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Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering.
Published in:
Microbiome, 2015, v. 3, n. 1, p. 1, doi. 10.1186/s40168-015-0105-6
By:
- Franzén, Oscar;
- Jianzhong Hu;
- Xiuliang Bao;
- Itzkowitz, Steven H.;
- Peter, Inga;
- Bashir, Ali
Publication type:
Article
Functional regulatory mechanism of smooth muscle cell-restricted LMOD1 coronary artery disease locus.
Published in:
PLoS Genetics, 2018, v. 14, n. 11, p. 1, doi. 10.1371/journal.pgen.1007755
By:
- Nanda, Vivek;
- Wang, Ting;
- Pjanic, Milos;
- Liu, Boxiang;
- Nguyen, Trieu;
- Matic, Ljubica Perisic;
- Hedin, Ulf;
- Koplev, Simon;
- Ma, Lijiang;
- Franzén, Oscar;
- Ruusalepp, Arno;
- Schadt, Eric E.;
- Björkegren, Johan L. M.;
- Montgomery, Stephen B.;
- Snyder, Michael P.;
- Quertermous, Thomas;
- Leeper, Nicholas J.;
- Miller, Clint L.
Publication type:
Article
Assembly and diploid architecture of an individual human genome via single-molecule technologies.
Published in:
Nature Methods, 2015, v. 12, n. 8, p. 780, doi. 10.1038/nmeth.3454
By:
- Pendleton, Matthew;
- Sebra, Robert;
- Pang, Andy Wing Chun;
- Ummat, Ajay;
- Franzen, Oscar;
- Rausch, Tobias;
- Stütz, Adrian M;
- Stedman, William;
- Anantharaman, Thomas;
- Hastie, Alex;
- Dai, Heng;
- Fritz, Markus Hsi-Yang;
- Cao, Han;
- Cohain, Ariella;
- Deikus, Gintaras;
- Durrett, Russell E;
- Blanchard, Scott C;
- Altman, Roger;
- Chin, Chen-Shan;
- Guo, Yan
Publication type:
Article
Plasmidome-Analysis of ESBL-Producing <i>Escherichia coli</i> Using Conventional Typing and High-Throughput Sequencing.
Published in:
PLoS ONE, 2013, v. 8, n. 6, p. 1, doi. 10.1371/journal.pone.0065793
By:
- Brolund, Alma;
- Franzén, Oscar;
- Melefors, Öjar;
- Tegmark-Wisell, Karin;
- Sandegren, Linus
Publication type:
Article
Intraclonal Variations Among Streptococcus pneumoniae Isolates Influence the Likelihood of Invasive Disease in Children.
Published in:
Journal of Infectious Diseases, 2014, v. 209, n. 3, p. 377, doi. 10.1093/infdis/jit481
By:
- Browall, Sarah;
- Norman, Martin;
- Tångrot, Jeanette;
- Galanis, Ilias;
- Sjöström, Karin;
- Dagerhamn, Jessica;
- Hellberg, Christel;
- Pathak, Anuj;
- Spadafina, Tiziana;
- Sandgren, Andreas;
- Bättig, Patrick;
- Franzén, Oscar;
- Andersson, Björn;
- Örtqvist, Åke;
- Normark, Staffan;
- Henriques-Normark, Birgitta
Publication type:
Article
Single-cell analysis of mosquito hemocytes identifies signatures of immune cell subtypes and cell differentiation.
Published in:
eLife, 2021, p. 1, doi. 10.7554/eLife.66192
By:
- Hyeogsun Kwon;
- Mohammed, Mubasher;
- Franzén, Oscar;
- Ankarklev, Johan;
- Smith, Ryan C.
Publication type:
Article
PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data.
Published in:
Database: The Journal of Biological Databases & Curation, 2019, v. 2019, p. N.PAG, doi. 10.1093/database/baz046
By:
- Franzén, Oscar;
- Gan, Li-Ming;
- Björkegren, Johan L M
Publication type:
Article
Preservation Analysis of Macrophage Gene Coexpression Between Human and Mouse Identifies PARK2 as a Genetically Controlled Master Regulator of Oxidative Phosphorylation in Humans.
Published in:
G3: Genes | Genomes | Genetics, 2016, v. 6, n. 10, p. 3361, doi. 10.1534/g3.116.033894
By:
- Codoni, Veronica;
- Blum, Yuna;
- Civelek, Mete;
- Proust, Carole;
- Franzén, Oscar;
- Björkegren, Johan L. M.;
- Le Goff, Wilfried;
- Cambien, Francois;
- Lusis, Aldons J.;
- Trégouët, David-Alexandre
Publication type:
Article
Cis-epistasis at the LPA locus and risk of cardiovascular diseases.
Published in:
Cardiovascular Research, 2022, v. 118, n. 4, p. 1088, doi. 10.1093/cvr/cvab136
By:
- Zeng, Lingyao;
- Moser, Sylvain;
- Mirza-Schreiber, Nazanin;
- Lamina, Claudia;
- Coassin, Stefan;
- Nelson, Christopher P;
- Annilo, Tarmo;
- Franzén, Oscar;
- Kleber, Marcus E;
- Mack, Salome;
- Andlauer, Till F M;
- Jiang, Beibei;
- Stiller, Barbara;
- Li, Ling;
- Willenborg, Christina;
- Munz, Matthias;
- Kessler, Thorsten;
- Kastrati, Adnan;
- Laugwitz, Karl-Ludwig;
- Erdmann, Jeanette
Publication type:
Article
Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNA-Seq.
Published in:
PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1003000
By:
- Franzén, Oscar;
- Jerlström-Hultqvist, Jon;
- Einarsson, Elin;
- Ankarklev, Johan;
- Ferella, Marcela;
- Andersson, Björn;
- Svärd, Staffan G.
Publication type:
Article
Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci.
Published in:
Nature Communications, 2016, v. 7, n. 7, p. 12092, doi. 10.1038/ncomms12092
By:
- Miller, Clint L.;
- Pjanic, Milos;
- Wang, Ting;
- Nguyen, Trieu;
- Cohain, Ariella;
- Lee, Jonathan D.;
- Perisic, Ljubica;
- Hedin, Ulf;
- Kundu, Ramendra K.;
- Majmudar, Deshna;
- Kim, Juyong B.;
- Wang, Oliver;
- Betsholtz, Christer;
- Ruusalepp, Arno;
- Franzén, Oscar;
- Assimes, Themistocles L.;
- Montgomery, Stephen B.;
- Schadt, Eric E.;
- Björkegren, Johan L.M.;
- Quertermous, Thomas
Publication type:
Article
Characterization of Evolutionarily Conserved Trypanosoma cruzi NatC and NatA-N-Terminal Acetyltransferase Complexes.
Published in:
Journal of Parasitology Research, 2019, p. 1, doi. 10.1155/2019/6594212
By:
- Ochaya, Stephen;
- Franzén, Oscar;
- Buhwa, Doreen Asiimwe;
- Foyn, Håvard;
- Butler, Claire E.;
- Stove, Svein Isungset;
- Tyler, Kevin M.;
- Arnesen, Thomas;
- Matovu, Enock;
- Åslund, Lena;
- Andersson, Björn
Publication type:
Article
Draft Genome Sequencing of Giardia intestinalis Assemblage B Isolate GS: Is Human Giardiasis Caused by Two Different Species?
Published in:
PLoS Pathogens, 2009, v. 5, n. 8, p. 1, doi. 10.1371/journal.ppat.1000560
By:
- Franzén, Oscar;
- Jerlström-Hultqvist, Jon;
- Castro, Elsie;
- Sherwood, Ellen;
- Ankarklev, Johan;
- Reiner, David S.;
- Palm, Daniel;
- Andersson, Jan O.;
- Andersson, Björn;
- Svärd, Staffan G.
Publication type:
Article
Correction to: Integrative analysis of loss-of-function variants in clinical and genomic data reveals novel genes associated with cardiovascular traits.
Published in:
2019
By:
- Glicksberg, Benjamin S.;
- Amadori, Letizia;
- Akers, Nicholas K.;
- Sukhavasi, Katyayani;
- Franzén, Oscar;
- Li, Li;
- Belbin, Gillian M.;
- Ayers, Kristin L.;
- Shameer, Khader;
- Badgeley, Marcus A.;
- Johnson, Kipp W.;
- Readhead, Ben;
- Darrow, Bruce J.;
- Kenny, Eimear E.;
- Betsholtz, Christer;
- Ermel, Raili;
- Skogsberg, Josefin;
- Ruusalepp, Arno;
- Schadt, Eric E.;
- Dudley, Joel T.
Publication type:
Correction Notice
Integrative analysis of loss-of-function variants in clinical and genomic data reveals novel genes associated with cardiovascular traits.
Published in:
BMC Medical Genomics, 2019, v. 12, n. 6, p. N.PAG, doi. 10.1186/s12920-019-0542-3
By:
- Glicksberg, Benjamin S.;
- Amadori, Letizia;
- Akers, Nicholas K.;
- Sukhavasi, Katyayani;
- Franzén, Oscar;
- Li, Li;
- Belbin, Gillian M.;
- Akers, Kristin L.;
- Shameer, Khader;
- Badgeley, Marcus A.;
- Johnson, Kipp W.;
- Readhead, Ben;
- Darrow, Bruce J.;
- Kenny, Eimear E.;
- Betsholtz, Christer;
- Ermel, Raili;
- Skogsberg, Josefin;
- Ruusalepp, Arno;
- Schadt, Eric E.;
- Dudley, Joel T.
Publication type:
Article
Global analysis of A-to-I RNA editing reveals association with common disease variants.
Published in:
PeerJ, 2018, p. 1, doi. 10.7717/peerj.4466
By:
- Franzén, Oscar;
- Ermel, Raili;
- Sukhavasi, Katyayani;
- Jain, Rajeev;
- Jain, Anamika;
- Betsholtz, Christer;
- Giannarelli, Chiara;
- Kovacic, Jason C.;
- Ruusalepp, Arno;
- Skogsberg, Josefin;
- Ke Hao;
- Schadt, Eric E.;
- Björkegren, Johan L. M.
Publication type:
Article
EnsembleCNV: an ensemble machine learning algorithm to identify and genotype copy number variation using SNP array data.
Published in:
Nucleic Acids Research, 2019, v. 47, n. 7, p. e39, doi. 10.1093/nar/gkz068
By:
- Zhang, Zhongyang;
- Cheng, Haoxiang;
- Hong, Xiumei;
- Di Narzo, Antonio F;
- Franzen, Oscar;
- Peng, Shouneng;
- Ruusalepp, Arno;
- Kovacic, Jason C;
- Bjorkegren, Johan L M;
- Wang, Xiaobin;
- Hao, Ke
Publication type:
Article
Multiple Mitochondrial Introgression Events and Heteroplasmy in Trypanosoma cruzi Revealed by Maxicircle MLST and Next Generation Sequencing.
Published in:
PLoS Neglected Tropical Diseases, 2012, v. 6, n. 4, p. 1, doi. 10.1371/journal.pntd.0001584
By:
- Messenger, Louisa A.;
- Llewellyn, Martin S.;
- Bhattacharyya, Tapan;
- Franzén, Oscar;
- Lewis, Michael D.;
- Ramírez, Juan David;
- Carrasco, Hernan J.;
- Andersson, Björn;
- Miles, Michael A.
Publication type:
Article
Multiple Mitochondrial Introgression Events and Heteroplasmy in Trypanosoma cruzi Revealed by Maxicircle MLST and Next Generation Sequencing.
Published in:
PLoS Neglected Tropical Diseases, 2012, v. 6, n. 4, p. 1, doi. 10.1371/journal.pntd.0001584
By:
- Messenger, Louisa A.;
- Llewellyn, Martin S.;
- Bhattacharyya, Tapan;
- Franzén, Oscar;
- Lewis, Michael D.;
- Ramírez, Juan David;
- Carrasco, Hernan J.;
- Andersson, Björn;
- Miles, Michael A.
Publication type:
Article
The Short Non-Coding Transcriptome of the Protozoan Parasite Trypanosoma cruzi.
Published in:
PLoS Neglected Tropical Diseases, 2011, v. 5, n. 8, p. 1, doi. 10.1371/journal.pntd.0001283
By:
- Franzén, Oscar;
- Arner, Erik;
- Ferella, Marcela;
- Nilsson, Daniel;
- Respuela, Patricia;
- Carninci, Piero;
- Hayashizaki, Yoshihide;
- Åslund, Lena;
- Andersson, Björn;
- Daub, Carsten O.
Publication type:
Article
The Short Non-Coding Transcriptome of the Protozoan Parasite Trypanosoma cruzi.
Published in:
PLoS Neglected Tropical Diseases, 2011, v. 5, n. 8, p. 1
By:
- Franzén, Oscar;
- Arner, Erik;
- Ferella, Marcela;
- Nilsson, Daniel;
- Respuela, Patricia;
- Carninci, Piero;
- Hayashizaki, Yoshihide;
- Åslund, Lena;
- Andersson, Björn;
- Daub, Carsten O.
Publication type:
Article
Shotgun Sequencing Analysis of Trypanosoma cruzi I Sylvio X10/1 and Comparison with T. cruzi VI CL Brener.
Published in:
PLoS Neglected Tropical Diseases, 2011, v. 5, n. 3, p. 1, doi. 10.1371/journal.pntd.0000984
By:
- Franzén, Oscar;
- Ochaya, Stephen;
- Sherwood, Ellen;
- Lewis, Michael D.;
- Llewellyn, Martin S.;
- Miles, Michael A.;
- Andersson, Björn
Publication type:
Article
Shotgun Sequencing Analysis of Trypanosoma cruzi I Sylvio X10/1 and Comparison with T. cruzi VI CL Brener.
Published in:
PLoS Neglected Tropical Diseases, 2011, v. 5, n. 3, p. 1, doi. 10.1371/journal.pntd.0000984
By:
- Franzén, Oscar;
- Ochaya, Stephen;
- Sherwood, Ellen;
- Lewis, Michael D.;
- Llewellyn, Martin S.;
- Miles, Michael A.;
- Andersson, Björn
Publication type:
Article
Comparative genomic analyses of freshly isolated Giardia intestinalis assemblage A isolates.
Published in:
BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1893-6
By:
- Ankarklev, Johan;
- Franzén, Oscar;
- Peirasmaki, Dimitra;
- Jerlström-Hultqvist, Jon;
- Lebbad, Marianne;
- Andersson, Jan;
- Andersson, Björn;
- Svärd, Staffan G.
Publication type:
Article
Comparative genomic analysis of human infective Trypanosoma cruzi lineages with the bat-restricted subspecies T. cruzi marinkellei.
Published in:
BMC Genomics, 2012, v. 13, n. 1, p. 531, doi. 10.1186/1471-2164-13-531
By:
- Franzén, Oscar;
- Talavera-López, Carlos;
- Ochaya, Stephen;
- Butler, Claire E.;
- Messenger, Louisa A.;
- Lewis, Michael D.;
- Llewellyn, Martin S.;
- Marinkelle, Cornelis J.;
- Tyler, Kevin M.;
- Miles, Michael A.;
- Andersson, Björn
Publication type:
Article
Genome analysis and comparative genomics of a Giardia intestinalis assemblage E isolate.
Published in:
BMC Genomics, 2010, v. 11, n. 1, p. 1, doi. 10.1186/1471-2164-11-543
By:
- Jerlström-Hultqvist, Jon;
- Franzén, Oscar;
- Ankarklev, Johan;
- Xu, Feifei;
- Nohýnková, Eva;
- Andersson, Jan O;
- Svärd, Staffan G;
- Andersson, Björn
Publication type:
Article
Genome analysis and comparative genomics of a Giardia intestinalis assemblage E isolate.
Published in:
BMC Genomics, 2010, v. 11, p. 543, doi. 10.1186/1471-2164-11-543
By:
- Jerlström-Hultqvist, Jon;
- Franzén, Oscar;
- Ankarklev, Johan;
- Feifei Xu;
- Nohýnková, Eva;
- Andersson, Jan O.;
- Svärd, Staffan G.;
- Andersson, Björn
Publication type:
Article
The HDAC9-associated risk locus promotes coronary artery disease by governing TWIST1.
Published in:
PLoS Genetics, 2022, v. 18, n. 6, p. 1, doi. 10.1371/journal.pgen.1010261
By:
- Ma, Lijiang;
- Bryce, Nicole S.;
- Turner, Adam W.;
- Di Narzo, Antonio F.;
- Rahman, Karishma;
- Xu, Yang;
- Ermel, Raili;
- Sukhavasi, Katyayani;
- d'Escamard, Valentina;
- Chandel, Nirupama;
- V'Gangula, Bhargavi;
- Wolhuter, Kathryn;
- Kadian-Dodov, Daniella;
- Franzen, Oscar;
- Ruusalepp, Arno;
- Hao, Ke;
- Miller, Clint L.;
- Björkegren, Johan L. M.;
- Kovacic, Jason C.
Publication type:
Article
alona: a web server for single-cell RNA-seq analysis.
Published in:
Bioinformatics, 2020, v. 36, n. 12, p. 3910, doi. 10.1093/bioinformatics/btaa269
By:
- Franzén, Oscar;
- Björkegren, Johan L M
Publication type:
Article

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