| REVIGO summarizes and visualizes long lists of gene ontology terms | PLoS ONE | 2011 | 3.3K |
| The UCSC Genome Browser database: update 2011 | Nucleic Acids Research | 2011 | 821 |
| Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems | Genome Biology | 2011 | 395 |
| MicroRNA profiling of Parkinson's disease brains identifies early downregulation of miR-34b/c which modulate mitochondrial function | Human Molecular Genetics | 2011 | 371 |
| Quantification of mRNA and protein and integration with protein turnover in a bacterium | Molecular Systems Biology | 2011 | 207 |
| Molecular mechanisms of epistasis within and between genes | Trends in Genetics | 2011 | 204 |
| The gap gene network | Cellular and Molecular Life Sciences | 2011 | 195 |
| Reduced fidelity of branch point recognition and alternative splicing induced by the anti-tumor drug spliceostatin A | Genes and Development | 2011 | 193 |
| Multi-domain conformational selection underlies pre-mRNA splicing regulation by U2AF | Nature | 2011 | 156 |
| ΔNp63α is an oncogene that targets chromatin remodeler Lsh to drive skin stem cell proliferation and tumorigenesis | Cell Stem Cell | 2011 | 155 |
| Human microRNAs miR-22, miR-138-2, miR-148a, and miR-488 are associated with panic disorder and regulate several anxiety candidate genes and related pathways | Biological Psychiatry | 2011 | 142 |
| Predicting mutation outcome from early stochastic variation in genetic interaction partners | Nature | 2011 | 137 |
| Biogenesis of a novel compartment for autophagosome-mediated unconventional protein secretion | Journal of Cell Biology | 2011 | 135 |
| Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing | Nucleic Acids Research | 2011 | 133 |
| PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions | Nucleic Acids Research | 2011 | 125 |
| The Ewing sarcoma protein regulates DNA damage-induced alternative splicing | Molecular Cell | 2011 | 122 |
| cTAGE5 mediates collagen secretion through interaction with TANGO1 at endoplasmic reticulum exit sites | Molecular Biology of the Cell | 2011 | 120 |
| Computational design of peptide ligands | Trends in Biotechnology | 2011 | 111 |
| Bacterial transcriptomics: what is beyond the RNA horiz-ome? | Nature Reviews Microbiology | 2011 | 107 |
| A complex of Pdi1p and the mannosidase Htm1p initiates clearance of unfolded glycoproteins from the endoplasmic reticulum | Molecular Cell | 2011 | 98 |
| From Saccharomyces cerevisiae to Candida glabratain a few easy steps: important adaptations for an opportunistic pathogen | FEMS Microbiology Letters | 2011 | 94 |
| The Long Non-Coding RNAs: A New (P)layer in the "Dark Matter" | Frontiers in Genetics | 2011 | 88 |
| Cytoplasmic polyadenylation and translational control | Current Opinion in Genetics and Development | 2011 | 88 |
| Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures | Nature Protocols | 2011 | 80 |
| Analysis of disease-linked rhodopsin mutations based on structure, function, and protein stability calculations | Journal of Molecular Biology | 2011 | 77 |
