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Cologne Center for Genomics (CCG)

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Publications 2025

Ahmed, S., Cesarato, N., Li, Y., Xiong, X., Ullah, K., Khan, H., Khan, M.J., Thiele, H., Ahmad, W., Hasni, M.S., and Betz, R.C. (2025). Bi-Allelic DSG1 Splice-Site Variant Identified in a Family With Non-Syndromic Striate Palmoplantar Keratoderma. J Dermatol 52: 1709-1712. 10.1111/1346-8138.17911 https://www.ncbi.nlm.nih.gov/pubmed/40878888.

Boehm, V., Wallmeroth, D., Wulf, P.O., Popp, O., Teixeira Alves, L.G., Reinecke, L., Riedel, M., Wyler, E., Franitza, M., Becker, K., Polkovnychenko, K., Del Giudice, S., Benlasfer, N., Mertins, P., Landthaler, M., and Gehring, N.H. (2025). Rapid UPF1 depletion illuminates the temporal dynamics of the NMD-regulated human transcriptome. Mol Cell 85: 3524-3546 e3512. 10.1016/j.molcel.2025.08.015 https://www.ncbi.nlm.nih.gov/pubmed/40934927.

Brunger, T., Ivaniuk, A., Perez-Palma, E., Montanucci, L., Cohen, S., Smith, L., Parthasarathy, S., Helbig, I., Nothnagel, M., May, P., and Lal, D. (2025). Conserved missense variant pathogenicity and correlated phenotypes across paralogous genes. Genome Biol 26: 197. 10.1186/s13059-025-03663-x https://www.ncbi.nlm.nih.gov/pubmed/40624578.

Dechow, A., Timonen, S., Ianevski, A., Jiang, Q., Wahnschaffe, L., Peng, Y., Jungherz, D., Becker, K., Neubauer, H.A., Schonefeldt, S., de Araujo, E., Gunning, P., Fleck, R., Schrader, A., Hallek, M., Pflug, N., Moriggl, R., Aittokallio, T., Mustjoki, S., Braun, T., and Herling, M. (2025). Dual STAT3/STAT5 inhibition as a novel treatment strategy in T-prolymphocytic leukemia. Leukemia 39: 1435-1448. 10.1038/s41375-025-02577-8 https://www.ncbi.nlm.nih.gov/pubmed/40234614.

Frazao, V.V., Sendel, S., Caliebe, A., and Nothnagel, M. (2025). Large-Scale Genotype-Phenotype Simulations for Genomic Studies. Genetic Epidemiology 49:  <Go to ISI>://WOS:001587862000111.

Hahnen, E., Hauke, J., Gelmon, K., Marme, F., Ernst, C., Martin, M., Untch, M., Bonnefoi, H., Knudsen, E., Im, S.A., DeMichele, A., Van't Veer, L., Kim, S.B., Bear, H., McCarthy, N., Rhiem, K., Turner, N., Witkiewicz, A., Rojo, F., Filipits, M., Martin, L.A., Fasching, P.A., Schem, C., Becker, K., Garcia-Saenz, J.A., Kelly, C.M., Reimer, T., Toi, M., Rugo, H.S., Denkert, C., Gnant, M., Makris, A., Liu, Y., Valota, O., Felder, B., Weber, K., Nekljudova, V., and Loibl, S. (2025). BRCA1/2 and Other Predisposition Genes in High-Risk Hormone Receptor+/Human Epidermal Growth Factor Receptor 2- Breast Cancer Treated With Endocrine Therapy With or Without Palbociclib: A Secondary PENELOPE-B Study Analysis. Jco Precis Oncol 9: e2400742. 10.1200/PO-24-00742 https://www.ncbi.nlm.nih.gov/pubmed/40209141.

Hahnen, E., Hauke, J., Gelmon, K., Marme, F., Ernst, C., Martin, M., Untch, M., Bonnefoi, H., Knudsen, E., Im, S.A., DeMichele, A., Van't Veer, L., Kim, S.B., Bear, H., McCarthy, N., Rhiem, K., Turner, N., Witkiewicz, A., Rojo, F., Filipits, M., Martin, L.A., Fasching, P.A., Schem, C., Becker, K., Garcia-Saenz, J.A., Kelly, C.M., Reimer, T., Toi, M., Rugo, H.S., Denkert, C., Gnant, M., Makris, A., Liu, Y., Valota, O., Felder, B., Weber, K., Nekljudova, V., and Loibl, S. (2025). Reply to: Germline and Somatic BRCA1/2 Mutations in Breast Cancer Treatment Strategies. Jco Precis Oncol 9: e2500588. 10.1200/PO-25-00588 https://www.ncbi.nlm.nih.gov/pubmed/40893049.

Harit, K., Yi, W., Jeron, A., Schmidt, J., Beckervordersandforth, R., Wyler, E., Manukyan, A., Deckert, M., Radbruch, H., Conrad, T., Altmuller, J., Landthaler, M., Wang, X., Nishanth, G., and Schluter, D. (2025). Astrocytic-OTUD7B ameliorates murine experimental autoimmune encephalomyelitis by stabilizing glial fibrillary acidic protein and preventing inflammation. Nature communications 16: 9279. 10.1038/s41467-025-65093-4 https://www.ncbi.nlm.nih.gov/pubmed/41115891.

Hernandez, C.F., Villaman, C., Leu, C., Lal, D., Mata, I., Klein, A.D., and Perez-Palma, E. (2025). Polygenic score analysis identifies distinct genetic risk profiles in Alzheimer's disease comorbidities. Scientific reports 15: 11407. 10.1038/s41598-025-95755-8 https://www.ncbi.nlm.nih.gov/pubmed/40181078.

Hernandez, C.F., Villaman, C., Tejos, C., Repetto, G.M., Leu, C., Lal, D., Mata, I.F., Klein, A.D., and Perez-Palma, E. (2025). Polygenic scores contribution to Parkinson's disease comorbidities. Brain Commun 7: fcaf325. 10.1093/braincomms/fcaf325 https://www.ncbi.nlm.nih.gov/pubmed/40980402.

Ishorst, N., Holzel, S., Greve, C., Yilmaz, O., Lindenberg, T., Lambertz, J., Drichel, D., Zametica, B., Mingardo, E., Kalanithy, J.C., Channab, K., Kibris, D., Henne, S., Degenhardt, F., Siewert, A., Dixon, M., Kruse, T., Ongkosuwito, E., Girisha, K.M., Pande, S., Nowak, S., Hagelueken, G., Geyer, M., Carels, C., van Rooij, I., Ludwig, K.U., Odermatt, B., and Mangold, E. (2025). Role of ZFHX4 in orofacial clefting based on human genetic data and zebrafish models. European journal of human genetics : EJHG 33: 595-606. 10.1038/s41431-024-01775-9 https://www.ncbi.nlm.nih.gov/pubmed/39702590.

Kachanov, M., Volk, A.E., Falkenbach, F., Mollring, A., Hauke, J., Rading, K., Frommolt, P., Becker, K., Graefen, M., Schmutzler, R.K., Maurer, T., Hahnen, E., and Budaus, L. (2025). Evaluation of Different National Comprehensive Cancer Network Clinical Practice Guidelines in Prostate Cancer for Germline Genetic Testing in Localized and Locally Recurrent Prostate Cancer. Eur Urol Focus 11: 848-854. 10.1016/j.euf.2025.05.021 https://www.ncbi.nlm.nih.gov/pubmed/40517093.

Kachanov, M., Volk, A.E., Falkenbach, F., Mollring, A., Hauke, J., Rading, K., Frommolt, P., Becker, K., Graefen, M., Schmutzler, R.K., Maurer, T., Hahnen, E., and Budaus, L. (2025). Reply to Lingyu Guo and Tian An's Letter to the Editor re: Mykyta Kachanov, Alexander E. Volk, Fabian Falkenbach, et al. Evaluation of Different National Comprehensive Cancer Network Clinical Practice Guidelines in Prostate Cancer for Germline Genetic Testing in Localized and Locally Recurrent Prostate Cancer. Eur Urol Focus. In press. https://doi.org/10.1016/j.euf.2025.05.021. Eur Urol Focus:  10.1016/j.euf.2025.08.001 https://www.ncbi.nlm.nih.gov/pubmed/40858408.

Kalanithy, J.C., Mingardo, E., Stegmann, J.D., Dhakar, R., Dakal, T.C., Rosenfeld, J.A., Tan, W.H., Coury, S.A., Woerner, A.C., Sebastian, J., Levy, P.A., Fleming, L.R., Waffenschmidt, L., Lindenberg, T.T., Yilmaz, O., Channab, K., Babra, B.K., Christ, A., Eiberger, B., Holzel, S., Vidic, C., Haberlein, F., Ishorst, N., Rodriguez-Gatica, J.E., Pezeshkpoor, B., Kupczyk, P.A., Vanakker, O.M., Loddo, S., Novelli, A., Dentici, M.L., Becker, A., Thiele, H., Posey, J.E., Lupski, J.R., Hilger, A.C., Reutter, H.M., Merz, W.M., Dworschak, G.C., and Odermatt, B. (2025). TFAP2E is implicated in central nervous system, orofacial and maxillofacial anomalies. J Med Genet 62: 126-137. 10.1136/jmg-2023-109799 https://www.ncbi.nlm.nih.gov/pubmed/39715634.

Khan, M.A., Blatterer, J., Kuster, M., Kaufmann, L., Kroisel, P.M., Vincent, J.B., Zubair, B.M., Muzammal, M., Ahmad, N., Abbas, S., Shah, W., Ali, M.Z., Hussain, M.S., Thiele, H., Nurnberg, P., Wagner, K., and Windpassinger, C. (2025). Genetic analysis in a consanguineous MCPH family revealed a refinement of the MCPH12 locus and a founder effect of the recurrent CDK6 variant [c.589G>A, p.(Ala197Thr)] in the Pakistani population. J Genet 104: 19  https://www.ncbi.nlm.nih.gov/pubmed/40801391.

Klapproth, H., Huerta Arana, M., Lackmann, J.W., Bopp, L., Hussain, M.S., Aloui, A., Becker, K., von Stebut, E., Klein Geltink, R.I., Tantcheva-Poor, I., and Fabri, M. (2025). Metformin in Necrobiotic Xanthogranuloma. Br J Dermatol:  10.1093/bjd/ljaf370 https://www.ncbi.nlm.nih.gov/pubmed/40966608.

Kraege, A., Chavarro-Carrero, E., Schnell, E., Heilmann-Heimbach, S., Becker, K., Kohrer, K., Huettel, B., Sargheini, N., Schiffer, P., Waldvogel, A.M., Thomma, B., and Rovenich, H. (2025). High quality genome assembly and annotation (v1) of the eukaryotic freshwater microalga Coccomyxa elongata SAG 216-3b. G3 (Bethesda) 15:  10.1093/g3journal/jkae294 https://www.ncbi.nlm.nih.gov/pubmed/39671565.

Landoulsi, Z., Lohmann, K., Vollstedt, E.J., Wedgwood-Benn, E., Niestroj, L.M., Laabs, B.H., Sendel, S., Balck, A., Borsche, M., Lal, D., Grunewald, A., Bruggemann, N., Franke, A., Hicks, A., Kasten, M., Zeuner, K.E., Lange, L.M., Lieb, W., Mollenhauer, B., Pawlack, H., Pramstaller, P.P., Caliebe, A., Konig, I.R., May, P., and Klein, C. (2025). Large-scale copy number variant analysis in genes linked to Parkinson s disease. NPJ Parkinsons Dis 11: 225. 10.1038/s41531-025-01076-y https://www.ncbi.nlm.nih.gov/pubmed/40750593.

Montanucci, L., Brunger, T., Bhattarai, N., Bosselmann, C.M., Kim, S., Allen, J.P., Zhang, J., Klockner, C., Krey, I., Fariselli, P., May, P., Lemke, J.R., Myers, S.J., Yuan, H., Traynelis, S.F., and Lal, D. (2025). Ligand distances as key predictors of pathogenicity and function in NMDA receptors. Hum Mol Genet 34: 128-139. 10.1093/hmg/ddae156 https://www.ncbi.nlm.nih.gov/pubmed/39535073.

Mushunuri, A., Adesoji, O., Krause, R., May, P., Lerche, H., Becker, A., Grimm, D., International League Against Epilepsy Consortium on Complex, E., Nothnagel, M., and Schulz, H. (2025). Genetic risk factor identification for common epilepsies guided by integrative omics data analysis. Epilepsia:  10.1111/epi.70021 https://www.ncbi.nlm.nih.gov/pubmed/41319129.

Nkouamedjo Fankep, R.C., Soylev, A., Kobiela, A.L., Blom, J., Ernst, C., and Motameny, S. (2025). SV-MeCa: an XGBoost-based meta-caller approach for structural variant calling from short-read data. BMC Bioinformatics 26: 218. 10.1186/s12859-025-06246-6 https://www.ncbi.nlm.nih.gov/pubmed/40836322.

Oztoprak, H., Gao, S., Guiglielmoni, N., Brandt, A., Zheng, Y., Errbii, M., Bednarski, V., Becker, C., Becker, K., Borgschulte, L., Burak, K.A., Dion-Cote, A.M., Leonov, V., Opherden, L., Shimano, S., and Bast, J. (2025). Chromosome-scale genome dynamics reveal signatures of independent haplotype evolution in the ancient asexual mite Platynothrus peltifer. Sci Adv 11: eadn0817. 10.1126/sciadv.adn0817 https://www.ncbi.nlm.nih.gov/pubmed/39854451.

Richters, L., Gluz, O., Weber-Lassalle, N., Christgen, M., Haverkamp, H., Kuemmel, S., Kayali, M., Kates, R.E., Grischke, E.M., Altmuller, J., Forstbauer, H., Thiele, H., Braun, M., Warm, M., Ossowski, A., Wuerstlein, R., Ernst, C., Graeser, M., Linn, S.C., Nitz, U., Hauke, J., Kreipe, H.H., Schmutzler, R.K., Hahnen, E., and Harbeck, N. (2025). Genetic Alterations, Therapy Response, and Survival Among Patients With Triple-Negative Breast Cancer: A Secondary Analysis of a Randomized Clinical Trial. Jama Netw Open 8: e2461639. 10.1001/jamanetworkopen.2024.61639 https://www.ncbi.nlm.nih.gov/pubmed/40009381.

Schlosser, R.M., Krumbach, F., Corrales, E., Andrieux, G., Preisinger, C., Liss, F., Golzmann, A., Boerries, M., Becker, K., Knuchel, R., Garczyk, S., and Luscher, B. (2025). Multidimensional OMICs reveal ARID1A orchestrated control of DNA damage, splicing, and cell cycle in normal-like and malignant urothelial cells. Molecular oncology 19: 3784-3805. 10.1002/1878-0261.70019 https://www.ncbi.nlm.nih.gov/pubmed/40170512.

Trombly, G., Said, A.M., Kudin, A.P., Hallmann, K., Kakabadze, A., Peeva, V., Becker, K., Kohrer, K., Zsurka, G., and Kunz, W.S. (2025). Ligase 3 prevents oxidative strand break-induced mitochondrial DNA loss but is not essential for replicative circularization. Nucleic Acids Res 53:  10.1093/nar/gkaf1000 https://www.ncbi.nlm.nih.gov/pubmed/41099692.

Wenzel, M.C., Dasmeh, P., Plum, P.S., Giel, A.S., Hoppe, S., Franitza, M., Jonas, C., Thieme, R., Zhao, Y., Heider, D., Palles, C., Fitzgerald, R.C., Bruns, C.J., Buettner, R., Quaas, A., Gockel, I., Maj, C., Chon, S.H., Schumacher, J., and Hillmer, A.M. (2025). Single-cell analysis of Barrett's esophagus and carcinoma reveals cell types conferring risk via genetic predisposition. Cell Genom 5: 100980. 10.1016/j.xgen.2025.100980 https://www.ncbi.nlm.nih.gov/pubmed/40925382.

Werr, L., Bartenhagen, C., Rosswog, C., Cartolano, M., Voegele, C., Sexton-Oates, A., Di Genova, A., Ernst, A., Kahlert, Y., Hemstedt, N., Hoppner, S., Mansuet Lupo, A., Pelosi, G., Brcic, L., Papotti, M., George, J., Bosco, G., Quaas, A., Tang, L.H., Robzyk, K., Kadota, K., Roh, M.S., Fanaroff, R.E., Falcon, C.J., Buttner, R., Lantuejoul, S., Rekhtman, N., Rudin, C.M., Travis, W.D., Alcala, N., Fernandez-Cuesta, L., Foll, M., Peifer, M., Thomas, R.K., Fischer, M., and Lung NEN Network. (2025). TERT Expression and Clinical Outcome in Pulmonary Carcinoids. Journal of clinical oncology : official journal of the American Society of Clinical Oncology 43: 214-225. 10.1200/JCO.23.02708 https://www.ncbi.nlm.nih.gov/pubmed/39348606.

Wong, K.M., Maroofian, R., Meier, K., Diegmann, S., Tkemaladze, T., Alvi, J.R., Tasharrofi, B., Efthymiou, S., Munchau, A., Korenke, G.C., Almontashiri, N., Eyaid, W., Kashgari, A., Alotaibi, M., Gartner, J., Huppke, B., Asadollahi, M., Chikvinidze, G., Keramatipour, M., Sultan, T., Thiele, H., Nurnberg, P., Graler, M.H., Houlden, H., and Huppke, P. (2025). Biallelic ELOVL1 Variants Are Linked to Hypomyelinating Leukodystrophy, Movement Disorder, and Ichthyosis. Mov Disord 40: 1836-1850. 10.1002/mds.30258 https://www.ncbi.nlm.nih.gov/pubmed/40590574.

Worf, K., Matosin, N., Gerstner, N., Frohlich, A.S., Koller, A.C., Degenhardt, F., Thiele, H., Rietschel, M., Udawela, M., Scarr, E., Dean, B., Theis, F.J., Mueller, N.S., and Knauer-Arloth, J. (2025). Exon-variant interplay and multi-modal evidence identify endocrine dysregulation in severe psychiatric disorders impacting excitatory neurons. Transl Psychiatry 15: 153. 10.1038/s41398-025-03366-8 https://www.ncbi.nlm.nih.gov/pubmed/40253403.