#### Filter Results:

#### Publication Year

2007

2016

#### Publication Type

#### Co-author

#### Key Phrase

#### Publication Venue

#### Method

#### Organism

Learn More

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)

- Luis Luna-Zurita, Christian U Stirnimann, Sebastian Glatt, Bogac L Kaynak, Sean Thomas, Florence Baudin +9 others
- Cell
- 2016

Transcription factors (TFs) are thought to function with partners to achieve specificity and precise quantitative outputs. In the developing heart, heterotypic TF interactions, such as between the T-box TF TBX5 and the homeodomain TF NKX2-5, have been proposed as a mechanism for human congenital heart defects. We report extensive and complex interdependent… (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)

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 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)

- Md Abul Hassan Samee, Bomyi Lim, Núria Samper, Hang Lu, Christine A Rushlow, Gerardo Jiménez +2 others
- Cell systems
- 2015

To understand the relationship between an enhancer DNA sequence and quantitative gene expression, thermodynamics-driven mathematical models of transcription are often employed. These "sequence-to-expression" models can describe an incomplete or even incorrect set of regulatory relationships if the parameter space is not searched systematically. Here, we… (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)