• 1. Gamero-Estevez, E., Hensel, I. V., Steinhauer, M., Müllertz, O., Savochkina, E., Sektioglu, I. M., Stoll, B., Derakhshani, S., Devriese, S., Kim, K. and Resnik-Docampo, M.(2025):
     Protocol for Immune Cell Isolation, Organoid Generation, and Co-culture Establishment from Cryopreserved Whole Human Intestine
     Bio-protocol 15(1)

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1. Ignashkova TI, Gendarme M, Peschk K, Eggenweiler HM, Lindemann RK, Reiling JH (2017):
   Cell survival and protein secretion associated with Golgi integrity in response to Golgi stress-inducing agents
   Traffic 18(8)
2. Ramírez-Peinado S, Ignashkova TI, van Raam BJ, Baumann J, Sennott EL, Gendarme M, Lindemann RK, Starnbach MN, Reiling JH (2017):
   TRAPPC13 modulates autophagy and the response to Golgi stress
   Journal of Cell Science 130
3. van Raam BJ, Lacina T, Lindemann RK, Reiling JH (2017):
   Secretory stressors induce intracellular death receptor accumulation to control apoptosis
   Cell Death and Disease 8(10)
4. Gendarme M, Baumann J, Ignashkova TI, Lindemann RK, Reiling JH (2017):
   Image-based drug screen identifies HDAC inhibitors as novel Golgi disruptors synergizing with JQ1
   Molecular Biology of the Cell 28(26)
5. Baumann J, Ignashkova TI, Chirasani SR, Ramírez-Peinado S, Alborzinia H, Gendarme M, Kuhnigk K, Kramer V, Lindemann RK, Reiling JH (2017):
   Golgi stress-induced transcriptional changes mediated by MAPK signaling and three ETS transcription factors regulate MCL1 splicing
   Molecular Biology of the Cell 29(1)
6. Alborzinia H, Ignashkova TI, Dejure FR, Gendarme M, Theobald J, Wölfl S, Lindemann RK, Reiling JH (2018):
   Golgi stress mediates redox imbalance and ferroptosis in human cells
   Communications Biology 1

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1. Volkamer A, Eid S, Turk S, Jaeger S, Rippmann F, Fulle S (2014):
   The pocketome of human kinases: Prioritizing the ATP binding sites of (yet) untapped protein kinases for drug discovery
   Journal of Chemical Information and Modeling 55(3)
2. Volkamer A, Eid S, Turk S, Rippmann F, Fulle S (2016):
   Identification and visualization of kinase-specific subpockets
   Journal of Chemical Information and Modeling 56(2)
3. Merget B, Turk S, Eid S, Rippmann F, Fulle S (2017):
   Profiling prediction of kinase inhibitors: Toward the virtual assay
   Journal of Medicinal Chemistry 60(1)
4. Eid S, Turk S, Volkamer A, Rippmann F, Fulle S (2017):
   KinMap: A web-based tool for interactive navigation through human kinome data
   BMC Bioinformatics 18
5. Turk S, Merget B, Rippmann F, Fulle S (2017):
   Coupling matched molecular pairs with machine learning for virtual compound optimization
   Journal of Chemical Information and Modeling 57(12)
6. Sorgenfrei FA, Fulle S, Merget B (2018):
   Kinome-wide profiling prediction of small molecules
   ChemMedChem 13(6)
7. Jaeger S, Fulle S, Turk S (2018):
   Mol2vec: Unsupervised machine learning approach with chemical intuition
   Journal of Chemical Information and Modeling 58(1)
8. Turk S, Merget B, Eid S, Fulle S (2018):
   From cancer to pain target by automated selectivity inversion of a clinical candidate
   Journal of Medicinal Chemistry 61(11)
9. Schwarz D, Merget B, Deane C, Fulle S (2019):
   Modelling conformational flexibility of kinases in inactive states
   Proteins 87(11)

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1. Schröder M, Loos S, Naumann SK, Bachran C, Krötschel M, Umansky V, Helming L, Swee LK (2017):
   Identification of inhibitors of myeloid-derived suppressor cells activity through phenotypic chemical screening
   OncoImmunology 6(1)
2. Bachran C, Schröder M, Conrad L, Cragnolini JJ, Tafesse FG, Helming L, Ploegh HL, Swee LK (2017):
   The activity of myeloid cell-specific VHH immunotoxins is target-, epitope-, subset- and organ dependent
   Scientific Reports 7(1)
3. Schröder M, Krötschel M, Conrad L, Naumann SK, Bachran C, Rolfe A, Umansky V, Helming L, Swee LK (2018):
   Genetic screen in myeloid cells identifies TNF-α autocrine secretion as a factor increasing MDSC suppressive activity via Nos2 up-regulation
   Scientific Reports 8
4. Wöll S, Schiller S, Bachran C, Swee LK, Scherließ R (2018):
   Pentaglycine lipid derivates – rp-HPLC analytics for bioorthogonal anchor molecules in targeted, multiple-composite liposomal drug delivery systems
   International Journal of Pharmaceutics 547(1-2)
5. Wöll S, Bachran C, Schiller S, Schröder M, Conrad L, Swee LK, Scherließ R (2018):
   Sortaggable liposomes: Evaluation of reaction conditions for single-domain antibody conjugation by Sortase-A and targeting of CD11b+ myeloid cells
   European Journal of Pharmaceutics and Biopharmaceutics 133
6. Wöll S, Bachran C, Schiller S, Schröder M, Conrad L, Scherließ R, Swee LK (2019):
   Sortagging of liposomes with a murine CD11b-specific VHH increases in vitro and in vivo targeting specificity of myeloid cells
   European Journal of Pharmaceutics and Biopharmaceutics 134

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1. Jurkowska RZ, Jurkowski TP (2019):
   Establishment, erasure and synthetic reprogramming of DNA methylation in mammalian cells
   In: The DNA, RNA, and histone methylomes (Springer)
2. Llamazares Prada M, Espinet E, Mijosek V, Schwartz U, Waszak SM, Lutsik P, Tamas R, Richter M, Behrendt A, Pohl S, Benz N, Muley T, Warth A, Heussel CP, Winter H, Herth F, Mertens T, Karmouty-Quintana H, Koch I, Benes V, Korbel JO, Trumpp A, Wyatt D, Stahl H, Plass C, Jurkowska RZ (2020):
   Versatile workflow for cell type resolved transcriptional and epigenetic profiles from cryopreserved human lung
   JCI Insight 6 (6)
3. Schwartz U, Llamazares Prada M, Pohl ST, Richter M, Tamas R, Schuler M, Keller C, Mijosek V, Muley T, Schneider MA, Quast K, Hey J, Heußel CP, Warth A, Winter H, Serçin Ö, Karmouty-Quintana H, Jyothula SS, Patel MK, Herth F, Koch I, Petrosino G, Titimeaua A, Mardin BR, Weichenhan D, Jurkowski TP, Imbusch CD, Brors B, Benes V, Jung B, Wyatt D, Stahl HF, Plass C, Jurkowska RZ (2023): High-resolution transcriptomic and epigenetic profiling identifies novel regulators of COPD
   The EMBO Journal Jun 15;42(12):e111272

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1. Gutiérrez-Sanz Ó, Andoy NM, Filipiak MS, Haustein N, Tarasov A (2017):
   Direct, label-free, and rapid transistor-based immunodetection in whole serum
   ACS Sensors 2(9)
2. Filipiak MS, Rother S, Andoy NM, Knudsen AC, Grimm S, Bachran C, Swee LK, Zaumseil J, Tarasov A (2018):
   Highly sensitive, selective and label-free protein detection in physiological solutions using carbon nanotube transistors with nanobody receptors
   Sensors and Actuators B: Chemical 255(2)
3. Andoy NM, Filipiak MS, Vetter D, Gutiérrez-Sanz Ó, Tarasov A (2018):
   Graphene-based electronic immunosensor with femtomolar detection limit in whole serum
   Advanced Materials Technologies 3(12)
4. Haustein N, Gutiérrez-Sanz Ó, Tarasov A (2019):
   Analytical model to describe the effect of poly-ethylene glycol on ionic screening of analyte charges in transistor-based immunosensing
   ACS Sensors 4(4)
5. Gutiérrez-Sanz Ó, Haustein N, Schroeter M, Oelschlaegel T, Filipiak MS, Tarasov A (2019):
   Transistor-based immunosensing in human serum samples without on-site calibration
   Sensors and Actuators B: Chemical 295
6. Filipiak MS, Vetter D, Thodkar K, Gutiérrez-Sanz Ó, Jönsson-Niedziółka M, Tarasov A (2020):
   Electron transfer from FAD-dependent glucose dehydrogenase to single-sheet graphene electrodes
   Electrochimica Acta 330
7. García-Chamé MA, Gutiérrez-Sanz Ó, Ercan-Herbst E, Haustein N, Filipiak MS, Ehrnhöfer DE, Tarasov A (2020):
   A transistor-based label-free immunosensor for rapid detection of tau protein
   Biosensors and Bioelectronics 159
8. Thodkar K, Cazade PA, Bergmann F, Lopez-Calle E, Thompson D, Heindl D (2021):
   Self-Assembled Pyrene Stacks and Peptide Monolayers Tune the Electronic Properties of Functionalized Electrolyte-Gated Graphene Field-Effect Transistors
   ACS Applied Materials & Interfaces 13

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1. Serçin Ö, Reither S, Roidos P, Ballin N, Palikyras S, Baginska A, Rein K, Llamazares M, Halavatyi A, Winter H, Muley T, Jurkowska RZ, Abdollahi A, Zenke FT, Neumann B, Mardin BR (2019):
   A solid-phase transfection platform for arrayed CRISPR screens
   Molecular Systems Biology 15 (12)
2. Drainas AP, Lambuta RA, Ivanova I, Serçin Ö, Sarropoulos I, Smith ML, Efthymiopoulos T, Raeder B, Stütz AM, Waszak SM, Mardin BR, Korbel JO (2020):
   Genome-wide Screens Implicate Loss of Cullin Ring Ligase 3 in Persistent Proliferation and Genome Instability in TP53-Deficient Cells
   Cell Reports 31(1)
3. Roidos P, Sungalee S, Benfatto S, Serçin Ö, Stütz AM, Abdollahi A, Mauer J, Zenke FT, Korbel JO, Mardin BR (2020):
   A scalable CRISPR/CAS9-based fluorescent reporter assay to study DNA double-strand break repair choice
   Nature Communications 11, 4077 (2020)
4. Dejure F, Butzer J, Lindemann RK, Mardin BR (2020):
   Exploiting the metabolic dependencies of the broad amino acid transporter SLC6A14
   Oncotarget. 2020; 11: 4490-4503
5. Benfatto S, Serçin Ö, Dejure FR, Abdollahi A, Zenke FT, Mardin BR (2021):
   Uncovering cancer vulnerabilities by machine learning prediction of synthetic lethality
   Molecular Cancer. 2021; 20:111

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1. Magdalena Tertil, Urszula Skupio, Justyna Barut, Valentyna Dubovyk, Agnieszka Wawrzczak-Bargiela, Zbigniew Soltys, Slawomir Golda, Lucja Kudla, Lucja Wiktorowska, Klaudia Szklarczyk, Michal Korostynski, Ryszard Przewlocki & Michal Slezak (2018):
   Glucocorticoid receptor signaling in astrocytes is required for aversive memory formation
   Translational Psychiatry 8
2. Agnieszka Plociennikowska, Jamie Frankish, Thais Moraes, Dolores Del Prete, Franziska Kahnt, Claudio Acuna, Michal Slezak, Marco Binder, Ralf Bartenschlager (2021):
   TLR3 activation by Zika virus stimulates inflammatory cytokine production which dampens the antiviral response induced by RIG-I-like receptors
   Journal of Virology 95(10)
3. Verena Nold, Michelle Portenhauser, Dolores Del Prete, Andrea Blasius, Isabella Harris, Eliza Koros, Tatiana Peleh, Bastian Hengerer, Iris-Tatjana Kolassa, Michal Slezak & Kelly Ann Allers (2022):
   Impact of Fkbp5 × early life adversity × sex in humanised mice on multidimensional stress responses and circadian rhythmicity
   Molecular Psychiatry

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1. Cetin M, Pinamonti V, Schmid T, Boschert T, Mellado Fuentes A, Kromer K, Lerner T, Zhang J, Herzig Y, Ehlert C, Hernandez-Hernandez M, Samaras G, Torres CM, Fisch L, Dragan V, Kouwenhoven A, Van Schoubroeck B, Wils H, Van Hove C, Platten M, Green EW, Stevenaert F, Felix NJ, Lindner JM (2024):
   T-FINDER: A highly sensitive, pan-HLA platform for functional T cell receptor and ligand discovery.
   Science Advances
2. Boschert T, Kromer K, Lerner T, Lindner K, Haltenhof G, Tan CL, Jähne K, Poschke I, Bunse L, Eisele P, Grassl N, Mildenberger I, Sahm K, Platten M, Lindner JM, Green EW (2024):
   H3K27M neoepitope vaccination in diffuse midline glioma induces B and T cell responses across diverse HLA loci of a recovered patient.
   Science Advances
3. Tan, CL, Lindner, K, Boschert, T, Meng, Z, Rodriguez Ehrenfried, A, De Roia, A, Haltenhof, G, Faenza, A, Imperatore, F, Bunse, L, Lindner, JM, Harbottle, RP, Ratliff, M, Offringa, R, Poschke, I, Platten, M, Green, EW (2024): Prediction of tumor-reactive T cell receptors from scRNA-seq data for personalized T cell therapy.
   Nat Biotechnol

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1. Hensel IV, Éliás S, Steinhauer M, Stoll B, Benfatto S, Merkt W, Krienke S, Lorenz HM, Haas J, Wildemann B, Resnik-Docampo M (2024):
   SLE serum induces altered goblet cell differentiation and leakiness in human intestinal organoids.
   EMBO Molecular Medicine

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1. Cetin M, Pinamonti V, Schmid T, Boschert T, Mellado Fuentes A, Kromer K, Lerner T, Zhang J, Herzig Y, Ehlert C, Hernandez-Hernandez M, Samaras G, Torres CM, Fisch L, Dragan V, Kouwenhoven A, Van Schoubroeck B, Wils H, Van Hove C, Platten M, Green EW, Stevenaert F, Felix NJ, Lindner JM (2024):
   T-FINDER: A highly sensitive, pan-HLA platform for functional T cell receptor and ligand discovery.
   Science Advances
2. Boschert T, Kromer K, Lerner T, Lindner K, Haltenhof G, Tan CL, Jähne K, Poschke I, Bunse L, Eisele P, Grassl N, Mildenberger I, Sahm K, Platten M, Lindner JM, Green EW (2024):
   H3K27M neoepitope vaccination in diffuse midline glioma induces B and T cell responses across diverse HLA loci of a recovered patient.
   Science Advances

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