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 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.
Daria Bunina (Postdoctoral EIPOD fellow joint with Noh lab) contact: daria.bunina [at] embl.de
Daria studied biochemistry at Lomonosov Moscow State University in Russia and did her PhD at Heidelberg University, during which she analyzed effects of non-coding transcripts on protein expression of yeast genes.
Her main research interest in the Zaugg and Noh labs is to understand the interplay between different levels of epigenetic regulation (such as chromatin structure, histone modifications and DNA methylation) responsible for plasticity in gene expression.
Apart from research, Daria likes freestyle swimming, travelling, learning languages, dancing and reading.
Brian (Mang Ching) Lai (Postdoctoral fellow) contact: mangching.lai [at] embl.de
Brian studied Biochemistry at Essex University, and did his Master’s degree in Clinical Neuroscience at University College London. He went on to complete his DPhil at Oxford University in Molecular Neurodegeneration, studying the allele-specific gene splicing mechanisms in parkinsonian disorders.
His main research interest in the Zaugg group is to understand the regulatory effects of chromatin and downstream changes in both physiological ageing and age-related disorders using multiomics approaches.
Apart from research, Brian likes tennis, going to the pub, spontaneous trips, gaming, and dancing.
Neha Daga (Postdoctoral fellow) contact: neha.daga [at] embl.de
Her main interest in the Zaugg group is to integrate disease-associated genetic variants with gene regulatory network reconstruction using large-scale gene regulatory networks in T-cells to study autoimmune diseases.
Apart from work, she likes travelling, hiking and meeting new people and knowing different cultures.
Mikael Marttinen (Postdoctoral fellow joint with Noh lab) contact: mikael.marttinen [at] embl.de
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 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.
Olga Sigalova (PhD student joint with Furlong lab) contact: olga.sigalova [at] embl.de
Olga studied mathematical modeling in economics at Lomonosov Moscow State University and did her Master thesis in behavioral game theory. After that, she completed Moscow Bioinformatics School and worked in a bioinformatic lab on projects related to bacterial comparative genomics.
Her main research interest in the Furlong and Zaugg labs is to understand robustness underlying gene regulatory programs in embryonic development.
Apart from research, Olga likes hiking, visiting historical places, reading and learning foreign languages.
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
Alumni of the Zaugg lab
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)