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Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
...-stimulated primary aortic endothelial cells isolated from human, mouse, and cow, we find that 55 TE subfamilies are associated with RELA-bound regions, many of which reside near TNF-responsive genes. A prominent example of lineage-specific contribution of transposons comes from the bovine SINE subfamilies Bov-tA1...
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Method: ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search
- Haotian Zhang,
- Yiming Zhang,
- Teng Gao,
- and Yufeng Wu
Genome Res. December 2025 35: 2781-2791; Published in Advance September 3, 2025, doi:10.1101/gr.280542.125
..., Boston, Massachusetts 02115, USA; 4Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269, USA Corresponding author: yufeng.wu@uconn.eduAbstractIn a multicellular organism, cell lineages share a common evolutionary history. Knowing this history can facilitate the study...
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Research: Epigenetic and evolutionary features of ape subterminal heterochromatin
- DongAhn Yoo,
- Katherine M. Munson,
- and Evan E. Eichler
Genome Res. January 2026 36: 38-49; Published in Advance October 22, 2025, doi:10.1101/gr.280987.125
...of these regions in chimpanzees and gorillas. Detailed analyses of the composition of the associated terminal 32 bp satellite array from chimpanzee (termed pCht) and intervening segmental duplication (SD) spacers confirm two independent origins in the Pan and gorilla lineages. In chimpanzee and bonobo, we estimate...
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Review: Advancements in prospective single-cell lineage barcoding and their applications in research
- Xiaoli Zhang,
- Yirui Huang,
- Yajing Yang,
- Qi-En Wang,
- and Lang Li
Genome Res. December 2024 34: 2147-2162; Published in Advance November 21, 2024, doi:10.1101/gr.278944.124
...University, Columbus, Ohio 43210, USA; 4Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, Ohio 43210, USA Corresponding author: xiaoli18@usf.eduAbstractSingle-cell lineage tracing (scLT) has emerged as a powerful tool, providing unparalleled resolution...
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Research: Genome-wide patterns of selection–drift variation strongly associate with organismal traits across the green plant lineage
- Kavitha Uthanumallian,
- Andrea Del Cortona,
- Susana M. Coelho,
- Olivier De Clerck,
- Sebastian Duchene,
- and Heroen Verbruggen
Genome Res. August 2024 34: 1130-1139; Published in Advance August 29, 2024, doi:10.1101/gr.279002.124
...Genome-wide patterns of selection–drift variation strongly associate with organismal traits across the green plant lineage Kavitha Uthanumallian1, Andrea Del Cortona2, Susana M. Coelho3, Olivier De Clerck2, Sebastian Duchene4,5 and Heroen Verbruggen1,6 1Melbourne Integrative Genomics, School of Bio...
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Method: Detecting ancient positive selection in humans using extended lineage sorting
- Stéphane Peyrégne,
- Michael James Boyle,
- Michael Dannemann,
- and Kay Prüfer
Genome Res. September 2017 27: 1563-1572; Published in Advance July 18, 2017, doi:10.1101/gr.219493.116
...of recombination rates along the human lineage could limit our power to detect selected regions, and we used an ancestral recombination map of the human-chimpanzee ancestor to annotate top candidate regions (Supplemental Table S9; Munch et al. 2014). Finally, we further characterized fixed or nearly fixed...
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Method: A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings
- Louxin Zhang,
- Niloufar Abhari,
- Caroline Colijn,
- and Yufeng Wu
Genome Res. July 2023 33: 1053-1060; Published in Advance May 22, 2023, doi:10.1101/gr.277669.123
...at least one child that is of indegree one. Here, we develop a new method that infers the minimum tree–child network by aligning lineage taxon strings in the phylogenetic trees. This algorithmic innovation enables us to get around the limitations of the existing programs for phylogenetic network inference...
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Research: Sympatric chimpanzees and gorillas harbor convergent gut microbial communities
- Andrew H. Moeller,
- Martine Peeters,
- Jean-Basco Ndjango,
- Yingying Li,
- Beatrice H. Hahn,
- and Howard Ochman
Genome Res. October 2013 23: 1715-1720; Published in Advance June 26, 2013, doi:10.1101/gr.154773.113
...microbiota from those of heritable factors is to compare sympatric (i.e., co-occurring) and allopatric (i.e., geographically separated) host populations. Gorillas diverged from the lineage leading to humans and chimpanzees/bonobos at least 6 million years ago (Glazko andNei 2003; Langergraber et al. 2012...
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Research: Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals
- Ulrike Böhme,
- Thomas D. Otto,
- James A. Cotton,
- Sascha Steinbiss,
- Mandy Sanders,
- Samuel O. Oyola,
- Antoine Nicot,
- Sylvain Gandon,
- Kailash P. Patra,
- Colin Herd,
- Ellen Bushell,
- Katarzyna K. Modrzynska,
- Oliver Billker,
- Joseph M. Vinetz,
- Ana Rivero,
- Chris I. Newbold,
- and Matthew Berriman
Genome Res. April 2018 28: 547-560; Published in Advance March 2, 2018, doi:10.1101/gr.218123.116
...Complete avian malaria parasite s reveal features associated with lineage-specific evolution in birds and mammals Ulrike Böhme1,7, Thomas D. Otto1,7,8, James A. Cotton1, Sascha Steinbiss1, Mandy Sanders1, Samuel O. Oyola1,2, Antoine Nicot3, Sylvain Gandon3, Kailash P. Patra4, Colin Herd1, Ellen...
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Research: Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements
- Yuyun Zhang,
- Zijuan Li,
- Yu'e Zhang,
- Kande Lin,
- Yuan Peng,
- Luhuan Ye,
- Yili Zhuang,
- Meiyue Wang,
- Yilin Xie,
- Jingyu Guo,
- Wan Teng,
- Yiping Tong,
- Wenli Zhang,
- Yongbiao Xue,
- Zhaobo Lang,
- and Yijing Zhang
Genome Res. December 2021 31: 2276-2289; Published in Advance September 9, 2021, doi:10.1101/gr.275658.121
...lineage-specific and embedded in TEsA comparison of the -wide TF binding patterns revealed that they are largely grouped by TF families (Fig. 3A). Different groups are preferentially localized to different chromosomal regions. The AP2 TFs mostly bind to the distal end of chromosomes, whereas NAC TFs bind...

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