Author details

Full Name

Nick Goldman

Affiliation

ORCID

Career Start Year

1988

Papers

115

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
36593407	Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design.	Nat Biotechnol	2023
37366056	DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies.		2023
37038003	Maximum likelihood pandemic-scale phylogenetics.		2023
35486906	phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets.	PLoS Computational Biology	2022
35701578	Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England.	Nature	2022
33406072	Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk.	PLoS Computational Biology	2021
32353118	Ambiguity Coding Allows Accurate Inference of Evolutionary Parameters from Alignments in an Aggregated State-Space.	Systematic Biology	2021
33895815	Mutation Rates and Selection on Synonymous Mutations in SARS-CoV-2.	Genome Biology and Evolution	2021
33469589	Mutation rates and selection on synonymous mutations in SARS-CoV-2.		2021
34049487	A phylogenetic approach for weighting genetic sequences.	BMC Bioinformatics	2021
33821270	A daily-updated database and tools for comprehensive SARS-CoV-2 mutation-annotated trees.	bioRxiv	2021
33651813	Short-range template switching in great ape genomes explored using pair hidden Markov models.	PLoS Genetics	2021
33649511	Want to track pandemic variants faster? Fix the bioinformatics bottleneck.	Nature	2021
33758852	phastSim: efficient simulation of sequence evolution for pandemic-scale datasets.		2021
32123117	Integrated structural and evolutionary analysis reveals common mechanisms underlying adaptive evolution in mammals.	Proceedings of the National Academy of Sciences of the United States of America	2020
31114882	Modeling Structural Constraints on Protein Evolution via Side-Chain Conformational States.	Mol Biol Evol	2019
29707196	Improving communication for interdisciplinary teams working on storage of digital information in DNA.	F1000Research	2018
29618097	Alignment Modulates Ancestral Sequence Reconstruction Accuracy.	Molecular Biology and Evolution	2018
28595363	More on the Best Evolutionary Rate for Phylogenetic Analysis.	Systematic Biology	2017
28385709	Short template switch events explain mutation clusters in the human genome.	Genome Research	2017
27820964	Long-term antibiotic treatment for non-cystic fibrosis bronchiectasis in adults: evidence, current practice and future use.		2016
26893301	Clustering Genes of Common Evolutionary History.	Mol Biol Evol	2016
26819408	ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments.	Nucleic Acids Research	2016
26615177	Maximum Likelihood Phylogenetic Inference is Consistent on Multiple Sequence Alignments, with or without Gaps.	Systematic Biology	2016
26031838	Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference.	Syst Biol	2015
25634226	The human blood DNA methylome displays a highly distinctive profile compared with other somatic tissues.	Epigenetics	2015
25564672	Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks.	Proc Natl Acad Sci U S A	2015
25237395	Sequence Bundles: a novel method for visualising, discovering and exploring sequence motifs.	BMC Proceedings	2014
25258084	Transcriptional diversity during lineage commitment of human blood progenitors.	Science	2014
24170395	Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment.	Methods Mol Biol	2014
25043003	Genome sequencing of normal cells reveals developmental lineages and mutational processes.	Nature	2014
24996414	Maximum likelihood inference of small trees in the presence of long branches.	Systematic Biology	2014
24532780	A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data.	Genetics	2014
24743184	Phylogenetic quantification of intra-tumour heterogeneity.	PLoS Comput Biol	2014
23354052	Towards practical, high-capacity, low-maintenance information storage in synthesized DNA.	Nature	2013
24348229	Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset.	PLoS Computational Biology	2013
24185836	Systematic evaluation of spliced alignment programs for RNA-seq data.	Nat Methods	2013
23563608	SMIM1 underlies the Vel blood group and influences red blood cell traits.	Nat Genet	2013
22049066	The effects of alignment error and alignment filtering on the sitewise detection of positive selection.	Molecular Biology and Evolution	2012
22398555	Insights into hominid evolution from the gorilla genome sequence.	Nature	2012
22531217	Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm.		2012
22377270	All Your Base: a fast and accurate probabilistic approach to base calling.		2012
22912860	An improved protocol for sequencing of repetitive genomic regions and structural variations using mutagenesis and next generation sequencing.	PLoS One	2012
22726842	Error-correcting properties of the SOLiD Exact Call Chemistry.	BMC Bioinformatics	2012
22490825	Looking for Darwin in genomic sequences--validity and success of statistical methods.	Molecular Biology and Evolution	2012
22451944	Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages.	Proc Natl Acad Sci U S A	2012
21993624	A high-resolution map of human evolutionary constraint using 29 mammals.	Nature	2011
21233085	What's in a likelihood? Simple models of protein evolution and the contribution of structurally viable reconstructions to the likelihood.	Systematic Biology	2011
21357752	RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.	RNA	2011
21504561	PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment.	BMC Bioinformatics	2011