[Preprints] [2023] [2022] [2021] [2020] [2019] [2018] [2017] [2016] [BibTeX file]
Preprints
Chopra A, Song J, Weiner J, Beule D, Schaefer AS (2024). “Genetic analysis of cis-enhancers associated with bone mineral density and periodontitis in the gene SOST.” ResearchSquare. ☞ Link
Opitz B, Essex M, Pascual-Leone BM, Loeber U, Kuhring M, Zhang B, Bruening U, Fritsche-Guenther R, Krzanowski M, Vernengo FF, Brumhard S, Röwekamp I, Bielecka A, Lesker T, Wyler E, Landthaler M, Mantei A, Meisel C, Caesar S, Thibeault C, Corman V, Marko L, Suttorp N, Strowig T, Kurth F, Sander L, Li Y, Kirwan J, Forslund S (2023). “Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in severe COVID-19.” doi:10.21203/rs.3.rs-2459463/v1 ☞ Link
Zuljan E, von der Emde B, Piwonski I, Pestana ACA, Klinghammer K, Mock A, Horak P, Heining C, Klauschen F, Pretzell M, Boerries I, Brandts C, Kreutzfeldt S, Teleanu M, Hübschmann D, Morris L, Keller U, Glimm H, Fröhling S, Ochsenreither S, Keilholz U, Blanc E, Beule D, Rieke D (2024). “Integrative analysis reveals a macrophage-predominant, immunosuppressive immune microenvironment and subtype-specific therapeutic vulnerabilities in advanced salivary gland cancer.” medRxiv, 2024-06. doi:10.1101/2024.06.11.24308538 ☞ Link
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
2024
Schmidt A, Danyel M, Grundmann K, Brunet T, Klinkhammer H, Hsieh T, Engels H, Peters S, Knaus A, Moosa S, Averdunk L, Boschann F, Sczakiel HL, Schwartzmann S, Mensah MA, Pantel JT, Holtgrewe M, Bösch A, Weiß C, Weinhold N, Suter A, Stoltenburg C, Neugebauer J, Kallinich T, Kaindl AM, Holzhauer S, Bührer C, Bufler P, Kornak U, Ott C, Schülke M, Nguyen HHP, Hoffjan S, Grasemann C, Rothoeft T, Brinkmann F, Matar N, Sivalingam S, Perne C, Mangold E, Kreiss M, Cremer K, Betz RC, Mücke M, Grigull L, Klockgether T, Spier I, Heimbach A, Bender T, Brand F, Stieber C, Morawiec AM, Karakostas P, Schäfer VS, Bernsen S, Weydt P, Castro-Gomez S, Aziz A, Grobe-Einsler M, Kimmich O, Kobeleva X, Önder D, Lesmann H, Kumar S, Tacik P, Basin MA, Incardona P, Lee-Kirsch MA, Berner R, Schuetz C, Körholz J, Kretschmer T, Donato ND, Schröck E, Heinen A, Reuner U, Hanßke A, Kaiser FJ, Manka E, Munteanu M, Kuechler A, Cordula K, Hirtz R, Schlapakow E, Schlein C, Lisfeld J, Kubisch C, Herget T, Hempel M, Weiler-Normann C, Ullrich K, Schramm C, Rudolph C, Rillig F, Groffmann M, Muntau A, Tibelius A, Schwaibold EMC, Schaaf CP, Zawada M, Kaufmann L, Hinderhofer K, Okun PM, Kotzaeridou U, Hoffmann GF, Choukair D, Bettendorf M, Spielmann M, Ripke A, Pauly M, Münchau A, Lohmann K, Hüning I, Hanker B, Bäumer T, Herzog R, Hellenbroich Y, Westphal DS, Strom T, Kovacs R, Riedhammer KM, Mayerhanser K, Graf E, Brugger M, Hoefele J, Oexle K, Mirza-Schreiber N, Berutti R, Schatz U, Krenn M, Makowski C, Weigand H, Schröder S, Rohlfs M, Vill K, Hauck F, Borggraefe I, Müller-Felber W, Kurth I, Elbracht M, Knopp C, Begemann M, Kraft F, Lemke JR, Hentschel J, Platzer K, Strehlow V, Jamra RA, Kehrer M, Demidov G, Beck-Wödl S, Graessner H, Sturm M, Zeltner L, Schöls LJ, Magg J, Bevot A, Kehrer C, Kaiser N, Turro E, Horn D, Grüters-Kieslich A, Klein C, Mundlos S, Nöthen M, Riess O, Meitinger T, Krude H, Krawitz PM, Haack T, Ehmke N, Wagner M (2024). “Next-generation phenotyping integrated in a national framework for patients with ultrarare disorders improves genetic diagnostics and yields new molecular findings.” Nature Genetics. ISSN 1546-1718, doi:10.1038/s41588-024-01836-1 ☞ Link
Marot-Lassauzaie V, Beneyto-Calabuig S, Obermayer B, Velten L, Beule D, Haghverdi L (2024). “Identifying cancer cells from calling single-nucleotide variants in scRNA-seq data.” Bioinformatics, 40(9), btae512. ISSN 1367-4811, doi:10.1093/bioinformatics/btae512 ☞ Link
Horn V, Cancino CA, Steinheuer LM, Obermayer B, Fritz K, Nguyen AL, Juhran KS, Plattner C, Bösel D, Oldenburg L, Burns M, Schulz AR, Saliutina M, Mantzivi E, Lissner D, Conrad T, Mashreghi M, Zundler S, Sonnenberg E, Schumann M, Haag L, Beule D, Flatz L, Atreya I, Atreya R, Bacher P, Becker C, Bojarski C, Britzen-Laurent N, Bosch-Voskens C, Chang H, Diefenbach A, Günther C, Hegazy AN, Hildner K, Klose CS, Koop K, Krug S, Kühl AA, Leppkes M, López-Posadas R, Ludwig LS, Neufert C, Neurath M, Patankar J, Prüß M, Radbruch A, Romagnani C, Ronchi F, Sanders A, Scheffold A, Schulzke J, Schumann M, Schürmann S, Siegmund B, Stürzl M, Trajanoski Z, Triantafyllopoulou A, Waldner M, Weidinger C, Wirtz S, Zundler S, Trjanoski Z, D’Haens G, Weidinger C, Mei HE, Siegmund B, Thurley K, Hegazy AN (2024). “Multimodal Profiling of Peripheral Blood Identifies Proliferating Circulating Effector CD4+ T Cells as Predictors for Response to Integrin α4β7–Blocking Therapy in Inflammatory Bowel Disease.” Gastroenterology. ISSN 0016-5085, doi:10.1053/j.gastro.2024.09.021 ☞ Link
Menzel M, Martis-Thiele M, Goldschmid H, Ott A, Romanovsky E, Siemanowski-Hrach J, Seillier L, Brüchle NO, Maurer A, Lehmann K, Begemann M, Elbracht M, Meyer R, Dintner S, Claus R, Meier-Kolthoff JP, Blanc E, Möbs M, Joosten M, Benary M, Basitta P, Hölscher F, Tischler V, Groß T, Kutz O, Prause R, William D, Horny K, Goering W, Sivalingam S, Borkhardt A, Blank C, Junk SV, Yasin L, Moskalev EA, Carta MG, Ferrazzi F, Tögel L, Wolter S, Adam E, Matysiak U, Rosenthal T, Dönitz J, Lehmann U, Schmidt G, Bartels S, Hofmann W, Hirsch S, Dikow N, Göbel K, Banan R, Hamelmann S, Fink A, Ball M, Neumann O, Rehker J, Kloth M, Murtagh J, Hartmann N, Jurmeister P, Mock A, Kumbrink J, Jung A, Mayr E, Jacob A, Trautmann M, Kirmse S, Falkenberg K, Ruckert C, Hirsch D, Immel A, Dietmaier W, Haack T, Marienfeld R, Fürstberger A, Niewöhner J, Gerstenmaier U, Eberhardt T, Greif PA, Appenzeller S, Maurus K, Doll J, Jelting Y, Jonigk D, Märkl B, Beule D, Horst D, Wulf A, Aust D, Werner M, Reuter-Jessen K, Ströbel P, Auber B, Sahm F, Merkelbach-Bruse S, Siebolts U, Roth W, Lassmann S, Klauschen F, Gaisa NT, Weichert W, Evert M, Armeanu-Ebinger S, Ossowski S, Schroeder C, Schaaf CP, Malek N, Schirmacher P, Kazdal D, Pfarr N, Budczies J, Stenzinger A (2024). “Benchmarking whole exome sequencing in the German network for personalized medicine.” European Journal of Cancer, 211, 114306. ISSN 0959-8049, doi:10.1016/j.ejca.2024.114306 ☞ Link
Fatykhova D, Fritsch VN, Siebert K, Methling K, Lalk M, Busche T, Kalinowski J, Weiner J, Beule D, Bertrams W, others (2024). “Microenvironmental acidification by pneumococcal sugar consumption fosters barrier disruption and immune suppression in the human alveolus.” European Respiratory Journal. doi:doi.org/10.1183/13993003.01983-2023 ☞ Link
Adhikary PP, Idowu T, Tan Z, Hoang C, Shanta S, Dumbani M, Mappalakayil L, Awasthi B, Bermudez M, Weiner J, Beule D, Wolber G, Page BD, Hedtrich S (2024). “Disrupting TSLP-TSLP receptor interactions via putative small molecule inhibitors yields a novel and efficient treatment option for atopic diseases.” EMBO Molecular Medicine, 1-27. doi:10.1038/s44321-024-00085-3 ☞ Link
Mattei D, Ivanov A, Hammer J, Ugursu B, Schalbetter S, Richetto J, Weber-Stadlbauer U, Mueller F, Scarborough J, Wolf SA, Kettenmann H, Wollscheid B, Beule D, Meyer U (2024). “Microglia undergo molecular and functional adaptations to dark and light phases in male laboratory mice.” Brain, Behavior, and Immunity, 120, 571-583. ISSN 0889-1591, doi:10.1016/j.bbi.2024.07.007 ☞ Link
Kopp J, Koch LA, Lyubenova H, Küchler O, Holtgrewe M, Ivanov A, Dubourg C, Launay E, Brachs S, Mundlos S, Pellerin L, Mameli M, Paolicelli RC (2024). “Loss-of-function variants affecting the STAGA complex component SUPT7L cause a developmental disorder with generalized lipodystrophy.” Human Genetics, 143(5), 683-694. doi:10.1007/s00439-024-02669-y ☞ Link
Ruiz-Orera J, Miller DC, Greiner J, Genehr C, Grammatikaki A, Blachut S, Mbebi J, Patone G, Myronova A, Adami E, others (2024). “Evolution of translational control and the emergence of genes and open reading frames in human and non-human primate hearts.” Nature Cardiovascular Research, 1-19. doi:10.1038/s44161-024-00544-7 ☞ Link
Fisch A, Pestana A, Sachse V, Doll C, Hofmann E, Heiland M, Obermueller T, Heidemann J, Dommerich S, Schoppe D, Schallenberg S, Piwonski I, Blanc E, Tinhofer I (2024). “Feasibility analysis of using patient-derived tumour organoids for treatment decision guidance in locally advanced head and neck squamous cell carcinoma.” European journal of cancer (Oxford, England : 1990), 213, 115100. ISSN 1879-0852, doi:10.1016/j.ejca.2024.115100 ☞ Link
Al-Diab O, Sünkel C, Blanc E, Catar RA, Ashraf MI, Zhao H, Wang P, Rinschen MM, Fritsche-Guenther R, Grahammer F, Bachmann S, Beule D, Kirwan JA, Rajewsky N, Huber TB, Gürgen D, Kusch A (2024). “Sex-specific molecular signature of mouse podocytes in homeostasis and in response to pharmacological challenge with rapamycin.” Biology of sex differences, 15, 72. ISSN 2042-6410, doi:10.1186/s13293-024-00647-7 ☞ Link
Trinks A, Milek M, Beule D, Kluge J, Florian S, Sers C, Horst D, Morkel M, Bischoff P (2024). “Robust detection of clinically relevant features in single-cell RNA profiles of patient-matched fresh and formalin-fixed paraffin-embedded (FFPE) lung cancer tissue.” Cellular Oncology, 47, 1-11. doi:10.5281/zenodo.7852154 ☞ Link
Šmid A, Štajdohar M, Milek M, Urbančič D, Kuželički NK, Tamm R, Metspalu A, Mlinarič-Raščan I (2024). “Transcriptome analysis reveals involvement of thiopurine S-methyltransferase in oxidation-reduction processes.” European Journal of Pharmaceutical Sciences, 192, 106616. doi:10.1016/j.ejps.2023.106616 ☞ Link
Dörner PJ, Anandakumar H, Röwekamp I, Vernengo FF, Pascual-Leone BM, Krzanowski M, Sellmaier J, Brüning U, Fritsche-Guenther R, Pfannkuch L, Kurth F, Milek M, Igbokwe V, Löber U, Gutbier B, Holstein M, Heinz GA, Mashreghi M, Schulte LN, Klatt A, Caesar S, Wienhold S, Offermanns S, Mack M, Witzenrath M, Jordan S, Beule D, Kirwan JA, Forslund SK, Wilck N, Bartolomaeus H, Heimesaat MM, Opitz B (2024). “Clinically used broad-spectrum antibiotics compromise inflammatory monocyte-dependent antibacterial defense in the lung.” Nature Communications, 15(1), 2788.
Röwekamp I, Maschirow L, Rabes A, Vernengo FF, Hamann L, Heinz GA, Mashreghi M, Caesar S, Milek M, Fonseca ACF, Wienhold S, Nouailles G, Yao L, Mousavi S, Bruder D, Boehme JD, Puzianowska-Kuznicka M, Beule D, Witzenrath M, Group CS, Löhning M, Klose CSN, Heimesaat MM, Diefenbach A, Opitz B, Fuchs A, Engelmann M, Paul G, Ayoub M, Groehl K, Riedl K, Stolz D, Bauer W, Diehl-Wiesenecker EC, Terue IvW, Galtung N, Suttorp N, Witzenrath M, Wildberg C, Pley C, Zessin E, Schmager S, Schaaf B, Kremling J, Nickoleit-Bitzenberger D, Azzaui H, Hower M, Hempel F, Prebeg K, Popkirova K, Kolditz M, Schulte-Hubbert B, Langner S, Rohde G, Bellinghausen C, Grϋnewaldt A, Endres A, Frigerio C, Fiedler B, Panning M, Welte T, Pink I, Drick N, Fϋhner T, Klooster Mv, Steinberg T, Barten-Neiner G, Kröner W, Unruh O, Adaskina N, Eberhardt F, Julius C, Illig T, Klopp N, Pletz M, Schleenvoigt BT, Bahrs C, Moeser A, Ankert J, Sommerwerck U, Wintermantel T, Drömann D, Parschke P, Franzen K, Rupp J, Waldeck F, Käding N, Spinner C, Erber J, Voit F, Schneider J, Falcone M, Tiseo G, Heigener D, Hering I, Albrich W, Rassouli F, Wirth B, Neurohr C, Essig A, Stenger S, Wallner M, Burgmann H, Traby L, Schubert L, nurses aas (2024). “IL-33 controls IL-22-dependent antibacterial defense by modulating the microbiota.” Proceedings of the National Academy of Sciences, 121(22), e2310864121. doi:10.1073/pnas.2310864121 ☞ Link
Wei T, Blanc E, Peidli S, Bischoff P, Trinks A, Horst D, Sers C, Blüthgen N, Beule D, Morkel M, Obermayer B (2024). “High-confidence calling of normal epithelial cells allows identification of a novel stem-like cell state in the colorectal cancer microenvironment.” International Journal of Cancer, n/a(n/a). doi:10.1002/ijc.35079 ☞ Link
Hramyka D, Sczakiel HL, Zhao MX, Stolpe O, Nieminen M, Adam R, Danyel M, Einicke L, Hägerling R, Knaus A, Mundlos S, Schwartzmann S, Seelow D, Ehmke N, Mensah MA, Boschann F, Beule D, Holtgrewe M (2024). “REEV: review, evaluate and explain variants.” Nucleic Acids Research, gkae366. doi:10.1093/nar/gkae366 ☞ Link
Ramberger E, Sapozhnikova V, Ng YLD, Dolnik A, Ziehm M, Popp O, Str"ang E, Kull M, Gr"unschl"ager F, Kr"uger J, Benary M, M"uller S, Gao X, Murgai A, Haji M, Schmidt A, Lutz R, Nogai A, Braune J, Laue D, Langer C, Khandanpour C, Bassermann F, D"ohner H, Engelhardt M, Straka C, Hundemer M, Beule D, Haas S, Keller U, Einsele H, Bullinger L, Knop S, Mertins P, Kr"onke J (2024). “The proteogenomic landscape of multiple myeloma reveals insights into disease biology and therapeutic opportunities.” Nature Cancer. ISSN 2662-1347, doi:10.1038/s43018-024-00784-3 ☞ Link
Habringer S, Ihlow J, Kleo K, Klostermann A, Schmidt M, Chai L, Knödler M, Leyvraz S, Sigler C, Sinn B, Maschmeyer G, Jegodka Y, Benary M, Ott C, Tinhofer I, Schäfer R, Möbs M, Keller U, Keilholz U, Rieke DT (2024). “A diagnostic challenge of KIT p.V559D and BRAF p.G469A mutations in a paragastric mass.” The Oncologist, oyae137. ISSN 1083-7159, doi:10.1093/oncolo/oyae137 ☞ Link
Shi W, Song J, Weiner J, Chopra A, Dommisch H, Beule D, Schaefer AS (2024). “lncRNA CDKN2B-AS1 regulates collagen expression.” Human Genetics. doi:10.1007/s00439-024-02674-1 ☞ Link
Shi W, Song J, Dommisch H, Weiner J, Schaefer A (2024). “STAT1 binds to CAD and periodontitis risk SNP rs10757278, causing inhibition of lncRNA CDKN2B-AS1 expression, which activates transcription of collagen genes in cells of the extracellular matrix.” In EUROPEAN JOURNAL OF HUMAN GENETICS, volume 32, 402-402. SPRINGERNATURE CAMPUS, 4 CRINAN ST, LONDON, N1 9XW, ENGLAND.
Zheng L, Chopra A, Weiner J, Dommisch H, Schaefer A (2024). “Systematic search for microRNA regulated genes with roles in the etiology of periodontitis.” In EUROPEAN JOURNAL OF HUMAN GENETICS, volume 32, 406-406. SPRINGERNATURE CAMPUS, 4 CRINAN ST, LONDON, N1 9XW, ENGLAND.
Lebedin M, Ratswohl C, Garg A, Schips M, García CV, Spatt L, Thibeault C, Obermayer B, Weiner J, Velásquez IM, others (2024). “Soluble ACE2 correlates with severe COVID-19 and can impair antibody responses.” iScience.
Tranter E, Frentsch M, Hütter-Krönke ML, Vuong GL, Busch D, Loyal L, Henze L, Rosnev S, Blau I, Thiel A, Beule D, Bullinger L, Obermayer B, Na I (2024). “Comparable CD8+ T-cell responses to SARS-CoV-2 vaccination in single-cell transcriptomics of recently allogeneic transplanted patients and healthy individuals.” Journal of Medical Virology, 96(3), e29539. doi:10.1002/jmv.29539 ☞ Link
Bhasin MA, Knaus A, Incardona P, Schmid A, Holtgrewe M, Elbracht M, Krawitz PM, Hsieh T (2024). “Enhancing Variant Prioritization in VarFish through On-Premise Computational Facial Analysis.” Genes, 15(3), 370.
Ermshaus A, Piechotta M, Rüter G, Keilholz U, Leser U, Benary M (2024). “preon: Fast and accurate entity normalization for drug names and cancer types in precision oncology.” Bioinformatics, 40(3), btae085. ISSN 1367-4811, doi:10.1093/bioinformatics/btae085 ☞ Link
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 (2024). “Increased beta2-adrenergic signaling promotes fracture healing through callus neovascularization in mice.” Science Translational Medicine, 16(743), eadk9129. doi:10.1126/scitranslmed.adk9129 ☞ Link
2023
Monsorno K, Ginggen K, Ivanov A, Buckinx A, Lalive AL, Tchenio A, Benson S, Vendrell M, D’Alessandro A, Beule D, others (2023). “Loss of microglial MCT4 leads to defective synaptic pruning and anxiety-like behavior in mice.” Nature Communications, 14(1), 5749. doi:10.1038/s41467-023-41502-4 ☞ Link
Markus D, Pelletier A, Boube M, Port F, Boutros M, Payre F, Obermayer B, Zanet J (2023). “The pleiotropic functions of Pri smORF peptides synchronize leg development regulators.” PLOS Genetics, 19(10), 1-27. doi:10.1371/journal.pgen.1011004 ☞ Link
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
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.” Genome Med, 15, 50. doi:10.1186/s13073-023-01206-2 ☞ 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
Holle J, Bartolomaeus H, Löber U, Behrens F, Bartolomaeus TUP, Anandakumar H, Wimmer MI, Vu DL, Kuhring M, Brüning U, Maifeld A, Geisberger S, Kempa S, Schumacher F, Kleuser B, Bufler P, Querfeld U, Kitschke S, Engler D, Kuhrt LD, Drechsel O, Eckardt K, Forslund SK, Thürmer A, McParland V, Kirwan JA, Wilck N, Müller D (2022). “Inflammation in Children with CKD Linked to Gut Dysbiosis and Metabolite Imbalance.” Journal of the American Society of Nephrology, 33(12), 2259. ISSN 1046-6673, doi:10.1681/ASN.2022030378 ☞ Link
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 6, 2024