Searching journal content for articles similar to Torarinsson et al. 16 (7): 885.

Displaying results 1-10 of 62
For checked items
  1. Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
    • Dongying Xie,
    • Pohao Ye,
    • Yiming Ma,
    • and Zhongying Zhao
    Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
    ...is primarily driven by differences in unalignable regionsWe next investigated the sequence divergences underpinning the larger sizes of C. nigoni strains relative to C. briggsae strains. To this end, we leveraged the genomic variation detection tool SyRI (Goel et al. 2019), which systematically identifies...
  2. Resource: Genetic features and genomic targets of human KRAB-zinc finger proteins
    • Jonas de Tribolet-Hardy,
    • Christian W. Thorball,
    • Romain Forey,
    • Evarist Planet,
    • Julien Duc,
    • Alexandre Coudray,
    • Bara Khubieh,
    • Sandra Offner,
    • Cyril Pulver,
    • Jacques Fellay,
    • Michael Imbeault,
    • Priscilla Turelli,
    • and Didier Trono
    Genome Res. August 2023 33: 1409-1423; Published in Advance September 20, 2023, doi:10.1101/gr.277722.123
    ...significantly bound SVAs, and 11 were rather found at DNA transposons. The remaining 71 KZFPs mapped to a mixture of low complexity or simple repeats, satellite DNAs and tRNAs. For 24, no particular class of genomic entity could be singled out perhaps due in part to difficulties in sequences alignment, notably...
    OPEN ACCESS ARTICLE
  3. Research: Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features
    • J. Omar Yáñez-Cuna,
    • Cosmas D. Arnold,
    • Gerald Stampfel,
    • Łukasz M. Boryń,
    • Daniel Gerlach,
    • Martina Rath,
    • and Alexander Stark
    Genome Res. July 2014 24: 1147-1156; Published in Advance April 8, 2014, doi:10.1101/gr.169243.113
    ...groups was reflected by the expression levels of the neighboring genes asmeasuredby RNA-seq (Fig. 1C). For example, genes next to S2-specific enhancers were specifically expressed in S2 cells but not in BG3 cells or OSCs, and the equivalent was true for BG3- or OSC-specific enhancers. Genes next...
    OPEN ACCESS ARTICLE
  4. Method: Alignment of single-cell RNA-seq samples without overcorrection using kernel density matching
    • Mengjie Chen,
    • Qi Zhan,
    • Zepeng Mu,
    • Lili Wang,
    • Zhaohui Zheng,
    • Jinlin Miao,
    • Ping Zhu,
    • and Yang I. Li
    Genome Res. April 2021 31: 698-712; Published in Advance March 19, 2021, doi:10.1101/gr.261115.120
    ...al. 2014), and cellular response to stress and stimulation (Shalek et al. 2014; Keren-Shaul et al. 2017; Golumbeanu et al. 2018). Gene expression levels in tens of thousands of single cells are now routinely measured in a single scRNA-seq experiment (Macosko et al. 2015), and more scRNA-seq data sets...
    OPEN ACCESS ARTICLE
  5. Research: The identification and functional annotation of RNA structures conserved in vertebrates
    • Stefan E. Seemann,
    • Aashiq H. Mirza,
    • Claus Hansen,
    • Claus H. Bang-Berthelsen,
    • Christian Garde,
    • Mikkel Christensen-Dalsgaard,
    • Elfar Torarinsson,
    • Zizhen Yao,
    • Christopher T. Workman,
    • Flemming Pociot,
    • Henrik Nielsen,
    • Niels Tommerup,
    • Walter L. Ruzzo,
    • and Jan Gorodkin
    Genome Res. August 2017 27: 1371-1383; Published in Advance May 9, 2017, doi:10.1101/gr.208652.116
    ...functional role. We computationally screened vertebrate s for conserved RNA structures (CRSs), leveraging structure-based, rather than sequence-based, alignments. After careful correction for sequence identity and GC content, we predict ∼516,000 human genomic regions containing CRSs. We find...
    OPEN ACCESS ARTICLE
  6. LETTER: Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions
    • Elfar Torarinsson,
    • Zizhen Yao,
    • Eric D. Wiklund,
    • Jesper B. Bramsen,
    • Claus Hansen,
    • Jørgen Kjems,
    • Niels Tommerup,
    • Walter L. Ruzzo,
    • and Jan Gorodkin
    Genome Res. February 2008 18: 242-251; Published in Advance December 20, 2007, doi:10.1101/gr.6887408
    ...Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions Elfar Torarinsson 1 , 2 , Zizhen Yao 3 , Eric D. Wiklund 4 , Jesper B. Bramsen 4 , Claus Hansen 5 , Jørgen Kjems 4 , Niels Tommerup...
  7. Research: Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/ enhancer-binding protein beta binding sites
    • Daniel Savic,
    • Brian S. Roberts,
    • Julia B. Carleton,
    • E. Christopher Partridge,
    • Michael A. White,
    • Barak A. Cohen,
    • Gregory M. Cooper,
    • Jason Gertz,
    • and Richard M. Myers
    Genome Res. December 2015 25: 1791-1800; Published in Advance October 20, 2015, doi:10.1101/gr.191593.115
    ...genomic features that accurately discriminate between active and inactive TF binding events remain ambiguous. Recent studies have identified promoter-distal RNA polymerase II (RNAP2) binding at enhancer elements, suggesting that these interactions may serve as a marker for active regulatory sequences...
  8. LETTER: Structured RNAs in the ENCODE selected regions of the human genome
    • Stefan Washietl,
    • Jakob S. Pedersen,
    • Jan O. Korbel,
    • Claudia Stocsits,
    • Andreas R. Gruber,
    • Jörg Hackermüller,
    • Jana Hertel,
    • Manja Lindemeyer,
    • Kristin Reiche,
    • Andrea Tanzer,
    • Catherine Ucla,
    • Carine Wyss,
    • Stylianos E. Antonarakis,
    • France Denoeud,
    • Julien Lagarde,
    • Jorg Drenkow,
    • Philipp Kapranov,
    • Thomas R. Gingeras,
    • Roderic Guigó,
    • Michael Snyder,
    • Mark B. Gerstein,
    • Alexandre Reymond,
    • Ivo L. Hofacker,
    • and Peter F. Stadler
    Genome Res. June 2007 17: 852-864; doi:10.1101/gr.5650707
    ...Structured RNAs in the ENCODE selected regions of the human genome Stefan Washietl 1 , 14 , Jakob S. Pedersen 2 , Jan O. Korbel 3 , 4 , Claudia Stocsits 5 , Andreas R. Gruber 1 , Jörg Hackermüller 6 , Jana Hertel 5...
    OPEN ACCESS ARTICLE
  9. Resource: RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development
    • Meng How Tan,
    • Kin Fai Au,
    • Arielle L. Yablonovitch,
    • Andrea E. Wills,
    • Jason Chuang,
    • Julie C. Baker,
    • Wing Hung Wong,
    • and Jin Billy Li
    Genome Res. January 2013 23: 201-216; Published in Advance September 7, 2012, doi:10.1101/gr.141424.112
    ...introns and in intergenic regions. We then developed a filtering pipeline to separate protein-coding transcripts from noncoding RNAs and identified a confident set of 6686 noncoding transcripts in 3859 genomic loci. Since the current reference genome, XenTro3, consists of hundreds of scaffolds instead...
  10. Research: Epigenetic and evolutionary features of ape subterminal heterochromatin
    • DongAhn Yoo,
    • Katherine M. Munson,
    • and Evan E. Eichler
    Genome Res. January 2026 36: 38-49; Published in Advance October 22, 2025, doi:10.1101/gr.280987.125
    ...insertions and lineage-specific duplicated genes. Our findings suggest independent evolution of subterminal caps converging on a common genetic and epigenetic structure that promoted ectopic exchange as well as the emergence of novel genes at transition regions between euchromatin and heterochromatin...
    OPEN ACCESS ARTICLE
For checked items

Search Results

Next 10 » New Search

Modify Results

Citation format:
Results / page:
Results order:

This search

  • Alert me when new articles matching this search are published
  • Download all citations on this page to my citation manager

Preprint Server



Current Issue

  1. March 2026, 36 (3)
  1. Current Issue
  1. Alert me to new issues of Genome Research