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Genetic structure of SARS-CoV-2 reflects clonal superspreading and multiple independent introduction events, North-Rhine Westphalia, Germany, February and March 2020.
Published in:
Eurosurveillance (15607917), 2020, v. 25, n. 22, p. 19, doi. 10.2807/1560-7917.ES.2020.25.22.2000746
By:
- Walker, Andreas;
- Houwaart, Torsten;
- Wienemann, Tobias;
- Kohns Vasconcelos, Malte;
- Strelow, Daniel;
- Senff, Tina;
- Hülse, Lisanna;
- Adams, Ortwin;
- Andree, Marcel;
- Hauka, Sandra;
- Feldt, Torsten;
- Jensen, Björn-Erik;
- Keitel, Verena;
- Kindgen-Milles, Detlef;
- Timm, Jörg;
- Pfeffer, Klaus;
- Dilthey, Alexander T.
Publication type:
Article
Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing.
Published in:
Nucleic Acids Research, 2018, v. 46, n. 13, p. 6712, doi. 10.1093/nar/gky442
By:
- Kim, Jung-Hyun;
- Dilthey, Alexander T;
- Nagaraja, Ramaiah;
- Lee, Hee-Sheung;
- Koren, Sergey;
- Dudekula, Dawood;
- Wood III, William H;
- Piao, Yulan;
- Ogurtsov, Aleksey Y;
- Utani, Koichi
Publication type:
Article
De novo assembly of haplotype-resolved genomes with trio binning.
Published in:
Nature Biotechnology, 2018, v. 36, n. 12, p. 1174, doi. 10.1038/nbt.4277
By:
- Koren, Sergey;
- Rhie, Arang;
- Walenz, Brian P;
- Dilthey, Alexander T;
- Bickhart, Derek M;
- Kingan, Sarah B;
- Hiendleder, Stefan;
- Williams, John L;
- Smith, Timothy P L;
- Phillippy, Adam M
Publication type:
Article
Nanopore sequencing and assembly of a human genome with ultra-long reads.
Published in:
Nature Biotechnology, 2018, v. 36, n. 4, p. 338, doi. 10.1038/nbt.4060
By:
- Jain, Miten;
- Koren, Sergey;
- Miga, Karen H;
- Quick, Josh;
- Rand, Arthur C;
- Sasani, Thomas A;
- Tyson, John R;
- Beggs, Andrew D;
- Dilthey, Alexander T;
- Fiddes, Ian T;
- Malla, Sunir;
- Marriott, Hannah;
- Nieto, Tom;
- O'Grady, Justin;
- Olsen, Hugh E;
- Pedersen, Brent S;
- Rhie, Arang;
- Richardson, Hollian;
- Quinlan, Aaron R;
- Snutch, Terrance P
Publication type:
Article
SARS‐CoV‐2 targets neurons of 3D human brain organoids.
Published in:
EMBO Journal, 2020, v. 39, n. 20, p. 1, doi. 10.15252/embj.2020106230
By:
- Ramani, Anand;
- Müller, Lisa;
- Ostermann, Philipp N;
- Gabriel, Elke;
- Abida‐Islam, Pranty;
- Müller‐Schiffmann, Andreas;
- Mariappan, Aruljothi;
- Goureau, Olivier;
- Gruell, Henning;
- Walker, Andreas;
- Andrée, Marcel;
- Hauka, Sandra;
- Houwaart, Torsten;
- Dilthey, Alexander;
- Wohlgemuth, Kai;
- Omran, Heymut;
- Klein, Florian;
- Wieczorek, Dagmar;
- Adams, Ortwin;
- Timm, Jörg
Publication type:
Article
Improved genome inference in the MHC using a population reference graph.
Published in:
Nature Genetics, 2015, v. 47, n. 6, p. 682, doi. 10.1038/ng.3257
By:
- Dilthey, Alexander;
- Iqbal, Zamin;
- McVean, Gil;
- Cox, Charles;
- Nelson, Matthew R
Publication type:
Article
Genetics of gene expression in primary immune cells identifies cell type-specific master regulators and roles of HLA alleles.
Published in:
Nature Genetics, 2012, v. 44, n. 5, p. 502, doi. 10.1038/ng.2205
By:
- Fairfax, Benjamin P;
- Makino, Seiko;
- Radhakrishnan, Jayachandran;
- Plant, Katharine;
- Leslie, Stephen;
- Dilthey, Alexander;
- Ellis, Peter;
- Langford, Cordelia;
- Vannberg, Fredrik O;
- Knight, Julian C
Publication type:
Article
Interaction between ERAP1 and HLA-B27 in ankylosing spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease susceptibility.
Published in:
Nature Genetics, 2011, v. 43, n. 8, p. 761, doi. 10.1038/ng.873
By:
- Evans, David M.;
- Spencer, Chris C. A.;
- Pointon, Jennifer J.;
- Zhan Su;
- Harvey, David;
- Kochan, Grazyna;
- Opperman, Udo;
- Dilthey, Alexander;
- Pirinen, Matti;
- Stone, Millicent A.;
- Appleton, Louise;
- Moutsianis, Loukas;
- Leslie, Stephen;
- Wordsworth, Tom;
- Kenna, Tony J.;
- Karaderi, Tugce;
- Thomas, Gethin P.;
- AWard, Michael M.;
- Weisman, Michael H.;
- Farrar, Claire
Publication type:
Article
A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1.
Published in:
Nature Genetics, 2010, v. 42, n. 11, p. 985, doi. 10.1038/ng.694
By:
- Strange, Amy;
- Capon, Francesca;
- Spencer, Chris C. A.;
- Knight, Jo;
- Weale, Michael E.;
- Allen, Michael H.;
- Barton, Anne;
- Band, Gavin;
- Bellenguez, Céline;
- Bergboer, Judith G. M.;
- Blackwell, Jenefer M.;
- Bramon, Elvira;
- Bumpstead, Suzannah J.;
- Casas, Juan P.;
- Cork, Michael J.;
- Corvin, Aiden;
- Deloukas, Panos;
- Dilthey, Alexander;
- Duncanson, Audrey;
- Edkins, Sarah
Publication type:
Article
An appeal for strengthening genomic pathogen surveillance to improve pandemic preparedness and infection prevention: the German perspective.
Published in:
Infection, 2023, v. 51, n. 4, p. 805, doi. 10.1007/s15010-023-02040-9
By:
- Salzberger, Bernd;
- Mellmann, Alexander;
- Bludau, Anna;
- Ciesek, Sandra;
- Corman, Victor;
- Dilthey, Alexander;
- Donker, Tjibbe;
- Eckmanns, Tim;
- Egelkamp, Richard;
- Gatermann, Sören G.;
- Grundmann, Hajo;
- Häcker, Georg;
- Kaase, Martin;
- Lange, Berit;
- Mielke, Martin;
- Pletz, Mathias W.;
- Semmler, Torsten;
- Thürmer, Andrea;
- Wieler, Lothar H.;
- Wolff, Thorsten
Publication type:
Article
SWGTS—a platform for stream-based host DNA depletion.
Published in:
Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae332
By:
- Spohr, Philipp;
- Ried, Max;
- Kühle, Laura;
- Dilthey, Alexander
Publication type:
Article
Haploflow: strain-resolved de novo assembly of viral genomes.
Published in:
Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02426-8
By:
- Fritz, Adrian;
- Bremges, Andreas;
- Deng, Zhi-Luo;
- Lesker, Till Robin;
- Götting, Jasper;
- Ganzenmueller, Tina;
- Sczyrba, Alexander;
- Dilthey, Alexander;
- Klawonn, Frank;
- McHardy, Alice Carolyn
Publication type:
Article
Haploflow: strain-resolved de novo assembly of viral genomes.
Published in:
Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02426-8
By:
- Fritz, Adrian;
- Bremges, Andreas;
- Deng, Zhi-Luo;
- Lesker, Till Robin;
- Götting, Jasper;
- Ganzenmueller, Tina;
- Sczyrba, Alexander;
- Dilthey, Alexander;
- Klawonn, Frank;
- McHardy, Alice Carolyn
Publication type:
Article
Characterisation of the changing genomic landscape of metastatic melanoma using cell free DNA.
Published in:
NPJ Genomic Medicine, 2017, v. 2, n. 1, p. N.PAG, doi. 10.1038/s41525-017-0030-7
By:
- Cutts, Anthony;
- Venn, Oliver;
- Dilthey, Alexander;
- Gupta, Avinash;
- Vavoulis, Dimitris;
- Dreau, Helene;
- Middleton, Mark;
- McVean, Gil;
- Taylor, Jenny C.;
- Schuh, Anna
Publication type:
Article
Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-10934-2
By:
- Dilthey, Alexander T.;
- Jain, Chirag;
- Koren, Sergey;
- Phillippy, Adam M.
Publication type:
Article
Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.
Published in:
Nature, 2011, v. 476, n. 7359, p. 214, doi. 10.1038/nature10251
By:
- Sawcer, Stephen;
- Hellenthal, Garrett;
- Pirinen, Matti;
- Spencer, Chris C. A.;
- Patsopoulos, Nikolaos A.;
- Moutsianas, Loukas;
- Dilthey, Alexander;
- Su, Zhan;
- Freeman, Colin;
- Hunt, Sarah E.;
- Edkins, Sarah;
- Gray, Emma;
- Booth, David R.;
- Potter, Simon C.;
- Goris, An;
- Band, Gavin;
- Bang Oturai, Annette;
- Strange, Amy;
- Saarela, Janna;
- Bellenguez, Céline
Publication type:
Article
Characterisation of Type II DNA Methyltransferases of Metamycoplasma hominis.
Published in:
Microorganisms, 2023, v. 11, n. 6, p. 1591, doi. 10.3390/microorganisms11061591
By:
- Vogelgsang, Lars;
- Nisar, Azlan;
- Scharf, Sebastian Alexander;
- Rommerskirchen, Anna;
- Belick, Dana;
- Dilthey, Alexander;
- Henrich, Birgit
Publication type:
Article
RNA transcription and degradation of Alu retrotransposons depends on sequence features and evolutionary history.
Published in:
G3: Genes | Genomes | Genetics, 2022, v. 12, n. 5, p. 1, doi. 10.1093/g3journal/jkac054
By:
- Baar, Till;
- Dümcke, Sebastian;
- Gressel, Saskia;
- Schwalb, Björn;
- Dilthey, Alexander;
- Cramer, Patrick;
- Tresch, Achim
Publication type:
Article
Characterisation of mobile genetic elements in Mycoplasma hominis with the description of ICEHo-II, a variant mycoplasma integrative and conjugative element.
Published in:
Mobile DNA, 2020, v. 11, n. 1, p. 1, doi. 10.1186/s13100-020-00225-9
By:
- Henrich, Birgit;
- Hammerlage, Stephanie;
- Scharf, Sebastian;
- Haberhausen, Diana;
- Fürnkranz, Ursula;
- Köhrer, Karl;
- Peitzmann, Lena;
- Fiori, Pier Luigi;
- Spergser, Joachim;
- Pfeffer, Klaus;
- Dilthey, Alexander T.
Publication type:
Article
Multi-Population Classical HLA Type Imputation.
Published in:
PLoS Computational Biology, 2013, v. 9, n. 2, p. 1, doi. 10.1371/journal.pcbi.1002877
By:
- Dilthey, Alexander;
- Leslie, Stephen;
- Moutsianas, Loukas;
- Shen, Judong;
- Cox, Charles;
- Nelson, Matthew R.;
- McVean, Gil
Publication type:
Article
The role of microbiome-host interactions in the development of Alzheimer's disease.
Published in:
Frontiers in Cellular & Infection Microbiology, 2023, p. 1, doi. 10.3389/fcimb.2023.1151021
By:
- Weber, Christian;
- Dilthey, Alexander;
- Finzer, Patrick
Publication type:
Article
Genetic fine mapping of systemic lupus erythematosus MHC associations in Europeans and African Americans.
Published in:
Human Molecular Genetics, 2018, v. 27, n. 21, p. 3813, doi. 10.1093/hmg/ddy280
By:
- Hanscombe, Ken B;
- Morris, David L;
- Noble, Janelle A;
- Dilthey, Alexander T;
- Tombleson, Philip;
- Kaufman, Kenneth M;
- Comeau, Mary;
- Langefeld, Carl D;
- Alarcon-Riquelme, Marta E;
- Gaffney, Patrick M
Publication type:
Article
Rapid Selection of Sotrovimab Escape Variants in Severe Acute Respiratory Syndrome Coronavirus 2 Omicron-Infected Immunocompromised Patients.
Published in:
Clinical Infectious Diseases, 2023, v. 76, n. 3, p. 408, doi. 10.1093/cid/ciac802
By:
- Gliga, Smaranda;
- Lübke, Nadine;
- Killer, Alexander;
- Gruell, Henning;
- Walker, Andreas;
- Dilthey, Alexander T;
- Thielen, Alexander;
- Lohr, Carolin;
- Flaßhove, Charlotte;
- Krieg, Sarah;
- Pereira, Joanna Ventura;
- Seraphin, Tobias Paul;
- Zaufel, Alex;
- Däumer, Martin;
- Orth, Hans-Martin;
- Feldt, Torsten;
- Bode, Johannes G;
- Klein, Florian;
- Timm, Jörg;
- Luedde, Tom
Publication type:
Article
High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs.
Published in:
PLoS Computational Biology, 2016, v. 12, n. 10, p. 1, doi. 10.1371/journal.pcbi.1005151
By:
- Dilthey, Alexander T.;
- Gourraud, Pierre-Antoine;
- Mentzer, Alexander J.;
- Cereb, Nezih;
- Iqbal, Zamin;
- McVean, Gil
Publication type:
Article
Complete sequences of six major histocompatibility complex haplotypes, including all the major MHC class II structures.
Published in:
HLA: Immune Response Genetics, 2023, v. 102, n. 1, p. 28, doi. 10.1111/tan.15020
By:
- Houwaart, Torsten;
- Scholz, Stephan;
- Pollock, Nicholas R.;
- Palmer, William H.;
- Kichula, Katherine M.;
- Strelow, Daniel;
- Le, Duyen B.;
- Belick, Dana;
- Hülse, Lisanna;
- Lautwein, Tobias;
- Wachtmeister, Thorsten;
- Wollenweber, Tassilo E.;
- Henrich, Birgit;
- Köhrer, Karl;
- Parham, Peter;
- Guethlein, Lisbeth A.;
- Norman, Paul J.;
- Dilthey, Alexander T.
Publication type:
Article
Horizontally transferred genes cluster spatially and metabolically.
Published in:
Biology Direct, 2015, v. 10, p. 1, doi. 10.1186/s13062-015-0102-5
By:
- Dilthey, Alexander;
- Lercher, Martin J.
Publication type:
Article
Psoriasis Patients Are Enriched for Genetic Variants That Protect against HIV-1 Disease.
Published in:
PLoS Genetics, 2012, v. 8, n. 2, p. 1, doi. 10.1371/journal.pgen.1002514
By:
- Haoyan Chen;
- Hayashi, Genki;
- Lai, Olivia Y.;
- Dilthey, Alexander;
- Kuebler, Peter J.;
- Wong, Tami V.;
- Martin, Maureen P.;
- Vina, Marcelo A. Fernandez;
- McVean, Gil;
- Wabl, Matthias;
- Leslie, Kieron S.;
- Maurer, Toby;
- Martin, Jeffrey N.;
- Deeks, Steven G.;
- Carrington, Mary;
- Bowcock, Anne M.;
- Nixon, Douglas F.;
- Liao, Wilson
Publication type:
Article
Microbial Community Profiling Protocol with Full‐length 16S rRNA Sequences and Emu.
Published in:
Current Protocols, 2024, v. 4, n. 3, p. 1, doi. 10.1002/cpz1.978
By:
- Curry, Kristen D.;
- Soriano, Sirena;
- Nute, Michael G.;
- Villapol, Sonia;
- Dilthey, Alexander;
- Treangen, Todd J.
Publication type:
Article
Ultraplexing: increasing the efficiency of long-read sequencing for hybrid assembly with k-mer-based multiplexing.
Published in:
Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-01974-9
By:
- Dilthey, Alexander T.;
- Meyer, Sebastian A.;
- Kaasch, Achim J.
Publication type:
Article
Etablierung der Genomischen Erreger-Surveillance zur Stärkung des Pandemie- und Infektionsschutzes in Deutschland.
Published in:
Bundesgesundheitsblatt - Gesundheitsforschung - Gesundheitsschutz, 2023, v. 66, n. 4, p. 443, doi. 10.1007/s00103-023-03680-w
By:
- Scheithauer, Simone;
- Dilthey, Alexander;
- Bludau, Anna;
- Ciesek, Sandra;
- Corman, Victor;
- Donker, Tjibbe;
- Eckmanns, Tim;
- Egelkamp, Richard;
- Grundmann, Hajo;
- Häcker, Georg;
- Kaase, Martin;
- Lange, Berit;
- Mellmann, Alexander;
- Mielke, Martin;
- Pletz, Mathias;
- Salzberger, Bernd;
- Thürmer, Andrea;
- Widmer, Andreas;
- Wieler, Lothar H.;
- Wolff, Thorsten
Publication type:
Article
HLA*LA—HLA typing from linearly projected graph alignments.
Published in:
Bioinformatics, 2019, v. 35, n. 21, p. 4394, doi. 10.1093/bioinformatics/btz235
By:
- Dilthey, Alexander T;
- Mentzer, Alexander J;
- Carapito, Raphael;
- Cutland, Clare;
- Cereb, Nezih;
- Madhi, Shabir A;
- Rhie, Arang;
- Koren, Sergey;
- Bahram, Seiamak;
- McVean, Gil;
- Phillippy, Adam M
Publication type:
Article
A fast adaptive algorithm for computing whole-genome homology maps.
Published in:
Bioinformatics, 2018, v. 34, n. 17, p. i748, doi. 10.1093/bioinformatics/bty597
By:
- Jain, Chirag;
- Koren, Sergey;
- Dilthey, Alexander;
- Phillippy, Adam M;
- Aluru, Srinivas
Publication type:
Article
HLA*IMP—an integrated framework for imputing classical HLA alleles from SNP genotypes.
Published in:
Bioinformatics, 2011, v. 27, n. 7, p. 968, doi. 10.1093/bioinformatics/btr061
By:
- Dilthey, Alexander T.;
- Moutsianas, Loukas;
- Leslie, Stephen;
- McVean, Gil
Publication type:
Article
Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing.
Published in:
Scientific Reports, 2024, v. 14, n. 1, p. 1, doi. 10.1038/s41598-024-53506-1
By:
- Spohr, Philipp;
- Scharf, Sebastian;
- Rommerskirchen, Anna;
- Henrich, Birgit;
- Jäger, Paul;
- Klau, Gunnar W.;
- Haas, Rainer;
- Dilthey, Alexander;
- Pfeffer, Klaus
Publication type:
Article
Distinct genetic architectures and environmental factors associate with host response to the γ2-herpesvirus infections.
Published in:
Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-17696-2
By:
- Sallah, Neneh;
- Miley, Wendell;
- Labo, Nazzarena;
- Carstensen, Tommy;
- Fatumo, Segun;
- Gurdasani, Deepti;
- Pollard, Martin O.;
- Dilthey, Alexander T.;
- Mentzer, Alexander J.;
- Marshall, Vickie;
- Cornejo Castro, Elena M.;
- Pomilla, Cristina;
- Young, Elizabeth H.;
- Asiki, Gershim;
- Hibberd, Martin L.;
- Sandhu, Manjinder;
- Kellam, Paul;
- Newton, Robert;
- Whitby, Denise;
- Barroso, Inês
Publication type:
Article

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