Author details

Full Name

Simon Whelan

Affiliation

ORCID

Career Start Year

1999

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
33289892	Automated Removal of Non-homologous Sequence Stretches with PREQUAL.	Methods in Molecular Biology	2021
31985800	Estimating Phylogenies from Shape and Similar Multidimensional Data: Why It Is Not Reliable.	Systematic Biology	2020
30668757	Physicochemical Amino Acid Properties Better Describe Substitution Rates in Large Populations.	Molecular Biology and Evolution	2019
31209473	Identifying Clusters of High Confidence Homologies in Multiple Sequence Alignments.	Molecular Biology and Evolution	2019
29868763	PREQUAL: detecting non-homologous characters in sets of unaligned homologous sequences.		2018
27633353	Phylogenetic Tree Estimation With and Without Alignment: New Distance Methods and Benchmarking.	Systematic Biology	2017
27896728	Inferring Trees.	Methods in Molecular Biology	2017
25209223	ModelOMatic: fast and automated model selection between RY, nucleotide, amino acid, and codon substitution models.	Systematic Biology	2015
25725494	GeLL: a generalized likelihood library for phylogenetic models.		2015
25944916	Covariation Is a Poor Measure of Molecular Coevolution.	Molecular Biology and Evolution	2015
26139831	Evidence of Statistical Inconsistency of Phylogenetic Methods in the Presence of Multiple Sequence Alignment Uncertainty.	Genome Biology and Evolution	2015
24631855	Impact of deep coalescence and recombination on the estimation of phylogenetic relationships among species using AFLP markers.	Molecular Phylogenetics and Evolution	2014
24391153	Assessing the state of substitution models describing noncoding RNA evolution.	Genome Biology and Evolution	2014
23144040	Class of multiple sequence alignment algorithm affects genomic analysis.	Molecular Biology and Evolution	2013
22076302	Characterizing the phylogenetic tree-search problem.	Systematic Biology	2012
22645563	Protein Phylogenetic Analysis of Ca(2+)/cation Antiporters and Insights into their Evolution in Plants.	Frontiers in Plant Science	2012
22528593	The interface of protein structure, protein biophysics, and molecular evolution.	Protein Sci	2012
22199391	Measuring the distance between multiple sequence alignments.		2012
22039210	Determining the evolutionary history of gene families.		2012
22070353	Developmental plasticity, morphological variation and evolvability: a multilevel analysis of morphometric integration in the shape of compound leaves.	J Evol Biol	2012
20724379	Phylogenetic substitution models for detecting heterotachy during plastid evolution.	Molecular Biology and Evolution	2011
20584772	The prevalence of multifurcations in tree-space and their implications for tree-search.	Molecular Biology and Evolution	2010
20981828	Dynamic expression patterns of 6-O endosulfatases during zebrafish development suggest a subfunctionalisation event for sulf2.	Developmental Dynamics	2010
18852102	The genetic code can cause systematic bias in simple phylogenetic models.	Philosophical Transactions of the Royal Society B: Biological Sciences	2008
18006548	Determination and validation of principal gene products.	Bioinformatics	2008
18566770	Inferring trees.	Methods in Molecular Biology	2008
18502771	Spatial and temporal heterogeneity in nucleotide sequence evolution.	Molecular Biology and Evolution	2008
17571346	Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.	Nature	2007
17567995	Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.	Genome Res	2007
17849327	New approaches to phylogenetic tree search and their application to large numbers of protein alignments.	Systematic Biology	2007
16381879	PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees.	Nucleic Acids Res	2006
16226061	Phylogenetics by likelihood: evolutionary modeling as a tool for understanding the genome.	Journal of Biomedical Informatics	2006
15107806	Functional needles in a genomic haystack.	Heredity	2004
15342538	Estimating the frequency of events that cause multiple-nucleotide changes.	Genetics	2004
12912837	Pandit: a database of protein and associated nucleotide domains with inferred trees.	Bioinformatics	2003
12529302	Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution.	Genome Res	2003
12411592	A novel use of equilibrium frequencies in models of sequence evolution.	Molecular Biology and Evolution	2002
12466850	Initial sequencing and comparative analysis of the mouse genome.	Nature	2002
11319253	A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach.	Molecular Biology and Evolution	2001
11335036	Molecular phylogenetics: state-of-the-art methods for looking into the past.	Trends Genet	2001
10833204	Statistical tests of gamma-distributed rate heterogeneity in models of sequence evolution in phylogenetics.	Molecular Biology and Evolution	2000
10189712	Evidence for mitochondrial DNA recombination in a human population of island Melanesia.	Proc Biol Sci	1999