Master’s position: Using bioinformatics to develop novel strategies to treat age-related pathologies

Ref. 2017-26


About the position

The Computational Systems Biology Laboratory of Dr. María Rodríguez Martínez, IBM Research – Zurich, and the Extracellular Matrix Rejuvenation Laboratory of Dr. Collin Y. Ewald, Department of Health Sciences and Technology at ETH Zurich, have an opening for a Master’s thesis researcher.

The aim of the project is to determine the molecular mechanism(s) that prolong health during aging, using bioinformatics, in order to develop novel strategies to treat age-related pathologies. Aging is the major risk factor for developing diseases such as cancer, diabetes, and neurodegenerative disorders. However, centenarians (individuals over the age of one hundred) seem to be protected against these diseases.

The successful applicant will join our research efforts to bioinformatically explore genome-wide association and expression profile data sets of centenarians to identify candidate gene alterations that could promote healthy aging. Furthermore, in the second part of the Master’s research, the student will test conserved gene alteration in C. elegans lifespan assays to gain functional insights. Studies will employ bioinformatics to analyze data from molecular biology, CRISPR-Cas9, microinjections, fluorescent microscopy, PCR, and C. elegans stress and longevity assays.


Requirements

The highly-motivated candidate should have great enthusiasm for aging research, the ability to solve problems creatively, and a Bachelor of Bioinformatics, Computer Science or similar. Specific requirements for this project are:

  • Working knowledge of at least one programming language (Phyton, C, C++ or equivalent).
  • Working knowledge of Matlab, R or equivalent.
  • Comfortable knowledge of statistics.
  • Prior experience of experimental work in molecular biology and/or C. elegans would be beneficial, but not required.

Diversity

IBM is committed to diversity at the workplace. With us you will find an open, multicultural environment. Excellent flexible working arrangements enable both women and men to strike the desired balance between their professional development and their personal lives.


How to apply

We look forward to receiving your online application that includes a CV (with publication list), academic transcripts and a one-page motivation letter. Furthermore, please provide the contact information of two potential referees. Please send the application to:

or to
ETH Zurich
Human Resources
Mrs. Nadja Lang
CH–8092 Zurich


Questions?

For further information, please contact or (no application documents) or visit our websites.
Computational Systems Biology, IBM Research – Zurich
Extracellular Matrix Rejuvenation Laboratory, ETH Zurich

Master’s thesis/semester project for ETH student: Demonstrating the computational advantages of spiking neural networks

Ref. 2017-25


About the position

Neural networksArtificial neural networks (ANNs) have been the driving force of artificial intelligence in recent years, currently transforming many industries. However, these conventional neural networks still suffer from several severe limitations, most importantly their need for human supervision in their training, the enormous data and energy consumption that they incur, and their lack in flexibility such as multitasking and adaptability to changing conditions. These challenges need to be overcome before industries such as data analytics, the Internet of Things, or autonomous drones can be fully equipped with cognitive computing capabilities.

Spiking neural networks (SNNs) are viewed as the next generation of neural networks. These networks can be very efficiently emulated by exploiting the physics of electronic devices. In addition, compared to conventional ANNs, SNNs in theory could yield higher computational power and could learn and compute in ways closely resembling the biological brain. However, algorithms practically demonstrating their theoretical advantages have been largely missing. In IBM Research – Zurich we have been contributing to advancing the field with hardware demonstrations of spiking neural elements with phase-change memory nanodevices and our current work focuses strongly also on the algorithmic front, aiming to identify and enable sources of computational superiority in SNNs compared to conventional ANNs.

We are inviting applications from ETH students to conduct their thesis work/semester project at IBM Research – Zurich on this exciting new topic. A successful project would have significant impact on the future of cognitive computing, by providing concrete experimental demonstrations of our theoretical work, making use of Big Data sources or video from neuromorphic vision sensors.


Requirements

The ideal candidate should have a multi-disciplinary background, strong mathematical aptitude and programming skills. Prior knowledge on spiking neural networks is a bonus.


Diversity

IBM is committed to diversity at the workplace. With us you will find an open, multicultural environment. Excellent flexible working arrangements enable both women and men to strike the desired balance between their professional development and their personal lives.


How to apply

If you are interested in this challenging position on an exciting new topic, please send your complete curriculum vitae including a transcript of grades by email to:


Exploratory Memory and Cognitive Technologies Group
IBM Research – Zurich

Pre-Doc researcher: Nanoscale thermal transport

Ref. 2017-24


About the position

We are looking for a highly motivated PhD student for our activities in nanoscale thermal transport. We aim to advance the understanding of heat generation and dissipation in nanoscale devices with the goal of developing technologies for future nanoelectronic devices and their energy challenge. Covering several projects, activities range from performing experiments of a fundamental nature to engineering devices and demonstrators.

The successful candidate will have access to a laboratory fully equipped to characterize nanoelectronic devices at high precision. Furthermore, a fully-equipped, state-of-the-art clean room is available for sample fabrication. This position is available for a duration of three years in a collaborative and creative group in a lively research environment.


Requirements

Applicants are expected to hold a Master’s degree in physics or engineering with a strong background in nanometer-scale physics. The ideal candidate is very talented, creative and highly motivated. He or she has excellent communication skills and is open to working in an international, multidisciplinary team.


Diversity

IBM is committed to diversity at the workplace. With us you will find an open, multicultural environment. Excellent flexible working arrangements enable both women and men to strike the desired balance between their professional development and their personal lives.


How to apply

If you are interested in this challenging position and fulfill the above requirements, please send your complete curriculum vitae and the names of three references by email to

Post-Doc researcher: Applied IoT and artificial intelligence

Ref. 2017-21


About the position

A post-doctoral position is available immediately in the Smart System Integration group at IBM Research – Zurich in the field of research and development of applied augmented intelligence. The research will take place within an inter-disciplinary team involving development and improving wearable sensing technology and analyzing the resulting data using cognitive algorithms including cutting-edge Watson APIs. This effort will contribute to IBM’s position as global leader in the development of radically innovative big data and augmented intelligence solutions.


Requirements

The successful candidate will have a strong interdisciplinary background in computer or informatics engineering, and experience in developing internet of things or wearable devices as well as pattern recognition and deep learning. The highly motivated individual will join our multi-disciplinary research team to advance our effort in the internet of the body project in the IBM Research Frontiers Institute with the goal to provide people with a healthier way of living and to augment their senses. The position will focus on experimental data gathering and software development for embedded wearable systems and edge computers. The objective is to apply advanced cognitive algorithms to the acquired data and contribute to develop the field of machine intelligence. These activities will support IBM’s vision on applied augmented intelligence.


Diversity

IBM is committed to diversity at the workplace. With us you will find an open, multicultural environment. Excellent flexible working arrangements enable both women and men to strike the desired balance between their professional development and their personal lives.


How to apply

Please send your CV including contact information for two or three references to:

Mgr. Smart System Integration
IBM Research GmbH
Säumerstrasse 4
CH – 8803 Rüschlikon, Switzerland

Post-Doc researcher: NLP and text mining

Ref. 2017-20


Project description

We are seeking to fill a postdoctoral research position available immediately at IBM Research – Zurich in the area of NLP and text mining.

The main focus of the postdoctoral researcher will be to provide solutions to the challenges of interpretation, analysis, information extraction and search (both semantic and keyword based) over large amounts of unstructured text documents, as well as connecting structured and unstructured data. Therefore, knowledge in the state-of-the-art NLP and text mining methods, as well as the ability, intelligence and creativity to modify them and advance beyond them is very important. Furthermore, experience with applying techniques for information extraction and harvesting knowledge from high-quality Web sources in order to automatically build and curate knowledge bases is highly relevant. Familiarity with deep learning methods and machine learning is a plus.

At IBM Research – Zurich, we are developing cognitive solutions for challenging NLP and text mining problems on very large, domain-specific, unstructured text documents comprising a mixture of both human and machine generated content. The successful candidate will be a part of a dedicated, international team that aims to provide efficient solutions to these problems.


Requirements

Candidates should have a PhD in Computer Science, NLP, machine learning, computational linguistics or equivalent with a track record in NLP, text mining, and/or machine learning. We expect strong analytical and problem solving skills, strong programming skills in Java/Python or similar, ability to conduct independent research, excellent communication and team skills. Software Engineering experience, familiarity with R and Big Data analytics is a plus.

The Post-doc position has a duration of 18 months.


Diversity

IBM is committed to diversity at the workplace. With us you will find an open, multicultural environment. Excellent flexible working arrangements enable both women and men to strike the desired balance between their professional development and their personal lives.


How to apply

If the above position fits your background, please send your complete CV, including a list of publications and skills, as well as contact information for three references to:

For technical information please contact Dr. Dorothea Wiesmann.

Post-Doc researcher: Deep learning for predictive analytics

Ref. 2017-19


About the position

We are seeking an outstanding post-doctoral researcher for research in state-of-the-art predictive analytics applied to IT as well as industrial components and systems. Applying and expanding state of the art machine learning methods including deep learning and model fusion, our research aims at identifying degradation indicators from rich historical event logs and telemetry data, and using those to accurately predict future failures and performance degradation events in the field.

This position is available from approximately September 2017 for a duration of 18 months. The successful candidate will enjoy an internationally competitive salary and work in a collaborative and creative group in an exclusive research environment.

The candidate will have the primary responsibility to advance new analytical models for predicting the reliability of IT components and/or wind turbine components, that will be applied in the wild. In addition, the candidate is expected to handle the data selection, cleaning and integration tasks prior to the modeling stage.


Requirements

  • The ideal candidate is expected to hold a PhD in Computer Science, preferred Machine Learning or Statistics
  • A strong background in machine learning with a specialization in time and event series analysis, deep learning and potentially survival models
  • Knowledge of reliability of IT components from a systems perspective is a strong plus
  • An excellent publication track record at top conferences and journals
  • Excellent coding skills in R, python, and potentially Scala
  • Familiarity with big data processing frameworks (e.g., Spark stack) would be highly beneficial
  • Familiarity with deep learning frameworks (e.g., TensorFlow) would be highly beneficial
  • The candidate must be self-driven, highly motivated and is required to multitask efficiently

The Post-doc position has a duration of 18 months.


Diversity

IBM is committed to diversity at the workplace. With us you will find an open, multicultural environment. Excellent flexible working arrangements enable both women and men to strike the desired balance between their professional development and their personal lives.


How to apply

If the above position fits your background, please send your complete CV, including a list of publications and skills, as well as contact information for three references to:

For technical information please contact Dr. Dorothea Wiesmann.

Post-Doc researcher: III–V MOCVD growth and photonics

Ref. 2017-18


The MIND (Materials Integration and Nanoscale Devices) group at IBM Research – Zurich is offering an opportunity for a highly motivated post-doc to work on the metal-organic vapor phase epitaxy MOCVD growth of different III–V materials on Si, combined with the structural, electrical and optical characterization of III–V semiconductor photonic devices. The project will be carried out in the framework of a FETOPEN project under H2020.

III-V MOCVD growth and photonicsThe research comprises the epitaxial growth as well as the detailed characterization of the structure and the optical and electrical properties of nanoscale photonic devices, ranging from photovoltaics to lasers. The work involves nanofabrication using our state-of-the-art cleanroom facility along with the selective growth of nanostructures [1,2] using (MOCVD) and development of different doping strategies. The crystalline and optical quality of the material will be investigated using, e.g., scanning electron microscopy, X-ray diffraction and optical spectroscopy. Additionally, electrical transport measurements of pn-junctions and heterostructures for photovoltaics will be done, along with various optical characterizations.

[1] M. Borg et al., Nano Lett. 14, 1914 (2014).
[2] H. Schmid et al., Appl. Phys. Lett., 106, 233101 (2015).


Requirements

The candidate is expected to hold a Ph.D. degree in physics, materials science, electrical engineering or similar with solid academic and publication record and should possess a high degree of motivation and creativity combined with good communication skills in English (spoken and written). Hands-on experience with III–V growth as well as knowledge of optical characterization techniques is mandatory.


Diversity

IBM is committed to diversity at the workplace. With us you will find an open, multicultural environment. Excellent flexible working arrangements enable both women and men to strike the desired balance between their professional development and their personal lives.


How to apply

Interested applicants should submit their curriculum vitae including references to:

PhD opportunity: COSMIC, COmbating disorders of adaptive immunity with Systems MedICine

Ref. 2017-15


A PhD research position is available at the IBM Research – Zurich Laboratory, as a part of the H2020 COSMIC consortium, focused on understanding disorders of the adaptive immune system.

Background: EU countries face large health challenges to combat chronic diseases. Recently, systems medicine has emerged as a promising discipline to accelerate the translation of basic research into applications for improved diagnostics and personalized treatment. Its power arises from the integration of laboratory and computational approaches crossing research disciplines and sectors to solve clinical questions.

Approach: COSMIC will focus on B-cell neoplasia and rheumatoid arthritis, prototypical diseases originating from abnormal functioning of immune cells, often resulting in similar antigen specificities. The successful candidate will develop new algorithms to understand the molecular mechanisms of these diseases, and to identify strategies for optimal personalized patient treatment.

Starting date: 01/01/18.


Requirements

  • Strong background in computer science, mathematics, physics or similar.
  • Working knowledge of C or C++.
  • Working knowledge of Matlab, R or equivalent.
  • Comfortable knowledge of statistics and mathematical modeling.

In addition, the following experience would be helpful, but not essential:

  • Experience in machine learning, deep learning, big data analysis, and high performance computing.
  • Experience in systems biology or systems medicine.

Diversity

IBM is committed to diversity at the workplace. With us you will find an open, multicultural environment. Excellent flexible working arrangements enable both women and men to strike the desired balance between their professional development and their personal lives.


How to apply

Interested candidates should apply through the COSMIC website under “Vacancies”. Please mention there that you wish to be considered for the position at the IBM Research – Zurich Lab.

Pre-Doc researcher: Optomechanics

Ref. 2016-21


Project description

We are seeking a highly motivated candidate for a Ph.D. position in the area of optomechanics as part of the project OMT – Optomechanics Technologies, a Marie Skłodowska-Curie Innovative Training Network funded by the European Union.

The work involves simulation and design of highly miniaturized photonic devices, cleanroom processing at the limits of nanofabrication, laser-based optical characterization, and high-speed electronic measurements. Quantum physics in mesoscopic mechanical oscillators will be explored as well as novel non-linear effects occurring where light is confined to exceedingly small volumes, with the aim of demonstrating efficient optomechanical microwave-to-optical transduction in ultra-compact photonic crystal devices.

The Ph.D. student will work in the Quantum Technologies group at IBM Research GmbH and be mentored by Dr. Paul Seidler. Prof. Tobias Kippenberg at the École Polytechnique Fédérale de Lausanne will serve as the official Ph.D. advisor.

The successful candidate will enjoy an internationally competitive salary and work with collaborative and creative groups in an exclusive research environment.

The position is available immediately.


Requirements

  • A master’s degree in engineering or physics
  • An outstanding academic record
  • Good communication and English language skills

Application is open to both EU and non-EU nationals. The rules for this position require that the candidate has not resided or carried out his/her main activity (work, studies, etc.) in Switzerland for more than 12 months during the past three years.

Preference will be given to applicants with at least one publication in a peer-reviewed journal. Previous research experience in optics, numerical simulation or nanoscale fabrication would be beneficial.


Diversity

IBM is committed to diversity at the workplace. With us you will find an open, multicultural environment. Excellent flexible working arrangements enable both women and men to strike the desired balance between their professional development and their personal lives.


How to apply

Please send a single PDF file containing a cover letter, curriculum vitae, transcripts, and contact information for at least two references to Dr. Paul Seidler.

Post-Doc researcher: NLP and medical ontologies in German for cognitive pre-clinical assessment of patients

Ref. 2016-13


Project description

RHÖN and IBM will join forces to accelerate pre-clinical assessment of patients through cognitive computing built on top of our Watson capabilities. The goal is to equip doctors and medical staff with evidence and data insights before the patient even enters the clinical phase. This will result in improved medical care during pre-clinical assessment both for ambulant and inpatient care so that the right patient receives the right treatment at the right time.

In this context we are looking to hire a Post-Doctoral Fellow into our research team. We look for an enthusiastic person skilled in Natural Language Processing and medical ontologies in German, who is capable of programming and keen on taking up new tools and approaches. We very much work in a team where each member complements the others. The work will have a direct impact on the client as well as on research in healthcare informatics.

In the future, RHÖN-KLINIKUM AG, one of the largest healthcare providers in Germany, will cooperate with IBM in order to optimise patient management. The concept of the joint project is to ensure data-assisted patient navigation providing the best possible healthcare at the pre-clinical stage already and subsequently moving into either the in-patient or out-patient treatment. Inappropriate patient referrals, which cost both time and money, can therefore be avoided. Better use of patient data can also help in providing further recommendations for treatment.

IBM will contribute innovative “cognitive computing“ technology to this joint project. In a first phase, a cognitive assistance system will be installed at the “Center for Undiagnosed and Rare Diseases” at the university hospital in Marburg to help in the very work-intensive processing of such medical cases. The IBM Research – Zurich Laboratory will be responsible for the technological management of the project. The knowledge obtained from the first project phase at the university hospital in Marburg will then be analyzed and used for other hospitals in the corporate group.


Diversity

IBM is committed to diversity at the workplace. With us you will find an open, multicultural environment. Excellent, flexible working arrangements enable both women and men to strike the desired balance between their professional development and their personal lives.


Contact

Matthias Reumann, PhD
Sustainable, resilient health systems research
IBM Research – Zurich
Saeumerstrasse 4, 8803 Rueschlikon, Switzerland
mre@zurich.ibm.com
office: +41 44 724 84 12
mobile +49 157 313 867 43

Master’s thesis project in Systems Biology group: Spatiotemporal modelling of DNA replication

Ref. 2016-12


Project description


DNA replication, the duplication of a cell’s genetic material, ensures the maintenance of the genetic information and is the basis of biological inheritance. In eukaryotic cells, DNA replication initiates at multiple locations in the genome, known as origins of replication, and continues from there in both directions, thereby creating replication forks.

This project aims at developing a stochastic hybrid model of DNA replication that incorporates spatial information on origin locations and protein mobility dynamics. The ultimate goal is to understand the relationship between 3D structure and DNA replication. The model will be tailored for the case of fission yeast using recent experimental data and will be simulated in a high-performance computing setup.

The research will be conducted in collaboration between the Automatic Control Laboratory of ETH Zurich and IBM Research – Zurich. More specifically, the project will involve:

  • Adapting an existing model of protein mobility [1, 2] for the case of fission yeast nucleus and model origin locations in 3D using experimental data.
  • Integrating the origin location and existing DNA replication models [3] to enable stochastic initiation of origin firing when activation factors diffuse and bind onto the origins.
  • Simulating the resulting integrated model to test various hypotheses, for example different kinetic parameters of the activation factors or different relative positioning of the origins.
  • Examining whether and how relative origin positioning affects replication timing and how the process is affected by the dynamics of activation factors.

Diversity

IBM is committed to diversity at the workplace. With us you will find an open, multicultural environment. Excellent, flexible working arrangements enable both women and men to strike the desired balance between their professional development and their personal lives.


Contact

For more information please contact J. Lygeros and M. Rapsomaniki.


References

[1] E. Cinquemani, V. Roukos, Z. Lygerou, and L. Lygeros,
“Numerical analysis of FRAP experiments for DNA replication and repair,” in IEEE Conference on Decision and Control, Cancun, Mexico, December 9-11, 2008.
[2] M. Rapsomaniki, E. Cinquemani, N. Giakoumakis, P. Kotsantis, J. Lygeros, and Z. Lygerou,
“Inference of protein kinetics by stochastic modeling and simulation of fuorescence recovery after photobleaching experiments,” Bioinformatics 31(3) 355-362, 2015.
[3] J. Lygeros, K. Koutroumpas, S. Dimopoulos, I. Legouras, P. Kouretas, C. Heichinger, P. Nurse, and Z. Lygerou,
“Stochastic hybrid modeling of DNA replication across a complete genome,” Proceedings of the National Academy of Sciences of the U.S.A., vol. 105, pp. 12295-12300, August 2008.


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