The Friedberg Lab is Recruiting Graduate Students
The Friedberg Lab is recruiting graduate students, for both Master’s and Ph.D.
WE ARE: A dynamic young lab interested in gene, gene cluster and genome evolution, understanding microbial communities and microbe-host interactions by metagenomic analyses, developing algorithms for understanding gene cluster evolution, and prediction of protein function from protein sequence and structure.
YOU ARE: an independent, hard-working problem-solving, energetic and motivated scientist-to-be. You have graduated or are about to graduate in computer science and/or biology or related fields. The Friedberg Lab is a “dry” lab, so some programming skills are required (Python preferred).
Existing and planned projects include:
1. Computational protein function prediction and assessment of function prediction algorithms. The Friedberg Lab is among the leaders of the Critical Assessment of Function Annotations (CAFA), an international effort of dozens of research groups to asess and improve function prediction algorithms. We are looking for students that are excited about prediction of protein function from sequence and structure. Also, how well can we assess how well our algorithms are doing? The next CAFA meeting will take place in Berlin, July 2013 and the Friedberg Lab will play a central role in answering these questions.
2. Metagenomics: we are studying the interaction between the microbiome and the host using metagenomic and metatranscriptomic data. In collaboration We are looking at how the human microbiome affects gene expression in the host. Together with Robb Chapkin’s lab at Texas A&M we are analyzing microbial genomes and their effect on transcription in the human gut. We are also developing algorithms for context-based function prediction in metagenomic data. Simply put: how well can we prediction the function of a gene from its neighbors? Since many of the genes in metagenomic data have no known homologs, we are developing creative ways to computationally discover their function.
3. Microbial Evolution: we are researching the evolution of Mycoplasma, a bacteria genus which serves us as model clade for understanding genome evolution. Mycoplasma have the smallest genomes of any organism, and being parasitic evolve quickly. Together with the Balish Lab we expect to sequence several new species and strains in the next year, and we are developing computational methods and a central community database for analyzing the Mycoplasma tree of life. Besides the biological aspect, this project is also a great opportunity to get into web programming, database design, and learn how top design and code community-based scientific software.
4. Biopython: Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. If you would like to become a Biopython developer, part of an international community of open-source scientific software developers, the Friedberg Lab is the place for you. This option is especially attractive for Master’s students seeking to enter bioinformatics in Industry.
5. Insert your brilliant idea here! I love new projects!
The lab is equipped with its own 10-node cluster computer, several workstations, and has access to Miami University’s Supercomputing Center, and the Ohio Supercomputer Center at Ohio State University. Students have an excellent research environment, and many opportunities to collaborate with labs on and off campus.
Students can apply to the Friedberg Lab via the following graduate programs at Miami University:
1. Microbiology (Master’s and PhD).
2. Cell, Molecular and Strcutural Biology (PhD only).
3. Computer Science (Master’s only).
You are welcome and encouraged to inquire further. I love talking with prospective students. If you would like to set up a phone/Skype chat please send your CV to:
friedberg.lab.jobs ‘at gmail ‘dot’ com
Looking forward to hearing from you.
Iddo Friedberg, PhD
Assistant Professor, Microbiology and Computer Science (affiliate)
Oxford, OH, USA
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