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Department of Biology

Photo: Uhh/Multhaupt

Evolutionary Immunogenomics

Prof. Dr. Tobias Lenz

Bild von Prof. Dr. Lenz

Photo: UHH/Lenz

Professor

Research Unit for Evolutionary Immunogenomics

Address

University of Hamburg
Faculty of Mathematics, Informatics and Natural Sciences
Biology
Institute of Cell and Systems Biology of Animals
Evolutionary Immunogenomics
Martin-Luther-King-Platz 3
20146 Hamburg

Office

Institute of Cell and Systems Biology of Animals
Room: 460

Office hours

By appointment only

Contact

Tel: +49 40 42838 5369

Key aspects of activity

  • Evolution of an optimal immune response
  • Dynamics of antigen prpesentation and recognition
  • Evolutionary genomics of the major histocompatibility complex (MHC)
  • Human population genetics and genomics

Secretary's office

Sabine Baumann
Team assistant
Institute of Cell and Systems Biology of Animals
Evolutionary Immunogenomics
Martin-Luther-King-Platz 3
20146 Hamburg
Room: 461
Tel: +49 40 42838 5639


Seit 2021 Heisenberg-Professor, Universität Hamburg
2014 - 2021 Forschungsgruppenleiter, Max-Planck-Institut für Evolutionsbiologie, Plön
2011 - 2014 Postdoc, Harvard Medical School/Brigham and Women's Hospital, Boston
2009 - 2011 Postdoc, Max-Planck-Institut für Evolutionsbiologie, Plön
2005 - 2009 Promotion, Max-Planck-Institut für Evolutionsbiologie, Plön
2005 Forschungsassistent, Universität Bern
2005 Forschungssemester, Harvard University, Cambridge
1998 - 2005 Biologiestudium, Universität Hamburg

For full publication list please see link on the right or view Google Scholar profile

COVID-19 Host Genetics Initiative (2023) A second update on mapping the human genetic architecture of COVID-19. Nature 621: E7-E26.

Sakaue S, Gurajala S, Curtis M, Luo Y, Choi W, Ishigaki K, Kang JB, Rumker L, Deutsch AJ, Schönherr S, Lukas Forer L, LeFaive J, Fuchsberger C, Han B, Lenz TL, de Bakker PIW, Okada Y, Smith AV, Raychaudhuri S (2023) A statistical genetics guide to identifying HLA alleles driving complex disease. Nature Protocols 18: 2625-2641.

Radwan J, Babik W, Kaufman J, Lenz TL, Winternitz J (2020) Advances in the evolutionary understanding of MHC polymorphism. Trends in Genetics 36: 298-311.

Severe Covid-19 GWAS Group (2020) Genome-wide association study in severe Covid-19 with respiratory failure. New England Journal of Medicine 383:1522-1534.

Arora J, Pierini F, McLaren PJ, Carrington M, Fellay J, Lenz TL (2020) HLA heterozygote advantage against HIV-1 is driven by quantitative and qualitative differences in HLA allele-specific peptide presentation. Molecular Biology and Evolution 37: 639-650.

Chowell D, Krishna C, Pierini F, Makarov V, Rizvi NA, Kuo F, Riaz N, Lenz TL*, Chan TA* (2019) Evolutionary divergence of HLA class I genotype impacts efficacy of cancer immunotherapy. Nature Medicine 25: 1715-1720.

Pierini F, Lenz TL (2018) Divergent allele advantage at human MHC genes: signatures of past and ongoing selection. Molecular Biology and Evolution 35: 2145-2158.

Krause-Kyora B, Nutsua M, Böhme L, Pierini F, Pedersen DD, Kornell S-C, Drichel D, Bonazzi M, Möbus L, Tarp P, Susat J, Bosse E, Willburger B, Schmidt AH, Sauter J, Franke A, Wittig M, Calibe A, Nothnagel M, Schreiber S, Boldsen J*, Lenz TL*, Nebel A* (2018) Ancient DNA study reveals HLA susceptibility loci for leprosy in medieval Europeans. Nature Communications 9: 1569.

Publications

Publication type
Sorted by:

Page 1: results 1 to 10 of 72

Page 1: results 1 to 10 of 72

@article{e2f9bb95771140f892f9982ee6a26d52,
title = "Complete sequencing of ape genomes",
abstract = "The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies1,2,3. Consequently, our understanding of the evolution of our species is incomplete. Here we present haplotype-resolved reference genomes and comparative analyses of six ape species: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan and siamang. We achieve chromosome-level contiguity with substantial sequence accuracy (<1 error in 2.7 megabases) and completely sequence 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, to provide in-depth evolutionary insights. Comparative analyses enabled investigations of the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference genome. Such regions include newly minted gene families in lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes and subterminal heterochromatin. This resource serves as a comprehensive baseline for future evolutionary studies of humans and our closest living ape relatives.",
author = "DongAhn Yoo and Arang Rhie and Prajna Hebbar and Francesca Antonacci and Logsdon, {Glennis A.} and Solar, {Steven J.} and Dmitry Antipov and Pickett, {Brandon D.} and Yana Safonova and Francesco Montinaro and Yanting Luo and Joanna Malukiewicz and Storer, {Jessica M.} and Jiadong Lin and Sequeira, {Abigail N.} and Mangan, {Riley J.} and Glenn Hickey and {Monfort Anez}, Graciela and Parithi Balachandran and Anton Bankevich and Beck, {Christine R.} and Arjun Biddanda and Matthew Borchers and Bouffard, {Gerard G.} and Emry Brannan and Brooks, {Shelise Y.} and Lucia Carbone and Laura Carrel and Chan, {Agnes P.} and Juyun Crawford and Mark Diekhans and Eric Engelbrecht and Cedric Feschotte and Giulio Formenti and Garcia, {Gage H.} and {de Gennaro}, Luciana and David Gilbert and Green, {Richard E.} and Andrea Guarracino and Ishaan Gupta and Diana Haddad and Junmin Han and Harris, {Robert S.} and Hartley, {Gabrielle A.} and Harvey, {William T.} and Michael Hiller and Kendra Hoekzema and Houck, {Marlys L.} and Hyeonsoo Jeong and Kaivan Kamali and Manolis Kellis and Bryce Kille and Chul Lee and Youngho Lee and William Lees and Lewis, {Alexandra P.} and Qiuhui Li and Mark Loftus and Loh, {Yong Hwee Eddie} and Hailey Loucks and Jian Ma and Yafei Mao and Martinez, {Juan F. I.} and Patrick Masterson and McCoy, {Rajiv C.} and Barbara McGrath and Sean McKinney and Meyer, {Britta S.} and Miga, {Karen H.} and Mohanty, {Saswat K.} and Munson, {Katherine M.} and Karol Pal and Matt Pennell and Pevzner, {Pavel A.} and David Porubsky and Tamara Potapova and Ringeling, {Francisca R.} and Rocha, {Joana L.} and Ryder, {Oliver A.} and Samuel Sacco and Swati Saha and Takayo Sasaki and Schatz, {Michael C.} and Schork, {Nicholas J.} and Cole Shanks and Linn{\'e}a Smeds and Son, {Dongmin R.} and Cynthia Steiner and Sweeten, {Alexander P.} and Tassia, {Michael G.} and Fran{\c c}oise Thibaud-Nissen and Edmundo Torres-Gonz{\'a}lez and Mihir Trivedi and Wenjie Wei and Julie Wertz and Muyu Yang and Panpan Zhang and Shilong Zhang and Yang Zhang and Zhenmiao Zhang and Zhao, {Sarah A.} and Yixin Zhu and Jarvis, {Erich D.} and Gerton, {Jennifer L.} and Iker Rivas-Gonz{\'a}lez and Benedict Paten and Szpiech, {Zachary A.} and Huber, {Christian D.} and Lenz, {Tobias L.} and Konkel, {Miriam K.} and Yi, {Soojin V.} and Stefan Canzar and Watson, {Corey T.} and Sudmant, {Peter H.} and Erin Molloy and Erik Garrison and Lowe, {Craig B.} and Mario Ventura and O{\textquoteright}Neill, {Rachel J.} and Sergey Koren and Makova, {Kateryna D.} and Phillippy, {Adam M.} and Eichler, {Evan E.}",
year = "2025",
month = apr,
day = "9",
doi = "10.1038/s41586-025-08816-3",
language = "English",
journal = "Nature",
issn = "0028-0836",
publisher = "Nature Research",

}

@article{1d77cb0eecde44318bf6abd3a66c7223,
title = "HLA-DQB1*03:01 and risk of HBV-related HCC",
abstract = "Background and Aims: The human leukocyte antigen (HLA) locus is implicated in HCC among chronic HBV carriers. We investigated associations of HLA variants, amino acid polymorphisms, zygosity, and evolutionary divergence with HBV-related HCC in Han Chinese and explored biological mechanisms. Approach and Results: We examined the associations of HLA variants (imputed 4-digit classical alleles and amino acid polymorphisms), zygosity, and evolutionary divergence with HBV-related HCC in a discovery set (706 HBV-related HCC cases, 6197 chronic HBV carriers in Taiwan). Significant signals were validated in an independent set (636 cases, 560 controls in Qidong, Mainland China). We used logistic regression adjusted for sex, age, and top 10 genetic principal components, with a Bonferroni correction for multiple testing (p",
keywords = "evolutionary divergence, HBV, HCC, human leukocyte antigen, zygosity",
author = "Ting Zhang and Chih-Jen Huang and Hai-Tao Chen and Yu-Han Huang and Mei-Hung Pan and Mei-Hsuan Lee and Mathias Viard and Allan Hildesheim and Pfeiffer, {Ruth M.} and Mary Carrington and Chien-Jen Chen and Bin Zhu and Lenz, {Tobias L.} and Deke Jiang and Hwai-I Yang and Zhiwei Liu",
year = "2025",
month = mar,
day = "14",
doi = "10.1097/HEP.0000000000001307",
language = "English",
journal = "Hepatology",
issn = "0270-9139",
publisher = "Lippincott Williams and Wilkins",

}

@article{a0baf0c9693a4d598835eb2d759dfd43,
title = "Admixture as a source for HLA variation in Neolithic European farming communities",
abstract = "Background: The northern European Neolithic is characterized by two major demographic events: immigration of early farmers from Anatolia at 7500 years before present, and their admixture with local western hunter-gatherers forming late farmers, from around 6200 years before present. The influence of this admixture event on variation in the immune-relevant human leukocyte antigen (HLA) region is understudied. Results: We analyzed genome-wide data of 125 individuals from seven archeological early farmer and late farmer sites located in present-day Germany. The late farmer group studied here is associated with the Wartberg culture, from around 5500–4800 years before present. We note that late farmers resulted from sex-biased admixture from male western hunter-gatherers. In addition, we observe Y-chromosome haplogroup I as the dominant lineage in late farmers, with site-specific sub-lineages. We analyze true HLA genotypes from 135 Neolithic individuals, the majority of which were produced in this study. We observe significant shifts in HLA allele frequencies from early farmers to late farmers, likely due to admixture with western hunter-gatherers. Especially for the haplotype DQB1*04:01-DRB1*08:01, there is evidence for a western hunter-gatherer origin. The HLA diversity increased from early farmers to late farmers. However, it is considerably lower than in modern populations. Conclusions: Both early farmers and late farmers exhibit a relatively narrow HLA allele spectrum compared to today. This coincides with sparse traces of pathogen DNA, potentially indicating a lower pathogen pressure at the time.",
keywords = "Admixture, Ancient DNA, European Neolithic, HLA diversity, Immune genes, Population genetics",
author = "{da Silva}, {Nicolas Antonio} and Onur {\"O}zer and Magdalena Haller-Caskie and Chen, {Yan Rong} and Daniel Kolbe and Sabine Schade-Lindig and Joachim Wahl and Carola Berszin and Michael Francken and Irina G{\"o}rner and Kerstin Schierhold and Joachim Pechtl and Gisela Grupe and Christoph Rinne and Johannes M{\"u}ller and Lenz, {Tobias L.} and Almut Nebel and Ben Krause-Kyora",
year = "2025",
month = feb,
day = "28",
doi = "10.1186/s13059-025-03509-6",
language = "English",
volume = "26",
journal = "Genome biology",
issn = "1474-7596",
publisher = "BioMed Central Ltd.",
number = "1",

}

@article{f18dc2f663d945dbbde23268d15fed30,
title = "Autoimmunity Against Surfactant Protein B Is Associated with Pneumonitis During Checkpoint Blockade",
abstract = "Rationale: Immune checkpoint inhibitor (ICI)–related pneumonitis is a serious autoimmune event affecting as many as 20% of patients with non–small-cell lung cancer (NSCLC), yet the factors underpinning its development in some patients and not others are poorly understood. Objectives: To investigate the role of autoantibodies and autoreactive T cells against surfactant-related proteins in the development of pneumonitis. Methods: The study cohort consisted of patients with NSCLC who provided blood samples before and during ICI treatment. Serum was used for proteomics analyses and to detect autoantibodies present during pneumonitis. T-cell stimulation assays and single-cell RNA sequencing were performed to investigate the specificity and functionality of peripheral autoreactive T cells. The findings were confirmed in a validation cohort comprising patients with NSCLC and patients with melanoma. Measurements and Main Results: Across both cohorts, patients in whom pneumonitis developed had higher pretreatment levels of immunoglobulin G autoantibodies targeting surfactant protein (SP)-B. At the onset of pneumonitis, these patients also exhibited higher frequencies of CD41 IFN-g-positive SP-B-specific T cells and expanding T-cell clonotypes recognizing this protein, accompanied by a proinflammatory serum proteomic profile. Conclusions: Our data suggest that the cooccurrence of SP-B-specific immunoglobulin G autoantibodies and CD41 T cells is associated with the development of pneumonitis during ICI therapy. Pretreatment levels of these antibodies may represent a potential biomarker for an increased risk of developing pneumonitis, and on-treatment levels may provide a diagnostic aid.",
keywords = "autoimmunity, immune checkpoint inhibitor, non–small-cell lung cancer, pneumonitis, surfactant protein B",
author = "Nina Wyss and Fiamma Berner and Vincent Walter and Jochum, {Ann Kristin} and Purde, {Mette T.} and Abdou, {Marie Therese} and Tobias Sinnberg and Kathrin Hofmeister and Pop, {Oltin T.} and Ali, {Omar Hasan} and Jens Bauer and Cheng, {Hung Wei} and Mechthild Lutge and Niklas Klumper and Stefan Diem and Zeynep Kosaloglu-Yalcin and Yizheng Zhang and Laura Sellmer and Boris Macek and Julia Karbach and David Konig and Heinz Laubli and Lars Zender and Meyer, {Britta S.} and Christoph Driessen and Schurch, {Christian M.} and Wolfram Jochum and Teresa Amaral and Lucie Heinzerling and Antonio Cozzio and Hegazy, {Ahmed N.} and Tino Schneider and Brutsche, {Martin H.} and Alessandro Sette and Lenz, {Tobias L.} and Juliane Walz and Rammensee, {Hans Georg} and Martin Fruh and Elke Jager and Burkhard Becher and Amanda Tufman and Nicolas Nu{\~n}ez and Markus Joerger and Lukas Flatz",
note = "Publisher Copyright: Copyright {\textcopyright} 2024 by the American Thoracic Society.",
year = "2024",
month = oct,
day = "1",
doi = "10.1164/rccm.202311-2136OC",
language = "English",
volume = "210",
pages = "919--930",
journal = "American journal of respiratory and critical care medicine",
issn = "1073-449X",
publisher = "American Thoracic Society",
number = "7",

}

@inbook{a5a6c6c386ee4ef18b79786781ec2562,
title = "HLA Genes - A Hallmark of Functional Genetic Variation and Complex Evolution",
abstract = "The major histocompatibility complex (MHC) with its highly polymorphic HLA genes represents one of the most intensely studied genomic regions in the genome. MHC proteins play a key role in antigen-specific immunity and are associated with a wide range of complex diseases. Despite decades of research and many advances in the field, the characterization and interpretation of its genetic and genomic variability remain challenging. Here an overview is provided of the MHC, the nature of its exceptional variability, and the complex evolutionary processes assumed to drive this variability. Highlighted are also recent advances in the field that promise to improve our understanding of the variability in the MHC and in antigen-specific immunity more generally.",
keywords = "Adaptive immunity, Antigen presentation, Antigen-specific immunity, Genetic variation, HLA genes, Host–pathogen coevolution, Human leukocyte antigen (HLA), Immunogenetics, Major histocompatibility complex (MHC)",
author = "Lenz, {Tobias L.}",
note = "Publisher Copyright: {\textcopyright} 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.",
year = "2024",
month = may,
doi = "10.1007/978-1-0716-3874-3_1",
language = "English",
isbn = "978-1-0716-3873-6",
series = "Methods in Molecular Biology",
publisher = "Springer Nature",
pages = "1--18",
editor = "Sebastian Boegel",
booktitle = "HLA Typing",
address = "Germany",

}

@article{489dd53710064811bb78af6a0ccd7822,
title = "Template-specific optimization of NGS genotyping pipelines reveals allele-specific variation in MHC gene expression",
abstract = "Using high-throughput sequencing for precise genotyping of multi-locus gene families, such as the major histocompatibility complex (MHC), remains challenging, due to the complexity of the data and difficulties in distinguishing genuine from erroneous variants. Several dedicated genotyping pipelines for data from high-throughput sequencing, such as next-generation sequencing (NGS), have been developed to tackle the ensuing risk of artificially inflated diversity. Here, we thoroughly assess three such multi-locus genotyping pipelines for NGS data, the DOC method, AmpliSAS and ACACIA, using MHC class IIβ data sets of three-spined stickleback gDNA, cDNA and “artificial” plasmid samples with known allelic diversity. We show that genotyping of gDNA and plasmid samples at optimal pipeline parameters was highly accurate and reproducible across methods. However, for cDNA data, the gDNA-optimal parameter configuration yielded decreased overall genotyping precision and consistency between pipelines. Further adjustments of key clustering parameters were required tο account for higher error rates and larger variation in sequencing depth per allele, highlighting the importance of template-specific pipeline optimization for reliable genotyping of multi-locus gene families. Through accurate paired gDNA-cDNA typing and MHC-II haplotype inference, we show that MHC-II allele-specific expression levels correlate negatively with allele number across haplotypes. Lastly, sibship-assisted cDNA-typing of MHC-I revealed novel variants linked in haplotype blocks, and a higher-than-previously-reported individual MHC-I allelic diversity. In conclusion, we provide novel genotyping protocols for the three-spined stickleback MHC-I and -II genes, and evaluate the performance of popular NGS-genotyping pipelines. We also show that fine-tuned genotyping of paired gDNA-cDNA samples facilitates amplification bias-corrected MHC allele expression analysis.",
keywords = "amplicon genotyping, AmpliSAS, bioinformatics pipelines, major histocompatibility complex, multigene families, next-generation sequencing",
author = "Artemis Efstratiou and Arnaud Gaigher and Sven K{\"u}nzel and Ana Teles and Lenz, {Tobias L.}",
note = "Publisher Copyright: {\textcopyright} 2024 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.",
year = "2024",
month = may,
doi = "10.1111/1755-0998.13935",
language = "English",
volume = "24",
journal = "Molecular Ecology Resources",
issn = "1755-098X",
publisher = "Wiley-Blackwell Publishing Ltd",
number = "4",

}

@article{df6960f4a9d44bceac538218e749909d,
title = "Disruption of a Plasmodium falciparum patatin-like phospholipase delays male gametocyte exflagellation",
abstract = "An essential process in transmission of the malaria parasite to the Anopheles vector is the conversion of mature gametocytes into gametes within the mosquito gut, where they egress from the red blood cell (RBC). During egress, male gametocytes undergo exflagellation, leading to the formation of eight haploid motile microgametes, while female gametes retain their spherical shape. Gametocyte egress depends on sequential disruption of the parasitophorous vacuole membrane and the host cell membrane. In other life cycle stages of the malaria parasite, phospholipases have been implicated in membrane disruption processes during egress, however their importance for gametocyte egress is relatively unknown. Here, we performed comprehensive functional analyses of six putative phospholipases for their role during development and egress of Plasmodium falciparum gametocytes. We localize two of them, the prodrug activation and resistance esterase (PF3D7_0709700) and the lysophospholipase 1 (PF3D7_1476700), to the parasite plasma membrane. Subsequently, we show that disruption of most of the studied phospholipase genes does neither affect gametocyte development nor egress. The exception is the putative patatin-like phospholipase 3 (PF3D7_0924000), whose gene deletion leads to a delay in male gametocyte exflagellation, indicating an important, albeit not essential, role of this enzyme in male gametogenesis.",
keywords = "egress, exflagellation, gametocyte, malaria, phospholipase",
author = "Emma Pietsch and Korbinian Niederm{\"u}ller and Mia Andrews and Meyer, {Britta S.} and Lenz, {Tobias L.} and Wilson, {Danny W.} and Gilberger, {Tim Wolf} and Burda, {Paul Christian}",
note = "Publisher Copyright: {\textcopyright} 2023 The Authors. Molecular Microbiology published by John Wiley & Sons Ltd.",
year = "2024",
month = mar,
doi = "10.1111/mmi.15211",
language = "English",
volume = "121",
pages = "529--542",
journal = "Molecular Microbiology",
issn = "0950-382X",
publisher = "John Wiley and Sons Inc.",
number = "3",

}

@article{016aebfe3af34235a1d5718c59e34702,
title = "An immunogenetic basis for lung cancer risk",
abstract = "Cancer risk is influenced by inherited mutations, DNA replication errors, and environmental factors. However, the influence of genetic variation in immunosurveillance on cancer risk is not well understood. Leveraging population-level data from the UK Biobank and FinnGen, we show that heterozygosity at the human leukocyte antigen (HLA)-II loci is associated with reduced lung cancer risk in smokers. Fine-mapping implicated amino acid heterozygosity in the HLA-II peptide binding groove in reduced lung cancer risk, and single-cell analyses showed that smoking drives enrichment of proinflammatory lung macrophages and HLA-II+ epithelial cells. In lung cancer, widespread loss of HLA-II heterozygosity (LOH) favored loss of alleles with larger neopeptide repertoires. Thus, our findings nominate genetic variation in immunosurveillance as a critical risk factor for lung cancer.",
author = "Chirag Krishna and Anniina Tervi and Miriam Saffern and Wilson, {Eric A.} and Yoo, {Seong Keun} and Nina Mars and Vladimir Roudko and Cho, {Byuri Angela} and Jones, {Samuel Edward} and Natalie Vaninov and Selvan, {Myvizhi Esai} and G{\"u}m{\"u}{\c s}, {Zeynep H.} and FinnGen and Lenz, {Tobias L.} and Miriam Merad and Paolo Boffetta and Francisco Mart{\'i}nez-Jim{\'e}nez and Ollila, {Hanna M.} and Samstein, {Robert M.} and Diego Chowell",
note = "Publisher Copyright: {\textcopyright} 2024 American Association for the Advancement of Science. All rights reserved.",
year = "2024",
month = feb,
day = "23",
doi = "10.1126/science.adi3808",
language = "English",
volume = "383",
pages = "1--18",
journal = "Science",
issn = "0036-8075",
publisher = "American Association for the Advancement of Science",
number = "6685",

}

@article{eabb13ae85504df3a383aadbf6822617,
title = "Origin matters: Using a local reference genome improves measures in population genomics",
abstract = "Genome sequencing enables answering fundamental questions about the genetic basis of adaptation, population structure and epigenetic mechanisms. Yet, we usually need a suitable reference genome for mapping population-level resequencing data. In some model systems, multiple reference genomes are available, giving the challenging task of determining which reference genome best suits the data. Here, we compared the use of two different reference genomes for the three-spined stickleback (Gasterosteus aculeatus), one novel genome derived from a European gynogenetic individual and the published reference genome of a North American individual. Specifically, we investigated the impact of using a local reference versus one generated from a distinct lineage on several common population genomics analyses. Through mapping genome resequencing data of 60 sticklebacks from across Europe and North America, we demonstrate that genetic distance among samples and the reference genomes impacts downstream analyses. Using a local reference genome increased mapping efficiency and genotyping accuracy, effectively retaining more and better data. Despite comparable distributions of the metrics generated across the genome using SNP data (i.e. π, Tajima's D and F ST), window-based statistics using different references resulted in different outlier genes and enriched gene functions. A marker-based analysis of DNA methylation distributions had a comparably high overlap in outlier genes and functions, yet with distinct differences depending on the reference genome. Overall, our results highlight how using a local reference genome decreases reference bias to increase confidence in downstream analyses of the data. Such results have significant implications in all reference-genome-based population genomic analyses.",
keywords = "Gasterosteus aculeatus, Genome assembly, Gynogenetic, Population genomics, Read mapping, Reference genomes, Reference mapping bias, Stickleback",
author = "DMJ Thorburn and K Sagonas and M Binzer-Panchal and FJJ Chain and PGD Feulner and E Bornberg-Bauer and TBH Reusch and IE Samonte-Padilla and M Milinski and TL Lenz and C Eizaguirre",
year = "2023",
month = oct,
doi = "10.1111/1755-0998.13838",
language = "English",
volume = "23",
pages = "1706--1723",
journal = "Molecular Ecology Resources",
issn = "1755-098X",
publisher = "Wiley-Blackwell Publishing Ltd",
number = "7",

}

@article{656d6f68fc694ea188137b1ae31070c5,
title = "A second update on mapping the human genetic architecture of COVID-19",
keywords = "Humans, COVID-19, Human Genetics",
author = "{COVID-19 Host Genetics Initiative} and Tobias Lenz and Ana Teles and Clinton Azuure and Onur {\"O}zer",
year = "2023",
month = sep,
day = "7",
doi = "10.1038/s41586-023-06355-3",
language = "English",
volume = "621",
pages = "E7--E26",
journal = "Nature",
issn = "0028-0836",
publisher = "Nature Research",
number = "7977",

}

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