| Basic local alignment search tool SF Altschul, W Gish, W Miller, EW Myers, DJ Lipman Journal of molecular biology 215 (3), 403-410, 1990 | 144250* | 1990 |
| Initial sequencing and comparative analysis of the mouse genome Mouse Genome Sequencing Consortium Nature 420 (6915), 520, 2002 | 6723 | 2002 |
| Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project ENCODE Project Consortium Nature 447 (7146), 799, 2007 | 4910 | 2007 |
| A greedy algorithm for aligning DNA sequences Z Zhang, S Schwartz, L Wagner, W Miller Journal of Computational biology 7 (1-2), 203-214, 2000 | 3924 | 2000 |
| Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes A Siepel, G Bejerano, JS Pedersen, AS Hinrichs, M Hou, K Rosenbloom, ... Genome research 15 (8), 1034-1050, 2005 | 2988 | 2005 |
| Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution International Chicken Genome Sequencing Consortium Nature 432 (7018), 695, 2004 | 2225 | 2004 |
| Genome sequence of the Brown Norway rat yields insights into mammalian evolution Rat Genome Sequencing Project Consortium Nature 428 (6982), 493, 2004 | 2045 | 2004 |
| Galaxy: a platform for interactive large-scale genome analysis B Giardine, C Riemer, RC Hardison, R Burhans, L Elnitski, P Shah, ... Genome research 15 (10), 1451-1455, 2005 | 1997 | 2005 |
| Complete genome sequence of Salmonella enterica serovar Typhimurium LT2 M McClelland, KE Sanderson, J Spieth, SW Clifton, P Latreille, L Courtney, ... Nature 413 (6858), 852, 2001 | 1899 | 2001 |
| Optimal alignments in linear space EW Myers, W Miller Bioinformatics 4 (1), 11-17, 1988 | 1703 | 1988 |
| Human–mouse alignments with BLASTZ S Schwartz, WJ Kent, A Smit, Z Zhang, R Baertsch, RC Hardison, ... Genome research 13 (1), 103-107, 2003 | 1387 | 2003 |
| Aligning multiple genomic sequences with the threaded blockset aligner M Blanchette, WJ Kent, C Riemer, L Elnitski, AFA Smit, KM Roskin, ... Genome research 14 (4), 708-715, 2004 | 1288 | 2004 |
| PipMaker—a web server for aligning two genomic DNA sequences S Schwartz, Z Zhang, KA Frazer, A Smit, C Riemer, J Bouck, R Gibbs, ... Genome research 10 (4), 577-586, 2000 | 1282 | 2000 |
| Evolutionary and biomedical insights from the rhesus macaque genome RA Gibbs, J Rogers, MG Katze, R Bumgarner, GM Weinstock, ER Mardis, ... Science 316 (5822), 222-234, 2007 | 1133 | 2007 |
| A time-efficient, linear-space local similarity algorithm X Huang, W Miller Advances in Applied Mathematics 12 (3), 337-357, 1991 | 1090 | 1991 |
| Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons GG Loots, RM Locksley, CM Blankespoor, ZE Wang, W Miller, EM Rubin, ... Science 288 (5463), 136-140, 2000 | 914 | 2000 |
| A computer program for aligning a cDNA sequence with a genomic DNA sequence L Florea, G Hartzell, Z Zhang, GM Rubin, W Miller Genome research 8 (9), 967-974, 1998 | 902 | 1998 |
| Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes WJ Kent, R Baertsch, A Hinrichs, W Miller, D Haussler Proceedings of the National Academy of Sciences 100 (20), 11484-11489, 2003 | 757 | 2003 |
| Comparative analyses of multi-species sequences from targeted genomic regions JW Thomas, JW Touchman, RW Blakesley, GG Bouffard, ... Nature 424 (6950), 788, 2003 | 714 | 2003 |
| Genome analysis of the platypus reveals unique signatures of evolution WC Warren, LDW Hillier, JAM Graves, E Birney, CP Ponting, F Grützner, ... Nature 453 (7192), 175, 2008 | 664 | 2008 |
