Searching journal content for articles similar to Smith et al. 34 (3): 341.

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  1. Method: Quantitative mitochondrial DNA copy number determination using droplet digital PCR with single-cell resolution
    • Ryan O'Hara,
    • Enzo Tedone,
    • Andrew Ludlow,
    • Ejun Huang,
    • Beatrice Arosio,
    • Daniela Mari,
    • and Jerry W. Shay
    Genome Res. November 2019 29: 1878-1888; Published in Advance September 23, 2019, doi:10.1101/gr.250480.119
    .... Number matters: control of mammalian mitochondrial DNA copy number. J Genet Genomics 36: 125–131. doi:10.1016/S1673-8527(08)60099-5 ↵Cohen T, Levin L, Mishmar D. 2016. Ancient out-of-Africa mitochondrial DNA variants associate with distinct mitochondrial gene expression patterns. PLoS Genet 12: e1006407...
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  2. Resource: A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination
    • Desislava P. Staneva,
    • Roberta Carloni,
    • Tatsiana Auchynnikava,
    • Pin Tong,
    • Juri Rappsilber,
    • A. Arockia Jeyaprakash,
    • Keith R. Matthews,
    • and Robin C. Allshire
    Genome Res. November 2021 31: 2138-2154; Published in Advance August 18, 2021, doi:10.1101/gr.275368.121
    ...suggest parallels to RNAPII promoter–associated complexes in conventional eukaryotes. Further, we identify likely components of TbSWR1 and TbNuA4 complexes whose enrichment coincides with the SWR1-C exchange substrate H2A.Z at RNAPII transcription start regions. The systematic approach used provides...
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  3. Resource: A biochemical landscape of A-to-I RNA editing in the human brain transcriptome
    • Masayuki Sakurai,
    • Hiroki Ueda,
    • Takanori Yano,
    • Shunpei Okada,
    • Hideki Terajima,
    • Toutai Mitsuyama,
    • Atsushi Toyoda,
    • Asao Fujiyama,
    • Hitomi Kawabata,
    • and Tsutomu Suzuki
    Genome Res. March 2014 24: 522-534; Published in Advance January 9, 2014, doi:10.1101/gr.162537.113
    ...A biochemical landscape of A-to-I RNA editing in the human brain transcriptome Masayuki Sakurai 1 , 4 , Hiroki Ueda 1 , 4 , Takanori Yano 1 , Shunpei Okada 1 , Hideki Terajima 1 , Toutai Mitsuyama 2 , Atsushi Toyoda 3...
  4. Research: OPA1 links human mitochondrial genome maintenance to mtDNA replication and distribution
    • Ghizlane Elachouri,
    • Sara Vidoni,
    • Claudia Zanna,
    • Alexandre Pattyn,
    • Hassan Boukhaddaoui,
    • Karen Gaget,
    • Patrick Yu-Wai-Man,
    • Giuseppe Gasparre,
    • Emmanuelle Sarzi,
    • Cécile Delettre,
    • Aurélien Olichon,
    • Dominique Loiseau,
    • Pascal Reynier,
    • Patrick F. Chinnery,
    • Agnès Rotig,
    • Valerio Carelli,
    • Christian P. Hamel,
    • Michela Rugolo,
    • and Guy Lenaers
    Genome Res. January 2011 21: 12-20; Published in Advance October 25, 2010, doi:10.1101/gr.108696.110
    ...human diseases. Mounting evidence suggests that the actors of the mitochondrial network dynamics, among which is the intramitochondrial dynamin OPA1, might be involved in these processes. Here, using siRNAs specific to OPA1 alternate spliced exons, we evidenced that silencing of the OPA1 variants...
  5. Methods: Systematic functional characterization of cis-regulatory motifs in human core promoters
    • Saurabh Sinha,
    • Adam S. Adler,
    • Yair Field,
    • Howard Y. Chang,
    • and Eran Segal
    Genome Res. March 2008 18: 477-488; Published in Advance February 6, 2008, doi:10.1101/gr.6828808
    ...Systematic functional characterization of cis -regulatory motifs in human core promoters Saurabh Sinha 1 , 4 , Adam S. Adler 2 , 4 , Yair Field 3 , Howard Y. Chang 2 , 5 , and Eran Segal 3 , 5 1 Department...
  6. Method: Benchmarking bulk and single-cell variant-calling approaches on Chromium scRNA-seq and scATAC-seq libraries
    • Matthew Wiens,
    • Hossein Farahani,
    • R. Wilder Scott,
    • T. Michael Underhill,
    • and Ali Bashashati
    Genome Res. August 2024 34: 1196-1210; Published in Advance August 15, 2024, doi:10.1101/gr.277066.122
    ...variant generated by each caller as the score threshold to generate precision and recall across different levels. We further computed the area under the precision-recall curve (AUPRC) to compare the overall performance of each caller. Precision and recall were computed for variants across multiple samples...
  7. Research: Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice
    • Leandros Boukas,
    • Teresa Romeo Luperchio,
    • Afrooz Razi,
    • Kasper D. Hansen,
    • and Hans T. Bjornsson
    Genome Res. May 2024 34: 696-710; Published in Advance May 3, 2024, doi:10.1101/gr.278416.123
    ...developmental disorders caused by coding variants in epigenetic regulators have now been discovered. Epigenetic regulators are broadly expressed, and each of these disorders typically shows phenotypic manifestations from many different organ systems. An open question is whether the chromatin disruption—the root...
  8. 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
    ...new regulatory elements in support of the Britten–Davidson hypothesis. We characterized inter-specific polymorphisms, structural variants, and polymorphic transposable element insertions and assessed their association to interspecies hybridization-induced gene expression dysregulation related...
  9. Method: Classification and clustering of RNA crosslink-ligation data reveal complex structures and homodimers
    • Minjie Zhang,
    • Irena T. Hwang,
    • Kongpan Li,
    • Jianhui Bai,
    • Jian-Fu Chen,
    • Tsachy Weissman,
    • James Y. Zou,
    • and Zhipeng Lu
    Genome Res. May 2022 32: 968-985; Published in Advance March 24, 2022, doi:10.1101/gr.275979.121
    ..., extracting structure information from such data presents unique challenges. Here, we introduce a set of computational tools for the systematic analysis of data from a wide variety of crosslink-ligation methods, specifically focusing on read mapping, alignment classification, and clustering. We design a new...
  10. Resource: Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions
    • Rodrigo P. Baptista,
    • Yiran Li,
    • Adam Sateriale,
    • Mandy J. Sanders,
    • Karen L. Brooks,
    • Alan Tracey,
    • Brendan R.E. Ansell,
    • Aaron R. Jex,
    • Garrett W. Cooper,
    • Ethan D. Smith,
    • Rui Xiao,
    • Jennifer E. Dumaine,
    • Peter Georgeson,
    • Bernard J. Pope,
    • Matthew Berriman,
    • Boris Striepen,
    • James A. Cotton,
    • and Jessica C. Kissinger
    Genome Res. January 2022 32: 203-213; Published in Advance November 11, 2021, doi:10.1101/gr.275325.121
    ...copy number variation, differences in gene regulation, and single-nucleotide variants (SNVs). Using the new assembly and annotation as reference, 190 genes are identified as evolving under positive selection, including many not detected previously. The new C. parvum IOWA reference assembly is larger...
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