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ArticlesPeer ReviewedFull Text
Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps
Author / Creator:Dilthey, Alexander T. ; Jain, Chirag ; Koren, Sergey ; Phillippy, Adam M.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2019-07, Vol.10 (1), p.3066-12, Article 3066
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High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs
Author / Creator:Dilthey, Alexander T. ; Gourraud, Pierre-Antoine ; Mentzer, Alexander J. ; Cereb, Nezih ; Iqbal, Zamin ; McVean, Gil
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2016-10, Vol.12 (10), p.e1005151-e1005151
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De novo assembly of haplotype-resolved genomes with trio binning
Author / Creator: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
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2018-12, Vol.36 (12), p.1174-1182
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Nanopore sequencing and assembly of a human genome with ultra-long reads
Author / Creator: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 ; Tee, Louise ; Paten, Benedict ; Phillippy, Adam M ; Simpson, Jared T ; Loman, Nicholas J ; Loose, Matthew
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2018-04, Vol.36 (4), p.338-345
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Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes
Author / Creator:Ebler, Jana ; Ebert, Peter ; Clarke, Wayne E. ; Rausch, Tobias ; Audano, Peter A. ; Houwaart, Torsten ; Mao, Yafei ; Korbel, Jan O. ; Eichler, Evan E. ; Zody, Michael C. ; Dilthey, Alexander T. ; Marschall, Tobias
Publisher:New York: Nature Publishing Group US
Journal title:Nature genetics, 2022-04, Vol.54 (4), p.518-525
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Molecular mimicry between Anoctamin 2 and Epstein-Barr virus nuclear antigen 1 associates with multiple sclerosis risk
Author / Creator:Tengvall, Katarina ; Huang, Jesse ; Hellström, Cecilia ; Kammer, Patrick ; Biström, Martin ; Ayoglu, Burcu ; Bomfim, Izaura Lima ; Stridh, Pernilla ; Butt, Julia ; Brenner, Nicole ; Michel, Angelika ; Lundberg, Karin ; Padyukov, Leonid ; Lundberg, Ingrid E. ; Svenungsson, Elisabet ; Ernberg, Ingemar ; Olafsson, Sigurgeir ; Dilthey, Alexander T. ; Hillert, Jan ; Alfredsson, Lars ; Sundström, Peter ; Nilsson, Peter ; Waterboer, Tim ; Olsson, Tomas ; Kockum, Ingrid
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2019-08, Vol.116 (34), p.16955-16960
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A diploid assembly-based benchmark for variants in the major histocompatibility complex
Author / Creator:Chin, Chen-Shan ; Wagner, Justin ; Zeng, Qiandong ; Garrison, Erik ; Garg, Shilpa ; Fungtammasan, Arkarachai ; Rautiainen, Mikko ; Aganezov, Sergey ; Kirsche, Melanie ; Zarate, Samantha ; Schatz, Michael C. ; Xiao, Chunlin ; Rowell, William J. ; Markello, Charles ; Farek, Jesse ; Sedlazeck, Fritz J. ; Bansal, Vikas ; Yoo, Byunggil ; Miller, Neil ; Zhou, Xin ; Carroll, Andrew ; Barrio, Alvaro Martinez ; Salit, Marc ; Marschall, Tobias ; Dilthey, Alexander T. ; Zook, Justin M.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2020-09, Vol.11 (1), p.4794-4794, Article 4794
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Ultraplexing: increasing the efficiency of long-read sequencing for hybrid assembly with k-mer-based multiplexing
Author / Creator:Dilthey, Alexander T. ; Meyer, Sebastian A. ; Kaasch, Achim J.
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2020-03, Vol.21 (1), p.68-68, Article 68
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DNA methylation as a mediator of HLA-DRB1 15:01 and a protective variant in multiple sclerosis
Author / Creator:Kular, Lara ; Liu, Yun ; Ruhrmann, Sabrina ; Zheleznyakova, Galina ; Marabita, Francesco ; Gomez-Cabrero, David ; James, Tojo ; Ewing, Ewoud ; Lindén, Magdalena ; Górnikiewicz, Bartosz ; Aeinehband, Shahin ; Stridh, Pernilla ; Link, Jenny ; Andlauer, Till F.M ; Gasperi, Christiane ; Wiendl, Heinz ; Zipp, Frauke ; Gold, Ralf ; Tackenberg, Björn ; Weber, Frank ; Hemmer, Bernhard ; Strauch, Konstantin ; Heilmann-Heimbach, Stefanie ; Rawal, Rajesh ; Schminke, Ulf ; Schmidt, Carsten O ; Kacprowski, Tim ; Franke, Andre ; Laudes, Matthias ; Dilthey, Alexander T ; Celius, Elisabeth Gulowsen ; Søndergaard, Helle Bach ; Tegnér, Jesper ; Harbo, Hanne Flinstad ; Oturai, Annette B ; Olafsson, Sigurgeir ; Eggertsson, Hannes P ; Halldorsson, Bjarni V ; Hjaltason, Haukur ; Olafsson, Elias ; Jonsdottir, Ingileif ; Stefansson, Kari ; Olsson, Tomas ; Piehl, Fredrik ; Ekström, Tomas J ; Kockum, Ingrid ; Feinberg, Andrew P ; Jagodic, Maja
Journal title:Nature communications, 2018, Vol.9 (1)
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Multi-Population Classical HLA Type Imputation
Author / Creator:Dilthey, Alexander ; Leslie, Stephen ; Moutsianas, Loukas ; Shen, Judong ; Cox, Charles ; Nelson, Matthew R. ; McVean, Gil
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2013-02, Vol.9 (2), p.e1002877-e1002877
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ArticlesPeer ReviewedFull Text
Differential characteristics of vaginal versus endometrial microbiota in IVF patients
Author / Creator:Polifke, Alina ; von Schwedler, Annika ; Gulba, Rebecca ; Bensmann, Ralf ; Dilthey, Alexander ; Nassar, Najib N. R. ; Finzer, Patrick
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2024-12, Vol.14 (1), p.30508-16, Article 30508
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Distinct genetic architectures and environmental factors associate with host response to the γ2-herpesvirus infections
Author / Creator: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
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2020-07, Vol.11 (1), p.3849-13, Article 3849
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Haploflow: strain-resolved de novo assembly of viral genomes
Author / Creator:Fritz, Adrian ; Bremges, Andreas ; Deng, Zhi-Luo ; Lesker, Till Robin ; Götting, Jasper ; Ganzenmueller, Tina ; Sczyrba, Alexander ; Dilthey, Alexander ; Klawonn, Frank ; McHardy, Alice Carolyn
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2021-07, Vol.22 (1), p.212-212, Article 212
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Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing
Author / Creator:Spohr, Philipp ; Scharf, Sebastian ; Rommerskirchen, Anna ; Henrich, Birgit ; Jäger, Paul ; Klau, Gunnar W. ; Haas, Rainer ; Dilthey, Alexander ; Pfeffer, Klaus
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2024-02, Vol.14 (1), p.4068-4068, Article 4068
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NanoCore: core-genome-based bacterial genomic surveillance and outbreak detection in healthcare facilities from Nanopore and Illumina data
Author / Creator:Fuchs, Sebastian A. ; Hülse, Lisanna ; Tamayo, Teresa ; Kolbe-Busch, Susanne ; Pfeffer, Klaus ; Dilthey, Alexander T.
Publisher:United States: American Society for Microbiology
Journal title:mSystems, 2024-11, Vol.9 (11), p.e0108024
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High-resolution African HLA resource uncovers HLA-DRB1 expression effects underlying vaccine response
Author / Creator:Mentzer, Alexander J. ; Dilthey, Alexander T. ; Pollard, Martin ; Gurdasani, Deepti ; Karakoc, Emre ; Carstensen, Tommy ; Muhwezi, Allan ; Cutland, Clare ; Diarra, Amidou ; da Silva Antunes, Ricardo ; Paul, Sinu ; Smits, Gaby ; Wareing, Susan ; Kim, HwaRan ; Pomilla, Cristina ; Chong, Amanda Y. ; Brandt, Debora Y. C. ; Nielsen, Rasmus ; Neaves, Samuel ; Timpson, Nicolas ; Crinklaw, Austin ; Lindestam Arlehamn, Cecilia S. ; Rautanen, Anna ; Kizito, Dennison ; Parks, Tom ; Auckland, Kathryn ; Elliott, Kate E. ; Mills, Tara ; Ewer, Katie ; Edwards, Nick ; Fatumo, Segun ; Webb, Emily ; Peacock, Sarah ; Jeffery, Katie ; van der Klis, Fiona R. M. ; Kaleebu, Pontiano ; Vijayanand, Pandurangan ; Peters, Bjorn ; Sette, Alessandro ; Cereb, Nezih ; Sirima, Sodiomon ; Madhi, Shabir A. ; Elliott, Alison M. ; McVean, Gil ; Hill, Adrian V. S. ; Sandhu, Manjinder S.
Publisher:New York: Nature Publishing Group US
Journal title:Nature medicine, 2024-05, Vol.30 (5), p.1384-1394
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RNA transcription and degradation of Alu retrotransposons depends on sequence features and evolutionary history
Author / Creator:Baar, Till ; Dümcke, Sebastian ; Gressel, Saskia ; Schwalb, Björn ; Dilthey, Alexander ; Cramer, Patrick ; Tresch, Achim
Publisher:England: Oxford University Press
Journal title:G3 : genes - genomes - genetics, 2022-05, Vol.12 (5)
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Evolutionary and epidemic dynamics of COVID-19 in Germany exemplified by three Bayesian phylodynamic case studies
Author / Creator:Översti, Sanni ; Weber, Ariane ; Baran, Viktor ; Kieninger, Bärbel ; Dilthey, Alexander ; Houwaart, Torsten ; Walker, Andreas ; Schneider-Brachert, Wulf ; Kühnert, Denise
Publisher:United States: SAGE Publications
Journal title:Bioinformatics and biology insights, 2025-01, Vol.19, p.11779322251321065
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Characterisation of mobile genetic elements in Mycoplasma hominis with the description of ICEHo-II, a variant mycoplasma integrative and conjugative element
Author / Creator:Henrich, Birgit ; Hammerlage, Stephanie ; Scharf, Sebastian ; Haberhausen, Diana ; Fürnkranz, Ursula ; Köhrer, Karl ; Peitzmann, Lena ; Fiori, Pier Luigi ; Spergser, Joachim ; Pfeffer, Klaus ; Dilthey, Alexander T.
Publisher:England: BioMed Central Ltd
Journal title:Mobile DNA, 2020-11, Vol.11 (1), p.30-30, Article 30
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Characterisation of Type II DNA Methyltransferases of Metamycoplasma hominis
Author / Creator:Vogelgsang, Lars ; Nisar, Azlan ; Scharf, Sebastian Alexander ; Rommerskirchen, Anna ; Belick, Dana ; Dilthey, Alexander ; Henrich, Birgit
Publisher:Switzerland: MDPI AG
Journal title:Microorganisms (Basel), 2023-06, Vol.11 (6), p.1591
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Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps

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High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs

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De novo assembly of haplotype-resolved genomes with trio binning

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Nanopore sequencing and assembly of a human genome with ultra-long reads

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Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes

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Molecular mimicry between Anoctamin 2 and Epstein-Barr virus nuclear antigen 1 associates with multiple sclerosis risk

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A diploid assembly-based benchmark for variants in the major histocompatibility complex

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Ultraplexing: increasing the efficiency of long-read sequencing for hybrid assembly with k-mer-based multiplexing

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DNA methylation as a mediator of HLA-DRB1 15:01 and a protective variant in multiple sclerosis

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Multi-Population Classical HLA Type Imputation

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Differential characteristics of vaginal versus endometrial microbiota in IVF patients

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Distinct genetic architectures and environmental factors associate with host response to the γ2-herpesvirus infections

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Haploflow: strain-resolved de novo assembly of viral genomes

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Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing

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NanoCore: core-genome-based bacterial genomic surveillance and outbreak detection in healthcare facilities from Nanopore and Illumina data

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High-resolution African HLA resource uncovers HLA-DRB1 expression effects underlying vaccine response

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RNA transcription and degradation of Alu retrotransposons depends on sequence features and evolutionary history

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Evolutionary and epidemic dynamics of COVID-19 in Germany exemplified by three Bayesian phylodynamic case studies

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Characterisation of mobile genetic elements in Mycoplasma hominis with the description of ICEHo-II, a variant mycoplasma integrative and conjugative element

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Characterisation of Type II DNA Methyltransferases of Metamycoplasma hominis

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