Modeling Host-Pathogen Interactions:
Computational Biology and Bioinformatics for Infectious disease research
Background/Motivation:
Pathogenic infections are a major cause of both human disease, and loss of crop yields and animal stocks and thus cause immense damage to the worldwide economy. The significance of infectious diseases is expected to grow in an increasingly connected and warming world where viral, bacterial and fungal pathogens gain ready access to new hosts and ecologic niches. Disturbingly, the complex mechanisms by which pathogenic agents evade host defenses and reprogram host physiology to support colonization and reproduction is still very incompletely understood especially from a systems perspective. Thus, understanding host-pathogen interactions is both a socially important and a scientifically fascinating topic.
Recent technological advances have afforded us exquisitely-detailed near-comprehensive molecular views of host-pathogen interactions; novel computational and analytical approaches are necessary to appreciate the richness of these data. Genome sequencing was pioneered on pathogens and related microbes, and the number of strains and variants of pathogens sequenced to date vastly outnumbers the number of host genomes available. Additionally, for both plant and human hosts more and more data on population level genomic variation becomes available and offers a rich field for analysis into the genetic interactions between host and pathogen.
On a molecular level deep-sequencing, increasingly sophisticated proteomic tools and interactome analyses are powerful tools to dissect pathogen virulence programs and to investigate how pathogens rewire cellular transcriptional and protein networks. The sheer magnitude of possible interactions and our ignorance of how subtle interactions are integrated to support pathogenesis pose great difficulties to data analysis, modeling, and making useful predictions. The relatively rapid evolution of pathogens, coupled with the strong selection exerted by the host defense system, results in pathogen genomic programs that are finely-tuned to their hosts. The adaptation of the pathogen to the host may result in a subtle strategy that is not readily deduced from experimental observations. Studying these interactions also have obvious and direct applications in terms of improved therapeutic strategies. Historical therapeutic strategies have focused on the differences in physiology between pathogens and their hosts, and have resulted in some of the most successful treatments of disease ever developed, for example vaccines, antibiotics and antivirals. However, pathogens are evolving resistance to our current therapies and we are running out of simple targets, thus we will need to develop more complex strategies that tip the balance of power in favor of the host immune response.
The field is diverse in terms of computational approaches used, but is united by common qualities of the host-pathogen interaction. The goal of this session is to learn about novel computational, experimental, and computation-driven experimental approaches for studying of host-pathogen interactions, and to illuminate points of synergy between different approaches as well identifying where we’re misssing the mark. It is anticipated that a session in which cutting-edge experimental and computational approaches are presented and a wide computational expertise is assembled in the audience, has a high potential for fostering collaborations.
Session topics:
We plan to solicit papers in the following areas:
1.New experimental approaches to understand plant-pathogen interactions
2.Systems biology and regulatory networks of virulence and host response
3.Data integration approaches to identifying virulence determinants
4.Modeling host-pathogen interactions
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5.Evolutionary studies of host-pathogen interactions
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6.Drug target and mechanism identification for antibiotics and antivirals
Other topics within the subject area are welcome. Note that all submitted papers should make clear their relevance for the study of Modeling Host-Pathogen Interactions. If unsure whether your paper fits the session theme, please contact one of the co-chairs.
Session co-chairs:
Jason McDermott
Computational Biology and Bioinformatics Group
Pacific Northwest National Laboratory (PNNL)
Pascal Braun
Center for Cancer Systems Biology (CCSB) and Dana-Farber Cancer Center (DFCI)
Harvard Medical School (HMS)
Daniel Hyduke
Systems Biology
University of California San Diego (UCSD)
Richard Bonneau
Departments of Biology and Computer Science
New York University (NYU)
Submission information:
Please note that the submitted papers are reviewed and accepted on a competitive basis. At least three reviewers will be assigned to each submitted manuscript.
Important Dates
•Paper submissions due: July 18, 2011 (This session only.)
•Notification of paper acceptance: September 9, 2011
•Camera-ready final paper deadline: September 23, 2011 at 11:59pm PT
•Abstract deadline for non-reviewed posters: November 28, 2011 at noon PT
Paper Format
Please see the PSB paper format template and instructions at:
http://psb.stanford.edu/psb-online/psb-submit.
The file formats we accept are: postscript (*.ps) and Adobe Acrobat (*.pdf)). Attached files should be named with the last name of the first author (e.g. altman.ps or altman.pdf). Hardcopy submissions or unprocessed TeX or LaTeX files will be rejected without review.
Each paper must be accompanied by a cover letter. The cover letter must state the following:
•The email address of the corresponding author.
•The specific PSB session that should review the paper or abstract.
•The submitted paper contains original, unpublished results, and is not currently under consideration elsewhere.
•All co-authors concur with the contents of the paper.
Submitted papers are limited to twelve (12) pages in our publication format. Please format your paper according to instructions found at http://psb.stanford.edu/psb-online/psb-submit/. If figures cannot be easily resized and placed precisely in the text, then it should be clear that with appropriate modifications, the total manuscript length would be within the page limit.
Contact Russ Altman for additional information about paper submission requirements.
Modeling host-pathogen interactions
