Curriculum Vitae Judith Zaugg June 2019 Personal Information Name: Judith B., Zaugg ORCID: 0000-0001-8324-4040

Nationality: Swiss

Website: http://www.zaugg.embl.de

Current Position 2018 – Group leader at Molecular Medicine Partnership Unit (MMPU) 2014 – Group leader at European Molecular Biology Laboratory (EMBL) / Structural

Computational Biology Unit (Germany), co-affiliation with Genome Biology Unit (Germany) and European Bioinformatics Institute (UK)

Research focus Our aim is to understand how genetic and epigenetic variation across individuals affects complex traits and diseases through gene regulatory mechanisms. In parallel we make use of variation in molecular phenotypes to better understand biological processes and disease mechanisms. To do so develop computational tools to integrate data across multiple scales and types and apply these principles of gene regulation and signalling pathways in two broad biological areas: (i) neuronal development and processes related to neurodegenerative diseases and (ii) the hematopoietic niche and diseases related to the misregulation of the immune system and blood cancer. Education 2011 PhD degree awarded by Cambridge University, UK; Thesis title: “A computational study of

promoter structure and transcriptional regulation in yeast on a genomic scale” 2004-2007 Diploma Studies (equivalent to MA) in Biological Chemistry at ETH Zurich, majoring in

molecular biology, biological chemistry, informatics supported biochemistry, bioinformatics and organic chemistry. Thesis title: “Two stable phenotypes during nutrient shift from glucose to acetate in Escherichia coli: mechanistic insights into the regulation from glycolysis to gluconeogenesis“ supervised by Dr. Matthias Heinemann and Prof. Uwe Sauer

2005 Visiting Student at Massachusetts Institute of Technology (MIT) (Cambridge, MA, USA) in the group of Prof. JoAnne Stubbe, experimentally characterizing enzyme kinetics (3 months)

Research Experience 2012-2014 Postdoctoral Fellow at Stanford University (CA, USA) with Prof. Lars Steinmetz in

personalized transcriptomics and epigenetics, using NGS data to understand regulation of gene expression across human individuals and its links to complex traits and diseases. Collaborations with Prof. Mike Snyder, Prof. Steven Montgomery, Prof. Jonathan Pritchard (Stanford)

2011-2012 Postdoctoral Fellow at EMBL-EBI (Cambridge, UK) with Dr. Nick Luscombe using tilling array data and bioinformatics to study the promoter architecture and its impact on gene regulation in S.cerevisiae. Collaboration with Prof. Françoise Stutz (University of Geneva)

2007-2011 PhD research at EMBL-EBI and University of Cambridge (Cambridge, UK) with Dr. Nick Luscombe, focusing on functional genomics in gene regulation using S.cerevisiae as model organism; Collaborations with Prof. Nicholas Proudfood (Oxford University, UK) and Françoise Stutz (Geneva University, Switzerland)

2007 Internship at Roland Berger Strategy Consulting in pharmaceutical team, (3 months, Germany)

Teaching and supervision of students, graduate students and postdoctoral fellows 2018- Scientific coordinator the EMBL PhD course 2015- Module coordinator of the ‘omics module of the EMBL PhD course 2015-2017 Master class lecture at Heidelberg University (Genetic Variation) 2014 – Supervision: 1 Staff Bioinformatician, 6 Postdoctoral Fellow, 4 PhD students Member of thesis advisory committee of 15 PhD students Member of thesis defense committee of 5 PhD students Selected publications (* joint first author, + joint corresponding author)

• Garg, S.*, Reyes-Palomares, A.*, He, L., Bergeron, A., Lavallée, V.-P., Lemieux, S., Gendron, P.,

Rohde, C., Xia, J., Jagdhane, P., Müller-Tidow, C., Lipka, D.B., Imren, S., Humphries, R.K., Waskow, C., Vick, B., Jeremias, I., Richard-Carpentier, G., Hébert, J., Zaugg, J.B.+, Sauvageau, G+. and Pabst, C+. 2019. Hepatic leukemia factor is a novel leukemic stem cell regulator in DNMT3A, NPM1, and FLT3-ITD triple-mutated AML. Blood.

• Rasmussen, K.D.+*, Berest, I.*, Keβler, S., Nishimura, K., Simón-Carrasco, L., Vassiliou, G.S., Pedersen, M.T., Christensen, J., Zaugg, J.B.+ and Helin, K.+ 2019. TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells. Genome Research 29(4), pp. 564–575.

• Hennrich ML*, Romanov N*, Horn P, … , Zaugg, JB, Pelagatti A, Gavin AC+, Ho A+. 2018. Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline. Nature Communications 9(1), p. 4004.

• Berest I*, Arnold C*, Reyes-Palomares A, Palla G, Rasmussen K, Helin K, Zaugg JB (2018). Quantification of differential transcription factor activity and multiomic-based classification into activators and repressors: diffTF. BioRxiv: doi: https://doi.org/10.1101/336008

• Ruiz-Velasco M., Kumar M, Lai MC, Bhat P, Solís-Pinson AB, Reyes A, Kleinsorg S, Noh KM, Gibson TJ, Zaugg JB (2017) CTCF-mediated chromatin loops between promoter and gene body regulate alternative splicing across individuals: Cell Systems 5 (6), 628-637.

• Ruiz-Velasco M, Zaugg JB (2017). Structure meets function: How chromatin organisation conveys functionality. Current Opinion in Systems Biology: 1, Feb 2017,129-136, ISSN 2452-3100

• Ignatiadis N, Klaus B, Zaugg JB, Huber W. (2016) Data-driven hypothesis weighting increases detection power in genome-scale multiple testing. Nat Methods. Jul;13(7):577-80

• Cakiroglu SA, Zaugg JB, Luscombe NM (2016) Backmasking in the yeast genome: encoding overlapping information for protein-coding and RNA degradation. Nucleic Acids Res (2016) 44 (17): 8065-8072.

• Arnold C, Bhat P & Zaugg JB. SNPhood: SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data. Bioinformatics (2016) doi:10.1093/bioinformatics/btw127

• Grubert F*, Zaugg JB*, Kasowski M*, Ursu O*, et al. Genetic Control of Chromatin States and Gene Expression in Humans Involves Local and Distal Chromosomal Interactions. Cell (2015) 162 (5): 1051-1065

• Castelnuovo M*, Zaugg JB*+, Guffanti E, Maffioletti A, Camblong J, Xu Z, Clauder-Münster S, Luscombe NM, Steinmetz LM, Stutz F+. Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast. Nucl. Acids Res. (2014) 42 (7): 4348-4362.

• Kasowski M*, Kyriazopoulou-Panagiotopoulou S*, Grubert F*, Zaugg JB*, Kundaje A*, Liu Y, Boyle AP, Zhang QC, Zakharia F, Spacek DV, et al. 2013. Extensive Variation in Chromatin States Across Humans. Science 342 (6159), 750-752.

• Tan-Wong SM*, Zaugg JB*, Camblong J*, Xu Z, Zhang DW, Mischo HE, Ansari AZ, Luscombe NM, Steinmetz LM, Proudfoot NJ. 2012. Gene Loops Enhance Transcriptional Directionality. Science 338 (6107), 671-675.

• Zaugg JB, Luscombe NM. 2012. A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast. Genome Res 22: 84–94.

Invited presentations at major international conferences since 2014 (selected): 2017 Speaker at EMBO | Wellcome Trust conference: Target Validation, Hinxton (UK) 2017 Speaker and organizer of EMBO conference: From Single to Multiomics, Heidelberg

(Germany) 2017 Speaker and organizer of EMBL|Stanford conference: Personalized Health, Stanford (US) 2017 Speaker at EMBO | Wellcome Trust conference: Big Data in Biology, Hinxton (UK) 2017 Speaker at Systems Biology in Human Disease conference, Heidelberg (Germany) 2017 Speaker at IMB conference: Gene Regulation by the Numbers, Mainz (Germany) 2016 Speaker at Cell Symposium: Technology. Data. Biology. Berkley (US) 2016 Speaker at EMBO|Wellcome Trust conference: Proteomics in Cell Biology and Disease

Mechanisms, Heidelberg (Germany) 2016 Speaker at EMBO|Wellcome Trust conference conference: Big Data in Biology, Heidelberg

(Germany)

2016 Keynote Speaker at Bioinformatics Symposium: Computational biology: from microbes to human health, Leiden (Netherlands)

2016 Speaker at EMBO conference: VIZBI - Visualizing Biological Data, Heidelberg (Germany) 2015 Speaker and organizer of EMBL|Stanford conference: Personalized Health, Heidelberg

(Germany) 2015 Invited speaker at Wellcome Trust conference: Functional Genomics and Systems Biology,

Hinxton (UK) 2015 Selected talk at international workshop: Statistical Learning of Biological Systems from

Perturbations, Ascona (Switzerland) 2015 Invited speaker at Epigenetics Minisymposium at LIMES, Bonn (Germany) 2014 Invited speaker at EMBO conference: From Functional Genomics to Systems Biology,

Heidelberg (Germany) Steering boards, scientific advisory boards, awards, and fellowships 2019- Steering board Heidelberg Leukemia Network (HeLeNe) 2019- Scientific Advisory Board of the Hungarian Center of Excellence in Molecular Medicine

(HCEMM) 2015- Search committee for group leader recruitment:

NCMM Norway (2015, 2018), CRG Spain (2016) 2013 Award for best Scientific Contribution (ex aequo) CSF foundation (Switzerland) 2013 Fellowship for Advanced Researchers awarded from the Swiss Study Foundation (Switzerland)

for postdoctoral research at Stanford University 2012 Fellowship for supporting future academic leaders awarded by Janggen-Poehn foundation

(Switzerland) for first year of postdoctoral research at Stanford University 2011 Travel scholarship received from Keystone symposium (USA) 2007 Honorary scholarship received from Cambridge Overseas Trust, Cambridge University (UK) 2005 Fellowship for research stay at MIT awarded by Swiss Study Foundation (Switzerland) Editorial boards and reviewing Activity 2019- Member of international experts panel for reviewing grants of the Swedish Foundation for

Strategic Research (https://strategiska.se/en/ ) 2018- Member of Faculty1000 2018- Editorial Board, FEBS Letters 2014- Regular reviewing for: eLife, Nat. Comm., Cell Reports, NAR, Bioinformatics, MSB 2017-2018 Editorial Board, Physiological Genomics, UK Organization of Scientific Meetings since 2014 2017 Co-organizer of EMBL|Stanford conference: Personalised Health Stanford (US) 2017, 2019 Main organizer of EMBL|EMBO conference: From Single to Multiomics (Heidelberg) 2015, 2019 Co-organizer of EMBL|Stanford conference: Personalised Health (Heidelberg) Memberships of Academic Societies and Consortia 2010-2011 Member of Training advisory board of EpiGeneSys, FP7 European Community-funded

Network of Excellence to bridge epigentics and systems biology (www.epigenesys.org) 2010-2012 Founding member of Cambridge Swiss Society, an association providing a platform for

exchange among Swiss people in Cambridge (www.societies.cam.ac.uk/camswiss/) Since 2004 Board member of Pantok Dialogos, an association promoting interdisciplinary exchange

between science and business in Switzerland (www.pantok.ch) 2004-2007 Head of SiROP ETH, a student founded association aiming to enhance student education and

support scientific research by giving interested students the opportunity to actively collaborate in ongoing research projects

2003-2011 Member of Swiss Study Foundation, an institution that supports talented students during their studies, by providing them with interdisciplinary seminars and workshops complementary to their field of study (www.studienstiftung.ch)