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Jacob, Divya R and Guiblet, Wilfried M and Mamayusupova, Hulkar and Shtumpf, Mariya and Ciuta, Isabella and Ruje, Luminita and Gretton, Svetlana and Bikova, Milena and Correa, Clark and Dellow, Emily and Agrawal, Shivam P and Shafiei, Navid and Drobysevskaja, Anastasija and Armstrong, Chris M and Lam, Jonathan DG and Vainshtein, Yevhen and Clarkson, Christopher T and Thorn, Graeme J and Sohn, Kai and Pradeepa, Madapura M and Chandrasekharan, Sankaran and Brooke, Greg N and Klenova, Elena and Zhurkin, Victor B and Teif, Vladimir B (2024) Nucleosome reorganisation in breast cancer tissues. Clinical Epigenetics, 16 (1). 50-. DOI https://doi.org/10.1186/s13148-024-01656-4

Shtumpf, Mariya and Jeong, Seihee and Bikova, Milena and Mamayusupova, Hulkar and Ruje, Luminita and Teif, Vladimir B (2024) Aging clock based on nucleosome reorganisation derived from cell-free DNA. Aging Cell, 23 (5). e14100-. DOI https://doi.org/10.1111/acel.14100

Teif, Vladimir and Peng, Yunhui and Song, Wei and Ovcharenko, Ivan and Landsman, David and Panchenko, Anna (2024) Detection of new pioneer transcription factors as cell-type specific nucleosome binders. eLife, 12. RP88936-. DOI https://doi.org/10.7554/eLife.88936

Belokopytova, Polina and Viesná, Emil and Chiliński, Mateusz and Qi, Yifeng and Salari, Hossein and Di Stefano, Marco and Esposito, Andrea and Conte, Mattia and Chiariello, Andrea M and Teif, Vladimir B and Plewczynski, Dariusz and Zhang, Bin and Jost, Daniel and Fishman, Veniamin (2022) 3DGenBench: a web-server to benchmark computational models for 3D Genomics. Nucleic Acids Research, 50 (W1). W4-W12. DOI https://doi.org/10.1093/nar/gkac396

Shtumpf, Mariya and Piroeva, Kristan V and Agrawal, Shivam P and Jacob, Divya R and Teif, Vladimir B (2022) NucPosDB: a database of nucleosome positioning in vivo and nucleosomics of cell-free DNA. Chromosoma, 131 (1-2). pp. 19-28. DOI https://doi.org/10.1007/s00412-021-00766-9

Thorn, Graeme J and Clarkson, Christopher T and Rademacher, Anne and Mamayusupova, Hulkar and Schotta, Gunnar and Rippe, Karsten and Teif, Vladimir B (2022) DNA sequence-dependent formation of heterochromatin nanodomains. Nature Communications, 13 (1). 1861-. DOI https://doi.org/10.1038/s41467-022-29360-y

Mohr, Andrea and Chu, Tianyuan and Clarkson, Christopher and Brooke, Greg and Teif, Vladimir and Zwacka, Ralf (2021) Fas-threshold Signalling in MSCs Promotes Pancreatic Cancer Progression and Metastasis. Cancer Letters, 519. pp. 63-77. DOI https://doi.org/10.1016/j.canlet.2021.06.017

Cucinotta, Christine E and Martin, Benjamin JE and Noé González, Melvin and Raman, Pravrutha and Teif, Vladimir B and Vlaming, Hanneke (2021) Strength is in engagement The rise of an online scientific community during the COVID‐19 pandemic. EMBO Reports, 22 (5). e52612-. DOI https://doi.org/10.15252/embr.202152612

Teif, Vladimir and Gould, Travis and Clarkson, Christopher and Boyd, Logan and Antwi, Enoch and Ishaque, Naveed and Olins, Ada and Olins, Donald (2020) Linker histone epitopes are hidden by in situ higher-order chromatin structure. Epigenetics and Chromatin, 13 (1). 26-. DOI https://doi.org/10.1186/s13072-020-00345-9

Teif, Vladimir (2020) Soft power of non-consensus protein-DNA binding. Biophysical Journal, 118 (8). pp. 1797-1798. DOI https://doi.org/10.1016/j.bpj.2020.02.026

Antwi, Enoch B and Olins, Ada and Teif, Vladimir B and Bieg, Matthias and Bauer, Tobias and Gu, Zuguang and Brors, Benedikt and Eils, Roland and Olins, Donald and Ishaque, Naveed (2020) Whole-genome fingerprint of the DNA methylome during chemically induced differentiation of the human AML cell line HL-60/S4. Biology Open, 9 (2). bio044222-. DOI https://doi.org/10.1242/bio.044222

Clarkson, Christopher T and Deeks, Emma A and Samarista, Ralph and Mamayusupova, Hulkar and Zhurkin, Victor B and Teif, Vladimir B (2019) CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length. Nucleic Acids Research, 47 (21). pp. 11181-11196. DOI https://doi.org/10.1093/nar/gkz908

Wiehle, Laura and Thorn, Graeme and Raddatz, Günter and Clarkson, Christopher and Rippe, Karsten and Lyko, Frank and Breiling, Achim and Teif, Vladimir (2019) DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries. Genome Research, 29 (5). pp. 750-761. DOI https://doi.org/10.1101/gr.239707.118

Mallm, Jan Philipp and Iskar, Murat and Ishaque, Naveed and Klett, Lara C and Kugler, Sabrina J and Muino, Jose M and Teif, Vladimir B and Poos, Alexandra M and Großmann, Sebastian and Erdel, Fabian and Tavernari, Daniele and Koser, Sandra D and Schumacher, Sabrina and Brors, Benedikt and König, Rainer and Remondini, Daniel and Vingron, Martin and Stilgenbauer, Stephan and Lichter, Peter and Zapatka, Marc and Mertens, Daniel and Rippe, Karsten (2019) Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks. Molecular Systems Biology, 15 (5). e8339-. DOI https://doi.org/10.15252/msb.20188339

Pavlaki, I and Docquier, F and Chernukhin, I and Kita, G and Gretton, S and Clarkson, CT and Teif, VB and Klenova, E (2018) Poly(ADP-ribosyl)ation associated changes in CTCF-chromatin binding and gene expression in breast cells. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 1861 (8). pp. 781-730. DOI https://doi.org/10.1016/j.bbagrm.2018.06.010

Vainshtein, Yevhen and Rippe, Karsten and Teif, Vladimir B (2017) NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data. BMC Genomics, 18 (1). 158-. DOI https://doi.org/10.1186/s12864-017-3580-2

Teif, Vladimir B and Mallm, Jan-Philipp and Sharma, Tanvi and Mark Welch, David B and Rippe, Karsten and Eils, Roland and Langowski, Jörg and Olins, Ada L and Olins, Donald E (2017) Nucleosome repositioning during differentiation of a human myeloid leukemia cell line. Nucleus, 8 (2). pp. 188-204. DOI https://doi.org/10.1080/19491034.2017.1295201

Teif, Vladimir B (2016) Nucleosome positioning: resources and tools online. Briefings in Bioinformatics, 17 (5). pp. 745-757. DOI https://doi.org/10.1093/bib/bbv086

Salih, Bilal F and Teif, Vladimir B and Tripathi, Vijay and Trifonov, Edward N (2015) Strong nucleosomes of mouse genome including recovered centromeric sequences. Journal of Biomolecular Structure and Dynamics, 33 (6). pp. 1164-1175. DOI https://doi.org/10.1080/07391102.2014.938700

Teif, Vladimir B and Kepper, Nick and Yserentant, Klaus and Wedemann, Gero and Rippe, Karsten (2015) Affinity, stoichiometry and cooperativity of heterochromatin protein 1 (HP1) binding to nucleosomal arrays. Journal of Physics: Condensed Matter, 27 (6). 064110-064110. DOI https://doi.org/10.1088/0953-8984/27/6/064110

Cherstvy, Andrey G and Teif, Vladimir B (2014) Electrostatic effect of H1-histone protein binding on nucleosome repeat length. Physical Biology, 11 (4). 044001-044001. DOI https://doi.org/10.1088/1478-3975/11/4/044001

Teif, Vladimir B and Beshnova, Daria A and Vainshtein, Yevhen and Marth, Caroline and Mallm, Jan-Philipp and Höfer, Thomas and Rippe, Karsten (2014) Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development. Genome Research, 24 (8). pp. 1285-1295. DOI https://doi.org/10.1101/gr.164418.113

Beshnova, Daria A and Cherstvy, Andrey G and Vainshtein, Yevhen and Teif, Vladimir B (2014) Regulation of the nucleosome repeat length in vivo by the DNA sequence, protein concentrations and long-range interactions. PLoS Computational Biology, 10 (7). e1003698-e1003698. DOI https://doi.org/10.1371/journal.pcbi.1003698

Teif, VB and Erdel, F and Beshnova, DA and Vainshtein, Y and Mallm, JP and Rippe, K (2013) Taking into account nucleosomes for predicting gene expression. Methods, 62 (1). pp. 26-38. DOI https://doi.org/10.1016/j.ymeth.2013.03.011

Teif, VB and Shkrabkou, AV and Egorova, VP and Krot, VI (2012) Nucleosomes in gene regulation: Theoretical approaches. Molecular Biology, 46 (1). pp. 1-10. DOI https://doi.org/10.1134/S002689331106015X

Teif, VB and Rippe, K (2011) Nucleosome mediated crosstalk between transcription factors at eukaryotic enhancers. Physical Biology, 8 (4). 044001-044001. DOI https://doi.org/10.1088/1478-3975/8/4/044001

Teif, VB and Rippe, K (2010) Statistical-mechanical lattice models for protein-DNA binding in chromatin. Journal of Physics: Condensed Matter, 22 (41). p. 414105. DOI https://doi.org/10.1088/0953-8984/22/41/414105

Book Section

Teif, Vladimir B and Clarkson, Christopher T (2019) Nucleosome positioning. In: Encyclopedia of Bioinformatics and Computational Biology (vol 2). Elsevier, pp. 308-317. ISBN 978-0-12-811432-2. Official URL: https://doi.org/10.1016/B978-0-12-809633-8.20242-2

Monograph

Clarkson, Christopher T and Deeks, Emma A and Samarista, Ralph and Mamayusupova, Hulkar and Zhurkin, Victor B and Teif, Vladimir B (2019) CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length. Working Paper. bioRxiv. (Unpublished)

Teif, VB (2013) Science 3.0: Corrections to the Science 2.0 paradigm. Working Paper. Arxiv.