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Research: Independent evolution of transcript abundance and gene regulatory dynamics
- Gat Krieger,
- Offir Lupo,
- Avraham A. Levy,
- and Naama Barkai
Genome Res. July 2020 30: 1000-1011; Published in Advance July 22, 2020, doi:10.1101/gr.261537.120
.... The majority of genes whose expression varied between the species maintained a conserved dynamic pattern. Cases of diverged dynamic pattern correspond to genes that were induced under distinct subsets of conditions in the two species. Profiling the interspecific hybrid allowed us to distinguish between genes...
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Research: Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control
- Todd P. Michael,
- Evan Ernst,
- Nolan Hartwick,
- Philomena Chu,
- Douglas Bryant,
- Sarah Gilbert,
- Stefan Ortleb,
- Erin L. Baggs,
- K. Sowjanya Sree,
- Klaus J. Appenroth,
- Joerg Fuchs,
- Florian Jupe,
- Justin P. Sandoval,
- Ksenia V. Krasileva,
- Ljudmylla Borisjuk,
- Todd C. Mockler,
- Joseph R. Ecker,
- Robert A. Martienssen,
- and Eric Lam
Genome Res. February 2021 31: 225-238; Published in Advance December 23, 2020, doi:10.1101/gr.266429.120
...specific example is in the evolutionarily conserved linkage between core circadian clock genes LATE ELONGATED HYPOCOTYL (LHY) and PSEUDO RESPONSE REGULATOR 37 (PRR37) on Chr 20 of the sp9509 that is found as far back as bryophytes and shared across other dicots and non-grass monocots (Fig. 2B). Although...
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ARTICLE: Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
- Adam Siepel,
- Gill Bejerano,
- Jakob S. Pedersen,
- Angie S. Hinrichs,
- Minmei Hou,
- Kate Rosenbloom,
- Hiram Clawson,
- John Spieth,
- LaDeana W. Hillier,
- Stephen Richards,
- George M. Weinstock,
- Richard K. Wilson,
- Richard A. Gibbs,
- W. James Kent,
- Webb Miller,
- and David Haussler
Genome Res. August 2005 15: 1034-1050; Published in Advance July 15, 2005, doi:10.1101/gr.3715005
...genes, but matching publicly available mRNA or spliced EST sequences (“other mRNA” in Fig. 3 ) show 9.2% coverage by conserved elements (a 2.1-fold enrichment), and regions not in known genes or other mRNAs, but transcribed according to data from the Affymetrix/NCI Human Transcriptome project (“other...
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Research: Fixation of allelic gene expression landscapes and expression bias pattern shape the transcriptome of the clonal Amazon molly
- Yuan Lu,
- David Bierbach,
- Jenny Ormanns,
- Wesley C. Warren,
- Ronald B. Walter,
- and Manfred Schartl
Genome Res. March 2021 31: 372-379; Published in Advance February 5, 2021, doi:10.1101/gr.268870.120
...-throughput transcriptome resequencing. Hum Mol Genet 19: 122–134. doi:10.1093/hmg/ddp473 ↵Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. 2013. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14: R36. doi:10.1186/gb-2013-14-4-r36 ↵Koboldt...
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Research: Circadian gene variants and the skeletal muscle circadian clock contribute to the evolutionary divergence in longevity across Drosophila populations
- Liam C. Hunt,
- Jianqin Jiao,
- Yong-Dong Wang,
- David Finkelstein,
- Deepti Rao,
- Michelle Curley,
- Maricela Robles-Murguia,
- Abbas Shirinifard,
- Vishwajeeth R. Pagala,
- Junmin Peng,
- Yiping Fan,
- and Fabio Demontis
Genome Res. August 2019 29: 1262-1276; Published in Advance June 27, 2019, doi:10.1101/gr.246884.118
...the s of Drosophila melanogaster strains with exceptional longevity that were obtained via multiple rounds of selection from a parental strain. Comparison of genomic, transcriptomic, and proteomic data revealed that changes in gene expression due to intergenic polymorphisms are associated with longevity...
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Research: Genomic evidence for adaptation by gene duplication
- Wenfeng Qian and
- Jianzhi Zhang
Genome Res. August 2014 24: 1356-1362; Published in Advance June 5, 2014, doi:10.1101/gr.172098.114
...genes, which need not promote adaptation. Hence, the general validity of the adaptation by gene duplication hypothesis remains uncertain. Indeed, a -scale experiment found similar fitness effects of deleting pairs of duplicate genes and deleting individual singleton genes from the yeast , leading...
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Research: Divergence patterns of genic copy number variation in natural populations of the house mouse (Mus musculus domesticus) reveal three conserved genes with major population-specific expansions
- Željka Pezer,
- Bettina Harr,
- Meike Teschke,
- Hiba Babiker,
- and Diethard Tautz
Genome Res. August 2015 25: 1114-1124; Published in Advance July 6, 2015, doi:10.1101/gr.187187.114
...the most copy-number variable genes are three highly conserved genes that encode the splicing factor CWC22, the spindle protein SFI1, and the Holliday junction recognition protein HJURP. These genes exhibit population-specific expansion patterns that suggest involvement in local adaptations. We found...
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METHODS: Identification of Novel Human Genes Evolutionarily Conserved in Caenorhabditis elegans by Comparative Proteomics
- Chun-Hung Lai,
- Chang-Yuan Chou,
- Lan-Yang Ch'ang,
- Chung-Shyan Liu,
- and Wen-chang Lin
Genome Res. May 1, 2000 10: 703-713; doi:10.1101/gr.10.5.703
...Identification of Novel Human Genes Evolutionarily Conserved in Caenorhabditis elegans by Comparative Proteomics Chun-Hung Lai 1 , Chang-Yuan Chou 1 , Lan-Yang Ch'ang 1 , Chung-Shyan Liu 2 , and Wen-chang Lin 1 , 3 1...
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LETTER: “Genome design” model: Evidence from conserved intronic sequence in human–mouse comparison
- Alexander E. Vinogradov
Genome Res. March 2006 16: 347-354; Published in Advance February 3, 2006, doi:10.1101/gr.4318206
...the balance of small insertions and deletions (indels) can explain the greater length of introns in tissue-specific genes. The length of the conserved intronic DNA in a gene is correlated with the number of functional domains in the protein encoded by that gene. These results suggest that the greater length...
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Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
...and transcriptomic levels, along with their regulatory effects on structural variations (SVs) and gene expression. Functional validation is performed using dual-luciferase assays and cell-based experiments. Our findings reveal that integrated HBV sequences form long concatemers, mediating inter- and intrachromosomal...

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