Searching journal content for articles similar to Clark et al. 15 (11): 1463.

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  1. Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
    • Øystein Monsen,
    • Lars Grønvold,
    • Alex Datsomor,
    • Thomas Harvey,
    • James Kijas,
    • Alexander Suh,
    • Torgeir R. Hvidsten,
    • and Simen Rød Sandve
    Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
    ...with smaller chances of having a negative fitness consequence for the host are evolutionarily more successful.A minority of TEs have CRE superspreader abilitiesNext we wanted to understand the contribution of specific TEs to the TE-CRE landscape. Overall, there was a positive linear relationship between...
  2. Research: Evidence for selfing in a vertebrate from whole-genome sequencing
    • Astrid Böhne,
    • Zeynep Oğuzhan,
    • Ioannis Chrysostomakis,
    • Simon Vitt,
    • Denis Meuthen,
    • Sebastian Martin,
    • Sandra Kukowka,
    • and Timo Thünken
    Genome Res. December 2023 33: 2133-2142; Published in Advance December 7, 2023, doi:10.1101/gr.277368.122
    ..., sex determination is notably diverse and can be influenced by the environment, and sequential hermaphroditism has been reported for some species. Here, we present evidence for a case of facultative selfing in the cichlid fish Benitochromis nigrodorsalis, which is otherwise known as biparentally...
  3. Method: Haplotype and population structure inference using neural networks in whole-genome sequencing data
    • Jonas Meisner and
    • Anders Albrechtsen
    Genome Res. August 2022 32: 1542-1552; Published in Advance July 6, 2022, doi:10.1101/gr.276813.122
    ...autoencoder methods have been very successful for large-scale data sets as they perform dimensionality reduction and clustering either sequentially or jointly to benefit from induced nonlinearity and scalability of deep learning architectures using neural networks (NNs) (Xie et al. 2016; Yang et al. 2017...
  4. Method: Whole-genome analysis of noncoding genetic variations identifies multiscale regulatory element perturbations associated with Hirschsprung disease
    • Alexander Xi Fu,
    • Kathy Nga-Chu Lui,
    • Clara Sze-Man Tang,
    • Ray Kit Ng,
    • Frank Pui-Ling Lai,
    • Sin-Ting Lau,
    • Zhixin Li,
    • Maria-Mercè Garcia-Barcelo,
    • Pak-Chung Sham,
    • Paul Kwong-Hang Tam,
    • Elly Sau-Wai Ngan,
    • and Kevin Y. Yip
    Genome Res. November 2020 30: 1618-1632; Published in Advance September 18, 2020, doi:10.1101/gr.264473.120
    ...(Badner et al. 1990; Chakravarti et al. 2006). Phenotypic severity of the disease is determined by the length of colonic aganglionosis and can be classified into short-segment HSCR (S-HSCR; 80% of cases), long-segment HSCR (L-HSCR; 15%–20% of cases), and total colonic aganglionosis (TCA; up to 5% of cases...
  5. Method: INTEGRATE: gene fusion discovery using whole genome and transcriptome data
    • Jin Zhang,
    • Nicole M. White,
    • Heather K. Schmidt,
    • Robert S. Fulton,
    • Chad Tomlinson,
    • Wesley C. Warren,
    • Richard K. Wilson,
    • and Christopher A. Maher
    Genome Res. January 2016 26: 108-118; Published in Advance November 10, 2015, doi:10.1101/gr.186114.114
    ...INTEGRATE: gene fusion discovery using whole genome and transcriptome data Jin Zhang 1 , 2 , Nicole M. White 2 , Heather K. Schmidt 1 , Robert S. Fulton 1 , 3 , Chad Tomlinson 1 , Wesley C. Warren 1 , Richard K. Wilson 1...
  6. Method: Detection of long repeat expansions from PCR-free whole-genome sequence data
    • Egor Dolzhenko,
    • Joke J.F.A. van Vugt,
    • Richard J. Shaw,
    • Mitchell A. Bekritsky,
    • Marka van Blitterswijk,
    • Giuseppe Narzisi,
    • Subramanian S. Ajay,
    • Vani Rajan,
    • Bryan R. Lajoie,
    • Nathan H. Johnson,
    • Zoya Kingsbury,
    • Sean J. Humphray,
    • Raymond D. Schellevis,
    • William J. Brands,
    • Matt Baker,
    • Rosa Rademakers,
    • Maarten Kooyman,
    • Gijs H.P. Tazelaar,
    • Michael A. van Es,
    • Russell McLaughlin,
    • William Sproviero,
    • Aleksey Shatunov,
    • Ashley Jones,
    • Ahmad Al Khleifat,
    • Alan Pittman,
    • Sarah Morgan,
    • Orla Hardiman,
    • Ammar Al-Chalabi,
    • Chris Shaw,
    • Bradley Smith,
    • Edmund J. Neo,
    • Karen Morrison,
    • Pamela J. Shaw,
    • Catherine Reeves,
    • Lara Winterkorn,
    • Nancy S. Wexler,
    • The US–Venezuela Collaborative Research Group,
    • David E. Housman,
    • Christopher W. Ng,
    • Alina L. Li,
    • Ryan J. Taft,
    • Leonard H. van den Berg,
    • David R. Bentley,
    • Jan H. Veldink,
    • and Michael A. Eberle
    Genome Res. November 2017 27: 1895-1903; Published in Advance September 8, 2017, doi:10.1101/gr.225672.117
    ...for use in precisionmedicine initiatives (Ashley 2015, 2016; Marx 2015) and large-scale research projects, a reliablemethod is needed that can identify the presence or absence of potentially pathogenic repeat expansions in WGS data and also determine their approximate length without additional tests. Here...
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  7. Method: Detection of structural mosaicism from targeted and whole-genome sequencing data
    • Daniel A. King,
    • Alejandro Sifrim,
    • Tomas W. Fitzgerald,
    • Raheleh Rahbari,
    • Emma Hobson,
    • Tessa Homfray,
    • Sahar Mansour,
    • Sarju G. Mehta,
    • Mohammed Shehla,
    • Susan E. Tomkins,
    • Pradeep C. Vasudevan,
    • Matthew E. Hurles,
    • and The Deciphering Developmental Disorders Study
    Genome Res. October 2017 27: 1704-1714; Published in Advance August 30, 2017, doi:10.1101/gr.212373.116
    ..., was randomly determined based on the site’s minor allele frequency, which was used in a multinomial function with probabilities corresponding to Hardy Weinberg–assumed genotype proportions (p2, 2pq, q2). For calculating the BAF for each heterozygote at site i (9), we adjusted the expected heterozygote...
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  8. Research: The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences
    • Cheng Xue,
    • Muthuswamy Raveendran,
    • R. Alan Harris,
    • Gloria L. Fawcett,
    • Xiaoming Liu,
    • Simon White,
    • Mahmoud Dahdouli,
    • David Rio Deiros,
    • Jennifer E. Below,
    • William Salerno,
    • Laura Cox,
    • Guoping Fan,
    • Betsy Ferguson,
    • Julie Horvath,
    • Zach Johnson,
    • Sree Kanthaswamy,
    • H. Michael Kubisch,
    • Dahai Liu,
    • Michael Platt,
    • David G. Smith,
    • Binghua Sun,
    • Eric J. Vallender,
    • Feng Wang,
    • Roger W. Wiseman,
    • Rui Chen,
    • Donna M. Muzny,
    • Richard A. Gibbs,
    • Fuli Yu,
    • and Jeffrey Rogers
    Genome Res. December 2016 26: 1651-1662; Published in Advance October 17, 2016, doi:10.1101/gr.204255.116
    ..., is accumulating at an accelerating pace. Genomic information is also becoming available for diverse nonhuman species (Hayes et al. 2013; Schoenebeck and Ostrander 2014; Lack et al. 2015). Rhesus macaques (Macaca mulatta) are one of themost evolutionarily successful and intensively studied nonhuman primates...
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  9. Resource: Alignathon: a competitive assessment of whole-genome alignment methods
    • Dent Earl,
    • Ngan Nguyen,
    • Glenn Hickey,
    • Robert S. Harris,
    • Stephen Fitzgerald,
    • Kathryn Beal,
    • Igor Seledtsov,
    • Vladimir Molodtsov,
    • Brian J. Raney,
    • Hiram Clawson,
    • Jaebum Kim,
    • Carsten Kemena,
    • Jia-Ming Chang,
    • Ionas Erb,
    • Alexander Poliakov,
    • Minmei Hou,
    • Javier Herrero,
    • William James Kent,
    • Victor Solovyev,
    • Aaron E. Darling,
    • Jian Ma,
    • Cedric Notredame,
    • Michael Brudno,
    • Inna Dubchak,
    • David Haussler,
    • and Benedict Paten
    Genome Res. December 2014 24: 2077-2089; Published in Advance October 1, 2014, doi:10.1101/gr.174920.114
    ...for protein and, to a lesser extent, global nucleotide MSAs are available, but less effort has been made to establish benchmarks in the more general problem of whole-genome alignment (WGA). Using the same model as the successful Assemblathon competitions, we organized a competitive evaluation in which teams...
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  10. Resource: Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads
    • Rei Kajitani,
    • Kouta Toshimoto,
    • Hideki Noguchi,
    • Atsushi Toyoda,
    • Yoshitoshi Ogura,
    • Miki Okuno,
    • Mitsuru Yabana,
    • Masayuki Harada,
    • Eiji Nagayasu,
    • Haruhiko Maruyama,
    • Yuji Kohara,
    • Asao Fujiyama,
    • Tetsuya Hayashi,
    • and Takehiko Itoh
    Genome Res. August 2014 24: 1384-1395; Published in Advance April 22, 2014, doi:10.1101/gr.170720.113
    ...been successful in meeting the functional goals of each sequencing project, all are costly compared with a simple whole- shotgun sequencing strategy. Model organisms whose lineages have been maintained in laboratories have long been the main targets of sequencing. However, various wild-type organisms...
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