Simultaneous gene finding in multiple genomes

Current methods for automated annotation of protein-coding genes

(2015) KJ Hoff et al.   Current Opinion in Insect Science

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A novel hybrid gene prediction method employing protein multiple sequence alignments

(2011) Oliver Keller et al.   BIOINFORMATICS

Cactus: Algorithms for genome multiple sequence alignment

(2011) B. Paten et al.   GENOME RESEARCH

Creating a Buzz About Insect Genomes

(2011) G. E. Robinson et al.   SCIENCE

MRF Energy Minimization and Beyond via Dual Decomposition

(2010) N Komodakis et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

(2009)   JOURNAL OF HEREDITY

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

A Lagrangian relaxation approach for the multiple sequence alignment problem

(2008) Ernst Althaus et al.   JOURNAL OF COMBINATORIAL OPTIMIZATION