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LETTER: Why do human diversity levels vary at a megabase scale?
- Ines Hellmann,
- Kay Prüfer,
- Hongkai Ji,
- Michael C. Zody,
- Svante Pääbo,
- and Susan E. Ptak
Genome Res. September 2005 15: 1222-1231; doi:10.1101/gr.3461105
...Why do human diversity levels vary at a megabase scale? Ines Hellmann 1 , 4 , Kay Prüfer 1 , Hongkai Ji 2 , Michael C. Zody 3 , Svante Pääbo 1 , and Susan E. Ptak 1 1 Max-Planck-Institute for Evolutionary...
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INSIGHT/OUTLOOK: What is Finished, and Why Does it Matter
- Elaine Mardis,
- John McPherson,
- Robert Martienssen,
- Richard K. Wilson,
- and W. Richard McCombie
Genome Res. May 1, 2002 12: 669-671; doi:10.1101/gr.032102
...Elaine Wilson, R Richard Wilson John, McPherson McCombie, W.R WR McCombie Robert, Martienssen Elaine Mardis 10.1101/gr.032102 1549-5469 genome;12/5/669 1088-9051 What is Finished, and Why Does it Matter What is Finished, and Why Does it Matter Elaine Mardis 1 , John McPherson 1 , Robert Martienssen 2...
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INSIGHT/OUTLOOK: Why Is the Centromere So Cold?
- K.H. Andy Choo
Genome Res. February 1, 1998 8: 81-82; doi:10.1101/gr.8.2.81
...KH Andy Choo Choo K.H. Andy KH Andy Choo, KA Choo Choo, K.A Choo, KH Andy KA Choo KH Choo K.A. Choo Choo, K KHAndy Choo K Choo KH Andy KH Andy, Choo 1549-5469 genome;8/2/81 10.1101/gr.8.2.81 1088-9051 Why Is the Centromere So Cold? Why Is the Centromere So Cold? K.H. Andy Choo 1 The Murdoch...
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Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
- A. Bernardo Carvalho,
- Bernard Y. Kim,
- and Fabiana Uno
Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
..., the clearest one against GA-rich repeats in the human . However, our study reveals a systematic failure of both technologies to sequence and assemble specific exons of Drosophila melanogaster genes, indicating an overlooked limitation. Namely, multiple Y-linked exons are nearly or completely absent from raw...
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Resource: The PanOryza pangene catalog of Asian cultivated rice
- Bruno Contreras-Moreira,
- Eshan Sharma,
- Shradha Saraf,
- Guy Naamati,
- Parul Gupta,
- Justin Elser,
- Dmytro Chebotarov,
- Kapeel Chougule,
- Zhenyuan Lu,
- Sharon Wei,
- Andrew Olson,
- Ian Tsang,
- Disha Lodha,
- Yong Zhou,
- Zhichao Yu,
- Wen Zhao,
- Jianwei Zhang,
- Sandeep Amberkar,
- Kawinnat Sue-Ob,
- Zhi Sun,
- Maria Martin,
- Kenneth L. McNally,
- Doreen Ware,
- Eric W. Deutsch,
- Dario Copetti,
- Rod A. Wing,
- Pankaj Jaiswal,
- Sarah Dyer,
- and Andrew R. Jones
Genome Res. January 2026 36: 226-238; Published in Advance December 12, 2025, doi:10.1101/gr.280790.125
...the group “domains with unknown function” (DUFs) versus the number of pangenes with the respective domain. DUFs present in more than 50 pangenes are highlighted in black text.Among the significantly enriched domains in the cloud pangenes, we found a domain named DNA-directed RNA polymerase III subunit RPC4...
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Research: Degrees of convergent evolution in rodent adaptations to arid environments
- Domitille Chalopin,
- Carine Rey,
- Jeremy Ganofsky,
- Juliana Blin,
- Pascale Chevret,
- Marion Mouginot,
- Laurent Guéguen,
- Bastien Boussau,
- Sophie Pantalacci,
- and Marie Sémon
Genome Res. March 2026 36: 472-486; Published in Advance January 21, 2026, doi:10.1101/gr.280089.124
...species living in arid environments and presumably adapted to arid environments (Fig. 2). For convenience, below we refer to them as “arid species,” whereas other species are named “mesic species.”To assess the independence of the transitions to arid environments and date them, we used a semiautomated...
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Method: Strain-level metagenomic profiling using pangenome graphs with PanTax
- Wenhai Zhang,
- Yuansheng Liu,
- Guangyi Li,
- Jialu Xu,
- Enlian Chen,
- Alexander Schönhuth,
- and Xiao Luo
Genome Res. February 2026 36: 405-420; Published in Advance January 14, 2026, doi:10.1101/gr.280858.125
...satisfactory results.The difficulties involved in the adaptation of tools from short-read sequencing to long-read sequencing, as just outlined, explains why developing novel approaches for long-read-based taxonomic classification is imperative. So far, only few related tools have been designed, such as Melon...
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Method: Batch correction methods used in single-cell RNA sequencing analyses are often poorly calibrated
- Sindri Emmanúel Antonsson and
- Páll Melsted
Genome Res. August 2025 35: 1832-1841; Published in Advance July 7, 2025, doi:10.1101/gr.279886.124
..., Seurat (Stuart et al. 2019) and SCANPY (Wolf et al. 2018), include various batch correction methods, namely BBKNN, Harmony, MNN, and Combat in SCANPY, and Harmony and SCVI in Seurat, in addition to the built-in method in Seurat. Finally, we included ComBat-seq, a newer model based on the older...
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Research: Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species
- Damira Veseljak,
- Evelin Despot-Slade,
- Marin Volarić,
- Lucija Horvat,
- Tanja Vojvoda Zeljko,
- Nevenka Meštrović,
- and Brankica Mravinac
Genome Res. November 2025 35: 2445-2460; Published in Advance September 16, 2025, doi:10.1101/gr.280516.125
...assembly Tfree1.0 (Volarić et al. 2022). The candidate sequences that were mapped in five or more consecutive copies were classified as satDNAs. In this way, we identified 135 satDNAs, one already known from previous studies (Juan et al. 1993) and 134 new ones. We named them TfSat01-135 and listed...
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Method: Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
- Fan Feng,
- Sean Moran,
- Anders S. Hansen,
- Xiaotian Zhang,
- and Jie Liu
Genome Res. January 2026 36: 159-168; Published in Advance November 12, 2025, doi:10.1101/gr.280132.124
...to classify our stripes into three categories, namely (1) CTCF-motif occupied by CTCF-stripes, “CTCF-stripes”; (2) CTCF-deficient stripes that intersect with EP-interacting regions, “EP-stripes”; and (3) CTCF-deficient stripes that are not EP-intersecting, “indeterminate.” We follow the convention of previous...
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