Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies von van der Valk, Tom, Vezzi, Francesco, Ormestad, Mattias, Dalén, Love, Guschanski, Katerina

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The Norway spruce genome sequence and conifer genome evolution von Nystedt, Björn, Street, Nathaniel R., Wetterbom, Anna, Zuccolo, Andrea, Lin, Yao-Cheng, Scofield, Douglas G., Vezzi, Francesco, Delhomme, Nicolas, Giacomello, Stefania, Alexeyenko, Andrey, Vicedomini, Riccardo, Sahlin, Kristoffer, Sherwood, Ellen, Elfstrand, Malin, Gramzow, Lydia, Holmberg, Kristina, Hällman, Jimmie, Keech, Olivier, Klasson, Lisa, Koriabine, Maxim, Kucukoglu, Melis, Käller, Max, Luthman, Johannes, Lysholm, Fredrik, Niittylä, Totte, Olson, Åke, Rilakovic, Nemanja, Ritland, Carol, Rosselló, Josep A., Sena, Juliana, Svensson, Thomas, Talavera-López, Carlos, Theißen, Günter, Tuominen, Hannele, Vanneste, Kevin, Wu, Zhi-Qiang, Zhang, Bo, Zerbe, Philipp, Arvestad, Lars, Bhalerao, Rishikesh, Bohlmann, Joerg, Bousquet, Jean, Garcia Gil, Rosario, Hvidsten, Torgeir R., de Jong, Pieter, MacKay, John, Morgante, Michele, Ritland, Kermit, Sundberg, Björn, Lee Thompson, Stacey, Van de Peer, Yves, Andersson, Björn, Nilsson, Ove, Ingvarsson, Pär K., Lundeberg, Joakim, Jansson, Stefan

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Reevaluating assembly evaluations with feature response curves: GAGE and assemblathons von Vezzi, Francesco, Narzisi, Giuseppe, Mishra, Bud

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Development and performance of a next generation sequencing (NGS) assay for monitoring of mixed chimerism von Pettersson, Linnea, Vezzi, Francesco, Vonlanthen, Sofie, Alwegren, Karin, Hedrum, Anders, Hauzenberger, Dan

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TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data [version 2; peer review: 2 approved] von Eisfeldt, Jesper, Vezzi, Francesco, Olason, Pall, Nilsson, Daniel, Lindstrand, Anna

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Comprehensive structural variation genome map of individuals carrying complex chromosomal rearrangements von Eisfeldt, Jesper, Pettersson, Maria, Vezzi, Francesco, Wincent, Josephine, Käller, Max, Gruselius, Joel, Nilsson, Daniel, Syk Lundberg, Elisabeth, Carvalho, Claudia M B, Lindstrand, Anna

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Whole‐Genome Sequencing of Cytogenetically Balanced Chromosome Translocations Identifies Potentially Pathological Gene Disruptions and Highlights the Importance of Microhomology in... von Nilsson, Daniel, Pettersson, Maria, Gustavsson, Peter, Förster, Alisa, Hofmeister, Wolfgang, Wincent, Josephine, Zachariadis, Vasilios, Anderlid, Britt‐Marie, Nordgren, Ann, Mäkitie, Outi, Wirta, Valtteri, Käller, Max, Vezzi, Francesco, Lupski, James R, Nordenskjöld, Magnus, Syk Lundberg, Elisabeth, Carvalho, Claudia M. B., Lindstrand, Anna

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Feature-by-feature--evaluating de novo sequence assembly von Vezzi, Francesco, Narzisi, Giuseppe, Mishra, Bud

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Replicative and non-replicative mechanisms in the formation of clustered CNVs are indicated by whole genome characterization von Nazaryan-Petersen, Lusine, Eisfeldt, Jesper, Pettersson, Maria, Lundin, Johanna, Nilsson, Daniel, Wincent, Josephine, Lieden, Agne, Lovmar, Lovisa, Ottosson, Jesper, Gacic, Jelena, Mäkitie, Outi, Nordgren, Ann, Vezzi, Francesco, Wirta, Valtteri, Käller, Max, Hjortshøj, Tina Duelund, Jespersgaard, Cathrine, Houssari, Rayan, Pignata, Laura, Bak, Mads, Tommerup, Niels, Lundberg, Elisabeth Syk, Tümer, Zeynep, Lindstrand, Anna

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GRM1 is upregulated through gene fusion and promoter swapping in chondromyxoid fibroma von Nord, Karolin H, Lilljebjörn, Henrik, Vezzi, Francesco, Nilsson, Jenny, Magnusson, Linda, Tayebwa, Johnbosco, de Jong, Danielle, Bovée, Judith V M G, Hogendoorn, Pancras C W, Szuhai, Karoly

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High-resolution detection of chromosomal rearrangements in leukemias through mate pair whole genome sequencing von Tran, Anh Nhi, Taylan, Fulya, Zachariadis, Vasilios, Ivanov Öfverholm, Ingegerd, Lindstrand, Anna, Vezzi, Francesco, Lötstedt, Britta, Nordenskjöld, Magnus, Nordgren, Ann, Nilsson, Daniel, Barbany, Gisela

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De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data von Ameur, Adam, Che, Huiwen, Martin, Marcel, Bunikis, Ignas, Dahlberg, Johan, Höijer, Ida, Häggqvist, Susana, Vezzi, Francesco, Nordlund, Jessica, Olason, Pall, Feuk, Lars, Gyllensten, Ulf

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TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data [version 1; peer review: 2 approved with reservations] von Eisfeldt, Jesper, Vezzi, Francesco, Olason, Pall, Nilsson, Daniel, Lindstrand, Anna

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BESST--efficient scaffolding of large fragmented assemblies von Sahlin, Kristoffer, Vezzi, Francesco, Nystedt, Björn, Lundeberg, Joakim, Arvestad, Lars

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GapFiller: a de novo assembly approach to fill the gap within paired reads von Nadalin, Francesca, Vezzi, Francesco, Policriti, Alberto

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GAM-NGS: genomic assemblies merger for next generation sequencing von Vicedomini, Riccardo, Vezzi, Francesco, Scalabrin, Simone, Arvestad, Lars, Policriti, Alberto

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SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population von Ameur, Adam, Dahlberg, Johan, Olason, Pall, Vezzi, Francesco, Karlsson, Robert, Martin, Marcel, Viklund, Johan, Kähäri, Andreas Kusalananda, Lundin, Pär, Che, Huiwen, Thutkawkorapin, Jessada, Eisfeldt, Jesper, Lampa, Samuel, Dahlberg, Mats, Hagberg, Jonas, Jareborg, Niclas, Liljedahl, Ulrika, Jonasson, Inger, Johansson, Åsa, Feuk, Lars, Lundeberg, Joakim, Syvänen, Ann-Christine, Lundin, Sverker, Nilsson, Daniel, Nystedt, Björn, Magnusson, Patrik Ke, Gyllensten, Ulf

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Fast, accurate, and lightweight analysis of BS-treated reads with ERNE 2 von Prezza, Nicola, Vezzi, Francesco, Käller, Max, Policriti, Alberto

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T-cell receptor-HLA-DRB1 associations suggest specific antigens in pulmonary sarcoidosis von Grunewald, Johan, Kaiser, Ylva, Ostadkarampour, Mahyar, Rivera, Natalia V, Vezzi, Francesco, Lötstedt, Britta, Olsen, Remi-André, Sylwan, Lina, Lundin, Sverker, Käller, Max, Sandalova, Tatiana, Ahlgren, Kerstin M, Wahlström, Jan, Achour, Adnane, Ronninger, Marcus, Eklund, Anders

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Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species von Bradnam, Keith R, Fass, Joseph N, Alexandrov, Anton, Baranay, Paul, Bechner, Michael, Birol, Inanç, Boisvert, Sébastien, Chapman, Jarrod A, Chapuis, Guillaume, Chikhi, Rayan, Chitsaz, Hamidreza, Chou, Wen-Chi, Corbeil, Jacques, Del Fabbro, Cristian, Docking, T Roderick, Durbin, Richard, Earl, Dent, Emrich, Scott, Fedotov, Pavel, Fonseca, Nuno A, Ganapathy, Ganeshkumar, Gibbs, Richard A, Gnerre, Sante, Godzaridis, Elénie, Goldstein, Steve, Haimel, Matthias, Hall, Giles, Haussler, David, Hiatt, Joseph B, Ho, Isaac Y, Howard, Jason, Hunt, Martin, Jackman, Shaun D, Jaffe, David B, Jarvis, Erich D, Jiang, Huaiyang, Kazakov, Sergey, Kersey, Paul J, Kitzman, Jacob O, Knight, James R, Koren, Sergey, Lam, Tak-Wah, Lavenier, Dominique, Laviolette, François, Li, Yingrui, Li, Zhenyu, Liu, Binghang, Liu, Yue, Luo, Ruibang, Maccallum, Iain, Macmanes, Matthew D, Maillet, Nicolas, Melnikov, Sergey, Naquin, Delphine, Ning, Zemin, Otto, Thomas D, Paten, Benedict, Paulo, Octávio S, Phillippy, Adam M, Pina-Martins, Francisco, Place, Michael, Przybylski, Dariusz, Qin, Xiang, Qu, Carson, Ribeiro, Filipe J, Richards, Stephen, Rokhsar, Daniel S, Ruby, J Graham, Scalabrin, Simone, Schatz, Michael C, Schwartz, David C, Sergushichev, Alexey, Sharpe, Ted, Shaw, Timothy I, Shendure, Jay, Shi, Yujian, Simpson, Jared T, Song, Henry, Tsarev, Fedor, Vezzi, Francesco, Vicedomini, Riccardo, Vieira, Bruno M, Wang, Jun, Worley, Kim C, Yin, Shuangye, Yiu, Siu-Ming, Yuan, Jianying, Zhang, Guojie, Zhang, Hao, Zhou, Shiguo, Korf, Ian F

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