From e2427276ac989dd59fb494c34be88d5d047ae26b Mon Sep 17 00:00:00 2001
From: January Weiner <january.weiner@gmail.com>
Date: Thu, 5 Dec 2024 11:49:37 +0100
Subject: [PATCH] Update publication-list.md (#186)

added all relevant CUBI publications 2019-2024 + preprints
---
 bih-cluster/docs/misc/publication-list.md | 721 ++++++++++++++++++++++
 1 file changed, 721 insertions(+)

diff --git a/bih-cluster/docs/misc/publication-list.md b/bih-cluster/docs/misc/publication-list.md
index 43b3cfd5..9b4cf41a 100644
--- a/bih-cluster/docs/misc/publication-list.md
+++ b/bih-cluster/docs/misc/publication-list.md
@@ -8,6 +8,34 @@ It has been used to support the publications listed below.
 
 ## Articles & Preprints
 
+### 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](https://www.researchsquare.com/article/rs-4409923/v1)
+
+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](https://www.researchsquare.com/article/rs-2459463/v1)
+
+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](https://www.medrxiv.org/content/10.1101/2024.06.11.24308538v2)
+
+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](https://www.biorxiv.org/content/early/2022/09/19/2022.09.18.508452)
+
+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](https://www.biorxiv.org/content/10.1101/2021.08.28.458010.abstract)
+
+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](https://www.biorxiv.org/content/10.1101/2021.08.06.455386.abstract)
+
+
+
 ### 2024
 
 Köhler RM, Binns TS, Merk T, Zhu G, Yin Z, Zhao B, Chikermane M, Vanhoecke J, Busch JL, Habets JGV, Faust K, Schneider GH, Cavallo A, Haufe S, Zhang J, Kühn AA, Haynes JD, Neumann WJ. Dopamine and deep brain stimulation accelerate the neural dynamics of volitional action in Parkinson’s disease. *Brain*. 2024 Oct 1;147(10):3358–69. [doi: 10.1093/brain/awae219](https://doi.org/10.1093/brain/awae219)
@@ -16,13 +44,541 @@ Binns TS, Köhler RM, Vanhoecke J, Chikermane M, Gerster M, Merk T, Pellegrini F
 
 Hollunder, B., Ostrem, J.L., Sahin, I.A., Rajamani, N., Oxenford, S., Butenko, K., Neudorfer, C., Reinhardt, P., Zvarova, P., Polosan, M., Akram, H., Vissani, M., Zhang, C., Sun, B., Navratil, P., Reich, M.M., Volkmann, J., Yeh, F.-C., Baldermann, J.C., Dembek, T.A., Visser-Vandewalle, V., Alho, E.J.L., Franceschini, P.R., Nanda, P., Finke, C., Kühn, A.A., Dougherty, D.D., Richardson, R.M., Bergman, H., DeLong, M.R., Mazzoni, A., Romito, L.M., Tyagi, H., Zrinzo, L., Joyce, E.M., Chabardes, S., Starr, P.A., Li, N., Horn, A., 2024. Mapping dysfunctional circuits in the frontal cortex using deep brain stimulation. Nat. Neurosci. 1–14. [doi: 10.1038/s41593-024-01570-1](https://doi.org/10.1038/s41593-024-01570-1)
 
+
+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](https://doi.org/10.1038/s41588-024-01836-1)
+
+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](https://doi.org/10.1093/bioinformatics/btae512)
+
+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](https://www.sciencedirect.com/science/article/pii/S0016508524055276)
+
+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](https://www.sciencedirect.com/science/article/pii/S0959804924009626)
+
+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](https://publications.ersnet.org/content/erj/early/2024/08/22/1399300301983-2023)
+
+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](https://www.embopress.org/doi/full/10.1038/s44321-024-00085-3)
+
+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](https://www.sciencedirect.com/science/article/pii/S088915912400477X)
+
+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](https://link.springer.com/article/10.1007/s00439-024-02669-y)
+
+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](https://www.nature.com/articles/s44161-024-00544-7)
+
+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](https://linkinghub.elsevier.com/retrieve/pii/S0959804924017076)
+
+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](https://bsd.biomedcentral.com/articles/10.1186/s13293-024-00647-7)
+
+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](https://link.springer.com/article/10.1007/s13402-024-00922-0)
+
+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](https://www.sciencedirect.com/science/article/pii/S0928098723002464)
+
+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](https://www.pnas.org/doi/abs/10.1073/pnas.2310864121)
+
+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](https://onlinelibrary.wiley.com/doi/abs/10.1002/ijc.35079)
+
+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](https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae366/7676836)
+
+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](https://doi.org/10.1038/s43018-024-00784-3)
+
+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](https://doi.org/10.1093/oncolo/oyae137)
+
+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](https://doi.org/10.1007/s00439-024-02674-1)
+
+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](https://onlinelibrary.wiley.com/doi/abs/10.1002/jmv.29539)
+
+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](https://doi.org/10.1093/bioinformatics/btae085)
+
+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](https://www.science.org/doi/10.1126/scitranslmed.adk9129)
+
+
+### 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
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+proteins.” _Nat Commun_, 13(1), 2727. doi:10.1038/s41467-022-30322-7  [☞ Link](https://doi.org/10.1038/s41467-022-30322-7)
+
+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](https://doi.org/10.1126/sciimmunol.abj0140)
+
+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](https://doi.org/10.3390/ijms232315388)
+
+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](https://doi.org/10.1038/s42003-022-03828-5)
+
+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](https://doi.org/10.1007/s00439-022-02461-w)
+
+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](https://doi.org/10.1016/j.neurobiolaging.2022.11.013)
+
+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](https://doi.org/10.1038/s10038-022-01018-z)
+
+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](https://doi.org/10.3390/jcdd9070216)
+
+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](https://doi.org/10.1093/bioinformatics/btac418)
+
+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](https://doi.org/10.1038/s41467-022-34053-7)
+
+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](https://doi.org/10.1186/s12916-022-02560-5)
+
+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](https://doi.org/10.1186/s13073-022-01108-9)
+
+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](https://doi.org/10.1177/00220345211029266)
+
+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](https://doi.org/10.1038/s41431-021-00983-x)
+
+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](https://doi.org/10.1136/jmedgenet-2021-107843)
+
 Kossen T, Hirzel MA, Madai VI, Boenisch F, Hennemuth A, Hildebrand K, Pokutta S, Sharma K, Hilbert A, Sobesky J, Galinovic I, Khalil AA, Fiebach JB and Frey D. Toward Sharing Brain Images: Differentially Private TOF-MRA Images With Segmentation Labels Using Generative Adversarial Networks. *Frontiers in
 Artificial Intelligence*. 5 (2022). issn: 2624-8212. [doi: 10.3389/frai.2022.813842](https://doi.org/10.3389/frai.2022.813842)
 
 ### 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](https://doi.org/10.1016/j.dib.2021.107320)
+
+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](https://doi.org/10.1016/j.eclinm.2021.101099)
+
+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](https://doi.org/10.3389/fimmu.2021.694680)
+
+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](https://erj.ersjournals.com/content/58/suppl_65/PA2355.abstract)
+
+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](https://doi.org/10.1038/s41388-021-02054-3)
+
+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](https://doi.org/10.15252/emmm.202114123)
+
+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](https://doi.org/10.1038/s41467-021-25030-7)
+
+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](https://doi.org/10.1164/rccm.202103-0620OC)
+
+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](https://doi.org/10.1038/s42003-021-02495-2)
+
+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](https://doi.org/10.1016/j.nbd.2021.105391)
+
+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](https://doi.org/10.15252/embj.2020106272)
+
+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](https://doi.org/10.1002/ijc.33523)
+
+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](https://doi.org/10.1016/j.molcel.2020.11.037)
+
+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](https://doi.org/10.1183/13993003.03492-2020)
+
+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](https://doi.org/10.1177/00220345211004498)
+
+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](https://doi.org/10.1093/cid/ciaa751)
+
+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](https://doi.org/10.1016/j.isci.2021.102151)
+
+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](https://doi.org/10.12688/f1000research.29032.2)
+
+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](https://doi.org/10.1038/s41598-021-84919-x)
+
+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](https://doi.org/10.1038/s41436-020-01091-9)
+
+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](https://doi.org/10.1002/jimd.12341)
+
+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](https://doi.org/10.1016/j.neurobiolaging.2021.03.001)
+
+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](https://doi.org/10.1007/s00439-021-02295-y)
+
+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](https://doi.org/10.1161/CIRCGEN.120.003250)
+
+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](https://doi.org/10.1007/s00439-021-02344-6)
+
+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](https://doi.org/10.1111/cge.14059)
+
 Li, N., Hollunder, B., Baldermann, J. C., Kibleur, A., Treu, S., Akram, H., Al-Fatly, B., Strange, B. A., Barcia, J. A., Zrinzo, L., Joyce, E. M., Chabardes, S., Visser-Vandewalle, V., Polosan, M., Kuhn, J., Kühn, A. A., & Horn, A. (2021). A Unified Functional Network Target for Deep Brain Stimulation in Obsessive-Compulsive Disorder. Biological Psychiatry. [doi: 10.1016/j.biopsych.2021.04.006](https://doi.org/10.1016/j.biopsych.2021.04.006)
 
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@@ -73,6 +629,124 @@ Paraskevopoulou S., Pirzer F., Goldmann N., Schmid J., Corman V.M., Gottula L.T.
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 [doi: 10.1073/pnas.2006750117](https://doi.org/10.1073/pnas.2006750117).
 
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+Targeted Metabolomics Studies: MeTaQuaC.” _Anal Chem_, 92, 10241-10245. doi:10.1021/acs.analchem.0c00136
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+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,
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+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
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+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.
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+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](https://doi.org/10.7717/peerj.8607)
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+Source Software_, 5(55), 1584. doi:10.21105/joss.01584  [☞ Link](http://edoc.mdc-berlin.de/19748/1/19748oa.pdf)
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+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](https://doi.org/10.1186/s12885-020-06937-8)
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+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](https://doi.org/10.1002/ijc.33123)
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+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.
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+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
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+ [☞ Link](https://doi.org/10.1200/JCO.2020.38.15_suppl.3082)
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+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
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+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
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+
+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
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+
+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
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+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
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+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
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+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
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+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_,
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+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
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+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
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+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,
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+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,
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+
+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](https://doi.org/10.1177/0271678X19827251)
+
+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](https://doi.org/10.1016/j.ejpn.2019.11.002)
+
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 Kircher, M., Xiong, C., Martin, B. et al.
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 Quade,A., Thiel,A., Kurth,I., Holtgrewe,M., Elbracht,M., Beule,D., Eggermann,K., Scholl,U.I. and Häusler,M. (2019) Paroxysmal tonic upgaze: A heterogeneous clinical condition responsive to carbonic anhydrase inhibition. European Journal of Paediatric Neurology, [10.1016/j.ejpn.2019.11.002](https://doi.org/10.1016/j.ejpn.2019.11.002).
 
+Holtgrewe M, Messerschmidt C, Nieminen M, Beule D (2019). “Digestiflow: From BCL to FASTQ with Ease.” _Bioinformatics_.
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+Schumann F, Blanc E, Messerschmidt C, Blankenstein T, Busse A, Beule D (2019). “SigsPack, a package for cancer mutational signatures.” _BMC
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+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](https://doi.org/10.1186/s12920-019-0611-7)
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+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
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+Pathology and Neuroinflammation-Related Expression Changes in 5xFAD Transgenic Mice.” _Cell Chem Biol_, 26, 109-120.e7.
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+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.
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+
+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
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+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
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+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
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+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
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+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
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+
+
+
+
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 Blanc, E., Holtgrewe, M., Dhamodaran, A., Messerschmidt, C., Willimsky, G., Blankenstein, T., Beule, D. (2018).