Nick Goldman
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Nick Goldmancomputer-science Degrees
Computer Science
#4616
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#4869
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Data Science
#160
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#163
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Machine Learning
#2968
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#3005
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Database
#4798
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#4984
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Nick Goldmanbiology Degrees
Biology
#4741
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#7036
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Bioinformatics
#57
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#58
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Systematics
#64
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#76
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Computational Biology
#222
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#223
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Computer Science Biology
Nick Goldman's Degrees
- PhD Bioinformatics University of Oxford
- Bachelors Genetics University of Oxford
Why Is Nick Goldman Influential?
(Suggest an Edit or Addition)According to Wikipedia, Nicholas Goldman is a group leader and senior scientist at the European Bioinformatics Institute , located on the Wellcome Genome Campus in Hinxton, Cambridgeshire, England. He began working at the EBI in 2002, and became a senior scientist there in 2009. His group's research focuses on evolutionary genetics and genomics. He and his EBI colleague Ewan Birney, along with other researchers, developed a tool for DNA digital data storage, on which they successfully encoded all the sonnets of William Shakespeare, Martin Luther King Jr.'s 1963 "I Have a Dream" speech, a PDF of the 1953 paper "Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid", and a photo of their own institute. They described their results in a 2013 paper in Nature.
Nick Goldman's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project (2007) (5196)
- Initial sequencing and comparative analysis of the mouse genome. (2002) (4609)
- A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. (2001) (2590)
- Codon-substitution models for heterogeneous selection pressure at amino acid sites. (2000) (2270)
- A codon-based model of nucleotide substitution for protein-coding DNA sequences. (1994) (1976)
- Likelihood-based tests of topologies in phylogenetics. (2000) (1082)
- A high-resolution map of human evolutionary constraint using 29 mammals (2011) (1081)
- An algorithm for progressive multiple alignment of sequences with insertions. (2005) (891)
- Towards practical, high-capacity, low-maintenance information storage in synthesized DNA (2013) (776)
- Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis (2008) (766)
- Insights into hominid evolution from the gorilla genome sequence (2012) (670)
- Accuracy and Power of Statistical Methods for Detecting Adaptive Evolution in Protein Coding Sequences and for Identifying Positively Selected Sites (2004) (575)
- Statistical tests of models of DNA substitution (1993) (546)
- Systematic evaluation of spliced alignment programs for RNA-seq data (2013) (494)
- Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. (1994) (451)
- Molecular phylogenetics: state-of-the-art methods for looking into the past. (2001) (408)
- webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser (2010) (387)
- Models of molecular evolution and phylogeny. (1998) (320)
- Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. (2003) (298)
- Genome sequencing of normal cells reveals developmental lineages and mutational processes (2014) (297)
- Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages (2012) (278)
- Transcriptional diversity during lineage commitment of human blood progenitors (2014) (269)
- MAXIMUM LIKELIHOOD TREES FROM DNA SEQUENCES: A PECULIAR STATISTICAL ESTIMATION PROBLEM (1995) (257)
- Assessing the impact of secondary structure and solvent accessibility on protein evolution. (1998) (253)
- Coevolving protein residues: maximum likelihood identification and relationship to structure. (1999) (251)
- Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. (2007) (221)
- Detecting Amino Acid Sites Under Positive Selection and Purifying Selection (2005) (214)
- Protein evolution with dependence among codons due to tertiary structure. (2003) (205)
- MAXIMUM LIKELIHOOD INFERENCE OF PHYLOGENETIC TREES, WITH SPECIAL REFERENCE TO A POISSON PROCESS MODEL OF DNA SUBSTITUTION AND TO PARSIMONY ANALYSES (1990) (199)
- Evidence for mitochondrial DNA recombination in a human population of island Melanesia (1999) (193)
- An empirical codon model for protein sequence evolution. (2007) (192)
- Genomic DNA k-mer spectra: models and modalities (2009) (186)
- RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. (2011) (183)
- Combining protein evolution and secondary structure. (1996) (176)
- Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference (2015) (168)
- The effects of alignment error and alignment filtering on the sitewise detection of positive selection. (2012) (166)
- Different versions of the Dayhoff rate matrix. (2005) (143)
- Bayesian Probabilities and Quartet Puzzling (1997) (140)
- Distributions of statistics used for the comparison of models of sequence evolution in phylogenetics (1999) (138)
- Phylogenetic Quantification of Intra-tumour Heterogeneity (2013) (136)
- Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm (2012) (135)
- Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses. (1996) (127)
- Statistical tests of gamma-distributed rate heterogeneity in models of sequence evolution in phylogenetics. (2000) (119)
- Nucleotide, dinucleotide and trinucleotide frequencies explain patterns observed in chaos game representations of DNA sequences. (1993) (108)
- Phylogenetic information and experimental design in molecular systematics (1998) (102)
- SMIM1 underlies the Vel blood group and influences red blood cell traits (2013) (98)
- Variation in evolutionary processes at different codon positions. (2006) (91)
- Estimating the Frequency of Events That Cause Multiple-Nucleotide Changes (2004) (88)
- Simple diagnostic statistical tests of models for DNA substitution (1993) (87)
- PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees (2005) (79)
- Want to track pandemic variants faster? Fix the bioinformatics bottleneck (2021) (75)
- Species Choice for Comparative Genomics: Being Greedy Works (2005) (71)
- Evolutionary footprints of nucleosome positions in yeast. (2008) (70)
- XRate: a fast prototyping, training and annotation tool for phylo-grammars (2006) (61)
- A new criterion and method for amino acid classification. (2004) (60)
- METHODS FOR DISCRETE CODING OF MORPHOLOGICAL CHARACTERS FOR NUMERICAL ANALYSIS (1988) (59)
- Genomic reconstruction of the SARS-CoV-2 epidemic in England (2021) (59)
- PASSML: combining evolutionary inference and protein secondary structure prediction (1998) (55)
- Pandit: a database of protein and associated nucleotide domains with inferred trees (2003) (55)
- Alignment Modulates Ancestral Sequence Reconstruction Accuracy (2018) (53)
- Amino Acid Changes in Disease-Associated Variants Differ Radically from Variants Observed in the 1000 Genomes Project Dataset (2013) (53)
- PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment (2011) (51)
- A Penalized-Likelihood Method to Estimate the Distribution of Selection Coefficients from Phylogenetic Data (2014) (51)
- Clustering Genes of Common Evolutionary History (2015) (51)
- Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment. (2012) (50)
- Using protein structural information in evolutionary inference: transmembrane proteins. (1999) (48)
- A model of evolution and structure for multiple sequence alignment (2008) (48)
- A novel use of equilibrium frequencies in models of sequence evolution. (2002) (48)
- Experimental design criteria in phylogenetics: where to add taxa. (2007) (47)
- MUTATION RATES AND SELECTION ON SYNONYMOUS MUTATIONS IN SARS-COV-2 (2021) (46)
- Further results on error minimization in the genetic code (1993) (45)
- The human blood DNA methylome displays a highly distinctive profile compared with other somatic tissues (2015) (44)
- More on the Best Evolutionary Rate for Phylogenetic Analysis (2017) (42)
- In defense of statistical methods for detecting positive selection (2009) (41)
- Resource-aware taxon selection for maximizing phylogenetic diversity. (2007) (41)
- A daily-updated database and tools for comprehensive SARS-CoV-2 mutation-annotated trees (2021) (37)
- All Your Base: a fast and accurate probabilistic approach to base calling (2012) (36)
- Mutation Rates and Selection on Synonymous Mutations in SARS-CoV-2 (2021) (35)
- Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk (2020) (34)
- Phylogenomics and bioinformatics of SARS-CoV (2004) (34)
- Looking for Darwin in genomic sequences--validity and success of statistical methods. (2012) (33)
- Determination and validation of principal gene products (2008) (29)
- Uniting Alignments and Trees (2009) (26)
- Addressing Inter-Gene Heterogeneity in Maximum Likelihood Phylogenomic Analysis: Yeasts Revisited (2011) (26)
- Variance to mean ratio, R(t), for poisson processes on phylogenetic trees. (1994) (26)
- Integrated structural and evolutionary analysis reveals common mechanisms underlying adaptive evolution in mammals (2020) (25)
- Are big trees indeed easy? (1997) (24)
- Maximum Likelihood Phylogenetic Inference is Consistent on Multiple Sequence Alignments, with or without Gaps (2015) (23)
- Maximum Likelihood Inference of Small Trees in the Presence of Long Branches (2014) (23)
- Short template switch events explain mutation clusters in the human genome (2016) (23)
- Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks (2015) (22)
- EDIBLE: experimental design and information calculations in phylogenetics (2000) (20)
- Effects of sequence alignment procedures on estimates of phylogeny (1998) (20)
- Introduction. Statistical and computational challenges in molecular phylogenetics and evolution (2008) (19)
- Rapidly evolving human promoter regions (2008) (18)
- QUANTITATIVE ANALYSIS OF SHAPE VARIATION IN POPULATIONS OF SURIRELLA FASTUOSA (1990) (18)
- Markovian and Non-Markovian Protein Sequence Evolution: Aggregated Markov Process Models (2011) (18)
- What's in a likelihood? Simple models of protein evolution and the contribution of structurally viable reconstructions to the likelihood. (2011) (17)
- 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. (1995) (16)
- Genomic reconstruction of the SARS-CoV-2 epidemic across England from September 2020 to May 2021 (2021) (15)
- Genetic Variability of the SARS-CoV-2 Pocketome (2021) (15)
- Optimization of the Ewens/Caswell neutral model program for community diversity analysis (1989) (14)
- Modeling Mitochondrial Protein Evolution Using Structural Information (2002) (13)
- A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees (2021) (13)
- An Improved Protocol for Sequencing of Repetitive Genomic Regions and Structural Variations Using Mutagenesis and Next Generation Sequencing (2012) (13)
- Realistic simulations reveal extensive sample-specificity of RNA-seq biases (2013) (12)
- Sequence Bundles: a novel method for visualising, discovering and exploring sequence motifs (2014) (12)
- Error-correcting properties of the SOLiD Exact Call Chemistry (2012) (11)
- Toward practical high-capacity low-maintenance storage of digital information in synthesised DNA (2013) (11)
- Statistics of the log-det estimator. (2007) (11)
- phastSim: efficient simulation of sequence evolution for pandemic-scale datasets (2021) (10)
- matUtils: Tools to Interpret and Manipulate Mutation Annotated Trees. (2021) (9)
- Improving communication for interdisciplinary teams working on storage of digital information in DNA (2018) (8)
- Modeling Structural Constraints on Protein Evolution via Side-Chain Conformational States (2019) (8)
- Short-range template switching in great ape genomes explored using pair hidden Markov models (2020) (7)
- ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments (2016) (7)
- Probabilistic Models for the Study of Protein Evolution (2019) (7)
- progenitors Transcriptional diversity during lineage commitment of human blood (2014) (5)
- Fewest variables coding method for multistate characters (1989) (5)
- BOSS-RUNS: a flexible and practical dynamic read sampling framework for nanopore sequencing (2020) (5)
- Avoiding ascertainment bias in the maximum likelihood inference of phylogenies based on truncated data (2017) (4)
- Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design (2022) (3)
- Modelling structural constraints on protein evolution via side-chain conformational states (2019) (3)
- The SARS-CoV-2 replication-transcription complex is a priority target for broad-spectrum pan-coronavirus drugs (2021) (2)
- A phylogenetic approach for weighting genetic sequences (2021) (2)
- Maximum likelihood pandemic-scale phylogenetics (2022) (2)
- [Evaluation and extension of Markov process models for the evolution of DNA]. (1994) (2)
- phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets (2022) (2)
- Phylogenetic Novelty Scores: a New Approach for Weighting Genetic Sequences (2020) (1)
- Chicken Toll-like Receptor 3 Recognizes Its Cognate Ligand When Ectopically 97 Expressed in Human Cells (2013) (1)
- All Your Base: a fast and accurate probabilistic approach to base calling (2012) (1)
- Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England (2021) (1)
- Ambiguity Coding Allows Accurate Inference of Evolutionary Parameters from Alignments in an Aggregated State-Space (2019) (1)
- Short template switch events in human evolution cause complex mutation patterns (2016) (1)
- Error-correcting properties of the SOLiD Exact Call Chemistry (2012) (1)
- Integrated evolutionary and structural analysis reveals xenobiotics and pathogens as the major drivers of mammalian adaptation (2019) (1)
- Prevalence , causes and significance of short-range template-switch mutations in humans and model organisms (0)
- SWAMPy: Simulating SARS-CoV-2 Wastewater Amplicon Metagenomes with Python (2022) (0)
- Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computional Biology 2004 (ISMB/ECCB 2004) (2004) (0)
- Genome analysis Determination and validation of principal gene products (2007) (0)
- Automated filtering of multiple sequence alignment worsens phylogenetic inference (2017) (0)
- insertions From The Cover : An algorithm for progressive multiple alignment of sequences with (2005) (0)
- The Performance of Transversion Based Distance Estimates (1996) (0)
- A phylogenetic approach for weighting genetic sequences (2021) (0)
- Maximum likelihood pandemic-scale phylogenetics. (2023) (0)
- Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England (2022) (0)
- 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 (2007) (0)
- Alignment and Evolutionary Analysis Phylogeny-Aware Gap Placement Prevents Errors in Sequence (2014) (0)
- 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 (2006) (0)
- A novel process of successive inter-strand template switches explains complex mutations and creates hair-pins (2016) (0)
- Information storage in DNA (2014) (0)
- A retroviral origin of vertebrate myelin (2022) (0)
- PASP — a whole-transcriptome poly(A) tail length determination assay for the Illumina platform (2016) (0)
- Music of the Spheres (2015) (0)
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