| Jalview Version 2--a multiple sequence alignment editor and analysis workbench | Bioinformatics | 2009 | 5.5K |
| Mutations in the FUS/TLS gene on chromosome 16 cause familial amyotrophic lateral sclerosis | Science | 2009 | 1.9K |
| SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas | Nature Genetics | 2009 | 733 |
| Unlocking the secrets of the genome | Nature | 2009 | 620 |
| Genome sequence, comparative analysis, and population genetics of the domestic horse | Science | 2009 | 559 |
| High-resolution mapping of copy-number alterations with massively parallel sequencing | Nature Methods | 2009 | 417 |
| Mechanoenzymatic cleavage of the ultralarge vascular protein von Willebrand factor | Science | 2009 | 410 |
| Evidence that inositol polyphosphate 4-phosphatase type II is a tumor suppressor that inhibits PI3K signaling | Cancer Cell | 2009 | 366 |
| Tumours with PI3K activation are resistant to dietary restriction | Nature | 2009 | 359 |
| The bacterial species challenge: making sense of genetic and ecological diversity | Science | 2009 | 322 |
| Halofuginone inhibits TH17 cell differentiation by activating the amino acid starvation response | Science | 2009 | 306 |
| Copper-mediated amidation of heterocyclic and aromatic C-H bonds | Organic Letters | 2009 | 273 |
| Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk | Nature Genetics | 2009 | 272 |
| Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung | Proceedings of the National Academy of Sciences of the United States of America | 2009 | 270 |
| Association of survival and disease progression with chromosomal instability: a genomic exploration of colorectal cancer | Proceedings of the National Academy of Sciences of the United States of America | 2009 | 262 |
| Nodal morphogens | Cold Spring Harbor Perspectives in Biology | 2009 | 207 |
| Stepwise acquisition of pyrimethamine resistance in the malaria parasite | Proceedings of the National Academy of Sciences of the United States of America | 2009 | 197 |
| IL2RA genetic heterogeneity in multiple sclerosis and type 1 diabetes susceptibility and soluble interleukin-2 receptor production | PLoS Genetics | 2009 | 183 |
| Regulation of microtubule dynamics by inhibition of the tubulin deacetylase HDAC6 | Journal of Cell Science | 2009 | 175 |
| Aberrant methylation of APC, MGMT, RASSF2A, and Wif-1 genes in plasma as a biomarker for early detection of colorectal cancer | Clinical Cancer Research | 2009 | 171 |
| Dampened Hedgehog signaling but normal Wnt signaling in zebrafish without cilia | Development (Cambridge) | 2009 | 165 |
| Understanding the role of DISC1 in psychiatric disease and during normal development | Journal of Neuroscience | 2009 | 147 |
| Non-B DNA conformations as determinants of mutagenesis and human disease | Molecular Carcinogenesis | 2009 | 119 |
| Soluble IL-2RA levels in multiple sclerosis subjects and the effect of soluble IL-2RA on immune responses | Journal of Immunology | 2009 | 113 |
| Differences in SMN1 allele frequencies among ethnic groups within North America | Journal of Medical Genetics | 2009 | 112 |
