• Accurate analysis of genuine CRISPR editing events with ampliCan 

      Labun, Kornel; Guo, Xiaoge; Chavez, Alejandro; Church, George M.; Gagnon, James A.; Valen, Eivind (Peer reviewed; Journal article, 2019)
      We present ampliCan, an analysis tool for genome editing that unites highly precise quantification and visualization of genuine genome editing events. ampliCan features nuclease-optimized alignments, filtering of experimental ...
    • A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection 

      Pettersson, Mats E.; Rochus, Christina M.; Han, Fan; Chen, Junfeng; Hill, Jason; Wallerman, Ola; Fan, Guangyi; Hong, Xiaoning; Xu, Qiwu; Zhang, He; Liu, Shanshan; Liu, Xin; Haggerty, Leanne; Hunt, Toby; Martin, Fergal J.; Flicek, Paul; Bunikis, Ignas; Folkvord, Arild; Andersson, Leif (Peer reviewed; Journal article, 2019)
      The Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies ...
    • The circular RNome of primary breast cancer 

      Smid, Marcel; Wilting, Saskia M.; Uhr, Katharina; Rodríguez-González, F. Germán; de Weerd, Vanja; Prager-Van der Smissen, Wendy J.C.; van der Vlugt-Daane, Michelle; van Galen, Anne; Nik-Zainal, Serena; Butler, Adam; Martin, Sancha; Davies, Helen R.; Staaf, Johan; van de Vijver, Marc J.; Richardson, Andrea L.; Macgrogan, Gaëtan; Salgado, Roberto; van den Eynden, Gert G.G.M.; Purdie, Colin A.; Thompson, Alastair M.; Caldas, Carlos; Span, Paul N.; Sweep, Fred C.G.J.; Simpson, Peter T.; Lakhani, Sunil R.; Van Laere, Steven; Desmedt, Christine; Paradiso, Angelo; Eyfjord, Jorunn; Broeks, Annegien; Vincent-Salomon, Anne; Futreal, Andrew P.; Knappskog, Stian; King, Tari; Viari, Alain; Børresen-Dale, Anne-Lise; Stunnenberg, Hendrik G.; Stratton, Mike; Foekens, John A.; Sieuwerts, Anieta M.; Martens, John W.M. (Peer reviewed; Journal article, 2019)
      Circular RNAs (circRNAs) are a class of RNAs that is under increasing scrutiny, although their functional roles are debated. We analyzed RNA-seq data of 348 primary breast cancers and developed a method to identify circRNAs ...
    • Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis 

      Nepal, Chirag; Hadzhiev, Yavor; Previti, A. Christopher; Haberle, Vanja; Li, Nan; Takahashi, Hazuki; Suzuki, Ana Maria; Sheng, Ying; Abdelhamid, Rehab; Anand, Santosh; Gehrig, Jochen; Akalin, Altuna; Kockx, Christel E.M.; van der Sloot, Antoine A.J.; van Ijcken, Wilfred F.J.; Armant, Olivier; Rastegar, Sepand; Watson, Craig; Strähle, Uwe; Stupka, Elia; Carninci, Piero; Lenhard, Boris; Müller, Ferenc (Peer reviewed; Journal article, 2013)
      Spatiotemporal control of gene expression is central to animal development. Core promoters represent a previously unanticipated regulatory level by interacting with cis-regulatory elements and transcription initiation in ...
    • Functional annotation of human long noncoding RNAs via molecular phenotyping 

      Ramilowski, Jordan; Yip, Chiu Wai Mickey; Agrawal, Saumya; Chang, Jen-Chien; Ciani, Yari; Kulakovskiy, Ivan; Mendez, Mickaël; Ching Ooi, Jasmine Li; Ouyang, John F; Parkinson, Nick; Kasukawa, Takeya; Kauppinen, Sakari; Kere, Juha; Lenhard, Boris; Schneider, Claudio; Suzuki, Harukazu; Yagi, Ken; De Hoon, Michiel J L; Shin, Jay W; Piero, Carninci (Journal article; Peer reviewed, 2020)
      Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression ...
    • Increased taxon sampling reveals thousands of hidden orthologs in flatworms 

      Martin Duran, Jose Maria; Ryan, Joseph Francis; Vellutini, Bruno Cossermelli; Pang, Kevin Scott; Hejnol, Andreas (Journal article; Peer reviewed, 2017)
      Gains and losses shape the gene complement of animal lineages and are a fundamental aspect of genomic evolution. Acquiring a comprehensive view of the evolution of gene repertoires is limited by the intrinsic limitations ...