Software Engineer/PostDoc: Distributed Systems and Blockchain

Ref. 2017–07


About the position

We are turning some of the most complex distributed systems designs and algorithms into real systems. We are also researching and inventing new scalable, fault-tolerant and secure distributed systems with the goal of changing the world of financial and digital transactions in general. We are researching, designing and building blockchains.

We are looking for highly motivated and enthusiastic software engineers to join the Industry Platforms and Blockchain group of the Cloud & Computing Infrastructure department at IBM Research - Zurich. In this role, you will be expected to contribute to the architecture definition and implementation in our blockchain projects, notably their aspects pertaining to distributed and fault-tolerant systems such as consensus and state-machine replication, concurrency control and distributed databases. You will be able to contribute directly and make an impact not only on IBM products, but also on the Hyperledger Fabric open-source project.

The Industry Platforms and Blockchain group consists of scientists and researchers with deep expertise and knowledge in these areas, who work together with our software engineers to deliver world-class results. Given that such results are expected to power hundreds or thousands of production blockchain deployments, software quality, modularity, maintainability, scalability and resilience are of paramount importance in the development process.


Requirements

Candidates applying for this position should fulfill the following requirements:

  • Degree in computer science, software engineering, software architecture, or equivalent
  • At least three years of experience in software-related positions (building systems in the scope of a graduate degree counts towards these three years)
  • Experience in distributed and parallel systems and large software architectures
  • Basic understanding/experience in one or more of the following protocols/ systems: Paxos, Raft, ZooKeeper, etc, Consul
  • Proficient in at least two of the following programming languages: Golang, C, C++, Java
  • Experience with standard engineering and coding practices
  • "Get-it-done" pragmatic attitude
  • Capable of participating actively in brainstorming sessions in multi-disciplinary teams. Able to propose, defend, and criticize ideas
  • Ability to conduct independent work, to work in a team, and to assume responsibility
  • Capable and eager to learn independently about the subject area(s) of the project(s) and underlying distributed systems technologies
  • Very good verbal English communication skills

In addition, the following skills are desired, but not necessarily required:

  • PhD in distributed systems/distributed databases
  • Security and networking knowledge
  • Deep understanding of designing protocols/systems such as Paxos, Raft, ZooKeeper, etcd, Consul, PBFT
  • Knowledge of proof-of-work blockchains (Bitcoin, Ethereum)
  • Experience with open-source development
  • Proficiency, familiarity and/or experience with additional programming languages

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

Candidates with a PhD degree and a good research publication record in the fields of distributed systems/distributed databases and who are willing to implement real systems are strongly encouraged to apply. Such candidates can be considered for a PostDoc position. This position is available for a duration of 24 months with the possibility of an extension.

If the above position fits your background and you are interested in this challenging position, please send your complete curriculum vitae, including a list of publications and the names of three references, to

Judith Blanc
Human Resources
IBM Research – Zurich
jko@zurich.ibm.com

PhD or Post-doc: Monolithic III–V integration on Si for nanowire-based photovoltaics

Ref. 2017–06


About the position

The MIND (Materials Integration and Nanoscale Devices) group at IBM Research – Zurich is offering an opportunity for a highly motivated student to carry out a PhD on the growth, structural, electrical and optical characterization of III–V semiconductor nanowires grown on silicon. The project will be carried out in the framework of a FETOPEN project under H2020. The aim of the project is to monolithically integrate [1] GaAsP and InGaP nanowire solar cell arrays on state-of-the-art silicon solar cells.

The research comprises the epitaxial growth as well as the detailed characterization of the structure and the optical and electrical properties of nanoscale nanowire devices. The work involves nanofabrication using our state-of-the-art cleanroom facility along with the selective growth of nanostructures [2] using metal-organic vapor phase epitaxy (MOCVD). 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 axial pn-junctions and heterostructures will help developing highly efficient multi-junction solar cells.

[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 Master’s degree in physics, materials science, electrical engineering or similar with outstanding academic record and should possess a high degree of motivation and creativity combined with communications skills in English (spoken and written). The student will be embedded in the MIND group for the duration of this project and closely collaborate with our EU project partners from NL, FR, SE, and DE.

Potentially we would consider an excellent candidate for a post-doc in this position as well.


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 students should submit their curriculum vitae including references to:
Dr. Kirsten Moselund, Heinz Schmid or Dr. Stephan Wirths, IBM Research – Zurich, Säumerstrasse 4, CH-8803 Rüschlikon, Switzerland.

Post-doc: Biomedical technologies with the microfluidic probe

Ref. 2017-05


About the position

A postdoctoral position is available for our activities on biomedical technologies at the Research Laboratory of IBM in Zurich. These activities aim at applying IBM’s expertise in microtechnology and microfluidics towards the development of next-generation bioanalytical tools. This multidisciplinary research is problem-oriented, involves microtechnologists, physicists, electrical engineers, biotechnologists and chemists, and is pursued within a dynamic network of partners and collaborators. In this postdoctoral position, research will focus on IBM’s microfluidic probe (MFP) technology. MFP is a non-contact, scanning microfluidic device that can pattern surfaces with proteins in an additive and subtractive manner, form gradients of proteins on surfaces and interacts with cells and tissue sections on surfaces.

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

The candidate will have the primary responsibility to advance methods and technologies for molecular profiling of cells/tissues using the microfluidic probe with group members and external partners.


Requirements

  • The candidate must have profound expertise in microfluidics, analytical/numerical modelling, and small-volume fluid handling/manipulation. The ideal candidate will additionally have experience in cell-based assays, immunoassays, molecular biology assays, optical microscopy and bioanalytical techniques (e.g. PCR, electrophoresis).
  • The candidate must be keen on driving an experimental program coupled with analytical/numerical analysis.
  • Systems design, implementation with the use of Matlab/LabView and troubleshooting skills will be beneficial.
  • The candidate must be self-driven, highly motivated and is required to multitask efficiently.

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

Candidates are welcome to send a single PDF file that includes a CV (a list of publications) and contact information for three references to:

Dr. Govind Kaigala, e-mail: gov@zurich.ibm.com
IBM Research – Zurich, Säumerstrasse 4 CH-8803 Rüschlikon, Switzerland

Further information

Application per e-mail is preferred.

Master’s thesis and internship opportunity:
Identifying mechanisms of action in association studies

Ref. 2017-04


Project description

Genome-wide association studies (GWAS) have emerged as a powerful tool for identifying genetic variants associated with complex phenotypes and disease. Despite the many newly discovered associations, the variants identified by these studies typically explain only a small fraction of the heritable component of disease risk. Furthermore, few genetic variants are found within coding regions of genes, and the elucidation of the molecular mechanism by which these loci influence the phenotype remains challenging.

GWAS

The Systems Biology group at IBM Research – Zurich has developed a new computational approach to elucidate the molecular mechanisms behind the association of genetic variants to breast cancer susceptibility. Specifically, the algorithm tests whether a genetic variant (e.g. a SNP) modulates the activity of a transcription factor by perturbing its interaction with specific targets.

The proposed internship will focus on its application to two independent breast cancer genomic and transcriptomic datasets and the analysis of results in a disease context. Furthermore, it is known that SNP variation explains only a fraction of heritable disease risks, a phenomenon known as “missing heritability”. Recent studies have proposed that DNA short tandem repeats (STRs) make up a significant amount of the missing variants. Therefore, ideally, the internship project will be extended to explore cancer associations with variation in short tandem repeats (STRs). We hypothesize that increased rates of STR-induced mutations in protein-coding sequences give rise to novel antigens, leading to an increased immune response in tumors with STR instabilities (known as MSI phenotype). Based on previous work on STRs (by M. Anisimova, ZHAW, and T. Bilgin, UZH), the project will aim to investigate the mechanisms responsible for the increased response to immunotherapy, while also identifying novel antigen targets.


Requirements

Candidates applying for this position should fulfill the following requirements:

  • Working knowledge of C or C++.
  • Working knowledge of Matlab, R or equivalent.
  • Comfortable knowledge of statistics and mathematical modeling.
  • In addition, some knowledge of molecular biology, genetic and systems biology, as well as high-throughput technologies for the molecular characterization of cancer samples would be beneficial, although it is not essential.

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, please, contact: Dr. María Rodríguez Martínez.

Software Engineer

Ref. 2017-03


Project description

We are looking for highly motivated and enthusiastic software engineers to join the Cognitive Computing & Industry Solutions department at IBM Research – Zurich. Software engineers contribute to the architecture definition and implementation of our projects, which cover diverse subject areas, e.g., healthcare, materials science and systems biology. In the context of these projects, we use — and very often develop — novel cutting-edge tools for cognitive systems in areas including natural language processing (NLP), machine learning (ML) and knowledge representation (KR). The department has a large group of scientists and researchers with deep expertise and knowledge in these areas, who work together with our software engineers to deliver world-class results. Given that such results are frequently developed with (or for) industry partners, software quality, modularity, maintainability, scalability, and resilience are of paramount importance in the development process.


Requirements

Candidates applying for this position should fulfill the following requirements:

  • Degree in computer science, software engineering, software architecture, or equivalent.
  • At least two years of industry experience in software-related positions.
  • Experience with standard engineering practices.
  • Proficient in at least two of the following programming languages: C, C++, Python, Java.
  • Capable of participating actively in brainstorming sessions in multi-disciplinary teams. Able to propose, defend, and criticize ideas.
  • “Get it done” pragmatic attitude.
  • Ability to conduct independent work, to work in a team, and to assume responsibility.
  • Very good verbal English communication skills.
  • Capable and eager to learn independently about the subject area(s) of the project(s) and underlying cognitive technologies.

In addition, the following skills are desired, but not necessarily required:

  • Experience in distributed and parallel systems and large software architectures.
  • Proficiency, familiarly and/or experience with additional programming languages.
  • Database and networking knowledge.
  • Knowledge of web/cloud application development.
  • Knowledge of natural language processing, machine learning, and/or knowledge representation.

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 application documents in a single PDF file by email to Mirjam Strebel. Besides your CV, we kindly ask you to describe in your cover letter how you fulfill the position requirements. Please also indicate which other additional skills you possess that you consider relevant to the application process.

Master’s project: Photonics

Ref. 2017-02


Project description

PhotonicsWe are seeking a highly motived candidate for a Master’s project in the Quantum Technologies group at IBM Research – Zurich for the development of III/V-on-silicon photonic devices with potential applications in communications technology, sensing, and quantum computing. The goal is to fabricate integrated compact III-V optical cavities on silicon substrates where the piezoelectric behavior of the III-V material can be exploited for optomechanical coupling.

This highly interdisciplinary Master’s project will involve the development of a fabrication process for photonic crystal devices made of gallium phosphide and will be carried out in the cleanroom of the Binnig and Rohrer Nanotechnology Center (BRNC). The BRNC is located at the renowned IBM laboratory in Rüschlikon, Switzerland, which provides a collaborative research environment comprising regular research staff as well as other Master’s and Ph.D. students.


Requirements

  • Interest in cleanroom work and process development. Previous experience with process technology would be advantageous
  • Current enrollment in a Master’s program in physics, electrical engineering, or micro- and nanosystems with permission to begin the Master’s thesis
  • A superior academic record
  • Good communication skills

Duration

The duration of the Master’s project will be determined in accordance with the regulations of the candidate’s university.


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, and transcripts to
Dr. Paul Seidler, preferably before March 1, 2017.

Post-Doc researcher: Control systems

Ref. 2017-01


We are seeking an outstanding post-doctoral researcher for research in state-of-the-art control systems applied to magnetic tape storage systems. Our research aims at developing technologies that enable the continued scaling of IBM’s magnetic tape data storage products to keep up with the explosive growth of digital data.

Tape storage

Requirements

The candidate should have a strong background in electrical or mechanical engineering with a specialization in control engineering and have excellent skills working “hands-on” in the laboratory. Familiarity in one or more of the following areas will be useful: H-infinity and state space control, system modeling, electronics, mechatronics, as well as knowledge of Matlab, VHDL, C and/or DSP programming languages. The candidate will work as part of an interdisciplinary team and should have excellent written and oral communication skills.

Applicants are expected to hold a PhD in engineering and have a good track record of research. The candidate should be creative and able to meet deadlines. This position is available starting in the spring of 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.


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 and if you are interested in this challenging position, please send your complete curriculum vitae, including a list of publications, and the names of three references to
Judith Blanc
Human Resources
IBM Research – Zurich
E-mail:

Post-Doc researcher: Transprecision Computing on FPGAs

Ref. 2016-23


Project description

The Cloud & Computing Infrastructure department at IBM Research – Zurich is seeking a postdoctoral Researcher to work on transprecision computing for applications in the areas of big-data analytics, cognitive computing and scientific computing. This research is focused on the architecture and design of mixed-precision accelerator for high-performance processors. Prototypes will be based on a co-design of a Field-Programmable Gate Array (FPGA)-based hardware implementation and the firmware/software of the target application.

The candidate will work on a collaborative project investigating how and to what extent the relaxation of accuracy requirements for intermediate calculations (transprecision computing) can boost the performance & energy efficiency of modern computer systems.

The postdoctoral researcher will work in a larger project that develops a complete framework for transprecision computing, covering devices, circuits, software tools, and algorithms, and will demonstrate its results through applying highly relevant algorithms in the field of Big Data, deep learning, and scientific computing to fully operational prototype systems.

Requirements

Candidates must have a strong background in Computer Engineering, Computer Science, Electrical Engineering, or equivalent, with an outstanding university track record.

We expect a high degree of expertise in FPGA design and development as well as strong programming skills (C/C++, Python, parallel programming).

The successful candidate should have some of the following areas in his/her field of expertise: machine learning algorithms, Big Data analytics, graph analytics, data mining, deep learning, numerical analysis.


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, please send an application to Dr. Heiner Giefers.

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: Foundations of Cognitive Solutions

Ref. 2016-18


Project description

We have an opening for a post-doctoral research position in our Foundations of Cognitive Solutions group.

The opening is in the context of the IBM Watson ecosystem with a focus on large-scale, cloud-related aspects of visual scene segmentation, object recognition and semantic mapping. The successful candidate will research and implement novel efficient methods for semantic data representation as well as data processing to aid machine cognition and human–machine interaction.


Requirements

The ideal candidate has a degree in Robotics (including Computer Science, Electrical Engineering, or similar fields), with a track record in simultaneous localization and mapping (SLAM) as well as computer vision related to robotics.

The ideal candidate demonstrates strong programming skills (C++; familiarity with relevant libraries and toolboxes such as ROS, OpenCV, etc), the ability to conduct independent research, to work in a team and to assume responsibility.


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, please send your application including CV and cover letter to

Dr. Martin Rufli

+41 44 724 8714

Applicant review will begin immediately.

3 PhD positions: NeMeCo - Near-memory computing - Scaling big-data processing into the next decade

Ref. 2016-16


Project description

The emerging knowledge economy relies increasingly on big-data applications to extract value out of huge amounts of data by searching for correlations that can be used to predict business trends, find the best medical treatment for diseases, perform financial risk management, determine the best locations to drill for oil and gas, fight crime, and for many other purposes. Big-data applications are very different from traditional workloads and put extremely high demands on the High Performance Computing (HPC) systems that are used to execute them.

One of the key challenges in designing new generations of HPC systems that can keep up with the ever-growing data volumes, is that current technological trends prevent large amounts of data to be transferred at acceptable power dissipation costs. Reducing expensive data transfers by “bringing computation closer to the data”, also known as near-memory computing, has emerged as a very promising solution to address this scaling issue in HPC systems in order to realize the Exascale computing systems that are required for handling future Big-data workloads. Near-memory computing, however, is still in its infancy, and many challenges have to be addressed before it can be established as an integral component of HPC systems.

NeMeCo is an ambitious Marie Skłodowska-Curie European Industrial Doctorates (EID) Innovative Training Network (ITN) programme, which addresses several of the above challenges. In particular, NeMeCo is an interdisciplinary training and research project aimed at developing power-efficient HPC systems for Big-data processing based on the exploitation of near-memory computing capabilities, and, in this way, making the world a better place by enabling important innovations in, for example, healthcare, energy consumption, traffic congestion and safety.

NeMeCo involves a three-partner network comprising the Eindhoven University of Technology in the Netherlands, IBM Research – Zurich, and the Netherlands Institute for Radio Astronomy, ASTRON. These partners provide a unique combination of academic and industrial expertise of Big-data applications, compilers, memory and processor technology, and high-performance computer architecture. NeMeCo offers early stage researchers (ESRs) an excellent multidisciplinary training program at the cross roads of hardware and software design, where complex trade-offs have to be made between performance, programmability and energy efficiency. A board of 8 experienced supervisors will work together across disciplines and sectors to train and mentor the ESRs who will have access to superb research facilities at all locations. A total of three individual PhD projects are available

  • ESR1: Run-time optimization
  • ESR2: Compiler technology
  • ESR3: Near-memory processor design

These three projects complement each other to cover the wide spectrum of aspects related to the following research objectives that build upon each other:

  1. Analysis of Big data workloads, their key algorithms, their complexity in terms of memory, compute and I/O operations, their data locality, their parallelization potential, their mappings to various platforms, possible algorithmic optimizations, etc. The purpose is to obtain a detailed understanding of their characteristics, and their static and dynamic processing requirements (ESR1+2+3).
  2. Modelling of selected Big data workloads, modelling of conventional computer architectures and of potential novel architectures based on near-memory computing, and modelling of the mapping of the workloads on those architectures. Objective is to enable a huge design space exploration, but still with sufficient detail based on accurate predictions of power consumption and performance (ESR1+2+3).
  3. Development of techniques for partitioning, mapping, and compiling Big data workloads on a hybrid HPC system combining conventional processing elements with near-memory computing capabilities (ESR2). Development of techniques for run-time optimization of the performance and power consumption (ESR1). Development of a system-level and accelerator level architecture for a near-memory computing device integrated into a hybrid HPC system (ESR3).
  4. Realization of a near-memory computing tool set and ecosystem including compiler, debugger, performance analysis, and run-time optimization tools (ESR1+2), and a near-memory computing device implementation in a hardware description language (ESR3).
  5. Translation of the expertise, models, tools and architecture, into a small-scale demonstrator of a computing system supporting near-memory computing (ESR1+2+3). This demonstrator will be integrated into an emerging ecosystem for HPC technologies, which increases the commercial relevance of the developed near-memory computing tool set and architecture while, at the same time, allowing evaluation of its application to a wide range of real-world problems. The latter is a key element of the proposed cutting-edge research program and will be instrumental for realizing break-through innovations.

The training is structured individually for each ESR based on a personal career development plan which covers scientific, personal and transferable skills. The ESRs will be employed for an initial period of three years by the Eindhoven University of Technology in the Netherlands, which will also award the PhD degrees. If successful, the employment will be extended by a fourth year. Each ESR will do secondments at IBM Research GmbH in Switzerland (for about 20 months) and at ASTRON in the Netherlands (for about 4 months).

As part of the NeMeCo project, the three ESRs will have access to an exceptionally wide range of state-of-the-art server and supercomputing technologies, including an on-site BlueGene BG/Q system, a collection of OpenPOWER hardware, various commercial GPUs, FPGAs, and DSPs, as well as technologies that are not on the market yet, such as the world’s first hot water cooled 64-bit microserver and an accelerator platform that is based on the direct attachment of FPGAs to the memory interconnect of a commercial server processor.

In addition, the DOME project, in which ASTRON and IBM jointly perform fundamental research on large-scale green Exascale computing for the Square Kilometre Array (SKA) radio telescope, offers the ESRs a unique opportunity to get experience with an “extremely Big”-data application, involving the processing of Exabytes of astronomical data collected by hundreds of thousands of antennas and dishes for exploring the universe. The SKA will become the biggest radio telescope on earth requiring enormous compute power when it becomes operational in the next decade.


More information on the job requirements, conditions of employment, and how to apply

Download PDF of this job description

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.

Post-Doc researcher: Developer of computational methods to support personalized medicine in cancer

Ref. 2015-18


Project description

A postdoctoral research position is available at IBM – Zurich Research Laboratory to develop computational methods to support personalized medicine in cancer. This highly interdisciplinary project involving the collaboration of several institutions across Europe and USA will focus on prostate cancer, a leading cause of cancer death amongst men, but also prone to over-treatment.

Maria Rodrigues Martinez on working in SwitzerlandThe project aims to develop computational models that can exploit molecular and clinical data in order to improve our understanding of cancer disease mechanisms and predict optimized strategies for therapeutic intervention. The models will be based on the exploitation of genomic, transcriptomic, proteomic, and clinical data in primary and metastatic tumors, prospective cohorts of well characterized prostate cancer patients, drug screenings in cell lines, and the use of the Watson technology, a last-generation cognitive computer developed at IBM.

The successful candidate will analyze molecular data in order to characterize tumor heterogeneity, and will develop methodologies to integrate disparate types of data into models that can help risk-stratify patients.


Requirements

Candidates should have a strong background in computer science, mathematics or physics and be interested in cancer-related research. Strong programming skills are necessary. Experience in machine learning, Big Data analysis, and high-performance computing is a plus.


About the group

The group of systems biology at IBM aims to develop new mathematical and computational approaches for the analysis and exploitation of the latest generation of biomedical data. In the context of cancer, the group focuses on the integration of high-throughput molecular datasets to build comprehensive molecular disease models; the development of new approaches to reconstruct signalling protein networks from single-cell time-series proteomic data; and the application of Bayesian approaches and high-performance computing to the problem of network reconstruction.


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, please send an application including CV and reference letters to:


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Innovating at IBM

At IBM, you have the op­por­tun­ity to work on real prob­lems. In the past few weeks I've spo­ken with cli­ents in ener­gy, auto­motive, health­care, chem­i­cals and the mater­ials sci­ences. The poten­tial for world-chang­ing im­pact is in­cred­ib­ly high.
In addition, whenever an IBMer has a good idea, he or she can be sure the com­pany will in­vest in it and put all re­sources necessary towards making it real.”

  • Interview with IBM's Cristiano MalossiCristiano Malossi
    IBM research scientist

Read more about what motivates Cristiano


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