Zaugg Group

Systems (epi)genetics to study the basis of complex traits and diseases


Judith Zaugg (Group Leader) contact: judith.zaugg [at] embl.de (Curriculum Vitae)

Judith studied Chemical Biology at ETH Zurich and did her PhD at the EMBL-EBI in computational functional genomics, investigating non-canonical transcriptional regulatory mechanism in yeast. For her postdoc she went to Stanford University where she studied the genetic basis of regulatory variation across healthy human individuals, integrating  multiple histone ChIP-Seq for multiple individuals with physical interactome data (Hi-C, ChIA-PET) to identify genetic associations between distal regulatory elements.
Her main research interest is to understand how the interplay of genetics, epigenetics and cellular signalling converge onto gene regulatory programmes that eventually gives rise to complex phenotypes, including diseases.
Apart from research, Judith likes mountain biking, skiing, running and having fun with her family.

Christian Arnold (Staff Bioinformatician) contact: christian.arnold [at] embl.de

Christian Arnold

Christian studied Bioinformatics at University Leipzig. After that, he worked as a research fellow at Harvard University for a year before starting his PhD at University of Leipzig in the field of epigenetics. Specifically, he regarded chromatin as a biological computer and studied its properties, computational power, and disease relevance.
His main research interests are efficient algorithm development, developing automated pipelines for biological data analysis, epigenetics, phylogenetics and, more generally, finding creative solutions for a wide range of bioinformatics challenges.
Apart from research, Christian likes to meet (new) people and to play chess. He is also a Bouldering aficionado and likes to travel.

Gwen Bauersachs (Laboratory Officer) contact: gwen.bauersachs [at] embl.de

Gwen studied Biosciences and did her PhD at Heidelberg University, during which she used iPSC-derived brain organoids to investigate glutamate-induced neurotoxicity. In the Zaugg group she´s taking care of organizational aspects and provides experimental support for single cell multiomic approaches and whatever else is needed.

In her free time, Gwen likes to go bouldering, hiking, doing yoga, cooking and spending time with friends and her cats.

Mikael Marttinen (Postdoctoral fellow joint with Noh lab) contact: mikael.marttinen [at] embl.de

Mikael studied Biochemistry and did his PhD at the University of Eastern Finland, during which he analysed the transcriptomic and phosphoproteomic alterations associated with Alzheimer’s disease-related neurofibrillary pathology in human brain.
His main interest in the Zaugg and Noh labs is to use a combination of in vitro generated neurons and glia cells and next generation sequencing techniques to study the molecular phenotypes of Alzheimer’s disease-associated risk variants.
Apart from research, Mikael likes bouldering, hiking/camping, and making music.

Annique Claringbould (Postdoctoral EIPOD fellow joint with Steinmetz lab) contact: annique.claringbould [at] embl.de

Annique studied Life Sciences at University College Utrecht in the Netherlands and continued to do an MSc in Human Molecular Genetics at Imperial College London. She did her PhD at the University Medical Centre in Groningen, the Netherlands, where she studied how human genetic variation influences gene expression levels. Her current research in the Zaugg and Steinmetz groups is in constructing and validating gene regulatory networks to better understand complex diseases.
When she is not doing research, Annique loves to dance, scuba dive and travel the world to discover beautiful places.

Karin Prummel (Postdoctoral fellow joint with the Saka lab) contact: karin.prummel [at] embl.de

Karin studied Biomedical Sciences at Utrecht University in the Netherlands and did her master’s degree in Cancer, Genomics, and Developmental Biology. She did her PhD at the University of Zurich in Switzerland, where she worked on the cell fate decisions of the mesoderm during embryology using various microscopy, sequencing, and genome editing approaches. Her main focus in the Zaugg group is studying the gene regulatory mechanisms involved in remodeling of the bone marrow niche upon leukemia, using single-cell ‘omics methods and multiplexed imaging.
Outside of the lab, Karin loves to climb, hike, snowboard, and play piano.

Nila Servaas (Postdoctoral fellow joint with GSK) contact: nila.servaas [at] embl.de

Nila studied Biomedical Sciences at Utrecht University in the Netherlands where she also continued to do her MSc in Drug Innovation. She did her PhD at the Center for Translational Immunology (CTI) at the University Medical Center Utrecht, the Netherlands, where she focused on integrating computational and experimental approaches to study immune cell dysregulation in the autoimmune disease Systemic Sclerosis. Her main research in the Zaugg group evolves around understanding the gene regulatory and signaling mechanisms driving immune cell differentiation.
When she is not in the lab, Nila likes to do weightlifting, biking, DJing or brew/enjoy craft beers.

Kristy Ou (Postdoctoral EIPOD fellow joint with the Saka lab) contact: kristy.ou [at] embl.de

Kristy studied Math and Applied Science at the University of California, Los Angeles in the US, where she first became exposed to biomedical research as an undergrad researcher in a systems biology lab. She continued with her PhD at the University of Pennsylvania, where she used targeted epigenetic editing approaches to induce cell cycle entry in pancreatic beta cells. Afterwards, Kristy did a short postdoc at Charité University in Berlin, Germany, where she profiled manufacturing-induced epigenetic changes in adoptive T cell therapies. As a postdoc in the Zaugg and Saka groups, Kristy aims to characterize regulatory networks driving drug resistance in lymphoma through single cell approaches.
In her free time, Kristy enjoys urban sketching, learning new languages, and being adventurous with friends.

Charles Dussiau (Postdoctoral fellow joint with Milsom lab) contact: charles.dussiau [at] embl.de

Charles studied Pharmacy at University of Tours in France, and continue with a four years residency in Medical Biology specialized in Hematology at Paris hospitals. He then worked as a clinical biologist for 2 years in Cochin hospital. Afterwards, during his PhD at Cochin Institute, he studied Hematopoietic and Progenitor Cells in myelodysplastic neoplasms. He then worked for 2 years as a clinical biologist in the Hematology laboratory of Bordeaux hospital. His main research interest in the Zaugg and Milsom groups is to integrate single cell omics with cellular and functional features to better understand how aging affects hematopoiesis.
In his free time, Charles enjoys swimming, running, playing guitar and go out with friends.

Dirk Hart (Postdoctoral fellow) contact: dirk.hart [at] embl.de

Dirk studied Medical sciences and did his MSc in Virology at Stellenbosch University, South Africa. He completed his PhD in Biomedical sciences at Fribourg University, Switzerland where he worked on gene transcription in human development and generation of a human ovarian granulosa cell model from iPSCs. In the Zaugg group his research focus will be to study the remodeling of the bone marrow niche upon leukemia, using 3D cell culture models and single cell omics.
In his free time Dirk is an avid sport follower, likes to keep active in the gym or outdoors, enjoys spending time with friends and to travel to new places.

Jonas Rauchhaus (PhD student at MMPU joint with Müller-Tidow lab) contact: jonas.rauchhaus [at] embl.de

Jonas obtained his M.Eng. in Biomedical Engineering at Imperial College London, where he investigated the impact of G-quadruplexes on DNA methylation changes during ageing and in cancer as part of his master thesis. In the Zaugg group, he researches the functions of RNA modifications (epitranscriptomics) in healthy cells and leukemia models by developing new CRISPR/Cas-based RNA editing tools that enable the targeted manipulation of epitranscriptomic marks.
During his free time, Jonas likes to make music (drums & guitar) or goes running and mountain biking.

Anna Mathioudaki (PhD student at MMPU joint with Pabst lab) contact: anna.mathioudaki [at] embl.de

Anna studied Biology in University of Patras, Greece. After that, she enrolled in the Joint Graduate Program of Molecular Biology and Biomedicine at University of Crete and IMBB-FORTH where she conducted her master thesis about disease variants in healthy populations. Anna’s main research interest in the Zaugg group is to assess the genome-wide chromatin accessibility and gene-expression profiles of the bone marrow niche stem cells, upon ageing and in acute myeloid leukemia, using bulk and single-cell sequencing approaches.
When Anna is not in the lab, she is most likely meeting new people, travelling, enjoying the sun or any combination of the above.

Aryan Kamal (PhD student) contact: aryan.kamal [at] embl.de

Aryan studied Computer Science at the Sharif University of Technology in Iran. He continued his studies in bioinformatics at Saarland University, where he implemented an algorithm for haplotype phasing of third-generation sequencing data. His main research interest in the Zaugg group are reconstruction and application of Gene Regulatory Networks from (single cell) RNA-seq and ATAC-seq data.
Apart from research, Aryan likes gaming, playing chess, reading history and traveling.

Guido Barzaghi (PhD student joint with Krebs lab) contact: guido.barzaghi [at] embl.de

Guido studied Biotechnology at the University of Turin in Italy to then transition to Bioinformatics for his MSc degree at the University of Copenhagen where he worked on single cell RNA-seq data of an in-vitro model of brain development.
His main research interest in the Zaugg and Krebs groups is the characterisation of cooperative TF binding through the integration of Single Molecule Footprinting and RNA-seq data.
Besides research, Guido enjoys listening to music, playing the guitar and watching movies

Sara Lobato Moreno (PhD student at MMPU joint with Pabst lab) contact: sara.lobato [at] embl.de

Sara studied Biology at the Autonomous University of Madrid (Spain) and then moved to Heidelberg where she joined the Master’s program in Molecular Biosciences with a focus on Neuroscience. Her main interest in the Zaugg group is to understand the relevance of the RNA binding factor RBM4 in acute myeloid leukemia.
Besides science Sara enjoys hiking trips, yoga, tennis, spending time with friends and family and she is making her first steps in bouldering.

Maksim Kholmatov (PhD student) contact: maksim.kholmatov [at] embl.de

Maksim finished Medical Biophysics programme at Saint-Petersburg State Pediatric Medical University, Russia. He did his thesis in N.N. Petrov National Medical Research Center of Oncology where he studied genetics of sporadic and hereditary oncogenesis. In the Zaugg lab his research interests revolve around using multiomics approaches to dissect gene regulation within bone marrow stem cell niche.
In his spare time Maksim likes playing football, finding new music, and fiddling around with his laptops.

Frosina Stojanovska (PhD student) contact: frosina.stojanovska [at] embl.de

Frosina studied Computer Science at “Ss. Cyril and Methodius” University – Skopje. After that, she graduated with an MSc in Bioinformatics at the same university with a master thesis on protein structure prediction with deep learning. Her main research interest at Zaugg group is a multi-modal analysis with in situ Cryo-ET imaging data and omics data using Mycoplasma pneumoniae as a model organism.
Apart from research, Frosina is also enthusiastic about travelling, photography and enjoying sunrises and sunsets

Josephine Brysting (PhD student at MMPU joint with the Müller-Tidow lab) contact: josephine.brysting [at] embl.de

Josephine studied Human Biology at Loughborough University in the United Kingdom and thereafter graduated with a Professional Scientific Masters in Biotechnology from the University of San Francisco, USA. In San Francisco, Josephine acquired an interest for engineered immune cell therapies whilst working at two start-ups, most recently as a Senior Research Associate at CERo Therapeutics Inc. As a PhD student in the Zaugg Lab, Josephine is interested in using a multi-omics approach to identify novel antigens in Acute Myeloid Leukemia (AML) for targeting by chimeric antigen receptor (CAR) T cells.
Outside the lab, you will find Josephine running the hills of Heidelberg, meeting with friends and staying up to date with start-ups and innovation.

Evi Vlachou (PhD student) contact: evi.vlachou [at] embl.de

Evi obtained a Bachelor’s in Biology from NKUA in Athens and a Master’s in Immunology from the University of Amsterdam, with a minor in Big Data. Her thesis at Dkfz-Heidelberg focused on understanding memory B cells while during her minor at Institute curie, Evi developed an interest in computational cancer biology. She then pursued a second Master’s in Bioinformatics from ENS, Paris, exploring retinoic acid resistance in Acute Promyelocytic leukemia. Currently, Evi’s main research interest is to infer gene regulatory networks in Acute Myeloid Leukemia and understand the cell interactions in the bone marrow employing a single-cell multimodal approach.
Outside the lab Evi enjoys yoga, dancing, techno festivals, and traveling.

Miguel Hernandez (Master student) contact: miguel.hernandez [at] embl.de

Miguel did his Bachelor’s in Biology at the Universidad de Guadalajara in Mexico. He then started his master’s in Molecular Biosciences at Heidelberg University with projects ranging from high-throughput screens of synthetic genomic sequences at DKFZ to data analysis of ex-vivo drug response profiling from blood cancer patients at the Uni Klinikum. He is interested in the integration of multiomics data to approach biological questions. He is currently working on his master’s thesis at the Zaugg group, where he is building gene regulatory networks to better understand the distinct phenotypes in T-cell subsets.
In his free time, Miguel enjoys having a beer with friends, eating, exercising and sometimes, helplessly, getting lost in Wikipedia.

Bogdan Avanesyan (Master student) contact: bogdan.avanesyan [at] embl.de

Bogdan studied molecular biology at Lomonosov Moscow State University in Russia. After that, he joined the Master’s program in Life Sciences at Skolkovo Institute of Science and Technology. His main research interest in the Zaugg group is the identification of gene regulatory networks driving drug resistance in non-Hodgkin lymphoma from single-cell RNA-seq and ATAC-seq data.
Apart from research, Bogdan likes spending time with friends and family, reading, and gaming.

Yaren Canten (Intern student) contact: yaren.canten [at] embl.de

Yaren studied Molecular Biology and Genetics at Middle East Technical University in Turkey. Afterwards, she did a Master’s in Molecular and Cellular Biology at Ludwig Maximilian University of Munich. Recently, she has finalized her master’s thesis on the humoral immune response in patients with inflammatory diseases of the central nervous system. Her main focus in the Zaugg and Saka groups is using multiplexed imaging and targeted spatial transcriptomics to understand remodeling of the bone marrow niche upon leukemia.
In her free time, Yaren enjoys learning new languages, spending time with family and friends, and dancing.

Gerard Deuner (Intern student) contact: gerard.deuner [at] embl.de

Gerard is a last year Bioinformatics bachelor’s degree student who is carrying out his final degree project in the Zaugg group. His main research interests within the genomics field rely upon understanding molecular mechanisms underlying diseases and other complex phenotypes by developing and making use of statistical-based tools. His project in the Zaugg group consists of contributing to the effort of moving from bulk to single cell enhancer-inclusive gene regulatory networks (eGRNS) through the implementation and benchmarking analysis of different sc-eGRN approaches.
Besides that, during his free time, Gerard enjoys practicing sports, reading and having fun with family or friends.

Victor Paton (Intern student) contact: victor.paton [at] embl.de

Victor studied Biotechnology at the Technical University of Madrid (Spain). After that, he moved to Heidelberg to start the Molecular Biosciences MSc, major in Systems Biology. His main research interests and previous work lie on the fields of machine learning, network inference and tool development via programming. His main activity in the Zaugg lab is to explore different approaches and strategies to draw robust conclusions from single cell eGRNs.
In his free time, Victor enjoys meeting friends, travelling, and cooking new recipes. He also goes often bouldering and, on a sunny day, you will probably find him having a beer outside.

Alumni of the Zaugg lab

Olga Sigalova (PhD student); now Postdoc in the Aerts lab, VIB-KU Leuven Center for Brain and Disease Research

Daria Bunina (Postdoctoral EIPOD fellow 2016-2022); now group leader at MDC Berlin

Brian (Mang Ching) Lai (Postdoctoral fellow 2016-2022); now at GSK/Cellzome

Neha Daga  (Postdoctoral fellow 2018-2022)

Lukas Jarosch (Master student 2021); now intern at Novartis

Irene de Teresa Trueba (EIPOD Postdoctoral fellow 2017-2021); now at ENGIE

Sophia Mueller-Dott (Master student 2020-21); now PhD student at HD University

Ivan Berest (PhD student 2016-2020, Postdoc 2020); now at Roche

Alexander Mattausch (Intern student 2019-2020); now student in Heidelberg

Mathias Andres Savar Cortes (Postdoc 2018-2020); now at Indivumed

Chaitra Rao (Master student 2019-2020); now at Novartis

Ignacio Ibarra (Predoc 2015-19, Postdoc 2019-2020); now Postdoc at the Helmholtz Center in Munich

Saudat Alishayeva (Intern student 2019); now student at Bahcesehir University, Istanbul

Frauke Huth (Master student 2019); now student at Oxford University, UK

Amirreza Shaeiri (Intern 2019); now student at Sharif University, Iran

Andrew Ó hEachteirn (Intern 2018-2019); now student at Cambridge University, UK

Mariana Ruiz-Velasco (Predoc 2014-2018, Postdoc 2018-2019); now Data Scientist at BASF

Armando Reyes Palomares (Postdoc 2015-2018); now Postdoc at Universidad Complutense Madrid

Giovanni Palla (Master student 2017/2018); now PhD student at Helmholtz Centre Munich

José Bautista (Visiting scholar 2017/2018)

Stefan Kleinsorg (Master Student 2016/2017)

Rafail Nikolaos Tasakis (Visiting Scientist 2016/2017); now PhD student at DKFZ Heidelberg

Gesa Hillmer (Master student 2016/2017); now at Springer in Heidelberg

Constantin Ahlmann-Eltze (Master student 2016/2017); now PhD student at EMBL

Manish Goel (Master student 2016); now PhD student at MPI Cologne

Rocío Rodríguez López (Visiting PhD student 2016); PhD student at University of Málaga

Ece Kartal (Visiting Scientist 2015); now PostDoc in the Saez-Rodriguez Group at Universität Heidelberg

Pooja Bhat (Visiting Scientist 2015); now PhD student at IMBA Vienna

Ana Belen Solis Pinson (Visiting Scientist 2014/2015)