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Review: Recent advances in methods to characterize archaic introgression in modern humans
- David Peede,
- Mayra M. Bañuelos,
- Jazeps Medina Tretmanis,
- Miriam Miyagi,
- and Emilia Huerta-Sánchez
Genome Res. February 2026 36: 239-256; Published in Advance January 16, 2026, doi:10.1101/gr.278993.124
...descends from an archaic proxy ancestor.Reference-based methodsOne strategy for identifying introgressed segments is to scan a modern human and label regions with a strong affinity to a sequenced archaic individual as introgressed. Because these approaches rely on an archaic “reference” as the putative...
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Research: Vertebrates show coordinated elevated expression of mitochondrial and nuclear genes after birth
- Hadar Medini and
- Dan Mishmar
Genome Res. March 2025 35: 459-474; Published in Advance March 4, 2025, doi:10.1101/gr.279700.124
...biogenesis (at E16.5 and E17.5), and 70% lethality of mice within 24 h after birth (Lai et al. 2008). Fourth, dysfunctional mitochondria in the embryonic mouse and human patients’ hearts led to severe cardiomyopathy and either embryonic or neonatal lethality (Zhao et al. 2019). Taken together...
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Review: De novo gene birth and the conundrum of ORFan genes in bacteria
- Md. Hassan uz-Zaman and
- Howard Ochman
Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
...in the database (Daubin and Ochman 2004a; Yomtovian et al. 2010; Vakirlis and Kupczok 2024; Pereira et al. 2025).De novo gene birth is the most tractable and traceable of these three routes because it is possible, in principle, to identify the ancestral noncoding sequence from which the new gene formed. Based...
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Research: Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon
- Koichi Kitao,
- Kenji Ichiyanagi,
- and So Nakagawa
Genome Res. June 2025 35: 1287-1300; Published in Advance May 8, 2025, doi:10.1101/gr.280007.124
.... Among transcription factors previously reported to promote human L1 transcription such as RUNX3, SP1, SOX2, and YY1 (Luqman-Fatah and Miyoshi 2023), RUNX3 binding sites were identified near the transcription start site (TSS) of the Lyosin isoform but not in the canonical MYL4 isoform in Anolis...
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Method: TFcomb identifies transcription factor combinations for cellular reprogramming based on single-cell multiomics data
- Chen Li,
- Sijie Chen,
- Yixin Chen,
- Haiyang Bian,
- Minsheng Hao,
- Lei Wei,
- and Xuegong Zhang
Genome Res. June 2025 35: 1429-1439; Published in Advance April 10, 2025, doi:10.1101/gr.279955.124
...-seq and ATAC-seq data. Benchmarking experiments on data of human embryonic stem cells demonstrate superior performance of TFcomb against existing methods for identifying individual TFs. We curate data sets of multiple cell reprogramming cases and demonstrate that TFcomb can efficiently identify reprogramming...
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Research: Optical genome mapping identifies rare structural variants in neural tube defects
- Nikhil S. Sahajpal,
- Jane Dean,
- Benjamin Hilton,
- Timothy Fee,
- Cindy Skinner,
- Alex Hastie,
- Barbara R. DuPont,
- Alka Chaubey,
- Michael J. Friez,
- and Roger E. Stevenson
Genome Res. April 2025 35: 798-809; Published in Advance March 19, 2025, doi:10.1101/gr.279318.124
...associated with NTDs in mouse have been identified in association with NTDs. Six of these genes are being proposed as human NTD-associated genes for the first time, with strong or moderate evidence for pathogenicity.Four cases carried deletions of genes associated with NTDs in mice (FOXD4, RBBP4, TGIF1...
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Research: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
- Jian-Hai Chen,
- Patrick Landback,
- Deanna Arsala,
- Alexander Guzzetta,
- Shengqian Xia,
- Jared Atlas,
- Dylan Sosa,
- Yong E. Zhang,
- Jingqiu Cheng,
- Bairong Shen,
- and Manyuan Long
Genome Res. March 2025 35: 379-392; Published in Advance February 14, 2025, doi:10.1101/gr.279498.124
...). To date, more than 4000 Mendelian disease genes have been identified, each contributing to a diverse array of human phenotypes (Boycott et al. 2013; https://mirror.omim.org/statistics/geneMap). These disease genes and associated phenotypes could provide insights into the evolutionary trajectory of human...
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Method: QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data
- Xiaoyu Song,
- Yuqing Shang,
- Michelle E. Ehrlich,
- Panos Roussos,
- Guo-Cheng Yuan,
- and Pei Wang
Genome Res. August 2025 35: 1821-1831; Published in Advance June 23, 2025, doi:10.1101/gr.279859.124
...QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data Xiaoyu Song1, Yuqing Shang1, Michelle E. Ehrlich2, Panos Roussos3,4, Guo-Cheng Yuan5 and Pei Wang6 1Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore 169857; 2Departments of Neurology...
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Research: Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population
- Agnese Viluma,
- Øystein Flagstad,
- Mikael Åkesson,
- Camilla Wikenros,
- Håkan Sand,
- Petter Wabakken,
- and Hans Ellegren
Genome Res. March 2022 32: 449-458; Published in Advance February 8, 2022, doi:10.1101/gr.276070.121
...alleles (Fig. 7). For the remaining time period up until 2014, wolves were split in two temporal subgroups of equal sample size (i.e., 1994–2005 and 2006–2014). The birth year of individual wolves was estimated based on aging using one of three methods: (a) tooth root sectioning and counting cementum...
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Research: Genomic variation within alpha satellite DNA influences centromere location on human chromosomes with metastable epialleles
- Megan E. Aldrup-MacDonald,
- Molly E. Kuo,
- Lori L. Sullivan,
- Kimberline Chew,
- and Beth A. Sullivan
Genome Res. October 2016 26: 1301-1311; Published in Advance August 10, 2016, doi:10.1101/gr.206706.116
...Genomic variation within alpha satellite DNA influences centromere location on human chromosomes with metastable epialleles Megan E. Aldrup-MacDonald 1 , 3 , Molly E. Kuo 1 , 3 , Lori L. Sullivan 1 , 3 , Kimberline Chew 1 and Beth A...

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