Publications

 

Publikationer rss feed

2018
 

The medical threat of mamba envenoming in sub-Saharan Africa revealed by genus-wide analysis of venom composition, toxicity and antivenomics profiling of available antivenoms

Ainsworth, Stuart ; Petras, Daniel ; Engmark, Mikael ; Süssmuth, Roderich D. ; Whiteley, Gareth ; Albulescu, Laura-Oana ; Kazandjian, Taline D. ; Wagstaff, Simon C. ; Rowley, Paul ; Wüster, Wolfgang ; Dorrestein, Pieter C. ; Arias, Ana Silvia ; M. Gutierrez, Jose ; Harrison, Robert ; Casewell, Nicholas R. ; Calvete, Juan J.
in journal: Journal of Proteomics (ISSN: 1874-3919) (DOI: http://dx.doi.org/10.1016/j.jprot.2017.08.016), vol: 172, pages: 173-189, 2018

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: http://dx.doi.org/10.1016/j.jprot.2017.08.016

 

Molecular profiling of short-term and long-term surviving patients identifies CD34 mRNA level as prognostic for glioblastoma survival

Michaelsen, Signe Regner ; Urup, Thomas ; Olsen, Lars Rønn ; Broholm, Helle ; Lassen, Ulrik ; Poulsen, Hans Skovgaard
in journal: Journal of Neuro-Oncology (ISSN: 0167-594X) (DOI: http://dx.doi.org/10.1007/s11060-017-2739-7), 2018

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2018     |    DOI: http://dx.doi.org/10.1007/s11060-017-2739-7

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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: Journal of Biomedicine and Biotechnology (ISSN: 1110-7243) (DOI: http://dx.doi.org/10.1155/2018/2087693), vol: 2018, 2018

Type: Journal article (Peer reviewed)

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

2017
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FurIOS: a web-based tool for identification of Vibrionaceae species using the fur gene

Machado, Henrique ; Cardoso, Joao ; Giubergia, Sonia ; Rapacki, Kristoffer ; Gram, Lone
in journal: BMC Microbiology (ISSN: 1471-2180) (DOI: http://dx.doi.org/10.3389/fmicb.2017.00414), vol: 8, 2017

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: http://dx.doi.org/10.3389/fmicb.2017.00414

 

A scored human protein-protein interaction network to catalyze genomic interpretation

Li, Taibo ; Wernersson, Rasmus ; Hansen, Rasmus B ; Horn, Heiko ; Mercer, Johnathan ; Slodkowicz, Grzegorz ; Workman, Christopher ; Rigina, Olga ; Rapacki, Kristoffer ; Stærfeldt, Hans Henrik ; Brunak, Søren ; Jensen, Thomas S. ; Lage, Kasper
in journal: Nature Methods (ISSN: 1548-7091) (DOI: http://dx.doi.org/10.1038/nmeth.4083), vol: 14, pages: 61–64, 2017

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: http://dx.doi.org/10.1038/nmeth.4083

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Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods

Ahrenfeldt, Johanne ; Skaarup, Carina ; Hasman, Henrik ; Pedersen, Anders Gorm ; Aarestrup, Frank Møller ; Lund, Ole
in journal: BMC Genomics (ISSN: 1471-2164) (DOI: http://dx.doi.org/10.1186/s12864-016-3407-6), vol: 18, 2017

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: http://dx.doi.org/10.1186/s12864-016-3407-6

 

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 journal: Tropical Medicine & International Health (ISSN: 1360-2276) (DOI: http://dx.doi.org/10.1111/tmi.12836), vol: 22, issue: 4, pages: 454-464, 2017

Type: Journal article (Peer reviewed)

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

 

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 journal: Clinical Microbiology and Infection (ISSN: 1198-743X) (DOI: http://dx.doi.org/10.1016/j.cmi.2016.12.035), vol: 23, issue: 6, 2017

Type: Journal article (Peer reviewed)

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

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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 Wairimu ; 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 journal: Scientific Reports (ISSN: 2045-2322) (DOI: http://dx.doi.org/10.1038/srep4035), vol: 7, 2017

Type: Journal article (Peer reviewed)

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

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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 journal: P L o S One (ISSN: 1932-6203) (DOI: http://dx.doi.org/10.1371/journal.pone.0168453), vol: 12, issue: 1, 2017

Type: Journal article (Peer reviewed)

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

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Exploration of immunoglobulin transcriptomes from mice immunized with three-finger toxins and phospholipases A2 from the Central American coral snake, Micrurus nigrocinctus

Laustsen, Andreas Hougaard ; Engmark, Mikael ; Clouser, Christopher ; Timberlake, Sonia ; Vigneault, Francois ; Gutiérrez, José María ; Lomonte, Bruno
in journal: PeerJ (ISSN: 2167-8359) (DOI: http://dx.doi.org/10.7717/peerj.2924), vol: 5, 2017

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: http://dx.doi.org/10.7717/peerj.2924

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Recombinant snakebite antivenoms: A cost-competitive solution to a neglected tropical disease?

Laustsen, Andreas Hougaard ; Johansen, Kristoffer H. ; Engmark, Mikael ; Andersen, Mikael Rørdam
in journal: P L o S Neglected Tropical Diseases (Online) (ISSN: 1935-2735) (DOI: http://dx.doi.org/10.1371/journal.pntd.0005361), vol: 11, issue: 2, 2017

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: http://dx.doi.org/10.1371/journal.pntd.0005361

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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 journal: European Journal of Clinical Microbiology & Infectious Diseases (ISSN: 0934-9723) (DOI: http://dx.doi.org/10.1007/s10096-017-2947-2), vol: 36, issue: 7, pages: 1325-1338, 2017

Type: Journal article (Peer reviewed)

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

 

WGS-based surveillance of third-generation cephalosporin-resistant Escherichia coli from bloodstream infections in Denmark

Roer, Louise ; Hansen, Frank ; Thomsen, Martin Christen Frølund ; Knudsen, Jenny Dahl ; Hansen, Dennis Schrøder ; Wang, Mikala ; Samulioniené, Jurgita ; Justesen, Ulrik Stenz ; Røder, Bent L ; Schumacher, Helga ; Østergaard, Claus ; Andersen, Leif Percival ; Dzajic, Esad ; Søndergaard, Turid Snekloth ; Stegger, Marc ; Hammerum, Anette Marie ; Hasman, Henrik
in journal: Journal of Antimicrobial Chemotherapy (ISSN: 0305-7453) (DOI: http://dx.doi.org/10.1093/jac/dkx092), vol: 72, pages: 1922-1929, 2017

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: http://dx.doi.org/10.1093/jac/dkx092

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MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads

Petersen, Thomas Nordahl ; Lukjancenko, Oksana ; Thomsen, Martin Christen Frølund ; Sperotto, Maria Maddalena ; Lund, Ole ; Aarestrup, Frank Møller ; Sicheritz-Pontén, Thomas
in journal: P L o S One (ISSN: 1932-6203) (DOI: http://dx.doi.org/10.1371/journal.pone.0176469), vol: 12, issue: 5, 2017

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: http://dx.doi.org/10.1371/journal.pone.0176469

 

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 journal: European Journal of Clinical Microbiology & Infectious Diseases (ISSN: 0934-9723) (DOI: http://dx.doi.org/10.1007/s10096-017-2993-9), vol: 36, issue: 7, pages: 1339-1342, 2017

Type: Journal article (Peer reviewed)

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

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Transcriptional changes induced by bevacizumab combination therapy in responding and non-responding recurrent glioblastoma patients

Urup, Thomas ; Staunstrup, Line Maersk ; Michaelsen, Signe Regner ; Vitting-Seerup, Kristoffer ; Bennedbaek, Marc ; Toft, Anders ; Olsen, Lars Rønn ; Jønson, Lars ; Issazadeh-Navikas, Shohreh ; Broholm, Helle ; Hamerlik, Petra ; Poulsen, Hans Skovgaard ; Lassen, Ulrik
in journal: B M C Cancer (ISSN: 1471-2407) (DOI: http://dx.doi.org/10.1186/s12885-017-3251-3), vol: 17, 2017

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: http://dx.doi.org/10.1186/s12885-017-3251-3

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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 journal: Scientific Reports (ISSN: 2045-2322) (DOI: http://dx.doi.org/10.1038/s41598-017-02724-x), vol: 7, issue: 1, 2017

Type: Journal article (Peer reviewed)

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

 

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: Journal of Clinical Microbiology (ISSN: 0095-1137) (DOI: http://dx.doi.org/10.1128/JCM.00737-17), vol: 55, issue: 8, pages: 2538-2543, 2017

Type: Journal article (Peer reviewed)

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

 

TANTIGEN: a comprehensive database of tumor T cell antigens

Olsen, Lars Rønn ; Tongchusak, Songsak ; Lin, Honghuang ; Reinherz, Ellis L. ; Brusic, Vladimir ; Zhang, Guang Lan
in journal: Cancer Immunology Immunotherapy (ISSN: 0340-7004) (DOI: http://dx.doi.org/10.1007/s00262-017-1978-y), vol: 66, pages: 731-735, 2017

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: http://dx.doi.org/10.1007/s00262-017-1978-y

 

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: http://dx.doi.org/10.1007/978-3-319-43751-4_5

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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 journal: Nature (ISSN: 0028-0836) (DOI: http://dx.doi.org/10.1038/nature23264), vol: 548, pages: 87-91, 2017

Type: Journal article (Peer reviewed)

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

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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 journal: P L o S Neglected Tropical Diseases (Print) (ISSN: 1935-2727) (DOI: http://dx.doi.org/10.1371/journal.pntd.0005768), vol: 11, issue: 7, 2017

Type: Journal article (Peer reviewed)

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

 

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 journal: Toxicon (ISSN: 0041-0101) (DOI: http://dx.doi.org/10.1016/j.toxicon.2017.08.028), vol: 138, pages: 151-158, 2017

Type: Journal article (Peer reviewed)

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

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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: Journal of Antimicrobial Chemotherapy (ISSN: 0305-7453) (DOI: http://dx.doi.org/10.1093/jac/dkx217), vol: 72, issue: 10, pages: 2764-2768, 2017

Type: Journal article (Peer reviewed)

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

 

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 journal: Scandinavian Journal of Immunology (ISSN: 0300-9475), vol: 86, issue: 4, pages: 318, 2017
Presented at:
44th Annual Meeting of the Scandinavian Society of Immunology, 2017, Stockholm

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 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 journal: P L o S Genetics (ISSN: 1553-7390) (DOI: http://dx.doi.org/10.1371/journal.pgen.1006834), vol: 13, issue: 8, 2017

Type: Journal article (Peer reviewed)

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

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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 journal: Bioinformatics (ISSN: 1367-4803) (DOI: http://dx.doi.org/10.1093/bioinformatics/btx526), vol: 33, issue: 24, pages: 3917-3921, 2017

Type: Journal article (Peer reviewed)

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

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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 journal: Eurosurveillance (Print) (ISSN: 1025-496X) (DOI: http://dx.doi.org/10.2807/1560-7917.ES.2017.22.42.17-00659), vol: 22, issue: 42, 2017

Type: Journal article (Peer reviewed)

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

 

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 journal: Tropical Medicine & International Health (ISSN: 1360-2276), vol: 22, issue: S1, pages: 359-359, 2017
Presented at:
10th European Congress on Tropical Medicine and International Health, 2017, Antwerp

Type: Conference abstract in journal (Peer reviewed)

Status: Published     |    Year: 2017

 

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 journal: Tropical Medicine & International Health (ISSN: 1360-2276), vol: 22, issue: S1, pages: 360-360, 2017
Presented at:
10th European Congress on Tropical Medicine and International Health, 2017, Antwerp

Type: Conference abstract in journal (Peer reviewed)

Status: Published     |    Year: 2017

 

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 journal: Tropical Medicine & International Health (ISSN: 1360-2276), vol: 22, issue: Suppl. 1, pages: 187, 2017
Presented at:
10th European Congress on Tropical Medicine and International Health, 2017, Antwerp

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, Frank Møller
in journal: Tropical Medicine & International Health (ISSN: 1360-2276), vol: 22, issue: Suppl. 1, pages: 34, 2017

Type: Conference abstract in journal (Peer reviewed)

Status: Published     |    Year: 2017

 

PATH-01. Identification of Prognastic Variables Based on Molecular Profiling of Long-Term and Short-Term Surviving Gglioblastoma Patients

Michaelsen, Signe Regner ; Urup, Thomas ; Olsen, Lars Rønn ; Gillberg, Linn ; Broholm, Helle ; Grunnet, Kirsten ; Grønbæk, Kirsten ; Hamerlik, Petra ; Lassen, Ulrik ; Poulsen, Hans Skovgaard
in journal: Neuro-Oncology (ISSN: 1522-8517) (DOI: http://dx.doi.org/10.1093/neuonc/nox168.692), vol: 19, issue: suppl_6, pages: vi170-vi170, 2017
Presented at:
22nd Annual Scientific Meeting and Education Day of the Society for Neuro-Oncology , 2017, San Fransisco

Type: Conference abstract in journal (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: http://dx.doi.org/10.1093/neuonc/nox168.692

 

Comparison of CyTOF assays across sites

Leipold, Michael D. ; Obermoser, Gerlinde ; Fenwick, Craig ; Kleinstuber, Katja ; Rashidi, Narges ; McNevin, John P. ; Nau, Allison N. ; Wagar, Lisa E. ; Rozot, Virginie ; Davis, Mark M. ; DeRosa, Stephen ; Pantaleo, Giuseppe ; Scriba, Thomas J. ; Walker, Bruce D. ; Olsen, Lars Rønn ; Maecker, Holden T.
in journal: Journal of Immunological Methods (ISSN: 0022-1759) (DOI: http://dx.doi.org/10.1016/j.jim.2017.11.008), 2017

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2017     |    DOI: http://dx.doi.org/10.1016/j.jim.2017.11.008

2016
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Using registries to integrate bioinformatics tools and services into workbench environments

Ménager, Hervé ; Kalaš, Matúš ; Rapacki, Kristoffer ; Ison, Jon
in journal: International Journal on Software Tools for Technology Transfer (ISSN: 1433-2779) (DOI: http://dx.doi.org/10.1007/s10009-015-0392-z), vol: 18, issue: 6, pages: 581-586, 2016

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: http://dx.doi.org/10.1007/s10009-015-0392-z

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Tools and data services registry

Ison, Jon ; Rapacki, Kristoffer ; Ménager, Hervé ; Kalaš, Matúš ; Rydza, Emil Karol ; Chmura, Piotr Jaroslaw ; Anthon, Christian ; Beard, Niall ; Berka, Karel ; Bolser, Dan ; Booth, Tim ; Bretaudeau, Anthony ; Brezovsky, Jan ; Casadio, Rita ; Cesareni, Gianni ; Coppens, Frederik ; Cornell, Michael ; Cuccuru, Gianmauro ; Davidsen, Kristian ; Vedova, Gianluca Della ; Dogan, Tunca ; Doppelt-Azeroual, Olivia ; Emery, Laura ; Gasteiger, Elisabeth ; Gatter, Thomas ; Goldberg, Tatyana ; Grosjean, Marie ; Grüning, Björn ; Helmer-Citterich, Manuela ; Ienasescu, Hans ; Ioannidis, Vassilios ; Jespersen, Martin Closter ; Jimenez, Rafael ; Juty, Nick ; Juvan, Peter ; Koch, Maximilian ; Laibe, Camille ; Li, Jing-Woei ; Licata, Luana ; Mareuil, Fabien ; Mičetić, Ivan ; Friborg, Rune Møllegaard ; Moretti, Sebastien ; Morris, Chris ; Möller, Steffen ; Nenadic, Aleksandra ; Peterson, Hedi ; Profiti, Giuseppe ; Rice, Peter ; Romano, Paolo ; Roncaglia, Paola ; Saidi, Rabie ; Schafferhans, Andrea ; Schwämmle, Veit ; Smith, Callum ; Sperotto, Maria Maddalena ; Stockinger, Heinz ; Vařeková, Radka Svobodová ; Tosatto, Silvio C. E. ; de la Torre, Victor ; Uva, Paolo ; Via, Allegra ; Yachdav, Guy ; Zambelli, Federico ; Vriend, Gert ; Rost, Burkhard ; Parkinson, Helen ; Løngreen, Peter ; Brunak, Søren
in journal: Nucleic Acids Research (ISSN: 0305-1048) (DOI: http://dx.doi.org/10.1093/nar/gkv1116), vol: 44, issue: D1, pages: D38-D47, 2016

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: http://dx.doi.org/10.1093/nar/gkv1116

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Propionibacterium acnes: disease-causing agent or common contaminant? Detection in diverse patient samples by next generation sequencing

Mollerup, Sarah ; Friis-Nielsen, Jens ; Vinner, Lasse ; Richter, Stine Raith ; Fridholm, Helena ; Herrera, Jose Romero ; Lund, Ole ; Brunak, Søren ; Gonzalez-Izarzugaza, Jose Maria ; Mourier, Tobias ; Nielsen, Lars Peter ; Hansen, Anders Johannes
in journal: Journal of Clinical Microbiology (ISSN: 0095-1137) (DOI: http://dx.doi.org/10.1128/jcm.02723-15), vol: 54, issue: 4, pages: 980-987, 2016

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: http://dx.doi.org/10.1128/jcm.02723-15

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Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers

Friis-Nielsen, Jens ; Kjartansdóttir, Kristín Rós ; Mollerup, Sarah ; Asplund, Maria ; Mourier, Tobias ; Holm Jensen, Randi ; Arn Hansen, Thomas ; Rey-Iglesia, Alba ; Vinner, Lasse ; Fridholm, Helena ; Nielsen, Lars Peter ; Willerslev, Eske ; Sicheritz-Pontén, Thomas ; Lund, Ole ; Hansen, Anders Johannes ; Gonzalez-Izarzugaza, Jose Maria ; Brunak, Søren
in journal: Viruses (ISSN: 1999-4915) (DOI: http://dx.doi.org/10.3390/v8020053), vol: 8, issue: 53, 2016

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: http://dx.doi.org/10.3390/v8020053

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ChemProt-3.0: a global chemical biology diseases mapping

Kringelum, Jens Vindahl ; Kjærulff, Sonny Kim ; Brunak, Søren ; Lund, Ole ; Oprea, Tudor ; Taboureau, Olivier
in journal: Database (ISSN: 1758-0463) (DOI: http://dx.doi.org/10.1093/database/bav123), vol: 2016, 2016

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: http://dx.doi.org/10.1093/database/bav123

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Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104

Leekitcharoenphon, Pimlapas ; Hendriksen, Rene S. ; Le Hello, Simon ; Weill, François-Xavier ; Baggesen, Dorte Lau ; Jun, Se-Ran ; Ussery, David ; Lund, Ole ; Crook, Derrick W ; Wilson, Daniel J ; Aarestrup, Frank Møller
in journal: Applied and Environmental Microbiology (ISSN: 0099-2240) (DOI: http://dx.doi.org/10.1128/AEM.03821-15), vol: 82, issue: 8, pages: 2516-2526, 2016

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: http://dx.doi.org/10.1128/AEM.03821-15

 

Benchtop Whole-Genome Sequencing for Identification of Nosocomial Outbreaks in Tanzania

Sonda, Tolbert ; Kumburu, Happiness ; Zwetselaar, Marco van ; Ahrenfeldt, Johanne ; Alifrangis, Michael ; Lund, Ole ; Kibiki, Gibson ; Aarestrup, Frank Møller
in journal: Infection Control & Hospital Epidemiology (ISSN: 0899-823X) (DOI: http://dx.doi.org/10.1017/ice.2016.28), vol: 37, issue: 5, pages: 622-623, 2016

Type: Comment/debate (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: http://dx.doi.org/10.1017/ice.2016.28

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Highlights from the eleventh ISCB Student Council Symposium 2015

Wilkins, Katie ; Hassan, Mehedi ; Francescatto, Margherita ; Jespersen, Jakob Berg ; Gonzalo Parra, R. ; Cuypers, Bart ; DeBlasio, Dan ; Junge, Alexander ; Jigisha, Anupama ; Rahman, Farzana
in journal: B M C Bioinformatics (ISSN: 1471-2105) (DOI: http://dx.doi.org/10.1186/s12859-016-0901-4), vol: 17, issue: Suppl. 3, pages: 203-205, 2016

Type: Conference abstract in journal (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: http://dx.doi.org/10.1186/s12859-016-0901-4

 

A comprehensive profile of recurrent glioblastoma

Campos, B. ; Olsen, Lars Rønn ; Urup, T. ; Poulsen, H. S.
in journal: Oncogene (ISSN: 0950-9232) (DOI: http://dx.doi.org/10.1038/onc.2016.85), vol: 35, pages: 5819-5825, 2016

Type: Review (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: http://dx.doi.org/10.1038/onc.2016.85

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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: Journal of Clinical Microbiology (ISSN: 0095-1137) (DOI: http://dx.doi.org/10.1128/JCM.00349-16), vol: 54, issue: 7, pages: 1782-1788, 2016

Type: Journal article (Peer reviewed)

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

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A Bacterial Analysis Platform: An Integrated System for Analysing Bacterial Whole Genome Sequencing Data for Clinical Diagnostics and Surveillance

Thomsen, Martin Christen Frølund ; Ahrenfeldt, Johanne ; Bellod Cisneros, Jose Luis ; Jurtz, Vanessa Isabell ; Larsen, Mette Voldby ; Hasman, Henrik ; Aarestrup, Frank Møller ; Lund, Ole
in journal: P L o S One (ISSN: 1932-6203) (DOI: http://dx.doi.org/10.1371/journal.pone.0157718), vol: 11, issue: 6, 2016

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: http://dx.doi.org/10.1371/journal.pone.0157718

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HostPhinder: A Phage Host Prediction Tool

Villarroel, Julia ; Kleinheinz, Kortine Annina ; Jurtz, Vanessa Isabell ; Zschach, Henrike ; Lund, Ole ; Nielsen, Morten ; Larsen, Mette Voldby
in journal: Viruses (ISSN: 1999-4915) (DOI: http://dx.doi.org/10.3390/v8050116), vol: 8, issue: 5, 2016

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: http://dx.doi.org/10.3390/v8050116

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Angiotensinogen and HLA class II predict bevacizumab response in recurrent glioblastoma patients

Urup, Thomas ; Michaelsen, Signe Regner ; Olsen, Lars Rønn ; Toft, Anders ; Christensen, Ib Jarle ; Grunnet, Kirsten ; Winther, Ole ; Broholm, Helle ; Kosteljanetz, Michael ; Issazadeh-Navikas, Shohreh ; Poulsen, Hans Skovgaard ; Lassen, Ulrik
in journal: Molecular Oncology (ISSN: 1574-7891) (DOI: http://dx.doi.org/10.1016/j.molonc.2016.05.005), vol: 10, issue: 8, pages: 1160-1168, 2016

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: http://dx.doi.org/10.1016/j.molonc.2016.05.005

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Meta-analysis of proportion estimates of Extended-Spectrum-Beta-Lactamase-producing Enterobacteriaceae in East Africa hospitals

Sonda, Tolbert ; Kumburu, Happiness ; van Zwetselaar, Marco ; Alifrangis, Michael ; Lund, Ole ; Kibiki, Gibson ; Aarestrup, Frank Møller
in journal: Antimicrobial Resistance and Infection Control (ISSN: 2047-2994) (DOI: http://dx.doi.org/10.1186/s13756-016-0117-4), vol: 5, 2016

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: http://dx.doi.org/10.1186/s13756-016-0117-4


http://www.bioinformatics.dtu.dk/english/research_new/metagenomics-and-epidemiology/genomic-epidemiology/gruppens-publikationer
22 JANUARY 2018