Max Planck Research Group Leaders

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Juanma Vaquerizas

Prof Juanma Vaquerizas · BMS

Max Planck Institute for Molecular Biomedicine · Muenster, Germany

Email
jmv [at] mpi-muenster [dot] mpg [dot] de
jvaquerizas [at] gmail [dot] com

Biography

I have a long-standing interest in understanding the molecular mechanisms that allow cells to use their genetic information to perform normal cellular and physiological functions, such as development and differentiation, and how the mis-regulation of these molecular mechanisms leads to disease, such as cancer. Towards the end of my undergraduate studies in Madrid, and with the advent of the first genome sequences, I became fascinated by the then recently acquired ability of using genomic tools to monitor biological processes, such as gene expression, for large number of genes. Using computational biology approaches, during my PhD I performed the first functional characterisation of the human repertoire of transcription factors, a dataset that became a reference in the field. For my postdoctoral training at the EMBL – European Bioinformatics Institute in Cambridge, I switched my interest to chromatin, in particular focusing on understanding how specific chromatin modifications are used by cells to regulate the difference in sex chromosome dosage between males and females. Unexpectedly, this work revealed a link between the spatial organisation of chromatin and gene regulation, which fuelled my interest in the most current research focus of my Max Planck Research Group: the understanding of the spatial organisation of the genome in development and disease.

Education and positions held

Research Summary

We focus on understanding how the two-meter long molecule of DNA in our cells is encapsulated in a few micron nucleus while all the regulatory mechanisms that make our genomes work properly keep doing so. To do so, we employ a wide range of experimental and computational techniques that allow us to monitor different aspects of gene and genome regulation, such as transcription, chromatin accessibility and chromatin architecture, in a genome-wide manner. Our work focuses mainly in two areas:

  1. Early embryonic development. We use early embryonic development since this is a critical developmental time point when the epigenetic programmes of the fully differentiated gametes need to be reverted back to a totipotent state following fertilisation to produce a new individual. Studies in early fruit fly and mammalian early embryonic development have allowed us to discover specific mechanisms that determine how chromatin architecture emerges at the awakening of the genome.
  2. Disease. Chromatin architecture is of critical importance for the correct regulation of gene expression. Mutations in key elements controlling this level of organisation lead to developmental disorders and diseases such as cancer. In order to examine how the 3D genome is affected in disease, we have developed experimental approaches to study chromatin conformation using small amounts of biological material. These techniques allow us to specifically examine changes in chromatin organisation for disease cells.

Key publications

  • Rhodes JDP, Feldmann A, Hernández-Rodríguez B, Díaz N, Brown JM, Fursova NA, Blackledge NP, Prathapan P, Dobrinic P, Huseyin MK, Szczurek A, Kruse K, Nasmyth KA, Buckle VJ, Vaquerizas JM*, Klose RJ*. Cohesin Disrupts Polycomb-Dependent Chromosome Interactions in Embryonic Stem Cells.
    Cell Rep. 2020 Jan 21; 30(3):820-835.e10 (* joint co-corresponding author)
  • Díaz N, Kruse K, Erdmann T, Staiger AM, Ott G, Lenz G, Vaquerizas JM. Chromatin conformation analysis of primary patient tissue using a low input Hi-C method.
    Nat Commun. 2018 Nov 29; 9(1):4938
  • Hug CB, Grimaldi AG, Kruse K, Vaquerizas JM. Chromatin Architecture Emerges during Zygotic Genome Activation Independent of Transcription.
    Cell. 2017 Apr 6; 169(2):216-228.e19
  • Vaquerizas JM*, Kummerfeld SK, Teichmann SA, Luscombe NM*. A census of human transcription factors: function, expression and evolution.
    Nat Rev Genet. 2009 Apr;10(4):252-63 (* joint co-corresponding author)
  • Kind J*, Vaquerizas JM*, Gebhardt P, Gentzel M, Luscombe NM, Bertone P, Akhtar A. Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila.
    Cell. 2008 May 30;133(5):813-28 (* joint first author)

Luisa F. Pallares

Luisa F. Luisa F. Pallares · BMS

Friedrich Miescher Laboratory · Tübingen, Germany

Email
luisa [dot] pallares [at] tuebingen [dot] mpg [dot] de

Biography

I was born in Ocaña, a city in northeast Colombia, and got my bachelor’s degree in Biology from the Universidad Nacional de Colombia in Bogotá. Then, with a fellowship from the Max-Planck Research School for Evolutionary Biology (IMPRS), I moved to Plön, Germany, where I did my Ph.D. at the Max-Planck Institute for Evolutionary Biology and the Christian-Albrechts-Universität zu Kiel, under the supervision of Diethard Tautz.

During my Ph.D. I studied the genetic basis of within and between species craniofacial morphology in outbred mice as a model for complex traits. Later on, with a Long-Term Postdoctoral Fellowship from the Human Frontiers Science Program (HFSP) I moved to Princeton University in the U.S. to study the genetic basis of complex traits in changing environments (genotype-by-environment interactions). During my postdoctoral work in the Ayroles lab, affiliated with the Ecology and Evolutionary Biology Department and the Lewis-Sigler Institute for Integrative Genomics, I used outbred Drosophila as model system and focused on gene expression variation at the population level. In February 2022, I moved back to Germany, to the Friedrich Miescher Laboratory (Tübingen), where I’m leading the Max Planck Research Group on Evolutionary Genomics of Complex Traits.

Education and positions held

  • 2016-2021:
    • HFSP Postdoctoral Fellow, Princeton University, USA 2022-present: Max Planck Research Group Leader, Friedrich Miescher Laboratory, Tübingen, Germany.
  •  2012-2015:
    • Ph.D. at MPI for Evolutionary Biology, Plön, Germany 2015-2016: Postdoctoral Researcher, MPI for Evolutionary Biology, Plön, Germany.

Research Summary

Our research focuses on understanding (a) the genetic basis of between-individual variation in complex traits and (b) how such complex genetic architectures, instead of being static properties of a trait, get re-shaped when populations are exposed to different environments (genotype-by-environment interactions or GxE). In addition, we are particularly interested in (c) understanding how phenotypic robustness is regulated in such traits.

That is, we aim to understand not only why individuals in a population look different from each other, but also why some individuals are more vulnerable than others when exposed to perturbations like stressful or new environments. To explore these questions within the context of natural genetic variation, we use wild-derived outbred Drosophila melanogaster populations as model system. We integrate experimental and analytical tools across the fields of quantitative and population genetics, molecular and computational biology, and use experimental evolution to generate and analyze large-scale genomics datasets. Conceptually, our research tackles long-standing questions in evolutionary biology including the genotype-phenotype map and its context-dependent nature, and the (apparent) conflict between robustness and evolvability.

Key publications

  • Tautz D, Reeves RG, Pallares LF. (2020). New experimental support for long standing concepts of poly-genic genetics implies that the Mendelian genetic paradigm needs to be revised. In: The New (Old) Genetics, Halle, eds. Wittinghofer, A. and Jäckle, H., NAL-live 2020.1, v1.0
  • Pallares LF, Picard S, Ayroles JF. (2020) TM3’seq: A Tagmentation-Mediated 3’ Sequencing Approach for Improving Scalability of RNA-seq Experiments. G3 10: 143-150
  • Pallares LF*, Ledevin R*, Pantalacci S, Turner LM, Steingrimsson E, Renaud S. (2017) Genomic regions controlling shape variation in the first upper molar of the house mouse. eLife 6:e29510
  • Pallares LF, Carbonetto P, Gopalakrishnan S, Parker CC, Ackert-Bicknell CL, Palmer AA, Tautz D (2015) Mapping of Craniofacial Traits in Outbred Mice Identifies Major Developmental Genes Involved in Shape Determination. PLoS Genet 11:e1005607

Eleanor Scerri

Dr. Eleanor Scerri · GSH

Max Planck Institute for the Science of Human History · Jena, Germany

Email
scerri [at] shh [dot] mpg [dot] de
eleanor [dot] scerri [at] icloud [dot] com

Biography

I am the Lise Meitner Professor at the Max Planck Institute for the Science of Human History (MPI-SHH), where I am leading the Pan African Evolution Research Group (Pan-Ev). I was formerly the first Marie Skłodowska-Curie Actions funded fellow at the MPI-SHH, where I set up and led the aWARE project. Prior to this, I was a British Academy Fellow in Archaeology at the School of Archaeology, University of Oxford where I was also a Junior Research Fellow at Jesus College. This position followed by my first, Fyssen Foundation funded postdoctoral fellowship which I held at the University of Bordeaux. I obtained my PhD in Archaeology from the University of Southampton, jointly funded by the Royal Anthropological Institute and the Sutasoma Trust.

Education and positions held

  • 2014 – 2018
    • University of Oxford, British Academy Postdoctoral Fellow
  • 2013 – 2014
    • University of Bordeaux, Fyssen Postdoctoral Fellow (2013-2014)
  • 2013
    • University of Southampton, PhD in Archaeology

Research Summary

I am an archaeological scientist interested in exploring the articulation between material culture, genetics, and biogeography to further theoretical, methodological and scientific advances in the field of human evolution. My group is exploring the pan-African evolution of our species, Homo sapiens through a number of diverse projects. We are conducting fieldwork in West Africa, generating new information and data for a range of analyses including environmental reconstruction, ancient DNA and palaeoanthropological studies. We are also conducted a range of modelling and simulation work, combining diverse African archives from palaeontology, climate models and genetics, as well as investing in the development of new methodologies for the analysis of archaeological materials.

Key publications

  • Scerri, E.M.L., Chikhi, L., Thomas, M.G. Beyond Multiregional and Simple Out of Africa Models of Human Evolution. Nature Ecology & Evolution 3, 1370–1372.
  • Scerri, E.M.L., Thomas, M.G., Manica, A., Gunz, P., Stock, J., Stringer, C.B., Grove, M., Groucutt, H.S., Timmermann A., Rightmire, G.P., d’Errico, F., Tryon, C., Drake, N.A., Brooks, A., Dennell, R., Durbin, R., Henn, B., Lee-Thorpe, J., deMenocal, P., Petraglia, M.D., Thompson, J., A., Scally, A., Chikhi, L. Did Our Species Evolve in Subdivided Populations across Africa, and Why Does It Matter? Trends in Ecology & Evolution 33, 582-594.
  • Groucutt, H.S., Grün, R., Zalmout, I.S.A., Drake, N.A., Armitage, S.J., Candy, I., Clark-Wilson, R., Louys, J., Breeze, P.S., Duval, M., Buck, L.T., Kivell, T., Pomeroy, E., Stephens, N., Stock, J.T., Stewart, M., Price, G.J., Kinsley, L., Sung, W.W., Alsharekh, A., Al-Omari, A., Zahir, M., Memesh, A.M., Abdulshakoor, A.J., Al-Masari, A.M., Bahameem, A.A., Al Murayyi, K.S.M., Zahrani, B., Scerri, E.M.L., Petraglia, M.D. 2018. Homo sapiens in Arabia 85 thousand years ago. Nature Ecology and Evolution 2, 800–809.
  • Scerri, E.M.L., Blinkhorn, J., Niang, K., Bateman, M., Groucutt, H.S. Persistence of Middle Stone Age technology to the Pleistocene/Holocene transition supports a complex hominin evolutionary scenario in West Africa. Journal of Archaeological Science Reports 11, 639-646.
  • Scerri, E. M. L., Drake, N., Groucutt, H. S., Jennings, R. Earliest Evidence for the Structure of Homo sapiens Populations in Africa. Quaternary Science Reviews 101, 207-216

Monika Scholz

Dr. Monika Scholz · BMS

Center of Advanced European Studies and Research (caesar) · Bonn, Germany

Email
monika [dot] scholz [at] caesar [dot] de

Biography

Monika Scholz studied Physics at the Julius-Maximilians-University in Würzburg, receiving her B.Sc. in 2010, and after further studies, she received her Diploma degree in Physics from the Technical University Dresden in 2012. After moving to the US and joining the PhD-Program of the University of Chicago she worked with Aaron Dinner and David Biron.

In 2014 she won a HHMI predoctoral fellowship, which supported her work on feeding behavior in C. elegans. She was awarded a William Rainey Harper Dissertation Fellowship and the Stephen B. H. Kent Prize in Biophysical Sciences for her dissertation. After obtaining her PhD-degree in Biophysics in 2017, she moved to Princeton University as a Dicke-Fellow in the Physics Department. There she used whole-brain calcium imaging of C. elegans to study the neural basis of behavior. She is now at caesar, Bonn to establish a Max Planck Research group with the long-term goal to discover and describe the principles underlying information transfer, processing, and compression in animals.

Education and positions held

  • 2019-present:
    • Max-Planck Group Leader (W2), research institute caesar, Bonn
  • 2017-2019:
    • Dicke Fellow, Department of Physics, Princeton University

Research Summary

We use the foraging behavior of the roundworm C. elegans to study how animals temporally coordinate locomotion and feeding behavior. Foraging is of particular interest, as locomotion and feeding are controlled in two entirely distinct neural circuits of the worm. These two sub-networks are only connected by a bilateral pair of gap junctions, forming a bottleneck between the two circuits. Intriguingly, sensory information is transmitted between those two networks: for example, a touch detected by the touch-sensory neurons of the somatic network causes a halt in feeding. How information is transmitted and how it is compressed in this bottleneck is a key question in my group. Bottlenecks are common both in biological networks as well as artificial networks and are often the crucial ingredient for separating relevant information from irrelevant information.

We follow the information flow through the bottleneck experimentally using behavioral assays, neural activity imaging, optogenetics, and genetic perturbations. Ultimately, the goal of the group ‘Neural Information Flow’ is to understand how animals integrate multiple sources of information and how this drives their foraging strategy. We expect that this approach will yield insight on decision making and attention in a small invertebrate brain.

Key publications

  • Hallinen, K. M.*, Dempsey, R.*,Scholz, M.*(*equal contribution), Yu, X., Linder, A. L., Randi, F., Sharma, A., Shaevitz, J. and Leifer, A. L. Decoding locomotion from population neural activity in moving C. elegans (submitted) Scholz, M., Dinner, A. R., Levine, E. and Biron, D. (2017). Stochastic feeding dynamics arise from the need for information and energy. PNAS 114,9261–9266
  • Lee, K. S., Iwanir, S., Kopito, R. B., Scholz, M., Calarco, J. A., Biron, D. and Levine, E. (2017).Serotonin-dependent kinetics of feeding bursts underlie a graded response to food availability in C. elegans. Nat Com 8, 14221 Scholz, M., Lynch, D. J., Lee, K. S., Levine, E. and Biron, D. (2016). A scalable method for automatically measuring pharyngeal pumping in C. elegans. J Neur Meth 274,172–178.

Nicolas Schuck

Dr. Nicolas Schuck · GSH

Max Planck Institute for Human Development · Berlin, Germany

Email
schuck [at] mpib-berlin [dot] mpg [dot] de

Biography

From 2004 to 2010 I studied Psychology at Humboldt University in Berlin, while also doing a Minor in Machine Learning at University of Toronto as a Exchange student (2007-2008). I then received a scholarship from the Max Planck society to do a PhD at the MPI for Human Development Berlin, which I finished in 2013. Next I did a postdoc at the Princeton Neuroscience Institute, Princeton University (2013-17). Since 2017 I am leading a Independent Max Planck Research Group at the MPI for Human Development.

Education and positions held

  • 2020-present:
    • PI at Max Planck-UCL
  • 2017-present:
    • Independent Max Planck Group Leader
  • 2013-2017:
    • Princeton University, Postdoc at Neuroscience Institute
  • 2010-2013:
    • Max Planck Institute for Human Development, Phd in Psychology
  • 2007-2008:
    • University of Toronto (Exchange), Minor in Machine Learning

Research Summary

My research aims to understand how decision making problems are represented in the brain. When playing chess, for instance, a novice will attend to and remember different aspects of a given position than an expert. In this sense, learning not only involves learning how to act, but also to how process, represent and store information. How are such adaptive representations learned, computationally? Where in the brain do they reside? And what role does replay, i.e. memory reactivation during idle wakefulness and sleep, play in this process? Unraveling how we learn representations that make complex tasks easy is the overarching goal of my research. I am addressing these questions by applying computational models and pattern recognition algorithms to experimental data from functional magnetic resonance imaging (fMRI). This approach allows me to decode the information hidden in the complex brain activation patterns of humans while they make decisions.

Key publications

  • Wittkuhn, L. & Schuck, N.W. (2021) Dynamics of fMRI patterns reflect sub-second activation sequences and reveal replay in human visual cortex. Nature Communications, 12(1795) doi:10.1038/s41467-021-21970-2
  • Schuck, N. W., & Niv, Y. (2019). Sequential replay of nonspatial task states in the human hippocampus. Science, 364(6447):eaaw5181. doi:10.1126/science.aaw5181
  • Kaplan*, R., Schuck*, N. W., Doeller, C. F. (2017). The role of mental maps in decision-making. Trends in Neurosciences, 40(5), 256–259. doi:10.1016/j.tins.2017.03.002
  • Schuck, N. W., Cai, M. B., Wilson, R. C. & Niv, Y. (2016). Human orbitofrontal cortex represents a cognitive map of state space. Neuron, 91(6), 1402–1412. doi: 10.1016/j.neuron.2016.08.019
  • Schuck, N. W., Gaschler, R., Wenke, D., Heinzle, J., Frensch, P. A., Haynes, J.-D. & Reverberi, C. (2015). Medial prefrontal cortex predicts internally driven strategy shifts. Neuron, 86(1), 331–340. doi: 10.1016/j.neuron.2015.03.015

Frank Ohme

Dr. Frank Ohme · CPTS

Max Planck Institute for Gravitational Physics · Hannover, Germany

Email
frank [dot] ohme [at] aei [dot] mpg [dot] de
frank [dot] ohme [at] ligo [dot] org

Biography

Grown up in the picturesque part of Germany called Thüringen, I studied Physics at the Friedrich Schiller University Jena and was one of the last students to receive a German diploma in 2008. (Now they all become Bachelors and Masters.)

Having enjoyed my first experiences in gravitational-wave data analysis with Prof. Schmeißer, and a one-year diploma project in the Numerical Relativity group of Prof. Brügmann, I moved on to the MPI for Gravitational Physics in Potsdam, also known as the Albert Einstein Institute, where I spent three and a half wonderful years (2009 – 2012) working on the interface of numerical relativity and gravitational-wave data analysis under the supervision of Bernard Schutz and Badri Krishnan.

After a few months as a post doc at the other Albert Einstein Institute in Hannover, I moved to Cardiff in September 2012, where I was a post-doctoral researcher under Stephen Fairhurst and later an ERC-funded Research Fellow under Mark Hannam.
My time in Cardiff had a great influence on me, and it also saw the (gravitational-wave) world changing on September 14, 2015. I was part of the international team of scientists that discovered and interpreted the first direct gravitational-wave observation of a black-hole binary. My small role in this gigantic endeavour was to help understanding what the signal we observed told us about the black holes it originated from. And it told us a lot!

Since November 2016 I have the honour to lead my own research group.

Education and positions held

  • 2012 – 2016
    • Research Fellow at Cardiff University
  • 2009 – 2012
    • PhD at MPI for Gravitational Physics (Postdam)
  • 2003 – 2008
    • Physics Diploma at University of Jena

Research Summary

Black holes are hard to find in the Universe. After all, nothing escapes them. However, when two of those mysterious object trap each other through their gravitational attraction, they typically perform a long-lasting dance around each other that warps space and time so much that they emit spacetime oscillations called gravitational waves. In my research group, we analyze data from kilometer-scale laser interferometers (called LIGO and Virgo) that can pick up those tiny spacetime distortions. The best chance we have to understand what we see (or rather, ‘hear’), is to model the gravitational-wave signal emitted by those coalescing black holes. We combine super computer simulations, pen-and-paper calculations and a fair amount of fancy statistics to extract more and more invisible secrets the Universe is holding.

Key publications

  • LIGO Scientific and Virgo Collaborations (B. P. Abbott et al.), GW190412: Observation of a Binary-Black-Hole Coalescence with Asymmetric Masses, accepted by Phys. Rev. D., arXiv:2004.08342 (2020)
  • Sebastian Khan, Frank Ohme, Katerina Chatziioannou, and Mark Hannam, Including higher order multipoles in gravitational-wave models for precessing binary black holes, Phys. Rev. D 101, 024056 (2020), arXiv: 1911.06050
  • LIGO Scientific and Virgo Collaborations (B. P. Abbott et al.), Properties of the Binary Black Hole Merger GW150914. Phys. Rev. Lett. 116, no. 24, 241102 (2016), arXiv:1602.03840
  • F. Pannarale and F. Ohme, Prospects for joint gravitational-wave and electromagnetic observations of neutron-star–black-hole coalescing binaries. Astrophys. J. 791 L7 (2014), arXiv:1406.6057
  • F. Ohme, A. B. Nielsen, D. Keppel and A. Lundgren, Statistical and systematic errors for gravitational-wave inspiral signals: A principal component analysis. Phys. Rev. D88 4 042002 (2013), arXiv:1304.7017

Danny Nedialkova

Prof. Dr. Danny Nedialkova · BMS

Max Planck Institute of Biochemistry · Martinsried, Germany

Email
nedialkova [at] biochem [dot] mpg [dot] de

Biography

Danny Nedialkova studied biotechnology at the University of Perugia (Italy) from 2001 to 2004 and received her doctorate in molecular virology from Leiden University (The Netherlands) in 2010. She later worked as a postdoc at the Max Planck Institute for Molecular Biomedicine in Münster, with a long-term fellowship from the European Molecular Biology Organization.

Since 2017, she leads the Max Planck Research Group “Mechanisms of Protein Biogenesis” at the MPI of Biochemistry in Martinsried. That same year, she was appointed as a Tenure-Track Professor for Biochemistry of Gene Expression at the Department of Chemistry (TU Munich) through the MaxPlanck@TUM program.

Education and positions held

  • 2017 – present:
    • Max Planck Research Group Leader (MPI of Biochemistry, Martinsried, DE)
  • 2017 – present:
    • Tenure-track Professor (Department of Chemistry, TU Munich, DE)
  • 2010 – 2016:
    • Postdoctoral Fellow (MPI of Molecular Biomedicine, Münster, DE)
  • 2004 – 2010:
    • Ph.D Student (Leiden University Medical Center, NL)
  • 2001 – 2004:
    • B.Sc Student (Universita degli Studi di Perugia, IT)

Research Summary

Proteins mediate most biological processes and function only after folding into complex three-dimensional shapes. To ensure protein homeostasis in a range of environments, cells rely on a complex molecular network that orchestrates timely and accurate protein synthesis, folding, and degradation.

Our research seeks to define how distinct metazoan cell proteomes are established and maintained, and to uncover why some cell types are selectively vulnerable to proteome damage. We address these questions at a systems level using genome-wide assays and gene inactivation screens in stem cell-derived models.

Key publications

  • Behrens, A., Rodschinka, G., Nedialkova D.D. 2021. “High-resolution quantitative profiling of tRNA abundance and modification status in eukaryotes by mim-tRNAseq”. Molecular Cell 81(8):1802-1815.e7.
  • Jungfleisch J., Nedialkova D.D.*, Dotu I.*, Sloan K.E., Bruening L., Raineri E., Bohnsack M., Leidel S.A., Diez J. 2017. “A novel and conserved translational control mechanism involving RNA structures within coding sequences“. Genome Res.; 27(1):95-106.*Equal contribution
  • Laguesse S.*, Creppe C.*, Nedialkova D.D., Prévot P.-P., Borgs L., Huysseune S., Franco B., Duysens G., Krusy N., Lee G., Thelen N., Thiry M., Close P., Chariot A., Malgrange B., Leidel S.A., Godin J.D., Nguyen L. 2015. “A dynamic unfolded protein response contributes to the control of cortical neurogenesis”. Dev Cell 35 (5): 553-67 *Equal contribution
  • Nedialkova D.D., Leidel S.A. 2015. “Optimization of codon translation rates via tRNA modifications maintains proteome integrity”. Cell 161 (7): 1606-1618.
  • Nedialkova D.D., Gorbalenya A.E., Snijder E.J. 2010. “Arterivirus nsp1 modulates the accumulation of minus-strand templates to control the relative abundance of viral mRNAs”. PLoS Pathog. 6(2): e1000772.
  • Nedialkova D.D., Ulferts R., van den Born E., Lauber C., Gorbalenya A.E., Ziebuhr J., Snijder E.J. 2009. “Biochemical characterization of arterivirus nonstructural protein 11 reveals the nidovirus-wide conservation of a replicative endoribonuclease”. J Virol. 83 (11): 5671–5682.

Edda G. Schulz

Dr. Edda G. Schulz · BMS

Max Planck Institute for Molecular Genetics · Berlin, Germany

Email
edda [dot] schulz [at] molgen [dot] mpg [dot] de

Biography

The main goal of my research is to understand how complex regulatory networks govern quantitative information processing and molecular decision-making during mammalian differentiation processes. During my PhD, I combined quantitative experiments and modeling to dissect the gene-regulatory network governing differentiation of type 1 T-helper lymphocytes, whereby I solved a long-standing question regarding the respective roles of IFN-γ and IL-12. For my postdoctoral research, funded by an HFSP long-term fellowship, I moved to a new field, epigenetics, because I believed that this layer of regulation was crucial to understand how transcriptional states are maintained in mammals. I learned how to apply genome-wide techniques and found that genes within the same topologically associating domain (TAD) tend to be co-regulated, providing a first indication for the functional role of TADs, which has since then been confirmed in numerous studies. Moreover, I discovered fundamental sex differences in embryonic stem cells with regard to pluripotency and differentiation that are only relieved once X-dosage compensation has occurred through X-chromosome inactivation. In 2015 I started as a Max Planck research group leader to identify the regulatory principles that control transcriptional states in mammals, using the onset of X-chromosome inactivation as a model.

Education and positions held

  • 2014 – present
    • Max Planck Research Group Leader at the MPI for Molecular Genetics, Berlin
  • 2010 – 2013
    • Institut Curie, Paris, France, Postdoc with Prof. Edith Heard, funded by HFSP long-term fellowship
  • 2005 – 2009
    • PhD, Biophysics, Humboldt Universität, Berlin
  • 1999 – 2005
    • Diplom, Biochemistry, Eberhard-Karls-Universität Tübingen

Research Summary

We are interested understanding how transcriptional states are established in response to multiple quantitative input signals and how they can then be stably maintained. As a model, we study the regulatory principles that restrict expression of Xist, the master regulator of X-chromosome inactivation, to exactly one randomly chosen X-chromosome in females. To this end, we combine theoretical, computational and experimental approaches. We have recently developed the first experimentally-validated mathematical model of the Xist regulatory network that can explain seemingly diverse Xist expression patterns in different species. Moreover, we use pooled CRISPR screens to identify missing regulators and cis-regulatory elements, combined with genome-engineering and (single-cell) genomics to quantitatively profile the players and interactions within the Xist regulatory network. In this way we aim to elucidate the principles the govern transcriptional and epigenetic regulation in the mammalian genome.

Key publications

  • Barros de Anrade e Sousa L*, Jonkers I*, Syx L, Dunkel I, Chaumeil J, Picard C, Foret B, Chen C, Lis JT#, Heard E#, Schulz EG# and Marsico A#. Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic features. Genome Research, 2019, doi:10.1101/gr.245027.118
  • Mutzel V, Okamoto I, Dunkel I, Saitou M, Giorgetti L, Heard E and Schulz EG. A symmetric toggle switch explains the onset of random X inactivation in different mammals. Nature Structural and Molecular Biology, 2019, 26.5, 350-360, doi:10.1038/s41594-019-0214-1
  • Schulz EG, Meisig J, Nakamura T, Okamoto I, Sieber A, Picard C, Borensztein M, Saitou M, Blüthgen N and Heard E. The two active X chromosomes in female embryonic stem cells block exit from the pluripotent state by inhibiting the MAPK signaling pathway,
    Cell Stem Cell, 2014, 14:203-2016, doi:10.1016/j.stem.2013.11.022
  • Nora EP, Lajoie BR*, Schulz EG*, Giorgetti L*, Okamoto I, Servant N, Piolot T, van Berkum NL, Meisig J, Sedat J, Gribnau J, Barillot E, Blüthgen N, Dekker J# and Heard E#. Spatial partitioning of the regulatory landscape of the X-inactivation centre, Nature, 2012, 485(7398):381-5, doi:10.1038/nature11049
  • Schulz EG, Mariani L, Radbruch A and Höfer T. Sequential polarization and imprinting of type 1 T-helper lymphocytes by interferon-γ and interleukin-12, IMMUNITY, 2009, 30 (5), 673-683, doi:10.1016/j.immuni.2009.03.013

Georg Martius

Dr. Georg Martius · CPTS

Max Planck Institute for Intelligent Systems · Tübingen, Germany

Email
georg [dot] martius [at] tuebingen [dot] mpg [dot] de

Biography

Georg Martius received his Diploma (Master equivalent) in Computer Science from University of Leipzig, Germany, in 2005. He pursued a Ph.D at the Bernstein Center for Computational Neuroscience in Göttingen, Germany finishing in 2009 with highest praise. Several postdoc positions at the Max Planck Institute (MPI) for Dynamics and Self-Organization, Göttingen, at the MPI for Mathematics in the Sciences in Leipzig and at the Institute of Science and Technology Austria have broadened his background. Since 2017 he is leading the Research group in Autonomous learning at MPI for Intelligent Systems in Tübingen, Germany, with the focus on Machine Learning for robotics.

Education and positions held

Education

  • 2005 – 2009
    • PhD at Bernstein Center for Computational Neuroscience (BCCN) Göttingen, Germany.
  • 1999 – 2005
    • Diploma in Computer Science.University of Leipzig, Faculty of Mathematics and Computer Science.
  • 2002 – 2003
    • Visiting Student, University of Edinburgh, Division of Informatics, Scotland, UK.

Positions

  • 2017 – present
    • Max Planck Research Group Leader, MPI for Intelligent Systems, Tübingen.
  • 2015 – 2017
    • IST-Fellow at Institute of Science and Technology Austria.
  • 2010 – 2015
    • Post-doctoral position at Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.
  • 2009 – 2010
    • Post-doctoral position at Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany.

Research Summary

I am interested in autonomous learning, that is how an embodied agent can determine what to learn, how to learn, and how to judge the learning success. I am using information theory and dynamical systems theory to formulate generic intrinsic motivations that lead to coherent behavior exploration – much like playful behavior. I am working on machine learning methods particularly suitable for reinforcement learning, internal models, and representation learning.

Key publications

  • G. Martius, R. Der, and N. Ay. Information driven self-organization of complex robotic behaviors. PLoS ONE, 8(5):e63400, 2013.
  • R. Der and G. Martius. Novel plasticity rule can explain the development of sensorimotor intelligence, PNAS, 2015, doi: 10.1073/pnas.1508400112
  • S. S. Sahoo, C. H. Lampert, and G. Martius. Learning equations for extrapolation and control. In Proc. Intl. Conf. on Machine Learning (ICML’18), volume 80, pages 4442-4450, PMLR, 2018
  • M. Rolinek, D. Zietlow and G. Martius. Variational Autoencoders Recover PCA Directions (by Accident), In Proc. Conference on Computer Vision and Pattern Recognition (CVPR’19), pages 12406–12415, 2019
  • S. Blaes, M. Vlastelica-Pogančić, J.-J. Zhu, and G. Martius. Control What You Can: Intrinsically motivated task-planning agent. In Advances in Neural Information Processing Systems 32 (NeurIPS’19), 2019.

John Weir

Dr. John Weir · BMS

Friedrich Miescher Laboratory · Tübingen, Germany

Email
john [dot] weir [at] tuebingen [dot] mpg [dot] de

Biography

Lacking an academic background, and initially unsure of what I was interested in, I studied a very broad Medical Sciences undergraduate degree in Leeds. I quickly realised I wanted to understand systems in great detail, and thus specialised in biochemistry. Upon graduation I moved to Cambridge to work as a research assistant in the MRC-LMB in the lab of Venki Ramakrishnan.

Working in the Ramakrishnan lab sparked my interest in structural biology, and after two years moved to pursue a PhD with Elena Conti. I was initially at the EMBL in Heidelberg, and later moved with Elena to the Max Planck in Martinsried. My PhD work revealed some unique structural features of an RNA helicase, and how this might contribute to its function with other cofactors and the RNA exosome.

I continued within the Max Planck Society as a Postdoc, moving to the group of Andrea Mussacchio at the MPI of Molecular Physiology in Dortmund. In Andrea’s lab I helped to unravel the biochemical puzzle of protein organisation within the kinetochore. Kinetochores are vast protein assemblies, built on chromosomes, that ensure that each chromosome is properly segregated during both mitosis (“normal” cell division) and meiosis; the generation of haploid germ cells for sexual reproduction. In my independent research group I now study the biochemical mechanisms of meiosis at the Friedrich Miescher Laboratory in Tübingen.

Education and positions held

  • 2017-Present:
    • MPRGL Friedrich Miescher Laboratory, Tübingen
  • 2011-2017:
    • Postdoc, MPI Molecular Physiology Dortmund
  • 2006-2011:
    • PhD Student EMBL Heidelberg & MPI Biochemistry, Martinsried, Germany
  • 2004-2006:
    • Research Assistant, MRC-LMB, Cambridge UK
  • 2001-2004:
    • BSc Medical Science, Leeds UK

 

Research Summary

Meiosis is at the very heart of both eukaryotic diversity and our very own genetic individuality. During meiosis, the parental genome needs to be reduced in order that the next generation receives the correct number of chromosomes. In order to achieve this task, the homologous chromosomes in the parental genome need to be linked and then segregated. We study how these meiotic chromosome linkages occur, and how they are regulated. Both complex mammals, and the simple unicellular yeast, use the same basic mechanisms to ensure that meiosis takes place properly. In order to link homologous chromosomes the cell introduces programmed double strand DNA breaks in its own genome.

These breaks are then repaired, using the homologous chromosome as a DNA repair template. Modifications to the normal DNA repair mechanisms lead to these DNA repair events to physically connect homologous chromosomes to one another. We are interested in understanding the regulation of meiotic DNA break formation, in number space and time. We are also interested in understanding how these breaks become crossovers through the activity of DNA helicases. Due to the difficulty in studying these processes in the cell directly, we try to rebuild these systems outside of the cell, using recombinant proteins and synthetic chromatin.

Key publications

  • Altmannova V, Blaha A, Astrinidis S, Reichle H, Weir JR. InteBac: An integrated bacterial and baculovirus expression vector suite. Protein Sci. 2021 Jan;30(1):108-114. doi: 10.1002/pro.3957. Epub 2020 Oct 13. PMID: 32955754; PMCID: PMC7737779.
  •  Weir JR*, Faesen AC*, Klare K*, Petrovic A, Basilico F, Fischböck J, Pentakota S, Keller J, Pesenti ME, Pan D, Vogt D, Wohlgemuth S, Herzog F, Musacchio A. Insights from biochemical reconstitution into the architecture of human kinetochores. Nature. 2016 Sep 8;537(7619):249-253. doi: 10.1038/nature19333. Epub 2016 Aug 31. PMID: 27580032.
  • Klare K*, Weir JR*, Basilico F, Zimniak T, Massimiliano L, Ludwigs N, Herzog F, Musacchio A. CENP-C is a blueprint for constitutive centromere-associated network assembly within human kinetochores. J Cell Biol. 2015 Jul 6;210(1):11-22. doi: 10.1083/jcb.201412028. Epub 2015 Jun 29. PMID: 26124289; PMCID: PMC4494010.
  • Falk S*, Weir JR*, Hentschel J, Reichelt P, Bonneau F, Conti E. The molecular architecture of the TRAMP complex reveals the organization and interplay of its two catalytic activities. Mol Cell. 2014 Sep 18;55(6):856-867. doi: 10.1016/j.molcel.2014.07.020. Epub 2014 Aug 28. PMID: 25175027.
  • Weir JR, Bonneau F, Hentschel J, Conti E. Structural analysis reveals the characteristic features of Mtr4, a DExH helicase involved in nuclear RNA processing and surveillance. Proc Natl Acad Sci U S A. 2010 Jul 6;107(27):12139-44. doi: 10.1073/pnas.1004953107. Epub 2010 Jun 21. PMID: 20566885; PMCID: PMC2901443.