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INSIGHT/OUTLOOK: Unlimited Hypothesis Research
- James C. Engert
Genome Res. March 1, 2000 10: 271-272; doi:10.1101/gr.10.3.271
...James C James Engert James James C, Engert Engert, J.C Engert, J JC Engert Engert, JC James C Engert J.C. Engert JamesC Engert J Engert Engert, James C Engert Engert James C. 10.1101/gr.10.3.271 1549-5469 genome;10/3/271 1088-9051 Unlimited Hypothesis Research Unlimited Hypothesis Research James C...
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PERSPECTIVE: Determinants of the success of whole-genome association testing
- Andrew G. Clark,
- Eric Boerwinkle,
- James Hixson,
- and Charles F. Sing
Genome Res. November 2005 15: 1463-1467; doi:10.1101/gr.4244005
...Determinants of the success of whole- association testing Andrew G. Clark 1 , 4 , Eric Boerwinkle 2 , James Hixson 2 , and Charles F. Sing 3 1 Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA 2 Human Genetics Center, University of Texas Health Science...
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Method: A simple method for finding related sequences by adding probabilities of alternative alignments
- Martin C. Frith
Genome Res. August 2024 34: 1165-1173; Published in Advance August 16, 2024, doi:10.1101/gr.279464.124
...evidence.A similar sum-over-alignments method has been used with great success in the HMMER software (Eddy 2008). So, it is curious that many sequence-search tools developed more recently than HMMER do not use this approach. No one has described a sum-over-alignments method that fits easily into typical...
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Research: The genomic consequences and persistence of sociality in spiders
- Jilong Ma,
- Jesper Bechsgaard,
- Anne Aagaard,
- Palle Villesen,
- Trine Bilde,
- and Mikkel Heide Schierup
Genome Res. March 2025 35: 499-511; Published in Advance February 20, 2025, doi:10.1101/gr.279503.124
...inbreeding over evolutionary time is likely to have resulted in purging but also elevated rates of fixation of segregating recessive deleterious alleles; this is supported by the absence of inbreeding depression and evidence for outbreeding depression (lower hatching success when individuals from isolated...
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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
...the dynamic nature of cell lineages in both developmental biology and cancer research. Additionally, the review navigates through critical considerations for successful experimental design in lineage tracing and addresses challenges inherent in this field, including technical limitations, complexities in data...
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INSIGHT/OUTLOOK: WABA Success: A Tool for Sequence Comparison between Large Genomes
- David L. Baillie and
- Ann M. Rose
Genome Res. August 1, 2000 10: 1071-1073; doi:10.1101/gr.10.8.1071
...M, Rose Baillie Ann M genome;10/8/1071 1549-5469 1088-9051 10.1101/gr.10.8.1071 WABA Success: A Tool for Sequence Comparison between Large Genomes WABA Success: A Tool for Sequence Comparison between Large Genomes David L. Baillie 1 and Ann M. Rose 2 , 3 1Department of Molecular Biology...
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Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
- Rita Tam,
- Mareike Möller,
- Runpeng Luo,
- Zhenyan Luo,
- Ashley Jones,
- Sambasivam Periyannan,
- John P. Rathjen,
- and Benjamin Schwessinger
Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
...-specific dikaryotic state in which two haploid s are contained in separate nuclei in the same cytoplasm and propagated in a coordinated manner during cell division (Anderson and Kohn 2014; Li et al. 2019; Sperschneider et al. 2023a,b). Dikaryotism is highly successful, with an estimated 400,000 taxa in the fungal...
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Research: Hydra has mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype
- Arne Sahm,
- Konstantin Riege,
- Marco Groth,
- Martin Bens,
- Johann Kraus,
- Martin Fischer,
- Hans Kestler,
- Christoph Englert,
- Ralf Schaible,
- Matthias Platzer,
- and Steve Hoffmann
Genome Res. December 2024 34: 2217-2228; Published in Advance December 4, 2024, doi:10.1101/gr.279025.124
...of freshwater polyps with remarkable regeneration abilities and a potentially unlimited life span under laboratory conditions. By sequencing of single cells and whole animals, we found that the mutation rates in Hydra’s stem cells are even slightly higher than in humans or mice. A potential explanation...
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Research: Fusion, fission, and scrambling of the bilaterian genome in Bryozoa
- Thomas D. Lewin,
- Isabel Jiah-Yih Liao,
- Mu-En Chen,
- John D.D. Bishop,
- Peter W.H. Holland,
- and Yi-Jyun Luo
Genome Res. January 2025 35: 78-92; Published in Advance January 6, 2025, doi:10.1101/gr.279636.124
...bryozoan , as a result of successive fusion and fission events (Fig. 6B). The main Hox cluster is located on orthologous chromosomes containing ALG B2 genes in each bryozoan assembly, and Hox genes separated from the cluster are also on a different orthologous chromosome that contains ALG B2 genes (Fig. 6C...
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Method: A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples
- Shuai Guo,
- Xiaoqian Liu,
- Xuesen Cheng,
- Yujie Jiang,
- Shuangxi Ji,
- Qingnan Liang,
- Andrew Koval,
- Yumei Li,
- Leah A. Owen,
- Ivana K. Kim,
- Ana Aparicio,
- Sanghoon Lee,
- Anil K. Sood,
- Scott Kopetz,
- John Paul Shen,
- John N. Weinstein,
- Margaret M. DeAngelis,
- Rui Chen,
- and Wenyi Wang
Genome Res. January 2025 35: 147-161; Published in Advance November 25, 2024, doi:10.1101/gr.278822.123
...high-grade serous ovarian cancer (HGSC) samples as a benchmark and discussed the impact of technological discrepancy on deconvolution analysis. However, current attempts to address these issues have achieved only limited success (Newman et al. 2019; Dong et al. 2021; Cobos et al. 2023). CIBERSORTx...
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