Publications |https://cgm.uni-frankfurt.de/publications/PublicationsHugoBlox Kit (https://hugoblox.com)en-usSat, 01 Aug 2026 00:00:00 +0000https://cgm.uni-frankfurt.de/media/logo.svgPublicationshttps://cgm.uni-frankfurt.de/publications/A categorization of spatial transcriptomics methods for cell–cell communication analysishttps://cgm.uni-frankfurt.de/publications/fischer-2026/Sat, 01 Aug 2026 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/fischer-2026/AtlasLens: Metadata-centric exploration and analysis of single-cell atlaseshttps://cgm.uni-frankfurt.de/publications/ashrafiyan-atlaslens-2026/Wed, 01 Jul 2026 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/ashrafiyan-atlaslens-2026/Comparing machine learning methods predicting transcriptome from epigenome with applications to association studieshttps://cgm.uni-frankfurt.de/publications/behjati-ardakani-comparing-2026/Wed, 01 Jul 2026 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/behjati-ardakani-comparing-2026/Improved RNA-DNA interaction calling suggests RNA-based gene regulation of phenotypic transitionshttps://cgm.uni-frankfurt.de/publications/zehr-improved-2026/Mon, 01 Jun 2026 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/zehr-improved-2026/Predicting gene-specific regulation with transcriptomic and epigenetic single-cell datahttps://cgm.uni-frankfurt.de/publications/rumpf-predicting-2026/Fri, 01 May 2026 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/rumpf-predicting-2026/Prediction and evaluation of Split-ORFs using Ribo-seq datahttps://cgm.uni-frankfurt.de/publications/kalk-prediction-2026/Fri, 01 May 2026 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/kalk-prediction-2026/Probing transcription factor subsets in gene regulatory networkshttps://cgm.uni-frankfurt.de/publications/geis-probing-2026/Fri, 01 May 2026 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/geis-probing-2026/Quantifying Components in a Model Vaccine with Machine-Learning-Augmented Raman Spectroscopyhttps://cgm.uni-frankfurt.de/publications/hahn-quantifying-2026/Fri, 01 May 2026 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/hahn-quantifying-2026/RANKOR: Direct Drug Prioritization from Bulk and Single-Cell Transcriptomic Signatureshttps://cgm.uni-frankfurt.de/publications/katsaouni-rankor-2026/Fri, 01 May 2026 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/katsaouni-rankor-2026/Cell type-specific epigenetic regulatory circuitry of coronary artery disease locihttps://cgm.uni-frankfurt.de/publications/hecker-cell-2026/Sun, 01 Mar 2026 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/hecker-cell-2026/Enhancing KLF15 activity in cardiomyocytes: a novel approach to prevent pathological reprogramming and fibrosis via nuclease-deficient dCas9VPRhttps://cgm.uni-frankfurt.de/publications/schoger-enhancing-2026/Sun, 01 Mar 2026 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/schoger-enhancing-2026/Comparative cross-methodological analysis of the IDH-wildtype glioblastoma tumor microenvironmenthttps://cgm.uni-frankfurt.de/publications/cakmak-comparative-2026/Sun, 01 Feb 2026 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/cakmak-comparative-2026/Hierarchical Representation Learning for Drug Mechanism-of-Action Prediction from Gene Expression Datahttps://cgm.uni-frankfurt.de/publications/katsaouni-hierarchical-2026/Sun, 01 Feb 2026 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/katsaouni-hierarchical-2026/miRXplain: explainable isomiR-aware microRNA target prediction using CLIP-L experiments and hybrid attention transformershttps://cgm.uni-frankfurt.de/publications/maji-mirxplain-2026/Sun, 01 Feb 2026 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/maji-mirxplain-2026/Cystine import and oxidative catabolism fuel vascular growth and repair via nutrient-responsive histone acetylationhttps://cgm.uni-frankfurt.de/publications/drekolia-cystine-2026/Thu, 01 Jan 2026 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/drekolia-cystine-2026/Epigenetic control of metabolic identity across cell typeshttps://cgm.uni-frankfurt.de/publications/pacheco-epigenetic-2025/Mon, 01 Dec 2025 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/pacheco-epigenetic-2025/The transaminase-ω-amidase pathway senses oxidative stress to control glutamine metabolism and α-ketoglutarate levels in endothelial cellshttps://cgm.uni-frankfurt.de/publications/herrle-transaminase-amidase-2025/Mon, 01 Dec 2025 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/herrle-transaminase-amidase-2025/TripLexicon: prediction and analysis of gene regulatory RNA-DNA interactionshttps://cgm.uni-frankfurt.de/publications/warwick-triplexicon-2025/Mon, 01 Dec 2025 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/warwick-triplexicon-2025/Decoding heart failure subtypes with neural networks via differential explanation analysishttps://cgm.uni-frankfurt.de/publications/ruz-jurado-decoding-2025/Sat, 01 Nov 2025 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/ruz-jurado-decoding-2025/Vascular Niches Are the Primary Hotspots in Cardiac Aginghttps://cgm.uni-frankfurt.de/publications/rodriguez-morales-vascular-2025/Sat, 01 Nov 2025 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/rodriguez-morales-vascular-2025/Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standardhttps://cgm.uni-frankfurt.de/publications/lin-pipeline-2025/Wed, 01 Oct 2025 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/lin-pipeline-2025/Revealing microRNA regulation in single cellshttps://cgm.uni-frankfurt.de/publications/maji-revealing-2025/Sun, 01 Jun 2025 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/maji-revealing-2025/STAT3 expression is reduced in cardiac pericytes in HFpEF and its loss reduces cellular adhesion and induces pericyte senescencehttps://cgm.uni-frankfurt.de/publications/vanicek-stat-3-2025/Sun, 01 Jun 2025 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/vanicek-stat-3-2025/A cell type-specific expression atlas of small and total RNA in the heart after myocardial infarctionhttps://cgm.uni-frankfurt.de/publications/maji-cell-2025/Thu, 01 May 2025 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/maji-cell-2025/GeneCOCOA: Detecting context-specific functions of individual genes using co-expression datahttps://cgm.uni-frankfurt.de/publications/zehr-genecocoa-2025/Wed, 01 Jan 2025 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/zehr-genecocoa-2025/Learning Enhancer-Gene associations from Bulk Transcriptomic and Epigenetic Sequencing Data with STITCHIThttps://cgm.uni-frankfurt.de/publications/rumpf-learning-2025/Wed, 01 Jan 2025 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/rumpf-learning-2025/Long non-coding RNAs direct the SWI/SNF complex to cell type-specific enhancershttps://cgm.uni-frankfurt.de/publications/oo-long-2025/Wed, 01 Jan 2025 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/oo-long-2025/Prediction of Enhancer-Gene Interactions Using Chromatin-Conformation Capture and Epigenome Data Using STAREhttps://cgm.uni-frankfurt.de/publications/hecker-prediction-2025/Wed, 01 Jan 2025 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/hecker-prediction-2025/Temporal Expression Analysis to Unravel Gene Regulatory Dynamics by microRNAshttps://cgm.uni-frankfurt.de/publications/maji-temporal-2025/Wed, 01 Jan 2025 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/maji-temporal-2025/A statistical approach for identifying single nucleotide variants that affect transcription factor bindinghttps://cgm.uni-frankfurt.de/publications/baumgarten-statistical-2024/Wed, 01 May 2024 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/baumgarten-statistical-2024/BI-3231, an enzymatic inhibitor of HSD17B13, reduces lipotoxic effects induced by palmitic acid in murine and human hepatocyteshttps://cgm.uni-frankfurt.de/publications/alcober-boquet-bi-3231-2024/Fri, 01 Mar 2024 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/alcober-boquet-bi-3231-2024/A systematic analysis of circRNAs in subnuclear compartmentshttps://cgm.uni-frankfurt.de/publications/brezski-systematic-2024/Mon, 01 Jan 2024 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/brezski-systematic-2024/An AI-based cell segmentation pipeline for studying immune markers from brightfield microscopy imageshttps://cgm.uni-frankfurt.de/publications/kohler-ai-based-2024/Mon, 01 Jan 2024 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/kohler-ai-based-2024/Improved integration of single-cell transcriptome data demonstrates common and unique signatures of heart failure in mice and humanshttps://cgm.uni-frankfurt.de/publications/ruz-jurado-improved-2024/Mon, 01 Jan 2024 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/ruz-jurado-improved-2024/Multiomics analysis identifies novel facilitators of human dopaminergic neuron differentiationhttps://cgm.uni-frankfurt.de/publications/gomez-ramos-multiomics-2024/Mon, 01 Jan 2024 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/gomez-ramos-multiomics-2024/Computational tools for inferring transcription factor activityhttps://cgm.uni-frankfurt.de/publications/hecker-computational-2023/Fri, 01 Dec 2023 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/hecker-computational-2023/The challenges of research data management in cardiovascular science: a DGK and DZHK position paper-executive summaryhttps://cgm.uni-frankfurt.de/publications/steffens-challenges-2023/Sun, 01 Oct 2023 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/steffens-challenges-2023/Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding modelshttps://cgm.uni-frankfurt.de/publications/grau-widespread-2023/Sun, 01 Oct 2023 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/grau-widespread-2023/Alterations in the hepatocyte epigenetic landscape in steatosishttps://cgm.uni-frankfurt.de/publications/maji-alterations-2023/Sat, 01 Jul 2023 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/maji-alterations-2023/Circular RNA circPLOD2 regulates pericyte function by targeting the transcription factor KLF4https://cgm.uni-frankfurt.de/publications/glaser-circular-2023/Sat, 01 Jul 2023 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/glaser-circular-2023/CVD-associated SNPs with regulatory potential reveal novel non-coding disease geneshttps://cgm.uni-frankfurt.de/publications/zhu-cvd-associated-2023/Sat, 01 Jul 2023 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/zhu-cvd-associated-2023/Pathogenetic mechanisms and therapeutic approaches of acute-to-chronic liver failurehttps://cgm.uni-frankfurt.de/publications/schierwagen-pathogenetic-2023/Sat, 01 Jul 2023 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/schierwagen-pathogenetic-2023/Efficiently quantifying DNA methylation for bulk- and single-cell bisulfite datahttps://cgm.uni-frankfurt.de/publications/fischer-efficiently-2023/Thu, 01 Jun 2023 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/fischer-efficiently-2023/A combined computational and functional approach identifies IGF2BP2 as a driver of chemoresistance in a wide array of pre-clinical models of colorectal cancerhttps://cgm.uni-frankfurt.de/publications/kendzia-combined-2023/Mon, 01 May 2023 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/kendzia-combined-2023/Interaction of inherited genetic variants in the NLRP3 inflammasome/IL-6 pathway with acquired clonal hematopoiesis to modulate mortality risk in patients with HFrEFhttps://cgm.uni-frankfurt.de/publications/cremer-interaction-2023/Mon, 01 May 2023 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/cremer-interaction-2023/TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factorshttps://cgm.uni-frankfurt.de/publications/hoffmann-tf-prioritizer-2023/Mon, 01 May 2023 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/hoffmann-tf-prioritizer-2023/Dataset of single nucleotide polymorphisms of immune-associated genes in patients with SARS-CoV-2 infectionhttps://cgm.uni-frankfurt.de/publications/katsaouni-dataset-2023/Sun, 01 Jan 2023 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/katsaouni-dataset-2023/Multimodal analysis methods in predictive biomedicinehttps://cgm.uni-frankfurt.de/publications/qoku-multimodal-2023/Sun, 01 Jan 2023 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/qoku-multimodal-2023/The adapted Activity-By-Contact model for enhancer-gene assignment and its application to single-cell datahttps://cgm.uni-frankfurt.de/publications/hecker-adapted-2023/Sun, 01 Jan 2023 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/hecker-adapted-2023/The endothelial-enriched lncRNA LINC00607 mediates angiogenic functionhttps://cgm.uni-frankfurt.de/publications/boos-endothelial-enriched-2023/Sun, 01 Jan 2023 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/boos-endothelial-enriched-2023/DOT1L regulates chamber-specific transcriptional networks during cardiogenesis and mediates postnatal cell cycle withdrawalhttps://cgm.uni-frankfurt.de/publications/cattaneo-dot-1-l-2022/Thu, 01 Dec 2022 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/cattaneo-dot-1-l-2022/A universal model of RNA.DNA:DNA triplex formation accurately predicts genome-wide RNA-DNA interactionshttps://cgm.uni-frankfurt.de/publications/warwick-universal-2022/Tue, 01 Nov 2022 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/warwick-universal-2022/HIF1α-AS1 is a DNA:DNA:RNA triplex-forming lncRNA interacting with the HUSH complexhttps://cgm.uni-frankfurt.de/publications/leisegang-hif-1-as-1-2022/Tue, 01 Nov 2022 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/leisegang-hif-1-as-1-2022/Broad domains of histone marks in the highly compact Paramecium macronuclear genomehttps://cgm.uni-frankfurt.de/publications/drews-broad-2022/Fri, 01 Apr 2022 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/drews-broad-2022/Nuclear receptor activation shapes spatial genome organization essential for gene expression control: lessons learned from the vitamin D receptorhttps://cgm.uni-frankfurt.de/publications/warwick-nuclear-2022/Fri, 01 Apr 2022 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/warwick-nuclear-2022/Energy efficient convolutional neural networks for arrhythmia detectionhttps://cgm.uni-frankfurt.de/publications/katsaouni-energy-2022/Tue, 01 Mar 2022 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/katsaouni-energy-2022/Comparative analysis of common alignment tools for single-cell RNA sequencinghttps://cgm.uni-frankfurt.de/publications/bruning-comparative-2022/Sat, 01 Jan 2022 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/bruning-comparative-2022/Two Piwis with Ago-like functions silence somatic genes at the chromatin levelhttps://cgm.uni-frankfurt.de/publications/drews-two-2021/Mon, 01 Nov 2021 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/drews-two-2021/Dysregulation of cholesterol homeostasis in human lung cancer tissue and tumour-associated macrophageshttps://cgm.uni-frankfurt.de/publications/hoppstadter-dysregulation-2021/Fri, 01 Oct 2021 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/hoppstadter-dysregulation-2021/Integrative analysis of epigenetics data identifies gene-specific regulatory elementshttps://cgm.uni-frankfurt.de/publications/schmidt-integrative-2021/Fri, 01 Oct 2021 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/schmidt-integrative-2021/Computational prediction of CRISPR-impaired non-coding regulatory regionshttps://cgm.uni-frankfurt.de/publications/baumgarten-computational-2021/Thu, 01 Jul 2021 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/baumgarten-computational-2021/Machine learning based disease prediction from genotype datahttps://cgm.uni-frankfurt.de/publications/katsaouni-machine-2021/Thu, 01 Jul 2021 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/katsaouni-machine-2021/Fast detection of differential chromatin domains with SCIDDOhttps://cgm.uni-frankfurt.de/publications/ebert-fast-2021/Tue, 01 Jun 2021 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/ebert-fast-2021/Fostering accessible online education using Galaxy as an e-learning platformhttps://cgm.uni-frankfurt.de/publications/serrano-solano-fostering-2021/Sat, 01 May 2021 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/serrano-solano-fostering-2021/A hierarchical regulatory network analysis of the vitamin D induced transcriptome reveals novel regulators and complete VDR dependency in monocyteshttps://cgm.uni-frankfurt.de/publications/warwick-hierarchical-2021/Mon, 01 Mar 2021 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/warwick-hierarchical-2021/Machine learning for deciphering cell heterogeneity and gene regulationhttps://cgm.uni-frankfurt.de/publications/scherer-machine-2021/Mon, 01 Mar 2021 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/scherer-machine-2021/SPONGEdb: a pan-cancer resource for competing endogenous RNA interactionshttps://cgm.uni-frankfurt.de/publications/hoffmann-spongedb-2021/Mon, 01 Mar 2021 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/hoffmann-spongedb-2021/CpG content-dependent associations between transcription factors and histone modificationshttps://cgm.uni-frankfurt.de/publications/fischer-cpg-2021/Fri, 01 Jan 2021 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/fischer-cpg-2021/Single cell sequencing reveals endothelial plasticity with transient mesenchymal activation after myocardial infarctionhttps://cgm.uni-frankfurt.de/publications/tombor-single-2021/Fri, 01 Jan 2021 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/tombor-single-2021/Synthesis of Power-Efficient Analog Neural Networks for Signal Processinghttps://cgm.uni-frankfurt.de/publications/florian-aul-synthesis-2020/Sun, 01 Nov 2020 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/florian-aul-synthesis-2020/Deletion of NoxO1 limits atherosclerosis development in female micehttps://cgm.uni-frankfurt.de/publications/buchmann-deletion-2020/Thu, 01 Oct 2020 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/buchmann-deletion-2020/Prediction of single-cell gene expression for transcription factor analysishttps://cgm.uni-frankfurt.de/publications/behjati-ardakani-prediction-2020/Thu, 01 Oct 2020 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/behjati-ardakani-prediction-2020/EpiRegio: analysis and retrieval of regulatory elements linked to geneshttps://cgm.uni-frankfurt.de/publications/baumgarten-epiregio-2020/Wed, 01 Jul 2020 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/baumgarten-epiregio-2020/Altered glucocorticoid metabolism represents a feature of macroph-aginghttps://cgm.uni-frankfurt.de/publications/valbuena-perez-altered-2020/Mon, 01 Jun 2020 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/valbuena-perez-altered-2020/The endocannabinoid anandamide has an anti-inflammatory effect on CCL2 expression in vascular smooth muscle cellshttps://cgm.uni-frankfurt.de/publications/pfluger-muller-endocannabinoid-2020/Wed, 01 Apr 2020 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/pfluger-muller-endocannabinoid-2020/Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Datahttps://cgm.uni-frankfurt.de/publications/chakraborty-chromatyping-2020/Sun, 01 Mar 2020 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/chakraborty-chromatyping-2020/Improved linking of motifs to their TFs using domain informationhttps://cgm.uni-frankfurt.de/publications/baumgarten-improved-2020/Sun, 01 Mar 2020 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/baumgarten-improved-2020/SRSF7 maintains its homeostasis through the expression of Split-ORFs and nuclear body assemblyhttps://cgm.uni-frankfurt.de/publications/konigs-srsf-7-2020/Sun, 01 Mar 2020 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/konigs-srsf-7-2020/Feeding exogenous dsRNA interferes with endogenous sRNA accumulation in Parameciumhttps://cgm.uni-frankfurt.de/publications/karunanithi-feeding-2020/Sat, 01 Feb 2020 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/karunanithi-feeding-2020/Integrative prediction of gene expression with chromatin accessibility and conformation datahttps://cgm.uni-frankfurt.de/publications/schmidt-integrative-2020/Sat, 01 Feb 2020 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/schmidt-integrative-2020/Yeast Viral Killer Toxin K1 Induces Specific Host Cell Adaptions via Intrinsic Selection Pressurehttps://cgm.uni-frankfurt.de/publications/gier-yeast-2020/Sat, 01 Feb 2020 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/gier-yeast-2020/AERON: Transcript quantification and gene-fusion detection using long readshttps://cgm.uni-frankfurt.de/publications/rautiainen-aeron-2020/Wed, 01 Jan 2020 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/rautiainen-aeron-2020/The mRNA-binding Protein TTP/ZFP36 in Hepatocarcinogenesis and Hepatocellular Carcinomahttps://cgm.uni-frankfurt.de/publications/krohler-mrna-binding-2019/Fri, 01 Nov 2019 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/krohler-mrna-binding-2019/Unique and assay specific features of NOMe-, ATAC- and DNase I-seq datahttps://cgm.uni-frankfurt.de/publications/nordstrom-unique-2019/Fri, 01 Nov 2019 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/nordstrom-unique-2019/Exogenous RNAi mechanisms contribute to transcriptome adaptation by phased siRNA clusters in Parameciumhttps://cgm.uni-frankfurt.de/publications/karunanithi-exogenous-2019/Sun, 01 Sep 2019 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/karunanithi-exogenous-2019/Phenotypic Plasticity of Fibroblasts during Mammary Carcinoma Developmenthttps://cgm.uni-frankfurt.de/publications/elwakeel-phenotypic-2019/Sun, 01 Sep 2019 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/elwakeel-phenotypic-2019/The lncRNA Locus Handsdown Regulates Cardiac Gene Programs and Is Essential for Early Mouse Developmenthttps://cgm.uni-frankfurt.de/publications/ritter-lncrna-2019/Sun, 01 Sep 2019 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/ritter-lncrna-2019/Large-scale inference of competing endogenous RNA networks with sparse partial correlationhttps://cgm.uni-frankfurt.de/publications/list-large-scale-2019/Mon, 01 Jul 2019 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/list-large-scale-2019/Transcriptomics of a KDELR1 knockout cell line reveals modulated cell adhesion propertieshttps://cgm.uni-frankfurt.de/publications/blum-transcriptomics-2019/Mon, 01 Jul 2019 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/blum-transcriptomics-2019/TEPIC 2-an extended framework for transcription factor binding prediction and integrative epigenomic analysishttps://cgm.uni-frankfurt.de/publications/schmidt-tepic-2019/Wed, 01 May 2019 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/schmidt-tepic-2019/Improving in-silico normalization using read weightshttps://cgm.uni-frankfurt.de/publications/durai-improving-2019/Fri, 01 Mar 2019 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/durai-improving-2019/Identification of transcription factor binding sites using ATAC-seqhttps://cgm.uni-frankfurt.de/publications/li-identification-2019/Fri, 01 Feb 2019 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/li-identification-2019/On the problem of confounders in modeling gene expressionhttps://cgm.uni-frankfurt.de/publications/schmidt-problem-2019/Fri, 01 Feb 2019 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/schmidt-problem-2019/Temporal enhancer profiling of parallel lineages identifies AHR and GLIS1 as regulators of mesenchymal multipotencyhttps://cgm.uni-frankfurt.de/publications/gerard-temporal-2019/Fri, 01 Feb 2019 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/gerard-temporal-2019/Automated analysis of small RNA datasets with RAPIDhttps://cgm.uni-frankfurt.de/publications/karunanithi-automated-2019/Tue, 01 Jan 2019 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/karunanithi-automated-2019/Hepatocellular Carcinoma and Nuclear Paraspeckles: Induction in Chemoresistance and Prediction for Poor Survivalhttps://cgm.uni-frankfurt.de/publications/kessler-hepatocellular-2019/Tue, 01 Jan 2019 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/kessler-hepatocellular-2019/Transcriptome Kinetics of Saccharomyces cerevisiae in Response to Viral Killer Toxin K1https://cgm.uni-frankfurt.de/publications/gier-transcriptome-2019/Tue, 01 Jan 2019 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/gier-transcriptome-2019/Analysis of Cell Type-Specific Effects of MicroRNA-92a Provides Novel Insights Into Target Regulation and Mechanism of Actionhttps://cgm.uni-frankfurt.de/publications/rogg-analysis-2018/Thu, 01 Nov 2018 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/rogg-analysis-2018/Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promotershttps://cgm.uni-frankfurt.de/publications/behjati-ardakani-integrative-2018/Thu, 01 Nov 2018 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/behjati-ardakani-integrative-2018/In silico read normalization using set multi-cover optimizationhttps://cgm.uni-frankfurt.de/publications/durai-silico-2018/Mon, 01 Oct 2018 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/durai-silico-2018/Transgenic expression of the RNA binding protein IMP2 stabilizes miRNA targets in murine microsteatosishttps://cgm.uni-frankfurt.de/publications/dehghani-amirabad-transgenic-2018/Mon, 01 Oct 2018 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/dehghani-amirabad-transgenic-2018/An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasetshttps://cgm.uni-frankfurt.de/publications/schmidt-ontology-based-2018/Sat, 01 Sep 2018 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/schmidt-ontology-based-2018/JAMI: fast computation of conditional mutual information for ceRNA network analysishttps://cgm.uni-frankfurt.de/publications/hornakova-jami-2018/Sat, 01 Sep 2018 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/hornakova-jami-2018/Environmental Temperature Controls Accumulation of Transacting siRNAs Involved in Heterochromatin Formationhttps://cgm.uni-frankfurt.de/publications/pirritano-environmental-2018/Thu, 01 Feb 2018 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/pirritano-environmental-2018/More than the \"Killer Trait\": Infection with the Bacterial Endosymbiont Caedibacter taeniospiralis Causes Transcriptomic Modulation in Paramecium Hosthttps://cgm.uni-frankfurt.de/publications/grosser-more-2018/Thu, 01 Feb 2018 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/grosser-more-2018/Predicting transcription factor binding using ensemble random forest modelshttps://cgm.uni-frankfurt.de/publications/behjati-ardakani-predicting-2018/Mon, 01 Jan 2018 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/behjati-ardakani-predicting-2018/The long non-coding RNA H19 suppresses carcinogenesis and chemoresistance in hepatocellular carcinomahttps://cgm.uni-frankfurt.de/publications/schultheiss-long-2017/Tue, 01 Aug 2017 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/schultheiss-long-2017/RegulatorTrail: a web service for the identification of key transcriptional regulatorshttps://cgm.uni-frankfurt.de/publications/kehl-regulatortrail-2017/Sat, 01 Jul 2017 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/kehl-regulatortrail-2017/Combining transcription factor binding affinities with open-chromatin data for accurate gene expression predictionhttps://cgm.uni-frankfurt.de/publications/schmidt-combining-2017/Sun, 01 Jan 2017 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/schmidt-combining-2017/Epigenomic Profiling of Human CD4+ T Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Developmenthttps://cgm.uni-frankfurt.de/publications/durek-epigenomic-2016/Tue, 01 Nov 2016 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/durek-epigenomic-2016/The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discoveryhttps://cgm.uni-frankfurt.de/publications/stunnenberg-international-2016/Tue, 01 Nov 2016 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/stunnenberg-international-2016/Two sets of RNAi components are required for heterochromatin formation in trans triggered by truncated transgeneshttps://cgm.uni-frankfurt.de/publications/gotz-two-2016/Fri, 01 Jul 2016 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/gotz-two-2016/Informed kmer selection for de novo transcriptome assemblyhttps://cgm.uni-frankfurt.de/publications/durai-informed-2016/Wed, 01 Jun 2016 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/durai-informed-2016/De novo ChIP-seq analysishttps://cgm.uni-frankfurt.de/publications/he-novo-2015/Tue, 01 Sep 2015 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/he-novo-2015/Epigenetic regulation of serotype expression antagonizes transcriptome dynamics in Paramecium tetraureliahttps://cgm.uni-frankfurt.de/publications/cheaib-epigenetic-2015/Sat, 01 Aug 2015 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/cheaib-epigenetic-2015/A general concept for consistent documentation of computational analyseshttps://cgm.uni-frankfurt.de/publications/ebert-general-2015/Thu, 01 Jan 2015 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/ebert-general-2015/Fiona: a parallel and automatic strategy for read error correctionhttps://cgm.uni-frankfurt.de/publications/schulz-fiona-2014/Mon, 01 Sep 2014 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/schulz-fiona-2014/Letting the data speak for themselves: a fully Bayesian approach to transcriptome assemblyhttps://cgm.uni-frankfurt.de/publications/schulz-letting-2014/Wed, 01 Jan 2014 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/schulz-letting-2014/Assessment of transcript reconstruction methods for RNA-seqhttps://cgm.uni-frankfurt.de/publications/steijger-assessment-2013/Sun, 01 Dec 2013 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/steijger-assessment-2013/Reconstructing dynamic microRNA-regulated interaction networkshttps://cgm.uni-frankfurt.de/publications/schulz-reconstructing-2013/Sun, 01 Sep 2013 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/schulz-reconstructing-2013/Probabilistic error correction for RNA sequencinghttps://cgm.uni-frankfurt.de/publications/le-probabilistic-2013/Wed, 01 May 2013 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/le-probabilistic-2013/Bayesian ontology querying for accurate and noise-tolerant semantic searcheshttps://cgm.uni-frankfurt.de/publications/bauer-bayesian-2012/Mon, 01 Oct 2012 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/bauer-bayesian-2012/DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression datahttps://cgm.uni-frankfurt.de/publications/schulz-drem-2012/Wed, 01 Aug 2012 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/schulz-drem-2012/Oases: robust de novo RNA-seq assembly across the dynamic range of expression levelshttps://cgm.uni-frankfurt.de/publications/schulz-oases-2012/Sun, 01 Apr 2012 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/schulz-oases-2012/Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerShttps://cgm.uni-frankfurt.de/publications/emde-detecting-2012/Thu, 01 Mar 2012 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/emde-detecting-2012/Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood countshttps://cgm.uni-frankfurt.de/publications/goke-estimation-2012/Thu, 01 Mar 2012 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/goke-estimation-2012/A tandem sequence motif acts as a distance-dependent enhancer in a set of genes involved in translation by binding the proteins NonO and SFPQhttps://cgm.uni-frankfurt.de/publications/roepcke-tandem-2011/Thu, 01 Dec 2011 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/roepcke-tandem-2011/Exact score distribution computation for ontological similarity searcheshttps://cgm.uni-frankfurt.de/publications/schulz-exact-2011/Tue, 01 Nov 2011 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/schulz-exact-2011/DECOD: fast and accurate discriminative DNA motif findinghttps://cgm.uni-frankfurt.de/publications/huggins-decod-2011/Thu, 01 Sep 2011 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/huggins-decod-2011/Integrative analysis of genomic, functional and protein interaction data predicts long-range enhancer-target gene interactionshttps://cgm.uni-frankfurt.de/publications/rodelsperger-integrative-2011/Fri, 01 Apr 2011 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/rodelsperger-integrative-2011/Prediction of alternative isoforms from exon expression levels in RNA-Seq experimentshttps://cgm.uni-frankfurt.de/publications/richard-prediction-2010/Tue, 01 Jun 2010 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/richard-prediction-2010/Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short readshttps://cgm.uni-frankfurt.de/publications/ye-pindel-2009/Sun, 01 Nov 2009 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/ye-pindel-2009/Short ultraconserved promoter regions delineate a class of preferentially expressed alternatively spliced transcriptshttps://cgm.uni-frankfurt.de/publications/rodelsperger-short-2009/Sun, 01 Nov 2009 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/rodelsperger-short-2009/Clinical diagnostics in human genetics with semantic similarity searches in ontologieshttps://cgm.uni-frankfurt.de/publications/kohler-clinical-2009/Thu, 01 Oct 2009 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/kohler-clinical-2009/A global view of gene activity and alternative splicing by deep sequencing of the human transcriptomehttps://cgm.uni-frankfurt.de/publications/sultan-global-2008/Fri, 01 Aug 2008 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/sultan-global-2008/Mapping translocation breakpoints by next-generation sequencinghttps://cgm.uni-frankfurt.de/publications/chen-mapping-2008/Tue, 01 Jul 2008 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/chen-mapping-2008/A short ultraconserved sequence drives transcription from an alternate FBN1 promoterhttps://cgm.uni-frankfurt.de/publications/guo-short-2008/Tue, 01 Jan 2008 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/guo-short-2008/The generalised k-Truncated Suffix Tree for time-and space-efficient searches in multiple DNA or protein sequenceshttps://cgm.uni-frankfurt.de/publications/schulz-generalised-2008/Tue, 01 Jan 2008 00:00:00 +0000https://cgm.uni-frankfurt.de/publications/schulz-generalised-2008/