| Proteome survey reveals modularity of the yeast cell machinery | Nature | 2006 | 2.1K |
| PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments | Nucleic Acids Research | 2006 | 1.7K |
| Toward automatic reconstruction of a highly resolved tree of life | Science | 2006 | 1.2K |
| The genome of the sea urchin Strongylocentrotus purpuratus | Science | 2006 | 886 |
| SMART 5: domains in the context of genomes and networks | Nucleic Acids Research | 2006 | 806 |
| mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes | Genes and Development | 2006 | 720 |
| Taverna: a tool for building and running workflows of services | Nucleic Acids Research | 2006 | 628 |
| BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems | Nucleic Acids Research | 2006 | 559 |
| A high-resolution map of transcription in the yeast genome | Proceedings of the National Academy of Sciences of the United States of America | 2006 | 546 |
| ATSAS2.1, a program package for small-angle scattering data analysis | Journal of Applied Crystallography | 2006 | 499 |
| Literature mining for the biologist: from information retrieval to biological discovery | Nature Reviews Genetics | 2006 | 468 |
| Chemokine signaling mediates self-organizing tissue migration in the zebrafish lateral line | Developmental Cell | 2006 | 395 |
| An integrated view of protein evolution | Nature Reviews Genetics | 2006 | 384 |
| Taverna: lessons in creating a workflow environment for the life sciences | Concurrency Computation Practice and Experience | 2006 | 378 |
| Activation of the canonical Wnt pathway leads to loss of hematopoietic stem cell repopulation and multilineage differentiation block | Nature Immunology | 2006 | 369 |
| Minimizing the risk of reporting false positives in large-scale RNAi screens | Nature Methods | 2006 | 362 |
| Nuclear pore components are involved in the transcriptional regulation of dosage compensation in Drosophila | Molecular Cell | 2006 | 331 |
| The Hippo pathway regulates the bantam microRNA to control cell proliferation and apoptosis in Drosophila | Cell | 2006 | 330 |
| Anopheles gambiae immune responses to human and rodent Plasmodium parasite species | PLoS Pathogens | 2006 | 329 |
| High-throughput fluorescence microscopy for systems biology | Nature Reviews Molecular Cell Biology | 2006 | 324 |
| High-throughput RNAi screening by time-lapse imaging of live human cells | Nature Methods | 2006 | 320 |
| Histone trimethylation and the maintenance of transcriptional ON and OFF states by trxG and PcG proteins | Genes and Development | 2006 | 313 |
| The crystal structure of the exon junction complex reveals how it maintains a stable grip on mRNA | Cell | 2006 | 306 |
| A Polycomb group protein complex with sequence-specific DNA-binding and selective methyl-lysine-binding activities | Genes and Development | 2006 | 287 |
| Structure of C3b reveals conformational changes that underlie complement activity | Nature | 2006 | 286 |
