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Heinig Lab

Genetic and Epigenetic Gene Regulation

Overview

The Heinig lab is located at the Institute of Computational Biology, which is part of the Computational Health Center of Helmholtz Munich.

Together with my research group, I develop AI solutions for personalized network based precision medicine.

Technological advances allow for an unprecedented in-depth characterization of the molecular basis of complex diseases. In particular SNP genotyping, DNA methylation assays and gene expression profiling in large cohorts and in single cells have been used to identify numerous disease associated loci and genes. However, a deeper mechanistic or systems level understanding of disease processes still remains elusive in most cases.

The aim of our research is the development and application of computational and statistical tools for the identification of molecular regulatory networks underlying common diseases and the genetic and epigenetic mechanisms controlling these networks from population level DNA and multi-omics data sets. In a second step we aim to personalize the networks based on single cell data. This will enable us to implement new concepts for precision medicine. A special focus is the molecular characterization of cardiovascular and metabolic diseases.

Computational methods to understand the systems genetics of complex traits

Our research group is dedicated to unraveling the intricate relationships between genetic variation, gene regulation, and complex diseases. We aim to bridge the gap between genome-wide association studies (GWAS) and underlying biological mechanisms through innovative approaches in complex trait genetics. We integrate multi-omics data using advanced computational techniques, including network algorithms, Bayesian modeling, and machine learning. Our work focuses on identifying regulatory networks and core genes implicated in complex traits, providing a systems-level view of genetic influences on biological processes. By examining the interplay between genes and their products, we identify key pathways and potential intervention points in disease processes. Our research contributes to the development of more accurate predictive models for disease risk and progression, driving progress towards personalized medicine. Ultimately, we strive to improve risk prediction, enable earlier interventions, and develop more effective treatments tailored to individual genetic profiles, transforming our understanding of complex diseases and individual variability in health outcomes.

Multi-omics in cardiovascular disease

Our research group pioneers the application of multi-omics approaches to revolutionize cardiovascular disease understanding. We integrate diverse molecular data types, from genomics to proteomics, to examine heart biology and pathology at unprecedented resolution. By combining large-scale genomic studies with cutting-edge single-cell analyses, we bridge the gap between genetic variation and disease manifestation at the cellular level. We develop innovative computational methods to analyze these complex datasets, including the identification of expression quantitative trait loci for transcripts (eQTL) and proteins (pQTL) in human heart tissue and the creation of detailed single-cell atlases in health and disease. Our integrative approach unveils novel insights into the molecular mechanisms underlying cardiovascular diseases, contributing to the AI driven identification of new biomarkers and potential therapeutic targets. Through active collaborations with international consortia such as the CZI seed network for the human heart, we aim to transform cardiovascular health understanding and pave the way for precision medicine. Our ultimate goal is to translate molecular insights into improved prediction of disease risk and patient outcomes, bringing us closer to personalized cardiovascular treatments.

Lab members

Andreas Schmidt

    PhD Student

    Email  •  Linkedin

    Porträt Bhavishya Nelakuditi

    Bhavishya Nelakuditi

      PhD Student

      Visha studied computer engineering with specialisation in bioinformatics and is now working on determining the genetic and clinical factors that influence cardiovascular vascular diseases in collaboration with AG Stark group at LMU Klinikum.

      Email  •  Linkedin

      Cem Gülec

        Software Engineer

        Cem studied computer science and currently involved in a project that leverages the availability of reference cell atlases to scale scPower, that optimizes the power of multi-sample single cell transcriptomics experiments.

        Email  •  LinkedIn  •  Github

        Corinna Losert

          PhD Student

          Corinna is a data scientist interested in understanding the gene regulatory mechanisms that underly (heart and immune system related) diseases. For this she analyzes and integrates bulk and single-cell multi-omics data in various different projects and collaborations.

          Email  •  Linkedin

          Porträt Florin Ratajczak

          Florin Ratajczak

            PhD Student

            Florin studied bioinformatics with specialisation in machine learning. He researches the domain-specific application of graph neural networks and how they can be leveraged to distill meaningful insights from genome-scale datasets.

            Email  •  Linkedin • GitHub

            Ilaria Looser

              PhD Student

              Ilaria studied Quantitative Biology and currently works on a data-driven leukaemia classification by integrating multi-modal diagnostic datasets of haematological diseases using machine learning. The project is a collaboration with the Munich Leukemia Laboratory (MLL).

               

              Email  •  Linkedin  •  GitHub

              Porträt Jiaqi Lu

              Jiaqi Lu

                PhD Student

                Jiaqi studied mathematics with a focus on statistics. Now her research interest lies in analyzing single-cell CRISPR data and revealing the GRN structure with causal inference.

                Email  •  LinkedIn  

                Porträt Korbinian Träuble

                Korbinian Träuble

                  PhD Student

                  Korbinian studied physics and is now working on cardiovascular immunology using single cell RNA sequencing data in a collaboration with an industry partner.

                  Email  •  LinkedIn  •  Twitter  •  GitHub

                   

                  Porträt Orhan Bellur

                  Orhan Bellur

                    PhD Student

                    Orhan studied Molecular Biology and Genetics and has a broad interest in investigating metabolic diseases, particularly neurodegenerative diseases, using a systems biology approach. Currently, he is pursuing his PhD, focusing on understanding the molecular mechanisms of Alzheimer's disease and identifying candidate drugs by employing several in silico drug repurposing algorithms.

                    Email  •  Linkedin

                    Porträt Raphael Lermer

                    Raphael Lermer

                      PhD Student

                      Raphael studied chemical engineering and is now focusing on survival analyses regarding cardiovascular diseases and investigates aging on the proteomic level by different machine learning approaches.

                      Email  •  LinkedIn

                      Porträt Sergey Vilov

                      Sergey Vilov

                        Postdoc

                        Sergey earned his PhD in Physics from Université Grenoble Alpes in 2019. In 2021, he joined Helmholtz Zentrum München, where he has been focusing on developing deep learning methods to study the effects of genomic alterations.

                        Email  •  Linkedin  •  Github

                        Porträt Simon Wengert

                        Simon Wengert

                          PhD Student

                          Simon is interested in characterising mitochondrial sequence variations across human tissues. To this end, he develops novel computational approaches to learn about their effects on donor phenotypes and the molecular pathways through with they are mediated. On top of that, he works on the analysis of single-cell and spatial transcriptomic data to study early mouse brain development.

                          Email  •  Website  •  Linkedin  •  Twitter  •  Github

                          Vladana Djacovic

                            PhD Student

                            After completing her master’s in Data Science, Vladana began a PhD project on snRNA and scRNA sequencing to study heart aging and cardiovascular diseases. The project is being done in collaboration with LMU Klinikum.

                            Email  •  Linkedin

                            Porträt Huang Ziming

                            Ziming Huang

                              PhD Student

                              Ziming studied at Shanghai Institute of Materia Medica and the University of the Chinese Academy of Sciences and is now working on identifying novel targets in heart failure. He aims to develop efficient and reliable computational methods with applications in understanding of immune signatures and inflammatory networks that underlie the development of heart failure. 

                              Email  •  Linkedin

                              Publications

                              2024 Nature Medicine

                              Kami Pekayvaz*, Corinna Losert*, Viktoria Knottenberg*, Christoph Gold, Irene V. van Blokland, Roy Oelen, Hilde E. Groot, Jan Walter Benjamins, Sophia Brambs, Rainer Kaiser, Adrian Gottschlich, Gordon Victor Hoffmann, Luke Eivers, Alejandro Martinez-Navarro, Nils Bruns, Susanne Stiller, Sezer Akgöl, Keyang Yue, Vivien Polewka, Raphael Escaig, Markus Joppich, Aleksandar Janjic, Oliver Popp, Sebastian Kobold, Tobias Petzold, Ralf Zimmer, Wolfgang Enard, Kathrin Saar, Philipp Mertins, Norbert Huebner, Pim van der Harst, Lude H. Franke, Monique G. P. van der Wijst, Steffen Massberg, Matthias Heinig†, Leo Nicolai†, Konstantin Stark†

                              Multiomic analyses uncover immunological signatures in acute and chronic coronary syndromes

                              2022 Nature Genetics

                              Hawe JS*, Wilson R*, Schmid KT*, Zhou L, Lakshmanan LN, Lehne BC, Kühnel B, Scott WR, Wielscher M, Yew YW, Baumbach C, Lee DP, Marouli E, Bernard M, Pfeiffer L, Matías-García PR, Autio MI, Bourgeois S, Herder C, Karhunen V, Meitinger T, Prokisch H, Rathmann W, Roden M, Sebert S, Shin J, Strauch K, Zhang W, Tan WLW, Hauck SM, Merl-Pham J, Grallert H, Barbosa EGV; MuTHER Consortium, Illig T, Peters A, Paus T, Pausova Z, Deloukas P, Foo RSY, Jarvelin MR, Kooner JS, Loh M†, Heinig M†, Gieger C†, Waldenberger M†, Chambers JC†.

                              Genetic variation influencing DNA methylation provides insights into molecular mechanisms regulating genomic function

                              Contact:

                              Herr Heinig, Matthias Dr.

                              Dr. Matthias Heinig

                              Junior Group Leader

                              58a / 104