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Resource: An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes
- Chong Li,
- Marc Jan Bonder,
- Sabriya Syed,
- Matthew Jensen,
- Human Genome Structural Variation Consortium (HGSVC),
- HGSVC Functional Analysis Working Group,
- Mark B. Gerstein,
- Michael C. Zody,
- Mark J.P. Chaisson,
- Michael E. Talkowski,
- Tobias Marschall,
- Jan O. Korbel,
- Evan E. Eichler,
- Charles Lee,
- and Xinghua Shi
Genome Res. December 2024 34: 2304-2318; Published in Advance December 5, 2024, doi:10.1101/gr.279419.124
...An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human s Chong Li1,2, Marc Jan Bonder3,4, Sabriya Syed5, Matthew Jensen6,7, Human Genome Structural Variation Consortium (HGSVC), HGSVC Functional Analysis Working Group, Mark B...
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Research: Differences in activity and stability drive transposable element variation in tropical and temperate maize
- Shujun Ou,
- Armin Scheben,
- Tyler Collins,
- Yinjie Qiu,
- Arun S. Seetharam,
- Claire C. Menard,
- Nancy Manchanda,
- Jonathan I. Gent,
- Michael C. Schatz,
- Sarah N. Anderson,
- Matthew B. Hufford,
- and Candice N. Hirsch
Genome Res. August 2024 34: 1140-1153; Published in Advance September 9, 2024, doi:10.1101/gr.278131.123
..., there have been a limited number of pan studies of TE variation within species owing to challenges in assembling and annotating genomic regions containing these highly repetitive elements (Ou et al. 2019). Instead, the vast majority of studies characterizing TE content have used resequencing data mapped...
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Research: High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis
- Yuan Lu,
- Edward Rice,
- Kang Du,
- Susanne Kneitz,
- Magali Naville,
- Corentin Dechaud,
- Jean-Nicolas Volff,
- Mikki Boswell,
- William Boswell,
- LaDeana Hillier,
- Chad Tomlinson,
- Kremitzki Milin,
- Ronald B. Walter,
- Manfred Schartl,
- and Wesley C. Warren
Genome Res. April 2023 33: 557-571; Published in Advance May 5, 2023, doi:10.1101/gr.277434.122
...Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; 6McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA; 7Department of Life Sciences, Texas A&M University, Corpus Christi, Texas 78412, USA; 8Developmental Biochemistry, Biozentrum...
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Resource: Structural variants in 3000 rice genomes
- Roven Rommel Fuentes,
- Dmytro Chebotarov,
- Jorge Duitama,
- Sean Smith,
- Juan Fernando De la Hoz,
- Marghoob Mohiyuddin,
- Rod A. Wing,
- Kenneth L. McNally,
- Tatiana Tatarinova,
- Andrey Grigoriev,
- Ramil Mauleon,
- and Nickolai Alexandrov
Genome Res. May 2019 29: 870-880; Published in Advance April 16, 2019, doi:10.1101/gr.241240.118
...needs an estimated 26% increase in yield to meet the global demand by the year 2030 under constraints such as less arable land, less water, and severe environmental stresses due to climate change (Seck et al. 2012).To help address this yield gap, we intend to catalog all natural variation that exists...
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Research: A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility
- Angelo A. Ruggieri,
- Luca Livraghi,
- James J. Lewis,
- Elizabeth Evans,
- Francesco Cicconardi,
- Laura Hebberecht,
- Yadira Ortiz-Ruiz,
- Stephen H. Montgomery,
- Alfredo Ghezzi,
- José Arcadio Rodriguez-Martinez,
- Chris D. Jiggins,
- W. Owen McMillan,
- Brian A. Counterman,
- Riccardo Papa,
- and Steven M. Van Belleghem
Genome Res. October 2022 32: 1862-1875; Published in Advance September 15, 2022, doi:10.1101/gr.276839.122
...for structural variation to serve as raw material for adaptive evolution.Structural variants (SVs) in s are a ubiquitous component of within and between species genomic variation (Mérot et al. 2020; Zhang et al. 2021). The larger size of SVs, when compared with single nucleotide polymorphisms (SNPs), may...
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Research: Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana
- Maximilian O. Press,
- Rajiv C. McCoy,
- Ashley N. Hall,
- Joshua M. Akey,
- and Christine Queitsch
Genome Res. August 2018 28: 1169-1178; Published in Advance July 3, 2018, doi:10.1101/gr.231753.117
...repeat variation in human and great ape populations and its impact on gene expression divergence. Genome Res 25: 1591–1599. ↵Boyle EA, O'Roak BJ, Martin BK, Kumar A, Shendure J. 2014. MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing. Bioinformatics 30: 2670...
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Research: Extensive de novo mutation rate variation between individuals and across the genome of Chlamydomonas reinhardtii
- Rob W. Ness,
- Andrew D. Morgan,
- Radhakrishnan B. Vasanthakrishnan,
- Nick Colegrave,
- and Peter D. Keightley
Genome Res. November 2015 25: 1739-1749; Published in Advance August 10, 2015, doi:10.1101/gr.191494.115
...Extensive de novo mutation rate variation between individuals and across the genome of Chlamydomonas reinhardtii Rob W. Ness 1 , Andrew D. Morgan 1 , Radhakrishnan B. Vasanthakrishnan 1 , Nick Colegrave 1 , 2 and Peter D. Keightley 1 , 2...
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Method: Efficient inference of population size histories and locus-specific mutation rates from large-sample genomic variation data
- Anand Bhaskar,
- Y.X. Rachel Wang,
- and Yun S. Song
Genome Res. February 2015 25: 268-279; Published in Advance January 6, 2015, doi:10.1101/gr.178756.114
...Efficient inference of population size histories and locus-specific mutation rates from large-sample genomic variation data Anand Bhaskar 1 , 2 , Y.X. Rachel Wang 3 and Yun S. Song 1 , 2 , 3 , 4 1 Simons Institute...
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Research: Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes
- Konstantinos Kritsas,
- Samuel E. Wuest,
- Daniel Hupalo,
- Andrew D. Kern,
- Thomas Wicker,
- and Ueli Grossniklaus
Genome Res. December 2012 22: 2455-2466; Published in Advance September 17, 2012, doi:10.1101/gr.129346.111
...have been proposed to play important roles in gene regulation, RNA processing, and maintaining genome integrity. However, because all of these functions can tolerate some sequence variation, their ultraconserved and ultraselected nature is not explained. We investigated whether there are highly...
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Review: Population genetic inference from genomic sequence variation
- John E. Pool,
- Ines Hellmann,
- Jeffrey D. Jensen,
- and Rasmus Nielsen
Genome Res. March 2010 20: 291-300; Published in Advance January 12, 2010, doi:10.1101/gr.079509.108
...Population genetic inference from genomic sequence variation John E. Pool 1 , 2 , Ines Hellmann 3 , Jeffrey D. Jensen 1 , 5 and Rasmus Nielsen 1 , 4 , 6 1 Department of Integrative Biology, University of California, Berkeley...

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