Dezső Módos

Imperial College London | Imperial · Department of Metabolism, Digestion and Reproduction

Extensive cross-talk between signaling pathways is required to integrate the myriad of extracellular signal combinations at the cellular level. Gene duplication events may lead to the emergence of novel functions, leaving groups of similar genes - termed paralogs - in the genome. To distinguish critical paralog groups (CPGs) from other paralogs in...

Even targeted chemotherapies against solid cancers show a moderate success increasing the need to novel targeting strategies. To address this problem, we designed a systems-level approach investigating the neighbourhood of mutated or differentially expressed cancer-related proteins in four major solid cancers (colon, breast, liver and lung). Using...

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represents an unprecedented worldwide health problem. Although the primary site of infection is the lung, growing evidence points towards a crucial role of the intestinal epithelium. Yet, the exact effects of viral infection and the role of intestinal epithelial-immune cell interactions i...

We describe a precision medicine workflow, the integrated single nucleotide polymorphism network platform (iSNP), designed to determine the mechanisms by which SNPs affect cellular regulatory networks, and how SNP co-occurrences contribute to disease pathogenesis in ulcerative colitis (UC). Using SNP profiles of 378 UC patients we map the regulator...

The toxicogenomics field aims to understand and predict toxicity by using ‘omics’ data in order to study systems-level responses to compound treatments. In recent years there has been a rapid increase in publicly available toxicological and ‘omics’ data, particularly gene expression data, and a corresponding development of methods for its analysis....

Macroautophagy/autophagy is a highly-conserved catabolic process eliminating dysfunctional cellular components and invading pathogens. Autophagy malfunction contributes to disorders such as cancer, neurodegenerative and inflammatory diseases. Understanding autophagy regulation in health and disease has been the focus of the last decades. We previou...

Autophagy is a highly-conserved catabolic process eliminating dysfunctional cellular components and invading pathogens. Autophagy malfunction contributes to disorders such as cancer, neurodegenerative and inflammatory diseases. Understanding autophagy regulation in health and disease has been the focus of the last decades. We previously provided an...

Background Single nucleotide polymorphisms (SNP) associated with Crohn’s disease (CD) are in both protein-coding and non-coding regions of the genome. Interpreting the effect of non-coding regulatory SNPs is challenging. We previously developed the iSNP pipeline, which determines how SNPs in transcription factor (TF) binding sites and miRNA target...

Background Cytokines are small peptides that signal between a variety of cell types and are one of the fundamental communication elements of the immune system. A variety of cytokine—cytokine interactions have previously been investigated in the literature, describing cytokines activating or inhibiting other cytokines in target cell types, and thus...

Increasing evidence points towards the key role of the epithelium in the systemic and over-activated immune response to viral infection, including SARS-CoV-2 infection. Yet, how viral infection alters epithelial–immune cell interactions regulating inflammatory responses, is not well known. Available experimental approaches are insufficient to prope...

Triple negative breast cancer (TNBC) is currently associated with a lack of treatment options. Arsenic derivatives have shown antitumoral activity both in vitro and in vivo; however, their mode of action is not completely understood. In this work we evaluate the response to arsenate of the double positive MCF-7 breast cancer cell line as well as of...

Patients with inflammatory bowel disease (IBD) are known to have perturbations in microRNA (miRNA) levels as well as altered miRNA regulation. Although experimental methods have provided initial insights into the functional consequences that may arise due to these changes, researchers are increasingly utilising novel bioinformatics approaches to fu...

Background Humans are colonized by complex microbial communities which contribute to physiological processes in the host. The communication between microbes and host is crucial to maintain the homeostasis and gut health. Disruption in the microbiome composition leads to increased inflammation and appearance of diseases, such as inflammatory bowel d...

Inflammatory bowel disease (IBD) is a chronic immune-mediated inflammatory disorder of the gastrointestinal tract that arises due to complex interactions between host genetic risk factors, environmental factors, and a dysbiotic gut microbiota. Although metagenomic approaches have attempted to characterise the dysbiosis occurring in IBD, the precise...

The gastrointestinal (GI) tract harbours a complex microbial community, which contributes to its homeostasis. A disrupted microbiome can cause GI-related diseases, including inflammatory bowel disease (IBD), therefore identifying host-microbe interactions is crucial for better understanding gut health. Bacterial extracellular vesicles (BEVs), relea...

Background A subset of mucosal CD4+ T-cells expressing the NK cell receptor NKG2D (encoded by the KLRK1 gene) are enriched in patients with Crohn’s Disease (CD). In pre-clinical models of colitis, NKG2D expression was confined to a subset of colonic CD4+ T-cells that hyper-expressed interferon gamma. However, the functional role of these cells in m...

Background Intercellular communication mediated by cytokines is critical to the development of immune responses, particularly in the context of chronic immune-mediated disorders such as inflammatory bowel disease (IBD). By releasing these small molecular weight peptides, the source cells can influence numerous intracellular processes in the target...

Analyzing the relationships among various drugs is an essential issue in the field of computational biology. Different kinds of informative knowledge, such as drug repurposing, can be extracted from drug-drug relationships. Scientific literature represents a rich source for the retrieval of knowledge about the relationships between biological conce...

Inflammatory bowel disease (IBD) is a chronic immune-mediated condition arising due to complex interactions between multiple genetic and environmental factors. Despite recent advances, the pathogenesis of the condition is not fully understood and patients still experience suboptimal clinical outcomes. Over the past few years, investigators are incr...

Signaling networks represent the molecular mechanisms controlling a cell's response to various internal or external stimuli. Most currently available signaling databases contain only a part of the complex network of intertwining pathways, leaving out key interactions or processes. Hence, we have developed SignaLink3 (http://signalink.org/), a value...

Intercellular communication mediated by cytokines is critical to the development of immune responses, particularly in the context of infectious and inflammatory diseases. By releasing these small molecular weight peptides, the source cells can influence numerous intracellular processes in the target cells, including the secretion of other cytokines...

Intercellular communication mediated by cytokines is critical to the development of immune responses, particularly in the context of infectious and inflammatory diseases. By releasing these small molecular weight peptides, the source cells can influence numerous intracellular processes in the target cells, including the secretion of other cytokines...

Recent work introduces a powerful new web tool that enables a faster and statistically more reliable data mining of transcriptomics and metatranscriptomics for inflammatory bowel disease (IBD) research.

Background Intercellular communication is essential for growing and differentiating in multicellular organisms by transducing the signal from cell to cell. Despite its importance, the molecular background is less discovered due to the lack of data. This gap has started to be addressed with the appearance of single-cell omics approaches providing an...

Background During inflammatory bowel disease the mucosal immune system is altered. The mucosal immune cells are communicating through the various cytokines. Single cell and small volume RNA-seq and proteomics approaches make the investigation of cytokine networks plausible However the lack of specific resources make such efforts hard. Methods To a...

Background Cell functions are regulated by signalling pathways that often cross-talk with each other. These cross-talks are usually cell-type specific and, as we showed earlier, often mediated by so called critical paralog proteins (proteins resulted due to gene duplication but then diverged both in terms of their regulation and their functions). A...

Background Ulcerative Colitis (UC) associated single nucleotide polymorphisms (SNP) are mostly in non-coding regions of the genome. Because of that, it has been challenging to determine their role in the disease onset and severity. We have previously developed an integrative workflow (termed iSNP) to understand better how these SNPs are involved in...

The gastrointestinal (GI) tract is inhabited by a complex microbial community, which contributes to its homeostasis. Disrupted microbiome can cause GI-related diseases, including inflammatory bowel disease, therefore identifying host-microbe interactions is crucial for better understanding gut health. Bacterial extracellular vesicles (BEVs), releas...

Hyper-induction of pro-inflammatory cytokines, also known as a cytokine storm or cytokine release syndrome (CRS), is one of the key aspects of the currently ongoing SARS-CoV-2 pandemic. This process occurs when a large number of innate and adaptive immune cells activate and start producing pro-inflammatory cytokines, establishing an exacerbated fee...

Molecular knowledge of biological processes is a cornerstone in omics data analysis. Applied to single-cell data, such analyses provide mechanistic insights into individual cells and their interactions. However, knowledge of intercellular communication is scarce, scattered across resources, and not linked to intracellular processes. To address this...

The SARS-CoV-2 pandemic of 2020 has mobilised scientists around the globe to research all aspects of the coronavirus virus and its infection. For fruitful and rapid investigation of viral pathomechanisms, a collaborative and interdisciplinary approach is required. Therefore, we have developed ViralLink: a systems biology workflow which reconstructs...

Dichapetalum madagascariense Poir (Dichapetalaceae) is traditionally used to treat bacterial infections, jaundice, urethritis and viral hepatitis in Africa. Its root contains a broad spectrum of biologically active dichapetalins. To evaluate the plant's effect on human MCF-7 cells and its' antibacterial and antiparasitic potentials, we isolated and...

The Traditional Chinese Medicine (TCM) formulation Shexiang Baoxin Pill (SBP) is commonly used in the treatment of coronary heart disease (CHD) in East Asia and regarded to promote the regulation of angiogenesis and to improve endothelial function. SBP comprises of seven TCM materials; however, the interactions of their effects in a biological syst...

It is becoming increasingly clear that bacterial extracellular vesicles (BEVs) produced by members of the intestinal microbiota can contribute to microbe-host cell interactions that impact on host health. A major unresolved question is the nature of the cargo packaged into these BEVs and how they can impact on host cell function. Here we have analy...

Hyper-induction of pro-inflammatory cytokines, also known as a cytokine storm or cytokine release syndrome (CRS) is one of the key aspects of the currently ongoing SARS-CoV-2 pandemic. This process occurs when a large number of innate and adaptive immune cells are activated, and start producing pro-inflammatory cytokines, establishing an exacerbate...

Pathway analysis is an informative method for comparing and contrasting drug-induced gene expression in cellular systems. Here, we define the effects of the marine natural product fucoxanthin, separately and in combination with the prototypic phosphatidylinositol 3-kinase (PI3K) inhibitor LY-294002, on gene expression in a well-established human gl...

Molecular knowledge of biological processes is a cornerstone in the analysis of omics data. Applied to single-cell data, such analyses can provide mechanistic insights into individual cells and their interactions. However, knowledge of intercellular communication is scarce, scattered across different resources, and not linked to intracellular proce...

Investigating the interactions among various drugs is an indispensable issue in the field of computational biology. Scientific literature represents a rich source for the retrieval of knowledge about the interactions between drugs. Predicting drug-drug interaction (DDI) types will help biologists to evade hazardous drug interactions and support the...

The SARS-CoV-2 pandemic of 2020 has mobilised scientists around the globe to research all aspects of the coronavirus virus and its infection. For fruitful and rapid investigation of viral pathomechanisms, a collaborative and interdisciplinary approach is required. Therefore, we have developed ViralLink: a systems biology workflow which reconstructs...

Background Genome-wide association studies have deciphered the single nucleotide poly- morphisms (SNPs) which are responsible for ulcerative colitis (UC) susceptibility. However, to understand how these SNPs are involved in UC, additional methods are necessary. One such approach is in silico network propagation modelling, which can discover how the...

Discovering important proteins in Protein-Protein Interaction (PPI) networks has attracted a lot of attention in recent years. Most of the previous work applies different network centrality measures such as Closeness, Betweenness, PageRank and many others to discover the most influential proteins in PPI networks. Although entropy is a well-known gr...

Background Genome-wide association studies have deciphered the single nucleotide polymorphisms (SNPs) which are responsible for ulcerative colitis (UC) susceptibility. However, to understand how these SNPs are involved in UC, additional methods are necessary. One such approach is in silico network propagation modelling, which can discover how the e...

Current in vitro models for hepatotoxicity commonly suffer from low detection rates due to incomplete coverage of bioactivity space. Additionally, in vivo exposure measures such as Cmax are used for hepatotoxicity screening which are unavailable early on. Here we propose a novel rule-based framework to extract interpretable and biologically meaning...

We describe a novel precision medicine workflow, the integrated single nucleotide polymorphism network platform (iSNP), designed to identify the exact mechanisms of how SNPs affect cellular regulatory networks, and how SNP co-occurrences contribute to disease pathogenesis in ulcerative colitis (UC). Using SNP profiles of 377 UC patients, we mapped...

Background ulcerative colitis (UC) is a complex disease with poorly understood pathogenesis. In recent years, enormous genome-wide association studies have identified 242 single-nucleotide polymorphisms (SNPs) which cause UC susceptibility. However, their exact functions and effects remain unknown. To help discover novel pathogenic pathways in UC,...

Background The pathogenic signalling pathways of ulcerative colitis (UC) are complex, making patient stratification for optimal therapeutic choices challenging. Disease associated single-nucleotide polymorphisms (SNPs) make the prospect of personalised disease stratification and therapeutics tantalisingly plausible, but forward movement has been di...

Introduction. Gastrointestinal and urogenital infections cause great costs to health system and are responsible for many deaths all over the world. Personal hygiene is the simplest, most cost-effective method of prevention against these infections. Aim. The aim of our study was to investigate personal hygiene habits of a selected Hungarian subpopul...

Understanding living systems requires an in-depth knowledge of the signaling networks that drive cellular homeostasis, regulate intercellular communication, and contribute to cell fates during development. Several resources exist to provide high-throughput data sets or manually curated interaction information from human or invertebrate model organi...

Understanding living systems requires an in depth knowledge of the signaling networks that drive cellular homeostasis, regulate intercellular communication and contribute to cell fates during development. Several resources exist to provide high-throughput datasets or manually curated interaction information from human or invertebrate model organism...