@article{UBHD-69262076,
  author={Bakr, Ali and Corte, Giuditta Della and Veselinov, Olivera and Kelekçi, Simge and Chen, Mei-Ju May and Lin, Yu-Yu and Sigismondo, Gianluca and Iacovone, Marika and Cross, Alice and Syed, Rabail and Jeong, Yunhee and Sollier, Etienne and Liu, Chun- Shan and Lutsik, Pavlo and Krijgsveld, Jeroen and Weichenhan, Dieter and Plass, Christoph and Popanda, Odilia and Schmezer, Peter},
  title={ARID1A regulates DNA repair through chromatin organization and its deficiency triggers DNA damage-mediated anti-tumor immune response},
  year={2024},
  pages={5698-5719},
  language={eng},
  issn={1362-4962},
  volume={52},
  number={10},
  note={Ver{\"o}ffentlicht: 08 April 2024 ; Gesehen am 14.10.2024},
  journal={Nucleic acids research},
  doi={10.1093/nar/gkae233},
}
@article{UBHD-68871334,
  author={Bakr, Ali and Hey, Joschka and Sigismondo, Gianluca and Liu, Chun-Shan and Sadik, Ahmed and Goyal, Ashish and Cross, Alice and Iyer, Ramya Lakshmana and M{\"u}ller, Patrick and Trauernicht, Max and Breuer, Kersten and Lutsik, Pavlo and Opitz, Christiane and Krijgsveld, Jeroen and Weichenhan, Dieter and Plass, Christoph and Popanda, Odilia and Schmezer, Peter},
  title={ID3 promotes homologous recombination via non-transcriptional and transcriptional mechanisms and its loss confers sensitivity to PARP inhibition},
  year={2021},
  pages={11666-11689},
  language={eng},
  issn={1362-4962},
  volume={49},
  number={20},
  note={Gesehen am 27.01.2022},
  journal={Nucleic acids research},
  doi={10.1093/nar/gkab964},
}
@article{UBHD-68979787,
  author={Chen, Yuanyuan and Toth, Reka and Chocarro, Sara and Weichenhan, Dieter and Hey, Joschka and Lutsik, Pavlo and Sawall, Stefan and Stathopoulos, Georgios and Plass, Christoph and Sotillo, Rocio},
  title={Club cells employ regeneration mechanisms during lung tumorigenesis},
  year={2022},
  pages={1-16},
  language={eng},
  issn={2041-1723},
  volume={13},
  number={Artikel-ID 4557},
  note={Gesehen am 28.10.2022},
  journal={Nature Communications},
  doi={10.1038/s41467-022-32052-2},
}
@article{UBHD-68374139,
  author={Gerh{\"a}user, Clarissa and Feuerbach, Lars and Assenov, Yassen and H{\"u}bschmann, Daniel and Kuryshev, Vladimir and Weichenhan, Dieter and Toth, Reka and Lutsik, Pavlo and Lawerenz, Christian and Eils, Roland and Schlesner, Matthias and Kalle, Christof von and S{\"u}ltmann, Holger and Brors, Benedikt and Plass, Christoph and Korbel, Jan Oliver},
  title={Molecular evolution of early-onset prostate cancer identifies molecular risk markers and clinical trajectories},
  year={2018},
  pages={996-1011.e8},
  language={eng},
  issn={1878-3686},
  volume={34},
  number={6},
  note={Gesehen am 29.03.2019},
  journal={Cancer cell},
  doi={10.1016/j.ccell.2018.10.016},
}
@article{UBHD-68556370,
  author={Goeppert, Benjamin and Toth, Reka and Albrecht, Thomas and Lipka, Daniel and Lutsik, Pavlo and Assenov, Yassen and Endris, Volker and Stenzinger, Albrecht and Mehrabi, Arianeb and Schirmacher, Peter and Plass, Christoph and Weichenhan, Dieter and R{\"o}ssler, Stephanie},
  title={Integrative analysis defines distinct prognostic subgroups of intrahepatic cholangiocarcinoma},
  year={2019},
  pages={2091-2106},
  language={eng},
  issn={1527-3350},
  volume={69},
  number={5},
  note={Gesehen am 27.03.2020},
  journal={Hepatology},
  doi={10.1002/hep.30493},
}
@article{UBHD-68559182,
  author={G{\"u}lmez Karaca, K{\"u}bra and Kupke, Janina and Brito, David V. C. and Zeuch, Benjamin and Thome, Christian and Weichenhan, Dieter and Lutsik, Pavlo and Plass, Christoph and Oliveira, Ana},
  title={Neuronal ensemble-specific DNA methylation strengthens engram stability},
  year={2020},
  pages={13 S.},
  language={eng},
  issn={2041-1723},
  volume={11(2020) Artikel-Nummer 639},
  number={13 Seiten},
  note={Gesehen am 30.03.2020},
  journal={Nature Communications},
  doi={10.1038/s41467-020-14498-4},
}
@article{UBHD-68351910,
  author={Haller, Florian and K{\"o}rner, Cindy and Weichenhan, Dieter and Lutsik, Pavlo and Kleinheinz, Kortine and Eils, Roland and Plass, Christoph and Wiemann, Stefan},
  title={Enhancer hijacking activates oncogenic transcription factor NR4A3 in acinic cell carcinomas of the salivary glands},
  year={2019},
  language={eng},
  issn={2041-1723},
  volume={10(2019) Artikel-Nummer 368},
  number={13 Seiten},
  note={Gesehen am 25.01.2019},
  journal={Nature Communications},
  doi={10.1038/s41467-018-08069-x},
}
@article{UBHD-69000470,
  author={Halperin, Coral and Hey, Joschka and Weichenhan, Dieter and Stein, Yaniv and Mayer, Shimrit and Lutsik, Pavlo and Plass, Christoph and Scherz-Shouval, Ruth},
  title={Global DNA methylation analysis of cancer-associated fibroblasts reveals extensive epigenetic rewiring linked with RUNX1 upregulation in breast cancer stroma},
  year={2022},
  pages={4139-4152},
  language={eng},
  issn={1538-7445},
  volume={82},
  number={22},
  note={Gesehen am 22.12.2022},
  journal={Cancer research},
  doi={10.1158/0008-5472.CAN-22-0209},
}
@article{UBHD-68800856,
  author={Hey, Joschka and Paulsen, Michelle and Toth, Reka and Weichenhan, Dieter and Butz, Simone and Schatterny, Jolanthe and Liebers, Reinhard and Lutsik, Pavlo and Plass, Christoph and Mall, Marcus A.},
  title={Epigenetic reprogramming of airway macrophages promotes polarization and inflammation in muco-obstructive lung disease},
  year={2021},
  pages={1-18},
  language={eng},
  issn={2041-1723},
  volume={12},
  number={Artikel-ID 6520},
  note={Gesehen am 12.11.2021},
  journal={Nature Communications},
  doi={10.1038/s41467-021-26777-9},
}
@article{UBHD-69365236,
  author={Jeong, Yunhee and Ronen, Jonathan and Kopp, Wolfgang and Lutsik, Pavlo and Akalin, Altuna},
  title={scMaui},
  subtitle={a widely applicable deep learning framework for single-cell multiomics integration in the presence of batch effects and missing data},
  year={2024},
  pages={1-22},
  language={eng},
  issn={1471-2105},
  volume={25},
  number={Artikel-ID 257},
  note={Gesehen am 14.07.2025},
  journal={BMC bioinformatics},
  doi={10.1186/s12859-024-05880-w},
}
@article{UBHD-69342401,
  author={Kelly, Katherine and Scherer, Michael and Braun, Martina Maria and Lutsik, Pavlo and Plass, Christoph},
  title={EpiCHAOS},
  subtitle={a metric to quantify epigenomic heterogeneity in single-cell data},
  year={2024},
  pages={1-19},
  language={eng},
  issn={1474-760X},
  volume={25},
  number={Artikel-ID 305},
  note={Gesehen am 06.05.2025},
  journal={Genome biology},
  doi={10.1186/s13059-024-03446-w},
}
@article{UBHD-69239913,
  author={Kupke, Janina and Klimmt, Julien and Mudlaff, Franziska and Schwab, Maximilian and Lutsik, Pavlo and Plass, Christoph and Sticht, Carsten and Oliveira, Ana},
  title={Dnmt3a1 regulates hippocampus-dependent memory via the downstream target Nrp1},
  year={2024},
  pages={1528-1539},
  language={eng},
  issn={1740-634X},
  volume={49},
  number={10},
  note={Gesehen am 02.08.2024},
  journal={Neuropsychopharmacology},
  doi={10.1038/s41386-024-01843-0},
}
@article{UBHD-68965896,
  author={Lipka, Daniel and Lutsik, Pavlo and Plass, Christoph},
  title={From basic knowledge to effective therapies},
  year={2018},
  pages={871-873},
  language={eng},
  issn={1878-3686},
  volume={34},
  number={6},
  journal={Cancer cell},
  doi={10.1016/j.ccell.2018.11.013},
}
@article{UBHD-68784437,
  author={Liu, Chun-Shan and Toth, Reka and Bakr, Ali and Goyal, Ashish and Islam, Md Saiful and Breuer, Kersten and Mayakonda Thippeswamy, Anand and Lin, Yu-Yu and Stepper, Peter and Jurkowski, Tomasz P. and Veldwijk, Marlon Romano and Sperk, Elena and Herskind, Carsten and Lutsik, Pavlo and Weichenhan, Dieter and Plass, Christoph and Schmezer, Peter and Popanda, Odilia},
  title={Epigenetic modulation of radiation-induced diacylglycerol kinase alpha expression prevents pro-fibrotic fibroblast response},
  year={2021},
  pages={1-26},
  language={eng},
  issn={2072-6694},
  volume={13},
  note={Gesehen am 29.09.2021},
  journal={Cancers},
  doi={10.3390/cancers13102455},
}
@article{UBHD-68730458,
  author={Llamazares Prada, Maria and Espinet, Elisa and Mijošek, Vedrana and Schwartz, Uwe and Lutsik, Pavlo and Tămaş, Raluca and Richter, Mandy and Behrendt, Annika and Pohl, Stephanie T. and Benz, Naja P. and Muley, Thomas and Warth, Arne and Heußel, Claus Peter and Winter, Hauke and Landry, Jonathan J. M. and Herth, Felix and Mertens, Tinne C. J. and Karmouty-Quintana, Harry and Koch, Ina and Benes, Vladimir and Korbel, Jan Oliver and Waszak, Sebastian Martin and Trumpp, Andreas and Wyatt, David M. and Stahl, Heiko F. and Plass, Christoph and Jurkowska, Renata Z.},
  title={Versatile workflow for cell type-resolved transcriptional and epigenetic profiles from cryopreserved human lung},
  year={2021},
  pages={1-18},
  language={eng},
  issn={2379-3708},
  volume={6},
  note={Gesehen am 29.07.2021},
  journal={JCI insight},
  doi={10.1172/jci.insight.140443},
}
@article{UBHD-68682321,
  author={Lutsik, Pavlo and Baude, Annika and Mancarella, Daniela and {\"O}z, Aliye Simin and K{\"u}hn, Alexander and Toth, Reka and Hey, Joschka and Toprak, Umut and Lim, Jinyeong and Viet Hanh Nguyen and Jiang, Chao and Mayakonda Thippeswamy, Anand and Hartmann, Mark and Rosemann, Felix and Breuer, Kersten and Vonficht, Dominik and Gr{\"u}nschl{\"a}ger, Florian and Lee, Suman and Schuhmacher, Maren Kirstin and Kusevic, Denis and Jauch, Anna and Weichenhan, Dieter and Zustin, Jozef and Schlesner, Matthias and Haas, Simon and Park, Joo Hyun and Park, Yoon Jung and Oppermann, Udo and Jeltsch, Albert and Haller, Florian and Fellenberg, J{\"o}rg and Lindroth, Anders M. and Plass, Christoph},
  title={Globally altered epigenetic landscape and delayed osteogenic differentiation in H3.3-G34W-mutant giant cell tumor of bone},
  year={2020},
  pages={16 S.},
  language={eng},
  issn={2041-1723},
  volume={11(2020) Artikel-Nummer 5414},
  number={16 Seiten},
  note={Gesehen am 21.01.2021},
  journal={Nature Communications},
  doi={10.1038/s41467-020-18955-y},
}
@article{UBHD-68778867,
  author={Mayakonda Thippeswamy, Anand and Sch{\"o}nung, Maximilian and Hey, Joschka and Batra, Rajbir and Feuerstein-Akg{\"o}z, Clarissa and K{\"o}hler, Kristin and Lipka, Daniel and Sotillo, Rocio and Plass, Christoph and Lutsik, Pavlo and Toth, Reka},
  title={Methrix},
  subtitle={an R/bioconductor package for systematic aggregation and analysis of bisulfite sequencing data},
  year={2020},
  pages={5524-5525},
  language={eng},
  issn={1367-4811},
  volume={36},
  number={22/23},
  note={Advance access publication date: 25 December 2020 ; Gesehen am 13.09.2021},
  journal={Bioinformatics},
  doi={10.1093/bioinformatics/btaa1048},
}
@article{UBHD-68711885,
  author={Niem{\"o}ller, Christoph and Plass, Christoph and Lutsik, Pavlo and Lipka, Daniel},
  title={Bisulfite-free epigenomics and genomics of single cells through methylation-sensitive restriction},
  year={2021},
  pages={1-10},
  language={eng},
  issn={2399-3642},
  volume={4},
  number={Artikel-ID 153},
  note={Gesehen am 26.11.2021},
  journal={Communications biology},
  doi={10.1038/s42003-021-01661-w},
}
@article{UBHD-69243896,
  author={Sch{\"o}nung, Maximilian and Hess, Jana and Bawidamann, Pascal and St{\"a}ble, Sina and Hey, Joschka and Langstein, Jens and Assenov, Yassen and Weichenhan, Dieter and Lutsik, Pavlo and Lipka, Daniel},
  title={AmpliconDesign},
  subtitle={an interactive web server for the design of high-throughput targeted DNA methylation assays},
  year={2021},
  pages={933-939},
  language={eng},
  issn={1559-2308},
  volume={16},
  number={9},
  note={"Published online: 24 Oct 2020".- Artikelvorschau ; Gesehen am 15.08.2024},
  journal={Epigenetics},
  doi={10.1080/15592294.2020.1834921},
}
@article{UBHD-69117632,
  author={Sch{\"o}nung, Maximilian and Hartmann, Mark and Kr{\"a}mer, Stephen and St{\"a}ble, Sina and Hakobyan, Mariam and Kleinert, Emely and Aurich, Theo and Cobanoglu, Defne and Heidel, Florian and Fr{\"o}hling, Stefan and Milsom, Michael and Schlesner, Matthias and Lutsik, Pavlo and Lipka, Daniel},
  title={Dynamic DNA methylation reveals novel cis-regulatory elements in mouse hematopoiesis},
  year={2023},
  pages={24-42.e7},
  language={eng},
  issn={1873-2399},
  volume={117},
  number={8 vom: Jan.},
  journal={Experimental hematology},
  doi={10.1016/j.exphem.2022.11.001},
}
@article{UBHD-69275607,
  author={Sollier, Etienne and Heilmann, Jessica and Gerh{\"a}user, Clarissa and Scherer, Michael and Plass, Christoph and Lutsik, Pavlo},
  title={Figeno},
  subtitle={multi-region genomic figures with long-read support},
  year={2024},
  pages={1-4},
  language={eng},
  issn={1367-4811},
  volume={40},
  note={Ver{\"o}ffentlicht: 10. Juni 2024 ; Gesehen am 21.11.2024},
  journal={Bioinformatics},
  doi={10.1093/bioinformatics/btae354},
}
@article{UBHD-68774051,
  author={Touzart, Aurore and Mayakonda Thippeswamy, Anand and Smith, Charlotte and Hey, Joschka and Toth, Reka and Cieslak, Agata and Andrieu, Guillaume P. and Quang, Christine Tran and Latiri, Mehdi and Ghysdael, Jacques and Spicuglia, Salvatore and Dombret, Hervé and Ifrah, Norbert and Macintyre, Elizabeth and Lutsik, Pavlo and Boissel, Nicolas and Plass, Christoph and Asnafi, Vahid},
  title={Epigenetic analysis of patients with T-ALL identifies poor outcomes and a hypomethylating agent-responsive subgroup},
  year={2021},
  pages={1-15},
  language={eng},
  issn={1946-6242},
  volume={13},
  note={Gesehen am 26.08.2021},
  journal={Science translational medicine},
  doi={10.1126/scitranslmed.abc4834},
}
@article{UBHD-69345197,
  author={Wagner, Rebecca E. and Arnetzl, Leonie and Britto-Borges, Thiago and Heit-Mondrzyk, Anke and Bakr, Ali and Sollier, Etienne and Gkatza, Nikoletta A. and Panten, Jasper and Delaunay, Sylvain and Sohn, Daniela and Schmezer, Peter and Odom, Duncan T. and M{\"u}ller-Decker, Karin and Plass, Christoph and Dieterich, Christoph and Lutsik, Pavlo and Bornel{\"o}v, Susanne and Frye, Michaela},
  title={SRSF2 safeguards efficient transcription of DNA damage and repair genes},
  year={2024},
  pages={1-26},
  language={eng},
  issn={2211-1247},
  volume={43},
  note={Online verf{\"u}gbar: 23. Oktober 2024, Artikelversion: 23. Oktober 2024 ; Gesehen am 15.05.2025},
  journal={Cell reports},
  doi={10.1016/j.celrep.2024.114869},
}
@article{UBHD-69338348,
  author={Weichenhan, Dieter and Riedel, Anna and Sollier, Etienne and Toprak, Umut and Hey, Joschka and Breuer, Kersten and Wierzbińska, Justyna Anna and Touzart, Aurore and Lutsik, Pavlo and B{\"a}hr, Marion and {\"O}stlund, Anders and Nilsson, Tina and Jacobsson, Susanna and Edler, Marcel and Waraky, Ahmed and Behrens, Yvonne Lisa and G{\"o}hring, Gudrun and Schlegelberger, Brigitte and Steinek, Clemens and Harz, Hartmann and Leonhardt, Heinrich and Dolnik, Anna and Reinhardt, Dirk and Bullinger, Lars and Palmqvist, Lars and Lipka, Daniel and Plass, Christoph},
  title={Altered enhancer-promoter interaction leads to MNX1 expression in pediatric acute myeloid leukemia with t(7;12)(q36;p13)},
  year={2024},
  pages={5100-5111},
  language={eng},
  issn={2473-9537},
  volume={8},
  number={19},
  note={Online verf{\"u}gbar: 27. September 2024 ; Gesehen am 23.04.2025},
  journal={Blood advances},
  doi={10.1182/bloodadvances.2023012161},
}
@article{UBHD-68966004,
  author={Weichenhan, Dieter and Lipka, Daniel and Lutsik, Pavlo and Goyal, Ashish and Plass, Christoph},
  title={Epigenomic technologies for precision oncology},
  year={2022},
  pages={60-68},
  language={eng},
  issn={1096-3650},
  volume={84},
  journal={Seminars in cancer biology},
  doi={10.1016/j.semcancer.2020.08.004},
}
@article{UBHD-68572616,
  author={Wierzbińska, Justyna Anna and Toth, Reka and Ishaque, Naveed and Rippe, Karsten and Mallm, Jan-Philipp and Klett, Lara C. and Mertens, Daniel and Zenz, Thorsten and Hielscher, Thomas and Seifert, Marc and K{\"u}ppers, Ralf and Assenov, Yassen and Lutsik, Pavlo and Stilgenbauer, Stephan and R{\"o}ßner, Philipp M. and Seiffert, Martina and Byrd, John and Oakes, Christopher C. and Plass, Christoph and Lipka, Daniel},
  title={Methylome-based cell-of-origin modeling (Methyl-COOM) identifies aberrant expression of immune regulatory molecules in CLL},
  year={2020},
  pages={1-19},
  language={eng},
  issn={1756-994X},
  volume={12},
  number={Artikel-ID 29},
  note={Gesehen am 30.04.2020},
  journal={Genome medicine},
  doi={10.1186/s13073-020-00724-7},
}
@article{UBHD-68980340,
  author={Zaremba, Anne and Jansen, Philipp and Murali, Rajmohan and Mayakonda Thippeswamy, Anand and Riedel, Anna and Krahl, Dieter and Burkhardt, Hans and John, Stefan and Géraud, Cyrill and Philip, Manuel and Kretz, Julia and M{\"o}ller, Inga and Stadtler, Nadine and Sucker, Antje and Paschen, Annette and Ugurel, Selma and Zimmer, Lisa and Livingstone, Elisabeth and Horn, Susanne and Plass, Christoph and Schadendorf, Dirk and Hadaschik, Eva and Lutsik, Pavlo and Griewank, Klaus},
  title={Genetic and methylation analysis of CTNNB1 in benign and malignant melanocytic lesions},
  year={2022},
  pages={1-18},
  language={eng},
  issn={2072-6694},
  volume={14},
  note={Gesehen am 31.10.2022},
  journal={Cancers},
  doi={10.3390/cancers14174066},
}