Works by Lutsik, Pavlo

Results: 33

AKSmooth: Enhancing low-coverage bisulfite sequencing data via kernel-based smoothing.

Published in:

Journal of Bioinformatics & Computational Biology, 2014, v. 12, n. 6, p. -1, doi. 10.1142/S0219720014420050

By:

Chen, Junfang;
Lutsik, Pavlo;
Akulenko, Ruslan;
Walter, Jörn;
Helms, Volkhard

Publication type:

Article

Heterogeneity in the gene regulatory landscape of leiomyosarcoma.

Published in:

NAR Cancer, 2023, v. 5, n. 3, p. 1, doi. 10.1093/narcan/zcad037

By:

Belova, Tatiana;
Biondi, Nicola;
Ping-Han Hsieh;
Lutsik, Pavlo;
Chudasama, Priya;
Kuijjer, Marieke L.

Publication type:

Article

Epigenetic Modulation of Radiation-Induced Diacylglycerol Kinase Alpha Expression Prevents Pro-Fibrotic Fibroblast Response.

Published in:

Cancers, 2021, v. 13, n. 10, p. 2455, doi. 10.3390/cancers13102455

By:

Liu, Chun-Shan;
Toth, Reka;
Bakr, Ali;
Goyal, Ashish;
Islam, Md Saiful;
Breuer, Kersten;
Mayakonda, Anand;
Lin, Yu-Yu;
Stepper, Peter;
Jurkowski, Tomasz P.;
Veldwijk, Marlon R.;
Sperk, Elena;
Herskind, Carsten;
Lutsik, Pavlo;
Weichenhan, Dieter;
Plass, Christoph;
Schmezer, Peter;
Popanda, Odilia;
Ávila-Flores, Antonia;
Torres-Ayuso, Pedro

Publication type:

Article

Epigenome data release: a participantcentered approach to privacy protection

Published in:

Genome Biology, 2015, v. 16, n. 1, p. 142, doi. 10.1186/s13059-015-0723-0

By:

Dyke, Stephanie O. M.;
Cheung, Warren A.;
Joly, Yann;
Ammerpohl, Ole;
Lutsik, Pavlo;
Rothstein, Mark A.;
Caron, Maxime;
Busche, Stephan;
Bourque, Guillaume;
Rönnblom, Lars;
Flicek, Paul;
Beck, Stephan;
Hirst, Martin;
Stunnenberg, Henk;
Siebert, Reiner;
Walter, Jörn;
Pastinen, Tomi

Publication type:

Article

Adult monozygotic twins discordant for intra-uterine growth have indistinguishable genome-wide DNA methylation profiles.

Published in:

Genome Biology, 2013, v. 14, n. 5, p. 1, doi. 10.1186/gb-2013-14-5-r44

By:

Souren, Nicole Y. P.;
Lutsik, Pavlo;
Gasparoni, Gilles;
Tierling, Sascha;
Gries, Jasmin;
Riemenschneider, Matthias;
Fryns, Jean-Pierre;
Derom, Catherine;
Zeegers, Maurice P.;
Walter, Jörn

Publication type:

Article

Reference-free deconvolution, visualization and interpretation of complex DNA methylation data using DecompPipeline, MeDeCom and FactorViz.

Published in:

Nature Protocols, 2020, v. 15, n. 10, p. 3240, doi. 10.1038/s41596-020-0369-6

By:

Scherer, Michael;
Nazarov, Petr V.;
Toth, Reka;
Sahay, Shashwat;
Kaoma, Tony;
Maurer, Valentin;
Vedeneev, Nikita;
Plass, Christoph;
Lengauer, Thomas;
Walter, Jörn;
Lutsik, Pavlo

Publication type:

Article

Methylome-based cell-of-origin modeling (Methyl-COOM) identifies aberrant expression of immune regulatory molecules in CLL.

Published in:

Genome Medicine, 2020, v. 12, n. 1, p. 1, doi. 10.1186/s13073-020-00724-7

By:

Wierzbinska, Justyna A.;
Toth, Reka;
Ishaque, Naveed;
Rippe, Karsten;
Mallm, Jan-Philipp;
Klett, Lara C.;
Mertens, Daniel;
Zenz, Thorsten;
Hielscher, Thomas;
Seifert, Marc;
Küppers, Ralf;
Assenov, Yassen;
Lutsik, Pavlo;
Stilgenbauer, Stephan;
Roessner, Philipp M.;
Seiffert, Martina;
Byrd, John;
Oakes, Christopher C.;
Plass, Christoph;
Lipka, Daniel B.

Publication type:

Article

EpiCHAOS: a metric to quantify epigenomic heterogeneity in single-cell data.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03446-w

By:

Kelly, Katherine;
Scherer, Michael;
Braun, Martina Maria;
Lutsik, Pavlo;
Plass, Christoph

Publication type:

Article

MeDeCom: discovery and quantification of latent components of heterogeneous methylomes.

Published in:

Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1182-6

By:

Lutsik, Pavlo;
Slawski, Martin;
Gasparoni, Gilles;
Vedeneev, Nikita;
Hein, Matthias;
Walter, Jörn

Publication type:

Article

DNA methylation signatures of monozygotic twins clinically discordant for multiple sclerosis.

Published in:

Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-09984-3

By:

Souren, Nicole Y.;
Gerdes, Lisa A.;
Lutsik, Pavlo;
Gasparoni, Gilles;
Beltrán, Eduardo;
Salhab, Abdulrahman;
Kümpfel, Tania;
Weichenhan, Dieter;
Plass, Christoph;
Hohlfeld, Reinhard;
Walter, Jörn

Publication type:

Article

Enhancer hijacking activates oncogenic transcription factor NR4A3 in acinic cell carcinomas of the salivary glands.

Published in:

Nature Communications, 2019, v. 10, n. 1, p. 1, doi. 10.1038/s41467-018-08069-x

By:

Haller, Florian;
Bieg, Matthias;
Will, Rainer;
Körner, Cindy;
Weichenhan, Dieter;
Bott, Alexander;
Ishaque, Naveed;
Lutsik, Pavlo;
Moskalev, Evgeny A.;
Mueller, Sarina K.;
Bähr, Marion;
Woerner, Angelika;
Kaiser, Birgit;
Scherl, Claudia;
Haderlein, Marlen;
Kleinheinz, Kortine;
Fietkau, Rainer;
Iro, Heinrich;
Eils, Roland;
Hartmann, Arndt

Publication type:

Article

DNA methylation analysis on purified neurons and glia dissects age and Alzheimer's disease-specific changes in the human cortex.

Published in:

Epigenetics & Chromatin, 2018, v. 11, n. 1, p. N.PAG, doi. 10.1186/s13072-018-0211-3

By:

Gasparoni, Gilles;
Bultmann, Sebastian;
Lutsik, Pavlo;
Kraus, Theo F. J.;
Sordon, Sabrina;
Vlcek, Julia;
Dietinger, Vanessa;
Steinmaurer, Martina;
Haider, Melanie;
Mulholland, Christopher B.;
Arzberger, Thomas;
Roeber, Sigrun;
Riemenschneider, Matthias;
Kretzschmar, Hans A.;
Giese, Armin;
Leonhardt, Heinrich;
Walter, Jörn

Publication type:

Article

Mitochondrial DNA Variation and Heteroplasmy in Monozygotic Twins Clinically Discordant for Multiple Sclerosis.

Published in:

Human Mutation, 2016, v. 37, n. 8, p. 765, doi. 10.1002/humu.23003

By:

Souren, Nicole Y.P.;
Gerdes, Lisa A.;
Kümpfel, Tania;
Lutsik, Pavlo;
Klopstock, Thomas;
Hohlfeld, Reinhard;
Walter, Jörn

Publication type:

Article

Epigenetic analysis of patients with T-ALL identifies poor outcomes and a hypomethylating agent-responsive subgroup.

Published in:

Science Translational Medicine, 2021, v. 13, n. 595, p. 1, doi. 10.1126/scitranslmed.abc4834

By:

Touzart, Aurore;
Mayakonda, Anand;
Smith, Charlotte;
Hey, Joschka;
Toth, Reka;
Cieslak, Agata;
Andrieu, Guillaume P.;
Tran Quang, Christine;
Latiri, Mehdi;
Ghysdael, Jacques;
Spicuglia, Salvatore;
Dombret, Hervé;
Ifrah, Norbert;
Macintyre, Elizabeth;
Lutsik, Pavlo;
Boissel, Nicolas;
Plass, Christoph;
Asnafi, Vahid

Publication type:

Article

Comprehensive analysis of DNA methylation data with RnBeads.

Published in:

Nature Methods, 2014, v. 11, n. 11, p. 1138, doi. 10.1038/nmeth.3115

By:

Assenov, Yassen;
Müller, Fabian;
Lutsik, Pavlo;
Walter, Jörn;
Lengauer, Thomas;
Bock, Christoph

Publication type:

Article

Figeno: multi-region genomic figures with long-read support.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae354

By:

Sollier, Etienne;
Heilmann, Jessica;
Gerhauser, Clarissa;
Scherer, Michael;
Plass, Christoph;
Lutsik, Pavlo

Publication type:

Article

Methrix: an R/Bioconductor package for systematic aggregation and analysis of bisulfite sequencing data.

Published in:

Bioinformatics, 2020, v. 36, n. 22/23, p. 5524, doi. 10.1093/bioinformatics/btaa1048

By:

Mayakonda, Anand;
Schönung, Maximilian;
Hey, Joschka;
Batra, Rajbir Nath;
Feuerstein-Akgoz, Clarissa;
Köhler, Kristin;
Lipka, Daniel B;
Sotillo, Rocio;
Plass, Christoph;
Lutsik, Pavlo;
Toth, Reka

Publication type:

Article

ID3 promotes homologous recombination via non-transcriptional and transcriptional mechanisms and its loss confers sensitivity to PARP inhibition.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 20, p. 11666, doi. 10.1093/nar/gkab964

By:

Bakr, Ali;
Hey, Joschka;
Sigismondo, Gianluca;
Liu, Chun-Shan;
Sadik, Ahmed;
Goyal, Ashish;
Cross, Alice;
Iyer, Ramya Lakshmana;
Müller, Patrick;
Trauernicht, Max;
Breuer, Kersten;
Lutsik, Pavlo;
Opitz, Christiane A;
Krijgsveld, Jeroen;
Weichenhan, Dieter;
Plass, Christoph;
Popanda, Odilia;
Schmezer, Peter

Publication type:

Article

Activation-induced deaminase is critical for the establishment of DNA methylation patterns prior to the germinal center reaction.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5057, doi. 10.1093/nar/gkab322

By:

Català-Moll, Francesc;
Ferreté-Bonastre, Anna G;
Li, Tianlu;
Weichenhan, Dieter;
Lutsik, Pavlo;
Ciudad, Laura;
Álvarez-Prado, Ángel F;
Rodríguez-Ubreva, Javier;
Klemann, Christian;
Speckmann, Carsten;
Vilas-Zornoza, Amaya;
Abolhassani, Hassan;
Martínez-Gallo, Mónica;
Dieli-Crimi, Romina;
Rivière, Jacques G;
Martín-Nalda, Andrea;
Colobran, Roger;
Soler-Palacín, Pere;
Kracker, Sven;
Hammarström, Lennart

Publication type:

Article

BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives.

Published in:

Nucleic Acids Research, 2014, v. 42, n. W1, p. W501, doi. 10.1093/nar/gku457

By:

Becker, Daniel;
Lutsik, Pavlo;
Ebert, Peter;
Bock, Christoph;
Lengauer, Thomas;
Walter, Jörn

Publication type:

Article

BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W551, doi. 10.1093/nar/gkr312

By:

Lutsik, Pavlo;
Feuerbach, Lars;
Arand, Julia;
Lengauer, Thomas;
Walter, Jörn;
Bock, Christoph

Publication type:

Article

AmpliconDesign – an interactive web server for the design of high-throughput targeted DNA methylation assays.

Published in:

Epigenetics, 2021, v. 16, n. 9, p. 933, doi. 10.1080/15592294.2020.1834921

By:

Schönung, Maximilian;
Hess, Jana;
Bawidamann, Pascal;
Stäble, Sina;
Hey, Joschka;
Langstein, Jens;
Assenov, Yassen;
Weichenhan, Dieter;
Lutsik, Pavlo;
Lipka, Daniel B.

Publication type:

Article

Bi-PROF.

Published in:

Epigenetics, 2013, v. 8, n. 7, p. 765, doi. 10.4161/epi.25242

By:

Gries, Jasmin;
Schumacher, Dirk;
Arand, Julia;
Lutsik, Pavlo;
Rivera Markelova, Maria;
Fichtner, Iduna;
Walter, Jörn;
Sers, Christine;
Tierling, Sascha

Publication type:

Article

Bisulfite-free epigenomics and genomics of single cells through methylation-sensitive restriction.

Published in:

Communications Biology, 2021, v. 4, n. 1, p. 1, doi. 10.1038/s42003-021-01661-w

By:

Niemöller, Christoph;
Wehrle, Julius;
Riba, Julian;
Claus, Rainer;
Renz, Nathalie;
Rhein, Janika;
Bleul, Sabine;
Stosch, Juliane M.;
Duyster, Justus;
Plass, Christoph;
Lutsik, Pavlo;
Lipka, Daniel B.;
Lübbert, Michael;
Becker, Heiko

Publication type:

Article

Globally altered epigenetic landscape and delayed osteogenic differentiation in H3.3-G34W-mutant giant cell tumor of bone.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-18955-y

By:

Lutsik, Pavlo;
Baude, Annika;
Mancarella, Daniela;
Öz, Simin;
Kühn, Alexander;
Toth, Reka;
Hey, Joschka;
Toprak, Umut H.;
Lim, Jinyeong;
Nguyen, Viet Ha;
Jiang, Chao;
Mayakonda, Anand;
Hartmann, Mark;
Rosemann, Felix;
Breuer, Kersten;
Vonficht, Dominik;
Grünschläger, Florian;
Lee, Suman;
Schuhmacher, Maren Kirstin;
Kusevic, Denis

Publication type:

Article

Neuronal ensemble-specific DNA methylation strengthens engram stability.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-14498-4

By:

Gulmez Karaca, Kubra;
Kupke, Janina;
Brito, David V. C.;
Zeuch, Benjamin;
Thome, Christian;
Weichenhan, Dieter;
Lutsik, Pavlo;
Plass, Christoph;
Oliveira, Ana M. M.

Publication type:

Article

ARID1A regulates DNA repair through chromatin organization and its deficiency triggers DNA damage-mediated anti-tumor immune response.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 10, p. 5698, doi. 10.1093/nar/gkae233

By:

Bakr, Ali;
Corte, Giuditta Della;
Veselinov, Olivera;
Kelekçi, Simge;
Chen, Mei-Ju May;
Lin, Yu-Yu;
Sigismondo, Gianluca;
Iacovone, Marika;
Cross, Alice;
Syed, Rabail;
Jeong, Yunhee;
Sollier, Etienne;
Liu, Chun- Shan;
Lutsik, Pavlo;
Krijgsveld, Jeroen;
Weichenhan, Dieter;
Plass, Christoph;
Popanda, Odilia;
Schmezer, Peter

Publication type:

Article

Club cells employ regeneration mechanisms during lung tumorigenesis.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-32052-2

By:

Chen, Yuanyuan;
Toth, Reka;
Chocarro, Sara;
Weichenhan, Dieter;
Hey, Joschka;
Lutsik, Pavlo;
Sawall, Stefan;
Stathopoulos, Georgios T.;
Plass, Christoph;
Sotillo, Rocio

Publication type:

Article

scMaui: a widely applicable deep learning framework for single-cell multiomics integration in the presence of batch effects and missing data.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05880-w

By:

Jeong, Yunhee;
Ronen, Jonathan;
Kopp, Wolfgang;
Lutsik, Pavlo;
Akalin, Altuna

Publication type:

Article

Systematic evaluation of cell-type deconvolution pipelines for sequencing-based bulk DNA methylomes.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 4, p. 1, doi. 10.1093/bib/bbac248

By:

Jeong, Yunhee;
Sousa, Lisa Barros de Andrade e;
Thalmeier, Dominik;
Toth, Reka;
Ganslmeier, Marlene;
Breuer, Kersten;
Plass, Christoph;
Lutsik, Pavlo

Publication type:

Article

A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-29625-6

By:

Llimos, Gerard;
Gardeux, Vincent;
Koch, Ute;
Kribelbauer, Judith F.;
Hafner, Antonina;
Alpern, Daniel;
Pezoldt, Joern;
Litovchenko, Maria;
Russeil, Julie;
Dainese, Riccardo;
Moia, Riccardo;
Mahmoud, Abdurraouf Mokhtar;
Rossi, Davide;
Gaidano, Gianluca;
Plass, Christoph;
Lutsik, Pavlo;
Gerhauser, Clarissa;
Waszak, Sebastian M.;
Boettiger, Alistair;
Radtke, Freddy

Publication type:

Article

Epigenetic reprogramming of airway macrophages promotes polarization and inflammation in muco-obstructive lung disease.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-26777-9

By:

Hey, Joschka;
Paulsen, Michelle;
Toth, Reka;
Weichenhan, Dieter;
Butz, Simone;
Schatterny, Jolanthe;
Liebers, Reinhard;
Lutsik, Pavlo;
Plass, Christoph;
Mall, Marcus A.

Publication type:

Article

RnBeads 2.0: comprehensive analysis of DNA methylation data.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1664-9

By:

Müller, Fabian;
Scherer, Michael;
Assenov, Yassen;
Lutsik, Pavlo;
Walter, Jörn;
Lengauer, Thomas;
Bock, Christoph

Publication type:

Article