Welcome to Algorithmic Biology Laboratory
The Algorithmic Biology Lab research focuses on quantitative modeling of various life phenomena at cellular and molecular levels. In particular, ABL research includes modeling RNA structure and ncRNA-mRNA interactions, de novo assembly of short and long sequencing reads for genomic and transcriptomic studies, de novo genomic variation detection, synthetic biology, bionics, and robotics. ABL is directed by Dr. Chitsaz and is located in the Computer Science Building on the Colorado State University campus.

Draft of a Japanese worm genome
The first genome draft of a japanese member of the planarians, characterized in collaboration with the Agata lab, has just been published in Zoological Letters. Make sure to check our genome browser for it.

Graph Traversal Edit Distance
Our polynomial time algorithm for graph traversal edit distance appeared at RECOMB 2018. Our algorithm is a Linear Programming relaxation that is guaranteed to yield and integer solution. Since LP has a polynomial-time algorithm (the interior methods), our algorithm has polynomial time complexity.

Principal Variety Analysis
Our method for minimum dimensional algebraic manifold learning, which we call Principal Variety Analysis (PVA), has been accepted at CoRL 2017 and will be published soon.

Role of Clp1 in Yeast
Our work on genomewide analysis of Clp1 function in budding yeast reveals transcription termination and antisense transcription inhibition roles of Clp1. The paper describing our methods and results has been accepted at Scientific Reports and will be published soon.

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