Publications

[Preprints] [2023] [2022] [2021] [2020] [2019] [2018] [2017] [2016] [BibTeX file]

Preprints

Jahn D, Knapstein PR, Otto E, Köhli P, Sevecke J, Graef F, Graffmann C, Fuchs M, Jiang S, Rickert M, Erdmann C, Appelt J, Revend L, Küttner Q, Witte J, Rahmani A, Duda G, Xie W, Donat A, Schinke T, Ivanov A, Tchouto MN, Beule D, Frosch K, Baranowsky A, Tsitsilonis S, Keller J (2023). “Increased beta2-adrenergic signaling is a targetable stimulus essential for bone healing by promoting callus neovascularization.” bioRxiv, 2023-07. doi:doi.org/10.1101/2023.07.14.548550 ☞ Link

Boeddrich A, Haenig C, Neuendorf N, Blanc E, Ivanov A, Kirchner M, Schleumann P, Bayraktaroglu I, Richter M, Molenda CM, Sporbert A, Zenkner M, Schnoegl S, Suenkel C, Schneider L, Rybak-Wolf A, Kochnowsky B, Byrne LM, Wild EJ, Nielsen JE, Dittmar G, Peters O, Beule D, Wanker EE (2023). “A proteomics analysis of 5xFAD mouse brain regions reveals the lysosome-associated protein Arl8b as a candidate biomarker for Alzheimer’s disease.” bioRxiv, 2023-01. doi:10.1101/2023.01.16.523715 ☞ Link

Ermshaus A, Piechotta M, Ruter G, Keilholz U, Leser U, Benary M (2023). “preon: Fast and accurate entity normalization for drug names and cancer types in precision oncology.” bioRxiv, 2023-05. doi:10.1101/2023.05.22.540912

Yerinde C, Keye J, Durlanik S, Freise I, Nowak F, Hsiao H, Letizia M, Schlickeiser S, Obermayer B, Huck A, Friedrich M, Wu H, Kunkel D, Kühl AA, Bauer S, Thiel A, Siegmund B, Glauben R, Weidinger C (2022). “HDAC7 controls anti-viral and anti-tumor immunity by CD8+ T cells.” bioRxiv. doi:10.1101/2022.09.18.508452 ☞ Link

Winkler W, Díaz C, Blanc E, Napieczynska H (2021). “Preclinical models of human multiple myeloma subgroups.” bioRxiv. doi:10.1101/2021.08.28.458010 ☞ Link

Göppel T, Obermayer B, Chen I, Gerland U (2021). “A kinetic error filtering mechanism for enzyme-free copying of nucleic acid sequences.” bioRxiv. doi:10.1101/2021.08.06.455386 ☞ Link

2023

Ludwik KA, Opitz R, Jyrch S, Megges M, Weiner J, Beule D, Kühnen P, Stachelscheid H (2023). “Generation of iPSC lines with SLC16A2: G410R or SLC16A2 knock out.” Stem Cell Research, 103256. doi:10.1016/j.scr.2023.103256 ☞ Link

Schneemann M, Heils L, Moos V, Weiß F, Krug SM, Weiner J, Beule D, Gerhard R, Schulzke J, Bücker R (2023). “A Colonic Organoid Model Challenged with the Large Toxins of Clostridioides difficile TcdA and TcdB Exhibit Deregulated Tight Junction Proteins.” Toxins, 15(11), 643. doi:10.3390/toxins15110643 ☞ Link

Monsorno K, Ginggen K, Ivanov A, Buckinx A, Lalive AL, Tchenio A, Benson S, Vendrell M, D’Alessandro A, Beule D, Pellerin L, Mameli M, Paolicelli RC (2023). “Loss of microglial MCT4 leads to defective synaptic pruning and anxiety-like behavior in mice.” Nature Communications, 14(1), 5749.

Zheng L, Chopra A, Weiner J, Beule D, Dommisch H, Schaefer A (2023). “miRNAs from inflamed gingiva link gene signaling to increased MET expression.” Journal of Dental Research, 00220345231197984. doi:10.1177/002203452311979 ☞ Link

Mhlekude B, Postmus D, Stenzel S, Weiner J, Jansen J, Zapatero-Belinchòn FJ, Olmer R, Richter A, Heinze J, Heinemann N, Mühlemann B, Schroeder S, Jones TC, Müller MA, Drosten C, Pich A, Thiel V, Martin U, Niemeyer D, Gerold G, Beule D, Goffinet C (2023). “Pharmacological inhibition of bromodomain and extra-terminal proteins induces an NRF-2-mediated antiviral state that is subverted by SARS-CoV-2 infection.” PLoS pathogens, 19(9), e1011657. doi:10.1371/journal.ppat.1011657 ☞ Link

Benary M, Wang XD, Schmidt M, Soll D, Hilfenhaus G, Nassir M, Sigler C, Knödler M, Keller U, Beule D, Keilholz U, Leser U, Rieke DT (2023). “Leveraging Large Language Models for Decision Support in Personalized Oncology.” JAMA Network Open, 6(11), e2343689-e2343689. doi:10.1001/jamanetworkopen.2023.43689

Briest F, Noerenberg D, Hennch C, Yoshida K, Hablesreiter R, Nimo J, Sasca D, Kirchner M, Mansouri L, Inoue Y, Wiegand L, Staiger AM, Casadei B, Korkolopoulou P, Weiner J, Lopez-Guillermo A, Warth A, Schneider T, Nagy Á, Klapper W, Hummel M, Kanellis G, Anagnostopoulos I, Mertins P, Bullinger L, Rosenquist R, Vassilakopoulos TP, Ott G, Ogawa S, Damm F (2023). “Frequent ZNF217 mutations lead to transcriptional deregulation of interferon signal transduction via altered chromatin accessibility in B cell lymphoma.” Leukemia, 1-13. doi:10.1038/s41375-023-02013-9 ☞ Link

Spranger L, Weiner J, Bredow J, Zeitz U, Grittner U, Boschmann M, Dickmann S, Stobäus N, Schwartzenberg RJ, Brachs M, Spranger J, Mai K (2023). “Thrifty energy phenotype predicts weight regain in postmenopausal women with overweight or obesity and is related to FGFR1 signaling.” Clinical Nutrition, 42(4), 559-567. doi:10.1016/j.clnu.2023.02.020 ☞ Link

Chopra A, Song J, Weiner J, Keceli HG, Dincer PR, Cruz R, Carracedo A, Blanco J, Dommisch H, Schaefer AS (2023). “RSPO4 is a potential risk gene of stages III-IV, grade C periodontitis through effects on innate immune response and oral barrier integrity.” Journal of Clinical Periodontology, 50(4), 476-486. doi:10.1111/jcpe.13758 ☞ Link

Lechner L, Opitz R, Silver MJ, Krabusch PM, Prentice AM, Field MS, Stachelscheid H, Leitão E, Schröder C, Vallone VF, Horsthemke B, Jöckel K, Schmidt B, Nöthen MM, Hoffmann P, Herms S, Kleyn PW, Megges M, Blume-Peytavi U, Weiss K, Mai K, Blankenstein O, Obermayer B, Wiegand S, Kühnen PKP (2023). “Early-set POMC methylation variability is accompanied by increased risk for obesity and is addressable by MC4R agonist treatment.” Science Translational Medicine, 15(705), eadg1659. doi:10.1126/scitranslmed.adg1659 ☞ Link

Obermayer B, Keilholz L, Conrad T, Frentsch M, Blau I, Vuong L, Lesch S, Movasshagi K, Tietze-Stolley C, Loyal L, Henze L, Penack O, Stervbo U, Babel N, Haas S, Beule D, Bullinger L, Wittenbecher F, Na I (2023). “Single-cell clonal tracking of persistent T-cells in allogeneic hematopoietic stem cell transplantation.” Frontiers in Immunology, 14. ISSN 1664-3224, doi:10.3389/fimmu.2023.1114368 ☞ Link

Gressier E, Schulte-Schrepping J, Petrov L, Brumhard S, Stubbemann P, Hiller A, Obermayer B, Spitzer J, Kostevc T, Whitney PG, Bachem A, Odainic A, van de Sandt C, Nguyen THO, Ashhurst T, Wilson K, Oates CVL, Gearing LJ, Meischel T, Hochheiser K, Greyer M, Clarke M, Kreutzenbeck M, Gabriel SS, Kastenmüller W, Kurts C, Londrigan SL, Kallies A, Kedzierska K, Hertzog PJ, Latz E, Chen YE, Radford KJ, Chopin M, Schroeder J, Kurth F, Gebhardt T, Sander LE, Sawitzki B, Schultze JL, Schmidt SV, Bedoui S (2023). “CD4+ T cell calibration of antigen-presenting cells optimizes antiviral CD8+ T cell immunity.” Nature Immunology, 24(6), 979-990. ISSN 1529-2916, doi:10.1038/s41590-023-01517-x ☞ Link

Loedige I, Baranovskii A, Mendonsa S, Dantsuji S, Popitsch N, Breimann L, Zerna N, Cherepanov V, Milek M, Ameres S, Chekulaeva M (2023). “mRNA stability and m6A are major determinants of subcellular mRNA localization in neurons.” Molecular Cell, 83(15), 2709-2725.e10. ISSN 1097-2765, doi:10.1016/j.molcel.2023.06.021 ☞ Link

de Bortoli T, Benary M, Horak P, Lamping M, Stintzing S, Tinhofer I, Leyvraz S, Schäfer R, Klauschen F, Keller U, Rieke DT, Jelas I (2023). “Tumour mutational burden and survival with molecularly matched therapy.” European Journal of Cancer, 190, 112925. doi:10.1016/j.ejca.2023.05.013 ☞ Link

Stellmach C, Sass J, Auber B, Boeker M, Wienker T, Heidel AJ, Benary M, Schumacher S, Ossowski S, Klauschen F, Möller Y, Schmutzler R, Ustjanzew A, Werner P, Tomczak A, Hölter T, Thun S (2023). “Creation of a structured molecular genomics report for Germany as a local adaption of HL7’s Genomic Reporting Implementation Guide.” Journal of the American Medical Informatics Association. ISSN 1527-974X, doi:10.1093/jamia/ocad061 ☞ Link

Winkler W, Díaz CF, Blanc E, Napieczynska H, Langner P, Werner M, Walter B, Wollert-Wulf B, Yasuda T, Heuser A, Beule D, Mathas S, Anagnostopoulos I, Rosenwald A, Rajewsky K, Janz M (2023). “Mouse models of human multiple myeloma subgroups.” Proceedings of the National Academy of Sciences of the United States of America, 120, e2219439120. ISSN 1091-6490, doi:10.1073/pnas.2219439120 ☞ Link

Spranger L, Weiner J, Bredow J, Zeitz U, Grittner U, Boschmann M, Dickmann S, Stobaus N, Schwartzenberg JJ, Brachs M, Spranger J, Mai K (2023). “Thrifty energy phenotype predicts weight regain in postmenopausal women with overweight or obesity and is related to FGFR1 signaling.” Clinical Nutrition, 42, 559-567. doi:10.1016/j.clnu.2023.02.020 ☞ Link

Freitag K, Eede P, Ivanov A, Sterczyk N, Schneeberger S, Borodina T, Sauer S, Beule D, Heppner F (2023). “Diverse but unique astrocytic phenotypes during embryonic stem cell differentiation, culturing and development.” Commun Biol, 6, 40. doi:10.1038/s42003-023-04410-3 ☞ Link

Nieminen M, Stolpe O, Kuhring M, Weiner J, Pett P, Beule D, Holtgrewe M (2023). “SODAR: managing multiomics study data and metadata.” Gigascience, 12, giad052. doi:10.1093/gigascience/giad052 ☞ Link

Graff P, Wilzopolski J, Voss A, Blimkie TM, Weiner J3, Kershaw O, Panwar P, Hackett T, Brömme D, Loyal L, Thiel A, Beule D, Hancock RE, Gruber AD, Bäumer W, Hedtrich S (2023). “Extracellular matrix remodeling in atopic dermatitis harnesses the onset of an asthmatic phenotype and is a potential contributor to the atopic march.” Journal of Investigative Dermatology. doi:10.1016/j.jid.2023.09.278

Müller R, Freitag-Wolf S, Weiner J3, Chopra A, Top T, Dommisch H, Schaefer A (2023). “Case-only design identifies interactions of genetic risk variants at SIGLEC5 and PLG with the lncRNA CTD-2353F22.1 implying the importance of periodontal wound healing for disease aetiology.” J Clin Periodontol, 50, 90-101. doi:10.1111/jcpe.13712 ☞ Link

Mothes R, Pascual-Reguant A, Koehler R, Liebeskind J, Liebheit A, Bauherr S, Philipsen L, Dittmayer C, Laue M, von Manitius R, Elezkurtaj S, Durek P, Heinrich F, Heinz GA, Guerra GM, Obermayer B, Meinhardt J, Ihlow J, Radke J, Heppner FL, Enghard P, Stockmann H, Aschman T, Schneider J, Corman VM, Sander LE, Mashreghi M, Conrad T, Hocke AC, Niesner RA, Radbruch H, Hauser AE (2023). “Distinct tissue niches direct lung immunopathology via CCL18 and CCL21 in severe COVID-19.” Nature Communications, 14(1), 791. ISSN 2041-1723, doi:10.1038/s41467-023-36333-2 ☞ Link

Rieke DT, Schröder S, Schafhausen P, Blanc E, Zuljan E, von der Emde B, Beule D, Keller U, Keilholz U, Klinghammer K (2023). “Targeted treatment in a case series of AR+, HRAS/PIK3CA co-mutation salivary duct carcinoma.” Frontiers in Oncology, 13. ISSN 2234-943X, doi:10.3389/fonc.2023.1107134

2022

Baumgardt M, Hülsemann M, Löwa A, Fatykhova D, Hoffmann K, Kessler M, Mieth M, Hellwig K, Frey D, Langenhagen A, Voss A, Obermayer B, Wyler E, Dökel S, Gruber AD, Tölch U, Hippenstiel S, Hocke AC, Hönzke K (2022). “State-of-the-art analytical methods of viral infections in human lung organoids.” PLOS ONE, 17(12), 1-8. doi:10.1371/journal.pone.0276115 ☞ Link

Pennitz P, Kirsten H, Friedrich VD, Wyler E, Goekeri C, Obermayer B, Heinz GA, Mashreghi M, B"uttner M, Trimpert J, Landthaler M, Suttorp N, Hocke AC, Hippenstiel S, T"onnies M, Scholz M, Kuebler WM, Witzenrath M, Hoenzke K, Nouailles G (2022). “A pulmonologist’s guide to perform and analyse cross-species single lung cell transcriptomics.” European Respiratory Review, 31(165). ISSN 0905-9180, doi:10.1183/16000617.0056-2022 ☞ Link

Bertrams W, Hönzke K, Obermayer B, Tönnies M, Bauer TT, Schneider P, Neudecker J, Rückert JC, Stiewe T, Nist A, Eggeling S, Suttorp N, Wolff T, Hippenstiel S, Schmeck B, Hocke AC (2022). “Transcriptomic comparison of primary human lung cells with lung tissue samples and the human A549 lung cell line highlights cell type specific responses during infections with influenza A virus.” Scientific Reports, 12(1), 20608. ISSN 2045-2322, doi:10.1038/s41598-022-24792-4 ☞ Link

Jarick K, Topczewska P, Jakob M, Yano H, Arifuzzaman M, Gao X, Boulekou S, Stokic-Trtica V, Leclère P, Preußer A, Rompe Z, Stamm A, Tsou A, Chu C, Heinrich F, Guerra G, Durek P, Ivanov A, Beule D, Helfrich S, Duerr C, Kühl A, Stehle C, Romagnani C, Mashreghi M, Diefenbach A, Artis D, Klose C (2022). “Non-redundant functions of group 2 innate lymphoid cells.” Nature, 611(7937), 794-800. doi:10.1038/s41586-022-05395-5 ☞ Link

Ivanov A, Mattei D, Radscheit K, Compagnion A, Pett J, Herzel H, Paolicelli R, Piwecka M, Meyer U, Beule D (2022). “Analyses of circRNA Expression throughout the Light-Dark Cycle Reveal a Strong Regulation of Cdr1as, Associated with Light Entrainment in the SCN.” Int J Mol Sci, 23. doi:10.3390/ijms232012347 ☞ Link

Wirges A, Bunse M, Joedicke J, Blanc E, Gudipati V, Moles M, Shiku H, Beule D, Huppa J, Höpken U, Rehm A (2022). “EBAG9 silencing exerts an immune checkpoint function without aggravating adverse effects.” Mol Ther, 30, 3358-3378. doi:10.1016/j.ymthe.2022.07.009 ☞ Link

Hönzke K, Obermayer B, Mache C, Fathykova D, Kessler M, Dökel S, Wyler E, Baumgardt M, Löwa A, Hoffmann K, Graff P, Schulze J, Mieth M, Hellwig K, Demir Z, Biere B, Brunotte L, Mecate-Zambrano A, Bushe J, Dohmen M, Hinze C, Elezkurtaj S, Tönnies M, Bauer T, Eggeling S, Tran H, Schneider P, Neudecker J, Rückert J, Schmidt-Ott K, Busch J, Klauschen F, Horst D, Radbruch H, Radke J, Heppner F, Corman V, Niemeyer D, Müller M, Goffinet C, Mothes R, Pascual-Reguant A, Hauser A, Beule D, Landthaler M, Ludwig S, Suttorp N, Witzenrath M, Gruber A, Drosten C, Sander L, Wolff T, Hippenstiel S, Hocke A (2022). “Human lungs show limited permissiveness for SARS-CoV-2 due to scarce ACE2 levels but virus-induced expansion of inflammatory macrophages.” Eur Respir J, 60. doi:10.1183/13993003.02725-2021 ☞ Link

Freitag K, Sterczyk N, Wendlinger S, Obermayer B, Schulz J, Farztdinov V, Mülleder M, Ralser M, Houtman J, Fleck L, Braeuning C, Sansevrino R, Hoffmann C, Milovanovic D, Sigrist S, Conrad T, Beule D, Heppner F, Jendrach M (2022). “Spermidine reduces neuroinflammation and soluble amyloid beta in an Alzheimer’s disease mouse model.” J Neuroinflammation, 19, 172. doi:10.1186/s12974-022-02534-7 ☞ Link

Schalbetter S, von Arx A, Cruz-Ochoa N, Dawson K, Ivanov A, Mueller F, Lin H, Amport R, Mildenberger W, Mattei D, Beule D, Földy C, Greter M, Notter T, Meyer U (2022). “Adolescence is a sensitive period for prefrontal microglia to act on cognitive development.” Sci Adv, 8, eabi6672. doi:10.1126/sciadv.abi6672 ☞ Link

Grunert C, Willimsky G, Peuker C, Rhein S, Hansmann L, Blankenstein T, Blanc E, Beule D, Keller U, Pezzutto A, Busse A (2022). “Isolation of Neoantigen-Specific Human T Cell Receptors from Different Human and Murine Repertoires.” Cancers (Basel), 14. doi:10.3390/cancers14071842 ☞ Link

Dannebaum R, Suwalski P, Asgharian H, Du ZG, Lin H, Weiner J, Holtgrewe M, Thibeault C, Müller M, Wang X, Karadeniz Z, Saccomanno J, Doehn J, Hübner R, Hinzmann B, Blüher A, Siemann S, Telman D, Suttorp N, Witzenrath M, Hippenstiel S, Skurk C, Poller W, Sander L, Beule D, Kurth F, Guettouche T, Landmesser U, Berka J, Luong K, Pa-COVID SG, Rubelt F, Heidecker B (2022). “Highly multiplexed immune repertoire sequencing links multiple lymphocyte classes with severity of response to COVID-19.” EClinicalMedicine, 48, 101438. doi:10.1016/j.eclinm.2022.101438 ☞ Link

Horak P, Griffith M, Danos A, Pitel B, Madhavan S, Liu X, Chow C, Williams H, Carmody L, Barrow-Laing L, Rieke D, Kreutzfeldt S, Stenzinger A, Tamborero D, Benary M, Rajagopal P, Ida C, Lesmana H, Satgunaseelan L, Merker J, Tolstorukov M, Campregher P, Warner J, Rao S, Natesan M, Shen H, Venstrom J, Roy S, Tao K, Kanagal-Shamanna R, Xu X, Ritter D, Pagel K, Krysiak K, Dubuc A, Akkari Y, Li X, Lee J, King I, Raca G, Wagner A, Li M, Plon S, Kulkarni S, Griffith O, Chakravarty D, Sonkin D (2022). “Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC).” Genet Med, 24, 986-998. doi:10.1016/j.gim.2022.01.001 ☞ Link

Weiner J, Obermayer B, Beule D (2022). “Venn Diagrams May Indicate Erroneous Statistical Reasoning in Transcriptomics.” Front Genet, 13, 818683. doi:10.3389/fgene.2022.818683 ☞ Link

Gloaguen Y, Kirwan J, Beule D (2022). “Deep Learning-Assisted Peak Curation for Large-Scale LC-MS Metabolomics.” Anal Chem, 94, 4930-4937. doi:10.1021/acs.analchem.1c02220 ☞ Link

Chopra A, Mueller R, Weiner J3, Rosowski J, Dommisch H, Grohmann E, Schaefer A (2022). “BACH1 Binding Links the Genetic Risk for Severe Periodontitis with ST8SIA1.” J Dent Res, 101, 93-101. doi:10.1177/00220345211017510 ☞ Link

Bischoff P, Trinks A, Wiederspahn J, Obermayer B, Pett J, Jurmeister P, Elsner A, Dziodzio T, Rückert J, Neudecker J, Falk C, Beule D, Sers C, Morkel M, Horst D, Klauschen F, Blüthgen N (2022). “The single-cell transcriptional landscape of lung carcinoid tumors.” Int J Cancer, 150, 2058-2071. doi:10.1002/ijc.33995 ☞ Link

Georg P, Astaburuaga-García R, Bonaguro L, Brumhard S, Michalick L, Lippert L, Kostevc T, Gäbel C, Schneider M, Streitz M, Demichev V, Gemünd I, Barone M, Tober-Lau P, Helbig E, Hillus D, Petrov L, Stein J, Dey H, Paclik D, Iwert C, Mülleder M, Aulakh S, Djudjaj S, Bülow R, Mei H, Schulz A, Thiel A, Hippenstiel S, Saliba A, Eils R, Lehmann I, Mall M, Stricker S, Röhmel J, Corman V, Beule D, Wyler E, Landthaler M, Obermayer B, von Stillfried S, Boor P, Demir M, Wesselmann H, Suttorp N, Uhrig A, Müller-Redetzky H, Nattermann J, Kuebler W, Meisel C, Ralser M, Schultze J, Aschenbrenner A, Thibeault C, Kurth F, Sander L, Blüthgen N, Sawitzki B, PA-COVID-19 SG (2022). “Complement activation induces excessive T cell cytotoxicity in severe COVID-19.” Cell, 185(3), 493-512.e25. ISSN 0092-8674, doi:10.1016/j.cell.2021.12.040 ☞ Link

Zinnall U, Milek M, Minia I, Vieira-Vieira C, Müller S, Mastrobuoni G, Hazapis O, Del GS, Schwefel D, Bley N, Voigt F, Chao J, Kempa S, Hüttelmaier S, Selbach M, Landthaler M (2022). “HDLBP binds ER-targeted mRNAs by multivalent interactions to promote protein synthesis of transmembrane and secreted proteins.” Nat Commun, 13(1), 2727. doi:10.1038/s41467-022-30322-7 ☞ Link

Dörr D, Obermayer B, Weiner J, Zimmermann K, Anania C, Wagner L, Lyras E, Sapozhnikova V, Lara-Astiaso D, Prósper F, Lang R, Lupiáñez D, Beule D, Höpken U, Leutz A, Mildner A (2022). “C/EBPβ regulates lipid metabolism and Pparg isoform 2 expression in alveolar macrophages.” Sci Immunol, 7(75), eabj0140. doi:10.1126/sciimmunol.abj0140 ☞ Link

Kedziora S, Obermayer B, Sugulle M, Herse F, Kräker K, Haase N, Langmia I, Müller D, Staff A, Beule D, Dechend R (2022). “Placental Transcriptome Profiling in Subtypes of Diabetic Pregnancies Is Strongly Confounded by Fetal Sex.” Int J Mol Sci, 23(23). ISSN 1422-0067, doi:10.3390/ijms232315388 ☞ Link

Pennitz P, Kirsten H, Wyler E, Goekeri C, Obermayer B, Heinz GA, Mashreghi MF, Trimpert J, Landthaler M, Suttorp N, Hocke AC, Hippenstiel S, Tönnies M, Scholz M, Kuebler WM, Witzenrath M, Hoenzke K, Nouailles G (2022). “Integrational approaches for cross-species analysis of lung pathologies at single-cell resolution.” Pneumologie, 76(S 01), FV 285. FV 285.

Hoffmann K, Obermayer B, Hönzke K, Fatykhova D, Demir Z, Löwa A, Alves L, Wyler E, Lopez-Rodriguez E, Mieth M, Baumgardt M, Hoppe J, Firsching T, Tönnies M, Bauer T, Eggeling S, Tran H, Schneider P, Neudecker J, Rückert J, Gruber A, Ochs M, Landthaler M, Beule D, Suttorp N, Hippenstiel S, Hocke A, Kessler M (2022). “Human alveolar progenitors generate dual lineage bronchioalveolar organoids.” Commun Biol, 5(1), 875. ISSN 2399-3642, doi:10.1038/s42003-022-03828-5 ☞ Link

Neitzel H, Varon R, Chughtai S, Dartsch J, Dutrannoy-Tönsing V, Nürnberg P, Nürnberg G, Schweiger M, Digweed M, Hildebrand G, Hackmann K, Holtgrewe M, Sarioglu N, Schulze B, Horn D, Sperling K (2022). “Transmission ratio distortion of mutations in the master regulator of centriole biogenesis PLK4.” Hum Genet, 141(11), 1785-1794. doi:10.1007/s00439-022-02461-w ☞ Link

Foddis M, Blumenau S, Holtgrewe M, Paquette K, Westra K, Alonso I, Macario M, Morgadinho A, Velon A, Santo G, Santana I, Mönkäre S, Kuuluvainen L, Schleutker J, Pöyhönen M, Myllykangas L, Pavlovic A, Kostic V, Dobricic V, Lohmann E, Hanagasi H, Santos M, Guven G, Bilgic B, Bras J, Beule D, Dirnagl U, Guerreiro R, Sassi C (2022). “TREX1 p.A129fs and p.Y305C variants in a large multi-ethnic cohort of CADASIL-like unrelated patients.” doi:10.1016/j.neurobiolaging.2022.11.013 ☞ Link

Boschann F, Moreno D, Mensah M, Sczakiel H, Skipalova K, Holtgrewe M, Mundlos S, Fischer-Zirnsak B (2022). “Xq27.1 palindrome mediated interchromosomal insertion likely causes familial congenital bilateral laryngeal abductor paralysis (Plott syndrome).” J Hum Genet, 67(7), 405-410. doi:10.1038/s10038-022-01018-z ☞ Link

Seidel F, Laser K, Klingel K, Dartsch J, Theisen S, Pickardt T, Holtgrewe M, Gärtner A, Berger F, Beule D, Milting H, Schubert S, Klaassen S, Kühnisch J (2022). “Pathogenic Variants in Cardiomyopathy Disorder Genes Underlie Pediatric Myocarditis-Further Impact of Heterozygous Immune Disorder Gene Variants?” J Cardiovasc Dev Dis, 9(7), 216. doi:10.3390/jcdd9070216 ☞ Link

May V, Koch L, Fischer-Zirnsak B, Horn D, Gehle P, Kornak U, Beule D, Holtgrewe M (2022). “ClearCNV: CNV calling from NGS panel data in the presence of ambiguity and noise.” Bioinformatics, 38(16), 3871-3876. doi:10.1093/bioinformatics/btac418 ☞ Link

Schöpflin R, Melo U, Moeinzadeh H, Heller D, Laupert V, Hertzberg J, Holtgrewe M, Alavi N, Klever M, Jungnitsch J, Comak E, Türkmen S, Horn D, Duffourd Y, Faivre L, Callier P, Sanlaville D, Zuffardi O, Tenconi R, Kurtas N, Giglio S, Prager B, Latos-Bielenska A, Vogel I, Bugge M, Tommerup N, Spielmann M, Vitobello A, Kalscheuer V, Vingron M, Mundlos S (2022). “Integration of Hi-C with short and long-read genome sequencing reveals the structure of germline rearranged genomes.” Nat Commun, 13(1), 6470. doi:10.1038/s41467-022-34053-7 ☞ Link

Rieke D, de BT, Horak P, Lamping M, Benary M, Jelas I, Rüter G, Berger J, Zettwitz M, Kagelmann N, Kind A, Fabian F, Beule D, Glimm H, Brors B, Stenzinger A, Fröhling S, Keilholz U (2022). “Feasibility and outcome of reproducible clinical interpretation of high-dimensional molecular data: a comparison of two molecular tumor boards.” BMC Med, 20, 367. ISSN 17417015, doi:10.1186/s12916-022-02560-5 ☞ Link

Hinze C, Kocks C, Leiz J, Karaiskos N, Boltengagen A, Cao S, Skopnik C, Klocke J, Hardenberg J, Stockmann H, Gotthardt I, Obermayer B, Haghverdi L, Wyler E, Landthaler M, Bachmann S, Hocke A, Corman V, Busch J, Schneider W, Himmerkus N, Bleich M, Eckardt K, Enghard P, Rajewsky N, Schmidt-Ott K (2022). “Single-cell transcriptomics reveals common epithelial response patterns in human acute kidney injury.” Genome Med, 14, 103. doi:10.1186/s13073-022-01108-9 ☞ Link

Richter G, Wagner G, Reichenmiller K, Staufenbiel I, Martins O, Löscher B, Holtgrewe M, Jepsen S, Dommisch H, Schaefer A (2022). “Exome Sequencing of 5 Families with Severe Early-Onset Periodontitis.” J Dent Res, 101(2), 151-157. doi:10.1177/00220345211029266 ☞ Link

Coutelier M, Holtgrewe M, Jäger M, Flöttman R, Mensah M, Spielmann M, Krawitz P, Horn D, Beule D, Mundlos S (2022). “Combining callers improves the detection of copy number variants from whole-genome sequencing.” Eur J Hum Genet, 30(2), 178-186. doi:10.1038/s41431-021-00983-x ☞ Link

Vogt G, Verheyen S, Schwartzmann S, Ehmke N, Potratz C, Schwerin-Nagel A, Plecko B, Holtgrewe M, Seelow D, Blatterer J, Speicher M, Kornak U, Horn D, Mundlos S, Fischer-Zirnsak B, Boschann F (2022). “Biallelic truncating variants in ATP9A cause a novel neurodevelopmental disorder involving postnatal microcephaly and failure to thrive.” J Med Genet, 59(7), 662-668. doi:10.1136/jmedgenet-2021-107843 ☞ Link

2021

Schinke C, Fernandez VV, Ivanov A, Peng Y, Körtvelyessy P, Nolte L, Huehnchen P, Beule D, Stachelscheid H, Boehmerle W, Endres M (2021). “Dataset for: Modeling chemotherapy induced neurotoxicity with human induced pluripotent stem cell (iPSC)-derived sensory neurons.” Data Brief, 38, 107320. doi:10.1016/j.dib.2021.107320 ☞ Link

Weiner J, Suwalski P, Holtgrewe M, Rakitko A, Thibeault C, Müller M, Patriki D, Quedenau C, Krüger U, Ilinsky V, Popov I, Balnis J, Jaitovich A, Helbig E, Lippert L, Stubbemann P, Real L, Macías J, Pineda J, Fernandez-Fuertes M, Wang X, Karadeniz Z, Saccomanno J, Doehn J, Hübner R, Hinzmann B, Salvo M, Blueher A, Siemann S, Jurisic S, Beer J, Rutishauser J, Wiggli B, Schmid H, Danninger K, Binder R, Corman V, Mühlemann B, Arjun AR, Fragiadakis G, Mick E, Comet C, Calfee C, Erle D, Hendrickson C, Kangelaris K, Krummel M, Woodruff P, Langelier C, Venkataramani U, García F, Zyla J, Drosten C, Alice B, Jones T, Suttorp N, Witzenrath M, Hippenstiel S, Zemojtel T, Skurk C, Poller W, Borodina T, Pa-Covid S, Ripke S, Sander L, Beule D, Landmesser U, Guettouche T, Kurth F, Heidecker B (2021). “Increased risk of severe clinical course of COVID-19 in carriers of HLA-C*04:01.” EClinicalMedicine, 40, 101099. doi:10.1016/j.eclinm.2021.101099 ☞ Link

Domaszewska T, Zyla J, Otto R, Kaufmann S, Weiner J (2021). “Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients.” Front Immunol, 12, 694680. doi:10.3389/fimmu.2021.694680 ☞ Link

Nouailles G, Wyler E, Pennitz P, Postmus D, Vladimirova D, Kazmierski J, Pott F, Dietert K, Muelleder M, Farztdinov V, Obermayer B, Wienhold S, Andreotti S, Hoefler T, Sawitzki B, Drosten C, Sander LE, Suttorp N, Ralser M, Beule D, Gruber AD, Goffinet C, Landthaler M, Trimpert J, Witzenrath M (2021). “Single-cell-sequencing in SARS-COV-2-infected hamsters sheds light on endothelial cell involvement in COVID-19.” European Respiratory Journal. doi:10.1183/13993003.congress-2021.PA2355 ☞ Link

Bischoff P, Trinks A, Obermayer B, Pett J, Wiederspahn J, Uhlitz F, Liang X, Lehmann A, Jurmeister P, Elsner A, Dziodzio T, Rückert J, Neudecker J, Falk C, Beule D, Sers C, Morkel M, Horst D, Blüthgen N, Klauschen F (2021). “Single-cell RNA sequencing reveals distinct tumor microenvironmental patterns in lung adenocarcinoma.” Oncogene, 40, 6748-6758. doi:10.1038/s41388-021-02054-3 ☞ Link

Uhlitz F, Bischoff P, Peidli S, Sieber A, Trinks A, Lüthen M, Obermayer B, Blanc E, Ruchiy Y, Sell T, Mamlouk S, Arsie R, Wei T, Klotz-Noack K, Schwarz R, Sawitzki B, Kamphues C, Beule D, Landthaler M, Sers C, Horst D, Blüthgen N, Morkel M (2021). “Mitogen-activated protein kinase activity drives cell trajectories in colorectal cancer.” EMBO Mol Med, 13, e14123. doi:10.15252/emmm.202114123 ☞ Link

Nouailles G, Wyler E, Pennitz P, Postmus D, Vladimirova D, Kazmierski J, Pott F, Dietert K, Muelleder M, Farztdinov V, Obermayer B, Wienhold S, Andreotti S, Hoefler T, Sawitzki B, Drosten C, Sander L, Suttorp N, Ralser M, Beule D, Gruber A, Goffinet C, Landthaler M, Trimpert J, Witzenrath M (2021). “Temporal omics analysis in Syrian hamsters unravel cellular effector responses to moderate COVID-19.” Nat Commun, 12, 4869. doi:10.1038/s41467-021-25030-7 ☞ Link

Paterson S, Kar S, Ung S, Gardener Z, Bergstrom E, Ascough S, Kalyan M, Zyla J, Maertzdorf J, Mollenkopf H, Weiner J, Jozwik A, Jarvis H, Jha A, Nicholson B, Veldman T, Woods C, Mallia P, Kon O, Kaufmann S, Openshaw P, Chiu C (2021). “Innate-like Gene Expression of Lung-Resident Memory CD8(+) T Cells during Experimental Human Influenza: A Clinical Study.” Am J Respir Crit Care Med, 204, 826-841. doi:10.1164/rccm.202103-0620OC ☞ Link

Rajasekaran S, Siddiqui J, Rakijas J, Nicolay B, Lin C, Khan E, Patel R, Morris R, Wyler E, Boukhali M, Balasubramanyam J, Ranjith KR, van Rechem C, Vogel C, Elchuri S, Landthaler M, Obermayer B, Haas W, Dyson N, Miles W (2021). “Integrated multi-omics analysis of RB-loss identifies widespread cellular programming and synthetic weaknesses.” Commun Biol, 4, 977. doi:10.1038/s42003-021-02495-2 ☞ Link

Schinke C, Fernandez VV, Ivanov A, Peng Y, Körtvelyessy P, Nolte L, Huehnchen P, Beule D, Stachelscheid H, Boehmerle W, Endres M (2021). “Modeling chemotherapy induced neurotoxicity with human induced pluripotent stem cell (iPSC) -derived sensory neurons.” Neurobiol Dis, 155, 105391. doi:10.1016/j.nbd.2021.105391 ☞ Link

Pei G, Zyla J, He L, Moura-Alves P, Steinle H, Saikali P, Lozza L, Nieuwenhuizen N, Weiner J, Mollenkopf H, Ellwanger K, Arnold C, Duan M, Dagil Y, Pashenkov M, Boneca I, Kufer T, Dorhoi A, Kaufmann S (2021). “Cellular stress promotes NOD1/2-dependent inflammation via the endogenous metabolite sphingosine-1-phosphate.” EMBO J, 40, e106272. doi:10.15252/embj.2020106272 ☞ Link

Herda S, Heimann A, Obermayer B, Ciraolo E, Althoff S, Ruß J, Grunert C, Busse A, Bullinger L, Pezzutto A, Blankenstein T, Beule D, Na I (2021). “Long-term in vitro expansion ensures increased yield of central memory T cells as perspective for manufacturing challenges.” Int J Cancer, 148, 3097-3110. doi:10.1002/ijc.33523 ☞ Link

Kraushar M, Krupp F, Harnett D, Turko P, Ambrozkiewicz M, Sprink T, Imami K, Günnigmann M, Zinnall U, Vieira-Vieira C, Schaub T, Münster-Wandowski A, Bürger J, Borisova E, Yamamoto H, Rasin M, Ohler U, Beule D, Mielke T, Tarabykin V, Landthaler M, Kramer G, Vida I, Selbach M, Spahn C (2021). “Protein Synthesis in the Developing Neocortex at Near-Atomic Resolution Reveals Ebp1-Mediated Neuronal Proteostasis at the 60S Tunnel Exit.” Mol Cell, 81, 304-322.e16. doi:10.1016/j.molcel.2020.11.037 ☞ Link

Heyckendorf J, Marwitz S, Reimann M, Avsar K, DiNardo A, Günther G, Hoelscher M, Ibraim E, Kalsdorf B, Kaufmann S, Kontsevaya I, van Leth F, Mandalakas A, Maurer F, Müller M, Nitschkowski D, Olaru I, Popa C, Rachow A, Rolling T, Rybniker J, Salzer H, Sanchez-Carballo P, Schuhmann M, Schaub D, Spinu V, Suárez I, Terhalle E, Unnewehr M, Weiner J3, Goldmann T, Lange C (2021). “Prediction of anti-tuberculosis treatment duration based on a 22-gene transcriptomic model.” Eur Respir J, 58. doi:10.1183/13993003.03492-2020 ☞ Link

Bao X, Weiner J3, Meckes O, Dommisch H, Schaefer A (2021). “Entamoeba gingivalis Exerts Severe Pathogenic Effects on the Oral Mucosa.” J Dent Res, 100, 771-776. doi:10.1177/00220345211004498 ☞ Link

Eckold C, Kumar V, Weiner J, Alisjahbana B, Riza A, Ronacher K, Coronel J, Kerry-Barnard S, Malherbe S, Kleynhans L, Stanley K, Ruslami R, Ioana M, Ugarte-Gil C, Walzl G, van Crevel R, Wijmenga C, Critchley J, Dockrell H, Cliff J, TANDEM c (2021). “Impact of Intermediate Hyperglycemia and Diabetes on Immune Dysfunction in Tuberculosis.” Clin Infect Dis, 72, 69-78. doi:10.1093/cid/ciaa751 ☞ Link

Wyler E, Mösbauer K, Franke V, Diag A, Gottula L, Arsiè R, Klironomos F, Koppstein D, Hönzke K, Ayoub S, Buccitelli C, Hoffmann K, Richter A, Legnini I, Ivanov A, Mari T, Del GS, Papies J, Praktiknjo S, Meyer T, Müller M, Niemeyer D, Hocke A, Selbach M, Akalin A, Rajewsky N, Drosten C, Landthaler M (2021). “Transcriptomic profiling of SARS-CoV-2 infected human cell lines identifies HSP90 as target for COVID-19 therapy.” iScience, 24, 102151. doi:10.1016/j.isci.2021.102151 ☞ Link

Mölder F, Jablonski K, Letcher B, Hall M, Tomkins-Tinch C, Sochat V, Forster J, Lee S, Twardziok S, Kanitz A, Wilm A, Holtgrewe M, Rahmann S, Nahnsen S, Köster J (2021). “Sustainable data analysis with Snakemake.” F1000Res, 10, 33. doi:10.12688/f1000research.29032.2 ☞ Link

Messerschmidt C, Foddis M, Blumenau S, Müller S, Bentele K, Holtgrewe M, Kun-Rodrigues C, Alonso I, do CMM, Morgadinho A, Velon A, Santo G, Santana I, Mönkäre S, Kuuluvainen L, Schleutker J, Pöyhönen M, Myllykangas L, Senatore A, Berchtold D, Winek K, Meisel A, Pavlovic A, Kostic V, Dobricic V, Lohmann E, Hanagasi H, Guven G, Bilgic B, Bras J, Guerreiro R, Beule D, Dirnagl U, Sassi C (2021). “PHACTR1 genetic variability is not critical in small vessel ischemic disease patients and PcomA recruitment in C57BL/6J mice.” Sci Rep, 11(1), 6072. doi:10.1038/s41598-021-84919-x ☞ Link

Zarate Y, Uehara T, Abe K, Oginuma M, Harako S, Ishitani S, Lehesjoki A, Bierhals T, Kloth K, Ehmke N, Horn D, Holtgrewe M, Anderson K, Viskochil D, Edgar-Zarate C, Sacoto M, Schnur R, Morrow M, Sanchez-Valle A, Pappas J, Rabin R, Muona M, Anttonen A, Platzer K, Luppe J, Gburek-Augustat J, Kaname T, Okamoto N, Mizuno S, Kaido Y, Ohkuma Y, Hirose Y, Ishitani T, Kosaki K (2021). “CDK19-related disorder results from both loss-of-function and gain-of-function de novo missense variants.” Genet Med, 23(6), 1050-1057. doi:10.1038/s41436-020-01091-9 ☞ Link

Vogt G, El CN, Herczegfalvi Á, Kölbel H, Lekaj A, Schara U, Holtgrewe M, Krause S, Horvath R, Schuelke M, Hübner C, Mundlos S, Roos A, Lochmüller H, Karcagi V, Kornak U, Fischer-Zirnsak B (2021). “Expanding the clinical and molecular spectrum of ATP6V1A related metabolic cutis laxa.” J Inherit Metab Dis, 44(4), 972-986. doi:10.1002/jimd.12341 ☞ Link

Yildirim F, Foddis M, Blumenau S, Müller S, Kajetan B, Holtgrewe M, Kola V, Beule D, Sassi C (2021). “Shared and oppositely regulated transcriptomic signatures in Huntington’s disease and brain ischemia confirm known and unveil novel potential neuroprotective genes.” Neurobiol Aging, 104, 122.e1-122.e17. doi:10.1016/j.neurobiolaging.2021.03.001 ☞ Link

Elsner J, Mensah M, Holtgrewe M, Hertzberg J, Bigoni S, Busche A, Coutelier M, de SD, Elçioglu N, Filges I, Gerkes E, Girisha K, Graul-Neumann L, Jamsheer A, Krawitz P, Kurth I, Markus S, Megarbane A, Reis A, Reuter M, Svoboda D, Teller C, Tuysuz B, Türkmen S, Wilson M, Woitschach R, Vater I, Caliebe A, Hülsemann W, Horn D, Mundlos S, Spielmann M (2021). “Genome sequencing in families with congenital limb malformations.” Hum Genet, 140(8), 1229-1239. doi:10.1007/s00439-021-02295-y ☞ Link

Seidel F, Holtgrewe M, Al-Wakeel-Marquard N, Opgen-Rhein B, Dartsch J, Herbst C, Beule D, Pickardt T, Klingel K, Messroghli D, Berger F, Schubert S, Kühnisch J, Klaassen S (2021). “Pathogenic Variants Associated With Dilated Cardiomyopathy Predict Outcome in Pediatric Myocarditis.” Circ Genom Precis Med, 14(4), e003250. doi:10.1161/CIRCGEN.120.003250 ☞ Link

Melo U, Piard J, Fischer-Zirnsak B, Klever M, Schöpflin R, Mensah M, Holtgrewe M, Arbez-Gindre F, Martin A, Guigue V, Gaillard D, Landais E, Roze V, Kremer V, Ramanah R, Cabrol C, Harms F, Kornak U, Spielmann M, Mundlos S, van Maldergem L (2021). “Complete lung agenesis caused by complex genomic rearrangements with neo-TAD formation at the SHH locus.” Hum Genet, 140(10), 1459-1469. doi:10.1007/s00439-021-02344-6 ☞ Link

Sczakiel H, Hülsemann W, Holtgrewe M, Abad-Perez A, Elsner J, Schwartzmann S, Horn D, Spielmann M, Mundlos S, Mensah M (2021). “GLI3 variants causing isolated polysyndactyly are not restricted to the protein’s C-terminal third.” Clin Genet, 100(6), 758-765. doi:10.1111/cge.14059 ☞ Link

2020

Mattei D, Ivanov A, van Oostrum M, Pantelyushin S, Richetto J, Mueller F, Beffinger M, Schellhammer L, Vom BJ, Wollscheid B, Beule D, Paolicelli R, Meyer U (2020). “Enzymatic Dissociation Induces Transcriptional and Proteotype Bias in Brain Cell Populations.” Int J Mol Sci, 21. doi:10.3390/ijms21217944 ☞ Link

Kuhring M, Eisenberger A, Schmidt V, Kränkel N, Leistner D, Kirwan J, Beule D (2020). “Concepts and Software Package for Efficient Quality Control in Targeted Metabolomics Studies: MeTaQuaC.” Anal Chem, 92, 10241-10245. doi:10.1021/acs.analchem.0c00136 ☞ Link

Koche R, Rodriguez-Fos E, Helmsauer K, Burkert M, MacArthur I, Maag J, Chamorro R, Munoz-Perez N, Puiggròs M, Dorado GH, Bei Y, Röefzaad C, Bardinet V, Szymansky A, Winkler A, Thole T, Timme N, Kasack K, Fuchs S, Klironomos F, Thiessen N, Blanc E, Schmelz K, Künkele A, Hundsdörfer P, Rosswog C, Theissen J, Beule D, Deubzer H, Sauer S, Toedling J, Fischer M, Hertwig F, Schwarz R, Eggert A, Torrents D, Schulte J, Henssen A (2020). “Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma.” Nat Genet, 52, 29-34. doi:10.1038/s41588-019-0547-z ☞ Link

Holtgrewe M, Stolpe O, Nieminen M, Mundlos S, Knaus A, Kornak U, Seelow D, Segebrecht L, Spielmann M, Fischer-Zirnsak B, Boschann F, Scholl U, Ehmke N, Beule D (2020). “VarFish: comprehensive DNA variant analysis for diagnostics and research.” Nucleic Acids Res, 48, W162-W169. doi:10.1093/nar/gkaa241 ☞ Link

Obermayer B, Holtgrewe M, Nieminen M, Messerschmidt C, Beule D (2020). “SCelVis: exploratory single cell data analysis on the desktop and in the cloud.” PeerJ, 8, e8607. doi:10.7717/peerj.8607 ☞ Link

Nieminen M, Stolpe O, Schumann F (2020). “SODAR Core: a Django-based framework for scientific data management and analysis web apps.” Journal of Open Source Software, 5(55), 1584. doi:10.21105/joss.01584 ☞ Link

Akpa C, Kleo K, Oker E, Tomaszewski N, Messerschmidt C, López C, Wagener R, Oehl-Huber K, Dettmer K, Schoeler A, Lenze D, Oefner P, Beule D, Siebert R, Capper D, Dimitrova L, Hummel M (2020). “Acquired resistance to DZNep-mediated apoptosis is associated with copy number gains of AHCY in a B-cell lymphoma model.” BMC Cancer, 20, 427. doi:10.1186/s12885-020-06937-8 ☞ Link

Messerschmidt C, Obermayer B, Klinghammer K, Ochsenreither S, Treue D, Stenzinger A, Glimm H, Fröhling S, Kindler T, Brandts C, Schulze-Osthoff K, Weichert W, Tinhofer I, Klauschen F, Keilholz U, Beule D, Rieke D (2020). “Distinct immune evasion in APOBEC-enriched, HPV-negative HNSCC.” Int J Cancer, 147, 2293-2302. doi:10.1002/ijc.33123 ☞ Link

Boschann F, Fischer-Zirnsak B, Wienker T, Holtgrewe M, Seelow D, Eichhorn B, Döhnert S, Fahsold R, Horn D, Graul-Neumann L (2020). “An intronic splice site alteration in combination with a large deletion affecting VPS13B (COH1) causes Cohen syndrome.” Eur J Med Genet, 63, 103973. doi:10.1016/j.ejmg.2020.103973 ☞ Link

Rieke D, Klinghammer K, Obermayer B, Blanc E, Messerschmidt C, Jöhrens K, Klauschen F, Tinhofer I, Beule D, Keilholz U, Ochsenreither S (2020). “Association of a STK11/KEAP1-Mutation Gene Expression Signature in Lung Adenocarcinoma with Immune Desertion in Squamous Cell Carcinomas and Mediation by NFE2L2 Deregulation.” J Clin Oncol, 38(15_suppl), 3082-3082. doi:10.1200/JCO.2020.38.15_suppl.3082 ☞ Link

Ehmke N, Cusmano-Ozog K, Koenig R, Holtgrewe M, Nur B, Mihci E, Babcock H, Gonzaga-Jauregui C, Overton J, Xiao J, Martinez A, Muenke M, Balzer A, Jochim J, El CN, Fischer-Zirnsak B, Huber C, Kornak U, Elsea S, Cormier-Daire V, Ferreira C (2020). “Biallelic variants in KYNU cause a multisystemic syndrome with hand hyperphalangism.” Bone, 133, 115219. doi:10.1016/j.bone.2019.115219 ☞ Link

Seidel E, Walenda G, Messerschmidt C, Obermayer B, Peitzsch M, Wallace P, Bahethi R, Yoo T, Choi M, Schrade P, Bachmann S, Liebisch G, Eisenhofer G, Beule D, Scholl U (2020). “Generation and characterization of a mitotane-resistant adrenocortical cell line.” Endocr Connect, 9, 122-134. doi:10.1530/EC-19-0510 ☞ Link

Melo U, Schöpflin R, Acuna-Hidalgo R, Mensah M, Fischer-Zirnsak B, Holtgrewe M, Klever M, Türkmen S, Heinrich V, Pluym I, Matoso E, Bernardo dSS, Louro P, Hülsemann W, Cohen M, Dufke A, Latos-Bieleńska A, Vingron M, Kalscheuer V, Quintero-Rivera F, Spielmann M, Mundlos S (2020). “Hi-C Identifies Complex Genomic Rearrangements and TAD-Shuffling in Developmental Diseases.” Am J Hum Genet, 106, 872-884. doi:10.1016/j.ajhg.2020.04.016 ☞ Link

Robinson P, Ravanmehr V, Jacobsen J, Danis D, Zhang X, Carmody L, Gargano M, Thaxton C, UNC BC, Karlebach G, Reese J, Holtgrewe M, Köhler S, McMurry J, Haendel M, Smedley D (2020). “Interpretable Clinical Genomics with a Likelihood Ratio Paradigm.” Am J Hum Genet, 107, 403-417. doi:10.1016/j.ajhg.2020.06.021 ☞ Link

Blumenau S, Foddis M, Müller S, Holtgrewe M, Bentele K, Berchtold D, Beule D, Dirnagl U, Sassi C (2020). “Investigating APOE, APP-Aβ metabolism genes and Alzheimer’s disease GWAS hits in brain small vessel ischemic disease.” Sci Rep, 10, 7103. doi:10.1038/s41598-020-63183-5 ☞ Link

Quade A, Thiel A, Kurth I, Holtgrewe M, Elbracht M, Beule D, Eggermann K, Scholl U, Häusler M (2020). “Paroxysmal tonic upgaze: A heterogeneous clinical condition responsive to carbonic anhydrase inhibition.” Eur J Paediatr Neurol, 25, 181-186. doi:10.1016/j.ejpn.2019.11.002 ☞ Link

Thole T, Toedling J, Sprüssel A, Pfeil S, Savelyeva L, Capper D, Messerschmidt C, Beule D, Groeneveld-Krentz S, Eckert C, Gambara G, Henssen A, Finkler S, Schulte J, Sieber A, Bluethgen N, Regenbrecht C, Künkele A, Lodrini M, Eggert A, Deubzer H (2020). “Reflection of neuroblastoma intratumor heterogeneity in the new OHC-NB1 disease model.” Int J Cancer, 146, 1031-1041. doi:10.1002/ijc.32572 ☞ Link

Lamping M, Benary M, Leyvraz S, Messerschmidt C, Blanc E, Kessler T, Schütte M, Lenze D, Jöhrens K, Burock S, Klinghammer K, Ochsenreither S, Sers C, Schäfer R, Tinhofer I, Beule D, Klauschen F, Yaspo M, Keilholz U, Rieke D (2020). “Support of a molecular tumour board by an evidence-based decision management system for precision oncology.” Eur J Cancer, 127, 41-51. doi:10.1016/j.ejca.2019.12.017 ☞ Link

Praktiknjo S, Obermayer B, Zhu Q, Fang L, Liu H, Quinn H, Stoeckius M, Kocks C, Birchmeier W, Rajewsky N (2020). “Tracing tumorigenesis in a solid tumor model at single-cell resolution.” Nat Commun, 11, 991. doi:10.1038/s41467-020-14777-0 ☞ Link

Suter A, Santos-Simarro F, Toerring P, Abad PA, Ramos-Mejia R, Heath K, Huckstadt V, Parrón-Pajares M, Mensah M, Hülsemann W, Holtgrewe M, Mundlos S, Kornak U, Bartsch O, Ehmke N (2020). “Variable pulmonary manifestations in Chitayat syndrome: Six additional affected individuals.” Am J Med Genet A, 182, 2068-2076. doi:10.1002/ajmg.a.61735 ☞ Link

Bockstahler M, Fischer A, Goetzke C, Neumaier H, Sauter M, Kespohl M, Müller A, Meckes C, Salbach C, Schenk M, Heuser A, Landmesser U, Weiner J, Meder B, Lehmann L, Kratzer A, Klingel K, Katus H, Kaya Z, Beling A (2020). “Heart-Specific Immune Responses in an Animal Model of Autoimmune-Related Myocarditis Mitigated by an Immunoproteasome Inhibitor and Genetic Ablation.” Circulation, 141, 1885-1902. doi:10.1161/CIRCULATIONAHA.119.043171 ☞ Link

Krishnamoorthy G, Kaiser P, Abu AU, Weiner J3, Moura-Alves P, Brinkmann V, Kaufmann S (2020). “FX11 limits Mycobacterium tuberculosis growth and potentiates bactericidal activity of isoniazid through host-directed activity.” Dis Model Mech, 13. doi:10.1242/dmm.041954 ☞ Link

Tregoning J, Weiner J, Cizmeci D, Hake D, Maertzdorf J, Kaufmann S, Leroux-Roels G, Maes C, Aerssens A, Calvert A, Jones C (2020). “Pregnancy has a minimal impact on the acute transcriptional signature to vaccination.” NPJ Vaccines, 5, 29. doi:10.1038/s41541-020-0177-6 ☞ Link

Weiner J, Domaszewska T, Donkor S, Kaufmann S, Hill P, Sutherland J (2020). “Changes in Transcript, Metabolite, and Antibody Reactivity During the Early Protective Immune Response in Humans to Mycobacterium tuberculosis Infection.” Clin Infect Dis, 71, 30-40. doi:10.1093/cid/ciz785 ☞ Link

Win Z, Weiner J, Listanco A, Patel N, Sharma R, Greenwood A, Maertzdorf J, Mollenkopf H, Pizzoferro K, Cole T, Bodinham C, Kaufmann S, Denoel P, Del GG, Lewis D (2020). “Systematic Evaluation of Kinetics and Distribution of Muscle and Lymph Node Activation Measured by (18)F-FDG- and (11)C-PBR28-PET/CT Imaging, and Whole Blood and Muscle Transcriptomics After Immunization of Healthy Humans With Adjuvanted and Unadjuvanted Vaccines.” Front Immunol, 11, 613496. doi:10.3389/fimmu.2020.613496 ☞ Link

Mochel F, Rastetter A, Ceulemans B, Platzer K, Yang S, Shinde D, Helbig K, Lopergolo D, Mari F, Renieri A, Benetti E, Canitano R, Waisfisz Q, Plomp A, Huisman S, Wilson G, Cathey S, Louie R, Gaudio D, Waggoner D, Kacker S, Nugent K, Roeder E, Bruel A, Thevenon J, Ehmke N, Horn D, Holtgrewe M, Kaiser F, Kamphausen S, Abou JR, Weckhuysen S, Dalle C, Depienne C (2020). “Variants in the SK2 channel gene (KCNN2) lead to dominant neurodevelopmental movement disorders.” Brain, 143(12), 3564-3573. doi:10.1093/brain/awaa346 ☞ Link

Foddis M, Winek K, Bentele K, Mueller S, Blumenau S, Reichhart NN, Crespo-Garcia S, Harnett D, Ivanov A, Meisel A, Joussen A, Strauss O, Beule D, Dirnagl U, Sassi C (2020). “An exploratory investigation of brain collateral circulation plasticity after cerebral ischemia in two experimental C57BL/6 mouse models.” J Cereb Blood Flow Metab, 40, 276-287. doi:10.1177/0271678X19827251 ☞ Link

Quade A, Thiel A, Kurth I, Holtgrewe M, Elbracht M, Beule D, Eggermann K, Scholl U, Häusler M (2020). “Paroxysmal tonic upgaze: A heterogeneous clinical condition responsive to carbonic anhydrase inhibition.” Eur J Paediatr Neurol, 25, 181-186. doi:10.1016/j.ejpn.2019.11.002 ☞ Link

2019

Holtgrewe M, Messerschmidt C, Nieminen M, Beule D (2019). “Digestiflow: From BCL to FASTQ with Ease.” Bioinformatics.

Schumann F, Blanc E, Messerschmidt C, Blankenstein T, Busse A, Beule D (2019). “SigsPack, a package for cancer mutational signatures.” BMC Bioinformatics, 20, 450. doi:10.1186/s12859-019-3043-7 ☞ Link

Blanc E, Holtgrewe M, Dhamodaran A, Messerschmidt C, Willimsky G, Blankenstein T, Beule D (2019). “Identification and ranking of recurrent neo-epitopes in cancer.” BMC Med Genomics, 12, 171. doi:10.1186/s12920-019-0611-7 ☞ Link

Boeddrich A, Babila J, Wiglenda T, Diez L, Jacob M, Nietfeld W, Huska M, Haenig C, Groenke N, Buntru A, Blanc E, Meier J, Vannoni E, Erck C, Friedrich B, Martens H, Neuendorf N, Schnoegl S, Wolfer D, Loos M, Beule D, Andrade-Navarro M, Wanker E (2019). “The Anti-amyloid Compound DO1 Decreases Plaque Pathology and Neuroinflammation-Related Expression Changes in 5xFAD Transgenic Mice.” Cell Chem Biol, 26, 109-120.e7. doi:10.1016/j.chembiol.2018.10.013 ☞ Link

Borgsmüller N, Gloaguen Y, Opialla T, Blanc E, Sicard E, Royer A, Le BB, Durand S, Migné C, Pétéra M, Pujos-Guillot E, Giacomoni F, Guitton Y, Beule D, Kirwan J (2019). “WiPP: Workflow for Improved Peak Picking for Gas Chromatography-Mass Spectrometry (GC-MS) Data.” Metabolites, 9. doi:10.3390/metabo9090171 ☞ Link

Buonfiglioli A, Efe I, Guneykaya D, Ivanov A, Huang Y, Orlowski E, Krüger C, Deisz R, Markovic D, Flüh C, Newman A, Schneider U, Beule D, Wolf S, Dzaye O, Gutmann D, Semtner M, Kettenmann H, Lehnardt S (2019). “let-7 MicroRNAs Regulate Microglial Function and Suppress Glioma Growth through Toll-Like Receptor 7.” Cell Rep, 29, 3460-3471.e7. doi:10.1016/j.celrep.2019.11.029 ☞ Link

Kühnisch J, Herbst C, Al-Wakeel-Marquard N, Dartsch J, Holtgrewe M, Baban A, Mearini G, Hardt J, Kolokotronis K, Gerull B, Carrier L, Beule D, Schubert S, Messroghli D, Degener F, Berger F, Klaassen S (2019). “Targeted panel sequencing in pediatric primary cardiomyopathy supports a critical role of TNNI3.” Clin Genet, 96, 549-559. doi:10.1111/cge.13645 ☞ Link

Kuhring M, Nieminen M, Kirwan J, Beule D, Holtgrewe M (2019). “AltamISA: A Python API for ISA-Tab Files.” JOSS, 4, 1610. doi:10.21105/joss.01610

Lamping M, Rieke D, Klauschen F, Jöhrens K, Anagnostopoulos I, Lenze D, Tinhofer I, Benary M, Ochsenreither S, Klinghammer K, Burock S, Jann H, Stüven A, Ditzen D, Beule D, Messerschmidt C, Blanc E, Schäfer R, Keilholz U (2019). “Clinical Impact of Comprehensive versus Targeted Genomic Analysis for Precision Oncology.” J Clin Oncol, 37(15_suppl), e13033-e13033. doi:10.1200/JCO.2019.37.15_suppl.e13033 ☞ Link

Herda S, Heimann A, Althoff S, Ruß J, Bullinger L, Beule D, Obermayer B, Na I (2019). “Long-Term T Cell Expansion Results in Increased Numbers of Central Memory T Cells with Sustained Functional Properties for Adoptive T Cell Therapy.” Blood. doi:10.1182/blood-2019-124736 ☞ Link

van~Heesch S, Witte F, Schneider-Lunitz V, Schulz J, Adami E, Faber A, Kirchner M, Maatz H, Blachut S, Sandmann C, Kanda M, Worth C, Schafer S, Calviello L, Merriott R, Patone G, Hummel O, Wyler E, Obermayer B, Mücke M, Lindberg E, Trnka F, Memczak S, Schilling M, Felkin L, Barton P, Quaife N, Vanezis K, Diecke S, Mukai M, Mah N, Oh S, Kurtz A, Schramm C, Schwinge D, Sebode M, Harakalova M, Asselbergs F, Vink A, de WR, Viswanathan S, Widjaja A, Gärtner-Rommel A, Milting H, Dos RC, Knosalla C, Mertins P, Landthaler M, Vingron M, Linke W, Seidman J, Seidman C, Rajewsky N, Ohler U, Cook S, Hubner N (2019). “The Translational Landscape of the Human Heart.” Cell, 178, 242-260.e29. doi:10.1016/j.cell.2019.05.010 ☞ Link

2018

Holtgrewe M, Knaus A, Hildebrand G, Pantel J, Santos M, Neveling K, Goldmann J, Schubach M, Jäger M, Coutelier M, Mundlos S, Beule D, Sperling K, Krawitz P (2018). “Multisite de novo mutations in human offspring after paternal exposure to ionizing radiation.” Sci Rep, 8, 14611. doi:10.1038/s41598-018-33066-x ☞ Link

Guneykaya D, Ivanov A, Hernandez D, Haage V, Wojtas B, Meyer N, Maricos M, Jordan P, Buonfiglioli A, Gielniewski B, Ochocka N, Cömert C, Friedrich C, Artiles L, Kaminska B, Mertins P, Beule D, Kettenmann H, Wolf S (2018). “Transcriptional and Translational Differences of Microglia from Male and Female Brains.” Cell Rep, 24, 2773-2783.e6. doi:10.1016/j.celrep.2018.08.001 ☞ Link

Rieke D, Lamping M, Klauschen F, Ochsenreither S, Schütte M, Kessler T, Klinghammer K, Jöhrens K, Messerschmidt C, Lenze D, Burock S, Ditzen D, Schäfer R, Pavel M, Tinhofer I, Sers C, Beule D, Yaspo M, Leyvraz S, Keilholz U (2018). “Efficacy of a Structured Workflow for the Interpretation of Comprehensive Genomic Analysis Data in Clinical Routine.” J Clin Oncol, 36(15_suppl), e24164-e24164. doi:10.1200/JCO.2018.36.15_suppl.e24164 ☞ Link

Salatzki J, Foryst-Ludwig A, Bentele K, Blumrich A, Smeir E, Ban Z, Brix S, Grune J, Beyhoff N, Klopfleisch R, Dunst S, Surma M, Klose C, Rothe M, Heinzel F, Krannich A, Kershaw E, Beule D, Schulze P, Marx N, Kintscher U (2018). “Adipose tissue ATGL modifies the cardiac lipidome in pressure-overload-induced left ventricular failure.” PLoS Genet, 14, e1007171. doi:10.1371/journal.pgen.1007171 ☞ Link

2017

Kammertoens T, Friese C, Arina A, Idel C, Briesemeister D, Rothe M, Ivanov A, Szymborska A, Patone G, Kunz S, Sommermeyer D, Engels B, Leisegang M, Textor A, Fehling H, Fruttiger M, Lohoff M, Herrmann A, Yu H, Weichselbaum R, Uckert W, Hübner N, Gerhardt H, Beule D, Schreiber H, Blankenstein T (2017). “Tumour ischaemia by interferon-γ resembles physiological blood vessel regression.” Nature, 545, 98-102. doi:10.1038/nature22311 ☞ Link

Mamlouk S, Childs L, Aust D, Heim D, Melching F, Oliveira C, Wolf T, Durek P, Schumacher D, Bläker H, von WM, Gastl B, Möhr K, Menne A, Zeugner S, Redmer T, Lenze D, Tierling S, Möbs M, Weichert W, Folprecht G, Blanc E, Beule D, Schäfer R, Morkel M, Klauschen F, Leser U, Sers C (2017). “DNA copy number changes define spatial patterns of heterogeneity in colorectal cancer.” Nat Commun, 8, 14093. doi:10.1038/ncomms14093 ☞ Link

Mattei D, Ivanov A, Ferrai C, Jordan P, Guneykaya D, Buonfiglioli A, Schaafsma W, Przanowski P, Deuther-Conrad W, Brust P, Hesse S, Patt M, Sabri O, Ross T, Eggen B, Boddeke E, Kaminska B, Beule D, Pombo A, Kettenmann H, Wolf S (2017). “Maternal immune activation results in complex microglial transcriptome signature in the adult offspring that is reversed by minocycline treatment.” Transl Psychiatry, 7, e1120. doi:10.1038/tp.2017.80 ☞ Link

Messerschmidt C, Holtgrewe M, Beule D (2017). “HLA-MA: simple yet powerful matching of samples using HLA typing results.” Bioinformatics, 33, 2241-2242. doi:10.1093/bioinformatics/btx132 ☞ Link

Rieke D, Messerschmidt C, Ochsenreither S, Klinghammer K, Tinhofer I, Jöhrens K, Klauschen F, Beule D, Keilholz U (2017). “Association of an APOBEC Mutational Signature, Mutational Load, and BRCAness with Inflammation and PD-L1 Expression in HNSCC.” J Clin Oncol, 35(15_suppl), e14613-e14613. doi:10.1200/JCO.2017.35.15_suppl.e14613 ☞ Link

Yaakov G, Lerner D, Bentele K, Steinberger J, Barkai N (2017). “Coupling phenotypic persistence to DNA damage increases genetic diversity in severe stress.” Nat Ecol Evol, 1, 16. doi:10.1038/s41559-016-0016 ☞ Link

2016

Holtgrewe M, Beule D (2016). “VCFPy: A Python 3 Library with Good Support for Both Reading and Writing VCF.” JOSS, 1(6), 85. doi:10.21105/joss.00085 ☞ Link

Last modified: Nov 28, 2023