Open Faculty Position Assistant or Associate Professor

Announcement Open Faculty Position Assistant or Associate Professor without tenure due to source of funding (WOT)

The Northwest Institute of Genetic Medicine in partnership with the University of Washington in Seattle is seeking a new biomedical and health informatics faculty member at the level of assistant or associate professor in the Division of Biomedical and Health Informatics (www.bhi.washington.edu) without tenure due to source of funding (WOT).

The Northwest Institute of Genetic Medicine (NWIGM) is a recently established multi-disciplinary multi-institutional program funded by the State of Washington Life Sciences Discovery Fund. The primary goals of the NWIGM are a) to facilitate the design, development, and execution of translational genetic studies that bridge basic and clinical research at academic institutions and biotechnology companies, and b) to promote outcomes research on the role of genetic testing in clinical medicine and its impact on the provision of healthcare. Key activities of the NWIGM include consultation related to study design, grant writing, and generation of pilot data.

Key disciplines involved in the NWIGM include the Division of Medical Genetics in the Department of Medicine, the Division of Genetics in the Department of Pediatrics, the Department of Genome Sciences, the Center for Biomedical Statistics in the Department of Biostatistics, and the Division of Biomedical and Health Informatics in the Department of Medical Education and Biomedical Informatics. The organizations that have partnered to form NWIGM include the University of Washington, Seattle Children's Research Institute, and the Center for Health Studies at Group Health in Seattle. NWIGM also partners with the regional Institute of Translational Health Sciences (www.iths.org) which is an NIH CTSA funded center for clinical/translational research. The leadership for the NWIGM includes Dr. Gail Jarvik (Director), Dr. Bruce Weir, Dr. Deborah Nickerson, Dr. Michael Bamshad, and Dr. Peter Tarczy-Hornoch.

We encourage applications from candidates committed to biomedical informatics research in the area of genetic medicine both in the area of fostering discovery and in the area of applying the new discoveries. The responsibilities of the position include the following areas of activity: a) developing an independent program of research in the general area of linking electronic medical record phenotypic data (including natural language processing of text notes) with biological/genomic data sets in the context of genomic medicine, b) working with students and post-docs interested in this research area, c) providing consultation related to informatics support in this area related to grant writing, study design, and generation of pilot data, d) establishing collaborations with NWIGM members, and e) overseeing the development of an informatics consult service within the NWIGM.

The primary appointment will be 100% FTE with a 12-month service period in the Department of Medical Education and Biomedical Informatics in the School of Medicine with opportunities for joint or adjunct appointment as appropriate. The initial appointment is without tenure due to funding (WOT). Generally, if an award of tenure would be proposed for consideration it would be after an individual has attained the full professor rank. Full funding through the NWIGM is available for 3 ½ years after which it is expected that the faculty member will be supported by a combination of grants and revenue from the NWIGM.

Candidates must have a doctoral degree in a core discipline of biomedical informatics, computer
science, or similar as well as training in biomedical informatics. Strong training in research methods is required; and experience with genetic association studies and/or natural language processing and/or electronic medical records is highly desirable. Demonstrated ability
to initiate and successfully conduct research is highly desired as well.

Review of applications will begin in Fall 2008 and continue until filled. We are seeking candidates available to start working Summer 2009 or earlier. Please send a statement of interest and qualifications, detailed curriculum vitae, and four letters of reference to:


NWIGM Informatics Faculty Search
c/o Donna Rowe
Department of Medical Education and Biomedical Informatics
Box 357240
University of Washington
Seattle, WA 98195-7430
www.bhi.washington.edu

email: zermatt@u.washington.edu
phone: 206-221-3322

Search committee chair:

Peter Tarczy-Hornoch, MD
Head and Professor
Division of Biomedical and Health Informatics
Department of Medical Education and Biomedical Informatics
School of Medicine

University of Washington faculty engage in teaching, research, and service. The University of Washington is an affirmative action, equal opportunity employer. The University is building a culturally diverse faculty and staff and strongly encourages applications from women, minorities, individuals with disabilities, and covered veterans.

Liaison Manager: National Centre for Text Mining and Biomedical ResearchCentre, University of Manchester

The Biomedical Research Centre and the National Centre for Text Mining (www.nactem.ac.uk) seek to appoint a liaison manager to support their research and commercialisation activities; to establish, maintain and develop strategic links with industry and tool/resource suppliers; and to contribute substantially to ensuring the sustainability of both centres.The post is available with immediate effect for 2 years in the first instance.

The National Centre for Text Mining forms part of the School of Computer Science at the University of Manchester. Its role is to provide text mining services to the academic community and to engage with industry. The successful candidate will provide industrial and research support for a strong and dynamic team in text mining, liaising between the Biomedical Research Centre and the National Centre for Text Mining activities.

Closing date for applications: 10/01/2009

Further details are available at:
http://www.manchester.ac.uk/aboutus/jobs/research/vacancy/index.htm?ref=144704

Please quote reference: EPS/81303

Informal enquiries should be made to sophia.ananiadou@manchester.ac.uk

PhD scholarship for computing in medicine and life sciences, Luebeck University, Germany

The Graduate School for Computing in Medicine and Life Sciences at the University of Luebeck (Germany), publishes 16 Ph.D. scholarships for 16 individual projects in the fields of bioinformatics and robotics.

PhD scholarship amounts to 1250 € per month. Students with a master's degree (or its equivalent) in computer science, mathematics or engineering are invited to apply for admission. The application deadline is January 15, 2009. In certain cases, students must submit, as part of their application, the results of one of the acknowledged language tests to prove their English proficiency.

For further information, please visit our website at www.gradschool.uni-luebeck.de. Do not hesitate to contact us if you have any further questions via email: management@gradschool.uni-luebeck.de before sending your application.

1. Correction of Susceptibility caused Distortions in Functional Magnetic Resonance Imaging

Recently a research group at the host university has discovered a method for computing the distortions of the static field in MRI. This method is based on multi-grid methods, and has been successfully applied to the correction of the geometric distortions in T1-weighted images.
Based on new registration methods, it was shown that the statistic measure of similarity between CT images and T1-MR images of the same anatomy increased after applying this new method. The goal of this project is to apply the techniques developed to fMRI images, in order to allow for the use of fMRI in navigation.

2. Endoscopic Optical Coherence Tomography in the Deep Brain

Optical Coherence Tomography (OCT) is a new high-resolution, real-time imaging modality. Institutes of Lübeck University have been instrumental in developing this emerging technology, which is now beginning to gain recognition in laboratories world-wide. We have shown that OCT is able to capture the difference between white and grey brain matter.

The goal of the project is to investigate Optical Coherence Tomography (OCT) as a minimal-invasive imaging modality for deep brain navigation and diagnosis in neurological disorders. The goals of the project are:

1. Development of endoscopic OCT, thus OCT that can be placed inside a thin endoscopic needle.
2. Development of signal processing methods for tissue identification and classification.
3. Integration of OCT in a stereotactic environment.
4. Integration of OCT into neuronavigation systems.

3. Transcranial sonography (TCS) in monogenic forms of Parkinsonism

The project: There are several open questions regarding ultrasound technology in genetic and nongenetic forms of parkinsonism:

1. Is there information other than aSN or LN hyperechogenicity in the ultrasound signal from the mesencephalic and diencephalic ultrasound images to characterise distinct forms of parkinsonism/PD?
2. Is the ultrasound investigation useful to screen a large population for genetic and other forms of PD?
3. Can SN hyperechogenicity serve as a preclinical marker?

Computer methods for automated investigator-independent detection of the SN and LN will be developed. After development of this tool for the detection of aSN and LN hyperechogenicity, a statistical image processing tool will be created to detect specific characteristics of the images.

4. Stroke Rehabilitation Robot

The robots under investigation must have novel sensory capabilities to adapt to the patient's individual needs. Interdisciplinary tracks of developments would aim at cheap, yet precise sensor-actuator combinations, high acceptability by ergonomic and psychologically optimised appearance, interactivity by smart sensors and signal analysis as well as therapeutically optimised movement paradigms.

5. Parallel mode of action control: from human studies to intelligent robotic interfaces

The goal of the project is to transfer knowledge about the function of the motor system into haptic interface systems and stroke rehabilitation robotics. We will first consider the well established task of reaching for / grasping an object. This complex action consists of two main components, which are processed in parallel channels. The phylogenetically "older" reaching component is processed in the fast dorso-dorsal channel and the "younger" component of grasping requires more programming of the hand-object interaction and is processed in the slower ventro-dorsal channel. Neuroimaging studies with fMRI, MEG and DTI will be used to validate models.

6. Cardiac pacemaker localisation

The Graduate School of Computing in Medicine and Life Sciences (funded by Deutsche Forschungsgemeinschaft, DFG, and the German Government within the German university excellence program) at the University of Luebeck is now offering a PhD scholarship for the project "Cardiac pacemaker localisation “ in the research field of Robotics and Neuro-Rehabilitation.

7. Brain Modelling

The Graduate School of Computing in Medicine and Life Sciences (funded by Deutsche Forschungsgemeinschaft, DFG, and the German Government within the German university excellence program) at the University of Luebeck is now offering a PhD scholarship for the project "Brain Modelling “ in the research field of Navigation Methods in the Deep Brain.

8. Robot assisted navigation guided OCT operating microscope

We have recently demonstrated that optical coherence tomography (OCT) of human brain in vivo can be done and that this optical tissue imaging delineates adjacent brain, tumour invaded brain and the highly cellular part of the tumour. In such a scenario, a robot-assisted and navigated microscope would be able to obtain consecutive images of a tumour resection cavity. These imaging data could be scored for residual tumour.

The goals of this project are: (1) Robotic microscope, (2) Integration of optical coherence tomography into the optical pathway of a neurosurgical operating microscope (3) 3D mapping data of the OCT tissue analysis and imaging data for navigation.

9. Definition of cortical networks for the control of eye and hand movements

One of our topics will be to define the possible modulation of these cerebro-cerebellar activation patterns depending on a variable context of the movement. This will be investigated by using different levels of complex tasks, or, as in "normal" life situations, different levels of attention to the tasks especially due to different levels of external distraction. This definition of certain cerebro-cerebellar networks allows a possibly more precise interaction with technical devices such as EEG or ECoG, for instance to control a computer or an external technical device in a more natural way.

10. 3-dimensional kinematic principles of eye, head and limb movements

The project addresses two hypotheses:

The central processing of convergent semicircular canal information in the human brain as assessed by head impulse tests is consistent with its prediction obtained from the alignment of 3D rotation vectors of the spontaneous nystagmus in patients with brain stem lesions and the vectors resulting from individual semicircular canal stimulation.

Eye-centred rather than body-centred mechanisms are governing the integration of target and hand position in programming reaching movements in patients with a vestibular lesion with the head unrestrained vs. restrained.

11. Interfaces based on EEG, ECoG and DBS

The goal of this project is to develop stationary medical grade signal processing hard- and software to record from 256 wideband channels while ignoring synchronous magnetic disturbances (TMS). The second step will deal with the improvement of the stationary system to a mobile platform, based on embedded signal processing. The goal is to develop optimal classifiers to interpret brain activity and utilise this analysis to provide a scarce command set for output devices.

12. Inhibitor Design

Three-dimensional models for the homologous Mip proteins from Chlamydia spp. will be constructed by homology-model building. Along with the X-ray structure of Legionella Mip, these will be used in virtual screening for and docking of potential new inhibitors. Hits found in this procedure will be synthesised in-house and tested for PPIase inhibition in vitro and for antibacterial effects in vivo.

13. Efficient Methods of Exact Solutions of Complex Problems in Molecular Biology

Finding an optimal alignment is a very difficult and time consuming task due to the inherent algorithmic complexity. Therefore, most software systems provide only approximate solutions. We have developed new exact sequential algorithms that give better performance. A current PhD project tries to parallelise our new methods in a suitable way such that further significant speedups by parallel processing can be achieved. The algorithms are tested on our high performance shared-memory parallel machine SunFire 15K. An important innovation for our solution is the reduction of the tasks to specific graph theoretical problems that can be solved efficiently also in parallel, for example to distance problems in specific regular graphs.

14. Synaptic Plasticity: Regulatory Mechanisms in Receptor Trafficking

The project deals with the modelling and the simulation of the molecular mechanisms of LTP and LTD in the synaptic transmissions. The proposed project aims in the explanation of fundamental mechanisms of multistable reactions both in synaptic plasticity and in more general context. An essential part of such reactions is a positive-feedback loop, which has been found in various biochemical and medical investigations.

15. Computational analysis of RNA structure

We propose to develop computer-based tools for the automated theoretical design of gene interruption and to implement suitable algorithms. The development will be based on novel machine learning methods for motif detection and classification.

16. Analysis of adult stem cells by computer vision

In this project, time-lapse imaging of living cells is combined with computer vision and machine learning technologies to discover patterns in the in vitro behaviour of the cells. This non-invasive approach has the advantage that the cells are left undisturbed, since already small perturbations may alter the growth and differentiation characteristics of the cells. Moreover, the method allows for the investigation of large cell numbers, thus ensuring the statistical relevance of the obtained data.

PhD/Posdoc Positions in Biomedical Data Mining

PhD/Posdoc Positions in Biomedical Data Mining
University of Geneva/University Hospitals of Geneva, Switzerland

Applications are invited for 2 PhD students and 1 Postdoc in data mining
applied to biomedical data. The candidates will work on a 4 year
European research project (FP7). The project will involve several
clinical sites across Europe, including the University Hospitals of
Geneva, as well as leading EHR vendors. The goal of the project is to
deliver computer tools and methods to advance the state of the art in
documenting, detecting and preventing antibiotics resistance at both
clinical and population levels.

Candidates should have the following qualifications:
-an outstanding academic record in computer science as well as strong
mathematical and programming skills;
-a solid background in at least two of the following areas: distributed
database management, quantitative analysis, machine learning,
information retrieval, business intelligence, ontology engineering,
multimodal data management (structured data/text/signals...).
-a clear aptitude for independent and creative research as evidenced by
an excellent Master or PhD thesis;
-good communication skills in English and French (or at least a clear
indication of willingness to learn the latter).

The salary for a research assistant at the University of Geneva starts
at about 50000 CHF (~45000 USD or 30000 Euro) per year. The University
and University Hospitals of Geneva are equal opportunity employers.
Please send your curriculum vitae, academic transcript, and contact
information to patrick.ruch@sim.hcuge.ch.

Postdoctoral or Research Fellow in Biomedical Text Mining

Postdoctoral or Research Fellow in Biomedical Text Mining
Faculty of Medicine CENTRE FOR HEALTH INFORMATICS
http://www.chi.unsw.edu.au
UNSW Sydney Australia

We are seeking to appoint a highly motivated and experienced researcher, as a postdoctoral or research fellow in the Centre for Health Informatics, with a background in computational linguistics, computer science or a related area to develop and evaluate advanced text mining techniques and apply them in knowledge management applications in the biomedical domain.

The Centre for Health Informatics is Australia's largest academic health informatics research group conducting fundamental and applied research focusing on the design, evaluation and application of decision-support technologies for healthcare and the biosciences. The Centre is located at the University of New South Wales and collaborates with researchers in computer science, health services research and with industry and the public and private sectors.

This position offers an outstanding opportunity to work in a unique multi-disciplinary research environment encompassing information, communication, cognitive and organisational science to support health service and biomedical innovation.

Requirements for the position are:

• A PhD in Computational Linguistics, Artificial Intelligence, Computer Science or a related area.
• A track record of publication in the peer reviewed literature.
• Skills in one or more of the following areas: text mining, information extraction, named entity and relation extraction, computational lexicon development, text categorization, automatic text
• summarization, information retrieval.
• Preferably a strong track record and experience in statistical machine learning approaches to natural language processing.
• Excellent programming skills (Java/Python/Perl/C++).
• Knowledge of research experimental methods; ability to develop, implement prototypes and validate algorithms.
• Good oral and written communication skills; ability to produce oral presentations and written
• technical reports of publishable quality.
• Demonstrated skills in working in a team and desire to coach junior researchers and students.

The position is for two years full time with the possibility of extension depending on further funding. This opportunity offers much flexibility in supporting individual career development, including the commencement of new initiatives. A part-time appointment may be considered.

FIXED TERM: This is a fixed term position available until June 2009. The salary range is: Postdoctoral Fellow (Level A) $50,014 - $66,686; Research Fellow - Level B $70,028 - $82,554 (plus up to 9% employer superannuation plus leave loading), depending on qualifications and experience. The salary includes a superable UNSW academic loading of $3,000 per annum payable to academic staff (pro rata for fractional academic staff). A part-time appointment may be considered..

Please direct any enquiries to Dr Grace Chung on 02 9385 9016 or by e-mail on graceyc@unsw.edu.au.

Applications close 29 February 2008.

Senior Researcher in Bio-text Mining

Senior Researcher in Bio-text Mining

National Centre for Text Mining (NaCTeM)
School of Computer Science
University of Manchester, UK

We are looking for one senior researcher in text mining to work for a new project at NaCTeM (www.nactem.ac.uk) in text mining for systems biology (ONDEX project http://ondex.sourceforge.net/ ). The post is available immediately and for a duration of three years. The successful candidate will be appointed at Research Fellow level (salary £33,779 - £41,545 p.a) and will be part of the growing team of researchers associated with NaCTeM which is hosted by the School of Computer Science.

Essential skills: a good first degree and a PhD in an area relevant to text mining as well as excellent software engineering skills. The ability to develop algorithms and software for NLP/TM systems and to produce experiments for text mining applications using large data sets. Excellent knowledge of natural language processing/text mining using machine learning techniques and in particular named entity recognition, parsing, information extraction; excellent knowledge of C, C++, Java, XML, Windows, Linux and Web Services. A strong publication record is a must. Experience with biomedical text mining would be an advantage.

Informal enquiries should be made to Dr Sophia Ananiadou, Sophia.Ananiadou[at]manchester.ac.uk

Closing date for applications: 8th February 2008

Further details are available at: http://www.manchester.ac.uk/aboutus/jobs/research/vacancy/index.htm?ref=130141

Please quote reference: EPS/80023

Text and Language Processing for Biomedical Applications

Researcher / Senior Researcher Positions in
Text and Language Processing for Biomedical Applications

NICTA Victoria Research Laboratory
Melbourne, Australia

National ICT Australia (NICTA) is looking to fill research positions for a new project in Text and Language Processing for Biomedical Applications. Appointments may be made at the Researcher or at the Senior Researcher level. Appointments are for at least 2 years, potentially renewable for a 3rd year, to commence in 2008. Remuneration is at an internationally competitive level.

To apply and to view full Position Descriptions, go to http://nicta.com.au/about/careers. For further information or any enquiries, contact Dr. Lawrence Cavedon at lawrence.cavedon@nicta.com.au .

Closing date is February 15, 2008.

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The appointee will work with NICTA research staff, engineering staff, University of Melbourne faculty and postgraduate students, and external biomedical collaborators (especially within Melbourne's Bio21 precinct) to develop new techniques in information access and presentation, document processing, and text mining, with application to the biomedical research and clinical domain. Expected outcomes will include fundamental research, publications in high-impact venues, development of novel IP, and prototype systems and demonstrators (developed together with engineering staff). Other duties will include working with external biomedical partners to understand and respond to needs, and supervision of University of Melbourne research students.

Key requirements and selection criteria for the positions include:

• a PhD in Computer Science, Computational Linguistics, Artificial Intelligence, or a related discipline;
• a strong track record of publication in respected journals and international conferences;
• demonstrated expertise in a research area related to the goals of the project, including: information retrieval, natural language processing, question answering, human computer interaction in an IR setting, parsing, named entity recognition and resolution, text summarisation, ontology building / integration, system efficiency;
• good interpersonal skills and a demonstrated commitment to working collaboratively in a research team and delivering on team goals;
• excellent communication skills in a variety of contexts, including presentation of research and liasing with external collaborators;
• a strong interest in collaborating with external domain partners to understand their needs and to jointly develop solutions;
• applicants to the Senior Researcher level are expected to have demonstrated ability to craft a research agenda and to effectively supervise junior staff and research students.

Other desirable skills and selection criteria include:

• previous experience in the biomedical domain;
• programming skills in a variety of languages, including C/C++, Java, Python, Perl;
• demonstrated experience in statistical techniques to NLP and/or experimental design and analysis for computer science research;
• an interest in developing Intellectual Property that may lead to commercial development by NICTA.

National ICT Australia (NICTA) is Australia's ICT Research Centre of Excellence. NICTA aims to bring together world-class researchers and professional staff, enhance their skills, and build a culture of entrepreneurship and achievement in use-inspired research that will build Australia's ICT capacity.

See http://www.nicta.com.au for more information.

NICTA's Victoria Research Laboratory (VRL) is housed on the University of Melbourne campus, in the Parkville precinct of Melbourne, and within walking distance to one of the world's richest congregation of biomedical hospitals and research institutions. NICTA VRL has made a strong commitment to developing its Bioiformatics research program; the Snr/Researcher will be encouraged to work with researchers from the wider Bioinformatics team, as well as the other researchers on this specific project. VRL has establised partnerships with a number of Melbourne's leading biomedical research institutions and biomedical projects with international profile; further collaborative partnerships are constantly being developed.