Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

Aravind Subramanian, Pablo Tamayo, Vamsi K. Mootha, +8

Proceedings of the National Academy of Sciences

GeneticsGenomicsGene RecognitionBioinformatics DatabaseGene Expression Profiling +21

High-Resolution Profiling of Histone Methylations in the Human Genome

Artem Barski, Suresh Cuddapah, Kairong Cui, +6

Cell

Histone ModificationsChromatinHistone MethylationsEpigenetic ChangeGenetics +5

miRBase: microRNA sequences, targets and gene nomenclature

Sam Griffiths‐Jones

Nucleic Acids Research

BiologySystems BiologyFunctional GenomicsBioinformatics DatabaseMicrorna Gene Nomenclature +13

Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs

John L. Rinn, Michael A. Kertesz, Jordon K. Wang, +8

Cell

ChromatinSystems BiologyEngineeringFunctional DemarcationChromatin Remodeling +10

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

Adam Siepel, Gill Bejerano, Jakob Skou Pedersen, +13

Genome Research

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

Tarjei S. Mikkelsen, Manching Ku, David B. Jaffe, +19

Nature

ChromatinChromatin StructureChromatin StateChromatin RemodelingNatural Sciences +10

The Transcriptional Landscape of the Mammalian Genome

Piero Carninci, Takeya Kasukawa, Shintaro Katayama, +185

Science

GeneticsGenomic MechanismGenomicsMammalian GenomeEpigenetics +15

RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription

Philipp Kapranov, Jill Cheng, Sujit Dike, +19

Science

BioinformaticsSystems BiologyPervasive TranscriptionEngineeringUnannotated Rnas +13

The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells

Yuin‐Han Loh, Qiang Wu, Joon-Lin Chew, +19

Nature Genetics

Nanog Transcription NetworkInduced Pluripotent Stem CellDevelopmental BiologyMedicineStem Cell Research +5

Identification of protein coding regions by database similarity search

Warren Gish, David J. States

Nature Genetics

Functional GenomicsBioinformatics DatabaseDatabase Similarity SearchMedicineNatural Sciences +7