Imaging

iNAMES

MDC-Weizmann Helmholtz International Research School for Imaging and Data Science from the NAno to the MESo

Mission & program

Imaging is an indispensable component of biological research and personalized medicine.

New molecular and cellular insights obtained from imaging technologies should be integrated with data science into a coherent picture of tissues, organs and organisms, with a goal of prevention, early interception and treatment of diseases.

To contribute to this goal, the Max Delbrück Center for Molecular Medicine; the Weizmann Institute of Science in Rehovot, Israel; the Humboldt-Universität zu Berlin and the Charité-Universitätsmedizin, Berlin have joined forces to establish iNAMES - MDC-Weizmann Helmholtz International Research School (HIRS) for Imaging and Data Science from the NAno to the MESo.

The mission of iNAMES is the training of outstanding imaging and data scientists in a truly international research school, along with answering some of the most important biomedical and clinical research challenges of our time. 

The focus of iNAMES Research School lies in the development of an independent, interdisciplinary research project, supported by an international team of mentors from partner institutions from Germany and Israel.

The contribution of participating labs through complementary research studies, models and technologies ensure highly innovative, interdisciplinary projects in the areas of:

  1. Development of next generation imaging technology, methodology, imaging markers and (nano)molecular probes, including MRI and high-end optical imaging
  2. Advancement of computational sciences, imaging data sciences, artificial intelligence, machine learning, biophysics and mathematical models
  3. Application of imaging and data science in molecular medicine, biology, life sciences and mechanistic biophysical research
  4. Swift translation into clinical imaging, large population imaging and public health sciences

The joint effort brings together the understanding of the mechanisms by which diseases originate from defects at the molecular and cellular levels, with developments in techniques that characterize how the cells and their molecular machinery functions at the nanoscopic level, and with emerging non-invasive methods that relate the characterization of tissues and major organ systems at the mesoscopic level.

Examples of cross-domain project topics, combining multiscale imaging with model based analysis, artificial intelligence and machine learning.

iNAMES Research School

The iNAMES program framework includes the following key elements:

  • PhD research is carried out within a joint project, closely supervised by a German-Israeli team of research mentor/ co-mentors
  • Personalized research training in a collegial environment, characterized by scientific excellence and innovation
  • iNAMES-specific scientific program, including annual symposia, summer/winter school and regular workshops, which provide a forum for networking and exchange of ideas
  • Personal and career development program, including Individual Development Plan, design to achieve personal and career goals by identifying the specific needs, as well as promoting and assessing the acquisition of relevant competences
  • Access to the well-established program of Helmholtz Skill Courses, supporting further interdisciplinary networking within the Helmholtz Association

We do not only provide our students with a peer network and practical scientific training, but also offer an outstanding opportunity to actively participate in the international scientific community, all ensuring a timely completion of the dissertation. Our overarching goal is to equip our graduates with the critical skills essential for life-long learning, enabling them to successfully compete in any international job market.

Supervision
 

The iNAMES PhD researchers are mentored by a tandem of a primary mentor and a co-mentor(s) from partner institutions in Germany and Israel. The mentors support the preparation and implementation of the research project, assist in developing the Individual Development Plan (IDP), introduce to their own professional networks and advise on future plans and career goals.

Besides day-to-day mentors supervision, iNAMES doctoral researchers present their project annually to the Thesis Advisory Committee (TAC), which accompanies them from the first presentation of the research proposal to the preparation of the doctoral thesis. The primary mentor and co-mentor(s), together with two additional independent scientists, form a Thesis Advisory Committee (TAC).

Research visits and mobility
 

International and cross-disciplinary mobility of scientists between partner sites is of crucial importance for the success of iNAMES. Joint PhD projects are carefully set-up to enable the contribution of participating labs through complementary research, ensuring highly innovative, interdisciplinary projects.

The iNAMES Research School supports short-term stays to learn particular techniques (e.g. for 2-4 weeks) as well as extended stays (e.g. to work on research sub-projects in collaboration with a partner lab, for up to 6 months).

Each iNAMES student is expected to spend at least 2 weeks a year in the partner lab abroad.

To further increase the visibility of iNAMES within the research community, all doctoral researchers are encouraged to network and present their research at international conferences, supported by iNAMES travel and training grants.

Funding
 

iNAMES doctoral researchers are fully funded through an initial 3-year employment contract with the MDC. iNAMES provides funding for a duration of three years, with a possible fourth year needing to be financed by the primary mentor, in accordance with recommendation of the Thesis Advisory Committee (TAC) members. All doctoral researchers are expected to complete their doctoral research and thesis in 4 years.

Salaries are competitive to national standards, according to 65% TVöD 13 (monthly net payment of approximately 1800 EUR). Health and social insurance are included in the contract. The university tuition fees per semester are approximately 350 EUR, and include public transportation ticket.

 

Training & Events

iNAMES Research School offers advanced, structured and integrated training program with a strong focus on biomedical imaging and data science, in a highly interdisciplinary environment.

Upon completion of the iNAMES training, the graduates:

  • will have outstanding expertise in imaging modalities, imaging applications, image analysis
  • are experts for the design of molecular and cellular imaging assays for the study of biological systems
  • are ready to contribute to the growth and development of physical or computer sciences
  • will progress life sciences and healthcare
  • have a strong foundation for transition into a position as an independent researchers in the field
  • have developed skills in scientific reasoning and logic, problem solving, interpersonal communication
  • are educated in principles of responsible research and innovation
  • are well versed in research integrity, ethics, and equity
  • are ready to take leadership positions in industry and academia
  • will fill the gap of severe shortage of biomedical imaging and data science experts
Scientific Development
 

The iNAMES scientific program is designed to provide doctoral researchers with advanced training on state-of-the-art imaging and data science technologies. A spectrum of iNAMES training activities includes lecture series, student seminars, on-site courses, e-learning courses, hands-on practical seminars, and various scientific events, such as joint international PhD retreats and summer/winter schools. 

"X-roads in Imaging and Data Science" Student Seminar

Every 3rd Wednesday of the month, iNAMES PhD students, associates and guests present their exciting research projects in the area of biomedical imaging and data science.

"Frontiers in Biomedical Imaging and Image Analysis" Lecture Series

The "Frontiers in Biomedical Imaging and Image Analysis" series was launched in January 2021. Every 1st Wednesday of the month, excellent scientists working in the area of biomedical imaging and image analysis present their outstanding research to the MDC community and our guests.

Courses and hands-on experience

A variety of relevant courses is organised for the iNAMES doctoral researchers on site regularly, such as courses in image analysis, programming, statistics, data visualisation and similar. Additionally, doctoral researchers have an opportunity to participate in external courses, supported by the iNAMES training grants. The iNAMES school furthermore organizes info sessions with the MDC technology platforms, hands-on sessions at imaging centers, visits to our clinical partners (Charité and Sheba Medical Center), as well as company visits (e.g. to Siemens, Bruker, Nikon, Zeiss and local start-ups), to foster practical competencies and the entrepreneurship spirit of our doctoral researchers.

External conferences

To further increase the visibility of iNAMES within the research community, all doctoral researchers are encouraged to network and present their research at international conferences, supported by iNAMES travel and training grants.

Key Competences
 

Becoming an expert in a specific scientific domain or technology is an important, but not the only aspect of the iNAMES training program. With a growing number of PhDs following careers outside of academia, it is crucial to foster a wider range of personal skills and to introduce relevant career pathways as early as possible.

Our doctoral researchers take responsibility for their professional growth by developing and implementing an Individual Development Plan (IDP). This includes a research plan, training activities, as well as personal skills assessment and progress plan, enabling planning and monitoring of academic and personal development. The IDP is adapted throughout the PhD, particularly as a part of the progress review at the annual TAC meetings.

Peer Mentor Group is introduced as an additional measure to support career development, providing a platform for open discussions on professional and personal skills needs, peer advice on career options, or matters of work/ life balance, and facilitating the integration of iNAMES researchers visiting from partner institutions.

Career Orientation Workshops inform about the available career choices and assist with decisions about the next professional steps.

Technology Transfer Training is essential in preparing for careers both in and outside of academia. The MDC and WIS Technology Transfer Offices offer regular courses and workshops on IPR, patenting, avenues for commercialization of research, translating research into a product, translating basic research into real-world clinical applications, and similar. 

Extracurricular and student-organized activities, such as organization of scientific events, teaching at the Life Science Learning Lab “Gläsernes Labor” on the Berlin-Buch campus, participation in public outreach activities during, e.g., “The Long Night of Sciences”, organization of social events, and similar, contribute to the development of the students’ professional skills. These activities are further facilitating the integration of international students, creating a particularly welcoming and lively atmosphere on the campus.

Events

iNAMES Kick-Off | September 2021

Despite complex circumstances for initiating and driving an international exchange research program in 2020/21, we dived into this task with dedication, passion and optimism. To share our enthusiasm with the community, we organised a virtual kick-off event in September 2021, aiming to introduce the concept of the iNAMES Helmholtz International Research School, its mission and plans for the future, as well as to present the first cohort of our PhD students and their exciting research projects. 

As part of the Frontiers in Biomedical Imaging and Image Analysis Lecture Series at the MDC, we were delighted to welcome Wojtek James Goscinski from the Australian National Imaging Facility. He provided a fascinating keynote on Crossroads of Data Science and Imaging: Infrastructure and Applications.

 

iNAMES Orientation Session | October 2021

In the iNAMES Orientation session, doctoral researchers are provided with all information regarding the Helmholtz Association and the MDC organizational structure, university regulations, university admission and enrollment, credit points system, obligatory annual Advisory Committee Meetings (TACs), travel details, training grants, training opportunities and more. Within the Orientation session held in September 2021, iNAMES students participated in the Design Thinking workshop, boosting their creativity and collaborative mindset.

iNAMES Orientation Session 2021 | Design Thinking Workshop

iNAMES Symposia

The annual iNAMES Symposia, organized alternating between Berlin and Rehovot, gathers a wider scientific and industrial community, stimulating discussion, collaboration and networking between the iNAMES doctoral researchers, faculty, and representatives of industry partners.

More experienced doctoral researchers present their research, providing insight into the state-of-the-art technology developments, while at the same time gaining valuable presentation skills and teaching experience.

A “science café” open to the general public supplements the scientific program of the annual symposia, providing a platform for science communication and outreach.

"Beyond IMAGEination I."; Berlin, November 2022
 

The 1st iNAMES Symposium "Beyond IMAGEination I." was held at the MDC-BIMSB on November 23-24, 2022. The event gathered 104 participants from 10 institutions, and 25 invited speakers from 6 institutions (EMBL, MPI for Multidisciplinary Sciences, MDC, Charité, HU, WIS) presented their research. In addition, the attendees had the opportunity to enjoy 9 students chalk-talks, 16 poster presentations and 2 networking evening events. The scientific program of the symposium is available here.

Attendees of the first iNAMES Symposiums at MDC-BIMSB.

"Beyond IMAGEination II."; Rehovot, November 2023
 

The 2nd iNAMES Symposium, "Beyond IMAGEination II." will be held at Weizmann Institute of Science in Rehovot, Israel on November 26-27, 2023. 


Summer / Winter School

Furthermore, faculty members and doctoral researchers gather at annual summer/ winter schools, dedicated workshops on current advanced topics in imaging and data science. 

Summer School 2022: "Intro to Statistics and Mixed Models", June 2022
 

June 20 – 24; 09:00 – 17:00h

Trainers: Dr. Elmar Spiegel, Dr. Marina Jiménez Muñoz; Helmholtz Zentrum Munich - German Research Center for Environmental Health, Core Facility Statistical Consulting

Introduction to Statistics and Mixed Models provides a foundation in statistical analysis for scientists and practitioners. The first part covers descriptive statistics, classical statistical tests (t-test, Wilcoxon/Mann-Whitney-U test, ANOVA, etc.), and linear regression and its extensions. The second part deals with repeated measurements, in particular Mixed Models. All methods are explained in an applied setting. By the end of the week, attendees will be able to identify appropriate statistical methods, apply them, and interpret your results. 

Summer School 2023: "Graphics with R", July 2023
 

June 29 – 30 (09:00 – 12:30h) + July 06 – 07 (09:00 – 12:30h)

Trainers: Dr. Elmar Spiegel, Dr. Marina Jiménez Muñoz; Helmholtz Zentrum Munich - German Research Center for Environmental Health, Core Facility Statistical Consulting

Graphics with R covers methods in customizing base R graphics. Additionally, an introduction to ggplot2, an advanced and powerful tool for building graphics with R, is provided. In this course you will learn how to create refined, meaningful graphs in R to visually describe your research outputs. All topics are accompanied with hands-on exercises.


International PhD Retreat

PhD retreats bring together doctoral researchers from partner institutions, providing opportunities to network, exchange ideas and experiences, brainstorm, establish collaborations and form friendships. Doctoral researchers are actively involved in the organization of these meetings, thus developing their organization and project management skills.

 

People

Doctoral Researchers

iNAMES doctoral researchers | October 2021

2020

Marius Weismehl

Project: Exploring the molecular mechanism of guanylate-binding proteins at high structural and temporal resolution
Mentor: Oliver Daumke, MDC
Co-mentor: Hagen Hofmann, WIS

iNAMES offers a truly interdisciplinary environment by providing its members with expertise from diverse research fields.
Marius_Weismehl
Marius Weismehl Daumke Lab

Guanylate-binding proteins are key to cell-autonomous immunity against microbial and viral pathogens. Exploring the molecular mechanism of guanylate-binding proteins requires a set of structural biological approaches in combination with biochemical and cell biological approaches. To this end, we will perform X-ray crystallography, cryo electron microscopy and tomography, single-molecule FRET, and membrane binding and remodeling assays. 

Contact: Marius.Weismehl@mdc-berlin.de

Publications

M. Weismehl, X. Chu, M. Kutsch, P. Lauterjung, C. Herrmann, M. Kudryashev, O. Daumke (2023): Elucidating the activation mechanism for GBP1 oligomerization. bioRxiv: 2023.2008.2001.551421 

 

Nandita Saha

The best thing about being part of an exchange program is, it creates awareness and acceptance of alternative together with multi-faceted approaches of learning and gaining knowledge.
Nandita Saha
Nandita Saha Niendorf Lab

Project: Development, validation and application of magnetic resonance radiofrequency coil technology: New instruments to define the role of MR imaging markers in biological systems and disease
Mentor: Thoralf Niendorf, MDC
Co-mentor: Lucio Frydman, WIS / Rita Schmidt, WIS

My project is to develop and implement of radiofrequency (RF) coil technology, which will provide rich opportunities for new ways of non-invasive mapping and probing morphology, function, physiology and metabolism and facilitates explorations into the benefits and challenges of ultrahigh field Magnetic Resonance (UHF-MR) with the ultimate goal to spatially resolve and characterize (patho)physiological processes and biophysical mechanisms to promote a transfer from basic research to clinical science and vice versa.


Publications:

P. Lacour, P. L. Dang, F. R. Heinzel, A. S. Parwani, F. Bähr, A. Kucher, F. Hohendanner, T. Niendorf, F. Rahimi, N. Saha, H. Han, K. Rubarth, M. Sherif, L.-H. Boldt, B. Pieske, F. Blaschke (2022): Magnetic field-induced interactions between phones containing magnets and cardiovascular implantable electronic devices: Flip it to be safe? Heart Rhythm, 19(3):372-380.  

N. Saha, J. M. Millward, C. J. J. Herrmann, F. Rahimi, H. Han, P. Lacour, F. Blaschke, T. Niendorf (2023): High-fidelity 3D stray magnetic field mapping of smartphones to address safety considerations with active implantable electronic medical devices. Sensors, 2023, 23(3):1209.

N. Saha, A. Kuehne, J. M. Millward, T. W. Eigentler, L. Starke, S. Waiczies, T. Niendorf (2023): Advanced Radio Frequency Applicators for Thermal Magnetic Resonance Theranostics of Brain Tumors. Cancers, 2023, 15(8):2303.

Contact: Nandita.Saha@mdc-berlin.de

 

Igor Tellez

Project: Where is the pain in the brain?
Mentor: Thoralf Niendorf, MDC
Co-mentor: Michal Ramot; WIS

The international collaboration and teamwork not only contribute to achieve a highly enriched project, but also allow me to get to know a different culture.
Igor Tellez
Igor Tellez Niendorf Lab

The project focuses on identifying functional biomarkers for pain to enhance our understanding of pain processing. Despite substantial progress in recent medicine, it is still not understood how pain is processed in the brain. We have no objective biomarkers to assess pain in the patient. Pain cannot be evaluated in comatose or demented patients, and its subjectivity puts an enormous psychological burden on chronic pain patients. 

ContactIgor.Tellez@mdc-berlin.de

 

Gamze Güney

Project: Optical imaging and activation of thermal perception
Mentor: James Poulet, MDC
Co-mentor: Ofer Yizhar, WIS

Getting to know other groups and working in different institutes is great for creating networks, which can lead to beautiful collaborations and opportunities.
Gamze Güney
Gamze Güney Poulet Lab

The ability to perceive temperature helps animals to maintain the homeostasis of body temperature, to avoid noxious temperature that may cause damage, and to identify objects during haptic exploration. My aim in this project is to understand the neural mechanisms of temperature perception in the mouse forelimb system. I plan to use a combination of approaches including two-photon calcium imaging, optogenetic manipulations and behavioural training, to investigate how the thermal cortex represents skin temperature and how this information is translated into thermal perception.

 

 

Publications:

M. Vestergaard, M. Carta, G. Güney & J. F. A. Poulet (2023): The cellular coding of temperature in the mammalian cortex, Nature, 614:725–731.

ContactGamze.Gueney@mdc-berlin.de

 

2021

Madhu Nagathihalli Kantharaju

Project: Computational methods to achieve real-time whole brain imaging in behaving animals
Mentor: Kyle Harrington / Hanna Hörnberg / Dagmar Kainmüller, MDC
Co-mentor: Takashi Kawashima, WIS

iNAMES program answers one of the most important aspects of Science – unification: a multi-disciplinary team working towards one solution.
Madhu_s
Madhu Nagathihalli Kantharaju Harrington Lab

The goal of the project is to develop automatic, real-time algorithms for artifact correction of live fluorescent imaging in the brain of behaving animals. This project especially focuses on cancelling the effect of motion and cerebral blood flow during imaging using a lightsheet microscope and aims to implement such a software module in an open-source microscope control software. We aim to develop novel algorithms to address the existing neural imaging challenges, and to achieve brain-wide voltage imaging, which is one of the technical milestones for neuroscience.

Publications:

R. Barbara, M. Nagathihalli Kantharaju, R. Haruvi, K. Harrington, T. Kawashima (2022): PyZebrascope: An Open-Source Platform for Brain-Wide Neural Activity Imaging in Zebrafish. Frontiers in Cell and Developmental Biology, 10:875044. 

L. Finotto, B. Cole, W. Giese, E. Baumann, A. Claeys, M. Vanmechelen, B. Decraene, M. Derweduwe, N. Lakic, G. Shankar, M. Nagathihalli Kantharaju, J. Albrecht, I. Geudens, F. Stanchi, K. Ligon, B. Boeckx, D. Lambrechts, K. Harrington, L. Van Den Bosch, H. Gerhardt (2023): Single‐cell profiling and zebrafish avatars reveal LGALS1 as immunomodulating target in glioblastoma. EMBO Molecular Medicine. 15.

ContactMadhu.NagathihalliKantharaju@mdc-berlin.de

 

Bakhrom Muinjonov

Project: Imaging organotypic chimeric human-murine brain slices as a model system for neurodegeneration
Mentor: Volker Siffrin, MDC/Charité 
Co-mentor: Michal Schwartz, WIS

The collaborative project, opportunity to be supported and co-mentored during my research project and to acquire shared experiences of involved institutions is the perfect environment to thrive as a young scientist.
Bakhrom
Bakhrom Muinjonov Siffrin Lab

Through my clinical work I have seen many patients suffering from neurodegenerative disorders such as Alzheimer`s disease or multiple sclerosis, who are burdened by the limitations of pharmacological agents unable to directly target etiological factors of development of brain degeneration. My project is focused on developing authentic model of neurodegeneration by means of xenografting human pluripotent stem cells from multiple sclerosis patients to develop chimeric brain slices. I will be imaging the cellular and synaptic changes in organ like context by using two photon laser scanning microscopy to visualize complex interplay among different CNS cell populations. These chronic slices might be used in a context of drug treatment, understanding pathological mechanisms of events in cellular and network level.

Publications:

J. Kerkering, B. Muinjonov, K. S. Rosiewicz, S. Diecke, C. Biese, J. Schiweck, C. Chien, D. Zocholl, T. Conrad, F. Paul, M. Alisch, V. Siffrin (2023): iPSC-derived reactive astrocytes from patients with multiple sclerosis protect cocultured neurons in inflammatory conditions. J Clin Invest, 133(13):e164637.  

K.S. Rosiewicz, B. Muinjonov, S. Kunz, H. Radbruch, J. Chen, R. Jüttner, J. Kerkering, J. Ucar, T. Crowley, B. Wielockx, F. Paul, M. Alisch, V. Siffrin (2023):  HIF prolyl hydroxylase 2/3 deletion disrupts astrocytic integrity and exacerbates neuroinflammation. Glia, 71(8), 2024–2044.

ContactBakhrom.Muinjonov@mdc-berlin.de

 

Henri Trang

Project: Microstructural tissue fingerprinting in neuroinflammatory disorders
Mentor:  Friedemann Paul, MDC/Charité / Alexander U. Brandt, University of California, Irvine/ECRC/Charité
Co-mentor: Assaf Tal, WIS

I have always been fascinated by non-invasive imaging techniques to help diagnosis and treatment of clinical pathologies. I find exciting the prospect of developing novel experimental techniques that will eventually find use in a clinical framework.
Henri
Henri Trang Paul Lab

Autoimmune neuroinflammatory disorders are chronic progressive diseases, leading to disabilities such as visual loss, motor and cognitive impairment. The most prevalent chronic inflammatory disease of the central nervous system is multiple sclerosis. It is characterized by dissemination of white matter and cortical lesions in space and time, driven by disease-specific mechanisms, including inflammation, demyelination, failure to remyelination, axonal damage and other gliopathies. Our aim ist to derive microstructural tissue measurements that are disease and pathology specific, using multiparametric quantitative MRI/MRS methods, and explore tailored analytical approaches for clinical application.

ContactHenri.Trang@mdc-berlin.de

 

Paula Santos Otte

Project: Combining single and ensemble-molecule imaging methods to visualize cellular membrane interactions of the human amyloid protein, alpha-synuclein
Mentor: Melissa Birol, MDC
Co-mentor: Phil Selenko, WIS

Although our main location is Berlin, the iNAMES program allows us to get to know the scientific community at the Weizmann institute, to travel there and to learn from its scientists via summer schools and lectures.
Paula
Paula Santos Otte Birol Lab

In my project, we are aiming to understand how lipid metabolism and more specifically, the interaction between alpha-synuclein with cellular lipoproteins affects its structure, fibril formation, (dis)function and localization in cells. In particular, we are seeking to understand how lipoproteins responsible in coupling the neuron-astrocyte lipid metabolism may affect the aggregation and function of alpha-synuclein. The amyloid fibril formation of alpha-synuclein has been recognized in various neurological diseases including Parkinson's disease. Therefore, understanding how this protein interacts with cellular lipoproteins that couple the neuron-astrocyte lipid metabolism may help us to identify certain parameters that trigger the aggregation and misfunction and thus, lead to the formation of pathogenic alpha-synuclein.

ContactPaula.SantosOtte@mdc-berlin.de


Tobias Klein

Project: Deep learning-based kidney segmentation and predictive analysis of multi-parametric MRI for the diagnosis and therapy monitoring of kidney disease
Mentor: Thoralf Niendorf, MDC 
Co-mentor: Lucio Frydman, WIS
Co-mentor: Erdmann Seeliger, Charité

Science never is a one-(wo)man-show, it is always a team performance. By being part of iNAMES, I can be part of a supportive and familial community which helps me growing and where I can help my colleagues as well.
Tobias
Tobias Klein Niendorf Lab

Kidney diseases are a major health issue, with increasing incidence and an estimated five to ten million deaths per year worldwide. While several biomarkers are currently being investigated for diagnosis of renal diseases, to date clinical point-of-care biomarkers are still lacking for major renal diseases. To address this urgent unmet clinical need, non-invasive imaging may provide markers to inform on the different stages of renal pathophysiology, improve prediction and interception of disease progression and evaluate treatment of renal disease. This project examines the feasibility and reliability of longitudinal monitoring of kidney size in MR images of rats using deep learning approaches. We hypothesize that this approach enables quantification of acute changes in kidney size in experimental setups mimicking realistic clinical scenarios. For this purpose, a deep learning approach for renal segmentation that provides a solution for deforming the kidney shape using a constrained statistical model-based algorithm trained upon a (or few) dataset(s) will be developed. For swift translation of the deep learning approach to clinical data, we will implement a transformative solution that helps to bridge the gap between preclinical and clinical MRI.

ContactTobias.Klein@mdc-berlin.de

Publications:

T. Klein, T. Gladytz, J. M. Millward, K. Cantow, L. Hummel, E. Seeliger, S. Waiczies, C. Lippert, T. Niendorf (2023): Dynamic Parametric MRI and Deep Learning: Unveiling Renal Pathophysiology through Accurate Kidney Size Quantification. NMR in Biomedicine, e5057. 

 

Letizia Dalmasso

Project: Molecular characterization of protein tethers required for touch sensation
Mentor: Gary Lewin, MDC
Co-mentor: Mike Fainzilber, WIS

The key word is networking. iNAMES gives PhD students a great opportunity to meet people and network with them.
Letizia Dalmasso
Letizia Dalmasso Lewin Lab

At the MDC, I am investigating touch at molecular level. It is striking how little we know about touch, compared to other senses. In the Lewin lab, we are working on a model to explain how the receptors in the skin can transform mechanical forces (i.e. tactile stimuli) into electrical signals, a process known as “mechanotransduction”. This is the first step in touch perception and implies the presence of special ion channels able to be gated by mechanical stimuli. Our model implies that such channels are physically connected to the extracellular matrix by means of large protein tethers and that the stretching of these tethers by mechanical forces opens the channels. My main goal is to visualize these tethers and unveil their molecular identity. Understanding how molecules assemble to function in a mechanotransduction complex will open up avenues to develop therapeutic strategies to modulate touch.

ContactLetizia.Dalmasso@mdc-berlin.de 

 

Bilguun Nurzed

Project: Development and application of radiofrequency technology for cardiac magnetic resonance imaging at Ultrahigh Field
Mentor: Thoralf Niendorf, MDC
Co-mentor: Rita Schmidt, WIS
Co-mentor: Tobias Schäffter; Physikalisch-Technische Bundesanstalt Nationales Metrologieinstitut (PTB)

Cardiac Magnetic Resonance (CMR) at ultrahigh magnetic fields (UHF, B0 ≥ 7.0 T) benefits from the gain in 

My favourite part of my project is designing and simulating the new technology. It's like playing a video game!
Bilguun Nurzed Niendorf Lab

sensitivity and enhanced spatial resolution. To push the boundaries of magnetic field strengths, the challenges and electrodynamic constraints of CMR towards 21.0 T will be explored. For this purpose, the feasibility of CMR at 14.0 T and 21.0 T is examined using high-density radiofrequency (RF) transceiver dipole arrays in conjunction with static parallel (transmission (pTx) field shimming. To find suitable antenna concepts, three antenna concepts from previous CMR at UHF will be investigated to be used as transceiver elements. Electromagnetic field (EMF) simulation with the local high-density transceiver arrays will be performed in CST Studio 2020 on the human voxel models from the Virtual Family. The antenna concepts will be benchmarked regarding their transmit efficiency (TXE), B1+ efficiency, SAR level, and parallel imaging performance. To overcome the more pronounced challenges at extreme fields (EF), recently reported dynamic pTx method with optimized kT-points for CMR at 7.0 T will be performed. The findings in this project will provide the technical foundation for the development of RF array technology dedicated to CMR at 14.0 T and beyond.

ContactBilguun.Nurzed@mdc-berlin.de

Publications

B. Nurzed, A. Kuehne, C.S. Aigner, S. Schmitter, T. Niendorf, T.W. Eigentler (2023): Radiofrequency antenna concepts for human cardiac MR at 14.0 T. Magn Reson Mater Phy 36, 257–277.

 

2023

Ali Osman Cetin

Project: Defining the ground signaling of glioblastoma states
Mentor: Gaetano Gargiulo, MDC
Co-mentor: Itay Tirosh, WIS

Being in a high-quality research institute is an amazing thing. Being in two, unbelievable...
Ali Osman Cetin
Ali Osman Cetin Gargiulo Lab

Glioblastoma is currently incurable and the most malignant brain tumor. There has not been much improvement of glioblastoma therapy in the past decades in spite of immense scientific effort. In my project, I am trying to identify embryonic roots of glioblastoma subtypes and their transcriptional program. Glioblastoma is a very heterogeneous cancer, it has different transcriptional subtypes. It is not known why different subtypes exist and how glioblastoma takes advantage of having different subtypes. I will be looking at how developing mouse embryos use transcriptional program of different glioblastoma subtypes by using synthetic genetic tracers specific to different subtypes. The findings may shed light to why glioblastoma has different subtypes, and lead to new therapeutic strategies.

ContactAliOsman.Cetin@mdc-berlin.de

 

Daniel Leopoldus

Project: Investigating RyR1 in differentiating skeletal muscle using cryo-electron tomography
Mentor: Mikhail Kudryashev, MDC
Co-mentor: Ori Avinoam, WIS

Through the collaboration I get to be part of two groups from different fields and can learn from their respective expertise.
Daniel Leopoldus
Daniel Leopoldus Kudryashev Lab

Muscle cells are multinucleated cells, formed by mononucleated precursors. These stem cells can not only generate but also regenerate skeletal muscle. Both processes consist of multiple steps and failure in one of them leads to myopathies. Several known cytoskeletal and membrane proteins are involved in the mechanisms. However, the detailed understanding of the molecular architecture and its changes over time are missing. We aim to establish a workflow for the visualization of these molecular details in different intermediate states of myoblast fusion. To this end, we will use a cell culture model for a combination of fluorescent imaging with cryo-FIB milling and cryo electron tomography. Elucidating the high-resolution information during muscle fusion has strong implications for disease mechanisms.

ContactDaniel.Leopoldus@mdc-berlin.de

 

Clara Unger

Project: Understanding sex-differences in psychiatric disorders
Mentor: Hanna Hörnberg, MDC
Co-mentor: Tali Kimchi, WIS

iNAMES not only offers cutting-edge training in Imaging and Data Science and the tremendous opportunity to work at Weizmann Institute of Science, but it also is a platform that connects doctoral researchers and provides them with a peer group.
Clara Unger
Clara Unger Hörnberg Lab

There is a sex-bias in many psychiatric disorders which to a large extent is not understood. I aim to develop a more detailed understanding of the genetic, hormonal, molecular and cellular mechanisms which contribute to vulnerability to stress and to the development of disorders like depression. Using mouse models exposed to stress paradigms, I will investigate the relationship between the stress axis and hormonal systems. Through different -omics approaches, complex behavioral analysis and advanced imaging techniques, I hope to gain insight into why sex can be a risk factor for certain psychiatric conditions. I hope that my project will rob some researchers of excuses to only use males in their experiment and that it will provide a basis for more personalized treatments in the future.

ContactClara.Unger@mdc-berlin.de

 

Lison Neige Guillaume

Project: Simultaneous mapping of pathology and therapy in multiple sclerosis using fluorine-19 MRI
Mentor: Sonia Waiczies, MDC
Co-mentor: Thoralf Niendorf, MDC
Co-mentor: Amnon Bar-Shir, WIS

The best thing about being part of an exchange program is the sharing of experiences, may it be intellectual or cultural. I am very excited about the cultural immersion this program offers.
Lison Neige Guillaume
Lison Neige Guillaume Niendorf Lab

At the MDC, I am investigating touch at molecular level. It is striking how little we know about touch, compared to other senses. In the Lewin lab, we are working on a model to explain how the receptors in the skin can transform mechanical forces (i.e. tactile stimuli) into electrical signals, a process known as “mechanotransduction”. This is the first step in touch perception and implies the presence of special ion channels able to be gated by mechanical stimuli. Our model implies that such channels are physically connected to the extracellular matrix by means of large protein tethers and that the stretching of these tethers by mechanical forces opens the channels. My main goal is to visualize these tethers and unveil their molecular identity. Understanding how molecules assemble to function in a mechanotransduction complex will open up avenues to develop therapeutic strategies to modulate touch.

ContactLison.Guillaume@mdc-berlin.de
 

Antonia Konle

Endothelial cell states and fates driving arterio-lympho-venous specification in zebrafish
Mentor: Holger Gerhardt, MDC
Co-mentor: Karina Yaniv, WIS
Co-mentor: Philipp Junker, MDC, Charité

I am genuinely excited about the opportunity to collaborate with scientists possessing diverse expertise in the field of imaging and data science.
Antonia Konle
Antonia Konle Gerhardt Lab

This project aims to understand endothelial cell state transitions shaping arterio-lympho- venous patterns in zebrafish. Distinct arterial and venous angioblast populations form the dorsal aorta (DA) and posterior cardinal vein (PCV) during early zebrafish embryogenesis. Secondary sprouts from the PCV induce venous remodeling or lymphatic structure formation in intersegmental vessels (ISVs) sprouting from the DA. Early heterogeneity in seemingly identical ISVs suggests pre-programming of endothelial cells (ECs) towards arterial or venous identities. A flow-mediated adaptive mechanism fine-tunes the artery-vein balance. Molecular mechanisms will be unraveled using a multicolor lineage tracing tool, 3D time-lapse imaging, and single-cell RNA sequencing to track EC behavior in zebrafish embryogenesis.

Contact: Antonia.Konle@mdc-berlin.de

 

Franziska Pupp

Generating next-generation CAR T cells to overcome the immunosuppressive tumour microenvironment in the bone marrow
Mentor: Uta E. Höpken, MDC
Co-mentor: Steffen Jung, WIS

The plan is to develop a 3D bone marrow model to test the functionality of CAR-T cells in the microenvironment of tumours in the bone marrow. This model may also allow us to demonstrate the direct interaction between CAR-T cells, the tumour microenvironment and cancer cells. We are also developing a dual CAR targeting human BCMA or mouse CD19 together with mouse CCR4 in multiple myeloma cells. Thirdly, a technical approach is aimed at increasing the efficacy of the BCMA CAR. Combinatorial targeting of BCMA-expressing MM cells together with microenvironmental factors that strongly promote MM cell survival and proliferation may be crucial to deepen MRD status after adoptive CAR-T cell therapy.

Contact: Franziska.Pupp@mdc-berlin.de


Adrià Gassó-Alern

Use of a genome-wide shRNA screening to uncover end-resection factors
Mentor: Michela Di Virgilio, MDC
Co-mentor: Ziv Shulman, WIS

There are two main pathways to repair DNA double-strand breaks (DSBs): non-homologous end joining (NHEJ) and homologous recombination (HR). Many proteins have already been discovered to regulate pathway choice in different cellular contexts. Once a DSB is induced, a group of well-known proteins are required to protect the DNA ends in order to prevent resection, such as 53BP1 or RIF1, which are crucial for the direct ligation of the blunt ends (NHEJ). On the other hand, if the DNA ends become resected, DSB will be repaired through HR. In this case, the generated 3' overhangs will search for and invade homology sequences to repair damage in an error-free manner. The project focuses on uncovering new factors that would participate and be involved in the end-resection induction.

Contact: Adria.Gasso-Alern@mdc-berlin.de

 

 


iNAMES Faculty

The joint German-Israeli faculty includes distinguished scientists whose scientific expertise covers a broad spectrum of modern imaging, computational and life science fields.

The international faculty represents a healthy mix of junior (45%) and senior scientists (55%) from multiple disciplines, ranging from imaging, physics, mathematics, computational sciences, bioengineering, biochemistry and pharmacology to biology, molecular medicine, systems medicine, neurosciences, epidemiology and public health. Female scientists comprise 38% of the members of the faculty, while the iNAMES board includes 50% female spokespersons. 20% of the faculty are MDs, which provides an excellent framework for PhD/MD tandems and translational projects.

 

iNAMES Scientific Advisory Board

Prof. Dr. Katrin Heinze, Rudolf Virchow Center for Integrative and Translational Bioimaging, Julius-Maximilians-University Würzburg, Germany

Prof. Dr. Christoph Lippert, Hasso-Plattner-Institut für Digital Engineering & Universität Potsdam, Germany

Prof. Dr. Kamil Ugurbil, Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, USA

 

 

imaging@MDC

Research Groups

 

Technology Platforms

 

Imaging Lecture Series

Frontiers in Biomedical Imaging and Image Analysis Lecture Series is organized every 1st Wednesday of the month (15:00-16:00h).  Excellent external speakers working in the area of biomedical imaging and image analysis present their exciting research to the MDC community and our guests. Please see the overview of the lectures here.

Join us!

To alleviate the surging incidence of the world’s deadliest diseases, the development of new strategies for early detection and treatment is of utmost relevance. 

This can only proceed by deepening our understanding of the underlying molecular mechanisms and pathophysiological processes, calling in turn for new ways to visualize complex biological systems and to image disease states at various length- and time-scales. 

If you are enthusiastic and passionate about tackling these challenges, join us!

 

We offer:

  • Excellent scientific, international and supportive environment 
  • Individual PhD supervision & dual mentoring by the experts from two leading institutions in the field, supported by the thesis committee
  • Research visits and short-term (1-4 weeks) or long-term (up to 12 months) exchange stays at partner institution abroad
  • Annual symposia and research winter & summer schools, as well as participation in PhD retreats & networking social events
  • Access to state-of-the-art infrastructure & core facilities
  • Regular lectures, journal clubs & seminar series 
  • Advanced scientific, research-related & methods training
  • Framework program for personal & career development
  • Travel grants for external courses & conferences


How to apply? 

iNAMES recruitment process is a part of recruitment for the International PhD Program at the MDC Berlin.

Contact

For general inquiries, please contact:

Dr. Sanja Drakulic
sanja.drakulic@mdc-berlin.de
inames@mdc-berlin.de

Phone: 030 9406-1506

Max-Delbrück-Centrum for Molecular Medicine (MDC) 
Robert-Rössle-Str. 10 
13092 Berlin, Germany

 

For any science-related questions, please contact one of the iNAMES spokespersons:

Germany

Prof. Dr. Thoralf Niendorf (Max-Delbrück Center)
thoralf.niendorf@mdc-berlin.de

Univ. Prof. Dr. Friedemann Paul (Charité)
friedemann.paul@charite.de

Prof. Dr. Jeanette Schulz-Menger (Charité)
jeanette.schulz-menger@charite.de

Prof. Dr. Dr. h.c. Edda Klipp (Humboldt-Universität zu Berlin)
edda.klipp@rz.hu-berlin.de


Israel

Prof. Dr. Lucio Frydman (Weizmann Institute of Science)
lucio.frydman@weizmann.ac.il

Prof. Dr. Michal Neeman (Weizmann Institute of Science)
michal.neeman@weizmann.ac.il

iNAMES logo

Spokespersons
 

Contact

 

Dr. Sanja Drakulic
Scientific Coordinator
sanja.drakulic@mdc-berlin.de


Phone: 030 9406-1506


Max-Delbrück-Centrum for Molecular Medicine (MDC) 
Robert-Rössle-Str. 10 
13092 Berlin, Deutschland


Building 84, Room 1015