Iris Dror, Tianyin Zhou, Lin Yang, Yael Mandel-Gutfreund, Remo Rohs

New approaches to genome analysis based on the integration of DNA sequence and shape (also see abstract for oral presentation by Remo Rohs)


Marie Trussart

The three-dimensional genome conformation of Mycoplasma pneumoniae


Christos Dimitrakopoulos, Marc Hulsman, Jeroen de Ridder

Scale-spaces from protein networks: how diffusion profiles reveal functional information in physical interaction topologies


Logan J. Everett, John Le Lay, Sabina Lukovac, David J. Steger, Diana Bernstein, Mitchell A. Lazar, and Klaus H. Kaestner

Cistromic analysis reveals novel insights into hepatic CREB regulatory mechanisms
(see oral presentation for abstract)


Richard McEachin, Ashwini Bhasi, Trista Schagat, Aaron Goldstrohm

Identifying PUF co-regulators by RNA-Seq coupled with conserved motif search


R. Taylor Raborn, Krishnakumar Sridharan, Daniel S. Standage, John M. Logsdon Jr., Volker Brendel

Comparative genome-wide analysis of transcription initiation and promoter architecture in eukaryotes


Pilib Broin, Terry Smith, Aaron Golden

A non-tree based approach to automated construction of familial binding profiles


Karsten Hokamp, Yuliana Pozdeeva, Juan-Pablo Labrador

A phylogenetic footprinting ensemble tool and a new scoring metric for evaluating the prediction of transcription factor binding sites in flies


Weronika Sikora Wohlfeld, Marit Ackermann, Eleni Christodoulou, Andreas Beyer

Predicting transcription factor target genes from ChIP-seq data


Alona Chubatiuk

Benchmarking of motif-finding algorithms


Dieter De Witte, Michiel Van Bel, Piet Demeester, Bart Dhoedt, Klaas Vandepoele and Jan Fostier

A high performance computing approach to the discovery of conserved motifs