Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation

The UCSC Genome Browser database: 2016 update

(2015) Matthew L. Speir et al.   NUCLEIC ACIDS RESEARCH

Alignathon: a competitive assessment of whole-genome alignment methods

(2014) Dent Earl et al.   GENOME RESEARCH

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

The UCSC Genome Browser database: 2015 update

(2014) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish

(2013) Michael Hiller et al.   NUCLEIC ACIDS RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features

(2012) Hiroaki Iwata et al.   NUCLEIC ACIDS RESEARCH

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

(2012) D. G. MacArthur et al.   SCIENCE

Human Developmental Enhancers Conserved between Deuterostomes and Protostomes

(2012) Shoa L. Clarke et al.   PLoS Genetics

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

RNAcode: Robust discrimination of coding and noncoding regions in comparative sequence data

(2011) S. Washietl et al.   RNA

Creating a Buzz About Insect Genomes

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

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner

(2009) David V. Lu et al.   BIOINFORMATICS

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

(2009)   JOURNAL OF HEREDITY

Direct mapping and alignment of protein sequences onto genomic sequence

(2008) Osamu Gotoh   BIOINFORMATICS

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

(2008) Mario Stanke et al.   BIOINFORMATICS

Comparative analysis of sequence features involved in the recognition of tandem splice sites

(2008) Ralf Bortfeldt et al.   BMC GENOMICS

Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs

(2008) B. Paten et al.   GENOME RESEARCH

The UCSC Genome Browser Database: update 2009

(2008) R. M. Kuhn et al.   NUCLEIC ACIDS RESEARCH

Widespread and subtle: alternative splicing at short-distance tandem sites

(2008) Michael Hiller et al.   TRENDS IN GENETICS

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY