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Post-Doctoral Fellows: marine meta-genomics and bioactive compounds of marine microbes
The King Abdullah University of Science and Technology (KAUST) and the Hong Kong University of Science and Technology (HKUST) are involved in an ongoing partnership research program in marine meta-genomics and bioactive compounds of marine microbes from the Red Sea. Under this program, the following Post-Doctoral positions are available:
osition 1: Bioinformatics.
Candidate must hold a PhD degree in molecular biology, microbial genomics, computational biology or bioinformatics with strong publication track-record in relevant fields. Experience in analyzing, mining and annotating genome data will be an asset. Strong programming skills (Perl, C, Python or Java) are desirable. The appointee will be responsible for the analysis of meta-genomic data from environmental samples.
Position 2: Natural Product Chemistry
Candidates must hold a PhD in natural product chemistry, analytic chemistry, or chemical biology with strong publication track-record in relevant fields. Experience in working with biological systems, preferably in marine or micro-organisms, will be an asset. The appointee will be responsible for screening and characterizing bioactive compounds from marine microbes for antifouling, anti-tumor and antibiotics
Position 3: Microbial meta-genomics.
Candidates must hold a PhD in microbiology/marine microbial ecology with strong publication track-record in relevant fields. The appointee must have solid training in molecular microbial ecology, proven technical skills for studying microbial community structures, and good understanding of marine ecosystems/ecology.
Position 4: Proteomics
Candidates must hold a PhD in molecular biology or a relevant field, and have a strong background in comparative proteomics research. The appointee must have a keen interest in developing, optimizing and applying proteomics platforms (LC-MALDI, and Q-TOF) for quantitative analysis, and have experience in sample preparation and data analysis. Knowledge of bioinformatics is desired.
As English is the official language between HKUST and KAUST, all candidates are required to be fully fluent and be proficient in writing.
All Post-Doctoral Fellows will be appointed as a HKUST Post-Doc for one or two years, with a back-to-back appointment as a KAUST Post-Doc for an additional two to three years. Accommodation will be provided during their service at KAUST campus. Salary will be highly competitive and depending on qualifications and experience. Medical, dental, insurance, and pension plan or gratuity will also be provided.
Interested applicants are requested to send a copy of detailed curriculum vitae to Cherry Kwan (email: htckwan@ust.hk) before June 15. He/she shall also arrange two reference letters directly sent to the above email before the deadline. Review of applications will continue until the positions are filled.
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Research assistant at the Marine Biological Laboratory
Woods Hole (US)
Please apply online at the Institute website.
Posting Number: 0000254 - Department: Bay Paul Center - Position Type: Research - Position Title: Research Assistant I/II- Evolutionary Dynamics
Position Summary: The MBL seeks a highly motivated individual to join the Simmons lab as a full time Research Assistant I or II beginning in the spring of 2010. The successful applicant will contribute to projects that employ molecular, bioinformatic, cultivation, and field-based approaches to understanding short-term evolutionary dynamics in microbial communities. The Simmons lab is housed within the Marine Biological Laboratory's Josephine Bay Paul Center, a collaborative research group with interests in microbial diversity, molecular evolution, and comparative genomics.
Additional Information: Responsibilities will include but are not limited to: DNA and RNA extractions, standard and quantitative PCR, in situ hybridization, laser microdissection microscopy, preparation of libraries for 454 and Illumina sequencing, bioinformatic analyses, cultivation of bacteria and/or archaea, general lab organization and maintenance. Opportunities for locally based field work may also be available.
Basic Qualifications: Applicants should have an interest in microbiology, genomics, and evolution and possess a genuine drive to perform basic research. This position requires an independent, organized, and very motivated individual with experience in molecular techniques and ideally some experience with bioinformatics as well. Educational requirements include a B.A., B.S., or M.S. in microbiology/molecular biology/evolutionary biology or a related field and prior experience in an active research lab. Excellent written, verbal, and interpersonal skills, attention to detail, and a superb work ethic are essential. Position level and salary will depend upon education and experience.
Required Applicant Documents: Resume/CV, Cover Letter, References, Unofficial Transcripts.
Special Instructions to Applicants: The application process consists of four items: (1) a letter describing your interests, skills, and prior research experience, including any specific experience with the job responsibilities listed above; (2) a curriculum vitae; (3) copies of your transcripts from undergraduate and, if applicable, graduate work; (4) the name and contact information of three referees.
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PhD position in Marine Bacteria Phylogenomics
DSMZ Braunschweig (Ger)
A position for a PhD student in bioinformatics is available in the Department of Microbiology at the German Collection of Microorganisms and Cell Cultures (DSMZ) in Braunschweig, Germany. The project is entitled 'Phylogenomics And Functional Genomics of The Roseobacter Clade' and part of the recently established Transregional Collaborative Research Centre - Special Research Field 'Roseobacter' funded by the German Research Foundation (DFG).
The Roseobacter clade is one of the most abundant and successful groups of non-obligately phototrophic prokaryotes in the marine environment. The major goal of the Special Research Field is the understanding of evolutionary, genetic and physiological principles which constitute the secret of success for these bacteria. Consequently, marine microbial ecologists, bacterial physiologists, biochemists, natural product chemists, geneticists and computer scientists from Braunschweig and Oldenburg join forces to investigate the Roseobacter clade from the ecosystem level down to systems biology of model organisms with respect to important metabolic processes.
The candidate's tasks include the implementation of a software pipeline for the phylogenomic analysis of completely sequenced genomes and its application to members of the Roseobacter clade. Particular emphasis will be laid on devising and assessing programs for species delimitation and phylogenetic reconstruction directly based on whole genomes.
This PhD project is also tightly integrated with the DSMZ's current research related to the Genomic Encyclopedia of Archaea and Bacteria (GEBA); see here. The successful candidate will hold a master or diploma degree in informatics or bioinformatics and will be experienced with programming in compiled languages such as Java or C++ and scripting languages such as Ruby or Python. Preferred students will also have experience in at least some of the following fields: database programming, web programming (e.g., Ruby on Rails, PHP), linux administration, phylogenetic inference and genomics.
The DSMZ -- Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (German Collection of Microorganisms and Cell Cultures; http://www.dsmz.de/) is the most comprehensive Biological Resource Centre in Europe. With more than 18.000 microorganisms, 1.200 plant viruses, 600 human and animal cell lines, 770 plant cell cultures and more than 7.100 cultures deposited for the purposes of patenting, we have demonstrated our obligation to serve science for decades. The DSMZ is an independent, non-profit organisation.
For further details regarding the position please contact Dr. Hans-Peter Klenk (e-mail: hans-peter.klenk@dsmz.de; phone: +49-(0)531-2616-227) or Dr. Markus Goeker (e-mail: markus.goeker@dsmz.de; phone: +49-(0)531-2616-272).
Applications should be addressed until 15/03/2010 to: Carl von Ossietzky Universitaet Oldenburg - ICBM - Prof. Dr. Meinhard Simon - 26111 Oldenburg, Germany (phone: 0441/798-5361; e-mail: m.simon@icbm.de)
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PhD position on Microbial Biofilms in Luxembourg
Expires: March 31, 2010
Job description: The Centre de Recherche Public – Gabriel Lippmann, a fast growing public establishment for applied scientific research and technology transfer in Luxembourg, has an opening on a fixed-term contract for its internationally recognized “Environment and Agro-biotechnologies” Department (EVA) for a PhD thesis position (m/f), topic: “Systems Biology of Microbial Biofilm Communities for Concomitant Wastewater Treatment and Bioenergy Production”.
Duties and responsibilities: The general aim of the PhD project is to study natural microbial biofilms using state-of-the-art analytical tools (genomics, transcriptomics, proteomics, metabolomics, bioinformatics and imaging) to devise processes for the integrated treatment of wastewater and production of bioenergy. The project falls within the remit of a recently awarded Luxembourg National Research Fund ATTRACT Programme grant.
Tasks to be carried out by the PhD candidate will include setup and operation of laboratory-scale bioreactors, routine chemical analyses, imaging, cultivation-based experiments, molecular biology analyses, stable isotope probing experiments, genomics, transcriptomics, proteomics, metabolomics and bioinformatics.
Qualifications: The candidate should hold a Master or equivalent degree in bioengineering, biotechnology, microbiology, microbial ecology, molecular biology and/or systems biology. It is a prerequisite that the candidate has a solid background in modern molecular biology techniques and a vivid interest in bioinformatic methodologies. He/she has to be motivated and work independently, structured and self-responsible in a young, diversified environmental research department. Proficiency in English (scientific exchanges) is a prerequisite.
Application:
For applying, the candidates should provide the following documents:
- a letter of motivation,
- a curriculum vitae.
Candidates who are interested in the position should send their application (with the reference EVA-7109-PHD) following infos on our website.
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The NIOZ (Royal Netherlands Institute for Sea Research) offers working opportunities for Students of Universities, Schools of Higher and Intermediate Professional Education, at several scientific Departments:
FYS - Physical Oceanography
MCG - Marine Chemistry & Geology
BGC - Marine Organic Biogeochemistry
BIO- Biological Oceanography
MEE - Marine Ecology & Evolution
Lab web sites: www.nioz.nl
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TWO PHD POSITIONS IN BACTERIAL EVOLUTIONARY GENOMICS
at the Biozentrum, University of Basel, Switzerland
Two PhD positions in bacterial evolutionary genomics are available in the group of Prof. E. van Nimwegen at the Biozentrum of the University of Basel, also a member of the Swiss Institute of Bioinformatics. The overarching research interests of our lab concern the evolution of entire genomes and the structure, functioning, and evolution of genome-wide molecular interaction networks that regulate cellular behavior, including transcription regulatory networks and signaling networks.
Our group is highly interdisciplinary with members whose backgrounds range from molecular biology, chemistry, biophysics, to theoretical physics. Although the main focus of the group is on theoretical analysis and modeling, we are currently adding a wet-lab component to study bacterial evolutionary genomics, and have two open positions in experimental evolutionary genomics. Both positions will be co-supervised by Prof. E. van Nimwegen and Dr. O. Silander, who will be heading the wet lab.
The main aim of the first research project is to uncover the selection forces that shape changes in gene-content and phenotypic abilities of bacteria on relatively short evolutionary time scales, and to characterize these selection forces quantitatively. We will use high-throughput phenotypic characterization of related bacterial strains, in combination with sequencing of the entire genomes of selected strains using next generation deep sequencing technology. An integral part of the project will be the theoretical analysis of the obtained data, and relating the results to recent theories that have been developed in our group based on the analysis large-scale analysis of genomics data (e.g. van Nimwegen, Trends in Genet 19:9:479-484 (2003), Molina and van Nimwegen, Biol Direct 3:51 (2008)). In particular, we are interested in characterizing the environmental and evolutionary forces that drive changes in genome complexity.
The main aim of the second project is to understand de novo evolution of transcriptional regulation and promoter architecture. We will use experimental evolution of bacteria to evolve novel promoter sequences. This will be followed by detailed sequence analysis of the evolved promoters using next generation sequencing technologies. A central part of this project will involve characterization of transcription factor binding motifs (e.g. van Nimwegen, E. BMC Bioinf 8(Suppl 6):S4 (2007)) and computational modeling to predict how transcription factor binding affects expression.
Requirements for the position are a master diploma in biology or biochemistry and a strong background in molecular biology. Knowledge and/or experience in microbiology, bioinformatics, applied mathematics, and programming would all be highly advantageous. The candidates should have good knowledge of English, German is helpful but not necessary. The salary is according to the guidelines of the Swiss National Science Foundation and the entrance date will by mutual arrangement.
To apply, please send your application letter, CV and the names of two or three references (preferably by email) to Prof. Erik van Nimwegen (erik.vannimwegen@unibas.ch), Department of Bioinformatics - Biozentrum, University of Basel. Klingelbergstrasse 50/70 - CH-4056 Basel / Switzerland
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PhD Position in Genetics of Host - Microbiota Interactions and Chronic Inflammatory Diseases
MPI Ploen, Germany
A PhD position is available in the labs of Prof. Saleh Ibrahim at the University of Luebeck and Prof. John Baines at the Max-Planck-Institute for Evolutionary Biology in Ploen as part of the German Research Foundation (DFG) Cluster of Excellence "Inflammation at Interfaces".
The successful candidate will be enrolled in the "Genes, Environment and Inflammation" research training program of the Cluster and participate in a large-scale collaborative effort to study the genetic basis of host - microbiota interactions and susceptibility to chronic inflammatory diseases in the house mouse system. The main task will be to apply metagenomics techniques (including 454 GS-FLX sequencing) to characterize the microbial communities of the gut and skin in inbred mouse strains that differ in susceptibility to chronic inflammatory diseases including colitis, arthritis, lupus and epidermolysis bullosa acquisitor. An advanced, 4-way intercross between resistant and susceptible mouse strains is available and will be used to map loci contributing to disease susceptibility and/or host - microbiota interactions. Candidate genes will be studied in the context of host - microbiota coevolution and the evolutionary origin of disease-associated variation.
Job requirements include a Master's Degree or equivalent in Biology, Bioinformatics or a related field and a strong interest and experience in one or more of the following: bioinformatics, immunogenetics, evolution, population genetics or microbiology. The position is available immediately and will remain open until a suitable candidate is found.
The work will be performed in close cooperation between the laboratories at the University of Luebeck and the MPI for Evolutionary Biology in Ploen (50 km, 40 min via public transport) and take advantage of the mouse and genomics facilities of both locations. The everyday working language in both groups is English. Basic knowledge of German would be helpful, but not required.
Applications should be submitted as a single pdf document containing: (1) a one page cover letter summarizing research interests and experience, (2) full CV and (3) contact information of at least 2 references.
Applications and informal inquiries should be sent via Email to Prof. Dr. John Baines (Tel: +49-4522-763-367)
Useful References
Yu X, Gimsa U, Wester-Rosenlöf L, Kanitz E, Otten W, Kunz M, Ibrahim SM. Dissecting the effects of mtDNA variations on complex traits using mouse
conplastic strains. Genome Res 2009;19:159-165
Johnsen JM, Teschke M, Pavlidis P, McGee BM, Tautz D, Ginsburg D, Baines JF. Selection on cis-regulatory variation at B4galnt2 and its influence on von Willebrand factor in house mice. Mol Biol Evol 2009;26:567-578
Yu X, Bauer K, Koczan D, Thiesen HJ, Ibrahim SM. Combining global genome and transcriptome approaches to identify the candidate genes of small-effect quantitative trait loci in collagen-induced arthritis. Arthritis Res Ther 2007;9:R3
Yu X, Bauer K, Wernhoff P, Koczan D, Möller S, Thiesen HJ, Ibrahim SM. Fine mapping of collagen-induced arthritis quantitative trait loci in an advanced intercross line. J Immunol 2006;177:7042-7049
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GRADUATE STUDENT POSITION
Biodiversity of Ciliates In Near-Shore Environments
University of Massachusetts - Amherst
We are looking for a highly motivated student to join our project, which aims to elucidate the patterns of diversity of ciliates from near-shore environments and to explore the ecological processes that underlie this diversity. The project is collaborative between Laura Katz's lab at Smith College and marine ecologist George McManus at the University of Connecticut. Work on the project combines culture-independent approaches with analyses of targeted morphospecies. Techniques include analyses of clone libraries, DGGE, and both light and fluorescence microscopy.
Graduate students in Laura Katz's laboratory join either through MS program at Smith College or the Ph.D. program in Organismic and Evolutionary Biology at the University of Massachusetts Amherst. Interested individuals should visit the web sites below and contact Dr. Laura Katz directly (lkatz@smith.edu)
Laura Katz, Smith College
http://www.science.smith.edu/departments/Biology/lkatz/
OEB at UMass Amherst
http://www.bio.umass.edu/oeb/
http://www.bio.umass.edu/oeb/admissions
Smith College MS in biology
http://www.science.smith.edu/departments/Biology/graduate.html
http://www.smith.edu/gradstudy/
Collaborator George McManus, University of Connecticut
http://microzooplankton.uconn.edu/
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Postdoctoral research associate with Dominique Schneider in the Laboratory "Adaptation et Pathogénie des Microorganismes", University Joseph Fourier, Grenoble, France.
The project will involve a strong collaboration with Richard Lenski (Michigan State University). The sequence of hundreds of bacterial genomes uncovered the extraordinary diversity and plasticity of metabolic and regulatory networks. However, the dynamics of evolution of such a wide range of functions, and especially the link between genomic modifications, diversity and overall performance of a living organism remains a challenging yet fascinating task. For most microbiologists, "mechanism" refers to the biochemical or regulatory interactions among genes, proteins and metabolites in a cell. All these interactions have however to be related to fitness, the measure of the reproductive ability of a genotype which is the ultimate parameter of ecological success. Dynamics of entire genomes is one key of fitness changes, ultimately driving the interactions among genotypes and between genotypes and their environment. By linking changes in genomes to changes in fitness, it is possible to investigate how natural selection is able to re-shape and improve entire genomes, and which functions are more plastic over evolutionary time. Using such an evolutionary perspective is fully complementary to most "Systems Biology " approaches, which try to understand the global functioning of an organism by the precise analysis of a reference clone and therefore provide a static description of metabolic or regulatory networks. Using an evolutionary perspective is however difficult mainly because the relevant adaptive events that allowed the emergence of the present genomic structure of the organism occurred some unknown time in the past, in unknown conditions, with unknown genomic constraints. To overcome these limitations, we can reproduce evolution in controlled conditions in the laboratory. In this project, we will use the longest-running evolution experiment, where an ancestral cell of Escherichia coli has been used to propagate twelve populations in a defined environment for 40,000 generations. The evolutionary dynamics of genomes will be investigated by performing Solexa-sequencing of genomes from 135 evolved clones sampled from the different populations at each of ten different time points during evolution. Among many questions that will be addressed, this project will enable us to understand the successive genetic events leading to the increased performance of bacteria in their environment. Rigorous genetic and functional phenotypic analyses will be combined to dissect the complete adaptive diversification paths that will be uncovered in key populations. We will study how adaptive mutation appearance is constrained by the presence of other mutations and how they affect the metabolic or regulatory networks.
We will therefore address for the first time how evolvable are genomic features and what are the molecular bases of such evolvability. Candidates must have a Ph.D. in Genetics, Molecular and Evolutionary Biology or related field. Expertise in sequence analyses is requested. All candidates are expected to have a background or interest in molecular evolutionary genetics. In addition, the candidates should have expertise in molecular biology, and computational skills for genome sequence analyses. To apply, please submit applications (by e-mail to Dominique Schneider), including (1) a CV, (2) brief statement of past accomplishments and PDFs of most relevant publications, (3) research interests and (4) names and contact information of three referees.
Dominique Schneider
Laboratoire Adaptation et Pathogénie des Microorganismes
CNRS-UMR5163
Université Joseph Fourier - Institut Jean Roget
Domaine de la Merci BP170 38042 Grenoble Cedex 9 - France
Phone: +33 (0) 4 76 63 74 90
Fax: +33 (0) 4 76 63 74 97
E-mail: dominique.schneider@ujf-grenoble.fr
Webpage: http://www-ijr.ujf-grenoble.fr/
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