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1.

Cognate recognition of microbial antigens defines constricted CD4⁺ T cell receptor repertoires in the inflamed colon.

Muschaweck, Moritz; Kopplin, Lydia; Ticconi, Fabio; Schippers, Angela; Iljazovic, Aida; Gálvez, Eric J C; Abdallah, Ali T; Wagner, Norbert; Costa, Ivan G; Strowig, Till; Pabst, Oliver.

Immunity ; 54(11): 2565-2577.e6, 2021 11 09.

Article in English | MEDLINE | ID: mdl-34582747

2.

Spatial multi-omic map of human myocardial infarction.

Kuppe, Christoph; Ramirez Flores, Ricardo O; Li, Zhijian; Hayat, Sikander; Levinson, Rebecca T; Liao, Xian; Hannani, Monica T; Tanevski, Jovan; Wünnemann, Florian; Nagai, James S; Halder, Maurice; Schumacher, David; Menzel, Sylvia; Schäfer, Gideon; Hoeft, Konrad; Cheng, Mingbo; Ziegler, Susanne; Zhang, Xiaoting; Peisker, Fabian; Kaesler, Nadine; Saritas, Turgay; Xu, Yaoxian; Kassner, Astrid; Gummert, Jan; Morshuis, Michiel; Amrute, Junedh; Veltrop, Rogier J A; Boor, Peter; Klingel, Karin; Van Laake, Linda W; Vink, Aryan; Hoogenboezem, Remco M; Bindels, Eric M J; Schurgers, Leon; Sattler, Susanne; Schapiro, Denis; Schneider, Rebekka K; Lavine, Kory; Milting, Hendrik; Costa, Ivan G; Saez-Rodriguez, Julio; Kramann, Rafael.

Nature ; 608(7924): 766-777, 2022 08.

Article in English | MEDLINE | ID: mdl-35948637

3.

HMGB2 Loss upon Senescence Entry Disrupts Genomic Organization and Induces CTCF Clustering across Cell Types.

Zirkel, Anne; Nikolic, Milos; Sofiadis, Konstantinos; Mallm, Jan-Philipp; Brackley, Chris A; Gothe, Henrike; Drechsel, Oliver; Becker, Christian; Altmüller, Janine; Josipovic, Natasa; Georgomanolis, Theodore; Brant, Lilija; Franzen, Julia; Koker, Mirjam; Gusmao, Eduardo G; Costa, Ivan G; Ullrich, Roland T; Wagner, Wolfgang; Roukos, Vassilis; Nürnberg, Peter; Marenduzzo, Davide; Rippe, Karsten; Papantonis, Argyris.

Mol Cell ; 70(4): 730-744.e6, 2018 05 17.

Article in English | MEDLINE | ID: mdl-29706538

4.

Human pluripotent stem cell-derived kidney organoids for personalized congenital and idiopathic nephrotic syndrome modeling.

Jansen, Jitske; van den Berge, Bartholomeus T; van den Broek, Martijn; Maas, Rutger J; Daviran, Deniz; Willemsen, Brigith; Roverts, Rona; van der Kruit, Marit; Kuppe, Christoph; Reimer, Katharina C; Di Giovanni, Gianluca; Mooren, Fieke; Nlandu, Quincy; Mudde, Helmer; Wetzels, Roy; den Braanker, Dirk; Parr, Naomi; Nagai, James S; Drenic, Vedran; Costa, Ivan G; Steenbergen, Eric; Nijenhuis, Tom; Dijkman, Henry; Endlich, Nicole; van de Kar, Nicole C A J; Schneider, Rebekka K; Wetzels, Jack F M; Akiva, Anat; van der Vlag, Johan; Kramann, Rafael; Schreuder, Michiel F; Smeets, Bart.

Development ; 149(9)2022 05 01.

Article in English | MEDLINE | ID: mdl-35417019

5.

Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT).

Joodaki, Mehdi; Shaigan, Mina; Parra, Victor; Bülow, Roman D; Kuppe, Christoph; Hölscher, David L; Cheng, Mingbo; Nagai, James S; Goedertier, Michaël; Bouteldja, Nassim; Tesar, Vladimir; Barratt, Jonathan; Roberts, Ian Sd; Coppo, Rosanna; Kramann, Rafael; Boor, Peter; Costa, Ivan G.

Mol Syst Biol ; 20(2): 57-74, 2024 Feb.

Article in English | MEDLINE | ID: mdl-38177382

6.

tRigon: an R package and Shiny App for integrative (path-)omics data analysis.

Hölscher, David L; Goedertier, Michael; Klinkhammer, Barbara M; Droste, Patrick; Costa, Ivan G; Boor, Peter; Bülow, Roman D.

BMC Bioinformatics ; 25(1): 98, 2024 Mar 05.

Article in English | MEDLINE | ID: mdl-38443821

7.

Induction of senescence upon loss of the Ash2l core subunit of H3K4 methyltransferase complexes.

Bochynska, Agnieszka; Stenzel, Alexander T; Sayadi Boroujeni, Roksaneh; Kuo, Chao-Chung; Barsoum, Mirna; Liang, Weili; Bussmann, Philip; Costa, Ivan G; Lüscher-Firzlaff, Juliane; Lüscher, Bernhard.

Nucleic Acids Res ; 50(14): 7889-7905, 2022 08 12.

Article in English | MEDLINE | ID: mdl-35819198

8.

RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data.

Li, Zhijian; Kuo, Chao-Chung; Ticconi, Fabio; Shaigan, Mina; Gehrmann, Julia; Gusmao, Eduardo Gade; Allhoff, Manuel; Manolov, Martin; Zenke, Martin; Costa, Ivan G.

BMC Bioinformatics ; 24(1): 79, 2023 Mar 06.

Article in English | MEDLINE | ID: mdl-36879236

9.

Deep learning-based clustering approaches for bioinformatics.

Karim, Md Rezaul; Beyan, Oya; Zappa, Achille; Costa, Ivan G; Rebholz-Schuhmann, Dietrich; Cochez, Michael; Decker, Stefan.

Brief Bioinform ; 22(1): 393-415, 2021 01 18.

Article in English | MEDLINE | ID: mdl-32008043

10.

MOJITOO: a fast and universal method for integration of multimodal single-cell data.

Cheng, Mingbo; Li, Zhijian; Costa, Ivan G.

Bioinformatics ; 38(Suppl 1): i282-i289, 2022 06 24.

Article in English | MEDLINE | ID: mdl-35758807

11.

Targeted DNA Methylation Analysis Facilitates Leukocyte Counts in Dried Blood Samples.

Hubens, Wouter H G; Maié, Tiago; Schnitker, Matthis; Bocova, Ledio; Puri, Deepika; Wessiepe, Martina; Kramer, Jan; Rink, Lothar; Koschmieder, Steffen; Costa, Ivan G; Wagner, Wolfgang.

Clin Chem ; 69(11): 1283-1294, 2023 11 02.

Article in English | MEDLINE | ID: mdl-37708296

12.

KIT D816V Mast Cells Derived from Induced Pluripotent Stem Cells Recapitulate Systemic Mastocytosis Transcriptional Profile.

de Toledo, Marcelo A S; Fu, Xuhuang; Maié, Tiago; Buhl, Eva M; Götz, Katrin; Schmitz, Susanne; Kaiser, Anne; Boor, Peter; Braunschweig, Till; Chatain, Nicolas; Costa, Ivan G; Brümmendorf, Tim H; Koschmieder, Steffen; Zenke, Martin.

Int J Mol Sci ; 24(6)2023 Mar 09.

Article in English | MEDLINE | ID: mdl-36982353

13.

Detection of cell markers from single cell RNA-seq with sc2marker.

Li, Ronghui; Banjanin, Bella; Schneider, Rebekka K; Costa, Ivan G.

BMC Bioinformatics ; 23(1): 276, 2022 Jul 12.

Article in English | MEDLINE | ID: mdl-35831796

14.

CrossTalkeR: analysis and visualization of ligand-receptorne tworks.

Nagai, James S; Leimkühler, Nils B; Schaub, Michael T; Schneider, Rebekka K; Costa, Ivan G.

Bioinformatics ; 37(22): 4263-4265, 2021 11 18.

Article in English | MEDLINE | ID: mdl-35032393

15.

Dissecting gene regulation with multimodal sequencing.

Costa, Ivan G.

Nat Methods ; 20(9): 1282-1284, 2023 09.

Article in English | MEDLINE | ID: mdl-37537350

16.

Isolation and genome-wide characterization of cellular DNA:RNA triplex structures.

Sentürk Cetin, Nevcin; Kuo, Chao-Chung; Ribarska, Teodora; Li, Ronghui; Costa, Ivan G; Grummt, Ingrid.

Nucleic Acids Res ; 47(5): 2306-2321, 2019 03 18.

Article in English | MEDLINE | ID: mdl-30605520

17.

Unique and assay specific features of NOMe-, ATAC- and DNase I-seq data.

Nordström, Karl J V; Schmidt, Florian; Gasparoni, Nina; Salhab, Abdulrahman; Gasparoni, Gilles; Kattler, Kathrin; Müller, Fabian; Ebert, Peter; Costa, Ivan G; Pfeifer, Nico; Lengauer, Thomas; Schulz, Marcel H; Walter, Jörn.

Nucleic Acids Res ; 47(20): 10580-10596, 2019 11 18.

Article in English | MEDLINE | ID: mdl-31584093

18.

Detection of RNA-DNA binding sites in long noncoding RNAs.

Kuo, Chao-Chung; Hänzelmann, Sonja; Sentürk Cetin, Nevcin; Frank, Stefan; Zajzon, Barna; Derks, Jens-Peter; Akhade, Vijay Suresh; Ahuja, Gaurav; Kanduri, Chandrasekhar; Grummt, Ingrid; Kurian, Leo; Costa, Ivan G.

Nucleic Acids Res ; 47(6): e32, 2019 04 08.

Article in English | MEDLINE | ID: mdl-30698727

19.

Cyclin E1 and cyclin-dependent kinase 2 are critical for initiation, but not for progression of hepatocellular carcinoma.

Sonntag, Roland; Giebeler, Nives; Nevzorova, Yulia A; Bangen, Jörg-Martin; Fahrenkamp, Dirk; Lambertz, Daniela; Haas, Ute; Hu, Wei; Gassler, Nikolaus; Cubero, Francisco Javier; Müller-Newen, Gerhard; Abdallah, Ali T; Weiskirchen, Ralf; Ticconi, Fabio; Costa, Ivan G; Barbacid, Mariano; Trautwein, Christian; Liedtke, Christian.

Proc Natl Acad Sci U S A ; 115(37): 9282-9287, 2018 09 11.

Article in English | MEDLINE | ID: mdl-30150405

20.

Deconvolution of cellular subsets in human tissue based on targeted DNA methylation analysis at individual CpG sites.

Schmidt, Marco; Maié, Tiago; Dahl, Edgar; Costa, Ivan G; Wagner, Wolfgang.

BMC Biol ; 18(1): 178, 2020 11 24.

Article in English | MEDLINE | ID: mdl-33234153

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