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@LabThoma

MEET THE LAB
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Nico was an undergraduate in Biochemistry at the University of Cambridge (UK), where he also completed his Ph.D. in enzymology and structural biology jointly with Peter Leadlay (University of Cambridge) and Phil Evans (MRC-LMB Cambridge). He then was a postdoc with Roger Goody (Max-Plank Institute, Dortmund) focusing on protein-ligand interactions. In 2001 he moved to the laboratory of Nikola Pavletich (Memorial Sloan Kettering, New York) to complete his training in X-ray crystallography. Nico became a group leader at the FMI in 2006, where he has been tenured as of 2011.

NICOLAS THOMÄ

Group Leader

Ph.D., University of Cambridge, UK

nicolas.thoma[at]fmi.ch

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Jake completed his Ph.D at the University of Western Ontario in 2017 studying RBR ubiquitin ligase activation under the supervision of Dr. Gary Shaw. In the Thomä lab, he is studying how cullin-RING ubiquitin ligases, the largest family of E3 enzymes, ensure faithful replication of genomic information. He uses a variety of biophysical and structural techniques, including cryo-EM, to elucidate these processes at the atomic level.

JACOB AGUIRRE

Postdoc, EMBO fellow

Ph.D., University of Western Ontario, Canada

jacob.aguirre[at]fmi.ch

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After finishing her Bachelor studies in Biochemistry, Amparo's PhD project focused on the regulation of the tumor suppressor PTEN (at CIPF, Valencia, Spain). As a postodoctoral fellow she researched the molecular mechanisms of cytokinesis in budding yeast and human (DKFZ, Heidelberg, Germany). She then moved to EMBL, Heidelberg, Germany, where she worked as a lab manager and did research on the field of nucleocytoplasmic transport. 

AMPARO ANDRES-PONS

Lab Manager

Ph.D., CIPF, Valencia, Spain

amparo.andres[at]fmi.ch

Anja received her Diploma in Molecular Medicine from the University of Freiburg, Germany. She then did her PhD in Freiburg studying different components of the ubiquitin-like ISG15 system by X-ray crystallography. In the Thomä lab her main interest is on understanding how multi-protein complexes control transcription within chromatin.

ANJA BASTERS

Postdoc, NIBR fellow

Ph.D., University of Freiburg

anja.basters[at]fmi.ch

Richard ...

RICHARD BUNKER

Research Associate

Ph.D., 

richard.bunker[at]fmi.ch

Simone studied chemistry at the Swiss Federal Institute of Technology in Lausanne (EPFL) where he received his PhD in 2009 for developing new NMR techniques to probe the structure and dynamics of biomolecules under the supervision of Prof. Geoffrey Bodenhausen. He then moved for a short period to the Institut Biochimique SA (IBSA) in Lugano, Switzerland, where he worked as a mass spectrometry scientist, helping to establish their mass spectrometry facility. In 2011 he joined the Thomä laboratory at FMI for post-doctoral studies on the CRL-CSN complexes before becoming a project leader in 2014. Since 2016 he holds a shared position between the group of Dr. Nicolas Thomä and the electron microscopy facility under Dr. Christel Genoud. Together with his colleague Dr. Andreas Schenk they support FMI users to utilise cryo-EM for their scientific research, contribute to the setup and development of the cryo-EM facility shared with Novartis and explore and validate new methods for single-particle cryo-EM.

SIMONE CAVADINI

Project Leader, EM Competency Center

simone.cavadini[at]fmi.ch

Susanne received her Diploma in Biology from Heidelberg University. For her thesis research, she went to Rockefeller University to work with Gunter Blobel and Andre Hoelz on structural studies of the nuclear pore complex. She then joined the Biophysics PhD program at the University of California, Berkeley, to study mechanisms of transcriptional regulation in the group of Eva Nogales. In the Thoma lab, she focuses on DNA repair mechanisms.

SUSANNE KASSUBE

Postdoc, EMBO fellow 

Ph.D., University of California, Berkeley

susanne.kassube[at]fmi.ch

Zuzanna received her Intergrated Masters degree in Chemistry from the University of Edinburgh. During the course of her studies, she also pursued research projects at ETH Zurich (Prof. Nenad Ban) and the University of Dundee (Prof. Alessio Ciulli). In the Thoma lab, she is working on finding novel chemical matter for targeted degradation of DNA-binding proteins.   

ZUZANNA KOZICKA

Ph.D. Student, UbiCODE fellow

Masters in Chemistry, University of Edinburgh

zuzanna.kozicka[at]fmi.ch

Syota has worked in DNA repair field for 10 years as a cell biologist and structural biologist. He received his Ph.D in Biology in 2015 from Kobe University, Japan, and then, he joined Nicolas Thomä Group in 2016. His current project in the lab is to solve the structures of DNA damage recognition proteins and investigate the mechanisms of initiation stage of DNA repair pathway in the context of chromatin.

SYOTA MATSUMOTO

Postdoc

Ph.D., Kobe University, Japan

syota.matsumoto[at]fmi.ch

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Alicia received her B.S. in Biochemistry from Western Washington University where she worked in an organometallic chemistry lab under the supervision of Dr. Timothy Clark. She then moved to sunny Santa Cruz, California to do her Ph.D with Carrie Partch, studying the molecular details of circadian rhythms. In the Thomä lab, she is working on  elucidating the structural basis of transcriptional regulatory complexes.

ALICIA MICHAEL

Postdoc, EMBO/HFSP fellow

Ph.D., University of California, Santa Cruz

alicia.michael[at]fmi.ch

Ganesh received his B.S. Agricultural Biotechnology in Mahatma Phule Agricultural University, India. He then moved to Europe and did his Masters research at the University of Uppsala, Sweden. He completed his Ph.D. at the Max Planck Institute for Biochemistry in Munich, Germany under the supervision of Wolfgang Baumeister studying the 26S proteasome.

GANESH PATHARE

Postdoc

Ph.D., Max Planck Institute for Biochemistry, Munich

ganesh.pathare[at]fmi.ch

Entering university having no idea about contemporary (molecular) biology, Georg was completely blown away when he first heard that biomolecules can be resolved at atomic resolution. This is what he wanted to do and nothing else. So he moved to Heidelberg University where he received his Diploma in Biochemistry/Biophysics doing X-ray crystallography on signal recognition particle (SRP)-like GTPases. He then joined the lab of Jan-Michael Peters - an expert in mitosis and cell cycle control - at the Research Institute of Molecular Pathology (IMP) in Vienna working on a huge ubiquitin ligase complex promoting chromosome segregation in anaphase (anaphase-promoting complex/cyclosome (APC/C)). In the Thomä lab, he is working on drug-induced target protein degradation, a new paradigm in pharmacology that exploits ubiquitin ligase activity to shred disease causing proteins.

GEORG PETZOLD

Postdoc, EMBO/HFSP fellow

Ph.D., Research Institute of Molecular Pathology, Vienna

georg.petzold[at]fmi.ch

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Eric did his Bachelors in Molecular Biology at the University of Basel. He is working on protein expression of complexes in different expression systems.

ERIC PFEIFFER

Masters Student

University of Basel

eric.pfeiffer[at]fmi.ch

Carlos completed a BSc. in Chemistry and an MSc. in Molecular Biology in Madrid, where he developed a fascination with the molecular basis of life. Following a years-long interest in structural biology, he spent the following year in the labs of Alessandro Vannini (Institute of Cancer Research, London) and Wojtek Galej (European Molecular Biology Laboratory, Grenoble). He there studied proteins involved in transcription by RNA pol III and mRNA maturation before joining the Thomä lab for his PhD. He is now interested in the ever-expanding role of ubiquitin ligases as regulators of key cellular processes and hopes to make great contributions to his field.

CARLOS PLA PRATS

Ph.D. Student

Bachelor of Science, Chemistry

carlos.pla-prats[at]fmi.ch

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Pooja received her Masters in Biotechnology from the Indian Institute of Technology, Roorkee, India and then her PhD in structural biology and biochemistry from the Helmholtz Center for Infection Research Braunschweig, Germany in 2017. As a postdoctoral researcher, she is working on analysing DNA double strand break repair mechanisms using structural biology.

POOJA SADANA

Postdoc

Ph.D.,  Hemholtz Center for Infection Research, Germany

pooja.sadana[at]fmi.ch

Andreas received his master’s degree in molecular biology in 2001 and his Ph.D. in 2006 from University of Basel where he worked at the Maurice E. Mueller institute for structural biology in the group of Dr. Andreas Engel. In 2009 he moved to Harvard Medical School in Boston, where as a postdoctoral fellow he studied lipid protein interactions by electron diffraction and viral polymerases with single-particle electron microscope in the group of Dr. Tom Walz. In parallel, he also developed software for processing of electron diffraction data (www.iplt.org). In 2015 he joined the FMI, where he has a shared appointment between the group of Dr. Nicolas Thomä and the electron microscopy facility under Dr. Christel Genoud. In this function he was critically involved in setting up the new electron microscopy facility shared between FMI and Novartis, which opened end of 2016. He is in charge of running the structural EM efforts at FMI together with his colleague Dr. Simone Cavadini; they support the research groups in their structural studies of protein complexes by single-particle EM. In addition, they develop new methodology, workflows and software to provide a cutting-edge electron microscopy platform.

ANDREAS SCHENK

Project Leader, EM Competency Center

Ph.D.,  University of Basel

andreas.schenk[at]fmi.ch

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Dakota received his Bachelors in Chemistry from the University of Michigan-Ann Arbor in 2012 and then his PhD in Analytical Chemistry from the University of North Carolina-Chapel Hill in 2017. He is currently working on the syntheses of new bifunctional degrader molecules that can utilize endogenous ubiquitin ligases to target a range of proteins (e.g., transcription factors).

DAKOTA SUCHYTA

Postdoc

Ph.D.,  University of North-Carolina Chapel Hill

dakota.suchyta[at]fmi.ch

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Suzanne completed her Bachelor honours degree in Human Biology from the University of St. Andrews in Scotland.  She then worked as a research assistant for nearly 6 years in two different epigenetics research laboratories in Singapore.  In her first 2.5 years, she worked under the supervision of Dr. Tan Ene Choo, on a project studying the genetic variants in oestrogen receptor genes and perinatal depression. The following years, she worked in a cardiovascular research lab and participated in multiple projects, mainly under supervision of Dr. Roger Foo Sik Yin and Dr. Eleanor Wong. Now she is working as a research associate in the Thomä lab.

SUZANNE TAN

Research Associate

Bachelor of Science, University of St. Andrews

hui-san.tan[at]fmi.ch

FORMER LAB MEMBERS

Postdoctoral fellows
Markus Vogel (2007-2010)
Andrea Scrima (2007-2011)
Nicolas Bocquet (2009-2013)
Manjappa Lingaraju G (2009-2014)
Kerstin Boehm (2010-2014)
Simone Cavadini (2010-2014)
Richard Bunker (2011-2016)
Wassim Abdul Rahman (2011-2014)
Julius Rabl (2011-2018)
Tianlai Shi (2012-2013)
Eric Fischer (2013-2015)
Michal Walczak (2015-2017)
Andreas Daniel Schenk (2015-2016)

PhD students
Frank Schmitges (2006-2011)
Cian Stutz (2008-2012)
Tianlai Shi (2008-2012)
Eric Fischer (2010-2013)
Weaam Ibrahim Mohamed (2012-2018)
Julia Reinert (2013-2018)
Alessandro Potenza (2014-2015)

Technical/Research associates
Mahamadou Faty (2006-2018)
Jacqueline Blunschi (2009)
Wassim Abdul Rahman (2014-2017)
Manjappa Lingaraju G (2014-2016)
Julia Toth (2015)
Alessandro Potenza (2015-2017)

Undergraduates
Philipp Amsler (2007-2009)
Renata Konickova (2007-2008)
Cian Stutz (2007-2008)
Jonathan Aiwazian (2008-2009)
Eric Fischer (2008-2010)
Ulrike Seeburg (2014-2015)

Visiting scientists
Mariko Yoshizawa (2010)
Lauren Monovich (2012)

Martin Renatus (2014)
Seth Rubin (2016)

 

MEET THE LAB

The lab has between 10-16 members form all over the world and varying scientific backgrounds. Typically half of the lab team has had prior experience in structural biology, while the remainder comes from different fields ranging from cell biology, biochemistry, chemistry to yeast biology. Working in the lab is supported by the FMI core facilities. The FMI structure facility supports robotics, crystallization, data collection, electron microscopy and provides training. Further mass-spectrometry supports are provided by FMI protein analysis facility.