda M. Kamath,
    • Ilan Shomorony,
    • Fei Xia,
    • Thomas A. Courtade,
    • and David N. Tse
    Genome Res. May 2017 27: 747-756; Published in Advance March 20, 2017, doi:10.1101/gr.216465.116
    ...to unnecessary fragmentation. We present HINGE, an assembler that seeks to achieve optimal repeat resolution by distinguishing repeats that can be resolved given the data from those that cannot. This is accomplished by adding “hinges” to reads for constructing an overlap graph where only unresolvable repeats...
    OPEN ACCESS ARTICLE
  6. Method: Automated interpretable artificial intelligence genomic prediction with AlGP
    • Lei Wei,
    • Ziqin Jiang,
    • Baoliang Fan,
    • Yidan Yan,
    • Zhenqiang Xu,
    • Xiaoxiang Hu,
    • and Yuzhe Wang
    Genome Res. March 5, 2026 ; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
    ...and optimizing the hyperparameters. We demonstrate how gene-related biometrics influence target traits and how accounting for interaction effects enhances prediction accuracy. In addition, we apply Shapley additive explanations (SHAP) to quantify the SNP additive and epistatic effects. To bridge the gap between...
  7. Method: EnDeep4mC predicts DNA N4-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
    • Shuyu Zhang,
    • Quan Zou,
    • Mengting Niu,
    • Zhibin Lv,
    • Antony Stalin,
    • and Ximei Luo
    Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
    ..., requires efficient computational detection methods due to experimental limitations. Although machine learning predictors have been proposed, their performance could be enhanced through systematic optimization of feature encoding schemes. Here, we propose EnDeep4mC, a dual-adaptive framework integrating...
    OPEN ACCESS ARTICLE
  8. Method: Mapping and quantifying nascent transcript start sites using TT-TSS-seq
    • Eleanor Elgood Hunt,
    • Claudia Vivori,
    • Richard Mitter,
    • Vedis Agnadottir,
    • and Folkert J. van Werven
    Genome Res. March 2026 36: 600-610; Published in Advance February 17, 2026, doi:10.1101/gr.280726.125
    ...optimize the TSS-seq protocol to enhance sensitivity and accuracy. Specifically, we refine enzymatic reactions for decapping and RNA ligation and incorporate 5′ oligonucleotides containing unique molecular identifiers (UMIs) and barcodes to enable accurate quantification and sample multiplexing. The TT...
    OPEN ACCESS ARTICLE
  9. Method: Pangenome-based genome inference using integer programming
    • Ghanshyam Chandra,
    • Md Helal Hossen,
    • Stephan Scholz,
    • Alexander T. Dilthey,
    • Daniel Gibney,
    • and Chirag Jain
    Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
    ...and repetitive regions, further impacting genotyping performance. Recent works highlight the advantage of pan graphs in addressing these challenges. Building on these developments, we propose a rigorous alignment-free genotyping method. Our optimization framework identifies a path through the pan graph...
  10. 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
    ...The genetic code is nearly optimal for allowing additional information within protein-coding sequences Shalev Itzkovitz 1 , 2 and Uri Alon 1 , 2 , 3 1 Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel...
    OPEN ACCESS ARTICLE
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