| Initial sequencing and comparative analysis of the mouse genome European Bioinformatics Institute: Birney Ewan 3 Goldman Nick 3 Kasprzyk ... Nature 420 (6915), 520-562, 2002 | 8780 | 2002 |
| Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Management Group Liefer Laura A. 51 Wetterstrand Kris A. 51 Good Peter J. 51 ... nature 447 (7146), 799-816, 2007 | 6134 | 2007 |
| A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach S Whelan, N Goldman Molecular biology and evolution 18 (5), 691-699, 2001 | 3086 | 2001 |
| Molecular phylogenetics: state-of-the-art methods for looking into the past S Whelan, P Liò, N Goldman TRENDS in Genetics 17 (5), 262-272, 2001 | 529 | 2001 |
| Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution RC Hardison, KM Roskin, S Yang, M Diekhans, WJ Kent, R Weber, ... Genome research 13 (1), 13-26, 2003 | 362 | 2003 |
| Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome EH Margulies, GM Cooper, G Asimenos, DJ Thomas, CN Dewey, A Siepel, ... Genome research 17 (6), 760-774, 2007 | 254 | 2007 |
| The interface of protein structure, protein biophysics, and molecular evolution DA Liberles, SA Teichmann, I Bahar, U Bastolla, J Bloom, ... Protein Science, 769-785, 2012 | 243 | 2012 |
| Evidence for mitochondrial DNA recombination in a human population of island Melanesia E Hagelberg, N Goldman, P Lio, S Whelan, W Schiefenhöel, JB Clegg, ... Proceedings of the Royal Society of London. Series B: Biological Sciences …, 1999 | 237 | 1999 |
| Developmental plasticity, morphological variation and evolvability: a multilevel analysis of morphometric integration in the shape of compound leaves CP Klingenberg, S Duttke, S Whelan, M Kim Journal of Evolutionary Biology 25, 115-129, 2012 | 218 | 2012 |
| Statistical tests of gamma-distributed rate heterogeneity in models of sequence evolution in phylogenetics N Goldman, S Whelan Molecular Biology and Evolution 17 (6), 975-978, 2000 | 148 | 2000 |
| Protein Phylogenetic Analysis of Ca2+/cation Antiporters and Insights into their Evolution in Plants L Emery, S Whelan, KD Hirschi, JK Pittman Frontiers in plant science 3, 1, 2012 | 139 | 2012 |
| Distributions of statistics used for the comparison of models of sequence evolution in phylogenetics S Whelan, N Goldman Molecular Biology and Evolution 16 (9), 1292-1292, 1999 | 136 | 1999 |
| PREQUAL: detecting non-homologous characters in sets of unaligned homologous sequences S Whelan, I Irisarri, F Burki Bioinformatics 34 (22), 3929-3930, 2018 | 121 | 2018 |
| Identifying clusters of high confidence homologies in multiple sequence alignments RH Ali, M Bogusz, S Whelan Molecular biology and evolution 36 (10), 2340-2351, 2019 | 117 | 2019 |
| Estimating the frequency of events that cause multiple-nucleotide changes S Whelan, N Goldman Genetics 167 (4), 2027-2043, 2004 | 101 | 2004 |
| PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees S Whelan, PIW de Bakker, E Quevillon, N Rodriguez, N Goldman Nucleic Acids Research 34 (suppl_1), D327-D331, 2006 | 88 | 2006 |
| Class of multiple sequence alignment algorithm affects genomic analysis BP Blackburne, S Whelan Molecular Biology and Evolution 30 (3), 642-53, 2013 | 87 | 2013 |
| Measuring the distance between multiple sequence alignments BP Blackburne, S Whelan Bioinformatics 28, 495-502, 2011 | 84 | 2011 |
| Covariation is a poor measure of molecular coevolution D Talavera, SC Lovell, S Whelan Molecular biology and evolution 32 (9), 2456-2468, 2015 | 64 | 2015 |
| Evidence for mitochondrial DNA recombination in a human population of island Melanesia: correction E Hagelberg, N Goldman, P Lio, S Whelan, W Schiefenhövel, JB Clegg, ... Proceedings of the Royal Society of London. Series B: Biological Sciences …, 2000 | 63 | 2000 |