Publications

 

Publikationer rss feed

2019
 

Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries

Asplund, Maria ; Kjartansdóttir, Kristín Rós ; Mollerup, Sarah ; Vinner, Lasse ; Fridholm, Helena ; Herrera, José A. R. ; Friis-Nielsen, Jens ; Hansen, Thomas Arn ; Jensen, Randi Holm ; Nielsen, Ida Broman ; Richter, Stine Raith ; Rey-Iglesia, Alba ; Matey-Hernandez, Maria Luisa ; Alquezar-Planas, David E. ; Olsen, Pernille V. S. ; Sicheritz-Pontén, Thomas ; Willerslev, Eske ; Lund, Ole ; Brunak, Søren ; Mourier, Tobias ; Nielsen, Lars Peter ; Izarzugaza, Jose M. G. ; Hansen, Anders Johannes
in: Clinical Microbiology and Infection

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.cmi.2019.04.028

 

Functional Interpretation of Single Amino Acid Substitutions in 1,330 Disease-Associated Genes

Iqbal, Sumaiya ; Jespersen, Jakob Berg ; Perez-Palma, Eduardo ; May, Patrick ; Palotie, Aarno ; Cottrell, Jeffrey R. ; Wagner, Florence F. ; Daly, Mark J. ; Campbell, Arthur J. ; Lal, Dennis
in: BIOPHYSICAL JOURNAL, vol: 116, issue: 3, pages: 420a-421a

Type: Conference abstract in journal (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.bpj.2018.11.2266

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Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

Hendriksen, Rene S. ; Munk, Patrick ; Njage, Patrick Murigu Kamau ; van Bunnik, Bram ; McNally, Luke ; Lukjancenko, Oksana ; Röder, Timo ; Nieuwenhuijse, David ; Karlsmose Pedersen, Susanne ; Kjeldgaard, Jette Sejer ; Kaas, Rolf Sommer ; Clausen, Philip Thomas Lanken Conradsen ; Vogt, Josef Korbinian ; Leekitcharoenphon, Pimlapas ; van de Schans, Milou G M ; Zuidema, Tina ; de Roda Husman, Ana Maria ; Rasmussen, Simon ; Petersen, Bent ; Global, Sewage Surveillance project consortium ; Amid, Clara ; Cochrane, Guy ; Sicheritz-Pontén, Thomas ; Schmitt, Heike ; Alvarez, Jorge Raul Matheu ; Aidara-Kane, Awa ; Pamp, Sünje Johanna ; Lund, Ole ; Hald, Tine ; Woolhouse, Mark ; Koopmans, Marion P ; Vigre, Håkan ; Petersen, Thomas Nordahl ; Aarestrup, Frank Møller
in: Nature Communications, vol: 10

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41467-019-08853-3

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Immunity and mental illness: findings from a Danish population-based immunogenetic study of seven psychiatric and neurodevelopmental disorders

Nudel, Ron ; Benros, Michael E. ; Krebs, Morten Dybdahl ; Allesøe, Rosa Lundbye ; Lemvigh, Camilla Koldbæk ; Bybjerg-Grauholm, Jonas ; Børglum, Anders D. ; Daly, Mark J. ; Nordentoft, Merete ; Mors, Ole ; Hougaard, David M. ; Mortensen, Preben Bo ; Buil, Alfonso ; Werge, Thomas ; Rasmussen, Simon ; Thompson, Wesley K
in: European journal of human genetics

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41431-019-0402-9

 

LRE-Finder, a Web tool for detection of the 23S rRNA mutations and the optrA, cfr, cfr(B) and poxtA genes encoding linezolid resistance in enterococci from whole-genome sequences

Hasman, Henrik ; Clausen, Philip Thomas Lanken Conradsen ; Kaya, Hülya ; Hansen, Frank ; Knudsen, Jenny Dahl ; Wang, Mikala ; Holzknecht, Barbara Juliane ; Samulioniené, Jurgita ; Røder, Bent L ; Frimodt-Møller, Niels ; Lund, Ole ; Hammerum, Anette Marie
in: Journal of Antimicrobial Chemotherapy, vol: 74, issue: 6, pages: 1473-1476

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1093/jac/dkz092

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Proof of concept: used malaria rapid diagnostic tests applied for parallel sequencing for surveillance of molecular markers of anti-malarial resistance in Bissau, Guinea-Bissau during 2014-2017

Nag, Sidsel ; Ursing, Johan ; Rodrigues, Amabelia ; Crespo, Marina ; Krogsgaard, Camilla ; Lund, Ole ; Aarestrup, Frank Møller ; Alifrangis, Michael ; Kofoed, PouL-Erik
in: Malaria Journal, vol: 18, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1186/s12936-019-2894-8

 

RNase H-dependent PCR-enabled T-cell receptor sequencing for highly specific and efficient targeted sequencing of T-cell receptor mRNA for single-cell and repertoire analysis

Li, Shuqiang ; Sun, Jing ; Allesøe, Rosa Lundbye ; Datta, Krishnalekha ; Bao, Yun ; Oliveira, Giacomo ; Forman, Juliet ; Jin, Roger ; Olsen, Lars Rønn ; Keskin, Derin B. ; Shukla, Sachet A. ; Wu, Catherine J. ; Livak, Kenneth J.
in: Nature Protocols, vol: 14, pages: 2571-2594

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41596-019-0195-x

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Using WGS to identify antibiotic resistance genes and predict antimicrobial resistance phenotypes in MDR Acinetobacter baumannii in Tanzania

Kumburu, Happiness H ; Sonda, Tolbert ; van Zwetselaar, Marco ; Leekitcharoenphon, Pimlapas ; Lukjancenko, Oksana ; Mmbaga, Blandina Theophil ; Alifrangis, Michael ; Lund, Ole ; Aarestrup, Frank Møller ; Kibiki, Gibson S
in: Journal of Antimicrobial Chemotherapy, vol: 74, issue: 6, pages: 1484-1493

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1093/jac/dkz055

2018
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Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries

Munk, Patrick ; Knudsen, Berith Elkær ; Lukjacenko, Oksana ; Duarte, Ana Sofia Ribeiro ; Van Gompel, Liese ; Luiken, Roosmarijn E.C. ; Smit, Lidwien A.M. ; Schmitt, Heike ; Garcia, Alejandro Dorado ; Hansen, Rasmus Borup ; Petersen, Thomas Nordahl ; Bossers, Alex ; Ruppé, Etienne ; Graveland, Haitske ; van Essen, Alieda ; Gonzalez-Zorn, Bruno ; Moyano, Gabriel ; Sanders, Pascal ; Chauvin, Claire ; David, Julie ; Battisti, Antonio ; Caprioli, Andrea ; Dewulf, Jeroen ; Blaha, Thomas ; Wadepohl, Katharina ; Brandt, Maximiliane ; Wasyl, Dariusz ; Skarzyńska, Magdalena ; Zajac, Magdalena ; Daskalov, Hristo ; Saatkamp, Helmut W. ; Stärk, Katharina D.C. ; Lund, Ole ; Hald, Tine ; Pamp, Sünje Johanna ; Vigre, Håkan ; Heederik, Dick ; Wagenaar, Jaap A. ; Mevius, Dik ; Møller Aarestrup, Frank ; ,
in: Nature Microbiology, vol: 3, issue: 8, pages: 898-908

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1038/s41564-018-0192-9

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Direct whole-genome sequencing of Plasmodium falciparum specimens from dried erythrocyte spots

Nag, Sidsel ; Kofoed, Poul Erik ; Ursing, Johan ; Lemvigh, Camilla Koldbæk ; Allesøe, Rosa Lundbye ; Rodrigues, Amabelia ; Svendsen, Christina Aaby ; Jensen, Jacob Dyring ; Alifrangis, Michael ; Lund, Ole ; Møller Aarestrup, Frank
in: Malaria Journal, vol: 17, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1186/s12936-018-2232-6

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Prevalence and risk factors for CTX-M gram-negative bacteria in hospitalized patients at a tertiary care hospital in Kilimanjaro, Tanzania

Sonda, Tolbert ; Kumburu, Happiness ; van Zwetselaar, Marco ; Alifrangis, Michael ; Mmbaga, Blandina T. ; Lund, Ole ; Møller Aarestrup, Frank ; Kibiki, Gibson
in: European Journal of Clinical Microbiology and Infectious Diseases, vol: 37, issue: 5, pages: 897-906

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1007/s10096-018-3196-8

 

Accurate genotyping across variant classes and lengths using variant graphs

Sibbesen, Jonas Andreas ; Maretty, Lasse ; Jensen, Jacob Malte ; Petersen, Bent ; Liu, Siyang ; Villesen, Palle ; Skov, Laurits ; Belling, Kirstine ; Theil Have, Christian ; Gonzalez-Izarzugaza, Jose Maria ; Grosjean, Marie ; Bork-Jensen, Jette ; Grove, Jakob ; Dam-Als, Thomas ; Huang, Shujia ; Chang, Yuqi ; Xu, Ruiqi ; Ye, Weijian ; Rao, Junhua ; Guo, Xiaosen ; Sun, Jihua ; Cao, Hongzhi ; Ye, Chen ; van Beusekom, Johan ; Espeseth, Thomas ; Flindt, Esben ; Friborg, Rune M. ; Halager, Anders Egerup ; Le Hellard, Stephanie ; Hultman, Christina M. ; Lescai, Francesco ; Li, Shengting ; Lund, Ole ; Løngren, Peter ; Mailund, Thomas ; Matey-Hernandez, María Luisa ; Mors, Ole ; Pedersen, Christian N. S. ; Sicheritz-Pontén, Thomas ; Sullivan, Patrick ; Ali , Syed ; Westergaard, David ; Yadav, Rachita ; Li, Ning ; Xu, Xun ; Hansen, Torben ; Krogh, Anders ; Bolund, Lars ; Sørensen, Thorkild I. A. ; Pedersen, Oluf ; Gupta, Ramneek ; Rasmussen, Simon ; Besenbacher, Søren ; Børglum, Anders D. ; Wang, Jun ; Eiberg, Hans ; Kristiansen, Karsten ; Brunak, Søren ; Schierup, Mikkel Heide
in: Nature Genetics

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1038/s41588-018-0145-5

 

AnOxPe-pred: Using deep learning for the prediction of antioxidative properties of peptides.

Olsen, Tobias Hegelund ; Pertseva, Margarita ; García Moreno, Pedro Jesús ; Jacobsen, Charlotte ; Lund, Ole ; Hansen, Egon Bech ; Marcatili, Paolo
part of: Sustain Conference 2018, 2018, Technical University of Denmark (DTU), Lyngby, Denmark
Presented at:
Sustain conference 2018: Creating Technology for a Sustainable Society

Type: Conference abstract in proceedings (Peer reviewed)

Status: Published     |    Year: 2018

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Antibody Cross-Reactivity in Antivenom Research

Ledsgaard, Line ; Jenkins, Timothy P ; Davidsen, Kristian ; Krause, Kamille Elvstrøm ; Martos-Esteban, Andrea ; Engmark, Mikael ; Andersen, Mikael Rørdam ; Lund, Ole ; Laustsen, Andreas Hougaard
in: Toxins, vol: 10, issue: 10

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.3390/toxins10100393

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Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios

Matey-Hernandez, María Luisa ; Maretty, Lasse ; Jensen, Jacob Malte ; Petersen, Bent ; Andreas Sibbesen, Jonas ; Liu, Siyang ; Villesen, Palle ; Skov, Laurits ; Belling, Kirstine ; Theil Have, Christian ; Gonzalez-Izarzugaza, Jose Maria ; Grosjean, Marie ; Bork-Jensen, Jette ; Grove, Jakob ; Als, Thomas D. ; Huang, Shujia ; Chang, Yuqi ; Xu, Ruiqi ; Ye, Weijian ; Rao, Junhua ; Guo, Xiaosen ; Sun, Jihua ; Cao, Hongzhi ; Ye, Chen ; Beusekom, Johan v. ; Espeseth, Thomas ; Flindt, Esben N. ; Friborg, Rune M. ; Halager, Anders Egerup ; Le Hellard, Stephanie ; Hultman, Christina M. ; Lescai, Francesco ; Li, Shengting ; Lund, Ole ; Løngren, Peter ; Mailund, Thomas ; Mors, Ole ; Pedersen, Christian N. S. ; Sicheritz-Pontén, Thomas ; Sullivan, Patrick F. ; Ali , Syed ; Westergaard, David ; Yadav, Rachita ; Li, Ning ; Xu, Xun ; Hansen, Torben ; Krogh, Anders ; Bolund, Lars ; Sørensen, Thorkild I. A. ; Pedersen, Oluf ; Gupta, Ramneek ; Besenbacher, Søren ; Børglum, Anders D. ; Wang, Jun ; Eiberg, Hans ; Kristiansen, Karsten ; Brunak, Søren ; Schierup, Mikkel Heide ; Izarzugaza, Jose M. G.
in: B M C Bioinformatics, vol: 19

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1186/s12859-018-2239-6

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CHTyper, a Web Tool for Subtyping of Extraintestinal Pathogenic Escherichia coli based on the fumC and fimH Alleles

Roer, Louise ; Johannesen, Thor Bech ; Hansen, Frank ; Stegger, Marc ; Tchesnokova, Veronika ; Sokurenko, Evgeni ; Garibay, Natasha ; Allesøe, Rosa Lundbye ; Thomsen, Martin C. F. ; Lund, Ole ; Hasman, Henrik ; Hammerum, Anette M.
in: Journal of Clinical Microbiology, vol: 56, issue: 4

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1128/JCM.00063-18

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Hospital Epidemiology of Methicillin-Resistant Staphylococcus aureus in a Tertiary Care Hospital in Moshi, Tanzania, as Determined by Whole Genome Sequencing

Kumburu, Happiness H. ; Sonda, Tolbert ; Leekitcharoenphon, Pimlapas ; van Zwetselaar, Marco ; Lukjancenko, Oksana ; Alifrangis, Michael ; Lund, Ole ; Mmbaga, Blandina T. ; Kibiki, Gibson ; Aarestrup, Frank Møller
in: Journal of Biomedicine and Biotechnology, vol: 2018

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1155/2018/2087693

 

Identification and Characterization of Variant Intolerant Sites across Human Protein 3-Dimensional Structures

Iqbal, Sumaiya ; Jespersen, Jakob Berg ; Perez-Palma, Eduardo ; May, Patrick ; Heyne, Henrike ; Lage, Kasper ; Steensbjerre Møller, Rikke ; Wagner, Florence F. ; Daly, Mark ; Campbell, Arthur J. ; Lal, Dennis
in: BIOPHYSICAL JOURNAL, vol: 114, issue: 3 s1, pages: 664a

Type: Conference abstract in journal (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1016/j.bpj.2017.11.3583

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Improved ontology for eukaryotic single-exon coding sequences in biological databases

Jorquera, Roddy ; González, Carolina ; Clausen, Philip ; Petersen, Bent ; Holmes, David S
in: Database, vol: 2018, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1093/database/bay089

 

Molecular epidemiology of virulence and antimicrobial resistance determinants in Klebsiella pneumoniae from hospitalised patients in Kilimanjaro, Tanzania

Sonda, Tolbert ; Kumburu, Happiness ; van Zwetselaar, Marco ; Alifrangis, Michael ; Mmbaga, Blandina T. ; Lund, Ole ; Kibiki, Gibson S. ; Møller Aarestrup, Frank
in: European Journal of Clinical Microbiology and Infectious Diseases, vol: 37, issue: 10, pages: 1901-1914

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1007/s10096-018-3324-5

 

Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial

Keskin, Derin B. ; Anandappa, Annabelle J. ; Sun, Jing ; Tirosh, Itay ; Mathewson, Nathan D. ; Li, Shuqiang ; Oliveira, Giacomo ; Giobbie-Hurder, Anita ; Felt, Kristen ; Gjini, Evisa ; Shukla, Sachet A. ; Hu, Zhuting ; Li, Letitia ; Le, Phuong M. ; Allesøe, Rosa Lundbye ; Richman, Alyssa R. ; Kowalczyk, Monika S ; Abdelrahman, Sara ; Geduldig, Jack E. ; Charbonneau, Sarah ; Pelton, Kristine ; Iorgulescu, J. Bryan ; Elagina, Liudmila ; Zhang, Wandi ; Olive, Oriol ; McCluskey, Christine ; Olsen, Lars Rønn ; Stevens, Jonathan ; Lane, William J. ; Salazar, Andres M. ; Daley, Heather ; Wen, Patrick Y. ; Chiocca, E. Antonio ; Harden, Maegan ; Lennon, Niall J. ; Gabriel, Stacey ; Getz, Gad ; Lander, Eric S. ; Regev, Aviv ; Ritz, Jerome ; Neuberg, Donna ; Rodig, Scott J. ; Ligon, Keith L. ; Suvà, Mario L. ; Wucherpfennig, Kai W. ; Hacohen, Nir ; Fritsch, Edward F. ; Livak, Kenneth J ; Ott, Patrick A ; Wu, Catherine J ; Reardon, David A.
in: Nature, vol: 565, pages: 234-239

Type: Letter (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1038/s41586-018-0792-9

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Public Health Surveillance using Decentralized Technologies

Bellod Cisneros, Jose Luis ; Aarestrup, Frank Møller ; Lund, Ole
in: Blockchain in Healthcare Today, vol: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.30953/bhty.v1.17

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Rapid and precise alignment of raw reads against redundant databases with KMA

Clausen, Philip Thomas Lanken Conradsen ; Aarestrup, Frank Møller ; Lund, Ole
in: B M C Bioinformatics, vol: 19, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1186/s12859-018-2336-6

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SCCmecFinder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome mec in Staphylococcus aureus Using Whole-Genome Sequence Data

Kaya, Hülya ; Hasman, Henrik ; Larsen, Jesper ; Stegger, Marc ; Johannesen, Thor Bech ; Allesøe, Rosa Lundbye ; Lemvigh, Camilla Koldbæk ; Aarestrup, Frank Møller ; Lund, Ole ; Larsen, Anders Rhod
in: mSphere, vol: 3, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1128/mSphere.00612-17

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Whole genome sequencing reveals high clonal diversity of Escherichia coli isolated from patients in a tertiary care hospital in Moshi, Tanzania

Sonda, Tolbert ; Kumburu, Happiness ; van Zwetselaar, Marco ; Alifrangis, Michael ; Mmbaga, Blandina T. ; Aarestrup, Frank Møller ; Kibiki, Gibson ; Lund, Ole
in: Antimicrobial Resistance and Infection Control, vol: 7

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1186/s13756-018-0361-x

2017
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Analysis of 62 hybrid assembled human Y chromosomes exposes rapid structural changes and high rates of gene conversion

Gonzalez-Izarzugaza, Jose Maria ; Skov, Laurits ; Maretty, Lasse ; Jensen, Jacob Malte ; Petersen, Bent ; Andreas Sibbesen, Jonas ; Liu, Siyang ; Villesen, Palle ; Belling, Kirstine González-Izarzugaza ; Theil Have, Christian ; Grosjean, Marie ; Bork-Jensen, Jette ; Grove, Jakob ; Als, Thomas D. ; Huang, Shujia ; Chang, Yuqi ; Xu, Ruiqi ; Ye, Weijian ; Rao, Junhua ; Guo, Xiaosen ; Sun, Jihua ; Cao, Hongzhi ; Ye, Chen ; van Beusekom, Johan ; Espeseth, Thomas ; Flindt, Esben ; Friborg, Rune M. ; Halager, Anders E. ; Le Hellard, Stephanie ; Hultman, Christina M. ; Lescai, Francesco ; Li, Shengting ; Lund, Ole ; Løngren, Peter ; Mailund, Thomas ; Matey-Hernandez, María Luisa ; Mors, Ole ; Pedersen, Christian N. S. ; Sicheritz-Pontén, Thomas ; Sullivan, Patrick F. ; Qaswar Ali Shah, Syed ; Westergaard, David ; Yadav, Rachita ; Li, Ning ; Xu, Xun ; Hansen, Torben ; Krogh, Anders ; Bolund, Lars ; Sørensen, Thorkild I. A. ; Pedersen, Oluf ; Gupta, Ramneek ; Rasmussen, Simon ; Besenbacher, Søren ; Børglum, Anders D. ; Wang, Jun ; Eiberg, Hans ; Kristiansen, Karsten ; Brunak, Søren ; Schierup, Mikkel Heide
in: P L o S Genetics, vol: 13, issue: 8

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1371/journal.pgen.1006834

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ArrayPitope: Automated Analysis of Amino Acid Substitutions for Peptide Microarray-Based Antibody Epitope Mapping

Hansen, Christian Skjødt ; Østerbye, Thomas ; Marcatili, Paolo ; Lund, Ole ; Buus, Søren ; Nielsen, Morten
in: P L o S One, vol: 12, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1371/journal.pone.0168453

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Cross-recognition of a pit viper (Crotalinae) polyspecific antivenom explored through high-density peptide microarray epitope mapping

Engmark, Mikael ; Lomonte, Bruno ; Gutiérrez, José María ; Laustsen, Andreas Hougaard ; De Masi, Federico ; Andersen, Mikael Rørdam ; Lund, Ole
in: P L o S Neglected Tropical Diseases (Online), vol: 11, issue: 7

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1371/journal.pntd.0005768

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Development of a web tool for Escherichia coli subtyping based on fimH alleles

Roer, Louise ; Tchesnokova, Veronika ; Allesøe, Rosa Lundbye ; Muradova, Mariya ; Chattopadhyay, Sujay ; Ahrenfeldt, Johanne ; Thomsen, Martin Christen Frølund ; Lund, Ole ; Hansen, Frank ; Hammerum, Anette Marie ; Sokurenko, Evgeni ; Hasman, Henrik
in: Journal of Clinical Microbiology, vol: 55, issue: 8, pages: 2538-2543

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1128/JCM.00737-17

 

Erratum to: Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease

Joensen, Katrine Grimstrup ; Engsbro, A. L. Ø. ; Lukjancenko, Oksana ; Kaas, Rolf Sommer ; Lund, Ole ; Westh, H. ; Aarestrup, Frank Møller
in: European Journal of Clinical Microbiology & Infectious Diseases, vol: 36, issue: 7, pages: 1339-1342

Type: Comment/debate (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1007/s10096-017-2993-9

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Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease

Joensen, Katrine Grimstrup ; Engsbro, A L Ø ; Lukjancenko, Oksana ; Kaas, Rolf Sommer ; Lund, Ole ; Westh, H. ; Aarestrup, Frank Møller
in: European Journal of Clinical Microbiology & Infectious Diseases, vol: 36, issue: 7, pages: 1325-1338

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1007/s10096-017-2947-2

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High-density peptide microarray exploration of the antibody response in a rabbit immunized with a neurotoxic venom fraction

Engmark, Mikael ; Jespersen, Martin Closter ; Lomonte, Bruno ; Lund, Ole ; Laustsen, Andreas Hougaard
in: Toxicon, vol: 138, pages: 151-158

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1016/j.toxicon.2017.08.028

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High throughput resistance profiling of Plasmodium falciparum infections based on custom dual indexing and Illumina next generation sequencing-technology

Nag, Sidsel ; Dalgaard, Marlene Danner ; Kofoed, Poul-Erik ; Ursing, Johan ; Crespo, Marina ; Andersen, Lee O'Brien ; Aarestrup, Frank Møller ; Lund, Ole ; Alifrangis, Michael
in: Scientific Reports, vol: 7, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1038/s41598-017-02724-x

 

Hospital epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) in a tertiary care hospital in Moshi Tanzania as determined by whole genome sequencing

Kumburu, H. H. ; Sonda, T. ; Leetcharoenphon, P. ; van Zwetselaar, M. ; Lukjancenko, Oksana ; Alifrangis, M. ; Lund, Ole ; Mmbaga, B. T. ; Kibiki, G. ; Aarestrup, Frank Møller
in: Tropical Medicine & International Health, vol: 22, issue: S1, pages: 359-359
Presented at:
10th European Congress on Tropical Medicine and International Health

Type: Conference abstract in journal (Peer reviewed)

Status: Published     |    Year: 2017

 

Meta-analysis of proportion estimates of extended-spectrum-beta-lactamase-producing Enterobacteriaceae in East Africa hospitals

Sonda, T. ; Kumburu, H. ; van Zwetselaar, M. ; Alifrangis, M. ; Lund, Ole ; Kibiki, G. ; Aarestrup, M. Frank F.
in: Tropical Medicine & International Health, vol: 22, issue: Suppl. 1, pages: 34

Type: Conference abstract in journal (Peer reviewed)

Status: Published     |    Year: 2017

 

Modifications of TIGIT expression contribute to CD8 T cell exhaustion in chronic virus infection

Tauriainen, Johanna ; Scharf, Lydia ; Frederiksen, Juliet Wairimu ; Naji, Ali ; Ljunggren, Hans-Gustaf ; Sonnerborg, Anders ; Lund, Ole ; Reyes-Teran, Gustavo ; Hecht, Frederick M. ; Deeks, Steven G. ; Betts, Michael R. ; Buggert, Marcus ; Karlsson, Annika C.
in: Scandinavian Journal of Immunology, vol: 86, issue: 4, pages: 318
Presented at:
44th Annual Meeting of the Scandinavian Society of Immunology

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1111/sji.12587

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Multidrug-resistant Neisseria gonorrhoeae infection with ceftriaxone resistance and intermediate resistance to azithromycin, Denmark, 2017

Terkelsen, David ; Tolstrup, Jacob ; Johnsen, Camilla Hundahl ; Lund, Ole ; Larsen, Helle Kiellberg ; Worning, Peder ; Unemo, Magnus ; Westh, Henrik
in: Eurosurveillance (Print), vol: 22, issue: 42

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.2807/1560-7917.ES.2017.22.42.17-00659

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Norwegian patients and retail chicken meat share cephalosporin-resistant Escherichia coli and IncK/blaCMY-2 resistance plasmids

Berg, E. S. ; Wester, A. L. ; Ahrenfeldt, Johanne ; Mo, S. S. ; Slettemeås, J. S. ; Steinbakk, M ; Samuelsen, Ø. ; Grude, N. ; Simonsen, G. S. ; Løhr, I. H. ; Jørgensen, S. B. ; Tofteland, S. ; Lund, Ole ; Dahle, U. R. ; Sunde, M.
in: Clinical Microbiology and Infection, vol: 23, issue: 6

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1016/j.cmi.2016.12.035

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Patterns of infections, aetiological agents, and antimicrobial resistance at a tertiary care hospital in northern Tanzania

Kumburu, Happiness Houka ; Sonda, Tolbert ; Mmbaga, Blandina Theophil ; Alifrangis, Michael ; Lund, Ole ; Kibiki, Gibson ; Aarestrup, Frank Møller
in: Tropical Medicine & International Health, vol: 22, issue: 4, pages: 454-464

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1111/tmi.12836

 

Patterns of infections, aetiological agents, and antimicrobial resistance at a tertiary care hospital in northern Tanzania

Kumburu, H. H. ; Sonda, T. ; Mmbaga, B. T. ; Alifrangis, M. ; Lund, Ole ; Kibiki, G. ; Aarestrup, Frank Møller
in: Tropical Medicine & International Health, vol: 22, issue: S1, pages: 360-360
Presented at:
10th European Congress on Tropical Medicine and International Health

Type: Conference abstract in journal (Peer reviewed)

Status: Published     |    Year: 2017

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Perturbed CD8+ T cell TIGIT/CD226/PVR axis despite early initiation of antiretroviral treatment in HIV infected individuals

Tauriainen, Johanna ; Scharf, Lydia ; Frederiksen, Juliet ; Naji, Ali ; Ljunggren, Hans-Gustaf ; Sönnerborg, Anders ; Lund, Ole ; Reyes-Terán, Gustavo ; Hecht, Frederick Mm ; Deeks, Steven G. ; Betts, Michael R. ; Buggert, Marcus ; Karlsson, Annika C.
in: Scientific Reports, vol: 7

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1038/srep4035

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PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens

Zankari, Ea ; Allesøe, Rosa Lundbye ; Joensen, Katrine Grimstrup ; Cavaco, Lina ; Lund, Ole ; Aarestrup, Frank Møller
in: Journal of Antimicrobial Chemotherapy, vol: 72, issue: 10, pages: 2764-2768

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1093/jac/dkx217

 

Prevalence and risk factors of CTX-M Enterobacteriaceae in hospitalised patients at a tertiary hospital in Kilimanjaro, Tanzania

Sonda, T. ; Kumburu, H. ; van Zwetselaar, M. ; Alifrangis, M. ; Mmbaga, B. ; Lund, Ole ; Aarestrup, Frank Møller ; Kibiki, G.
in: Tropical Medicine & International Health, vol: 22, issue: Suppl. 1, pages: 187
Presented at:
10th European Congress on Tropical Medicine and International Health

Type: Conference abstract in journal (Peer reviewed)

Status: Published     |    Year: 2017

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RUCS: Rapid identification of PCR primers for unique core sequences

Thomsen, Martin Christen Frølund ; Hasman, Henrik ; Westh, Henrik ; Kaya, Hülya ; Lund, Ole
in: Bioinformatics, vol: 33, issue: 24, pages: 3917-3921

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1093/bioinformatics/btx526

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Sequencing and de novo assembly of 150 genomes from Denmark as a population reference

Maretty, Lasse ; Jensen, Jacob Malte ; Petersen, Bent ; Sibbesen, Jonas Andreas ; Liu, Siyang ; Villesen, Palle ; Skov, Laurits ; Belling, Kirstine González-Izarzugaza ; Theil Have, Christian ; Gonzalez-Izarzugaza, Jose Maria ; Grosjean, Marie ; Bork-Jensen, Jette ; Grove, Jakob ; Als, Thomas D. ; Huang, Shujia ; Chang, Yuqi ; Xu, Ruiqi ; Ye, Weijian ; Rao, Junhua ; Guo, Xiaosen ; Sun, Jihua ; Cao, Hongzhi ; Ye, Chen ; van Beusekom, Johan ; Espeseth, Thomas ; Flindt, Esben N. ; Friborg, Rune M. ; Halager, Anders E. ; Le Hellard, Stephanie ; Hultman, Christina M. ; Lescai, Francesco ; Li, Shengting ; Lund, Ole ; Løngreen, Peter ; Mailund, Thomas ; Matey-Hernandez, María Luisa ; Mors, Ole ; Pedersen, Christian N. S. ; Sicheritz-Pontén, Thomas ; Sullivan, Patrick F. ; Syed, Ali ; Westergaard, David ; Yadav, Rachita ; Li, Ning ; Xu, Xun ; Hansen, Torben ; Krogh, Anders ; Bolund, Lars ; Sørensen, Thorkild I. A. ; Pedersen, Oluf ; Gupta, Ramneek ; Rasmussen, Simon ; Besenbacher, Søren ; Börglum, Anders D. ; Wang, Jun ; Eiberg, Hans ; Kristiansen, Karsten ; Brunak, Søren ; Schierup, Mikkel Heide
in: Nature, vol: 548, pages: 87-91

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1038/nature23264

 

The CGE Tool Box

Larsen, Mette Voldby ; Joensen, Katrine Grimstrup ; Zankari, Ea ; Ahrenfeldt, Johanne ; Lukjancenko, Oksana ; Kaas, Rolf Sommer ; Roer, Louise ; Leekitcharoenphon, Pimlapas ; Saputra, Dhany ; Cosentino, S. ; Thomsen, Martin Christen Frølund ; Bellod Cisneros, Jose Luis ; Jurtz, Vanessa Isabell ; Rasmussen, Simon ; Petersen, Thomas Nordahl ; Hasman, Henrik ; Sicheritz-Pontén, Thomas ; Aarestrup, Frank Møller ; Lund, Ole
part of: Applied Genomics of Foodborne Pathogens, pages: 65-90, 2017, Springer, Switzerland

Type: Book chapter (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1007/978-3-319-43751-4_5

2016
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Application of WGS data for O-specific antigen analysis and in silico serotyping of Pseudomonas aeruginosa isolates

Thrane, Sandra Wingaard ; Taylor, Véronique L. ; Lund, Ole ; Lam, Joseph S. ; Jelsbak, Lars
in: Journal of Clinical Microbiology, vol: 54, issue: 7, pages: 1782-1788

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1128/JCM.00349-16


https://www.bioinformatics.dtu.dk/research2018/research-groups/genomic-epidemiology1/gruppens-publikationer
20 SEPTEMBER 2019