N. Goldman

发表

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

William Stafford Noble, Nancy R. Zhang, Stephen C. J. Parker, 2007, Nature.

Models of molecular evolution and phylogeny.

P. Lio’, N. Goldman, 1998, Genome research.

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.

Colin N. Dewey, Richard A. Moore, James B. Brown, 2007, Genome research.

Combining protein evolution and secondary structure.

David C. Jones, D. T. Jones, N. Goldman, 1996, Molecular biology and evolution.

Initial sequencing and comparative analysis of the mouse genome.

Colin N. Dewey, Simon C. Potter, James A. Cuff, 2002 .

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

A. Löytynoja, N. Goldman, 2008, Science.

Systematic evaluation of spliced alignment programs for RNA-seq data

J. Harrow, R. Guigó, T. Hubbard, 2013, Nature Methods.

Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses.

David C. Jones, D. T. Jones, N. Goldman, 1996, Journal of molecular biology.

A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach.

S. Whelan, N. Goldman, 2001, Molecular biology and evolution.

A codon-based model of nucleotide substitution for protein-coding DNA sequences.

N. Goldman, Z. Yang, Ziheng Yang, 1994, Molecular biology and evolution.

Molecular phylogenetics: state-of-the-art methods for looking into the past.

P. Lio’, S. Whelan, N. Goldman, 2001, Trends in genetics : TIG.

Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation.

N. Goldman, Z. Yang, Ziheng Yang, 1994, Molecular biology and evolution.

QUANTITATIVE ANALYSIS OF SHAPE VARIATION IN POPULATIONS OF SURIRELLA FASTUOSA

N. Goldman, T. Paddock, K. M. Shaw, 1990 .

Protein evolution with dependence among codons due to tertiary structure.

David T. Jones, N. Goldman, H. Kishino, 2003, Molecular biology and evolution.

Bayesian Probabilities and Quartet Puzzling

K. Strimmer, N. Goldman, A. Haeseler, 1997 .

Clustering Genes of Common Evolutionary History

N. Goldman, Kevin Gori, Tomasz Suchan, 2015, Molecular biology and evolution.

Addressing Inter-Gene Heterogeneity in Maximum Likelihood Phylogenomic Analysis: Yeasts Revisited

N. Goldman, J. Hess, Jaqueline Hess, 2011, PloS one.

Simple diagnostic statistical tests of models for DNA substitution

N. Goldman, 1993, Journal of Molecular Evolution.

A high-resolution map of human evolutionary constraint using 29 mammals

Albert J. Vilella, Matthew D. Rasmussen, André L. Martins, 2011, Nature.

The effects of alignment error and alignment filtering on the sitewise detection of positive selection.

Nick Goldman, Gregory E. Jordan, N. Goldman, 2012, Molecular biology and evolution.

Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference

Matthieu Muffato, Manuel Gil, Christophe Dessimoz, 2015, Systematic biology.

Statistics of the log-det estimator.

T. Massingham, N. Goldman, Nick Goldman, 2007, Molecular biology and evolution.

Stability of SARS-CoV-2 phylogenies

Conor R. Walker, Jason D. Fernandes, D. Haussler, 2020, PLoS genetics.

Codon-substitution models for heterogeneous selection pressure at amino acid sites.

N. Goldman, Z. Yang, R. Nielsen, 2000, Genetics.

Maximum Likelihood Inference of Small Trees in the Presence of Long Branches

N. Goldman, Sarah L. Parks, 2014, Systematic biology.

Looking for Darwin in genomic sequences--validity and success of statistical methods.

R. Nielsen, N. Goldman, Ziheng Yang, 2012, Molecular biology and evolution.

Genomic DNA k-mer spectra: models and modalities

B. Chor, D. Horn, T. Massingham, 2009, Genome Biology.

Detecting Amino Acid Sites Under Positive Selection and Purifying Selection

T. Massingham, N. Goldman, Tim Massingham, 2005, Genetics.

Insights into hominid evolution from the gorilla genome sequence

Albert J. Vilella, Gregory E. Jordan, Petra C. Schwalie, 2012, Nature.

Different versions of the Dayhoff rate matrix.

N. Goldman, C. Kosiol, 2005, Molecular biology and evolution.

Likelihood-based tests of topologies in phylogenetics.

A. Rodrigo, N. Goldman, J. P. Anderson, 2000, Systematic biology.

Genome sequencing of normal cells reveals developmental lineages and mutational processes

Asif U. Tamuri, M. Stratton, P. Campbell, 2014, Nature.

Coevolving protein residues: maximum likelihood identification and relationship to structure.

W R Taylor, D D Pollock, W. Taylor, 1999, Journal of molecular biology.

Sequence Bundles: a novel method for visualising, discovering and exploring sequence motifs

James King, Nick Goldman, Marek Kultys, 2014, BMC Proceedings.

ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments

Asif U. Tamuri, Nick Goldman, Jörg Schultz, 2016, Nucleic acids research.

Distributions of statistics used for the comparison of models of sequence evolution in phylogenetics

Simon Whelan, Nick Goldman, S. Whelan, 1999 .

Statistical tests of models of DNA substitution

Nick Goldman, N. Goldman, 1993, Journal of Molecular Evolution.

A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees

Russell B. Corbett-Detig, D. Haussler, A. Hinrichs, 2021, bioRxiv.

Improving communication for interdisciplinary teams working on storage of digital information in DNA

N. Goldman, J. Sayir, E. E. Hesketh, 2018, F1000Research.

Alignment Modulates Ancestral Sequence Reconstruction Accuracy

Asif U. Tamuri, Nick Goldman, Ricardo Assunção Vialle, 2018, Molecular biology and evolution.

Accuracy and Power of Statistical Methods for Detecting Adaptive Evolution in Protein Coding Sequences and for Identifying Positively Selected Sites

Nick Goldman, Ziheng Yang, Wendy S W Wong, 2004, Genetics.

Species Choice for Comparative Genomics: Being Greedy Works

Nick Goldman, Fabio Pardi, F. Pardi, 2005, PLoS genetics.

Resource-aware taxon selection for maximizing phylogenetic diversity.

Nick Goldman, Fabio Pardi, F. Pardi, 2007, Systematic biology.

Uniting Alignments and Trees

Ari Löytynoja, Nick Goldman, A. Löytynoja, 2009, Science.

Co-president Organizing Committee ______________________committees______________________ Scientific Committee 8:30 Extracting Organismal Phylogeny from Genomic Data -- 11:00 Concaterpillar: a New Method for Teasing Apart Conflicting Signals in Phylogenomic Analyses the Evolution of Rod from Cone Ops

N. Goldman, E. Rocha, 2006 .

MAXIMUM LIKELIHOOD TREES FROM DNA SEQUENCES: A PECULIAR STATISTICAL ESTIMATION PROBLEM

Nick Goldman, Ziheng Yang, N. Goldman, 1995 .

Phylogenetic information and experimental design in molecular systematics

Nick Goldman, N. Goldman, 1998, Proceedings of the Royal Society of London. Series B: Biological Sciences.

Assessing the impact of secondary structure and solvent accessibility on protein evolution.

David C. Jones, D. T. Jones, N. Goldman, 1998, Genetics.

A new criterion and method for amino acid classification.

Nick Goldman, Carolin Kosiol, N. Goldman, 2004, Journal of theoretical biology.

Statistical tests of gamma-distributed rate heterogeneity in models of sequence evolution in phylogenetics.

S. Whelan, N. Goldman, N Goldman, 2000, Molecular biology and evolution.

Effects of sequence alignment procedures on estimates of phylogeny

Nick Goldman, N. Goldman, 1998 .

MAXIMUM LIKELIHOOD INFERENCE OF PHYLOGENETIC TREES, WITH SPECIAL REFERENCE TO A POISSON PROCESS MODEL OF DNA SUBSTITUTION AND TO PARSIMONY ANALYSES

Nick Goldman, N. Goldman, 1990 .

Markovian and Non-Markovian Protein Sequence Evolution: Aggregated Markov Process Models

Nick Goldman, Carolin Kosiol, N. Goldman, 2011, Journal of molecular biology.

More on the Best Evolutionary Rate for Phylogenetic Analysis

T. Massingham, N. Goldman, S. Klopfstein, 2017, Systematic biology.

Probabilistic Models for the Study of Protein Evolution

N. Goldman, J. Thorne, 2019, Handbook of Statistical Genomics.

Phylogenomics and bioinformatics of SARS-CoV

P. Lio’, N. Goldman, 2004, Trends in Microbiology.

Experimental design criteria in phylogenetics: where to add taxa.

T. Massingham, N. Goldman, P. Darius, 2007, Systematic biology.

An Improved Protocol for Sequencing of Repetitive Genomic Regions and Structural Variations Using Mutagenesis and Next Generation Sequencing

A. Stütz, T. Massingham, N. Goldman, 2012, PloS one.

Integrated structural and evolutionary analysis reveals common mechanisms underlying adaptive evolution in mammals

N. Goldman, G. Slodkowicz, Greg Slodkowicz, 2020, Proceedings of the National Academy of Sciences.

From The Cover: An algorithm for progressive multiple alignment of sequences with

A. Löytynoja, N. Goldman, 2022 .

Integrated evolutionary and structural analysis reveals xenobiotics and pathogens as the major drivers of mammalian adaptation

N. Goldman, G. Slodkowicz, Greg Slodkowicz, 2019, bioRxiv.

What's in a likelihood? Simple models of protein evolution and the contribution of structurally viable reconstructions to the likelihood.

Nick Goldman, N. Goldman, M. Holder, 2011, Systematic biology.

progenitors Transcriptional diversity during lineage commitment of human blood

William J. Astle, Asif U. Tamuri, Sjoert B. G. Jansen, 2014 .

MUTATION RATES AND SELECTION ON SYNONYMOUS MUTATIONS IN SARS-COV-2

Conor R. Walker, Russell B. Corbett-Detig, R. Lanfear, 2021, bioRxiv.

A novel process of successive inter-strand template switches explains complex mutations and creates hair-pins

A. Löytynoja, N. Goldman, 2016 .

Genome analysis Determination and validation of principal gene products

J. Harrow, A. Frankish, M. Tress, 2007 .

phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets

Conor R. Walker, Russell B. Corbett-Detig, N. Goldman, 2022, PLoS Comput. Biol..

Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk

N. Goldman, S. Guindon, G. Baele, 2020, bioRxiv.

SMIM1 underlies the Vel blood group and influences red blood cell traits

Asif U. Tamuri, Gregory E. Jordan, C. A. Albers, 2013, Nature Genetics.

Maximum likelihood pandemic-scale phylogenetics

Russell B. Corbett-Detig, N. Goldman, R. Corbett-Detig, 2022, bioRxiv.

Optimization of the Ewens/Caswell neutral model program for community diversity analysis

N. Goldman, P. Lambshead, 1989 .

Chicken Toll-like Receptor 3 Recognizes Its Cognate Ligand When Ectopically 97 Expressed in Human Cells

N. Goldman, S. Baron, J. Hernandez, 2013 .

Genomic reconstruction of the SARS-CoV-2 epidemic in England

William T. Harvey, William L. Hamilton, Richard J. Goater, 2021, Nature.

SWAMPy: Simulating SARS-CoV-2 Wastewater Amplicon Metagenomes with Python

N. Goldman, N. De Maio, William Boulton, 2022, bioRxiv.

Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England

Richard J. Goater, Alexander W. Jung, E. Birney, 2021, Nature.

Genomic reconstruction of the SARS-CoV-2 epidemic across England from September 2020 to May 2021

Richard J. Goater, Alexander W. Jung, E. Birney, 2021, medRxiv.

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser

Ari Löytynoja, Nick Goldman, A. Löytynoja, 2010, BMC Bioinformatics.

Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm

Albert J. Vilella, Ari Löytynoja, Nick Goldman, 2012, Bioinform..

Transcriptional diversity during lineage commitment of human blood progenitors

Randy J. Read, William J. Astle, Paul Flicek, 2014, Science.

Short-range template switching in great ape genomes explored using pair hidden Markov models

Nicola De Maio, Nick Goldman, Conor R. Walker, 2020, bioRxiv.

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.

Nick Goldman, Peter F Stadler, Stefan Washietl, 2011, RNA.

Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution.

David Haussler, Francesca Chiaromonte, Mark Diekhans, 2003, Genome research.

Using protein structural information in evolutionary inference: transmembrane proteins.

P. Lio’, N. Goldman, P Liò, 1999, Molecular biology and evolution.

Towards practical, high-capacity, low-maintenance information storage in synthesized DNA

Ewan Birney, Christophe Dessimoz, Siyuan Chen, 2013, Nature.

Amino Acid Changes in Disease-Associated Variants Differ Radically from Variants Observed in the 1000 Genomes Project Dataset

Janet M. Thornton, Nick Goldman, Roman A. Laskowski, 2013, PLoS Comput. Biol..

Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages

N. Goldman, G. McLachlan, Piero Carninci, 2012, Proceedings of the National Academy of Sciences.

A phylogenetic approach for weighting genetic sequences

Jakub Truszkowski, Nicola De Maio, Alexander V. Alekseyenko, 2021, BMC Bioinformatics.

Mutation Rates and Selection on Synonymous Mutations in SARS-CoV-2

Conor R. Walker, Russell B. Corbett-Detig, R. Lanfear, 2021, Genome biology and evolution.

Phylogenetic Novelty Scores: a New Approach for Weighting Genetic Sequences

Alexander V. Alekseyenko, Marc A. Suchard, Nicola De Maio, 2020, bioRxiv.

Avoiding ascertainment bias in the maximum likelihood inference of phylogenies based on truncated data

Asif U. Tamuri, N. Goldman, 2017, bioRxiv.

Maximum Likelihood Phylogenetic Inference is Consistent on Multiple Sequence Alignments, with or without Gaps

Jakub Truszkowski, Nick Goldman, N. Goldman, 2015, Systematic biology.

A model of evolution and structure for multiple sequence alignment

Ari Löytynoja, Nick Goldman, A. Löytynoja, 2008, Philosophical Transactions of the Royal Society B: Biological Sciences.

XRate: a fast prototyping, training and annotation tool for phylo-grammars

Ian Holmes, Carolin Kosiol, Nick Goldman, 2006, BMC Bioinformatics.

A novel use of equilibrium frequencies in models of sequence evolution.

Simon Whelan, Nick Goldman, S. Whelan, 2002, Molecular biology and evolution.

EDIBLE: experimental design and information calculations in phylogenetics

Nick Goldman, Tim Massingham, T. Massingham, 2000, Bioinform..

Phylogenetic Quantification of Intra-tumour Heterogeneity

James D. Brenton, Nick Goldman, Florian Markowetz, 2013, PLoS Comput. Biol..

Evidence for mitochondrial DNA recombination in a human population of island Melanesia

E. Hagelberg, P. Lio’, S. Whelan, 1999, Proceedings of the Royal Society of London. Series B: Biological Sciences.

Variation in evolutionary processes at different codon positions.

Nick Goldman, Lee Bofkin, N. Goldman, 2006, Molecular biology and evolution.

The human blood DNA methylome displays a highly distinctive profile compared with other somatic tissues

N. Goldman, V. Rakyan, G. Slodkowicz, 2015, Epigenetics.

Variance to mean ratio, R(t), for poisson processes on phylogenetic trees.

N. Goldman, 1994, Molecular phylogenetics and evolution.

All Your Base: a fast and accurate probabilistic approach to base calling

Tim Massingham, Nick Goldman, T. Massingham, 2012, Genome Biology.

A Penalized-Likelihood Method to Estimate the Distribution of Selection Coefficients from Phylogenetic Data

Asif U. Tamuri, Nick Goldman, N. Goldman, 2014, Genetics.

Ambiguity Coding Allows Accurate Inference of Evolutionary Parameters from Alignments in an Aggregated State-Space

Ziheng Yang, Claudia C Weber, Umberto Perron, 2019, bioRxiv.

Short template switch events explain mutation clusters in the human genome

A. Löytynoja, N. Goldman, 2016, bioRxiv.

An empirical codon model for protein sequence evolution.

Ian Holmes, Nick Goldman, Carolin Kosiol, 2007, Molecular biology and evolution.

An algorithm for progressive multiple alignment of sequences with insertions.

Ari Löytynoja, Nick Goldman, A. Löytynoja, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design

E. Birney, N. Goldman, Lukas Weilguny, 2022, bioRxiv.

Rapidly evolving human promoter regions

Martin S. Taylor, Piero Carninci, Y. Hayashizaki, 2008, Nature Genetics.

Short template switch events in human evolution cause complex mutation patterns

Ari Löytynoja, Nick Goldman, A. Löytynoja, 2016 .

Estimating the Frequency of Events That Cause Multiple-Nucleotide Changes

Simon Whelan, Nick Goldman, S. Whelan, 2004, Genetics.

A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees

Russell B. Corbett-Detig, D. Haussler, A. Hinrichs, 2021, Molecular biology and evolution.

A daily-updated database and tools for comprehensive SARS-CoV-2 mutation-annotated trees

Russell B. Corbett-Detig, D. Haussler, A. Hinrichs, 2021, bioRxiv.

Modeling Structural Constraints on Protein Evolution via Side-Chain Conformational States

Alexey M. Kozlov, N. Goldman, A. Stamatakis, 2019, Molecular biology and evolution.

Modelling structural constraints on protein evolution via side-chain conformational states

Alexey M. Kozlov, N. Goldman, A. Stamatakis, 2019, bioRxiv.

Want to track pandemic variants faster? Fix the bioinformatics bottleneck

R. Lanfear, N. Goldman, A. Stamatakis, 2021, Nature.

In defense of statistical methods for detecting positive selection

N. Goldman, R. Nielsen, Ziheng Yang, 2009, Proceedings of the National Academy of Sciences.

A retroviral origin of vertebrate myelin

N. Goldman, D. Rowitch, Chao Zhao, 2022, bioRxiv.

phastSim: efficient simulation of sequence evolution for pandemic-scale datasets

Conor R. Walker, Russell B. Corbett-Detig, N. Goldman, 2021, bioRxiv.

PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment

Nick Goldman, Tim Massingham, Botond Sipos, 2011, BMC Bioinformatics.

Determination and validation of principal gene products

Alfonso Valencia, Jennifer L. Harrow, Michael L. Tress, 2008, Bioinform..

Evolutionary footprints of nucleosome positions in yeast.

Rainer Machné, Nick Goldman, Stefan Washietl, 2008, Trends in genetics : TIG.

Genetic Variability of the SARS-CoV-2 Pocketome

N. Goldman, M. Schapira, V. Shahani, 2021, Journal of proteome research.

PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees

Nicolas Rodriguez, Simon Whelan, Nick Goldman, 2005, Nucleic Acids Res..

Human immunodeficiency virus type 2 ( HIV-2 ) e n v gene analysis : prediction of glycoprotein epitopes important for heterotypic neutralization and evidence for three genotype clusters within the HIV-2 a subtype

N. Goldman, R. Daniels, N. Douglas, 2007 .

Human immunodeficiency virus type 2 (HIV-2) env gene analysis: prediction of glycoprotein epitopes important for heterotypic neutralization and evidence for three genotype clusters within the HIV-2a subtype.

N. Goldman, R. Daniels, N. Douglas, 1995, The Journal of general virology.

Realistic simulations reveal extensive sample-specificity of RNA-seq biases

Nick Goldman, Tim Massingham, Botond Sipos, 2013, 1308.3172.

Modeling Mitochondrial Protein Evolution Using Structural Information

P. Lio’, N. Goldman, 2002, Journal of Molecular Evolution.

PASP — a whole-transcriptome poly(A) tail length determination assay for the Illumina platform

J. Korbel, A. Stütz, T. Massingham, 2016, bioRxiv.

Maximum likelihood pandemic-scale phylogenetics

Russell B. Corbett-Detig, N. Goldman, R. Corbett-Detig, 2023, Nature Genetics.

Toward practical high-capacity low-maintenance storage of digital information in synthesised DNA

Ewan Birney, Christophe Dessimoz, Botond Sipos, 2013 .

Nucleotide, dinucleotide and trinucleotide frequencies explain patterns observed in chaos game representations of DNA sequences.

N. Goldman, N Goldman, 1993, Nucleic acids research.

Pandit: a database of protein and associated nucleotide domains with inferred trees

Simon Whelan, Nick Goldman, Paul I. W. de Bakker, 2003, Bioinform..

Further results on error minimization in the genetic code

Nick Goldman, N. Goldman, 1993, Journal of Molecular Evolution.

DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies

N. Goldman, Ziheng Yang, M. Telford, 2023, Systematic biology.

Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment.

Manuel Gil, Christophe Dessimoz, Nick Goldman, 2012, Methods in molecular biology.

METHODS FOR DISCRETE CODING OF MORPHOLOGICAL CHARACTERS FOR NUMERICAL ANALYSIS

Nick Goldman, N. Goldman, 1988 .

Are big trees indeed easy?

N. Goldman, Z. Yang, 1997, Trends in ecology & evolution.

The SARS-CoV-2 replication-transcription complex is a priority target for broad-spectrum pan-coronavirus drugs

N. Goldman, M. Schapira, N. de Maio, 2021, bioRxiv.

Markovian and non-Markovian protein sequence evolution: aggregated Markov process models.

N. Goldman, C. Kosiol, 2011, Journal of molecular biology.

SWAMPy: Simulating SARS-CoV-2 Wastewater Amplicon Metagenomes with Python

N. Goldman, N. de Maio, H. Denise, 2023, bioRxiv.

Error-correcting properties of the SOLiD Exact Call Chemistry

T. Massingham, N. Goldman, 2012, BMC Bioinformatics.

Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks

Manuel Gil, Christophe Dessimoz, Nick Goldman, 2015, Proceedings of the National Academy of Sciences.

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

A. Löytynoja, N. Goldman, 2008, Science.

Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design

Ewan Birney, Nick Goldman, Matthew Loose, 2020, bioRxiv.

Maximum likelihood pandemic-scale phylogenetics

Russell B. Corbett-Detig, N. Goldman, B. Minh, 2022, bioRxiv.

: Tools to Interpret and Manipulate Mutation Annotated Trees

Russell B. Corbett-Detig, D. Haussler, A. Hinrichs, 2021 .

Determination and validation of principal gene products

J. Harrow, A. Frankish, M. Tress, 2008, Bioinform..

Error-correcting properties of the SOLiD Exact Call Chemistry

Nick Goldman, Tim Massingham, N. Goldman, 2012, BMC Bioinformatics.