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Iddo Friedberg

 

 

Two immediate positions for a postdoc and a programmer are availabe. See: here.

The Friedberg Lab is always looking for postdocs and for 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?

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 predict 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. 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 graduate students seeking to enter bioinformatics in Industry.

4. The Biological Database of Images and Genomes (BioDIG) is a software infrastructure linking imaging data with biological data, which is part of the GMOD project.

5. Bacterial Genome Evolution: Gene blocks are a common occurrence in bacteria: these are genes which lie close together on the chromosome, and may participate in a common cellular or biochemical function. Operons are gene blocks whose member genes are co-transcribed. We have developed a new method to describe the evolution of operons and gene blocks in bacteria. We describe a small set of evolutionary events that can take place in gene block evolution, and count these events to create a new type of molecular clock that tells us how fast or how slow certain gene blocks may have evolved. We hope to learn how new functions are acquired by ensembles of genes such as these.

6. Insert your brilliant idea here! I love new projects!

The lab is equipped with its own cluster computer, several workstations, and the usage of Iowa State University's High Performance Computing Center. Students and postdocs have an excellent research environment, and many opportunities to collaborate with labs on and off campus.

Graduate students can apply to the lab via the Bioinformatics and Computational Biology Program or the Genetics and Genomics Program at Iowa State University. You are welcome and encouraged to inquire further. I love talking with prospective students and trainees. 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, Ph.D.

Associate Professor, Veterinary Microbiology and Preventive Medicine

Iowa State University

Ames, IA, USA