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- Majid Kazemian, Kushal Suryamohan, Jia-Yu Chen, Yinan Zhang, Md. Abul Hassan Samee, Marc S. Halfon +1 other
- Genome biology and evolution
- 2014

Many genes familiar from Drosophila development, such as the so-called gap, pair-rule, and segment polarity genes, play important roles in the development of other insects and in many cases appear to be deployed in a similar fashion, despite the fact that Drosophila-like "long germband" development is highly derived and confined to a subset of insect… (More)

Quantitative models of cis-regulatory activity have the potential to improve our mechanistic understanding of transcriptional regulation. However, the few models available today have been based on simplistic assumptions about the sequences being modeled, or heuristic approximations of the underlying regulatory mechanisms. We have developed a… (More)

An upward planar drawing of a digraph G is a planar drawing of G where every edge is drawn as a simple curve monotone in the vertical direction. A digraph is upward planar if it has an embedding that admits an upward planar drawing. The problem of testing whether a digraph is upward planar is NP-complete. In this paper we give a linear-time algorithm to… (More)

Modeling a gene's expression from its intergenic locus and trans-regulatory context is a fundamental goal in computational biology. Owing to the distributed nature of cis-regulatory information and the poorly understood mechanisms that integrate such information, gene locus modeling is a more challenging task than modeling individual enhancers. Here we… (More)

- Thyago Duque, Md. Abul Hassan Samee, Majid Kazemian, Hannah N. Pham, Michael H. Brodsky, Saurabh Sinha
- Molecular biology and evolution
- 2014

There is growing interest in models of regulatory sequence evolution. However, existing models specifically designed for regulatory sequences consider the independent evolution of individual transcription factor (TF)-binding sites, ignoring that the function and evolution of a binding site depends on its context, typically the cis-regulatory module (CRM) in… (More)

An upward drawing of a rooted tree T is a planar straight-line drawing of T where the vertices of T are placed on a set of horizontal lines, called layers, such that for each vertex u of T , no child of u is placed on a layer vertically above the layer on which u has been placed. In this paper we give a linear-time algorithm to obtain an upward drawing of a… (More)

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