Publications from the Genomic Epidemiology Research Group

A compartmental model to investigate the dynamics of the COVID-19 pandemic: A case study in five countries

Apenteng, Ofosuhene Okofrobour ; Oduro, Bismark ; Owusu-Mensah, Isaac
in: International Journal of Biomathematics

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2021 | DOI: https://doi.org/10.1142/S1793524521500273

A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes

VanOeffelen, Margo ; Nguyen, Marcus ; Aytan-Aktug, Derya ; Brettin, Thomas ; Dietrich, Emily M ; Kenyon, Ronald W. ; Machi, Dustin ; Mao, Chunhong ; Olson, Robert ; Pusch, Gordon D ; Shukla, Maulik ; Stevens, Rick ; Vonstein, Veronika ; Warren, Andrew S. ; Wattam, Alice R. ; Yoo, Hyunseung ; Davis, James J.
in: Briefings in Bioinformatics

Type: Review (Peer reviewed)

Status: Accepted/In press | Year: 2021 | DOI: https://doi.org/10.1093/bib/bbab313

Antimicrobial PDMS Surfaces Prepared through Fastand Oxygen-Tolerant SI-SARA-ATRP, Using Na₂SO₃ as a Reducing Agent

Andersen, Christian ; Zverina, Libor ; Ehtiati, Koosha ; Thormann, Esben ; Mordhorst, Hanne ; Pamp, Sünje J. ; Madsen, Niels J. ; Daugaard, Anders E.
in: ACS Omega, vol: 6, issue: 22, pages: 14551–14558

Type: Journal article (Peer reviewed)

Status: Published | Year: 2021 | DOI: https://doi.org/10.1021/acsomega.1c01611

A Peek into the Plasmidome of Global Sewage

Kirstahler, Philipp ; Teudt, Frederik ; Otani, Saria ; Aarestrup, Frank Møller ; Pamp, Sünje Johanna
in: mSystems, vol: 6, issue: 3

Type: Journal article (Peer reviewed)

Status: Published | Year: 2021 | DOI: https://doi.org/10.1101/2021.03.08.434362

A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing

Petrillo, Mauro ; Fabbri, Marco ; Kagkli, Dafni Maria ; Querci, Maddalena ; Van den Eede, Guy ; Alm, Erik ; Aytan, Derya ; Capella-Gutierrez, Salvador ; Carrillo, Catherine ; Cestaro, Alessandro ; Chan, Kok-Gan ; Coque, Teresa ; Endrullat, Christoph ; Gut, Ivo ; Hammer, Paul ; Kay, Gemma L. ; Madec, Jean-Yves ; Mather, Alison E. ; McHardy, Alice Carolyn ; Naas, Thierry ; Paracchini, Valentina ; Peter, Silke ; Pightling, Arthur ; Raffael, Barbara ; Rossen, John ; Ruppé, Etienne ; Schlaberg, Robert ; Vanneste, Kevin ; Weber, Lukas ; Westh, Henrik ; Angers-Loustau, Alexandre
in: F1000Research, vol: 10

Type: Journal article (Peer reviewed)

Status: Published | Year: 2021 | DOI: https://doi.org/10.12688/f1000research.39214.1

Article outcome of different sequencing and assembly approaches on the detection of plasmids and localization of antimicrobial resistance genes in commensal escherichia coli

Juraschek, Katharina ; Borowiak, Maria ; Tausch, Simon H. ; Malorny, Burkhard ; Käsbohrer, Annemarie ; Otani, Saria ; Schwarz, Stefan ; Meemken, Diana ; Deneke, Carlus ; Hammerl, Jens Andre
in: Microorganisms, vol: 9, issue: 3

Type: Journal article (Peer reviewed)

Status: Published | Year: 2021 | DOI: https://doi.org/10.3390/microorganisms9030598

Attribution of illnesses transmitted by food and water to comprehensive transmission pathways using structured expert judgment, United States

Beshearse, Elizabeth ; Bruce, Beau B. ; Nane, Gabriela F. ; Cooke, Roger M. ; Aspinall, Willy ; Hald, Tine ; Crim, Stacy M. ; Griffin, Patricia M. ; Fullerton, Kathleen E. ; Collier, Sarah A. ; Benedict, Katharine M. ; Beach, Michael J. ; Hall, Aron J. ; Havelaar, Arie H.
in: Emerging Infectious Diseases , vol: 27, issue: 1, pages: 182-195

Type: Journal article (Peer reviewed)

Status: Published | Year: 2021 | DOI: https://doi.org/10.3201/eid2701.200316

Automated download and clean-up of family specific databases for kmer-based virus identification

Allesøe, Rosa Lundbye ; Lemvigh, Camilla Koldbæk ; Phan, My V T ; Clausen, Philip Thomas Lanken Conradsen ; Florensa, Alfred Ferrer ; Koopmans, Marion P G ; Lund, Ole ; Cotten, Matthew
in: Bioinformatics, vol: 37, issue: 5, pages: 705–710

Type: Journal article (Peer reviewed)

Status: Published | Year: 2021 | DOI: https://doi.org/10.1093/bioinformatics/btaa857

Burden of foodborne diseases

Pires, Sara Monteiro ; Desta, Binyam N. ; Mughini-Gras, Lapo ; Mmbaga, Blandina T. ; Fayemi, Olanrewaju E. ; Salvador, Elsa M. ; Gobena, Tesfaye ; Majowicz, Shannon E. ; Hald, Tine ; Hoejskov, Peter S. ; Minato, Yuki ; Devleesschauwer, Brecht
in: Current Opinion in Food Science, vol: 39, pages: 152-159

Type: Review (Peer reviewed)

Status: Published | Year: 2021 | DOI: https://doi.org/10.1016/j.cofs.2021.01.006

Campylobacter jejuni ST50, a pathogen of global importance

Wallace, Rhiannon L. ; Cribb, Danielle M. ; Bulach, Dieter M. ; Ingle, Danielle J. ; Joensen, Katrine G. ; Nielsen, Eva Møller ; Leekitcharoenphon, Pimlapas ; Stingl, Kerstin ; Kirk, Martyn D.
in: Zoonoses and Public Health

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2021 | DOI: https://doi.org/10.1111/zph.12853