List of works - Nick Goldman

Initial sequencing and comparative analysis of the mouse genome

scientific article

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

scientific article published in June 2007

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

scientific article (publication date: May 2001)

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

scientific article (publication date: May 2000)

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

scientific article (publication date: September 1994)

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

scientific article

An algorithm for progressive multiple alignment of sequences with insertions

scientific article

Likelihood-based tests of topologies in phylogenetics

scientific article (publication date: December 2000)

Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis

scientific article

Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites

scientific article

Insights into hominid evolution from the gorilla genome sequence

scientific article

Systematic evaluation of spliced alignment programs for RNA-seq data

scientific article published on November 3, 2013

Statistical tests of models of DNA substitution

scientific article published on February 1, 1993

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

scientific article

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

scientific article published on November 26, 2010

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

scientific article

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

scientific article published in June 2007

Genome sequencing of normal cells reveals developmental lineages and mutational processes

scientific article published on 29 June 2014

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

scientific article

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

scientific article

Transcriptional diversity during lineage commitment of human blood progenitors

scientific article

Detecting amino acid sites under positive selection and purifying selection

scientific article published on 16 January 2005

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

scientific article

Protein evolution with dependence among codons due to tertiary structure

scientific article

An empirical codon model for protein sequence evolution

scientific article

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

scientific article

The Effects of Alignment Error and Alignment Filtering on the Sitewise Detection of Positive Selection

scientific article published on November 1, 2011

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

scientific article

Models of molecular evolution and phylogeny

scientific article

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

article

Combining protein evolution and secondary structure

scientific article published in May 1996

Phylogenetic quantification of intra-tumour heterogeneity

scientific article (publication date: April 2014)

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

scientific article

Genomic DNA k-mer spectra: models and modalities

scientific article published on 08 October 2009

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

article

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

scientific article (publication date: 7 March 1999)

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

scientific article published on April 23, 2012

Evolutionary footprints of nucleosome positions in yeast

article published in 2008

Different versions of the Dayhoff rate matrix

scientific article

Phylogenetic information and experimental design in molecular systematics

scientific article

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

scientific article

Using Evolutionary Trees in Protein Secondary Structure Prediction and Other Comparative Sequence Analyses

Estimating the frequency of events that cause multiple-nucleotide changes

scientific article

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

scientific article

Variation in evolutionary processes at different codon positions

scientific article published on 21 November 2006

Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset

scientific article

In defense of statistical methods for detecting positive selection

scientific article published on 31 August 2009

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

scientific article

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

scientific article

A novel use of equilibrium frequencies in models of sequence evolution

article

List of works by Nick Goldman

Initial sequencing and comparative analysis of the mouse genome

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

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

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

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

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

An algorithm for progressive multiple alignment of sequences with insertions

Likelihood-based tests of topologies in phylogenetics

Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis

Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites

Insights into hominid evolution from the gorilla genome sequence

Systematic evaluation of spliced alignment programs for RNA-seq data

Statistical tests of models of DNA substitution

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

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

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

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

Genome sequencing of normal cells reveals developmental lineages and mutational processes

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

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

Transcriptional diversity during lineage commitment of human blood progenitors

Detecting amino acid sites under positive selection and purifying selection

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

Protein evolution with dependence among codons due to tertiary structure

An empirical codon model for protein sequence evolution

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

The Effects of Alignment Error and Alignment Filtering on the Sitewise Detection of Positive Selection

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

Models of molecular evolution and phylogeny

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

Combining protein evolution and secondary structure

Phylogenetic quantification of intra-tumour heterogeneity

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

Genomic DNA k-mer spectra: models and modalities

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

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

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

Evolutionary footprints of nucleosome positions in yeast

Different versions of the Dayhoff rate matrix

Phylogenetic information and experimental design in molecular systematics

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

Using Evolutionary Trees in Protein Secondary Structure Prediction and Other Comparative Sequence Analyses

Estimating the frequency of events that cause multiple-nucleotide changes

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

Variation in evolutionary processes at different codon positions

Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset

In defense of statistical methods for detecting positive selection

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

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

A novel use of equilibrium frequencies in models of sequence evolution