A5061096065- Epigenetics and DNA Methylation
- RNA modifications and cancer
- Genetic diversity and population structure
- Chromosomal and Genetic Variations
- Reproductive Biology and Fertility
- RNA Research and Splicing
- Avian ecology and behavior
- Pluripotent Stem Cells Research
- Animal Behavior and Reproduction
- CRISPR and Genetic Engineering
- Genomics and Phylogenetic Studies
- Genetic and phenotypic traits in livestock
- Molecular Biology Techniques and Applications
- Galectins and Cancer Biology
- Hippo pathway signaling and YAP/TAZ
- Pharmacogenetics and Drug Metabolism
- Plant biochemistry and biosynthesis
- Bioinformatics and Genomic Networks
- Glycosylation and Glycoproteins Research
- Cellular Mechanics and Interactions
- Lung Cancer Research Studies
- Chemotherapy-induced cardiotoxicity and mitigation
- Cancer Genomics and Diagnostics
- Mast cells and histamine
- Plant Virus Research Studies
Max Planck Institute for Molecular Genetics
2010-2023
Max Planck Society
2010
Freie Universität Berlin
2010
Abstract Though clinical trials for medical applications of dimethyl sulfoxide (DMSO) reported toxicity in the 1960s, later, FDA classified DMSO safest solvent category. became widely used many biomedical fields and biological effects were overlooked. Meanwhile, science has evolved towards sensitive high-throughput techniques new research areas, including epigenomics microRNAs. Considering its wide use, especially cryopreservation vitro assays, we evaluated effect using these technological...
Presumably, due to a rapid early diversification, major parts of the higher-level phylogeny birds are still resolved controversially in different analyses or considered unresolvable. To address this problem, we produced an avian tree life, which includes molecular sequences one several species ∼90% currently recognized family-level taxa (429 species, 379 genera) including all 106 nonpasserines and 115 passerines (Passeriformes). The unconstrained noncoding 3-prime untranslated region...
Background Colorectal cancer (CRC) is with approximately 1 million cases the third most common worldwide. Extensive research ongoing to decipher underlying genetic patterns hope improve early diagnosis and treatment. In this direction, recent progress in next generation sequencing technologies has revolutionized field of genomics. However, one caveat these studies remains large amount variations identified their interpretation. Methodology/Principal Findings Here we present first work on...
// Pedro Castelo-Branco 1, 2, 3, * , Ricardo Leão 4, 5, Tatiana Lipman 1 Brittany Campbell Donghyun Lee Aryeh Price Cindy Zhang Abolfazl Heidari Derek Stephens Stefan Boerno 6 Hugo Coelho 5 Ana Gomes Celia Domingos 3 Joana D. Apolonio Georg Schäfer 11 Robert G. Bristow 7 Michal R. Schweiger 8, 9 Hamilton 4 Alexandre Zlotta 10 Arnaldo Figueiredo Helmut Klocker Holger Sültmann 12 Uri Tabori Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children,...
When a species successfully colonizes an urban habitat it can be expected that its population rapidly adapts to the new environment but also experiences demographic perturbations. It is, therefore, essential gain understanding of structure and history neighbouring rural populations before studying adaptation at genome level. Here, we investigate burrowing owl (Athene cunicularia), colonized South American cities just few decades ago. We assembled high-quality re-sequenced 137 owls from three...
Abstract Uncovering cellular responses from heterogeneous genomic data is crucial for molecular medicine in particular drug safety. This can be realized by integrating the activities networks of interacting proteins. As proof-of-concept we challenge network modeling with time-resolved proteome, transcriptome and methylome measurements iPSC-derived human 3D cardiac microtissues to elucidate adverse mechanisms anthracycline cardiotoxicity measured four different drugs (doxorubicin, epirubicin,...
Non-small cell lung cancer (NSCLC) is the most common cause of cancer-related deaths worldwide and primarily treated with radiation, surgery, platinum-based drugs like cisplatin carboplatin. The major challenge in treatment NSCLC patients intrinsic or acquired resistance to chemotherapy. Molecular markers predicting outcome are urgently needed.Here, we employed patient-derived xenografts (PDXs) detect predictive methylation biomarkers for platin-based therapies. We used MeDIP-Seq generate...
When a species colonizes an urban habitat, differences in the environment can create novel selection pressures. Successful colonization will further lead to demographic perturbations and genetic drift, which interfere with selection. Here, we test for consistent signals multiple populations of burrowing owl (Athene cunicularia), that colonized South American cities just few decades ago. We sequenced 213 owls from three urban-rural population pairs performed genome-wide comparison against...
Abstract Background The heat shock protein 90 (Hsp90) is required for the stability of many signalling kinases. As a target cancer therapy it allows simultaneous inhibition several pathways. However, its in healthy cells could also lead to severe side effects. This first comprehensive analysis response Hsp90 at kinome level. Methods We quantitatively profiled effects by geldanamycin on one primary (Hs68) and three tumour cell lines (SW480, U2OS, A549) affinity proteomics based immobilized...
Bone is a remarkable dynamic structure, which integrates mechanical and biochemical signaling inputs. Interstitial fluid in the intramedullary space transmits signals derived from compression-induced shear stress (FSS) to stimulate osteoblasts for bone formation. Using flow system human osteoblasts, this study demonstrates how BMP/TGF-β stimuli FSS YAP/TAZ confirms these findings by transcriptome analyses. Here, positively affects phosphorylation of both SMAD1/5 SMAD2/3, respective BMP-...
Owls (Strigiformes) evolved specific adaptations to their nocturnal predatory lifestyle, such as asymmetrical ears, a facial disk, and feather structure allowing silent flight. also share some traits with diurnal raptors other birds, cryptic plumage patterns, reversed sexual size dimorphism, acute vision hearing. The genetic basis of these lifestyle has been studied by candidate gene approaches but rarely genome-wide scans. Here, we used comparative analysis test for selection in the early...
Abstract The data currently described was generated within the EU/FP7 HeCaToS project ( He patic and Ca rdiac To xicity S ystems modeling). aimed to develop an in silico prediction system contribute drug safety assessment for humans. For this purpose, multi-omics of repeated dose toxicity were obtained 10 hepatotoxic cardiotoxic compounds. Most gained from vitro experiments which 3D microtissues (either hepatic or cardiac) exposed a therapeutic (physiologically relevant concentrations...
Abstract Long-read transcriptome sequencing (LRTS) holds the promise to boost our understanding of alternative splicing. Recent advances in accuracy and throughput have diminished major limitations enabled direct quantification isoforms. Considering complexity data broad range potential applications, it is clear that highly flexible, accurate analysis tools are crucial. Here, we present IsoTools, a comprehensive Python-based package, for improvement differential splicing analysis. Iso-Tools...
Abstract Long-read transcriptome sequencing (LRTS) holds the promise to refine our understanding of alternative splicing, however, nature splicing is highly complex, and computational tools need cope with this complexity by maximum flexibility at different steps work-flow. For purpose we developed IsoTools, a Python-based LRTS analysis package. IsoTools provides broad functionality for reconstruction quantification isoforms. Additionally, implemented graph-based method identification events...
Summary IBD is characterized by altered immune reactions and infections are thought to trigger the chronic inflammatory response in IBD. The gut represents a productive reservoir for SARS-CoV-2 aforementioned factors together with immunosuppression used treat likely influencing outcomes of patients COVID-19. We large small intestinal organoids from controls comparatively assess transcriptional epithelium during SARS- CoV-2 infection. Our analysis showed that epithelia exhibit reduced viral...
<h3>Background</h3> Systemic sclerosis (SSc) is an immune-mediated disease, which affects mostly women over 50 years old. Recently, single cell mRNA sequencing techniques (scRNA-seq) have contributed to establish the relevance of different immune types in SSc. However, little known about diversity peripheral blood monocytes, play a central role early inflammatory response and maintenance inflammation <h3>Objectives</h3> Our aim analyze composition monocyte compartment SSc patients disease...