Publications

COVID-19 Host Genetics Initiative.
A second update on mapping the human genetic architecture of COVID-19.
Nature, 2023, 621(7977):E7-E26. doi: 10.1038/s41586-023-06355-3.

R. Furrer, B. Heim, S. Schmid, S. Dilbaz, V. Adak, K.J.V. Nordström, D. Ritz, S.A. Steurer, J. Walter and C. Handschin.
Molecular control of endurance training adaptation in male mouse skeletal muscle.
Nat Metab, 2023 Sep 11. doi: 10.1038/s42255-023-00891-y.

K. Mohan, G. Gasparoni, A. Salhab, M.M. Orlich, R. Geffers, S. Hoffmann, R.H. Adams, J. Walter and A. Nordheim.
Age-Associated Changes in Endothelial Transcriptome and Epigenetic Landscapes Correlate With Elevated Risk of Cerebral Microbleeds.
J Am Heart Assoc, 2023, 12(17):e031044. doi: 10.1161/JAHA.123.031044.

R.K. Maji, B. Czepukojc, M. Scherer, S. Tierling, C. Cadenas, K. Gianmoena, N. Gasparoni, K. Nordström, G. Gasparoni, S. Laggai, X. Yang, A. Sinha, P. Ebert, M. Falk-Paulsen, S. Kinkley, J.  Hoppstädter, H.R. Chung, P. Rosenstiel, J.G. Hengstler, J. Walter, M.H. Schulz, S.M. Kessler and A.K. Kiemer. 
Alterations in the hepatocyte epigenetic landscape in steatosis.
Epigenetics Chromatin, 2023, 16(1):30. doi: 10.1186/s13072-023-00504-8.

M. Cheraghpour, M. Askari, S. Tierling, S. Shojaee, A. Sadeghi, P.K. Moghadam, M. Khazdouz, H. Asadzadeh Aghdaei, M. Piroozkhah, E. Nazemalhosseini-Mojarad and N. Fatemi.
A systematic review and meta-analysis for the association of the insulin-like growth factor pathway genetic polymorphisms with colorectal cancer susceptibility.
Front Oncol, 2023, 13. doi: 10.3389/fonc.2023.1168942.

V. Götz, S. Qiao, D. Das, P. Wartenberg, A. Wyatt, V. Wahl, I. Gamayun, S. Alasmi, C. Fecher-Trost, M.R. Meyer, R. Rad, T. Kaltenbacher, K. Kattler, P. Lipp, U. Becherer, P. Mollard, M. Candlish and U. Boehm.
Ovulation is triggered by a cyclical modulation of gonadotropes into a hyperexcitable state.
Cell Rep, 2023, 42(6):112543. doi: 10.1016/j.celrep.2023.112543.

Q. Yu, I. Gamayun, P. Wartenberg, Q. Zhang, S. Qiao, S. Kusumakshi, S. Candlish, V. Götz, S. Wen, D. Das, A. Wyatt, V. Wahl, F. Ectors, K. Kattler, D. Yildiz, V. Prevot, M. Schwaninger, G. Ternier, P.  Giacobini, P. Ciofi, T.D. Müller and U. Boehm.
Bitter taste cells in the ventricular walls of the murine brain regulate glucose homeostasis.
Nat Commun, 2023, 14(1):1588. doi: 10.1038/s41467-023-37099-3.

S. Qiao, S. Alasmi, A. Wyatt, P. Wartenberg, H. Wang, M. Candlish, D. Das, M. Aoki, R. Grünewald, Z. Zhou, Q. Tian, Q. Yu, V. Götz, A. Belkacemi, A. Raza, F. Ectors, K. Kattler, G. Gasparoni, J. Walter, P. Lipp, P. Mollard, D.J. Bernard, E. Karatayli, S.C. Karatayli, F. Lammert and U. Boehm.
Intra-pituitary follicle-stimulating hormone signaling regulates hepatic lipid metabolism in mice.
Nat Commun, 2023, 14(1):1098. doi: 10.1038/s41467-023-36681-z

P. Carius, A. Jungmann, M. Bechtel, A. Grißmer, A. Boese, G. Gasparoni, A. Salhab, R. Seipelt, K. Urbschat, C. Richter, C. Meier, D. Bojkova, J. Vinatl, J. Walter, N. Schneider-Daum and C.M. Lehr.
A Monoclonal Human Alveolar Epithelial Cell Line (“Arlo”) with Pronounced Barrier Function for Studying Drug Permeability and Viral Infections.
Adv Science, 2023, doi: 10.1002/advs.202207301.

J. Walter and N. Gasparoni, Eds: B. Fehse, J. Walter.
The importance of RNA for molecular diagnostics.
"In Focus: RNA. A current stocktaking of the Working", 2022, pp 84-95, ISBN: 978-3-00-074152-4, 2022, doi: 10.17169/refubium-36831.

B. Fehse, J. Walter, AG Gentechnologiebericht (Hrsg./Ed.).
In Focus: RNA. A current stocktaking of the Working Group Gene Technology Report. Video: https://1drv.ms/u/s!AsonYJMo588TlxyE4muaZ67x9zda?e=2yETlV 
ISBN: 978-3-00-074152-4, 2022, doi: 10.17169/refubium-36831.

J. Kärcher, B. Schulze, A. Dörr, S. Tierling and J. Walter.
Transfer of blocker-based qPCR reactions for DNA methylation analysis into a microfluidic LoC system using thermal modeling.
Biomicrofluidics, 2022, 16:064102. doi: 10.1063/5.0108374.

N. Mishra, K. Aden, J.I. Blase, N. Baran, D. Bordoni, F. Tran, C. Conrad, D. Avalos, C. Jaeckel, M. Scherer, S.B. Sørensen, S.H. Overgaard, B. Schulte, S. Nikolaus, G. Rey, G. Gasparoni, P.A. Lyons, J.L. Schultze, J. Walter, V. Andersen; SYSCID Consortium, E.T. Dermitzakis, S. Schreiber and P. Rosenstiel.
Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease.
Genome Med, 2022, 14(1):110. doi: 10.1186/s13073-022-01112-z.

V. Petrova, R. Song; DEEP Consortium, K.J.V. Nordström, J. Walter, J.J.L. Wong, N.J. Armstrong, J.E.J. Rasko and U. Schmitz.
Increased chromatin accessibility facilitates intron retention in specific cell differentiation states.
Nucleic Acids Res, 2022, gkac994. doi: 10.1093/nar/gkac994

J. Radke, E. Schumann, J. Onken, R. Koll, G. Acker, B. Bodnar, C. Senger, S. Tierling, M. Möbs, P. Vajkoczy, A. Vidal, S. Högler, P. Kodajova, D. Westphal, F. Meier, F. Heppner, S. Kreuzer-Redmer, F.  Grebien, K. Jürchott and T. Redmer.
Decoding molecular programs in melanoma brain metastases.
Nat Commun, 2022, 26;13(1):7304. doi: 10.1038/s41467-022-34899-x.

M. M. Nicolai, M. Pirritano, G. Gasparoni, M. Aschner, M. Simon and J. Bornhorst.
Manganese-Induced Toxicity in C. elegans: What Can We Learn from the Transcriptome?
Int J Mol Sci, 2022, 23(18):10748. doi: 10.3390/ijms231810748.

H. Dubois-Pot-Schneider, C. Aninat, K. Kattler, K. Fekir, K. Jarnouen, V. Cerec, D. Glaise, A. Salhab, G. Gasparoni, K. Takashi, S. Ishida, J. Walter and A. Corlu.
Transcriptional and Epigenetic Consequences of DMSO Treatment on HepaRG Cells.
Cells, 2022, 11:2298. doi:10.3390/cells11152298.

P. Nell, K. Kattler, D. Feuerborn, B. Hellwig, A. Riek, A. Salhab, K. Lepikhov, G. Gasparoni, A. Thomitzek, K. Belgasmi, N. Blüthgen, M. Morkel, B. Küppers-Munther, P. Godoy, D.C. Hay, C. Cadenas, R. Marchan, N. Vartak, K. Edlund, J. Rahnenführer, J. Walter and J.G. Hengstler.
Identification of an FXR-modulated liver-intestine hybrid state in iPSC-derived hepatocyte-like cells.
J Hepatol, 2022, doi: 10.1016/j.jhep.2022.07.009.

N. Fatemi, S. Tierling, H.A. Es, M. Varkiani, E.N. Mojarad, H.A. Aghdaei, J. Walter and M. Totonchi.
DNA Methylation Biomarkers in Colorectal Cancer: Clinical Applications for Precision Medicine.
Int J Cancer, 2022, doi: 10.1002/ijc.34186.

C. Cendón, W. Du, P. Durek, Y.C. Liu, T. Alexander, L. Serene, X. Yang, G. Gasparoni, A. Salhab, K. Nordström, T. Lai, A.R. Schulz, A. Rao, G.A. Heinz, A.L. Stefanski, A. Claußnitzer, K. Siewert, T. Dörner, H.D. Chang, H.D. Volk, C. Romagnani, Z. Qin, S. Hardt, C. Perka, S. Reinke, J. Walter, M.F. Mashreghi, K. Thurley, A. Radbruch and J. Dong. 
Resident memory CD4+ T lymphocytes mobilize from bone marrow to contribute to a systemic secondary immune reaction.
Eur J Immunol, 2022, doi: 10.1002/eji.202149726.

C. Kyriakopoulos, K. Nordström, P.L. Kramer, J.Y. Gottfreund, A. Salhab, J. Arand, F. Muller, F. von Meyenn, G. Ficz, W. Reik, V. Wolf,  J. Walter and P. Giehr.
A comprehensive approach for genome-wide efficiency profiling of DNA modifying enzymes.
Cell Rep Methods, 2022, doi: 10.1016/j.crmeth.2022.100187.

S. Tierling, W.M. Jürgens-Wemheuer, A. Leismann, J. Becker-Kettern, M. Scherer, A. Wrede, D. Breuskin, S. Urbschat, C. Sippl, J. Oertel, W.J. Schulz-Schaeffer and J. Walter.
Bisulfite profiling of the MGMT promoter and comparison with routine testing in glioblastoma diagnostics.
Clin Epigenetics, 2022, 14(1):26. doi: 10.1186/s13148-022-01244-4.

N. Katzmarski, J. Domínguez-Andrés, B. Cirovic, G. Renieris, E. Ciarlo, D. Le Roy, K. Lepikhov, K. Kattler, G. Gasparoni, K. Händler, H. Theis, M. Beyer, J.W.M. van der Meer, L.A.B. Joosten, J. Walter, J.L. Schultze, T. Roger, E.J. Giamarellos-Bourboulis, A. Schlitzer and M.G. Netea.
Reply to: 'Lack of evidence for intergenerational inheritance of immune resistance to infections'.
Nat Immunol, 2022, 23(2):208-209. doi: 10.1038/s41590-021-01103-z.

C. Fallerini, N. Picchiotti, M. Baldassarri, K. Zguro, S. Daga, F. Fava, E. Benetti, S. Amitrano, M. Bruttini, M. Palmieri, S. Croci, M. Lista, G. Beligni, F. Valentino, I. Meloni, M. Tanfoni, F. Minnai, F. Colombo, E. Cabri, M. Fratelli, C. Gabbi, S. Mantovani, E. Frullanti, M. Gori, F.P. Crawley, G. Butler-Laporte, B. Richards, H. Zeberg, M. Lipcsey, M. Hultström, K.U. Ludwig, E.C. Schulte, E. Pairo-Castineira, J.K. Baillie, A. Schmidt, R. Frithiof; WES/WGS Working Group Within the HGI; GenOMICC Consortium; GEN-COVID Multicenter Study, F. Mari, A. Renieri, S. Furini.
Common, low-frequency, rare, and unltra-rare coding variants contribute to COVID-19 severity.
Hum Genet, 2022, 141(1):147-173. doi: 10.1007/s00439-021-02397-7.

M.E.K. Niemi, COVID-19 Host Genetics Initiative.
Mapping the human genetic architecture of COVID-19.
Nature, 2021, 600: 472-477. doi: 10.1038/s41586-021-03767-x.

K. Ou, D. Hamo, A. Schulze, A. Roemhild, D. Kaiser, G. Gasparoni, A. Salhab, G. Zarrinrad, L. Amini, S. Schlickeiser, M. Streitz, J. Walter, H.D. Volk, M. Schmueck-Henneresse, P. Reinke and J. Polansky.
Strong expansion of human regulatory T cells for adoptive cell therapy results in epigenetic changes which may impact their survival and function.
Frontiers in Cell and Developmental Biology, 2021. doi: 10.3389/fcell.2021.751590.

A. Becker, G. Pierre Schmartz, L. Gröger, N. Grammes, V. Galata, H. Philippeit, J. Weiland, N. Ludwig, E. Meese, S. Tierling, J. Walter, A. Schwiertz, J. Spiegel, G. Wagenpfeil, K. Faßbender, A. Keller and M.M. Unger.
Effects of Resistant Starch on Symptoms, Fecal Markers and Gut Microbiota in Parkinson's Disease - the RESISTA-PD Trial.
Genomics Proteomics Bioinformatics, 2021, S1672-0229(21)00245-X. doi:10.1016/j.gpb.2021.08.009.

B. Krämer, R. Knoll, L. Bonaguro, M. ToVinh, J. Raabe, R. Astaburuaga-García, J. Schulte-Schrepping, K.M. Kaiser, G.J. Rieke, J. Bischoff, M.B. Monin, C. Hoffmeister, S. Schlabe, E. De Domenico, N. Reusch, K. Händler, G. Reynolds, N. Blüthgen, G. Hack, C. Finnemann, H.D. Nischalke, C.P. Strassburg, E. Stephenson, Y. Su, L. Gardner, D. Yuan, D. Chen, J. Goldman, P. Rosenstiel, S.V. Schmidt, E. Latz, K. Hrusovsky, A.J. Ball, J.M. Johnson, P.A. Koenig, F.I. Schmidt, M. Haniffa, J.R. Heath, B.M. Kümmerer, V. Keitel, B. Jensen, P. Stubbemann, F. Kurth, L.E. Sander, B. Sawitzki, Deutsche COVID-19 OMICS Initiative (DeCOI), A.C. Aschenbrenner, J.L. Schultze and J. Nattermann.
Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19.
Immunity, 2021, S1074-7613(21)00365-4. doi: 10.1016/j.immuni.2021.09.002.

N. Katzmarski, J. Domínguez-Andrés, B. Cirovic, G. Renieris, E. Ciarlo, D. Le Roy, K. Lepikhov, K. Kattler, G. Gasparoni, K. Händler, H. Theis, M. Beyer, J.W.M. van der Meer, L.A.B. Joosten, J. Walter, J.L. Schultze, T. Roger, E.J. Giamarellos-Bourboulis, A. Schlitzer and M.G. Netea.
Transmission of trained immunity and heterologous resistance to infections across generations.
Nat Immunol, 2021. doi:10.1038/s41590-021-01052-7.

M. Aoki, I. Gamayun, A. Wyatt, R. Grünewald, M. Simon-Thomas, S.E. Philipp, O. Hummel, S. Wagenpfeil, K. Kattler, G. Gasparoni, J. Walter, S. Qiao, D. Grattan and U. Boehm.
Prolactin-sensitive olfactory sensory neurons regulate male preference in female mice by modulating responses to chemosensory cues.
Science Advances, 2021,  7 (41), eabg4074.

K. Mattonet, N. Nowack-Weyers, V. Vogel, D. Moser, S. Tierling, M. Kasper-Sonnenberg, M. Wilhelm, M. Scherer, J. Walter, J. G. Hengstler, A. Schölmerich and R. Kumsta.
Prenatal exposure to endocrine disrupting chemicals is associated with altered DNA methylation in cord blood.
Epigenetics, 2021. doi:10.1080/15592294.2021.1975917.

M. Scherer, G. Gasparoni, S. Rahmouni, T. Shashkova, M. Arnoux, E. Louis, A. Nostaeva, D. Avalos, E. T. Dermitzakis, Y. S. Aulchenko, T. Lengauer, P. A. Lyons, M. Georges and J. Walter.
Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR.
Epigenetics & Chromatin, 2021, 14:44.

K. Gianmoena, N. Gasparoni, A. Jashari, P. Gabrys, K. Grgas, A. Ghallab, K. Nordström, G. Gasparoni, J. Reinders, K. Edlund, P. Godoy, A. Schriewer, H. Hayen, C.A. Hudert, G. Damm, D. Seehofer, T.S. Weiss,P.Boor, H-J. Anders,M. Motrapu, P. Jansen, T.S. Schiergens, M. Falk-Paulsen, P. Rosenstiel,C. Lisowski, E. Salido, R. Marchan, J. Walter, J.G. Hengstler and C. Cadenas
Epigenomic and transcriptional profiling identifies impaired glyoxylate detoxification in NAFLD as a risk factor for hyperoxaluria.
Cell Reports, 2021, 36(8):109526. doi:10.1016/j.celrep.2021.109526.

L. de Boni, G. Gasparoni, A. Welle, S. Tierling, I. Schmitt, J. Walter, J. Walter and U. Wüllner.
Epigenetic and gene expression changes of neuronal cells from MSA patients are pronounced in enzymes for cell metabolism and calcium-regulated protein kinases.
Acta Neuropathol, 2021. doi: 10.1007/s00401-021-02357-5.

S. Tierling, K. Kattler, M. Vogelgesang, T. Pfuhl, S. Lohse, C. Lo Porto, B. Schmitt, N. Seiwert, A. Salhab, S. Smola and J. Walter.
Rapid base-specific calling of SARS-CoV-2 variants of concern using combined RT-PCR melting curve screening and SIRPH technology.
Open Forum Infectious Diseases, 2021, ofab364. doi: 10.1093/ofid/ofab364.

K. Filipski, M. Scherer, K.N. Zeiner, A. Bucher, J. Kleemann, P. Jurmeister, T.I. Hartung, M. Meissner, K.H. Plate, T.R. Fenton, J. Walter, S. Tierling, B. Schilling, P.S. Zeiner and P.N. Harter.
DNA methylation-based prediction of response to immune checkpoint inhibition in metastatic melanoma.
J Immunother Cancer, 2021, 9(7):e002226. doi: 10.1136/jitc-2020-002226.

C. Haggerty, H. Kretzmer, Riemenschneider C, Kumar AS, Mattei AL, Bailly N, Gottfreund J, Giesselmann P, Weigert R, Brändl B, Giehr P, Buschow R, Galonska C, von Meyenn F, Pappalardi MB, McCabe MT, Wittler L, Giesecke-Thiel C, Mielke T, Meierhofer D, Timmermann B, Müller FJ, Walter J, Meissner A.
Dnmt1 has de novo activity targeted to transposable elements.
Nat Struct Mol Biol, 2021, Jun 17. doi: 10.1038/s41594-021-00603-8.

Beckmann D, Römer-Hillmann A, Krause A, Hansen U, Wehmeyer C, Intemann J, de Gorter DJJ, Dankbar B, Hillen J, Heitzmann M, Begemann I, Galic M, Weinhage T, Foell D, Ai R, Kremerskothen J, Kiener HP, Müller S, Kamradt T, Schröder C, Leitão E, Horsthemke B, Rosenstiel P, Nordström K, Gasparoni G, Gasparoni N, Walter J, Li N, Yang X, Chung HR, Pavenstädt H, Lindemann N, Schnittler HJ, Wang W, Firestein GS, Pap T, Korb-Pap A.
Lasp1 regulates adherens junction dynamics and fibroblast transformation in destructive arthritis.
Nat Commun, 2021, 12(1):3624. doi: 10.1038/s41467-021-23706-8.

RG Smith, E Pishva, Shireby G, Smith AR, Roubroeks JAY, Hannon E, Wheildon G, Mastroeni D, Gasparoni G, Riemenschneider M, Giese A, Sharp AJ, Schalkwyk L, Haroutunian V, Viechtbauer W, van den Hove DLA, Weedon M, Brokaw D, Francis PT, Thomas AJ, Love S, Morgan K, Walter J, Coleman PD, Bennett DA, De Jager PL, Mill J, Lunnon K.
A meta-analysis of epigenome-wide association studies in Alzheimer's disease highlights novel differentially methylated loci across cortex.
Nat Commun, 2021 Jun 10;12(1):3517. doi: 10.1038/s41467-021-23243-4.

A. Welle, C.V. Kasakow, A.M. Jungmann, D. Gobbo, L. Stopper, K. Nordström, A. Salhab, G. Gasparoni, A. Scheller, F. Kirchhoff and J. Walter.
Epigenetic control of region-specific transcriptional programs in mouse cerebellar and cortical astrocytes.
Glia, 2021 May 24. doi: 10.1002/glia.24016.

Warnat-Herresthal S, Schultze H, Shastry KL, Manamohan S, Mukherjee S, Garg V, Sarveswara R, Händler K, Pickkers P, Aziz NA, Ktena S, Tran F, Bitzer M, Ossowski S, Casadei N, Herr C, Petersheim D, Behrends U, Kern F, Fehlmann T, Schommers P, Lehmann C, Augustin M, Rybniker J, Altmüller J, Mishra N, Bernardes JP, Krämer B, Bonaguro L, Schulte-Schrepping J, De Domenico E, Siever C, Kraut M, Desai M, Monnet B, Saridaki M, Siegel CM, Drews A, Nuesch-Germano M, Theis H, Heyckendorf J, Schreiber S, Kim-Hellmuth S; COVID-19 Aachen Study (COVAS), Nattermann J, Skowasch D, Kurth I, Keller A, Bals R, Nürnberg P, Rieß O, Rosenstiel P, Netea MG, Theis F, Mukherjee S, Backes M, Aschenbrenner AC, Ulas T; Deutsche COVID-19 Omics Initiative (DeCOI), Breteler MMB, Giamarellos-Bourboulis EJ, Kox M, Becker M, Cheran S, Woodacre MS, Goh EL, Schultze JL.
Swarm Learning for decentralized and confidential clinical machine learning.
Nature, 2021, 594(7862):265-270. doi: 10.1038/s41586-021-03583-3.

J. Fischer, F.Ardakani, K. Kattler, J. Walter and M.H. Schulz.
CpG content-dependent associations between transcription factors and histone modifications.
PLOS One, 2021. doi: 10.1371/journal.pone.0249985.

S.J. Schunk, M.E. Kleber, ..., S. Tierling, J. Walter, E. Ampofo, B.A. Niemeyer, P. Lipp, H. Schunkert, M. Böhm, W. Koenig, D. Fliser, U. Laufs, T. Speer, eQTLGen consortium, BIOS consortium.
Genetically determined NLRP3 inflammasome activation associates with systemic inflammation and cardiovascular mortality.
Eur Heart J, 2021, Mar 22:ehab107. doi: 10.1093/eurheartj/ehab107.

M. Scherer, F. Schmidt, O. Lazareva, J. Walter, J. Baumbach, M.H. Schulz and M. List.
Machine Learning for Deciphering Cell Heterogeneity and Gene Regulation.
Nature Computational Science, 2021, doi: 10.1038/s43588-021-00038-7.

A.C. Aschenbrenner, M. Mouktaroudi, ..., M.G. Netea, J.L. Schultze, M. Kox, M.M.B. Breteler, J. Nattermann, A. Koutsoukou, E.J. Giamarellos-Bourboulis, T. Ulas, German COVID-19 Omics Initiative (DeCOI).
Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients.
Genome Med, 2021, 13;13(1):7. doi: 10.1186/s13073-020-00823-5.

A. Wiedemann, M. Lettau, I. Wirries, A. Jungmann, A. Salhab, G. Gasparoni, H.E. Mei, C. Perka, J. Walter, A. Radbruch, A.C. Lino and T. Dörner.
Human IgA-Expressing Bone Marrow Plasma Cells Characteristically Upregulate Programmed Cell Death Protein-1 Upon B Cell Receptor Stimulation.
Front Immunol, 2021, 12;11:628923. doi: 10.3389/fimmu.2020.628923.

L.K. Feiner, S. Tierling, S. Holländer, M. Glanemann and C. Rubie.
An aging and p53 related marker: HOXA5 promoter methylation negatively correlates with mRNA and protein expression in old age.
Aging (Albany NY), 2021, Feb 5;13. doi: 10.18632/aging.202621.

C. Kressler, G. Gasparoni, K. Nordström, D. Hamo, A. Salhab, C. Dimitropoulos, S. Tierling, P. Reinke, H.D. Volk, J. Walter, A. Hamann and J.K. Polansky.
Targeted De-Methylation of the FOXP3-TSDR Is Sufficient to Induce Physiological FOXP3 Expression but Not a Functional Treg Phenotype.
Front Immunol, 2021 Jan 7;11:609891. doi: 10.3389/fimmu.2020.609891.

J.L. Berg, B. Perfler, S. Hatzl, M.C. Mayer, S. Wurm, B. Uhl, A. Reinisch, I. Klymiuk, S. Tierling, G. Pregartner, G. Bachmaier, A. Berghold, K. Geissler, M. Pichler, G. Hoefler, H. Strobl, A. Wölfler, H. Sill and A. Zebisch.
Micro-RNA-125a mediates the effects of hypomethylating agents in chronic myelomonocytic leukemia.
Clin Epigenetics, 2021 Jan 6;13(1):1. doi: 10.1186/s13148-020-00979-2.

S.O.M. Dyke, C.A. Ennis, Y. Joly, J. Walter, R. Siebert and T. Pastinen.
Communicating science: epigenetics in the spotlight.
Environ Epigenet, 2020 Nov 18;6(1):dvaa015. doi: 10.1093/eep/dvaa015. eCollection 2020. PMID: 33240528

P. Lo Riso, C.E. Villa, G. Gasparoni, A. Vingiani, R. Luongo, A. Manfredi, A. Jungmann, A. Bertolotti, F. Borgo, A. Garbi, M. Lupia, P. Laise, V. Das, G. Pruneri, G. Viale, N. Colombo, T. Manzo, L. Nezi, U. Cavallaro, D. Cacchiarelli, J. Walter and G. Testa.
A cell-of-origin epigenetic tracer reveals clinically distinct subtypes of high-grade serous ovarian cancer.
Genome Med, 2020 Oct 30;12:94. doi: 10.1186/s13073-020-00786-7.

F. Behjati Ardakani, K. Kattler, T. Heinen, F. Schmidt, D. Feuerborn, G. Gasparoni, K. Lepikhov, P. Nell, J. Hengstler, J. Walter and M.H. Schulz.
Prediction of single-cell gene expression for transcription factor analysis,
GigaScience, 2020, giaa113, https://doi.org/10.1093/gigascience/giaa113.

M. Scherer, P.V. Nazarov, R. Toth, S. Sahay, T. Kaoma, V. Maurer, N. Vedeneev, C. Plass, T. Lengauer, J. Walter and P. Lutsik.
Reference-free deconvolution, visualization and interpretation of complex DNA methylation data using DecompPipeline, MeDeCom and FactorViz.
Nature Protocols, 2020. https://doi.org/10.1038/s41596-020-0369-6.

S. Böhm, V. Splith, L.M. Riedmayr, R.D. Rötzer, G. Gasparoni, K.J.V. Nordström, J.E. Wagner, K.S. Hinrichsmeyer, J. Walter, C. Wahl-Schott, S. Fenske, M. Biel, S. Michalakis and E. Becirovic.
A gene therapy for inherited blindness using dCas9-VPR-mediated transcriptional activation.
Sci Adv, 2020 Aug 19;6:eaba5614. doi: 10.1126/sciadv.aba5614.

A.L. Panagiotopoulos, N. Karguth, M. Pavlou, S. Böhm, G. Gasparoni, J. Walter, A. Graf, H. Blum, M. Biel, L.M. Riedmayr and E. Becirovic.
Antisense Oligonucleotide- and CRISPR-Cas9-Mediated Rescue of mRNA Splicing for a Deep Intronic CLRN1 Mutation.
Mol Ther Nucleic Acids, 2020 Sep 4;21:1050-1061. doi: 10.1016/j.omtn.2020.07.036.

N. Rajewsky, G. Almouzni, S.A. Gorski, S. Aerts, I. Amit, M.G. Bertero, C. Bock, A.L. Bredenoord, G. Cavalli, S. Chiocca, H. Clevers, B. De Strooper, A. Eggert, J. Ellenberg, X.M. Fernández, M. Figlerowicz, S.M. Gasser, N. Hubner, J. Kjems, J.A. Knoblich, G. Krabbe, P. Lichter, S. Linnarsson, J.C. Marine, J. Marioni, M.A. Marti-Renom, M.G. Netea, D. Nickel, M. Nollmann, H.R. Novak, H. Parkinson, S. Piccolo, I. Pinheiro, A. Pombo, C. Popp, W. Reik, S. Roman-Roman, P. Rosenstiel, J.L. Schultze, O. Stegle, A. Tanay, G. Testa, D. Thanos, F.J. Theis, M.E. Torres-Padilla, A. Valencia, C. Vallot, A. van Oudenaarden, M. Vidal and T. Voet; LifeTime Community.
LifeTime and improving European healthcare through cell-based interceptive medicine.
Nature, 2020 Sep 7. doi: 10.1038/s41586-020-2715-9.

J. Schulte-Schrepping, N. Reusch, D. Paclik, K. Baßler, S. Schlickeiser, B. Zhang, B. Krämer, T. Krammer, S. Brumhard, L. Bonaguro, E. De Domenico, D. Wendisch, M. Grasshoff, T.S. Kapellos, M. Beckstette, T. Pecht, A. Saglam, O. Dietrich, H.E. Mei, A.R. Schulz, C. Conrad, D. Kunkel, E. Vafadarnejad, C.J. Xu, A. Horne, M. Herbert, A. Drews, C. Thibeault, M. Pfeiffer, S. Hippenstiel, A. Hocke, H. Müller-Redetzky, K.M. Heim, F. Machleidt, A. Uhrig, L. Bosquillon de Jarcy, L. Jürgens, M. Stegemann, C.R. Glösenkamp, H.D. Volk, C. Goffinet, M. Landthaler, E. Wyler, P. Georg, M. Schneider, C. Dang-Heine, N. Neuwinger, K. Kappert, R. Tauber, V. Corman, J. Raabe, K.M. Kaiser, M.T. Vinh, G. Rieke, C. Meisel, T. Ulas, M. Becker, R. Geffers, M. Witzenrath, C. Drosten, N. Suttorp, C. von Kalle, F. Kurth, K. Händler, J.L. Schultze, A.C. Aschenbrenner, Y. Li, J. Nattermann, B. Sawitzki, A.E. Saliba and L.E. Sander; Deutsche COVID-19 OMICS Initiative (DeCOI).
Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment.
Cell, 2020 Aug 5:S0092-8674(20)30992-2. doi: 10.1016/j.cell.2020.08.001.

L. Schnöder, G. Gasparoni, K. Nordström, A. Schottek, I. Tomic, A. Christmann, K.H. Schäfer, M.D. Menger, J. Walter, K. Fassbender and Y. Liu.
Neuronal deficiency of p38α-MAPK ameliorates symptoms and pathology of APP or Tau-transgenic Alzheimer's mouse models.
FASEB J, 2020 May 31. doi: 10.1096/fj.201902731RR.

N. Gerstner, T. Kehl, K. Lenhof, A. Müller, C. Mayer, L. Eckhart, N.L. Grammes, C. Diener, M. Hart, O. Hahn, J. Walter, T. Wyss-Coray, E. Meese, A. Keller and H.P. Lenhof.
GeneTrail 3: advanced high-throughput enrichment analysis.
Nucleic Acids Res, 2020 May 7:gkaa306. doi: 10.1093/nar/gkaa306.

L. Frach, S. Tierling, M. Schwaiger, D. Moser, M. Heinrichs, J. G.Hengstler, J.Walter and R. Kumsta
The mediating role of KITLG DNA methylation in the association between childhood adversity and cortisol stress reactivity does not replicate in monocytes.
Psychoneuroendocrinology, 2020, doi: 10.1016/j.psyneuen.2020.104653.

M. Scherer, A. Nebel, A. Franke, J. Walter, T. Lengauer, C. Bock, F. Müller and M. List.
Quantitative comparison of within-sample heterogeneity scores for DNA methylation data.
Nucleic Acids Res, 2020, pii: gkaa120. doi: 10.1093/nar/gkaa120.

A. Ramisch, V. Heinrich, L.V. Glaser, A. Fuchs, X. Yang, P. Benner, R. Schöpflin, N. Li, S. Kinkley, A. Römer-Hillmann, J. Longinotto, S. Heyne, B. Czepukojc, S.M. Kessler, A.K. Kiemer, C. Cadenas, L. Arrigoni, N. Gasparoni, T. Manke, T. Pap, J.A. Pospisilik, J. Hengstler, J. Walter, S.H. Meijsing, H.R. Chung and M. Vingron.
CRUP: a comprehensive framework to predict condition-specific regulatory units.
Genome biology, 2019, 20(1):227.

S.Y. Weißenberg , F. Szelinski, E. Schrezenmeier, A.L. Stefanski, A. Wiedemann, H. Rincon-Arevalo, A. Welle, A. Jungmann, K. Nordström, J. Walter, J. Imgenberg-Kreuz, G. Nordmark, L. Rönnblom, P. Bachali, M.D. Catalina, A.C. Grammer, P.E. Lipsky, A.C. Lino and T. Dörner.
Identification and Characterization of Post-activated B Cells in Systemic Autoimmune Diseases.
Front Immunol, 2019, 10:2136. doi: 10.3389/fimmu.2019.02136. eCollection 2019.

J. Walter & H. Schickl (Eds.) on behalf of the Interdisciplinary Research Group (IAG) Gene Technology Report at the Berlin-Brandenburg Academy of Sciences and Humanities
Single Cell Analysis in Research and Medicine.
Berlin BBAW, 2019, 91 pages, ISBN: 978-3-939818-85-4.

K. Nordström, F. Schmidt, N. Gasparoni, A. Salhab, G. Gasparoni, K. Kattler, F. Müller, P. Ebert, I.G. Costa, DEEP consortium, N. Pfeifer, T. Lengauer, M.H.Schulz and J.Walter.
Unique and assay-specific features of NOMe-, ATAC- and DNase I-seq data.
Nucleic Acids Res, 2019, pii: gkz799, doi: 10.1093/nar/gkz799. 

B. Czepukojc, A. Barghash, S. Tierling, Y. Simon, C. Körbel, C. Cadenas, N. van Hul, A. Sachinidis, J.G.G. Hengstler, V. Helms, M.W. Laschke, J. Walter, J. Haybaeck, I. Leclercq, A.K. Kiemer and S.M. Kessler.
IGF2 mRNA binding protein 2 transgenic mice are more prone to develop a ductular reaction and to progress towards cirrhosis.
Front Med, 2019, doi: 10.3389/fmed.2019.00179.

S.O.M. Dyke, K.M. Saulnier, C. Dupras, A.P. Webster, K. Maschke, M. Rothstein, R. Siebert, J.Walter, S. Beck, T. Pastinen and Y. Joly.
Points-to-consider on the return of results in epigenetic research.
Genome Medicine, 2019, 11:31. doi: 10.1186/s13073-019-0646-6.

N.Y. Souren, L.A. Gerdes, P. Lutsik, G. Gasparoni, E. Beltrán, A. Salhab, T. Kümpfel, D. Weichenhan, C. Plass, R. Hohlfeld and J. Walter.
DNA methylation signatures of monozygotic twins clinically discordant for multiple sclerosis.
Nat Commun, 2019, 10(1):2094. doi: 10.1038/s41467-019-09984-3.

A. Lück, P. Giehr, K. Nordstrom, J. Walter and V. Wolf.
Hidden Markov modelling reveals neighborhood dependence of Dnmt3a and 3b activity.
IEEE/ACM Trans Comput Biol Bioinform, 2019. doi:10.1109/TCBB.2019.2910814.

F. Müller, M. Scherer, Y. Assenov, P. Lutsik, J. Walter, T. Lengauer and C. Bock.
RnBeads 2.0: comprehensive analysis of DNA methylation data.
Genome Biol, 2019, 20:55. doi:10.1186/s13059-019-1664-9.

J. Matthias, J. Maul , R. Noster, H. Meinl, Y.Y. Chao, H. Gerstenberg, F. Jeschke, G. Gasparoni, A. Welle, J. Walter, K. Nordström, K. Eberhardt, D. Renisch, S. Donakonda, P. Knolle, D. Soll, S.Grabbe, N. Garzorz-Stark, K. Eyerich, T. Biedermann, D. Baumjohann and C.E. Zielinski.
Sodium chloride is an ionic checkpoint for human TH2 cells and shapes the atopic skin microenvironment.
Sci Transl Med, 2019 Feb 20;11(480). doi: 0.1126/scitranslmed.aau0683.

A. Becker, G. Vella, V. Galata, K. Rentz, C. Beisswenger, C. Herr, J. Walter, S. Tierling, H. Slevogt, A. Keller and R. Bals.
The composition of the pulmonary microbiota in sarcoidosis – an observational study.
Respir Res, 2019 Feb 28;20(1):46. doi: 10.1186/s12931-019-1013-2.

A.U. Fischer, N.I. Müller, T. Deller, D.D. Turco, J.O. Fisch, D. Griesemer, K. Kattler, A. Maraslioglu, V. Roemer, M.A. Xu-Friedman, J. Walter and E. Friauf.
GABA is a Modulator, Rather than a Classical Transmitter, in the MNTB-LSO Sound Localization Circuit.
J Physiol, 2019 Feb 18. doi: 10.1113/JP277566.

F. Behjati Ardakani, K. Kattler, K. Nordström, N. Gasparoni, G. Gasparoni, S. Fuchs, A. Sinha, M. Barann, P. Ebert, J. Fischer, B. Hutter, G. Zipprich, C.D. Imbusch, B. Felder, J. Eils, B. Brors, T. Lengauer, T. Manke, P. Rosenstiel, J. Walter and M.H. Schulz.
Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters.
Epigenetics Chromatin, 2018, 11(1):66. doi: 10.1186/s13072-018-0236-7.

M. Brosch, K. Kattler, A. Herrmann, W. von Schönfels, K. Nordström, D. Seehofer, G. Damm, T. Becker, S. Zeissig, S. Nehring, F. Reichel, V. Moser, V. Raghavan Thangapandi, F. Stickel, G. Baretton, C. Röcken, M. Muders, M. Matz, M. Krawczak, G. Gasparoni, H. Hartmann, A. Dahl, C. Schafmayer, J. Walter and J. Hampe.
Epigenomic map of human liver reveals principles of zonated morphogenic and metabolic control.
Nature Communications, 2018, doi:10.1038/s41467-018-06611-5.

F. Bormann, S. Stinzing, S. Tierling, M. Morkel, M. Rivera Markelova, J. Walter, W. Weichert, F. Roßner, N. Kuhn, J. Perner, J. Dietz, S. Ispasanie, M. Dietel, R. Schäfer, V. Heinemann and C. Sers.
Epigenetic regulation of Amphiregulin and Epiregulin in colorectal cancer.
Int J Cancer, 2018, doi: 10.1002/ijc.31892.

S. Rupf, C.C. Laczny, V. Galata, C. Backes, A. Keller, N. Umanskaya, A. Erol, S. Tierling, C. Lo Porto, J. Walter, J. Kirsch, M. Hannig and C. Hannig.
Comparison of initial oral microbiomes of young adults with and without cavitated dentin caries lesions using an insitu biofilm model.
Sci Rep, 2018, doi: 10.1038/s41598-018-32361-x.

N. Jafari, P. Giehr, M. Hesaraki, R. Baas, P. de Graaf, H.T.M. Timmers, J. Walter, H. Baharvand and M. Totonchi.
Genomic integrity of ground-state pluripotency.
J Cell Biochem, 2018, doi: 10.1002/jcb.27296.

T. Kehl, L. Schneider, K. Kattler, D. Stöckel, J. Wegert, N. Gerstner, N. Ludwig, U. Distler, S. Tenzer, M. Gessler, J. Walter, A. Keller, N. Graf, E. Meese and H.P. Lenhof.
The role of TCF3 as potential master regulator in blastemal Wilms tumors.
Int J Cancer, 2018, doi: 10.1002/ijc.31834.

A. Salhab, K. Nordström, K. Kattler, P. Ebert, F. Ramirez, L. Arrigoni, F. Müller, C. Cadenas, J. Hengstler, T. Lengauer, T. Manke, DEEP Consortium and J.Walter
A comprehensive analysis of 195 DNA methylomes reveals shared and cell specific features of partially methylated domains.
Genome Biology, 2018, https://doi.org/10.1186/s13059-018-1510-5.

G. Gasparoni, S. Bultmann, P. Lutsik, T.F.J. Kraus, S. Sordon, J. Vlcek, V. Dietinger, M. Steinmaurer, M. Haider, C.B. Mulholland, T. Arzberger, S. Roeber, M. Riemenschneider, H.A. Kretzschmar, A. Giese, H. Leonhardt and J. Walter.
DNA methylation analysis on purified neurons and glia dissects age and Alzheimer's disease-specific changes in the human cortex.
Epigenetics Chromatin, 2018, 11(1):41, doi:10.1186/s13072-018-0211-3.

A.C. Lino, V.D. Dang, V. Lampropoulou, A. Welle, J. Joedicke, J. Pohar, Q. Simon, J. Thalmensi. A. Baures, V. Flühler, I. Sakwa, U. Stervbo, S. Ries, L. Jouneau, P. Boudinot, T. Tsubata, T. Adachi, A. Hutloff, ..., J. Walter and S. Fillatreau
LAG-3 Inhibitory Receptor Expression Identifies Immunosuppressive Natural Regulatory Plasma Cells.
Immunity, 2018, 49(1):120-133.e9, doi: 10.1016/j.immuni.2018.06.007.

P. Giehr, C. Kyriakopoulos, K. Lepikhov, S. Wallner, V. Wolf and J. Walter.
Two are better than one: HPoxBS - hairpin oxidative bisulfite sequencing.
Nucleic Acids Res, 2018, doi: 10.1093/nar/gky422.

P. Godoy, W. Schmidt-Heck, B. Hellwig, P. Nell, D. Feuerborn, J. Rahnenführer, K. Kattler, J. Walter, N. Blüthgen and J.G. Hengstler.
Assessment of stem cell differentiation based on genome-wide expression profiles.
Philos Trans R Soc Lond B Biol Sci, 2018, 373(1750). pii: 20170221. doi: 10.1098/rstb.2017.0221.

T. Kehl, L. Schneider, K. Kattler, D. Stöckel, J. Wegert, N. Gerstner, N. Ludwig, U. Distler, M. Schick, U. Keller, S. Tenzer, M. Gessler, J. Walter, A. Keller, N. Graf, E. Meese and H.P. Lenhof.
REGGAE: a novel approach for the identification of key transcriptional regulators.
Bioinformatics, 2018, doi: 10.1093/bioinformatics/bty372.

W.H. Pan, F. Sommer, M. Falk-Paulsen, T. Ulas, P. Best, A. Fazio, P. Kachroo, A. Luzius, M. Jentzsch, A. Rehman, F. Müller, T. Lengauer, J. Walter, S. Künzel, J.F. Baines, S. Schreiber, A. Franke, J.L. Schultze, F. Bäckhed and P. Rosenstiel.
Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development.
Genome Med, 2018, 10(1):27. doi: 10.1186/s13073-018-0534-5.

M. Totonchi, S.N. Hassani, A. Sharifi-Zarchi, N. Tapia, K. Adachi, J. Arand, B. Greber, D. Sabour, M.J. Araúzo-Bravo, J. Walter, M. Pakzad, H. Gourabi, H.R. Schöler and H. Baharvand.
Blockage of the Epithelial-to-Mesenchymal Transition Is Required for Embryonic Stem Cell Derivation.
Stem Cell Reports, 2017, 9(4):1275-1290. doi: 10.1016/j.stemcr.2017.08.006.

Y. Alkhaled, M. Laqqan, S. Tierling, C. Lo Porto and M.E. Hammadeh.
DNA methylation level of spermatozoa from subfertile and proven fertile and its relation to standard sperm parameters.
Andrologia, 2018, doi: 10.1111/and.13011.

S. Tierling, B. Schmitt and J. Walter.
Comprehensive Evaluation of Commercial Bisulfite-Based DNA Methylation Kits and Development of an Alternative Protocol With Improved Conversion Performance.
Genet Epigenet, 2018, doi: 10.1177/1179237X18766097.

Q. Hammer, E. Borst, T. Rückert, A. Haubner, M. Babic, A. Tomic, G. Pietra, J. Dunst, M. Nienen, I. Blau, J. Hofmann, I.-K. Na, P. Hemmati, N.Babel, R. Arnold, M. Messerle, P. Durek, F. Heinrich, G. Gasparoni, I. Prinz, C. Koenecke, J. Walter, K. Thurley, M.F. Mashreghi and C. Romagnani.
Peptide-Specific Recognition of Human Cytomegalovirus Strains Controls Adaptive Natural Killer Cells.
Nat Immunol, 2018 May;19(5):453-463. doi: 10.1038/s41590-018-0082-6. 

A. Nowak , D. Lock. P. Bacher, T. Hohnstein, K. Vogt, J. Gottfreund ,P. Giehr, JK Polansky, B. Sawitzki, A. Kaiser, J. Walter, A. Scheffold.
CD137+CD154- Expression As a Regulatory T Cell (Treg)-Specific Activation Signature for Identification and Sorting of Stable Human Tregs from In Vitro Expansion Cultures.
Front Immunol, 2018 Feb 7;9:199. doi: 10.3389/fimmu.2018.00199.

L. de Boni, G. Gasparoni, C. Haubenreich, S. Tierling, I. Schmitt, M. Peitz, P. Koch, J. Walter, U. Wüllner and O. Brüstle.
DNA methylation alterations in iPSC- and hESC-derived neurons: potential implications for neurological disease modeling.
Clin Epigenetics, 2018. doi: 10.1186/s13148-018-0440-0.

Y. Alkhaled, M. Laqqan, S. Tierling, C. Lo Porto, H. Amor and M.E. Hammadeh.
Impact of cigarette-smoking on sperm DNA methylation and its effect on sperm parameters.
Andrologia, 2018. doi: 10.1111/and.12950.

P. Giehr and J. Walter.
Hairpin Bisulfite Sequencing: Synchronous Methylation Analysis on Complementary DNA Strands of Individual Chromosomes.
Methods Mol Biol, 2017, 1708:573-586. doi: 10.1007/978-1-4939-7481-8_29.

A. Lück, P. Giehr, J.Walter, V. Wolf
A Stochastic Model for the Formation of Spatial Methylation Patterns.
Comp Methods in Systems Biol, 2017, pp 160-178.

M. Totonchi, H. S.-N. Hassani, A. Sharifi-Zarchi, N. Tapia,K. Adachi, J. Arand, B. Greber, D. Sabour, M. J. Araúzo-Bravo, J. Walter, M. Pakzad, H. Gourabi, H. R. Schöler and H. Baharvand.
Blockage of the Epithelial-to-Mesenchymal Transition Is Required for Embryonic Stem Cell Derivation.
Stem Cell Reports, 2017, 9(4):1275-1290. doi: 10.1016/j.stemcr.2017.08.006.

M. Laqqan, S. Tierling, Y. Alkhaled, C. LoPorto and M.E. Hammadeh.
Alterations in sperm DNA methylation patterns of oligospermic males.
Reprod Biol, 2017, pii: S1642-431X(17)30169-9. doi: 10.1016/j.repbio.2017.10.007.

C.S. Schultheiss, S. Laggai, B. Czepukojc, U.K. Hussein, M. List, A. Barghash, S. Tierling, K. Hosseini, N. Golob-Schwarz, J. Pokorny, M. Schulz, V. Helms, J. Walter, V.K. Zimmer, F. Lammert, R.M. Bohle, L. Dandolo, J. Haybaeck, A.K. Kiemer and S.M. Kessler.
The long non-coding RNA H19 suppresses carcinogenesis and chemoresistance in hepatocellular carcinoma.
Cell Stress, 2017, 1(1):37-54. doi: 10.15698/cst2017.10.105.

C. Kyriakopoulos, P. Giehr and V. Wolf V.
H(O)TA: estimation of DNA methylation and hydroxylation levels and efficiencies from time course data.
Bioinformatics, 2017, 1;33(11):1733-1734. doi: 10.1093/bioinformatics/btx042.

Interdisciplinary Research Group Gene Technology Report, Berlin Brandenburg Academy of Sciences and Humanities (J. Walter, A. Hümpel, Editors)
Epigenetics - Implications for the Life Sciences and the Humanities.
Berlin BBAW, 2017, ISBN: 97-3-939818-70-0. 

M. Laqqan, S. Tierling, Y. Al Khaled, C. Lo Porto, E.F. Solomayer and M.E. Hammadeh.
Aberrant DNA methylation patterns of human spermatozoa in current smoker males.
Reprod Toxicol, 2017. doi: 10.1016/j.reprotox.2017.05.010.

M. Laqqan, S. Tierling, Y. Al Khaled, C. Lo Porto, E.F. Solomayer and M.E. Hammadeh.
Spermatozoa from males with reduced fecundity exhibit differential DNA methylation patterns.
Andrology, 2017. doi: 10.1111/andr.12362.

Y. Al Khaled, S. Tierling, M. Laqqan, C. Lo Porto and M.E. Hammadeh.
Cigarette smoking induces only marginal changes in sperm DNA methylation levels of patients undergoing intra-cytoplasmic sperm injection treatment.
Andrologia, 2017. doi: 10.1111/and.12818.

P. Lutsik, M. Slawski, G. Gasparoni, N. Vendeev, M. Hein and J. Walter.
MeDeCom: discovery and quantification of latent components of heterogeneous methylomes.
Genome Biology, 2017. doi: 10.1186/s13059-017-1182-6.

J. Lan, K. Lepikhov, P. Giehr and J. Walter.
Histone and DNA methylation control by H3 serine 10/threonine 11 phosphorylation in the mouse zygote.
Epigenetics & Chromatin, 2017. doi: 10.1186/s13072-017-0112-x.

B.A. Szilagyi, J. Triebus, C. Kressler, M. de Almeida†, S. Tierling, P. Durek, M. Mardahl, A. Szilagyi, S. Floess, J. Huehn, U. Syrbe, J. Walter, J.K. Polansky and A. Hamann.
Gut memories don’t fade: Epigenetic regulation of lasting gut homing receptor expression in CD4+ memory T cells.
Mucosal Immunol, 2017. doi: 10.1038/mi.2017.7.

F. Schmidt, N. Gasparoni, G. Gasparoni, K. Gianmoena, C. Cadenas, J.K. Polansky, P. Ebert, K. Nordström, M. Barann, A. Sinha, S. Fröhler, J. Xiong, A. Dehghani Amirabad, F. Behjati Ardakani, B. Hutter, G. Zipprich, B. Felder, J. Eils, B. Brors, W. Chen, J.G. Hengstler, A. Hamann, T. Lengauer, P. Rosenstiel, J. Walter and M.H. Schulz.
Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction.
Nucleic Acids Res, 2017, 9;45(1):54-66. doi: 10.1093/nar/gkw1061.

S. Mamlouk, L.H. Childs, D. Aust, D. Heim, F. Melching, C. Oliveira, T. Wolf, P. Durek, D. Schumacher, H. Bläker, M. von Winterfeld, B. Gastl, K. Möhr, A. Menne, S. Zeugner, T. Redmer, D. Lenze, S. Tierling, M. Möbs, W. Weichert, G. Folprecht, E. Blanc, D. Beule, R. Schäfer, M. Morkel, F. Klauschen, U. Leser and C. Sers.
DNA copy number changes define spatial patterns of heterogeneity in colorectal cancer.
Nat Commun, 2017, 8:14093. doi: 10.1038/ncomms14093.

H.G. Stunnenberg; International Human Epigenome Consortium., M. Hirst.
The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery.
Cell, 2016, 17;167(5):1145-1149. doi: 10.1016/j.cell.2016.11.007.

P. Durek, K. Nordström, G. Gasparoni, A. Salhab, C. Kressler, M. de Almeida, K. Bassler, T. Ulas, F. Schmidt, J. Xiong, P. Glažar, F. Klironomos, A. Sinha, S. Kinkley, X. Yang, L. Arrigoni, A.D. Amirabad et al.; DEEP Consortium.
Epigenomic Profiling of Human CD4+ T Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Development.
Immunity, 2016, 15;45(5):1148-1161. doi: 10.1016/j.immuni.2016.10.022.

M. A. Eckersley-Maslin, V. Svensson, C. Krueger, T.M. Stubbs, P. Giehr, F. Krueger, R.J. Miragaia, C. Kyriakopoulos, R.V. Berrens, I. Milagre, J. Walter, S.A. Teichmann and W. Reik.
MERVL/Zscan4 Network Activation Results in Transient Genome-wide DNA Demethylation of mESCs.
Cell Reports, 2016, 17:179 - 192.

M. Pink, B.A. Ratsch, M. Mardahl, P. Durek, J.K. Polansky, M. Karl, R. Baumgrass, S. Wallner, C. Cadenas, K. Gianmoena, S. Floess, W. Chen, K. Nordstroem, S. Tierling, S. Olek, J. Walter and A. Hamann.
Imprinting of Skin/Inflammation Homing in CD4+ T Cells Is Controlled by DNA Methylation within the Fucosyltransferase 7 Gene.
J Immunol, 2016, pii: 1502434.

S. Kinkley, J. Helmuth, J.K. Polansky, I. Dunkel, G. Gasparoni, S. Fröhler S, W. Chen, J. Walter, A. Hamann and H.R. Chung.
reChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4(+) memory T cells.
Nat Commun, 2016, 7:12514. doi: 10.1038/ncomms12514.

S. Wallner, C. Schröder, E. Leitão, T. Berulava, C. Haak, D. Beißer, S. Rahmann, A.S. Richter, T. Manke, U. Bönisch et al.
Epigenetic dynamics of monocyte-to-macrophage differentiation.
Epigenetics Chromatin, 2016 29;9:33. doi: 10.1186/s13072-016-0079-z.

C. Bock, F. Halbritter, F.J. Carmona, S. Tierling, P. Datlinger, Y. Assenov, M. Berdasco, A.K. Bergmann, K. Booher, F. Busato et al.
Quantitative comparison of DNA methylation assays for biomarker development and clinical applications.
Nat Biotechnol, 2016, doi:10.1038/nbt.3605.

N.Y. Souren, L.A. Gerdes, T. Kümpfel, P. Lutsik, T. Klopstock, R. Hohlfeld and J. Walter.
Mitochondrial DNA Variation and Heteroplasmy in Monozygotic Twins Clinically Discordant for Multiple Sclerosis.
Hum Mutat, 2016 Apr 27. doi:10.1002/humu.23003.

P. Giehr, C. Kyriakopoulos, G. Ficz, V. Wolf and J. Walter.
The Influence of Hydroxylation on Maintaining CpG Methylation Patterns: A Hidden Markov Model Approach.
PLoS Comput Biol, 2016, 12(5):e1004905. doi:10.1371/journal.pcbi.1004905.

S. Qiao, K. Nordström, L. Muijs, G. Gasparoni, S. Tierling, E. Krause, J. Walter and U. Boehm.
Molecular plasticity of male and female murine gonadotropes revealed by mRNA sequencing.
Endocrinology, 2016, 157(3):1082-93. doi:10.1210/en.2015-1836.

M. Döring, G.Gasparoni, J Gries, K. Nordström, P. Lutsik, J Walter and N. Pfeifer.
Identification and analysis of methylation call differences between bisulfite microarray and bisulfite sequencing data with statistical learning techniques.
BMC Bioinformatics, 2015, 16(Suppl 3):A7 doi:10.1186/1471-2105-16-S3-A7.

S. O. Dyke, W. A. Cheung, Y. Joly, O. Ammerpohl, P. Lutsik, M. A. Rothstein, M. Caron, S. Busche, G. Bourque, L. Rönnblom, P. Flicek, S. Beck, M. Hirst, H. Stunnenberg, R. Siebert, J. Walter and T. Pastinen.
Epigenome data release: a participant-centered approach to privacy protection.
Genome Biology, 2015, 16:142 doi:10.1186/s13059-015-0723-0.

D. Drogan, H. Boeing, J. Janke, B. Schmitt, Y. Zhou, J. Walter, T. Pischon and S. Tierling.
Regional distribution of body fat in relation to DNA methylation within the LPL, ADIPOQ and PPARγ promoters in subcutaneous adipose tissue.
Nutr Diabetes, 2015. doi: 10.1038/nutd.2015.19.

K. Lepikhov, J. Arand, S. Fuchs, J. Lan, M. Wossidlo and J. Walter.
DNA Methylation Reprogramming in Preimplantation Development.
Epigenetic Mechanisms in Cellular Reprogramming (pp. 69-99). Epigenetics and Human Health Meissner, Alexander, Walter, Jörn (Eds.) 2015, XVIII, 230 p. Springer Berlin Heidelberg 2015.

J. Arand, M. Wossidlo, K. Lepikhov, J. Peat, W. Reik and J. Walter.
Selective impairment of methylation maintenance is the major cause of DNA methylation reprogramming in the early embryo.
Epigenetics & Chromatin, 2015, 8:1 doi: 10.1186/1756-8935-8-1.

A. Meissner and J. Walter (Eds.)
Epigenetic Mechanisms in Cellular Reprogramming.
Epigenetics and Human Health. 2015 Volume V , 230 pages. ISBN 978-3-642-31974-7 Springer Berlin Heidelberg 2015.

J. Chen, P. Lutsik, R. Akulenko, J. Walter and V. Helms.
AKSmooth: Enhancing low-coverage bisulfite sequencing data via kernel-based smoothing.
Journal of Bioinformatics and Computational Biology, 2014, doi: 10.1142/S0219720014420050.

M. Luetke-Eversloh, Q. Hammer, P. Durek, K. Nordström, G. Gasparoni, M. Pink, A. Hamann, J. Walter, H. Chang, J. Dong and C. Romagnani.
Human Cytomegalovirus Drives Epigenetic Imprinting of the IFNG Locus in NKG2Chi Natural Killer Cells.
PloS Pathogens, 2014, doi: 10.1371/journal.ppat.1004441.

Y. Assenov, F. Müller, P. Lutsik, J. Walter, T. Lengauer and C. Bock.
Comprehensive analysis of DNA methylation data with RnBeads.
Nat Methods, 2014, doi:10.1038/nmeth.3115.

M. Unterberg, L. Leffers, F. Hübner, H.-U. Humpf, K. Lepikhov, J. Walter, F. Ebert and T. Schwerdtle
Toxicity of arsenite and thio-DMAV after long-term (21 days) incubation of human urothelial cells: cytotoxicity, genotoxicity and epigenetics.
Toxicol Res, 2014, doi: 10.1039/C4TX00036F.

D. Becker, P. Lutsik, P. Ebert, C. Bock, T. Lengauer and J. Walter.
BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives.
Nucleic Acids Res, 2014; doi: 10.1093/nar/gku457.

A.Bulut-Karslioglu, I. A. De La Rosa-Velázquez, F. Ramirez, M. Barenboim, M. Onishi-Seebacher, J. Arand, C.Galán, G.E. Winter, B.Engist, B. Gerle, R. J. O’Sullivan, J. H. A. Martens, J. Walter, T. Manke, M. Lachner and T. Jenuwein.
Suv39h-dependent H3K9me3 marks intact retrotransposons and silences LINE elements in mouse embryonic stem cells.
Mol Cell, 2014, 55(2):277-90. doi: 10.1016/j.molcel.2014.05.029.

A.J. Deutsch, B. Rinner, K. Wenzl, M. Pichler, K. Troppan, E. Steinbauer, D. Schwarzenbach, S. Reitter, J. Feichtinger, S. Tierling, A. Prokesch, M. Scheideler, A. Krogsdam, G.G. Thallinger, H. Schaider, C. Beham-Schmid and P. Neumeister.
NR4A1-mediated apoptosis suppresses lymphomagenesis and is associated with a favorable cancer specific survival in patients with aggressive B-cell lymphomas.
Blood, 2014, 123(15):2367-77. doi: 10.1182/blood-2013-08-518878. 

U.C. Lange, S. Siebert, M. Wossidlo, T. Weiss, C. Ziegler-Birling, J. Walter, M.E. Torres-Padilla, S. Daujat and R. Schneider.
Dissecting the role of H3K64me3 in mouse pericentromeric heterochromatin.
Nat Commun, 2013, 4:2233. doi: 10.1038/ncomms3233.

G. Ficz, T.A. Hore, F. Santos, H.J. Lee, W. Dean, J. Arand, F. Krueger, D. Oxley, Y.L. Paul, J. Walter, S.J. Cook, S. Andrews, M.R. Branco and W. Reik.
FGF Signaling Inhibition in ESCs Drives Rapid Genome-wide Demethylation to the Epigenetic Ground State of Pluripotency.
Cell Stem Cell, 2013. doi: 10.1016/j.stem.2013.06.004.

E. Habibi, A.B. Brinkman, J. Arand, L.I. Kroeze, H.H.D. Kerstens, F. Matarese, K. Lepikhov, M. Gut, I. Brun-Heath, N.C. Hubner, R. Benedetti, L. Altucci, J.H. Jansen, J. Walter, I.G. Gut, H. Marks and H.G. Stunnenberg.
Whole-Genome Bisulfite Sequencing of Two Distinct Interconvertible DNA Methylomes of Mouse Embryonic Stem Cells.
Cell Stem Cell, 2013. doi: 10.1016/j.stem.2013.06.002.

J. Gries, D. Schumacher, J. Arand, P. Lutsik, M.R. Markelova, I. Fichtner, J. Walter, C. Sers and S. Tierling.
Bi-PROF: Bisulfite profiling of target regions using 454 GS FLX Titanium technology.
Epigenetics, 2013, 8(7):765-71. doi: 10.4161/epi.25242.

D. Hatakeyama, S. Tierling, T. Kuzuhara and U. Müller.
Epigenetic regulation of gene expression in the nervous system.
Methods in Neuroethical Research, Springer Japan, 2013, due July 31.

N.Y.P. Souren, P. Lutsik, G. Gasparoni, S. Tierling, J. Gries, M. Riemenschneider, J.P. Fryns, C. Derom, M.P. Zeegers and J. Walter.
Adult monozygotic twins discordant for intra-uterine growth have indistinguishable genome-wide DNA methylation profiles.
Genome Biol, 2013, 14:R44. doi:10.1186/gb-2013-14-5-r44. Featured in http://f1000.com/prime/718021970.

C.F. Classen, V. Riehmer, C. Landwehr, A. Kosfeld, S. Heilmann, C. Scholz, S. Kabisch, H. Engels, S. Tierling, M. Zivicnjak, F. Schacherer, D. Haffner and R.G. Weber.
Dissecting the genotype in syndromic intellectual disability using whole exome sequencing in addition to genome-wide copy number analysis.
Hum Genet, 2013, 132(7):825-41. doi: 10.1007/s00439-013-1296-1.

C.G. Spruijt, F. Gnerlich, A.H. Smits, T. Pfaffeneder, P.W.T.C. Jansen, C. Bauer, M. Münzel, M. Wagner, M. Müller, F. Khan, H.C. Eberl, A. Mensinga, A.B. Brinkman, K. Lepikhov, U. Müller, J. Walter, R. Boelens, H. van Ingen, H. Leonhardt, T. Carell and M. Vermeulen.
Dynamic Readers for 5-(Hydroxy)Methylcytosine and Its Oxidized Derivatives.
Cell, 2013, doi: 10.1016/j.cell.2013.02.004.

A. Toker, D. Engelbert, G. Garg, J.K. Polansky, S. Floess, T. Miyao, U. Baron, S. Düber, R. Geffers, P. Giehr, S. Schallenberg, K. Kretschmer, S. Olek, J. Walter, S. Weiss, S. Hori, A. Hamann and J. Huehn.
Active Demethylation of the Foxp3 Locus Leads to the Generation of Stable Regulatory T Cells within the Thymus.
J Immunol, 2013, 190(7):3180-8. doi: 10.4049/jimmunol.1203473.

C. Grimm, L. Chavez, M. Vilardell, A.L. Farrall, S. Tierling, J.W. Boehm, P. Grote, M. Lienhard, J. Dietrich, B. Timmermann, J. Walter, M.R. Schweiger, H. Lehrach, R. Herwig, B.G. Herrmann and M. Morkel.
DNA–Methylome Analysis of Mouse Intestinal Adenoma Identifies a Tumour-Specific Signature That Is Partly Conserved in Human Colon Cancer.
PLoS Genet, 2013, 9(2):e1003250. doi: 10.1371/journal.pgen.1003250.

S. Seisenberger, S. Andrews, F. Krueger, J. Arand, J. Walter, F. Santos, C. Popp, B. Thienpont, W. Dean and W. Reik.
The Dynamics of Genome-wide DNA Methylation Reprogramming in Mouse Primordial Germ Cells.
Mol Cell, 2012 Dec 6. doi: 10.1016/j.molcel.2012.11.001.

A. Schmidt, H.J. Wöhrmann, M.T. Raissig, J. Arand, J. Gheyselinck, V. Gagliardini, C. Heichinger, J. Walter and U. Grossniklaus.
The Polycomb group protein MEDEA and the DNA methyltransferase MET1 interact in Arabidopsis to repress autonomous endosperm development.
Plant J, 2012 Nov 12. doi: 10.1111/tpj.12070.

H.J. Wöhrmann, V. Gagliardini, M.T. Raissig, W. Wehrle, J. Arand, A. Schmidt, S. Tierling, D.R. Page, H. Schöb, J. Walter and U. Grossniklaus.
Identification of a DNA methylation-independent imprinting control region at the Arabidopsis MEDEA locus.
Genes Dev, 2012, 26(16):1837-50. doi: 10.1101/gad.195123.112..

J. Arand, D. Spieler, T. Karius, M.R. Branco, D. Meilinger, A. Meissner, T. Jenuwein, G. Xu, H. Leonhardt, V. Wolf and J. Walter.
In Vivo Control of CpG and Non-CpG DNA Methylation by DNA Methyltransferases.
PLoS Genetics, 2012, Volume 8, Issue 6: e1002750.
(see also comment in Nature Reviews Genetics)
DNA methylation: In vivo enzyme action.
Nature Reviews Genetics, 2012, 13: p520. doi: 10.1038/nrg3284.

Adams D, Altucci L, Antonarakis SE, Ballesteros J, Beck S, Bird A, Bock C, Boehm B, Campo E, Caricasole A, Dahl F, Dermitzakis ET, Enver T, Esteller M,Estivill X, Ferguson-Smith A, Fitzgibbon J, Flicek P, Giehl C, Graf T, Grosveld F, Guigo R, Gut I, Helin K, Jarvius J, K?ºppers R, Lehrach H, Lengauer T, Lernmark Ö, Leslie D, Loeffler M, Macintyre E, Mai A, Martens JH, Minucci S, Ouwehand WH, Pelicci PG, Pendeville H, Porse B, Rakyan V, Reik W, Schrappe M, Schübeler D, Seifert M, Siebert R, Simmons D, Soranzo N, Spicuglia S, Stratton M, Stunnenberg HG, Tanay A, Torrents D, Valencia A, Vellenga E, Vingron M, Walter J and Willcocks S.
BLUEPRINT to decode the epigenetic signature written in blood.
Nat Biotechnol, 2012, 30(3):224-6.

J. Arand, K. Lepikhov, M. Wossidlo and J. Walter.
Active DNA demethylation: the enigma starts in the zygote.
Epigenomics - From Chromatin Biology to Therapeutics, 2012, Edited by Krishnarao Appasani, Cambride University Press, Cambridge UK 201, pp 91-103.

B. van den Borst, N. Souren, R. Loos, A. Paulussen, C. Derom, A. Schols and M. Zeegers.
Genetics of maximally attained lung function: A role for leptin?
Respir Med, 2011, 106(2):235-42. doi: 10.1016/j.rmed.2011.08.001.

L. de Boni, S. Tierling, S. Roeber, J. Walter, A. Giese and H.A. Kretschmar.
Next-Generation Sequencing Reveals Regional Differences of the a-Synuclein Methylation State Independent of Lewy Body Disease.
Neuromolecular Med, 2011, 13(4):310-20. doi: 10.1007/s12017-011-8163-9.

B. Diesel, N. Ripoche, R.T. Risch, S. Tierling, J. Walter and A.K. Kiemer.
Inflammation-induced up-regulation of TLR2 expression in human endothelial cells is independent of differential methylation in the TLR2 promoter CpG island.
Innate Immunity, 2011, 18(1):112-23. doi: 10.1177/1753425910394888.

P. Lutsik, L. Feuerbach, J. Arand, T. Lengauer, J. Walter and C. Bock.
BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing.
Nucleic Acids Res, 2011, 39(Web Server issue):W551-6. doi: 10.1093/nar/gkr312.

N. Souren, M. Zeegers.
Is Hardy-Weinberg on its retreat?
J Clin Epidemiol, 2011, 64(8):819-20. doi: 10.1016/j.jclinepi.2011.03.001.

T. Karius, M. Schnekenburger, J. Gelfi, J. Walter, M. Dicato and M. Diederich.
Reversible epigenetic fingerprint-mediated glutathione-S-transferase P1 gene silencing in human leukemia cell lines.
Biochem Pharmacol, 2011, 81(11):1329-42. doi: 10.1016/j.bcp.2011.03.014.

M. Wossidlo, T. Nakamura, K. Lepikhov, C.J. Marques, V. Zakhartchenko, M. Boiani, J. Arand, T. Nakano, W. Reik and J. Walter.
5-hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming.
Nat Commun, 2011, 2:241. doi: 10.1038/ncomms1240.

S. Tierling, C. Sers, A. Lehmann and J. Walter.
A fast, cost-efficient and sensitive approach for KRAS mutation detection using multiplexed primer extension with IP/RP-HPLC separation.
Int J Cancer, 2011, 130(3):567-74. doi: 10.1002/ijc.26040.

N.Y. Souren, S. Tierling, J.P. Fryns, C. Derom, J. Walter and M.P. Zeegers.
DNA Methylation variability at growth-related imprints does not contribute to overweight in monozygotic twins discordant for BMI.
Obesity, 2011, 19(7):1519-22. doi: 10.1038/oby.2010.353.

Walter J.
An epigenetic tet a tet with pluripotency.
Cell Stem Cell, 2011, 8(2):121-2. doi: 10.1016/j.stem.2011.01.009.