Searching journal content for articles similar to Forster and Church 17 (1): 000.

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  1. Method: De novo individualized disease modules reveal the synthetic penetrance of genes and inform personalized treatment regimens
    • Taylor M. Weiskittel,
    • Choong Y. Ung,
    • Cristina Correia,
    • Cheng Zhang,
    • and Hu Li
    Genome Res. January 2022 32: 124-134; Published in Advance December 7, 2021, doi:10.1101/gr.275889.121
    ...disease modules de novo, which enables us to elucidate the importance of mutated genes in specific patients and to understand the synthetic penetrance of these genes across patients. We reveal that importance of the notorious cancer drivers TP53 and PIK3CA fluctuate widely across breast cancers and peak...
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  2. Method: Genome-wide prediction of DNA mutation effect on nucleosome positions for yeast synthetic genomics
    • Etienne Routhier,
    • Edgard Pierre,
    • Ghazaleh Khodabandelou,
    • and Julien Mozziconacci
    Genome Res. February 2021 31: 317-326; Published in Advance December 18, 2020, doi:10.1101/gr.264416.120
    ...rewriting projects (Ostrov et al. 2019). A first paradigmatic example of this effort, the Saccharomyces cerevisiae 2.0 (Sc 2.0) project (Richardson et al. 2017), will soon deliver the first example of a complete synthetic eukaryotic . Several projects are now starting with the aim to design more synthetic s...
  3. Method: Tn5 transposase and tagmentation procedures for massively scaled sequencing projects
    • Simone Picelli,
    • Åsa K. Björklund,
    • Björn Reinius,
    • Sven Sagasser,
    • Gösta Winberg,
    • and Rickard Sandberg
    Genome Res. December 2014 24: 2033-2040; Published in Advance July 30, 2014, doi:10.1101/gr.177881.114
    ...Tn5 transposase and tagmentation procedures for massively scaled sequencing projects Simone Picelli 1 , Åsa K. Björklund 1 , 2 , Björn Reinius 1 , 2 , Sven Sagasser 1 , 2 , Gösta Winberg 1 , 2 and Rickard...
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  4. Research: SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes
    • Yue Shen,
    • Giovanni Stracquadanio,
    • Yun Wang,
    • Kun Yang,
    • Leslie A. Mitchell,
    • Yaxin Xue,
    • Yizhi Cai,
    • Tai Chen,
    • Jessica S. Dymond,
    • Kang Kang,
    • Jianhui Gong,
    • Xiaofan Zeng,
    • Yongfen Zhang,
    • Yingrui Li,
    • Qiang Feng,
    • Xun Xu,
    • Jun Wang,
    • Jian Wang,
    • Huanming Yang,
    • Jef D. Boeke,
    • and Joel S. Bader
    Genome Res. January 2016 26: 36-49; Published in Advance November 13, 2015, doi:10.1101/gr.193433.115
    ...relating to features such as chromatin structure, splicing, and linear chromosomes with telomeres, centromeres, and recombinations that are absent from prokaryotes. With the goal of answering these questions, the Sc2.0 Project has designed and synthesized synthetic chromosomes that function in yeast...
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  5. Research: In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors
    • F.X. Reymond Sutandy,
    • Stefanie Ebersberger,
    • Lu Huang,
    • Anke Busch,
    • Maximilian Bach,
    • Hyun-Seo Kang,
    • Jörg Fallmann,
    • Daniel Maticzka,
    • Rolf Backofen,
    • Peter F. Stadler,
    • Kathi Zarnack,
    • Michael Sattler,
    • Stefan Legewie,
    • and Julian König
    Genome Res. May 2018 28: 699-713; Published in Advance April 11, 2018, doi:10.1101/gr.229757.117
    ...and is crucial for proteome diversity in eukaryotes. The RNA-binding protein (RBP) U2AF2 is central to splicing decisions, as it recognizes 3′ splice sites and recruits the spliceosome. We establish “in vitro iCLIP” experiments, in which recombinant RBPs are incubated with long transcripts, to study how U2AF2...
  6. Method: Chromosome-scale shotgun assembly using an in vitro method for long-range linkage
    • Nicholas H. Putnam,
    • Brendan L. O'Connell,
    • Jonathan C. Stites,
    • Brandon J. Rice,
    • Marco Blanchette,
    • Robert Calef,
    • Christopher J. Troll,
    • Andrew Fields,
    • Paul D. Hartley,
    • Charles W. Sugnet,
    • David Haussler,
    • Daniel S. Rokhsar,
    • and Richard E. Green
    Genome Res. March 2016 26: 342-350; Published in Advance February 4, 2016, doi:10.1101/gr.193474.115
    ...generated by proximity ligation of DNA in chromatin of living tissue can address this problem, dramatically increasing the scaffold contiguity of assemblies. Here, we describe a simpler approach (“Chicago”) based on in vitro reconstituted chromatin. We generated two Chicago data sets with human DNA...
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  7. Method: Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants
    • Ilaria Mogno,
    • Jamie C. Kwasnieski,
    • and Barak A. Cohen
    Genome Res. November 2013 23: 1908-1915; Published in Advance August 6, 2013, doi:10.1101/gr.157891.113
    ...variation (The 1000 Genomes Project Consortium 2012) and the role of noncoding polymorphisms in complex traits and disease (Degner et al. 2012; Maurano et al. 2012). Progress in this field requiresmethods to study the effects of combinations of TFBS variants inside cells. Synthetic promoters are powerful...
  8. Resource: Synthetic spike-in standards for RNA-seq experiments
    • Lichun Jiang,
    • Felix Schlesinger,
    • Carrie A. Davis,
    • Yu Zhang,
    • Renhua Li,
    • Marc Salit,
    • Thomas R. Gingeras,
    • and Brian Oliver
    Genome Res. September 2011 21: 1543-1551; Published in Advance August 4, 2011, doi:10.1101/gr.121095.111
    .... 2011). While there are clear advantages to RNA-seq, it is less clear how well the procedure performs, as several studies have reported conflicting RNA-seq accuracy results. RNA-seq–determined concentrations of six in vitro synthetic transcripts show good linearity (Mortazavi et al. 2008...
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  9. Resource: Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource
    • Elizabeth G. King,
    • Chris M. Merkes,
    • Casey L. McNeil,
    • Steven R. Hoofer,
    • Saunak Sen,
    • Karl W. Broman,
    • Anthony D. Long,
    • and Stuart J. Macdonald
    Genome Res. August 2012 22: 1558-1566; Published in Advance April 10, 2012, doi:10.1101/gr.134031.111
    ...Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource Elizabeth G. King 1 , Chris M. Merkes 2 , Casey L. McNeil 2 , Steven R. Hoofer 2 , Saunak Sen 3 , Karl W. Broman 4 , Anthony D...
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  10. Research: A transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
    • Zohar Rosenwasser,
    • Roni Cohen-Fultheim,
    • Ofir Shliefer,
    • Erez Y. Levanon,
    • and Eli Eisenberg
    Genome Res. March 12, 2026 ; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
    ...-mediated editing, as demonstrated in synthetic dsRNA substrates (Bass and Weintraub 1988; Wagner et al. 1989; Nishikura et al. 1991; Polson and Bass 1994; Bass 1997), viral dsRNA (Pfaller et al. 2018), and engineered guide RNA systems (Katrekar et al. 2022). If they exist, these long perfect dsRNAs may pose a risk...
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