Publications

You can find all my publications on my Google Scholar page.

You can also find my ORCID profile at https://orcid.org/0000-0003-3252-7758.

Otherwise, listed below you can find all my publications, sorted by year.

2025

John N, Fleming T, Kolb J, Lyraki O, Vásquez-Sepúlveda S, Parmar A, Kim K, Tarczewska M, Gupta P, Singh K, Marini F, Singh SP, Falk S, Franze K, Guck J, Wehner D. Biphasic inflammation control by dedifferentiated fibroblasts enables axon regeneration after spinal cord injury in zebrafish. Published online January 27, 2025. doi:10.1101/2025.01.27.635043 DOI: 10.1101/2025.01.27.635043
Cihan M, More P, Sprang M, Marini F, Andrade-Navarro MA. Target-site Dynamics and Alternative Polyadenylation Explain Large Share of Apparent MicroRNA Differential Expression. Published online October 1, 2025. doi:10.1101/2025.09.29.679194 DOI: 10.1101/2025.09.29.679194
Ries F, Klein M, Rogmann N, Többen S, Marini F, Heidel F, Radsak MP. Characterization of the TREM-1 Signaling Landscape in Human Neutrophils. Published online September 25, 2025. doi:10.1101/2025.09.23.678160 DOI: 10.1101/2025.09.23.678160
Beumer N, Imbusch CD, Kaufmann T, Schmidleithner L, Gütter K, Stüve P, Marchel H, Weichenhan D, Bähr M, Ruhland B, Marini F, Sanderink L, Ritter U, Simon M, Braband KL, Voss MM, Helbich SS, Mihoc DM, Hotz-Wagenblatt A, Nassabi H, Eigenberger A, Prantl L, Gebhard C, Rehli M, Strieder N, Singh K, Schmidl C, Plass C, Huehn J, Hehlgans T, Polansky JK, Brors B, Delacher M, Feuerer M. DNA hypomethylation traits define human regulatory T cells in cutaneous tissue and identify their blood recirculating counterparts. Nature Immunology. 2025;26(8):1315-1328. doi:10.1038/s41590-025-02210-x DOI: 10.1038/s41590-025-02210-x
Wilgenbus P, Pott J, Pagel S, Witzler C, Royce J, Marini F, Reyda S, Madhusudhan T, Kindler T, Hausen A, Gaida MM, Weiler H, Ruf W, Graf C. Coagulation proteases modulate nucleic acid uptake and cGAS-STING-IFN induction in the tumor microenvironment. JCI Insight. 2025;10(17). doi:10.1172/jci.insight.190311 DOI: 10.1172/jci.insight.190311
Hou C, Ghazanfar S, Marini F, Morgan M, Hicks SC. HuBMAPR: an R client for the HuBMAP data portal. Ma L, ed. Bioinformatics Advances. 2024;5(1). doi:10.1093/bioadv/vbaf048 DOI: 10.1093/bioadv/vbaf048
Ustjanzew A, Marini F, Wagner S, Wingerter A, Sandhoff R, Faber J, Paret C. Predicting GD2 expression across cancer types by the integration of pathway topology and transcriptome data. Published online May 24, 2025. doi:10.1101/2025.05.21.655303 DOI: 10.1101/2025.05.21.655303
Wild P, Khatami SG, Baumkötter R, Koeck T, Alam ASM, Yilmaz S, Chalabi J, Rapp S, Marini F, Schepers M, Bopp T, Bittner S, Schuster A, Beutel ME, Munzel T, Lackner K, Cate VT. Proteomic Atlas of Post-COVID Sequelae. Published online March 5, 2025. doi:10.21203/rs.3.rs-6024310/v1 DOI: 10.21203/rs.3.rs-6024310/v1
Salah A, Wollschläger D, Callari M, Schmidberger H, Marini F, Zahnreich S. Genome-wide transcriptomic response of whole blood to radiation. Scientific Reports. 2025;15(1). doi:10.1038/s41598-025-04898-1 DOI: 10.1038/s41598-025-04898-1
Huang J, Marini F, Solari FA, Swieringa F, de Laat B, De Simone I, Grassi L, Gui X, Li K, Middleton EA, Morgan NV, Provenzale I, Santos C, Schols S, Westbury S, Sickmann A, Rondina MT, Ruf W, Frontini M, Heemskerk JWM. Human and mouse platelet transcriptomes and proteomes for phenotyping 3474 genes with hemostatic and platelet traits. Blood Vessels, Thrombosis & Hemostasis. 2025;2(3):100068. doi:10.1016/j.bvth.2025.100068 DOI: 10.1016/j.bvth.2025.100068
Eski SE, Mi J, Pozo-Morales M, Hovhannisyan GG, Perazzolo C, Manco R, Ez-Zammoury I, Barbhaya D, Lefort A, Libert F, Marini F, Gurzov EN, Andersson O, Singh SP. Cholangiocytes contribute to hepatocyte regeneration after partial liver injury during growth spurt in zebrafish. Nature Communications. 2025;16(1). doi:10.1038/s41467-025-60334-y DOI: 10.1038/s41467-025-60334-y
Braband KL, Kaufmann T, Beumer N, Simon M, Helbich SS, Mihoc DM, Voss MM, Nedwed AS, Bauer K, Mallm JP, Ziesmann T, Distler U, Tenzer S, Eckert C, Volkmar M, Weichenhan D, Bähr M, Plass C, Linke M, Diederich S, Klein M, Bopp T, Schild H, Henkel A, Filippi E, Marini F, Brors B, Gaida MM, Delacher M. Single-cell chromatin landscape and DNA methylation patterns reveal shared molecular programs in human tumor and non-tumor tissue CCR8+Treg cells. Published online May 17, 2025. doi:10.1101/2025.05.14.653926 DOI: 10.1101/2025.05.14.653926
Weinmann-Menke J, Gonzalez-Sanchez HM, Iwata Y, Meineck M, Abassi N, Marini F, Granados-Contreras F, Takakura A, Noda M, Kelley VR. Ptprz Signaling, Tubule-Mediated and Macrophage-Mediated Kidney Injury, and Subsequent CKD. Journal of the American Society of Nephrology. 2025;36(7):1295-1309. doi:10.1681/asn.0000000640 DOI: 10.1681/ASN.0000000640

2024

Dietrich A, Merotto L, Pelz K, Eder B, Zackl C, Reinisch K, Edenhofer F, Marini F, Sturm G, List M, Finotello F. omnideconv: a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data. Published online June 11, 2024. doi:10.1101/2024.06.10.598226 DOI: 10.1101/2024.06.10.598226
Al Ajami A, Schuck J, Marini F, Imkeller K. A comprehensive workflow for allele-specific immune gene quantification and expression analysis in single-cell RNA-seq data. Published online December 15, 2024. doi:10.1101/2024.12.10.627679 DOI: 10.1101/2024.12.10.627679
Florin L, Strunk J, Hüppner A, Sial M, Plath M, Wagner S, Freitag K, Mikuličić S, Bopp T, Klein M, Rajalingam K, Harms G, Marini F, Ludt A, Hankeln T, Osterhof C, Henrich A, Nubbemeyer A, Suchan M, Schrörs B, Kreiter S, Kölsch A, Diken M, Döring T. The MYB-related transcription factor MYPOP acts as a selective regulator of cancer cell growth. Published online March 5, 2024. doi:10.21203/rs.3.rs-3673301/v1 DOI: 10.21203/rs.3.rs-3673301/v1
Ustjanzew A, Nedwed AS, Sandhoff R, Faber J, Marini F, Paret C. Unraveling the glycosphingolipid metabolism by leveraging transcriptome-weighted network analysis on neuroblastic tumors. Cancer & Metabolism. 2024;12(1). doi:10.1186/s40170-024-00358-y DOI: 10.1186/s40170-024-00358-y
Massoni-Badosa R, Aguilar-Fernández S, Nieto JC, Soler-Vila P, Elosua-Bayes M, Marchese D, Kulis M, Vilas-Zornoza A, Bühler MM, Rashmi S, Alsinet C, Caratù G, Moutinho C, Ruiz S, Lorden P, Lunazzi G, Colomer D, Frigola G, Blevins W, Romero-Rivero L, Jiménez-Martínez V, Vidal A, Mateos-Jaimez J, Maiques-Diaz A, Ovejero S, Moreaux J, Palomino S, Gomez-Cabrero D, Agirre X, Weniger MA, King HW, Garner LC, Marini F, Cervera-Paz FJ, Baptista PM, Vilaseca I, Rosales C, Ruiz-Gaspà S, Talks B, Sidhpura K, Pascual-Reguant A, Hauser AE, Haniffa M, Prosper F, Küppers R, Gut IG, Campo E, Martin-Subero JI, Heyn H. An atlas of cells in the human tonsil. Immunity. 2024;57(2):379-399.e18. doi:10.1016/j.immuni.2024.01.006 DOI: 10.1016/j.immuni.2024.01.006

2023

Ha CSR, Müller-Nurasyid M, Petrera A, Hauck SM, Marini F, Bartsch DK, Slater EP, Strauch K. Proteomics biomarker discovery for individualized prevention of familial pancreatic cancer using statistical learning. Batra SK, ed. PLOS ONE. 2023;18(1):e0280399. doi:10.1371/journal.pone.0280399 DOI: 10.1371/journal.pone.0280399
Johann L, Soldati S, Müller K, Lampe J, Marini F, Klein M, Schramm E, Ries N, Schelmbauer C, Palagi I, Karram K, Assmann JC, Khan MA, Wenzel J, Schmidt MHH, Körbelin J, Schlüter D, van Loo G, Bopp T, Engelhardt B, Schwaninger M, Waisman A. A20 regulates lymphocyte adhesion in murine neuroinflammation by restricting endothelial ICOSL expression in the CNS. Journal of Clinical Investigation. 2023;133(24). doi:10.1172/jci168314 DOI: 10.1172/JCI168314
Rosellini M, Omer EA, Schulze A, Ali NT, Boulos JC, Marini F, Küpper JH, Efferth T. Impact of plastic-related compounds on the gene expression signature of HepG2 cells transfected with CYP3A4. Archives of Toxicology. 2023;98(2):525-536. doi:10.1007/s00204-023-03648-4 DOI: 10.1007/s00204-023-03648-4
Grandt CL, Brackmann LK, Foraita R, Schwarz H, Hummel-Bartenschlager W, Hankeln T, Kraemer C, Zahnreich S, Drees P, Mirsch J, Spix C, Blettner M, Schmidberger H, Binder H, Hess M, Galetzka D, Marini F, Poplawski A, Marron M. Gene expression variability in long-term survivors of childhood cancer and cancer-free controls in response to ionizing irradiation. Molecular Medicine. 2023;29(1). doi:10.1186/s10020-023-00629-2 DOI: 10.1186/s10020-023-00629-2
ten Cate V, Rapp S, Schulz A, Pallares Robles A, Jurk K, Koeck T, Espinola-Klein C, Halank M, Seyfarth HJ, Beutel ME, Schuster AK, Marini F, Hobohm L, Lankeit M, Lackner KJ, Ruf W, Münzel T, Andrade-Navarro MA, Prochaska JH, Konstantinides SV, Wild PS. Circulating microRNAs predict recurrence and death following venous thromboembolism. Journal of Thrombosis and Haemostasis. 2023;21(10):2797-2810. doi:10.1016/j.jtha.2023.07.010 DOI: 10.1016/j.jtha.2023.07.010
Rosellini M, Schulze A, Omer EA, Ali NT, Marini F, Küpper JH, Efferth T. The Effect of Plastic-Related Compounds on Transcriptome-Wide Gene Expression on CYP2C19-Overexpressing HepG2 Cells. Molecules. 2023;28(16):5952. doi:10.3390/molecules28165952 DOI: 10.3390/molecules28165952
Bartneck J, Hartmann AK, Stein L, Arnold-Schild D, Klein M, Stassen M, Marini F, Pielenhofer J, Meiser SL, Langguth P, Mack M, Muth S, Probst HC, Schild H, Radsak MP. Tumor-infiltrating CCR2+ inflammatory monocytes counteract specific immunotherapy. Frontiers in Immunology. 2023;14. doi:10.3389/fimmu.2023.1267866 DOI: 10.3389/fimmu.2023.1267866
Nedwed AS, Helbich SS, Braband KL, Volkmar M, Delacher M, Marini F. Using combined single-cell gene expression, TCR sequencing and cell surface protein barcoding to characterize and track CD4+ T cell clones from murine tissues. Frontiers in Immunology. 2023;14. doi:10.3389/fimmu.2023.1241283 DOI: 10.3389/fimmu.2023.1241283
Braband KL, Nedwed AS, Helbich SS, Simon M, Beumer N, Brors B, Marini F, Delacher M. Using single-cell chromatin accessibility sequencing to characterize CD4+ T cells from murine tissues. Frontiers in Immunology. 2023;14. doi:10.3389/fimmu.2023.1232511 DOI: 10.3389/fimmu.2023.1232511
Bryce-Smith S, Burri D, Gazzara MR, Herrmann CJ, Danecka W, Fitzsimmons CM, Wan YK, Zhuang F, Fansler MM, Fernández JM, Ferret M, Gonzalez-Uriarte A, Haynes S, Herdman C, Kanitz A, Katsantoni M, Marini F, McDonnel E, Nicolet B, Poon CL, Rot G, Schärfen L, Wu PJ, Yoon Y, Barash Y, Zavolan M. Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data. RNA. 2023;29(12):1839-1855. doi:10.1261/rna.079849.123 DOI: 10.1261/rna.079849.123
Kirschner F, Arnold-Schild D, Leps C, Łącki MK, Klein M, Chen Y, Ludt A, Marini F, Kücük C, Stein L, Distler U, Sielaff M, Michna T, Riegel K, Rajalingam K, Bopp T, Tenzer S, Schild H. Modulation of cellular transcriptome and proteome composition by azidohomoalanine—implications on click chemistry–based secretome analysis. Journal of Molecular Medicine. 2023;101(7):855-867. doi:10.1007/s00109-023-02333-4 DOI: 10.1007/s00109-023-02333-4
Grandt CL, Brackmann LK, Poplawski A, Schwarz H, Marini F, Hankeln T, Galetzka D, Zahnreich S, Mirsch J, Spix C, Blettner M, Schmidberger H, Marron M. Identification of lncRNAs involved in response to ionizing radiation in fibroblasts of long-term survivors of childhood cancer and cancer-free controls. Frontiers in Oncology. 2023;13. doi:10.3389/fonc.2023.1158176 DOI: 10.3389/fonc.2023.1158176
Johann L, Soldati S, Müller K, Lampe J, Marini F, Klein M, Schramm E, Ries N, Schelmbauer C, Palagi I, Karram K, Assmann JC, Khan MA, Wenzel J, Schmidt MHH, Körbelin J, Schlüter D, van Loo G, Bopp T, Engelhardt B, Schwaninger M, Waisman A. A20 regulates lymphocyte adhesion in murine neuroinflammation by restricting endothelial ICOSL expression in the CNS. Journal of Clinical Investigation. 2023;133(24). doi:10.1172/jci168314 DOI: 10.1172/JCI168314
Pontarollo G, Kollar B, Mann A, Khuu MP, Kiouptsi K, Bayer F, Brandão I, Zinina VV, Hahlbrock J, Malinarich F, Mimmler M, Bhushan S, Marini F, Ruf W, Belheouane M, Baines JF, Endres K, Reba SM, Raker VK, Deppermann C, Welsch C, Bosmann M, Soshnikova N, Chassaing B, Bergentall M, Sommer F, Bäckhed F, Reinhardt C. Commensal bacteria weaken the intestinal barrier by suppressing epithelial neuropilin-1 and Hedgehog signaling. Nature Metabolism. 2023;5(7):1174-1187. doi:10.1038/s42255-023-00828-5 DOI: 10.1038/s42255-023-00828-5
Müller M, Förschler S, Wehrmann T, Marini F, Gockel I, Eckardt AJ. Atypical presentations and pitfalls of achalasia. Diseases of the Esophagus. 2023;36(10). doi:10.1093/dote/doad029 DOI: 10.1093/dote/doad029

2022

Kaps L, Huppertsberg A, Choteschovsky N, Klefenz A, Durak F, Schrörs B, Diken M, Eichler E, Rosigkeit S, Schmitt S, Leps C, Schulze A, Foerster F, Bockamp E, De Geest BG, Koynov K, Räder HJ, Tenzer S, Marini F, Schuppan D, Nuhn L. pH-degradable, bisphosphonate-loaded nanogels attenuate liver fibrosis by repolarization of M2-type macrophages. Proceedings of the National Academy of Sciences. 2022;119(12). doi:10.1073/pnas.2122310119 DOI: 10.1073/pnas.2122310119
Mooz J, Riegel K, PS H, Sadanandam A, Marini F, Klein M, Werner U, Roth W, Wilken-Schmitz A, Tegeder I, Rajalingam K. ARAF suppresses ERBB3 expression and metastasis in a subset of lung cancers. Science Advances. 2022;8(11). doi:10.1126/sciadv.abk1538 DOI: 10.1126/sciadv.abk1538
Saragovi A, Zheng X, Abramovich I, Cohen-Daniel L, Zhuoning L, Raifer H, Omar I, Swisa A, Kuchersky M, Drori A, Marini F, Toker O, Somech R, Schmidl C, Hendrickson R, Gottlieb E, Huber M, Berger M. Enhanced methionine cycle suppresses naïve CD8+ T-cell maturation. Published online August 16, 2022. doi:10.1101/2022.08.16.504136 DOI: 10.1101/2022.08.16.504136
Grandt CL, Brackmann LK, Poplawski A, Schwarz H, Hummel-Bartenschlager W, Hankeln T, Kraemer C, Marini F, Zahnreich S, Schmitt I, Drees P, Mirsch J, Grabow D, Schmidberger H, Binder H, Hess M, Galetzka D, Marron M. Radiation-response in primary fibroblasts of long-term survivors of childhood cancer with and without second primary neoplasms: the KiKme study. Molecular Medicine. 2022;28(1). doi:10.1186/s10020-022-00520-6 DOI: 10.1186/s10020-022-00520-6
Dietrich A, Sturm G, Merotto L, Marini F, Finotello F, List M. SimBu: bias-aware simulation of bulk RNA-seq data with variable cell-type composition. Bioinformatics. 2022;38(Supplement_2):ii141-ii147. doi:10.1093/bioinformatics/btac499 DOI: 10.1093/bioinformatics/btac499
Sohl J, Hartmann AK, Hahlbrock J, Bartneck J, Stassen M, Klein M, Bros M, Grabbe S, Marini F, Woods K, Guezguez B, Mack M, Schild H, Muth S, Melchior F, Probst HC, Langguth P, Radsak MP. Dithranol as novel co-adjuvant for non-invasive dermal vaccination. npj Vaccines. 2022;7(1). doi:10.1038/s41541-022-00530-9 DOI: 10.1038/s41541-022-00530-9
Ludt A, Ustjanzew A, Binder H, Strauch K, Marini F. Interactive and Reproducible Workflows for Exploring and Modeling RNA‐seq Data with pcaExplorer, Ideal, and GeneTonic. Current Protocols. 2022;2(4). doi:10.1002/cpz1.411 DOI: 10.1002/cpz1.411
Das Gupta D, Paul C, Samel N, Bieringer M, Staudenraus D, Marini F, Raifer H, Menke L, Hansal L, Camara B, Roth E, Daum P, Wanzel M, Mernberger M, Nist A, Bauer UM, Helmprobst F, Buchholz M, Roth K, Bastian L, Hartmann AM, Baldus C, Ikuta K, Neubauer A, Burchert A, Jäck HM, Klein M, Bopp T, Stiewe T, Pagenstecher A, Lohoff M. IRF4 deficiency vulnerates B-cell progeny for leukemogenesis via somatically acquired Jak3 mutations conferring IL-7 hypersensitivity. Cell Death & Differentiation. 2022;29(11):2163-2176. doi:10.1038/s41418-022-01005-z DOI: 10.1038/s41418-022-01005-z
Britto-Borges T, Ludt A, Boileau E, Gjerga E, Marini F, Dieterich C. Magnetique: an interactive web application to explore transcriptome signatures of heart failure. Journal of Translational Medicine. 2022;20(1). doi:10.1186/s12967-022-03694-z DOI: 10.1186/s12967-022-03694-z
Bensaoud C, Tenzer S, Poplawski A, Medina JM, Jmel MA, Voet H, Mekki I, Aparicio‐Puerta E, Cuveele B, Distler U, Marini F, Hackenberg M, Kotsyfakis M. Quantitative proteomics analysis reveals core and variable tick salivary proteins at the tick‐vertebrate host interface. Molecular Ecology. 2022;31(15):4162-4175. doi:10.1111/mec.16561 DOI: 10.1111/mec.16561
Nührenberg TG, Stöckle J, Marini F, Zurek M, Grüning BA, Benes V, Hein L, Neumann FJ, Stratz C, Cederqvist M, Hochholzer W. Impact of high platelet turnover on the platelet transcriptome: Results from platelet RNA-sequencing in patients with sepsis. James K, ed. PLOS ONE. 2022;17(1):e0260222. doi:10.1371/journal.pone.0260222 DOI: 10.1371/journal.pone.0260222
Hill P, Zellmann F, Vukova T, Marini F, Kolmar S, Kaina B, Hofmann TG, Nikolova T. Dose response to methylating agents in the γH2AX, SCE and colony formation assays: Effect of MGMT and MPG overexpression. Mutation Research/Genetic Toxicology and Environmental Mutagenesis. 2022;876-877:503462. doi:10.1016/j.mrgentox.2022.503462 DOI: 10.1016/j.mrgentox.2022.503462
Hill P, Zellmann F, Vukova T, Marini F, Kolmar S, Kaina B, Hofmann TG, Nikolova T. Dose response to methylating agents in the γH2AX, SCE and colony formation assays: Effect of MGMT and MPG overexpression. Mutation Research/Genetic Toxicology and Environmental Mutagenesis. 2022;876-877:503462. doi:10.1016/j.mrgentox.2022.503462 DOI: 10.1016/j.mrgentox.2022.503462
Joo R, Sánchez-Tapia A, Mortara S, Bellini Saibene Y, Turner H, Hug Peter D, Morandeira NS, Bannert M, Almazrouq B, Hare E, Ación L, Narváez-Gómez JP, Alfaro Córdoba M, Marini F, Giordano R, Canelón S, Ebou A, Upadhya AR, Chávez J, Ravi J. Ten simple rules to host an inclusive conference. PLOS Computational Biology. 2022;18(7):e1010164. doi:10.1371/journal.pcbi.1010164 DOI: 10.1371/journal.pcbi.1010164

2021

Paret C, Lehmann N, Bender H, Sprang M, Sommer CJ, Cana D, Seidmann L, Wingerter A, Neu MA, El Malki K, Alt F, Roth L, Marini F, Ottenhausen M, Glaser M, Knuf M, Russo A, Faber J. Identification of an Immunogenic Medulloblastoma-Specific Fusion Involving EPC2 and GULP1. Cancers. 2021;13(22):5838. doi:10.3390/cancers13225838 DOI: 10.3390/cancers13225838
Lapuente-Santana Ó, Marini F, Ustjanzew A, Finotello F, Eduati F. easier: interpretable predictions of antitumor immune response from bulk RNA-seq data. Published online November 27, 2021. doi:10.1101/2021.11.26.470099 DOI: 10.1101/2021.11.26.470099
Ustjanzew A, Desuki A, Ritzel C, Dolezilek AC, Wagner DC, Christoph J, Unberath P, Kindler T, Faber J, Marini F, Panholzer T, Paret C. cbpManager: a web application to streamline the integration of clinical and genomic data in cBioPortal to support the Molecular Tumor Board. BMC Medical Informatics and Decision Making. 2021;21(1). doi:10.1186/s12911-021-01719-z DOI: 10.1186/s12911-021-01719-z
Notarbartolo S, Ranzani V, Bandera A, Gruarin P, Bevilacqua V, Putignano AR, Gobbini A, Galeota E, Manara C, Bombaci M, Pesce E, Zagato E, Favalli A, Sarnicola ML, Curti S, Crosti M, Martinovic M, Fabbris T, Marini F, Donnici L, Lorenzo M, Mancino M, Ungaro R, Lombardi A, Mangioni D, Muscatello A, Aliberti S, Blasi F, De Feo T, Prati D, Manganaro L, Granucci F, Lanzavecchia A, Francesco RD, Gori A, Grifantini R, Abrignani S. Integrated longitudinal immunophenotypic, transcriptional, and repertoire analyses delineate immune responses in patients with COVID-19. Science Immunology. 2021;6(62). doi:10.1126/sciimmunol.abg5021 DOI: 10.1126/sciimmunol.abg5021
Marini F, Scherzinger D, Danckwardt S. TREND-DB—a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation. Nucleic Acids Research. 2020;49(D1):D243-D253. doi:10.1093/nar/gkaa722 DOI: 10.1093/nar/gkaa722
Bogucka K, Marini F, Rosigkeit S, Schloeder J, Jonuleit H, David K, Schlackow M, Rajalingam K. ERK3/MAPK6 is required for KRAS-mediated NSCLC tumorigenesis. Cancer Gene Therapy. 2020;28(5):359-374. doi:10.1038/s41417-020-00245-w DOI: 10.1038/s41417-020-00245-w
Krämer B, Knoll R, Bonaguro L, ToVinh M, Raabe J, Astaburuaga-García R, Schulte-Schrepping J, Kaiser KM, Rieke GJ, Bischoff J, Monin MB, Hoffmeister C, Schlabe S, De Domenico E, Reusch N, Händler K, Reynolds G, Blüthgen N, Hack G, Finnemann C, Nischalke HD, Strassburg CP, Stephenson E, Su Y, Gardner L, Yuan D, Chen D, Goldman J, Rosenstiel P, Schmidt SV, Latz E, Hrusovsky K, Ball AJ, Johnson JM, Koenig PA, Schmidt FI, Haniffa M, Heath JR, Kümmerer BM, Keitel V, Jensen B, Stubbemann P, Kurth F, Sander LE, Sawitzki B, Aschenbrenner AC, Schultze JL, Nattermann J, Altmüller J, Angelov A, Aschenbrenner AC, Bals R, Bartholomäus A, Becker A, Becker M, Bezdan D, Bitzer M, Blumert C, Bonifacio E, Bork P, Boyke B, Blum H, Casadei N, Clavel T, Colome-Tatche M, Cornberg M, De La Rosa Velázquez IA, Diefenbach A, Dilthey A, Fischer N, Förstner K, Franzenburg S, Frick JS, Gabernet G, Gagneur J, Ganzenmueller T, Gauder M, Geißert J, Goesmann A, Göpel S, Grundhoff A, Grundmann H, Hain T, Hanses F, Hehr U, Heimbach A, Hoeper M, Horn F, Hübschmann D, Hummel M, Iftner T, Iftner A, Illig T, Janssen S, Kalinowski J, Kallies R, Kehr B, Keller A, et al. Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19. Immunity. 2021;54(11):2650-2669.e14. doi:10.1016/j.immuni.2021.09.002 DOI: 10.1016/j.immuni.2021.09.002
Marini F, Ludt A, Linke J, Strauch K. GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data. BMC Bioinformatics. 2021;22(1). doi:10.1186/s12859-021-04461-5 DOI: 10.1186/s12859-021-04461-5

2020

Marini F, Linke J, Binder H. ideal: an R/Bioconductor package for interactive differential expression analysis. BMC Bioinformatics. 2020;21(1). doi:10.1186/s12859-020-03819-5 DOI: 10.1186/s12859-020-03819-5
Soneson C, Marini F, Geier F, Love MI, Stadler MB. ExploreModelMatrix: Interactive exploration for improved understanding of design matrices and linear models in R. F1000Research. 2020;9:512. doi:10.12688/f1000research.24187.1 DOI: 10.12688/f1000research.24187.1
Mohebiany AN, Ramphal NS, Karram K, Di Liberto G, Novkovic T, Klein M, Marini F, Kreutzfeldt M, Härtner F, Lacher SM, Bopp T, Mittmann T, Merkler D, Waisman A. Microglial A20 Protects the Brain from CD8 T-Cell-Mediated Immunopathology. Cell Reports. 2020;30(5):1585-1597.e6. doi:10.1016/j.celrep.2019.12.097 DOI: 10.1016/j.celrep.2019.12.097
Gaonkar KS, Marini F, Rathi KS, Jain P, Zhu Y, Chimicles NA, Brown MA, Naqvi AS, Zhang B, Storm PB, Maris JM, Raman P, Resnick AC, Strauch K, Taroni JN, Rokita JL. annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions. BMC Bioinformatics. 2020;21(1). doi:10.1186/s12859-020-03922-7 DOI: 10.1186/s12859-020-03922-7
Hauptmann J, Johann L, Marini F, Kitic M, Colombo E, Mufazalov IA, Krueger M, Karram K, Moos S, Wanke F, Kurschus FC, Klein M, Cardoso S, Strauß J, Bolisetty S, Lühder F, Schwaninger M, Binder H, Bechman I, Bopp T, Agarwal A, Soares MP, Regen T, Waisman A. Interleukin-1 promotes autoimmune neuroinflammation by suppressing endothelial heme oxygenase-1 at the blood–brain barrier. Acta Neuropathologica. 2020;140(4):549-567. doi:10.1007/s00401-020-02187-x DOI: 10.1007/s00401-020-02187-x
Amezquita RA, Lun ATL, Becht E, Carey VJ, Carpp LN, Geistlinger L, Marini F, Rue-Albrecht K, Risso D, Soneson C, Waldron L, Pagès H, Smith ML, Huber W, Morgan M, Gottardo R, Hicks SC. Orchestrating single-cell analysis with Bioconductor. Nature Methods. 2019;17(2):137-145. doi:10.1038/s41592-019-0654-x DOI: 10.1038/s41592-019-0654-x
Roewe J, Stavrides G, Strueve M, Sharma A, Marini F, Mann A, Smith SA, Kaya Z, Strobl B, Mueller M, Reinhardt C, Morrissey JH, Bosmann M. Bacterial polyphosphates interfere with the innate host defense to infection. Nature Communications. 2020;11(1). doi:10.1038/s41467-020-17639-x DOI: 10.1038/s41467-020-17639-x
Bogucka K, Pompaiah M, Marini F, Binder H, Harms G, Kaulich M, Klein M, Michel C, Radsak MP, Rosigkeit S, Grimminger P, Schild H, Rajalingam K. ERK3/MAPK6 controls IL-8 production and chemotaxis. eLife. 2020;9. doi:10.7554/elife.52511 DOI: 10.7554/eLife.52511

2019

Lückel C, Picard F, Raifer H, Campos Carrascosa L, Guralnik A, Zhang Y, Klein M, Bittner S, Steffen F, Moos S, Marini F, Gloury R, Kurschus FC, Chao YY, Bertrams W, Sexl V, Schmeck B, Bonetti L, Grusdat M, Lohoff M, Zielinski CE, Zipp F, Kallies A, Brenner D, Berger M, Bopp T, Tackenberg B, Huber M. IL-17+ CD8+ T cell suppression by dimethyl fumarate associates with clinical response in multiple sclerosis. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-13731-z DOI: 10.1038/s41467-019-13731-z
Akhtar J, More P, Albrecht S, Marini F, Kaiser W, Kulkarni A, Wojnowski L, Fontaine JF, Andrade-Navarro MA, Silies M, Berger C. TAF-ChIP: an ultra-low input approach for genome-wide chromatin immunoprecipitation assay. Life Science Alliance. 2019;2(4):e201900318. doi:10.26508/lsa.201900318 DOI: 10.26508/lsa.201900318
Marini F, Binder H. pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components. BMC Bioinformatics. 2019;20(1). doi:10.1186/s12859-019-2879-1 DOI: 10.1186/s12859-019-2879-1
Akhtar J, Kreim N, Marini F, Mohana G, Brüne D, Binder H, Roignant JY. Promoter-proximal pausing mediated by the exon junction complex regulates splicing. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-08381-0 DOI: 10.1038/s41467-019-08381-0
Graf C, Wilgenbus P, Pagel S, Pott J, Marini F, Reyda S, Kitano M, Macher-Göppinger S, Weiler H, Ruf W. Myeloid cell–synthesized coagulation factor X dampens antitumor immunity. Science Immunology. 2019;4(39). doi:10.1126/sciimmunol.aaw8405 DOI: 10.1126/sciimmunol.aaw8405
Auer TA, Breit HC, Marini F, Renovanz M, Ringel F, Sommer CJ, Brockmann MA, Tanyildizi Y. Evaluation of the apparent diffusion coefficient in patients with recurrent glioblastoma under treatment with bevacizumab with radiographic pseudoresponse. Journal of Neuroradiology. 2019;46(1):36-43. doi:10.1016/j.neurad.2018.04.002 DOI: 10.1016/j.neurad.2018.04.002

2018

Rue-Albrecht K, Marini F, Soneson C, Lun ATL. iSEE: Interactive SummarizedExperiment Explorer. F1000Research. 2018;7:741. doi:10.12688/f1000research.14966.1 DOI: 10.12688/f1000research.14966.1
Ogorodnikov A, Levin M, Tattikota S, Tokalov S, Hoque M, Scherzinger D, Marini F, Poetsch A, Binder H, Macher-Göppinger S, Probst HC, Tian B, Schaefer M, Lackner KJ, Westermann F, Danckwardt S. Transcriptome 3′end organization by PCF11 links alternative polyadenylation to formation and neuronal differentiation of neuroblastoma. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-07580-5 DOI: 10.1038/s41467-018-07580-5
Haase T, Müller C, Krause J, Röthemeier C, Stenzig J, Kunze S, Waldenberger M, Münzel T, Pfeiffer N, Wild PS, Michal M, Marini F, Karakas M, Lackner KJ, Blankenberg S, Zeller T. Novel DNA Methylation Sites Influence GPR15 Expression in Relation to Smoking. Biomolecules. 2018;8(3):74. doi:10.3390/biom8030074 DOI: 10.3390/biom8030074
Nührenberg TG, Cederqvist M, Marini F, Stratz C, Grüning BA, Trenk D, Binder H, Gilsbach R, Neumann FJ, Hein L. Uncontrolled Diabetes Mellitus Has No Major Influence on the Platelet Transcriptome. BioMed Research International. 2018;2018:1-9. doi:10.1155/2018/8989252 DOI: 10.1155/2018/8989252
Dietrich K, Baumgart J, Eshkind L, Reuter L, Gödtel-Armbrust U, Butt E, Musheev M, Marini F, More P, Grosser T, Niehrs C, Wojnowski L, Mathäs M. Health-Relevant Phenotypes in the Offspring of Mice Given CAR Activators Prior to Pregnancy. Drug Metabolism and Disposition. 2018;46(11):1827-1835. doi:10.1124/dmd.118.082925 DOI: 10.1124/dmd.118.082925

2017

Yurugi H, Marini F, Weber C, David K, Zhao Q, Binder H, Désaubry L, Rajalingam K. Targeting prohibitins with chemical ligands inhibits KRAS-mediated lung tumours. Oncogene. 2017;36(33):4778-4789. doi:10.1038/onc.2017.93 DOI: 10.1038/onc.2017.93
Campos Carrascosa L, Klein M, Kitagawa Y, Lückel C, Marini F, König A, Guralnik A, Raifer H, Hagner-Benes S, Rädler D, Böck A, Kang C, Lohoff M, Garn H, Schaub B, Berberich-Siebelt F, Sakaguchi S, Bopp T, Huber M. Reciprocal regulation of the Il9 locus by counteracting activities of transcription factors IRF1 and IRF4. Nature Communications. 2017;8(1). doi:10.1038/ncomms15366 DOI: 10.1038/ncomms15366
Auer TA, Renovanz M, Marini F, Brockmann MA, Tanyildizi Y. Ischemic stroke and intracranial hemorrhage in patients with recurrent glioblastoma multiforme, treated with bevacizumab. Journal of Neuro-Oncology. 2017;133(3):571-579. doi:10.1007/s11060-017-2467-z DOI: 10.1007/s11060-017-2467-z
Tanyildizi Y, Gökce S, Marini F, Mayer AK, Kirschner S, Hennermann JB, Brockmann MA. Vessel shape alterations of the vertebrobasilar arteries in Mucopolysaccharidosis type IVa (Morquio A) patients. European Journal of Radiology. 2017;93:128-133. doi:10.1016/j.ejrad.2017.05.026 DOI: 10.1016/j.ejrad.2017.05.026
Nikolova T, Marini F, Kaina B. Genotoxicity testing: Comparison of the γH2AX focus assay with the alkaline and neutral comet assays. Mutation Research/Genetic Toxicology and Environmental Mutagenesis. 2017;822:10-18. doi:10.1016/j.mrgentox.2017.07.004 DOI: 10.1016/j.mrgentox.2017.07.004

2016

Poplawski A, Marini F, Hess M, Zeller T, Mazur J, Binder H. Systematically evaluating interfaces for RNA-seq analysis from a life scientist perspective. Briefings in Bioinformatics. 2015;17(2):213-223. doi:10.1093/bib/bbv036 DOI: 10.1093/bib/bbv036
Marini F, Binder H. Development of Applications for Interactive and Reproducible Research: a Case Study. Genomics and Computational Biology. 2016;3(1):39. doi:10.18547/gcb.2017.vol3.iss1.e39 DOI: 10.18547/gcb.2017.vol3.iss1.e39

2015

Bruttger J, Karram K, Wörtge S, Regen T, Marini F, Hoppmann N, Klein M, Blank T, Yona S, Wolf Y, Mack M, Pinteaux E, Müller W, Zipp F, Binder H, Bopp T, Prinz M, Jung S, Waisman A. Genetic Cell Ablation Reveals Clusters of Local Self-Renewing Microglia in the Mammalian Central Nervous System. Immunity. 2015;43(1):92-106. doi:10.1016/j.immuni.2015.06.012 DOI: 10.1016/j.immuni.2015.06.012

2012

Fumagalli M, Fracassetti M, Cagliani R, Forni D, Pozzoli U, Comi GP, Marini F, Bresolin N, Clerici M, Sironi M. An evolutionary history of the selectin gene cluster in humans. Heredity. 2012;109(2):117-126. doi:10.1038/hdy.2012.20 DOI: 10.1038/hdy.2012.20
Cagliani R, Guerini FR, Fumagalli M, Riva S, Agliardi C, Galimberti D, Pozzoli U, Goris A, Dubois B, Fenoglio C, Forni D, Sanna S, Zara I, Pitzalis M, Zoledziewska M, Cucca F, Marini F, Comi GP, Scarpini E, Bresolin N, Clerici M, Sironi M. A Trans-Specific Polymorphism in ZC3HAV1 Is Maintained by Long-Standing Balancing Selection and May Confer Susceptibility to Multiple Sclerosis. Molecular Biology and Evolution. 2012;29(6):1599-1613. doi:10.1093/molbev/mss002 DOI: 10.1093/molbev/mss002

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