18th EMBL PhD Symposium
Life by Numb3rs
Towards Quantitative Biology
17th–19th November, 2016
EMBL Heidelberg, Germany

About the Symposium

Current research in biology demands an increasingly quantitative focus where system-wide approaches and theoretical modeling play a central role. Modern techniques allow the collection of vast amounts of data, yet analysing the underlying mechanisms and rules from this data remains challenging. This is further complicated by the fact that many of these processes are inherently stochastic and rarely accompanied by exact functional descriptions. Faced with these challenges, we still need to find ways to draw accurate conclusions and gain higher-level understanding.

The aim of this conference is to highlight recent advances and applications of quantitative research. In addition, we hope this symposium will inspire young researchers to see the implications of their work beyond a single process or correlation. This may help us get closer to predicting complex biological behavior by well-established principles comparable to those found in fundamental physics. At the core of this idea stands an interdisciplinary approach, which is also an integral part of the research here at EMBL. Finally, the symposium will consider quantification across multiple scales of biology, ranging from the sub-cellular to the multi-cellular level.

We hope that an increased focus on quantitative and interdisciplinary approaches on a systems-level will help us reveal underlying mechanistic principles in biology.


Photo of Luis Serrano

The EMBO Keynote Lecture

Dr. Luis Serrano - (website)
Friday 18th - 09:00-10:00

Centre for Genome Regulation - Spain

Dr Serrano graduated with a Bachelor's of Biological Sciences (1981) and Master’s in Science (1982) from the Complutense University of Madrid. He then completed a PhD in Biochemistry in the Universidad Autónoma de Madrid (1985) and in Cell Biology at the Centro de Biología Molecular (CSIC-UAM) in 1987 and the University of Cambridge in 1991. Subsequently he spent 4 years in the laboratory of Professor A.R. Fehrs, at the Medical Research Council (MRC), UK, where he focused his research on protein folding. Currently Dr Serrano is the director of Centro de Regulación Genómica (CRG) and a member of the Spanish Society for Biochemistry and Molecular Biology (SEBBM), member of the European Molecular Biology Organisation (EMBO) and member of the Royal Spanish Academy of Sciences (Spain).

Photo of Raymond E. Goldstein

Prof. Raymond E. Goldstein - (website)
Saturday 19th - 09:00-10:00

Department of Applied Mathematics and Theoretical Physics, University of Cambridge - UK

Professor Goldstein graduated from the Massachusetts Institute of Technology (MIT) with a double-major Bachelor of Science degrees in Physics and Chemistry in 1983. He continued his education at Cornell University, where he was awarded a Master of Science degree in Physics in 1986, followed by a PhD in 1988 for research on phase transitions and critical phenomena supervised by Neil Ashcroft. Prof Goldstein is a Fellow of the American Physical Society, the Institute of Physics, the Institute of Mathematics and its Applications, and the Royal Society. He is currently a Schlumberger Professor of Complex Physical Systems at University of Cambridge, focusing his research on non-equilibrium biological systems.

Photo of L. Mahadevan

Prof. L. Mahadevan - (website)
Thursday 17th - 09:30-10:30

Harvard University - USA

Professor Mahadevan graduated from the Indian Institute of Technology, Madras, and then received an M.S from the University of Texas at Austin, and an M.S. and Ph.D. from Stanford University in 1995. He started his independent career on the faculty at the Massachusetts Institute of Technology (MIT) in 1996.
Professor Lakshminarayanan Mahadevan is currently the Lola England de Valpine Professor of Applied Mathematics, Organismic and Evolutionary Biology and Physics at Harvard University. His work centers on using mathematics to understand the organization of matter in space and time.

Photo of Jean-Karim Hériché

Dr. Jean-Karim Hériché
Thursday 17th - 14:30-15:15

EMBL Heidelberg - Germany

Jean-Karim Hériché was trained as an engineer and obtained a PhD in biology from Université Joseph Fourier in Grenoble, France for work carried out at the French Atomic Energy Commission. He did post-doctoral research on cell cycle control during Drosophila development in Patrick O'Farrell's lab at the University of California, San Francisco and then moved to Richard Durbin's group at the Wellcome Trust Sanger Institute where he implemented bioinformatics tools and analysis methods for the MitoCheck project. He is now in the Cell Biology and Biophysics Unit at EMBL-Heidelberg where he works on image-based systems biology and bioimage informatics projects.

Photo of Dagmar Iber

Prof. Dagmar Iber - (website)
Saturday 19th - 10:00-10:45

Department of Biosystems Science and Engineering, ETH Zürich - Switzerland

Dagmar Iber studied mathematics and biochemistry in Regensburg, Cambridge and Oxford. She holds Master degrees and PhDs in both disciplines. After three years as a Junior Research Fellow in St John’s College, Oxford Dagmar became a lecturer in Applied Mathematics at Imperial College London. Dagmar has joined ETH Zuerich in 2008 after returning from an investment bank where she worked as an oil option trader for one year. Prof Iber’s group develops data-based, predictive models to understand the spatio-temporal dynamics of signaling networks. Her recent work focuses on mouse organogenesis and patterning systems to further understand the control of organ growth and robustness of signalling mechanisms in response to evolutionary changes.

Photo of Irene Miguel-Aliaga

Dr. Irene Miguel-Aliaga - (website)
Saturday 19th - 11:15-12:00

Imperial College London - UK

Irene Miguel-Aliaga is Professor of Genetics and Physiology at Imperial College London and Programme Leader at the London MRC Clinical Sciences Centre. She obtained her DPhil in Genetics from the University of Oxford, and explored how neurons acquire their identity during postdoctoral work at Harvard, Linkoping University and NIMR (now Crick Institute), London. First at Cambridge and now in London, her research group is investigating cellular and organ plasticity and exploring the mechanisms by which organs sense change and respond to it. Their work has primarily focused on the fly intestine and its neurons, investigating the links between gut neural system, reproduction and metabolic adaptation processes. Irene was elected to the EMBO YIP programme in 2012 and is the recipient of an ERC Starting Grant.

Photo of Peter de Peinder

Dr. Peter de Peinder - (website)
Thursday 17th - 16:45-17:30

VibSpec - The Netherlands

Peter de Peinder studied Chemistry at Utrecht University and then became a member of the Vibrational Spectroscopy department as a junior scientist. In 1999 he got a position of a senior scientist at the Material Analysis department of Philips Research and from 2000-2004 a part-time scientist position at Utrecht University. In 2006 he left Philips Research Eindhoven and focused on his activities at VibSpec. In 2009 he obtained his PhD in chemistry on the characterisation of crude oils by a combination of spectroscopy and chemometrics. As a part-time member of the Inorganic Chemistry and Catalysis group of Utrecht University he is involved in in-situ vibrational spectroscopy of homogeneous and heterogeneous catalysts.

Photo of Lucas Pelkmans

Prof. Lucas Pelkmans - (website)
Thursday 17th - 11:15-12:00

Institute of Molecular Life Sciences, University of Zürich - Switzerland

Prof Pelkmans studied at the University of Utrecht in The Netherlands and obtained his PhD from the ETH Zurich in 2003, after which he got a position as a postdoctoral fellow at the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, Germany. In 2005 he became assistant professor at the ETH Zurich and in 2010 the full professor at the University of Zurich, where he currently holds the Ernst Hadorn Chair. His lab operates at the forefront of research in quantitative cell biology, in the study of cell-to-cell variability, as well as in systems approaches based on large-scale genetic perturbations and network biology.

Photo of Leïla Perié

Dr. Leïla Perié - (website)
Friday 18th - 10:00-10:45

Institut Curie - France

Dr. Leila Perie completed her PhD from the Cochin Institute, Paris in 2009. After that, she has worked on cell differentiation at College de France, National Cancer Institute in Amsterdam and Utrecht University. In 2015, she started a young research group at Curie Institute in Paris focussing on deciphering the hematopoietic tree using single cell lineage tracing methods in combination with mathematical modeling, as well as modeling T cell dynamics. Apart from the intensive research in the field of quantitative immunology, Leila is also providing training for scientists and promoting the use of scientific communication as a tool of empowerment.

Photo of Paola Picotti

EMBO Young Investigator

Prof. Paola Picotti - (website)
Friday 18th - 16:15-17:00

Department of Biochemistry, ETH Zürich - Switzerland

Prof. Paola Picotti has obtained her PhD from the University of Padova. In 2006, she joined Prof. Ruedi Aebersold’s group at ETH Zurich, where her research received the ETH Latsis Prize 2011. At the beginning of 2011, she started her own research group and was appointed assistant professor at the Institute of Biochemistry at ETH Zurich. Her team focuses on the study of the effects of intracellular protein misfolding and aggregation using novel proteomics approaches. Among her pioneering achievements is the development of a method to analyze protein structural changes in biological samples and on large scale. In 2015 she was selected as an EMBO Young Investigator, while recently she won the 2016 Robert J. Cotter new investigator award for her significant contribution in the field of proteomics.

Photo of Leonie Ringrose

Prof. Leonie Ringrose - (website)
Friday 18th - 11:15-12:00

IRI Life Sciences - Germany

Prof. Leonie Ringrose has been a professor since 2015 at the IRI for Life Sciences, Humboldt University, Berlin. From 2006 to 2014 she was a junior group leader at the Institute of Molecular Biotechnology (IMBA) in Vienna, Austria. In 2014 she visited the John Innes Centre, Norwich UK for a sabbatical in systems biology. Her group works on the epigenetic regulation in Drosophila and mouse development. They combine strategies of quantitative live imaging, mathematical modeling, computational approaches with molecular developmental biology to understand the interaction of the Polycomb and Trithorax proteins with their chromatin targets.

Photo of Timothy Ryan

Prof. Timothy Ryan - (website)
Saturday 19th - 15:15-16:00

Weill Cornell Medical College - USA

Prof. Ryan received his Bachelor of Science in Physics at McGill University and his PhD in Physics at Cornell in the laboratory of Watt Webb. After carrying out postdoctoral work at Stanford Medical School he started his own Weill Cornell Medical College, USA where he is currently a Tri-Institutional Professor. The focus of his lab is on the molecular basis of synaptic transmission in mammalian brain. His prime interest lies in understanding the regulation of presynaptic strength. Dr Ryan's group uses biophysical tools to measure physiological parameters at synapses, including exocytosis, endocytosis, action potential waveforms and voltage-triggered calcium fluxes in individual presynaptic boutons. Dr Ryan's team develops state-of-the-art optical methods to obtain a quantitative understanding of presynaptic function and attempts to reduce the complexities of synaptic transmission in a physico-chemical framework.

Photo of Jonas Hartmann

Science & Society

Mr. Jonas Hartmann
Thursday 17th - 13:45-14:30

EMBL Heidelberg - Germany

Following his apprenticeship as a restaurant chef, Jonas Hartmann decided to study cell biology, receiving his master's degree from the University of Zurich in 2014. As a PhD student at EMBL, he is now investigating the interplay of signaling and morphogenesis, developing experimental and computational tools for single-cell perturbation and analysis. However, his fascination with philosophy also has Jonas ask some very different questions, including how the paradigms of modern biology were established, how they shape today's research, and how their limitations might be overcome. He is convinced that an understanding of such questions can help us do good science.

Photo of Russ Hodge

EMBO Science Policy

Mr. Russ Hodge - (website)
Saturday 19th - 13:45-14:30

Russ Hodge is currently working as a science writer at the Max Delbrück Center for Molecular Medicine in Berlin, Germany. His latest book is The Case of the Short-fingered Musketeer, about a 20-year search for the causes of essential hypertension. Previously he ran the Office of Information and Public Affairs at the European Molecular Biology Laboratory in Heidelberg, where he was heavily involved in science education. He was instrumental in writing the grants that established the science teaching magazine 'Science in School', the European Learning Laboratory for the Life Sciences at EMBL, and the international Science on Stage project. His work involves writing stories about science for the general public and more specialized audiences, creating new teaching materials for workshops, helping scientists develop their communication skills, and helping institutes improve their communication, outreach and education activities.

Photo of John Liebler

Mr. John Liebler - (website)
Friday 18th - 13:45-14:30

Founder of "Art of the Cell", Director of 3D Animation.

As a former Lead Medical Animator of XVIVO Scientific Animation, John Liebler is best known for his work with Harvard University/Biovisions on the pivotal molecular movie “The Inner Life of the Cell”. He has over 20 years of experience creating scientific images and interactive 3D videos for a wide range of pharmaceutical, biomedical and educational companies. From science animation videos used to explain cell biology to students to scientific method animations clarifying the research of pioneers in the field of biosciences. John’s biomedical animations educate and inspire audiences of all backgrounds and interests across the globe.

Luis Serrano Luis Serrano Raymond E. Goldstein Raymond E. Goldstein L. Mahadevan L. Mahadevan Jean-Karim Hériché Jean-Karim Hériché Dagmar Iber Dagmar Iber Irene Miguel-Aliaga Irene Miguel-Aliaga Peter de Peinder Peter de Peinder Lucas Pelkmans Lucas Pelkmans Leïla Perié Leïla Perié Paola Picotti Paola Picotti Leonie Ringrose Leonie Ringrose Timothy Ryan Timothy Ryan Jonas Hartmann Jonas Hartmann Russ Hodge Russ Hodge John Liebler John Liebler

Programme (on your calendar Calendar ICS) (or abstract book PDF)

Day 1, Thursday, November 17th

Multilevel System Regulation

08:00-09:00 Registration
09:00-09:30 Symposium Opening & Welcome
09:30-10:30 Keynote lecture: Lakshminarayanan Mahadevan
On the growth and form of the gut
10:30-10:45 Short Talk 1: Svend Dahl-Jensen
Deconstructing the formation of the ductal network in the pancreas
10:45-11:15 Coffee Break
11:15-12:00 Lecture: Lucas Pelkmans
Emergence of predictable patterns of cell-to-cell variability amongst genetically identical mammalian cells
12:00-12:15 Short Talk 2: Christoph Fritzsch
Modulation of transcriptional bursting by estradiol at a single endogenous allele
12:15-13:45 Lunch
13:45-14:30 Science and society: Jonas Hartmann
Philosophy for science: Can scientists rediscover the philosophy of science for themselves?

Data Management and Interpretation

14:30-15:15 Lecture: Jean-Karim Hériché
Systems biology of mitosis: a data perspective
15:15-15:45 Flash talks
15:45-16:45 Poster Session 1
(Coffee Break)
16:45-17:30 Lecture: Peter de Peinder
Life is great but complex...like quantitative vibrational spectroscopy
17:30-17:45 Short Talk 3: Klaus Yserentant
Towards quantitative 3D fluorescence microscopy with CoPS and array tomography
17:45-18:00 Short Talk 4: Sarah Noel Galleguillos
Quantifying cellular robustness in genome-scale metabolic reconstructions
18:00-18:15 Thank the speakers
18:15-19:00 Blackboard Session
19:00-20:00 Dinner
21:00 Science Show

Day 2, Friday, November 18th

From Genome to Proteome

09:00-10:00 The EMBO Keynote lecture: Luis Serrano
Transcriptome analysis of a small bacterium reveals non-TF predominant regulation which could be an ancient mode of responding to medium perturbations
10:00-10:45 Lecture: Leila Perie
Deciphering the hematopoietic differentiation pathway at the single cell level
10:45-11:15 Coffee Break
11:15-12:00 Lecture: Leonie Ringrose
"In vivo biochemistry": Absolute quantification and kinetic modelling applied to Polycomb and Trithorax regulation
12:00-12:15 Short Talk 1: Lara Urban
Prediction of rare regulatory variants using deep learning
12:15-13:45 Lunch
13:45-14:30 Science and society: John Liebler
OK, But what does it look like?
14:30-14:45 Short Talk 2: Tadek Krassowski
Breaking the genetic code: Multiple reassignments of the codon CUG during yeast evolution
14:45-15:15 Flash talks
15:15-16:15 Poster Session 2
(Coffee Break)
16:15-17:00 Lecture: Paola Piccotti
Monitoring protein structural changes on a large scale
17:00-17:15 Short Talk 3: Andrew Tuckwell
An engineering approach to molecular assembly of the type 3 secretion system
17:15-17:30 Short Talk 4: Éric Durandau
Dynamic measurement of kinase activity in live single cell
17:30-18:15 Blackboard Session
18:15-18:45 Panel Discussion - Is a PhD thesis obsolete?
18:45-19:00 Thank the speakers
19:00-20:00 Dinner

Day 3, Saturday, November 19th

Cell communication shaping tissues

09:00-10:00 Keynote lecture: Raymond E. Goldstein
Upside Down and Inside Out: The biomechanics of cell sheet folding
10:00-10:45 Lecture: Dagmar Iber
From Networks to Function – Computational models of organogenesis
10:45-11:15 Coffee Break
11:15-12:00 Lecture: Irene Miguel-Aliaga
Homeostatic plasticity
12:00-12:15 Short Talk 1: Erika Tsingos
How tissues coordinate growth in an organ: Insights from modeling clonal lineages in fish
12:15-13:45 Lunch
13:45-14:30 Science and society: Russ Hodge
How to see a ghost, think like a molecule, and write like a scientist
14:30-14:45 Short Talk 2: Gabriel Cavalheiro
Myc transcription factors regulate mouse lens development and eye organogenesis
14:45-15:15 Coffee Break
15:15-16:00 Lecture: Timothy A. Ryan
Power supplies for brain cells: the cost of thinking
16:00-16:15 Short Talk 3: Jason Cosgrove
Mapping the distribution of chemokines in lymphoid tissues: Combining super-resolution imaging with multiscale modelling
16:15-16:30 Short Talk 4: Amit Singh
Growth and form in 4th Dimension: Non-invasive, in vivo quantification of growth anatomy and morphology through time
16:30-17:00 Coffee Break
17:00-17:45 Blackboard Session
17:45-18:15 Panel Discussion - Is biology biology or math?
18:15-18:30 Thank the speakers
18:30-19:00 Award ceremony
19:00-20:00 Dinner
21:00 Closing Party

Travel and Accommodation

How to get to Heidelberg

Heidelberg is easily reached by train, car or plane from any country in the world. The EMBL campus is located in Heidelberg's neighbourhood area of Boxberg which is approximately 10 minutes by car from Heidelberg's city centre.

Reaching us by train, plane, car

During the Symposium

Getting to EMBL

In addition to public transportation we will provide buses from Heidelberg to EMBL. The bus timetable is provided below.
Locations of stops and other points of interest are shown on this map.

On Saturday there is no public bus with a direct connection to EMBL. You will have to use the buses provided by us.

Thursday, November 17th

Bus leaving from Heidelberg to EMBL

Bismarck- platz Crowne Plaza Hans- Böckler-Str. Alois-Link-Platz Exzellenz Hotel ISG Hotel Boxberg- ring EMBL
07:30 07:32 07:34 07:46
07:45 07:50 08:00
07:50 07:52 07:54 08:06
08:15 08:17 08:25
08:10 08:12 08:14 08:26
08:30 08:32 08:34 08:46

Bus leaving from EMBL to Heidelberg

EMBL Boxberg- ring ISG Hotel Exzellenz Hotel Alois-Link-Platz Hans- Böckler-Str. Crowne Plaza Bismarck- platz
19:11 19:24 19:26 19:28
20:47 21:00 21:02 21:04
22:00 22:05 22:10
22:20 22:25 22:30
22:50 22:55 23:00
23:10 23:15 23:20

Friday, November 18th

Bus leaving from Heidelberg to EMBL

Bismarck- platz Crowne Plaza Hans- Böckler-Str. Alois-Link-Platz Exzellenz Hotel ISG Hotel Boxberg- ring EMBL
08:10 08:15 08:25
08:10 08:12 08:14 08:26
08:35 08:37 08:45
08:30 08:32 08:34 08:46

Bus leaving from EMBL to Heidelberg

EMBL Boxberg- ring ISG Hotel Exzellenz Hotel Alois-Link-Platz Hans- Böckler-Str. Crowne Plaza Bismarck- platz
19:11 19:24 19:26 19:28
20:30 20:35 20:40
20:47 21:00 21:02 21:04
21:00 21:05 21:10

Saturday, November 19th

Bus leaving from Heidelberg to EMBL

Crowne Plaza Exzellenz Hotel ISG Hotel Boxbergring EMBL
08:10 08:15 08:25
08:35 08:37 08:45

Bus leaving from EMBL to Heidelberg

EMBL Boxbergring ISG Hotel Exzellenz Hotel Crowne Plaza
20:30 20:35 20:40
20:50 20:55 21:00
23:00 23:05 23:10
23:20 23:25 23:30
02:00 02:05 02:10
02:20 02:25 02:30

Travel Documents and Visas

Prior to travelling to Germany, some applicants from certain countries may have to acquire special travel documents, such as a visa. Applicants are strongly encouraged to check with the local German Authorities (Embassies or Consulates) about the need of special travelling documents. Since the process may be time consuming, applicants are advised to make such arrangements as soon as possible. Failure to obtain a visa after the deadline for participation in the conference will not result in a refund. Applicants are responsible for providing the right documentation needed for their entry into Germany. However, upon request, the Organizing Committee can issue a formal letter of acceptance to the symposium for the purposes of obtaining a visa. Please be aware that no visa letters will be issued before payment of the registration fee. The organizing committee can not be held responsible in the case of a refusal by German authorities to enter German territory.


The registration fee does not include accommodation, which has to be personally arranged. However, we have reserved a few rooms at the EMBL/ISG Hotel. The costs are 77 EUR per person/per night incl. breakfast in a single and 49,50 EUR in a twin or double room. If you are happy to share a twin/double room with a fellow participant, please indicate this when making the booking.

Please call or email the ISG Hotel for your booking and use the code “PhD Symposium 2016” to receive the EMBL special rate.

A shuttle bus will run between EMBL and the ISG Hotel during the conference.

Financial Support

Below you can find a list of travel or support grants:

Please note that you need to apply independently to these grants.
If you require any assistance please do not hesitate to contact the Symposium Organisers.

Registration - is now closed

For any question or urgent matter please contact the PhD Symposium Organisation

Open until September 15th
Abstract submission deadline: September 15th

Fee Registration
General €150 Registration closed
Industry €200 Registration closed
EMBL internal Registration closed

Abstract submission

Please note:


Sponsorship Information

The EMBL PhD symposium will provide an invaluable networking environment for your company to enhance the profile amongst the molecular biosciences research community, especially towards the young generation. The symposium will offer prime opportunities for your company to promote your new products, latest technology, and services. If you are interested in sponsoring our symposium and would like to have more information, please download our sponsorship brochure or direct your enquires to us.


Also kindly supported by:

EMBL CPP founder partners

Leica Microsystems Olympus

EMBL CPP corporate partners

BD Boehringer Ingelheim Glaxo Smith Kline Illumina ThermoFisher Scientific

EMBL CPP associate partners

Eppendorf Merck Nikon Sanofi

Gold sponsors

The Company of Biologists

Silver sponsors

Avanti Galton Institute

Bronze sponsors

AHF Biotrend

Prizes kindly offered by



PhD Symposium 2016

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