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Mapping the human genetic architecture of COVID-19.

Nature 600 (7889): 472-477. December 2021

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.

Nucleic Acids Research 44 (D1): D27-D37. 4 January 2016

Fine mapping and chromosome walking towards the Ror1 locus in barley (Hordeum vulgare L.).
Acevedo-Garcia, J., Collins, N.C., Ahmadinejad, N., Ma, L., Houben, A., Bednarek, P., Benjdia, M., Freialdenhoven, A., Altmüller, J., Nürnberg, P., Reinhardt, R., Schulze-Lefert, P. and Panstruga, R.
Theoretical and Applied Genetics 126 (12): 2969-2982. December 2013

A mechanistic classification of clinical phenotypes in neuroblastoma.
Ackermann, S., Cartolano, M., Hero, B., Welte, A., Kahlert, Y., Roderwieser, A., Bartenhagen, C., Walter, E., Gecht, J., Kerschke, L., Volland, R., Menon, R., Heuckmann, J.M., Gartlgruber, M., Hartlieb, S., Henrich, K.O., Okonechnikov, K., Altmüller, J., Nürnberg, P., Lefever, S., de Wilde, B., Sand, F., Ikram, F., Rosswog, C., Fischer, J., Theissen, J., Hertwig, F., Singhi, A.D., Simon, T., Vogel, W., Perner, S., Krug, B., Schmidt, M., Rahmann, S., Achter, V., Lang, U., Vokuhl, C., Ortmann, M., Büttner, R., Eggert, A., Speleman, F., O'Sullivan, R.J., Thomas, R.K., Berthold, F., Vandesompele, J., Schramm, A., Westermann, F., Schulte, J.H., Peifer, M. and Fischer, M.
Science 362 (6419): 1165-1170. 7 December 2018

Exome sequencing identifies biallelic MSH3 germline mutations as a recessive subtype of colorectal adenomatous polyposis.
Adam, R., Spier, I., Zhao, B., Kloth, M., Marquez, J., Hinrichsen, I., Kirfel, J., Tafazzoli, A., Horpaopan, S., Uhlhaas, S., Stienen, D., Friedrichs, N., Altmüller, J., Laner, A., Holzapfel, S., Peters, S., Kayser, K., Thiele, H., Holinski-Feder, E., Marra, G., Kristiansen, G., Nöthen, M.M., Büttner, R., Möslein, G., Betz, R.C., Brieger, A., Lifton, R.P. and Aretz, S.
American Journal of Human Genetics 99 (2): 337-51. 4 August 2016

De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics.
Adamidi, C., Wang, Y., Gruen, D., Mastrobuoni, G., You, X., Tolle, D., Dodt, M., Mackowiak, S.D., Gogol-Doering, A., Oenal, P., Rybak, A., Ross, E., Alvarado, A.S., Kempa, S., Dieterich, C., Rajewsky, N. and Chen, W.
Genome Research 21 (7): 1193-1200. July 2011

HDHL-INTIMIC: a European knowledge platform on food, diet, intestinal microbiomics, and human health.
Agamennone, V., Abuja, P.M., Basic, M., De Angelis, M., Gessner, A., Keijser, B., Larsen, M., Pinart, M., Nimptsch, K., Pujos-Guillot, E., Schlicht, K., Sharon, I., Untersmayr, E., Laudes, M., Pischon, T. and Bouwman, J.
Nutrients 14 (9): 1881. 29 April 2022

An unconventional gatekeeper mutation sensitizes inositol hexakisphosphate kinases to an allosteric inhibitor.
Aguirre, T., Hostachy, S., Dornan, G.L., Neuenschwander, M., Seyffarth, C., Haucke, V., Schütz, A., von Kries, J.P. and Fiedler, D.
eLife 21 : RP88982. 16 October 2023

Genetic heterogeneity in Pakistani microcephaly families revisited.
Ahmad, I., Baig, S.M., Abdulkareem, A.R., Hussain, M.S., Sur, I., Toliat, M.R., Nürnberg, G., Dalibor, N., Moawia, A., Waseem, S.S., Asif, M., Nagra, H., Sher, M., Khan, M.M.A., Hassan, I., Rehman, S.U., Thiele, H., Altmüller, J., Noegel, A.A. and Nürnberg, P.
Clinical Genetics 92 (1): 62-68. July 2017

The interleukin-11 receptor variant p.W307R results in craniosynostosis in humans.
Ahmad, I., Lokau, J., Kespohl, B., Malik, N.A., Baig, S.M., Hartig, R., Behme, D., Schwab, R., Altmüller, J., Jameel, M., Mucha, S., Thiele, H., Tariq, M., Nürnberg, P., Erdmann, J. and Garbers, C.
Scientific Reports 13 (1): 13479. 18 August 2023

Conserved miRNAs are candidate post-transcriptional regulators of developmental arrest in free-living and parasitic nematodes.
Ahmed, R., Chang, Z., Younis, A.E., Langnick, C., Li, N., Chen, W., Brattig, N. and Dieterich, C.
Genome Biology and Evolution 5 (7): 1246-1260. 2013

The FGFR inhibitor PD173074 binds to the C-terminus of oncofetal HMGA2 and modulates its DNA-binding and transcriptional activation functions.
Ahmed, S.M., Ragunathan, P., Shin, J., Peter, S., Kleissle, S., Neuenschwander, M., Schäfer, R., von Kries, J.P., Grüber, G. and Dröge, P.
FEBS Letters 597 (15): 1977-1988. August 2023

A common building block for the syntheses of amorfrutin and cajaninstilbene acid libraries toward efficient binding with peroxisome proliferator-activated receptors.
Aidhen, I.S., Mukkamala, R., Weidner, C. and Sauer, S.
Organic Letters 17 (2): 194-197. 16 January 2015

Transcriptional features of genomic regulatory blocks.
Akalin, A., Fredman, D., Arner, E, Dong, X, Bryne, JC, Suzuki, H., Daub, CO, Hayashizaki, Y and Lenhard, B
Genome Biology 10 (4): R38. 19 April 2009

Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia.
Akalin, A., Garrett-Bakelman, F.E., Kormaksson, M., Busuttil, J., Zhang, L., Khrebtukova, I., Milne, T.A., Huang, Y., Biswas, D., Hess, J.L., Allis, C.D., Roeder, R.G., Valk, P.J.M., Loewenberg, B., Delwel, R., Fernandez, H.F., Paietta, E., Tallman, M.S., Schroth, G.P., Mason, C.E., Melnick, A. and Figueroa, M.E.
PLoS Genetics 8 (6): e1002781. 21 June 2012

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles.
Akalin, A., Kormaksson, M., Li, S., Garrett-Bakelman, F.E., Figueroa, M.E., Melnick, A. and Mason, C.E.
Genome Biology 13 (10): R87. 3 October 2012

genomation: a toolkit to summarize, annotate and visualize genomic intervals.
Akalin, A., Franke, V., Vlahoviček, K., Mason, C.E. and Schübeler, D.
Bioinformatics 31 (7): 1127-1129. 1 April 2015

Acquired resistance to DZNep-mediated apoptosis is associated with copy number gains of AHCY in a B-cell lymphoma model.
Akpa, C.A., Kleo, K., Oker, E., Tomaszewski, N., Messerschmidt, C., López, C., Wagener, R., Oehl-Huber, K., Dettmer, K., Schoeler, A., Lenze, D., Oefner, P.J., Beule, D., Siebert, R., Capper, D., Dimitrova, L. and Hummel, M.
BMC Cancer 20 (1): 427. 14 May 2020

Sex-specific molecular signature of mouse podocytes in homeostasis and in response to pharmacological challenge with rapamycin.
Al-Diab, O., Sünkel, C., Blanc, E., Catar, R.A., Ashraf, M.I., Zhao, H., Wang, P., Rinschen, M.M., Fritsche-Guenther, R., Grahammer, F., Bachmann, S., Beule, D., Kirwan, J.A., Rajewsky, N., Huber, T.B., Gürgen, D. and Kusch, A.
Biology of Sex Differences 15 (1): 72. 15 September 2024

Late diagnosis of a truncating WISP3 mutation entails a severe phenotype of progressive pseudorheumatoid dysplasia.
Alawbathani, S., Kawalia, A., Karakaya, M., Altmüller, J., Nürnberg, P. and Cirak, S.
Cold Spring Harbor Molecular Case Studies 4 (1): a002139. 19 December 2017

MYCN mediates cysteine addiction and sensitizes neuroblastoma to ferroptosis.
Alborzinia, H., Flórez, A.F., Kreth, S., Brückner, L.M., Yildiz, U., Gartlgruber, M., Odoni, D.I., Poschet, G., Garbowicz, K., Shao, C., Klein, C., Meier, J., Zeisberger, P., Nadler-Holly, M., Ziehm, M., Paul, F., Burhenne, J., Bell, E., Shaikhkarami, M., Würth, R., Stainczyk, S.A., Wecht, E.M., Kreth, J., Büttner, M., Ishaque, N., Schlesner, M., Nicke, B., Stresemann, C., Llamazares-Prada, M., Reiling, J.H., Fischer, M., Amit, I., Selbach, M., Herrmann, C., Wölfl, S., Henrich, K.O., Höfer, T., Trumpp, A. and Westermann, F.
Nature Cancer 3 (4): 471-485. 28 April 2022

Integrative and comparative genomic analyses identify clinically relevant pulmonary carcinoid groups and unveil the supra-carcinoids.
Alcala, N., Leblay, N., Gabriel, A.A.G., Mangiante, L., Hervas, D., Giffon, T., Sertier, A.S., Ferrari, A., Derks, J., Ghantous, A., Delhomme, T.M., Chabrier, A., Cuenin, C., Abedi-Ardekani, B., Boland, A., Olaso, R., Meyer, V., Altmuller, J., Le Calvez-Kelm, F., Durand, G., Voegele, C., Boyault, S., Moonen, L., Lemaitre, N., Lorimier, P., Toffart, A.C., Soltermann, A., Clement, J.H., Saenger, J., Field, J.K., Brevet, M., Blanc-Fournier, C., Galateau-Salle, F., Le Stang, N., Russell, P.A., Wright, G., Sozzi, G., Pastorino, U., Lacomme, S., Vignaud, J.M., Hofman, V., Hofman, P., Brustugun, O.T., Lund-Iversen, M., Thomas de Montpreville, V., Muscarella, L.A., Graziano, P., Popper, H., Stojsic, J., Deleuze, J.F., Herceg, Z., Viari, A., Nuernberg, P., Pelosi, G., Dingemans, A.M.C., Milione, M., Roz, L., Brcic, L., Volante, M., Papotti, M.G., Caux, C., Sandoval, J., Hernandez-Vargas, H., Brambilla, E., Speel, E.J.M., Girard, N., Lantuejoul, S., McKay, J.D., Foll, M. and Fernandez-Cuesta, L.
Nature Communications 10 (1): 3407. 20 August 2019

Sites of transcription initiation drive mRNA isoform selection.
Alfonso-Gonzalez, C., Legnini, I., Holec, S., Arrigoni, L., Ozbulut, H.C., Mateos, F., Koppstein, D., Rybak-Wolf, A., Bönisch, U., Rajewsky, N. and Hilgers, V.
Cell 186 (11): 2438-2455. 25 May 2023

Relationship between genome and epigenome - challenges and requirements for future research.
Almouzni, G., Altucci, L., Amati, B., Ashley, N., Baulcombe, D., Beaujean, N., Bock, C., Bongcam-Rudloff, E., Bousquet, J., Braun, S., Bressac-de Paillerets, B., Bussemakers, M., Clarke, L., Conesa, A., Estivill, X., Fazeli, A., Grgurević, N., Gut, I., Heijmans, B.T., Hermouet, S., Houwing-Duistermaat, J., Iacobucci, I., Ilaš, J., Kandimalla, R., Krauss-Etschmann, S., Lasko, P., Lehmann, S., Lindroth, A., Majdič, G., Marcotte, E., Martinelli, G., Martinet, N., Meyer, E., Miceli, C., Mills, K., Moreno-Villanueva, M., Morvan, G., Nickel, D., Niesler, B., Nowacki, M., Nowak, J., Ossowski, S., Pelizzola, M., Pochet, R., Potočnik, U., Radwanska, M., Raes, J., Rattray, M., Robinson, M.D., Roelen, B., Sauer, S., Schinzer, D., Slagboom, E., Spector, T., Stunnenberg, H.G., Tiligada, E., Torres-Padilla, M.E., Tsonaka, R., Van Soom, A., Vidaković, M. and Widschwendter, M.
BMC Genomics 15 : 487. 18 June 2014

DNA sonication inverse PCR for genome scale analysis of uncharacterized flanking sequences.
Alquezar‐Planas, D.E., Löber, U., Cui, P., Quedenau, C., Chen, W. and Greenwood, A.D.
Methods in Ecology and Evolution 22 September 2020

A palladium-catalyzed domino reaction to access 3-amino-2H-indazoles from hydrazines and 2-halobenzonitriles.
Alsalim, R., Lindemann, P., López-Alberca, M.P., Miksche, S., Czechtizky, W., Halland, N. and Nazaré, M.
Organic Letters 22 (18): 7393-7396. 18 September 2020

The immunoproteasome-specific inhibitor ONX 0914 reverses susceptibility to acute viral myocarditis.
Althof, N., Goetzke, C.C., Kespohl, M., Voss, K., Heuser, A., Pinkert, S., Kaya, Z., Klingel, K. and Beling, A.
EMBO Molecular Medicine 10 (2): 200-218. 1 February 2018

Single-nucleus and spatial transcriptome reveal adrenal homeostasis in normal and tumoural adrenal glands.
Altieri, B., Secener, A.K., Sai, S., Fischer, C., Sbiera, S., Arampatzi, P., Kircher, S., Herterich, S., Landwehr, L.S., Vitcetz, S.N., Braeuning, C., Fassnacht, M., Ronchi, C.L. and Sauer, S.
Clinical and Translational Medicine 14 (8): e1798. August 2024

Predicting the binding affinity of MHC class II peptides.
Altiparmak, F., Akalin, A. and Ferhatosmanoglu, H.
Computational Systems Bioinformatics 2006 : 331-334. August 2006

Enrichment of target sequences for next-generation sequencing applications in research and diagnostics.
Altmüller, J., Budde, B.S. and Nürnberg, P.
Biological Chemistry 395 (2): 231-237. 1 February 2014

Mutational profiling in the peripheral blood leukocytes of patients with systemic mast cell activation syndrome using next-generation sequencing.
Altmüller, J., Haenisch, B., Kawalia, A., Menzen, M., Nöthen, M.M., Fier, H. and Molderings, G.J.
Immunogenetics 69 (6): 359-369. June 2017

A systematic comparison of two new releases of exome sequencing products: the aim of use determines the choice of product.
Altmüller, J., Motameny, S., Becker, C., Thiele, H., Chatterjee, S., Wollnik, B. and Nürnberg, P.
Biological Chemistry 397 (8): 791-801. 1 August 2016

Mutations in AP3D1 associated with immunodeficiency and seizures define a new type of Hermansky-Pudlak syndrome.
Ammann, S., Schulz, A., Krägeloh-Mann, I., Dieckmann, N.M.G., Niethammer, K., Fuchs, S., Eckl, K.M., Plank, R., Werner, R., Altmüller, J., Thiele, H., Nürnberg, P., Bank, J., Strauss, A., von Bernuth, H., Zur Stadt, U., Grieve, S., Griffiths, G.M., Lehmberg, K., Hennies, H.C. and Ehl, S.
Blood 127 (8): 997-1006. 25 February 2016

Retargeting transposon insertions by the adeno-associated virus Rep protein.
Ammar, I., Gogol-Doering, A., Miskey, C., Chen, W., Cathomen, T., Izsvak, Z. and Ivics, Z.
Nucleic Acids Research 40 (14): 6693-6712. 1 August 2012

Feasibility of a culturally adapted dietary weight-loss intervention among Ghanaian migrants in Berlin, Germany: the ADAPT study.
Amoah, S., Ennin, R., Sagoe, K., Steinbrecher, A., Pischon, T., Mockenhaupt, F.P. and Danquah, I.
International Journal of Environmental Research and Public Health 18 (2): 510. 9 January 2021

TAT-apoptosis repressor with caspase recruitment domain protein transduction rescues mice from fulminant liver failure.
An, J., Harms, C., Lättig-Tünnemann, G., Sellge, G., Mandic, A.D., Malato, Y., Heuser, A., Endres, M., Trautwein, C. and Donath, S.
Hepatology 56 (2): 715-726. August 2012

In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation.
Anania, C., Acemel, R.D., Jedamzick, J., Bolondi, A., Cova, G., Brieske, N., Kühn, R., Wittler, L., Real, F.M. and Lupiáñez, D.G.
Nature Genetics 54 (7): 1026-1036. July 2022

doRiNA: a database of RNA interactions in post-transcriptional regulation.
Anders, G., Mackowiak, S.D., Jens, M., Maaskola, J., Kuntzagk, A., Rajewsky, N., Landthaler, M. and Dieterich, C.
Nucleic Acids Research 40 (1): D180-D186. January 2012

Furin-, ADAM 10-, and γ-secretase-mediated cleavage of a receptor tyrosine phosphatase and regulation of β-catenin's transcriptional activity.
Anders, L., Mertins, P., Lammich, S., Murgia, M., Hartmann, D., Saftig, P., Haass, C. and Ullrich, A.
Molecular and Cellular Biology 26 (10): 3917-3934. May 2006

Automated genome sequence analysis and annotation.
Andrade, M.A., Brown, N.P., Leroy, C., Hoersch, S., de Daruvar, A., Reich, C., Franchini, A., Tamames, J., Valencia, A., Ouzounis, C. and Sander, C.
Bioinformatics 15 (5): 391-412. May 1999

Putative mobilized colistin resistance genes in the human gut microbiome.
Andrade, B.G.N., Goris, T., Afli, H., Coutinho, F.H., Dávila, A.M.R. and Cuadrat, R.R.C.
BMC Microbiology 21 : 220. 22 July 2021

Mitochondrial vesicles: an ancient process providing new links to peroxisomes.
Andrade-Navarro, M.A., Sanchez-Pulido, L. and McBride, H.M.
Current Opinion in Cell Biology 21 (4): 560-567. August 2009

Enhanced efficiency through nuclear localization signal fusion on phage PhiC31-integrase: activity comparison with Cre and FLPe recombinase in mammalian cells.
Andreas, S., Schwenk, F., Kueter-Luks, B., Faust, N. and Kühn, R.
Nucleic Acids Research 30 (11): 2299-2306. 1 June 2002

De novo whole genome assembly of the Roborovski dwarf hamster (Phodopus roborovskii) genome, an animal model for severe/critical COVID-19.
Andreotti, S., Altmüller, J., Quedenau, C., Borodina, T., Nouailles, G., Teixeira Alves, L.G., Landthaler, M., Bieniara, M., Trimpert, J. and Wyler, E.
Genome Biology and Evolution 14 (7): evac100. July 2022

High-resolution intravital microscopy.
Andresen, V., Pollok, K., Rinnenthal, J.L., Oehme, L., Guenther, R., Spiecker, H., Radbruch, H., Gerhard, J., Sporbert, A., Cseresnyes, Z., Hauser, A.E. and Niesner, R.
PLoS ONE 7 (12): e50915. 14 December 2012

Floral induction in Arabidopsis by FLOWERING LOCUS T requires direct repression of BLADE-ON-PETIOLE genes by the homeodomain protein PENNYWISE.
Andrés, F., Romera-Branchat, M., Martínez-Gallegos, R., Patel, V., Schneeberger, K., Jang, S., Altmüller, J., Nürnberg, P. and Coupland, G.
Plant Physiology 169 (3): 2187-2199. November 2015

Two deubiquitylases act on mitofusin and regulate mitochondrial fusion along independent pathways.
Anton, F., Dittmar, G., Langer, T. and Escobar-Henriques, M.
Molecular Cell 49 (3): 487-498. 7 February 2013

Discovery of a novel series of tankyrase inhibitors by a hybridization approach.
Anumala, U.R., Waaler, J., Nkizinkiko, Y., Ignatev, A., Lazarow, K., Lindemann, P., Olsen, P.A., Murthy, S., Obaji, E., Majouga, A.G., Leonov, S., von Kries, J.P., Lehtiö, L., Krauss, S. and Nazaré, M.
Journal of Medicinal Chemistry 60 (24): 10013-10025. 28 December 2017

The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators.
Appel, L.M., Franke, V., Benedum, J., Grishkovskaya, I., Strobl, X., Polyansky, A., Ammann, G., Platzer, S., Neudolt, A., Wunder, A., Walch, L., Kaiser, S., Zagrovic, B., Djinovic-Carugo, K., Akalin, A. and Slade, D.
Nature Communications 14 (1): 166. 11 January 2023

PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC.
Appel, L.M., Franke, V., Bruno, M., Grishkovskaya, I., Kasiliauskaite, A., Kaufmann, T., Schoeberl, U.E., Puchinger, M.G., Kostrhon, S., Ebenwaldner, C., Sebesta, M., Beltzung, E., Mechtler, K., Lin, G., Vlasova, A., Leeb, M., Pavri, R., Stark, A., Akalin, A., Stefl, R., Bernecky, C., Djinovic-Carugo, K. and Slade, D.
Nature Communications 12 (1): 6078. 19 October 2021

Proteomics, post-translational modifications, and integrative analyses reveal molecular heterogeneity within medulloblastoma subgroups.
Archer, T.C., Ehrenberger, T., Mundt, F., Gold, M.P., Krug, K., Mah, C.K., Mahoney, E.L., Daniel, C.J., LeNail, A., Ramamoorthy, D., Mertins, P., Mani, D.R., Zhang, H., Gillette, M.A., Clauser, K., Noble, M., Tang, L.C., Pierre-François, J., Silterra, J., Jensen, J., Tamayo, P., Korshunov, A., Pfister, S.M., Kool, M., Northcott, P.A., Sears, R.C., Lipton, J.O., Carr, S.A., Mesirov, J.P., Pomeroy, S.L. and Fraenkel, E.
Cancer Cell 34 (3): 396-410. 10 September 2018

Allosteric inhibition of a mammalian lectin.
Aretz, J., Anumala, U.R., Fuchsberger, F.F., Molavi, N., Ziebart, N., Zhang, H., Nazaré, M. and Rademacher, C.
Journal of the American Chemical Society 140 (44): 14915-14925. 7 November 2018

High serum prevalence of autoreactive IgG antibodies against peripheral nerve structures in patients with neurological post-COVID-19 vaccination syndrome.
Arlt, F.A., Breuer, A., Trampenau, E., Boesl, F., Kirchner, M., Mertins, P., Sánchez-Sendín, E., Nasouti, M., Mayrhofer, M., Blüthner, M., Endres, M., Prüss, H. and Franke, C.
Frontiers in Immunology 15 : 1404800. 2 August 2024

Inhibiting PHGDH with NCT-503 reroutes glucose-derived carbons into the TCA cycle, independently of its on-target effect.
Arlt, B., Mastrobuoni, G., Wuenschel, J., Astrahantseff, K., Eggert, A., Kempa, S. and Deubzer, H.E.
Journal of Enzyme Inhibition and Medicinal Chemistry 36 (1): 1282-1289. 30 June 2021

Inhibiting phosphoglycerate dehydrogenase counteracts chemotherapeutic efficacy against MYCN-amplified neuroblastoma.
Arlt, B., Zasada, C., Baum, K., Wuenschel, J., Mastrobuoni, G., Lodrini, M., Astrahantseff, K., Winkler, A., Schulte, J.H., Finkler, S., Forbes, M., Hundsdoerfer, P., Guergen, D., Hoffmann, J., Wolf, J., Eggert, A., Kempa, S. and Deubzer, H.E.
International Journal of Cancer 148 (5): 1219-1232. 1 March 2021

Quantification of transients using empirical orthogonal functions.
Arndt, J., Herzel, H., Bose, S., Falcke, M. and Scholl, E.
Chaos Solitons & Fractals 8 (12): 1911-1920. December 1997

SNT: a unifying toolbox for quantification of neuronal anatomy.
Arshadi, C., Günther, U., Eddison, M., Harrington, K.I.S. and Ferreira, T.A.
Nature Methods 18 : 374-377. April 2021

Regulation of influenza a virus mRNA splicing by CLK1.
Artarini, A., Meyer, M., Shin, Y.J., Huber, K., Hilz, N., Bracher, F., Eros, D., Orfi, L., Keri, G., Goedert, S., Neuenschwander, M., von Kries, J., Domovich-Eisenberg, Y., Dekel, N., Szabadkai, I., Lebendiker, M., Horváth, Z., Danieli, T., Livnah, O., Moncorgé, O., Frise, R., Barclay, W., Meyer, T.F. and Karlas, A.
Antiviral Research 168 : 187-196. August 2019

LABKIT: labeling and segmentation toolkit for big image data.
Arzt, M., Deschamps, J., Schmied, C., Pietzsch, T., Schmidt, D., Tomancak, P., Haase, R. and Jug, F.
Frontiers in Computer Science 4 : 777728. 10 February 2022

A Canadian genome-wide association study and meta-analysis confirm HLA as a risk factor for peanut allergy independent of asthma.
Asai, Y., Eslami, A., van Ginkel, C.D., Akhabir, L., Wan, M., Yin, D., Ellis, G., Ben-Shoshan, M., Marenholz, I., Martino, D., Ferreira, M.A., Allen, K., Mazer, B., de Groot, H., de Jong, N.W., Gerth van Wijk, R., Dubois, A.E.J., Grosche, S., Ashley, S., Rüschendorf, F., Kalb, B., Beyer, K., Nöthen, M.M., Lee, Y.A., Chin, R., Cheuk, S., Hoffman, J., Jorgensen, E., Witte, J.S., Melles, R.B., Hong, X., Wang, X., Hui, J., Musk, A.W.B., Hunter, M., James, A.L., Koppelman, G.H., Sandford, A.J., Clarke, A.E. and Daley, D.
Journal of Allergy and Clinical Immunology 141 (4): 1513-1516. April 2018

Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients.
Aschenbrenner, A.C., Mouktaroudi, M., Krämer, B., Oestreich, M., Antonakos, N., Nuesch-Germano, M., Gkizeli, K., Bonaguro, L., Reusch, N., Baßler, K., Saridaki, M., Knoll, R., Pecht, T., Kapellos, T.S., Doulou, S., Kröger, C., Herbert, M., Holsten, L., Horne, A., Gemünd, I.D., Rovina, N., Agrawal, S., Dahm, K., van Uelft, M., Drews, A., Lenkeit, L., Bruse, N., Gerretsen, J., Gierlich, J., Becker, M., Händler, K., Kraut, M., Theis, H., Mengiste, S., Domenico, E., Schulte-Schrepping, J., Seep, L., Raabe, J., Hoffmeister, C., ToVinh, M., Keitel, V., Rieke, G., Talevi, V., Skowasch, D., Aziz, N.A., Pickkers, P., van de Veerdonk, F.L., Netea, M.G., Schultze, J.L., Kox, M., Breteler, M.M.B., Nattermann, J., Koutsoukou, A., Giamarellos-Bourboulis, E.J. and Ulas, T.
Genome Medicine 13 (1): 7. 13 January 2021

Attenuated BMP1 function compromises osteogenesis, leading to bone fragility in humans and zebrafish.
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Fumarate is cardioprotective via activation of the Nrf2 antioxidant pathway.
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De novo variants of CSNK2B cause a new intellectual disability-craniodigital syndrome by disrupting the canonical Wnt signaling pathway.
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A novel missense variant of SCN4A co-segregates with congenital essential tremor in a consanguineous Kurdish family.
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American Journal of Medical Genetics A 188 (4): 1251-1258. April 2022

Genome sequencing reveals loci under artificial selection that underlie disease phenotypes in the laboratory rat.
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Expanding the spectrum of EEF1D neurodevelopmental disorders: biallelic variants in the guanine exchange domain.
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A microRNA screen reveals that elevated hepatic ectodysplasin A expression contributes to obesity-induced insulin resistance in skeletal muscle.
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A homozygous nonsense mutation identified in COL7A1 in a family with autosomal recessive dystrophic epidermolysis bullosa.
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Designed nanomolar small-molecule inhibitors of Ena/VASP EVH1 interaction impair invasion and extravasation of breast cancer cells.
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Chronic overexpression of bradykinin in kidney causes polyuria and cardiac hypertrophy.
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Three-layered proteomic characterization of a novel ACTN4 mutation unravels its pathogenic potential in FSGS.
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Enhancement of CRISPR-Cas9 induced precise gene editing by targeting Histone H2A-K15 ubiquitination.
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Mutations in POGLUT1, encoding protein o-glucosyltransferase 1, cause autosomal-dominant Dowling-Degos disease.
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Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation.
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Gain-of-function mutations in KCNN3 encoding the small-conductance Ca(2+)-activated K(+) channel SK3 cause Zimmermann-Laband syndrome.
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Investigating the role of GLUL as a survival factor in cellular adaptation to glutamine depletion via targeted stable isotope resolved metabolomics.
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SUMOylation of the chromodomain factor MRG-1 in C. elegans affects chromatin-regulatory dynamics.
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Genetic information from discordant sibling pairs points to ESRP2 as a candidate trans-acting regulator of the CF modifier gene SCNN1B.
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7 Tesla MRI of Balo's concentric sclerosis versus multiple sclerosis lesions.
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Investigating APOE, APP-Aβ metabolism genes and Alzheimer's disease GWAS hits in brain small vessel ischemic disease.
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Structural insights into crista junction formation by the Mic60-Mic19 complex.
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Identification and characterization of hypoxia-regulated endothelial circular RNA.
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Identification and regulation of the long non-coding RNA Heat2 in heart failure.
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The anti-amyloid compound DO1 decreases plaque pathology and neuroinflammation-related expression changes in 5xFAD transgenic mice.
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A proteomics analysis of 5xFAD mouse brain regions reveals the lysosome-associated protein Arl8b as a candidate biomarker for Alzheimer's disease.
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Creation of targeted genomic deletions using TALEN or CRISPR/Cas nuclease pairs in one-cell mouse embryos.
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Micro-RNA networks in T-cell prolymphocytic leukemia reflect T-cell activation and shape DNA damage response and survival pathways.
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Noncanonical function of AGO2 augments T-cell receptor signaling in T-cell prolymphocytic leukemia.
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ISG15 blocks cardiac glycolysis and ensures sufficient mitochondrial energy production during Coxsackievirus B3 infection.
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Claudin-10a deficiency shifts proximal tubular Cl(-) permeability to cation selectivity via claudin-2 redistribution.
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Journal of the American Society of Nephrology 33 (4): 699-717. April 2022

The histone H4 lysine 20 demethylase DPY-21 regulates the dynamics of condensin DC binding.
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An activatable lanthanide luminescent probe for time-gated detection of nitroreductase in live bacteria.
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Development of a species-specific RNA polymerase I-based shRNA expression vector.
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Mutations in plasmalemma vesicle-associated protein cause severe syndromic protein-losing enteropathy.
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Immunosuppression with cyclosporine versus tacrolimus shows distinctive nephrotoxicity profiles within renal compartments.
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Nuclear organization in the spinal cord depends on motor neuron lamination orchestrated by catenin and afadin function.
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Differential mRNA distribution of components of the ERK/MAPK signalling cascade in the adult mouse brain.
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N-desalkylquetiapine activates ERK1/2 to induce GDNF release in C6 glioma cells: a putative cellular mechanism for quetiapine as antidepressant.
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Local knockdown of ERK2 in the adult mouse brain via adeno-associated virus-mediated RNA interference.
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RNA-sequencing and somatic mutation status of adrenocortical tumors: novel pathogenetic insights.
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Update on the ACTG1-associated Baraitser–Winter cerebrofrontofacial syndrome.
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Mutations in EXOSC2 are associated with a novel syndrome characterised by retinitis pigmentosa, progressive hearing loss, premature ageing, short stature, mild intellectual disability and distinctive gestalt.
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A comparison of solvent-based extraction methods to assess the central carbon metabolites in mouse bone and muscle.
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Structural characterization of Thogoto Virus nucleoprotein provides insights into viral RNA encapsidation and RNP assembly.
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Complement is activated by IgG hexamers assembled at the cell surface.
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From tube to structure: SPA Cryo-EM workflow using apoferritin as an example.
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Conical Fourier shell correlation applied to electron tomograms.
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Cryoelectron tomography of the NAIP5/NLRC4 inflammasome: implications for NLR activation.
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Second generation codon optimized minicircle (CoMiC) for nonviral reprogramming of human adult fibroblasts.
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Susceptibility to diet-induced obesity at thermoneutral conditions is independent of UCP1.
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Design, construction, and evaluation of a dynamic MR compatible cardiac left ventricle model.
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Design and application of a four-channel transmit/receive surface coil for functional cardiac imaging at 7T.
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Annotating regulatory DNA based on man-mouse genomic comparison.
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Bioinformatics 18 (Suppl 2): S84-S90. 2002

Comparative promoter region analysis powered by CORG.
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BMC Genomics 6 (1): 24. 2005

Exploring potential target genes of signaling pathways by predicting conserved transcription factor binding sites.
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Bioinformatics 19 (Suppl 2): ii50-ii56. October 2003

Functional inference from non-random distributions of conserved predicted transcription factor binding sites.
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Bioinformatics 20 (Suppl 1): i109-i115. 4 August 2004

In vitro reconstructed human epithelia reveal contributions of Candida albicans EFG1 and CPH1 to adhesion and invasion.
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Microbiology 148 (Pt 2): 497-506. February 2002

CORG: a database for COmparative Regulatory Genomics.
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The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism.
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Developments in CORG: a gene-centric comparative genomics resource.
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Pristionchus.org: a genome-centric database of the nematode satellite species Pristionchus pacificus.
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A Caenorhabditis motif compendium for studying transcriptional gene regulation.
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Comparative promoter analysis in vertebrate genomes with the CORG workbench.
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Adhesion of pancreatic tumor cell clusters by desmosomal molecules enhances early liver metastases formation.
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Status of the neonatal rat brain after NMDA-induced excitotoxic injury as measured by MRI, MRS and metabolic imaging.
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Old discovery leading to new era: metabolic imaging of cancer with Deuterium MRI.
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T- and L-type calcium channels maintain calcium oscillations in the murine zona glomerulosa.
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Claudin peptidomimetics modulate tissue barriers for enhanced drug delivery.
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PRISMA: Protein Interaction Screen on Peptide Matrix reveals interaction footprints and modifications- dependent interactome of intrinsically disordered C/EBPb.
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Role of a ubiquitin-like modification in polarized morphogenesis.
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Reassessment of marker genes in human induced pluripotent stem cells for enhanced quality control.
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Laminar shear stress inhibits endothelial cell metabolism via KLF2-mediated repression of PFKFB3.
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Arteriosclerosis Thrombosis and Vascular Biology 35 (1): 137-145. January 2015

FLEXBAR: flexible barcode and adapter processing for next-generation sequencing platforms.
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Biology 1 (3): 895-905. 14 December 2012

Identifying tumor cells at the single-cell level using machine learning.
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Genome Biology 23 (1): 123. 30 May 2022

On the relation between filament density, force generation and protrusion rate in mesenchymal cell motility.
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Translog, a web browser for studying the expression divergence of homologous genes.
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BMC Bioinformatics 11 (Suppl 1): S59. 18 January 2010

Therapeutic targeting of ATR in alveolar rhabdomyosarcoma.
Dorado Garcia, H., Pusch, F., Bei, Y., von Stebut, J., Ibáñez, G., Guillan, K., Imami, K., Gürgen, D., Rolff, J., Helmsauer, K., Meyer-Liesener, S., Timme, N., Bardinet, V., Chamorro González, R., MacArthur, I.C., Chen, C.Y., Schulz, J., Wengner, A.M., Furth, C., Lala, B., Eggert, A., Seifert, G., Hundsoerfer, P., Kirchner, M., Mertins, P., Selbach, M., Lissat, A., Dubois, F., Horst, D., Schulte, J.H., Spuler, S., You, D., Dela Cruz, F., Kung, A.L., Haase, K., Di Virgilio, M., Scheer, M., Ortiz, M.V. and Henssen, A.G.
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Neuroblastoma signalling models unveil combination therapies targeting feedback-mediated resistance.
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3D spheroid and organoid models to study neuroinfection of RNA viruses.
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Increase in mental disorders during the COVID-19 pandemic -- the role of occupational and financial strains. An analysis of the German National Cohort (NAKO) Study.
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Temporal and regional changes during focal ischemia in rat brain studied by proton spectroscopic imaging and quantitative diffusion NMR imaging.
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Impaired myocardial development resulting in neonatal cardiac hypoplasia alters postnatal growth and stress response in the heart.
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A second cohort of CHD3 patients expands the molecular mechanisms known to cause Snijders Blok-Campeau syndrome.
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European Journal of Human Genetics 28 (10): 1422-1431. October 2020

Pharmacological restoration and therapeutic targeting of the B-cell phenotype in classical Hodgkin's lymphoma.
Du, J., Neuenschwander, M., Yu, Y., Däbritz, J.H.M., Neuendorff, N.R., Schleich, K., Bittner, A., Milanovic, M., Beuster, G., Radetzki, S., Specker, E., Reimann, M., Rosenbauer, F., Mathas, S., Lohneis, P., Hummel, M., Dörken, B., von Kries, J.P., Lee, S. and Schmitt, C.A.
Blood 129 (1): 71-81. 5 January 2017

Integrated epigenome profiling of repressive histone modifications, DNA methylation and gene expression in normal and malignant urothelial cells.
Dudziec, E., Gogol-Doering, A., Cookson, V., Chen, W. and Catto, J.
PLoS ONE 7 (3): e32750. 7 March 2012

Uncovering the contribution of moderate-penetrance susceptibility genes to breast cancer by whole-exome sequencing and targeted enrichment sequencing of candidate genes in women of European ancestry.
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Cancers 14 (14): 3363. 11 July 2022

S-palmitoylation is required for the control of growth cone morphology of DRG neurons by CNP-induced cGMP signaling.
Dumoulin, A., Dagane, A., Dittmar, G. and Rathjen, F.G.
Frontiers in Molecular Neuroscience 11 : 345. 24 September 2018

In vivo imaging of MMP-13 activity using a specific polymer-FRET peptide conjugate detects early osteoarthritis and inhibitor efficacy.
Duro-Castano, A., Lim, N.H., Tranchant, I., Amoura, M., Beau, F., Wieland, H., Kingler, O., Herrmann, M., Nazaré, M., Plettenburg, O., Dive, V., Vicent, M.J. and Nagase, H.
Advanced Functional Materials 28 (37): 1802738. 12 September 2018

Propionic acid shapes the multiple sclerosis disease course by an immunomodulatory mechanism.
Duscha, A., Gisevius, B., Hirschberg, S., Yissachar, N., Stangl, G.I., Eilers, E., Bader, V., Haase, S., Kaisler, J., David, C., Schneider, R., Troisi, R., Zent, D., Hegelmaier, T., Dokalis, N., Gerstein, S., Del Mare-Roumani, S., Amidror, S., Staszewski, O., Poschmann, G., Stühler, K., Hirche, F., Balogh, A., Kempa, S., Träger, P., Zaiss, M.M., Holm, J.B., Massa, M.G., Nielsen, H.B., Faissner, A., Lukas, C., Gatermann, S.G., Scholz, M., Przuntek, H., Prinz, M., Forslund, S.K., Winklhofer, K.F., Müller, D.N., Linker, R.A., Gold, R. and Haghikia, A.
Cell 180 (6): 1067-1080. 19 March 2020

The choice of embedding media affects image quality, tissue R(2)*, and susceptibility behaviors in post‐mortem brain MR microscopy at 7.0T.
Dusek, P., Madai, V.I., Huelnhagen, T., Bahn, E., Matej, R., Sobesky, J., Niendorf, T., Acosta-Cabronero, Julio and Wuerfel, J.
Magnetic Resonance in Medicine 81 (4): 2688-2701. April 2019

Brain iron and metabolic abnormalities in C19orf12 mutation carriers: a 7.0 tesla MRI study in mitochondrial membrane protein-associated neurodegeneration.
Dusek, P., Mekle, R., Skowronska, M., Acosta-Cabronero, J., Huelnhagen, T., Robinson, S.D., Schubert, F., Deschauer, M., Els, A., Ittermann, B., Schottmann, G., Madai, V.I., Paul, F., Klopstock, T., Kmiec, T., Niendorf, T., Wuerfel, J. and Schneider, S.A.
Movement Disorders 35 (1): 142-150. January 2020

Brain iron accumulation in Wilson's disease: a longitudinal imaging case study during anticopper treatment using 7.0T MRI and transcranial sonography.
Dusek, P., Skoloudik, D., Maskova, J., Huelnhagen, T., Bruha, R., Zahorakova, D., Niendorf, T., Ruzicka, E., Schneider, S.A. and Wuerfel, J.
Journal of Magnetic Resonance Imaging 47 (1): 282-285. January 2018

Mechanical forces couple bone matrix mineralization with inhibition of angiogenesis to limit adolescent bone growth.
Dzamukova, M., Brunner, T.M., Miotla-Zarebska, J., Heinrich, F., Brylka, L., Mashreghi, M.F., Kusumbe, A., Kühn, R., Schinke, T., Vincent, T.L.. and Löhning, M.
Nature Communications 13 (1): 3059. 1 June 2022

Long-term follow-up after the application of mesenchymal stromal cells in children and adolescents with steroid-refractory graft-versus-host disease.
Döring, M., Cabanillas Stanchi, K.M., Lenglinger, K., Treuner, C., Gieseke, F., Erbacher, A., Mezger, M., Vaegler, M., Schlegel, P.G., Greil, J., Bettoni da Cunha Riehm, C., Faul, C., Schumm, M., Lang, P., Handgretinger, R. and Müller, I.
Stem Cells and Development 30 (5): 234-246. 19 February 2021

Clinically used broad-spectrum antibiotics compromise inflammatory monocyte-dependent antibacterial defense in the lung.
Dörner, P.J., Anandakumar, H., Röwekamp, I., Fiocca Vernengo, F., Millet Pascual-Leone, B., Krzanowski, M., Sellmaier, J., Brüning, U., Fritsche-Guenther, R., Pfannkuch, L., Kurth, F., Milek, M., Igbokwe, V., Löber, U., Gutbier, B., Holstein, M., Heinz, G.A., Mashreghi, M.F., Schulte, L.N., Klatt, A.B., Caesar, S., Wienhold, S.M., Offermanns, S., Mack, M., Witzenrath, M., Jordan, S., Beule, D., Kirwan, J.A., Forslund, S.K., Wilck, N., Bartolomaeus, H., Heimesaat, M.M. and Opitz, B.
Nature Communications 15 (1): 2788. 30 March 2024

C/EBPβ regulates lipid metabolism and Pparg isoform 2 expression in alveolar macrophages.
Dörr, D., Obermayer, B., Weiner, J.M., Zimmermann, K., Anania, C., Wagner, L.K., Lyras, E.M., Sapozhnikova, V., Lara-Astiaso, D., Prósper, F., Lang, R., Lupiáñez, D.G., Beule, D., Höpken, U.E., Leutz, A. and Mildner, A.
Science Immunology 7 (75): eabj0140. September 2022

Synthetic lethal metabolic targeting of cellular senescence in cancer therapy.
Dörr, J.R., Yu, Y., Milanovic, M., Beuster, G., Zasada, C., Däbritz, J.H.M., Lisec, J., Lenze, D., Gerhardt, A., Schleicher, K., Kratzat, S., Purfürst, B., Walenta, S., Mueller-Klieser, W., Gräler, M., Hummel, M., Keller, U., Buck, A.K., Dörken, B., Willmitzer, L., Reimann, M., Kempa, S., Lee, S. and Schmitt, C.A.
Nature 501 (7467): 421-425. 19 September 2013

Characterization of the molecular mechanisms underlying increased ischemic damage in the aldehyde dehydrogenase 2 genetic polymorphism using a human induced pluripotent stem cell model system.
Ebert, A.D., Kodo, K., Liang, P., Wu, H., Huber, B.C., Riegler, J., Churko, J., Lee, J., de Almeida, P., Lan, F., Diecke, S., Burridge, P.W., Gold, J.D., Mochly-Rosen, D. and Wu, J.C.
Science Translational Medicine 6 (255): 255ra130. 24 September 2014

Protective alpha1-antitrypsin effects in autoimmune vasculitis are compromised by methionine oxidation.
Ebert, M.J., Jerke, U., Eulenberg-Gustavus, C., Kling, L., Jenne, D.E., Kirchner, M., Mertins, P., Bieringer, M., Elitok, S., Eckardt, K.U., Schreiber, A., Salama, A.D. and Kettritz, R.
Journal of Clinical Investigation 132 (23): e160089. 1 December 2022

Silent witness: dual-species transcriptomics reveals epithelial immunological quiescence to helminth larval encounter and fostered larval development.
Ebner, F., Kuhring, M., Radonic, A., Midha, A., Renard, B.Y. and Hartmann, S.
Frontiers in Immunology 9 : 1868. 15 August 2018

A helminth-derived chitinase structurally similar to mammalian chitinase displays immunomodulatory properties in inflammatory lung disease.
Ebner, F., Lindner, K., Janek, K., Niewienda, A., Malecki, P.H., Weiss, M.S., Sutherland, T.E., Heuser, A., Kühl, A.A., Zentek, J., Hofmann, A. and Hartmann, S.
Journal of Immunology Research 2021 : 234836. 25 November 2021

Bimodal antagonism of PKA signalling by ARHGAP36.
Eccles, R.L., Czajkowski, M.T., Barth, C., Müller, P.M., McShane, E., Grunwald, S., Beaudette, P., Mecklenburg, N., Volkmer, R., Zühlke, K., Dittmar, G., Selbach, M., Hammes, A., Daumke, O., Klussmann, E., Urbé, S. and Rocks, O.
Nature Communications 7 : 12963. 7 October 2016

Cystatin M/E variant causes autosomal dominant keratosis follicularis spinulosa decalvans by dysregulating cathepsins L and V.
Eckl, K.M., Gruber, R., Brennan, L., Marriott, A., Plank, R., Moosbrugger-Martinz, V., Blunder, S., Schossig, A., Altmüller, J., Thiele, H., Nürnberg, P., Zschocke, J., Hennies, H.C. and Schmuth, M.
Frontiers in Genetics 12 : 689940. July 2021

Impaired epidermal ceramide synthesis causes autosomal recessive congenital ichthyosis and reveals the importance of ceramide acyl chain length.
Eckl, K.M., Tidhar, R., Thiele, H., Oji, V., Hausser, I., Brodesser, S., Preil, M.L., Önal-Akan, A., Stock, F., Müller, D., Becker, K., Casper, R., Nürnberg, G., Altmüller, J., Nürnberg, P., Traupe, H., Futerman, A.H. and Hennies, H.C.
Journal of Investigative Dermatology 133 (9): 2202-2211. September 2013

Drug resistance mechanisms in colorectal cancer dissected with cell type-specific dynamic logic models.
Eduati, F., Doldan-Martelli, V., Klinger, B., Cokelaer, T., Sieber, A., Kogera, F., Dorel, M., Garnett, M.J., Blüthgen, N. and Saez-Rodriguez, J.
Cancer Research 77 (12): 3364-3375. 15 June 2017