Systems-Biology

Intership/Student project: PARTICLE SIMULATION OF ANTIBODY - TARGET INTERACTION

Wed, 07 May 2008 20:34:12 +0900

Description:

To design a new generation of monoclonal antibody (mAb) drugs we are applying novel modeling and simulation approaches. An accurate modeling of antibody-target interaction is critical for reliable predictions which directly feed into the drug development process. The current project aims to study the fundamentals of antibody-target interaction. Commonly this system is modeled with ordinary differential equations. For a one-to-one partner binding system this model is an accurate description. However, for the case of cell surface targets or where the target has multiple binding sites it is unclear how the interactions must be modeled in an ODE framework. The idea is to develop a particle simulation tool that can be used to study the fundamentals of antibody dynamics and derive the appropriate ODEs. This study is also expected to impact the design of more complex biological constructs and is therefore at the leading edge of modeling and simulation in drug development.

Position for plant-related Systems Biology

Wed, 07 May 2008 19:22:39 +0900

Job Description:
The Dow Chemical Company is making strategic investments to enable new product development in the BioSciences arena. This emerging market space targets R&D in new biotechnology-derived products ranging from agricultural commodities, to biomaterials, biomimetics, and biofuels. Computational modeling and biological systems analysis are foundational competencies for this field of research and development. Dow is building a Bioanalytical Center of Expertise located at the Dow AgroSciences facility in Indianapolis, IN. As a member of this Bioanalytical Center you will be accountable for leading the development and implementation of plant-related Systems Biology capabilities for Dow AgroSciences and Dow BioSciences projects and product platforms.

Key responsibilities will include:

Advance our computational biology capability and apply biological modeling approaches to enable or accelerate R&D projects
Act as an internal technical expert to develop a robust infrastructure for computational modeling in biology, and lead efforts that utilize external collaborations in this arena
Apply relevant computational tools for the analysis of plant metabolic networks
Assess, implement and document various bioinformatics and Systems Biology tools to streamline data management, data analysis and experimental design

Frontiers in Multi-Scale Systems Biology

Thu, 01 May 2008 12:37:47 +0900

Atlanta, GA
http://www.ibsi.gatech.edu/frontiers/

Submission deadline for poster abstracts: July 1, 2008.

PhD Scholarship in B-Cell Autoreactivity and its Role in Solid Organ Transplantation

Thu, 01 May 2008 11:59:18 +0900

Applications are invited for a 3-year PhD scholarship at DTU Nanotech with starting date soon, but negotiable. The project is part of a larger collaboration between DTU Nanotech, Technical University of Denmark (DTU), Copenhagen University Hospital (Rigshospitalet), Denmark, and the Weizmann Institute of Science, Israel, and is funded by the Danish Agency for Science, Technology and Innovation and DTU through DTU's Graduate Programme in Medicine and Technology.

Application Due: July 1, 2008

Call for Applications: ISCB Student Council DREAM Team

Wed, 30 Apr 2008 16:31:57 +0900

The ISCB Student Council is looking for highly motivated Bioinformatics students to join our team for the DREAM 2008 network reconstruction competition. The team will be mentored and advised by a senior researcher and expert in the field of network reverse engineering, Dr Alberto de la Fuente.

It's not necessary to be a member of the ISCB to apply - we will sponsor a one year ISCB membership for the successful applicants!

For details please see http://www.iscbsc.org/dreamteam.

This is a unique opportunity for students from all over the world to participate in an international, high-profile research competition. The students will collaborate and network with peers from other parts of the world and work under the guidance of an expert in Computational Biology.

Best regards,

Nils Gehlenborg
Chair, ISCB Student Council

Post-doc position for the European Project "APO-SYS - Apoptosis systems biology applied to cancer and AIDS", at Institut Curie, Paris, France

Wed, 30 Apr 2008 16:15:06 +0900

This position is created to support participation of Institut Curie to the EU-FP7-HEALTH-2007-2.1.2-4 project "Apoptosis systems biology applied to cancer and AIDS: An integrated approach of experimental biology, data mining, mathematical modeling, biostatistics and molecular medicine". One of the goal of Institut Curie in the project is the creation of a generic mathematical model of apoptosis pathways, based on quantitative (using ODEs) and qualitative (using logical formalism developed by R. Thomas) approaches. The final model should recapitulate existing models of different aspects of apoptosis and integrate data that will be provided by molecular biologists involved in the project. The mathematical model will be formally analyzed (robustness, parameter sensitivity study, bifurcation analysis, model-checking). Finally the model will be used to facilitate experimental design and make predictions for the biological systems under study.

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Summer Schools 2008

Tue, 22 Apr 2008 14:00:00 +0900

Find your Summer Schools 2008. More Job Postings.

Summer Schools 2008

Tue, 22 Apr 2008 12:52:34 +0900

Find your favorite Summer schools:

Summerschool on Data Analysis June 30 - July 11, 2008, Madrid, Spain
CSHL Summer School in Computational Cell Biology, June 27 - July 17, 2008. Cold Spring Harbor Lab, USA
A FEBS Advanced Lecture Course - New Developments in Quantitative Molecular Bioscience Sept 10-17, 2008, Island of Spetses, Greece
2nd summer school on Systems Biology for Medical Application September 30 - October 2, 2008, Costa Adeje Gran Hotel, Tenerife

Systems Biology of Human Disease

Tue, 22 Apr 2008 12:34:34 +0900

Joseph B. Martin Conference Center at Harvard Medical School, Boston, MA, USA
http://www.csb2.org/events/sbhd_2008

Registration deadline: May 15

Two Post-Doctoral Positions

Tue, 22 Apr 2008 12:25:09 +0900

1. Biological Modeling Post-Doctoral Position.
2. Metabolic Modeling Post-Doctoral Position.

Jennifer Reed
University of Wisconsin-Madison
Dept of Chemical and Biological Engineering
1415 Engineering Dr, 3639 Engineering Hall Madison, WI 53706
jlreed @ wisc.edu

PhD-studentship or Postdoctoral position in Systems Biology

Mon, 21 Apr 2008 11:48:39 +0900

The department of Systemic Cell Biology at the Max Planck Institute of Molecular Physiology in Dortmund, Germany, invites applications for a PhD-studentship or a Postdoctoral researcher

Senior Electron Microscopy Technician & Postdoctoral Fellow

Fri, 18 Apr 2008 13:07:22 +0900

POSITION AVAILABLE Senior Electron Microscopy Technician & Postdoctoral Fellow

A Senior Electron Microscopy Technician and a Postdoctoral Fellow are sought to carry out research work on the structure of actin filament complexes that (1) are associated with cardiac and skeletal muscle regulatory proteins to control muscle activity and (2) interact with smooth muscle actin-binding proteins to modulate the assembly of the smooth muscle cytoskeleton. Applicants must have experience in high-resolution EM work and first-rate facility with computer-assisted image analysis. Prior familiarity with preserving and recording macromolecular assemblies in negative stain and by cryo-EM methods would be invaluable. Experience in supervising research students would also be important.

Interested applicants should contact Dr. William Lehman at the meeting or send their CV with three references to:

Dr. William Lehman
Professor of Physiology & Biophysics Department of Physiology & Biophysics
Boston University School of Medicine
715 Albany Street Boston, MA 02118 Or
Email: wlehman @ bu.edu
Dr. Lehman's research is summarized on his home page: http://biophysics.bumc.bu.edu/faculty/lehman/index.html

PhD student researcher

Wed, 16 Apr 2008 12:43:02 +0900

FORSYS Junior Research Group
Systems biology of pancreatic cancer

Systems Biology and Bioinformatics group
University of Rostock
www.sbi.uni-rostock.de

Job description:

Research in systems biology of pancreatic cancer in an interdisciplinary junior research team working in collaboration with the Department of Gastroenterology at the Medical Faculty
Mathematical modelling of chemical kinetics and transport processes of cellular signal transduction pathways in pancreatic cancer on basis of quantitative experimental data
Analyzing model properties using methods from dynamical systems theory
Development of mathematical tools for experimental design
Statistical analysis of QTPCR and western blot data

Requirements:

Degree in Systems Biology, Physics, Mathematics, Engineering or Biochemistry
Experiences in the above research fields
Interest in interdisciplinary research in the life sciences

Salary: E13, full time job
Starting date: June-September 2008
Project duration: 2 years, with the possibility for extension (five years maximally)
Deadline: May 20, 2008.

Further information: Dr. Katja Rateitschak Tel. +49 381 498 7573

Application expenses cannot be reimbursed.
Submit your application (CV, certificates, etc.) in pdf format to:

Dr. Katja Rateitschak
FORSYS Nachwuchsgruppe
LS Systembiologie und Bioinformatik
Institut fuer Informatik Universitaet Rostock
D-18051 Rostock Germany
katja.rateitschak @ uni-rostock.de

Tenure Track/Tenure Investigator Positions in Systems Immunology and Infectious Disease Modeling

Mon, 14 Apr 2008 14:03:32 +0900

The National Institute of Allergy and Infectious Diseases (NIAID), Division of Intramural Research (DIR) is seeking several outstanding individuals for its new Program in Systems Immunology and Infectious Disease Modeling (PSIIM).

Modern technology allows the analysis of immune responses and hostpathogen interactions at multiple levels - from intracellular signaling networks, to individual cell behavior, to the functioning of a tissue, organ, and even the whole organism. The challenge is not only to collect the large amounts of data, but also to organize it in a manner that enhances our understanding of how the immune system operates or how pathogens affect their hosts. To do this, it is necessary to develop detailed quantitative models that can be used to predict the behavior of a complex biological system. These models can help explain the mechanisms underlying physiological and pathological responses to infection or vaccination, which can then be employed to design better therapies or vaccines.

Achieving these goals requires an interdisciplinary effort and for this reason the PSIIM is organized as an integrated team of scientists and support staff. Within the PSIIM, there will be groups with expertise in the areas of computational biology, bioinformatics, proteomics, genomics, cell biology, immunology, and infectious diseases. These teams will have access to the latest technology for gene expression profiling, high content screening of RNAi libraries for the discovery of pathway components, imaging tools, genomic and proteomic analysis, cores for the genetic manipulation of animals, and a substantial computer infrastructure. They will also have access to BSL3 facilities for working with infectious agents of high priority for human health and biodefense. Although the PSIIM has been established within NIAID and has an immune / infectious disease focus, it is also expected to play a major role in fostering the growth of systems biology efforts throughout the NIH and involving diverse biomedical areas.

Current teams in the PSIIM include Immunology, Computational Biology - Modeling and Simulation, and Molecular / Cell Biology - High-throughput screening. The PSIIM is now recruiting for tenure track or tenure level team leader appointments in the following areas:

Bioinformatics / Biostatistics: the incumbent will lead a group focused on developing and implementing computational tools and statistical methods for the analysis of genomic and proteomic data. The ideal candidate will have a strong background in statistics, mathematics, programming, and modeling biological systems as well as a strong interest in collaboration with biologists for the elucidation of biological mechanisms. The group will include expertise in software development (C++, Java, Perl, SQL etc.), knowledge of bioinformatic tools, databases and algorithms, and experience with heterogeneous computer environments (UNIX, Windows, Mac).

Proteomics: the incumbent will lead a group involved in the development and application of new methods for the determination of protein number, binding affinities, post-translational modification, and other qualitative and quantitative aspects of protein expression and behavior that are necessary for computer modeling and simulation. Tools such as mass spectrometry and microfluidic-based multiplexed binding assays are expected to be key elements in the efforts of this group. A strong background in protein biochemistry and the relevant instrumentation needed for high-throughput, high-sensitivity analysis is required.

Genomics: the incumbent will be responsible for developing novel approaches to the systems-wide analysis of such issues as transcription factor and epigenetic control of gene expression, the effects of allelic polymorphism on gene expression and function, quantitative measurement of gene expression, and the role of non-coding regions and transcripts such as miRNAs in regulating gene/gene product expression patterns.

Knowledge of modern methods in high-throughput analysis of gene transcription, transcription factor binding site identification, analysis of epigenetic modifications, and analysis of gene regulatory circuits is required; bioinformatics experience is desirable. These positions and the research activities they conduct are fully funded by the intramural research program of NIAID. Each team leader is expected to build a working group consisting of postdoctoral fellows, students, technicians, and staff scientists. The team leaders will work with the Program Director to help set the goals for the PSIIM and to determine how best to reach these goals as an integrated group. To ensure appropriate career trajectories for those joining the PSIIM team effort, the NIH has modified its tenure policies to take specific account of contributions made in such a team science setting. Applicants should be seeking a difficult
challenge in which creativity, technical expertise, and a strong desire to achieve in a team setting will be critical for success.

Interested candidates may contact Dr. Ronald Germain, Program Director, PSIIM, DIR, NIAID at (301) 496-1904 or email (rgermain @ niaid.nih.gov) for additional information about these positions.

To apply, submit your curriculum vitae, bibliography, and a detailed statement of how your expertise can contribute to the success of the PSIIM program, to Wanda Jackson at NIAID.DIR.Search @ niaid.nih.gov.
In addition, three letters of reference must be sent directly from your three referees to Dr. Robert Hohman, Chair, NIAID Search Committee, c/o Wanda Jackson at NIAID.DIR.Search @ niaid.nih.gov or 10 Center Drive, MSC 1356, Building 10, Room 4A22, Bethesda, Maryland 20892-1356.
Email is preferred. Completed applications MUST be received by Friday, May 23rd.
Please refer to ad #019 for bioinformatics/biostatistics, #020 for proteomics, and #021 for genomics on all correspondence.
Further information regarding the DIR laboratories is available at:http://www3.niaid.nih.gov/about/organization/dir/default.htm and information on working at NIAID is available on our website at: http://healthresearch.niaid.nih.gov

For more information about the NIAID systems biology program, please visit http://www.nih.gov/catalyst/2006/06.09.01/page1.html

Group leader biomodeling and biosystems analysis

Fri, 11 Apr 2008 21:36:11 +0900

Netherlands Institute for Systems Biology (NISB, www.sysbio.nl)
Amsterdam, The Netherlands

The Netherlands Institute for Systems Biology (NISB, www.sysbio.nl) is a joint venture of the two Amsterdam universities (the Vrije Universiteit and the University of Amsterdam) and two national research institutes in Amsterdam (the CWI (Netherlands research institute for mathematics and computer science) and AMOLF (FOM Institute for Atomic and Molecular Physics)).

The Netherlands Genomics Initiative (NGI, www.genomics.nl) has recently initiated the Netherlands Consortium for Systems Biology (NCSB), a 15 million Euro national research program to implement systems biology in ongoing research lines of seven high ranking Dutch research groups in the fields of biomedical and biotechnological research. As part of this investment a Biomodeling and Biosystems Analysis Group will be set up in the Netherlands Institute for Systems Biology (NISB) in Amsterdam.

The task of the Biomodeling and Biosystems Analysis Group is to develop generic as well as
specific tools and approaches for modeling and analysis of complex biological systems, specifically those that are addressed in the context of the NCSB program. The group will be housed in Amsterdam in the premises of one of the four parties that constitute the NISB (two universities and two national research institutes in Amsterdam). The group leader has a budget of 1.5 million Euro for a period of five years. A tenure position can be negotiated for this function.

In addition to the postdocs, PhD students and other personnel in the group, the group leader will be responsible for the modeling and system analysis activities of about twelve investigators (postdocs and PhD students) that are positioned in the different biomedical and biotechnological research groups that participate in the NCSB program. In this, the Biomodeling and Biosystems Analysis Group plays a central role in the NCSB program.

Candidates should fulfill the following criteria.

Strong track record in modeling and analysis of complex biological systems based on experimental data sets.
Able to build bridges between mathematicians/physicists/informaticians and experimental biologists
Proven leadership.
Able to communicate with researchers in the fields of biomedical and biotechnological research.

Application should be send to the director of the Netherlands Institute for Systems Biology (NISB): prof. Dr Roel van Driel, c/o University of Amsterdam, Kruislaan 318, 1098SM Amsterdam, the Netherlands. Information can be obtained from the same person (office: +31 (0)20 525 5150; home: +31 (0)251 657 356; mail: van.driel @ science.uva.nl).
Deadline May 1st, 2008.