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1. Full Text HLAIMP-an integrated framework for imputing classical HLA alleles from SNP genotypes
by Dilthey, Alexander T and Moutsianas, Loukas and Leslie, Stephen and McVean, Gil
Bioinformatics, ISSN 1367-4803, 04/2011, Volume 27, Issue 7, pp. 968 - 972
Motivation: Genetic variation at classical HLA alleles influences many phenotypes, including susceptibility to autoimmune disease, resistance to pathogens and... 
IMPUTATION | SUSCEPTIBILITY | BIOCHEMICAL RESEARCH METHODS | HODGKIN-LYMPHOMA | HOTSPOTS | MHC HAPLOTYPES | LINKAGE DISEQUILIBRIUM | GENE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | DISEASE | MATHEMATICAL & COMPUTATIONAL BIOLOGY | MAP | GENOME-WIDE ASSOCIATION | Genome-Wide Association Study | Psoriasis - genetics | Algorithms | Humans | Alleles | Genotype | Polymorphism, Single Nucleotide | Software | HLA Antigens - genetics | Original Papers
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2. Full Text Nanopore sequencing and assembly of a human genome with ultra-long reads
by Jain, Miten and Koren, Sergey and Miga, Karen H and Quick, Josh and Rand, Arthur C and Sasani, Thomas A and Tyson, John R and Beggs, Andrew D and Dilthey, Alexander T and Fiddes, Ian T and Malla, Sunir and Marriott, Hannah and Nieto, Tom and O'Grady, Justin and Olsen, Hugh E and Pedersen, Brent S and Rhie, Arang and Richardson, Hollian and Quinlan, Aaron R and Snutch, Terrance P and Tee, Louise and Paten, Benedict and Phillippy, Adam M and Simpson, Jared T and Loman, Nicholas J and Loose, Matthew
Nature Biotechnology, ISSN 1087-0156, 04/2018, Volume 36, Issue 4, pp. 338 - 345
We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore... 
METHYLATION | VARIANTS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | DNA | LENGTH | GENES | TIME | GAPS | Methods | Nucleotide sequencing | DNA sequencing | Genomes | Major histocompatibility complex | Porosity | Histocompatibility | Assembly | Gene sequencing
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3. Full Text High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs
by Dilthey, Alexander T and Gourraud, Pierre-Antoine and Mentzer, Alexander J and Cereb, Nezih and Iqbal, Zamin and McVean, Gil
PLoS Computational Biology, ISSN 1553-734X, 10/2016, Volume 12, Issue 10, p. e1005151
Genetic variation at the Human Leucocyte Antigen (HLA) genes is associated with many autoimmune and infectious disease phenotypes, is an important element of... 
CLASS-I | HIGH-RESOLUTION HLA | SUSCEPTIBILITY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Genetics, Population | Algorithms | Hemochromatosis Protein - genetics | Chromosome Mapping - methods | Humans | Reference Values | High-Throughput Nucleotide Sequencing - methods | Genome, Human - genetics | Immunogenetics | Histocompatibility antigens | Genes | Genomics | HLA histocompatibility antigens | Genomes | Genetic aspects | Nucleotide sequencing | DNA sequencing | Health aspects | Methods | Antigens | Accuracy | Infectious diseases | Laboratories | Funding | Quality | Colleges & universities | Population | Genetics | Life Sciences | Human health and pathology
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4. Full Text Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps
by Dilthey, AT and Jain, C and Koren, S and Phillippy, AM
NATURE COMMUNICATIONS, ISSN 2041-1723, 07/2019, Volume 10, Issue 1, pp. 3066 - 12
Metagenomic sequence classification should be fast, accurate and information-rich. Emerging long-read sequencing technologies promise to improve the balance... 
SEQUENCES | GENE | MULTIDISCIPLINARY SCIENCES | PHYLOGENETIC CLASSIFICATION | FAST GENOME | TIME | TOOL | Composition | Databases | Computer simulation | Species classification | Classification | Mapping | Genomes | Gene mapping | Data bases | Genera
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5. Full Text HLALA—HLA typing from linearly projected graph alignments
by Dilthey, Alexander T and Mentzer, Alexander J and Carapito, Raphael and Cutland, Clare and Cereb, Nezih and Madhi, Shabir A and Rhie, Arang and Koren, Sergey and Bahram, Seiamak and McVean, Gil and Phillippy, Adam M
Bioinformatics, ISSN 1367-4803, 11/2019, Volume 35, Issue 21, pp. 4394 - 4396
Abstract Summary HLA*LA implements a new graph alignment model for human leukocyte antigen (HLA) type inference, based on the projection of linear alignments... 
Applications Notes
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6. Full Text Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis
by Beecham, Ashley H and Patsopoulos, Nikolaos A and Xifara, Dionysia K and Davis, Mary F and Kemppinen, Anu and Cotsapas, Chris and Shah, Tejas S and Spencer, Chris and Booth, David and Goris, An and Oturai, Annette and Saarela, Janna and Fontaine, Bertrand and Hemmer, Bernhard and Martin, Claes and Zipp, Frauke and D'Alfonso, Sandra and Martinelli-Boneschi, Filippo and Taylor, Bruce and Harbo, Hanne F and Kockum, Ingrid and Hillert, Jan and Olsson, Tomas and Ban, Maria and Oksenberg, Jorge R and Hintzen, Rogier and Barcellos, Lisa F and Agliardi, Cristina and Alfredsson, Lars and Alizadeh, Mehdi and Anderson, Carl and Andrews, Robert and Søndergaard, Helle Bach and Baker, Amie and Band, Gavin and Baranzini, Sergio E and Barizzone, Nadia and Barrett, Jeffrey and Bellenguez, Céline and Bergamaschi, Laura and Bernardinelli, Luisa and Berthele, Achim and Biberacher, Viola and Binder, Thomas M.C and Blackburn, Hannah and Bomfim, Izaura L and Brambilla, Paola and Broadley, Simon and Brochet, Bruno and Brundin, Lou and Buck, Dorothea and Butzkueven, Helmut and Caillier, Stacy J and Camu, William and Carpentier, Wassila and Cavalla, Paola and Celius, Elisabeth G and Coman, Irène and Comi, Giancarlo and Corrado, Lucia and Cosemans, Leentje and Cournu-Rebeix, Isabelle and Cree, Bruce A.C and Cusi, Daniele and Damotte, Vincent and Defer, Gilles and Delgado, Silvia R and Deloukas, Panos and Di Sapio, Alessia and Dilthey, Alexander T and Donnelly, Peter and Dubois, Bénédicte and Duddy, Martin and Edkins, Sarah and Elovaara, Irina and Esposito, Federica and Evangelou, Nikos and Fiddes, Barnaby and Field, Judith and Franke, Andre and Freeman, Colin and Frohlich, Irene Y and Galimberti, Daniela and Gieger, Christian and Gourraud, Pierre-Antoine and Graetz, Christiane and Graham, Andrew and Grummel, Verena and Guaschino, Clara and Hadjixenofontos, Athena and Hakonarson, Hakon and Halfpenny, Christopher and Hall, Gillian and Hall, Per and Hamsten, Anders and Harley, James and Harrower, Timothy and Hawkins, Clive and Hellenthal, Garrett and Hillier, Charles and ... and Wellcome Trust Case Control Consor and Int IBD Genetics Consortium IIBDGC and International Multiple Sclerosis Genetics Consortium (IMSGC) and Wellcome Trust Case Control Consortium 2 (WTCCC2) and International IBD Genetics Consortium (IIBDGC) and Institutionen för fysik, kemi och biologi and Linköpings universitet and Bioinformatik and Tekniska högskolan
Nature Genetics, ISSN 1061-4036, 2013, Volume 45, Issue 11, pp. 1353 - 1362
Using the ImmunoChip custom genotyping array, we analyzed 14,498 subjects with multiple sclerosis and 24,091 healthy controls for 161,311 autosomal variants... 
AUTOIMMUNE | ALLELES | METAANALYSIS | GENOTYPE IMPUTATION | GENETIC RISK | INFORMATION | ANNOTATION | PRIMARY BILIARY-CIRRHOSIS | DISEASE | GENETICS & HEREDITY | GENOME-WIDE ASSOCIATION | Genetic Variation | European Continental Ancestry Group - genetics | Genetic Predisposition to Disease | Genome-Wide Association Study | Gene Frequency | Humans | Multiple Sclerosis - immunology | Genotype | Multiple Sclerosis - genetics | Chromosome Mapping | Polymorphism, Single Nucleotide | Genetic Loci | Multiple sclerosis | Chromosome mapping | Genetic susceptibility | Genetic variation | Genetic aspects | Identification and classification | Methods | Testing | Confidence intervals | Disease | Quality control | Genomes | Stratigraphy | Autoimmune diseases | Gene expression | Meta-analysis | Teknik och teknologier | TEKNIKVETENSKAP | Engineering and Technology | TECHNOLOGY
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7. Full Text Class II HLA interactions modulate genetic risk for multiple sclerosis
by Moutsianas, Loukas and Jostins, Luke and Beecham, Ashley H and Dilthey, Alexander T and Xifara, Dionysia K and Ban, Maria and Shah, Tejas S and Patsopoulos, Nikolaos A and Alfredsson, Lars and Anderson, Carl A and Attfield, Katherine E and Baranzini, Sergio E and Barrett, Jeffrey and Binder, Thomas M.C and Booth, David and Buck, Dorothea and Celius, Elisabeth G and Cotsapas, Chris and D'Alfonso, Sandra and Dendrou, Calliope A and Donnelly, Peter and Dubois, Bénédicte and Fontaine, Bertrand and Fugger, Lars and Goris, An and Gourraud, Pierr-Antoine and Graetz, Christiane and Hemmer, Bernhard and Hillert, Jan and Kockum, Ingrid and Leslie, Stephen and Lill, Christina M and Martinelli-Boneschi, Filippo and Oksenberg, Jorge R and Olsson, Tomas and Oturai, Annette and Saarela, Janna and SØndergaard, Helle Bach and Spurkland, Anne and Taylor, Bruce and Winkelmann, Juliane and Zipp, Frauke and L Haines, Jonathan and Pericak-Vance, Margaret A and Spencer, Chris C.A and Stewart, Graeme and Hafler, David A and Ivinson, Adrian J and Harbo, Hanne F and Hauser, Stephen L and De Jager, Philip L and Compston, Alastair and McCauley, Jacob L and Sawcer, Stephen and McVean, Gil and Int Multiple Sclerosis Genetics and Int IBD Genetics Consortium IIBDGC and International IBD Genetics Consortium (IIBDGC) and the International Multiple Sclerosis Genetics Consortium
Nature Genetics, ISSN 1061-4036, 09/2015, Volume 47, Issue 10, pp. 1107 - 1113
Association studies have greatly refined the understanding of how variation within the human leukocyte antigen (HLA) genes influences risk of multiple... 
POPULATION | METAANALYSIS | VARIANTS | DISEASE | ERAP1 | GENETICS & HEREDITY | SUSCEPTIBILITY LOCI | MHC | EPISTASIS | HLA-DRB1 | GENOME-WIDE ASSOCIATION | Genetic Predisposition to Disease | Histocompatibility Antigens Class II - immunology | Epistasis, Genetic | Humans | Alleles | Multiple Sclerosis - genetics | Polymorphism, Single Nucleotide | Histocompatibility Antigens Class II - genetics | Multiple sclerosis | Histocompatibility antigens | Genetic susceptibility | HLA histocompatibility antigens | Genetic research | Genetic aspects | Research | Single nucleotide polymorphisms | Health aspects | Risk factors
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8. Full Text De novo assembly of haplotype-resolved genomes with trio binning
by Koren, Sergey and Rhie, Arang and Walenz, Brian P and Dilthey, Alexander T and Bickhart, Derek M and Kingan, Sarah B and Hiendleder, Stefan and Williams, John L and Smith, Timothy P. L and Phillippy, Adam M
Nature Biotechnology, ISSN 1087-0156, 12/2018, Volume 36, Issue 12, pp. 1174 - 1182
Complex allelic variation hampers the assembly of haplotype-resolved sequences from diploid genomes. We developed trio binning, an approach that simplifies... 
VARIANTS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | SEQUENCE | TOOL | Haplotypes | Heterozygosis | Genomics | Analysis | Genomes | Genetic aspects | Research | Heterozygosity | Offspring | Cattle | Genetic crosses | Heredity | Variation | Assembly | Gene sequencing
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9. Full Text Molecular mimicry between Anoctamin 2 and Epstein-Barr virus nuclear antigen 1 associates with multiple sclerosis risk
by Tengvall, Katarina and Huang, Jesse and Hellstrom, Cecilia and Kammer, Patrick and Biström, Martin and Ayoglu, Burcu and Bomfim, Izaura Lima and Stridh, Pernilla and Butt, Julia and Brenner, Nicole and Michel, Angelika and Lundberg, Karin and Padyukov, Leonid and Lundberg, Ingrid E and Svenungsson, Elisabet and Ernberg, Ingemar and Olafsson, Sigurgeir and Dilthey, Alexander T and Hillert, Jan and Alfredsson, Lars and Sundström, Peter and Nilsson, Peter and Waterboer, Tim and Olsson, Tomas and Kockum, Ingrid and Medicinska fakulteten and Klinisk neurovetenskap and Umeå universitet and Institutionen för farmakologi och klinisk neurovetenskap
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 2019, Volume 116, Issue 34, p. 16955
Multiple sclerosis (MS) is a chronic inflammatory, likely autoimmune disease of the central nervous system with a combination of genetic and environmental risk... 
Clinical Medicine | Neurology | Neurologi | molecular mimicry | Medical and Health Sciences | Medicin och hälsovetenskap | multiple sclerosis | Epstein-Barr virus | Klinisk medicin | Anoctamin 2 | ANO2
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10. Full Text Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing
by Kim, Jung-Hyun and Dilthey, Alexander T and Nagaraja, Ramaiah and Lee, Hee-Sheung and Koren, Sergey and Dudekula, Dawood and Wood III, William H and Piao, Yulan and Ogurtsov, Aleksey Y and Utani, Koichi and Noskov, Vladimir N and Shabalina, Svetlana A and Schlessinger, David and Phillippy, Adam M and Larionov, Vladimir
Nucleic Acids Research, ISSN 0305-1048, 07/2018, Volume 46, Issue 13, pp. 6712 - 6725
Abstract Despite the key role of the human ribosome in protein biosynthesis, little is known about the extent of sequence variation in ribosomal DNA (rDNA) or... 
RECOMBINATION | HUMAN GENOME | ACID | RDNA | ALIGNMENT | VARIANTS | DNA | BIOCHEMISTRY & MOLECULAR BIOLOGY | ARCHITECTURE | NUCLEOLAR ORGANIZER REGIONS | INHERITANCE | Genomics
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11. Full Text DNA methylation as a mediator of HLA-DRB1 15:01 and a protective variant in multiple sclerosis
by Kular, Lara and Liu, Yun and Ruhrmann, Sabrina and Zheleznyakova, Galina and Marabita, Francesco and Gomez-Cabrero, David and James, Tojo and Ewing, Ewoud and Lindén, Magdalena and Górnikiewicz, Bartosz and Aeinehband, Shahin and Stridh, Pernilla and Link, Jenny and Andlauer, Till F. M and Gasperi, Christiane and Wiendl, Heinz and Zipp, Frauke and Gold, Ralf and Tackenberg, Björn and Weber, Frank and Hemmer, Bernhard and Strauch, Konstantin and Heilmann-Heimbach, Stefanie and Rawal, Rajesh and Schminke, Ulf and Schmidt, Carsten O and Kacprowski, Tim and Franke, Andre and Laudes, Matthias and Dilthey, Alexander T and Celius, Elisabeth G and Søndergaard, Helle B and Tegnér, Jesper and Harbo, Hanne F and Oturai, Annette B and Olafsson, Sigurgeir and Eggertsson, Hannes P and Halldorsson, Bjarni V and Hjaltason, Haukur and Olafsson, Elias and Jonsdottir, Ingileif and Stefansson, Kari and Olsson, Tomas and Piehl, Fredrik and Ekström, Tomas J and Kockum, Ingrid and Feinberg, Andrew P and Jagodic, Maja
Nature Communications, ISSN 2041-1723, 12/2018, Volume 9, Issue 1
The human leukocyte antigen (HLA) haplotype DRB1(star)15:01 is the major risk factor for multiple sclerosis (MS). Here, we find that DRB1(star)15:01 is... 
DIFFERENTIAL EXPRESSION | GENETIC RISK | MICROGLIA | MACROPHAGES | MULTIDISCIPLINARY SCIENCES | DISEASE | SUSCEPTIBILITY | TRANSCRIPTION | MONOCYTES | WIDE ASSOCIATION | LOCUS
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12. Full Text Molecular mimicry between Anoctamin 2 and Epstein-Barr virus nuclear antigen 1 associates with multiple sclerosis risk
by Tengvall, K and Huang, J and Hellstrom, C and Kammer, P and Bistrom, M and Ayoglu, B and Bomfim, IL and Stridh, P and Butt, J and Brenner, N and Michel, A and Lundberg, K and Padyukov, L and Lundberg, IE and Svenungsson, E and Ernberg, I and Olafsson, S and Dilthey, AT and Hillert, J and Alfredsson, L and Sundstrom, P and Nilsson, P and Waterboer, T and Olsson, T and Kockum, I and Science for Life Laboratory, SciLifeLab and Centra and Proteinvetenskap and KTH and Skolan för kemi, bioteknologi och hälsa (CBH)
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, ISSN 0027-8424, 08/2019, Volume 116, Issue 34, pp. 16955 - 16960
Multiple sclerosis (MS) is a chronic inflammatory, likely autoimmune disease of the central nervous system with a combination of genetic and environmental risk... 
TARGET | molecular mimicry | RESPONSES | multiple sclerosis | MULTIDISCIPLINARY SCIENCES | Epstein-Barr virus | INFECTION | Anoctamin 2 | ANO2 | T-CELLS | LYMPHOCYTES | Antigen-antibody reactions | Autoimmunity | Multiple sclerosis | Histocompatibility antigens | Autoantibodies | Peptides | Immunoglobulin G | HLA histocompatibility antigens | T cells | Health aspects | Risk factors | IgG antibody | Central nervous system | Viruses | Lymphocytes T | Mapping | Serology | Inflammatory diseases | Mimicry | Chloride ions | Confidence intervals | Lymphocytes | Drb1 protein | Ion channels | Antigens | Cross-reactivity | Risk analysis | Environmental risk | Peptide mapping | Reactivity | Histocompatibility antigen HLA | Gene mapping | Autoimmune diseases | Medical Biotechnology | Medical and Health Sciences | Medicin och hälsovetenskap | Medicinsk bioteknologi
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