| Year |
Citation |
Score |
| 2023 |
Kapli P, Kotari I, Telford MJ, Goldman N, Yang Z. DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies. Systematic Biology. PMID 37366056 DOI: 10.1093/sysbio/syad036 |
0.727 |
|
| 2023 |
De Maio N, Kalaghatgi P, Turakhia Y, Corbett-Detig R, Minh BQ, Goldman N. Maximum likelihood pandemic-scale phylogenetics. Nature Genetics. PMID 37038003 DOI: 10.1038/s41588-023-01368-0 |
0.32 |
|
| 2023 |
Weilguny L, De Maio N, Munro R, Manser C, Birney E, Loose M, Goldman N. Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design. Nature Biotechnology. PMID 36593407 DOI: 10.1038/s41587-022-01580-z |
0.364 |
|
| 2022 |
De Maio N, Boulton W, Weilguny L, Walker CR, Turakhia Y, Corbett-Detig R, Goldman N. phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets. Plos Computational Biology. 18: e1010056. PMID 35486906 DOI: 10.1371/journal.pcbi.1010056 |
0.367 |
|
| 2022 |
De Maio N, Kalaghatgi P, Turakhia Y, Corbett-Detig R, Minh BQ, Goldman N. Maximum likelihood pandemic-scale phylogenetics. Biorxiv : the Preprint Server For Biology. PMID 35350209 DOI: 10.1101/2022.03.22.485312 |
0.312 |
|
| 2021 |
McBroome J, Thornlow B, Hinrichs AS, Kramer A, De Maio N, Goldman N, Haussler D, Corbett-Detig R, Turakhia Y. A daily-updated database and tools for comprehensive SARS-CoV-2 mutation-annotated trees. Molecular Biology and Evolution. PMID 34469548 DOI: 10.1093/molbev/msab264 |
0.329 |
|
| 2021 |
De Maio N, Alekseyenko AV, Coleman-Smith WJ, Pardi F, Suchard MA, Tamuri AU, Truszkowski J, Goldman N. A phylogenetic approach for weighting genetic sequences. Bmc Bioinformatics. 22: 285. PMID 34049487 DOI: 10.1186/s12859-021-04183-8 |
0.803 |
|
| 2021 |
De Maio N, Weilguny L, Walker CR, Turakhia Y, Corbett-Detig R, Goldman N. phastSim: efficient simulation of sequence evolution for pandemic-scale datasets. Biorxiv : the Preprint Server For Biology. PMID 33758852 DOI: 10.1101/2021.03.15.435416 |
0.364 |
|
| 2021 |
Hodcroft EB, De Maio N, Lanfear R, MacCannell DR, Minh BQ, Schmidt HA, Stamatakis A, Goldman N, Dessimoz C. Want to track pandemic variants faster? Fix the bioinformatics bottleneck. Nature. 591: 30-33. PMID 33649511 DOI: 10.1038/d41586-021-00525-x |
0.513 |
|
| 2020 |
Turakhia Y, De Maio N, Thornlow B, Gozashti L, Lanfear R, Walker CR, Hinrichs AS, Fernandes JD, Borges R, Slodkowicz G, Weilguny L, Haussler D, Goldman N, Corbett-Detig R. Stability of SARS-CoV-2 phylogenies. Plos Genetics. 16: e1009175. PMID 33206635 DOI: 10.1371/journal.pgen.1009175 |
0.833 |
|
| 2020 |
Weber CC, Perron U, Casey D, Yang Z, Goldman N. Ambiguity Coding Allows Accurate Inference of Evolutionary Parameters from Alignments in an Aggregated State-Space. Systematic Biology. PMID 32353118 DOI: 10.1093/Sysbio/Syaa036 |
0.724 |
|
| 2020 |
Slodkowicz G, Goldman N. 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. 117: 5977-5986. PMID 32123117 DOI: 10.1073/Pnas.1916786117 |
0.805 |
|
| 2019 |
Perron U, Kozlov AM, Stamatakis A, Goldman N, Moal IH. Modelling structural constraints on protein evolution via side-chain conformational states. Molecular Biology and Evolution. PMID 31114882 DOI: 10.1093/Molbev/Msz122 |
0.412 |
|
| 2018 |
Vialle RA, Tamuri AU, Goldman N. Alignment modulates ancestral sequence reconstruction accuracy. Molecular Biology and Evolution. PMID 29618097 DOI: 10.1093/Molbev/Msy055 |
0.791 |
|
| 2017 |
Klopfstein S, Massingham T, Goldman N. More on the Best Evolutionary Rate for Phylogenetic Analysis. Systematic Biology. PMID 28595363 DOI: 10.1093/Sysbio/Syx051 |
0.803 |
|
| 2017 |
Löytynoja A, Goldman N. Short template switch events explain mutation clusters in the human genome. Genome Research. PMID 28385709 DOI: 10.1101/Gr.214973.116 |
0.728 |
|
| 2017 |
Tan G, Muffato M, Ledergerber C, Herrero J, Goldman N, Gil M, Dessimoz C. Automated filtering of multiple sequence alignment worsens phylogenetic inference F1000research. 6. DOI: 10.7490/F1000Research.1115083.1 |
0.634 |
|
| 2016 |
Gori K, Suchan T, Alvarez N, Goldman N, Dessimoz C. Clustering genes of common evolutionary history. Molecular Biology and Evolution. PMID 26893301 DOI: 10.1093/Molbev/Msw038 |
0.78 |
|
| 2016 |
Schwarz RF, Tamuri AU, Kultys M, King J, Godwin J, Florescu AM, Schultz J, Goldman N. ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments. Nucleic Acids Research. PMID 26819408 DOI: 10.1093/Nar/Gkw022 |
0.815 |
|
| 2015 |
Truszkowski J, Goldman N. Maximum likelihood phylogenetic inference is consistent on multiple sequence alignments, with or without gaps. Systematic Biology. PMID 26615177 DOI: 10.1093/Sysbio/Syv089 |
0.801 |
|
| 2015 |
Tan G, Muffato M, Ledergerber C, Herrero J, Goldman N, Gil M, Dessimoz C. Current methods for automated filtering of multiple sequence alignments frequently worsen single-gene phylogenetic inference. Systematic Biology. PMID 26031838 DOI: 10.1093/Sysbio/Syv033 |
0.62 |
|
| 2015 |
Lowe R, Slodkowicz G, Goldman N, Rakyan VK. The human blood DNA methylome displays a highly distinctive profile compared with other somatic tissues. Epigenetics : Official Journal of the Dna Methylation Society. 10: 274-81. PMID 25634226 DOI: 10.1080/15592294.2014.1003744 |
0.767 |
|
| 2015 |
Tan G, Gil M, Löytynoja AP, Goldman N, Dessimoz C. Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks. Proceedings of the National Academy of Sciences of the United States of America. 112: E99-100. PMID 25564672 DOI: 10.1073/Pnas.1417526112 |
0.801 |
|
| 2014 |
Chen L, Kostadima M, Martens JH, Canu G, Garcia SP, Turro E, Downes K, Macaulay IC, Bielczyk-Maczynska E, Coe S, Farrow S, Poudel P, Burden F, Jansen SB, Astle WJ, ... ... Goldman N, et al. Transcriptional diversity during lineage commitment of human blood progenitors. Science (New York, N.Y.). 345: 1251033. PMID 25258084 DOI: 10.1126/Science.1251033 |
0.773 |
|
| 2014 |
Kultys M, Nicholas L, Schwarz R, Goldman N, King J. Sequence Bundles: a novel method for visualising, discovering and exploring sequence motifs. Bmc Proceedings. 8: S8. PMID 25237395 DOI: 10.1186/1753-6561-8-S2-S8 |
0.731 |
|
| 2014 |
Behjati S, Huch M, van Boxtel R, Karthaus W, Wedge DC, Tamuri AU, Martincorena I, Petljak M, Alexandrov LB, Gundem G, Tarpey PS, Roerink S, Blokker J, Maddison M, Mudie L, ... ... Goldman N, et al. Genome sequencing of normal cells reveals developmental lineages and mutational processes. Nature. 513: 422-5. PMID 25043003 DOI: 10.1038/Nature13448 |
0.746 |
|
| 2014 |
Parks SL, Goldman N. Maximum likelihood inference of small trees in the presence of long branches. Systematic Biology. 63: 798-811. PMID 24996414 DOI: 10.1093/Sysbio/Syu044 |
0.568 |
|
| 2014 |
Schwarz RF, Trinh A, Sipos B, Brenton JD, Goldman N, Markowetz F. Phylogenetic quantification of intra-tumour heterogeneity. Plos Computational Biology. 10: e1003535. PMID 24743184 DOI: 10.1371/Journal.Pcbi.1003535 |
0.757 |
|
| 2014 |
Tamuri AU, Goldman N, dos Reis M. A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data. Genetics. 197: 257-71. PMID 24532780 DOI: 10.1534/Genetics.114.162263 |
0.804 |
|
| 2014 |
Iantorno S, Gori K, Goldman N, Gil M, Dessimoz C. Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment. Methods in Molecular Biology (Clifton, N.J.). 1079: 59-73. PMID 24170395 DOI: 10.1007/978-1-62703-646-7_4 |
0.805 |
|
| 2013 |
de Beer TA, Laskowski RA, Parks SL, Sipos B, Goldman N, Thornton JM. Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset. Plos Computational Biology. 9: e1003382. PMID 24348229 DOI: 10.1371/Journal.Pcbi.1003382 |
0.743 |
|
| 2013 |
Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P. Systematic evaluation of spliced alignment programs for RNA-seq data. Nature Methods. 10: 1185-91. PMID 24185836 DOI: 10.1038/Nmeth.2722 |
0.587 |
|
| 2013 |
Cvejic A, Haer-Wigman L, Stephens JC, Kostadima M, Smethurst PA, Frontini M, van den Akker E, Bertone P, Bielczyk-Maczyńska E, Farrow S, Fehrmann RS, Gray A, de Haas M, Haver VG, Jordan G, ... ... Goldman N, et al. SMIM1 underlies the Vel blood group and influences red blood cell traits. Nature Genetics. 45: 542-5. PMID 23563608 DOI: 10.1038/Ng.2603 |
0.77 |
|
| 2013 |
Goldman N, Bertone P, Chen S, Dessimoz C, LeProust EM, Sipos B, Birney E. Towards practical, high-capacity, low-maintenance information storage in synthesized DNA. Nature. 494: 77-80. PMID 23354052 DOI: 10.1038/Nature11875 |
0.678 |
|
| 2012 |
Sipos B, Massingham T, Stütz AM, Goldman N. An improved protocol for sequencing of repetitive genomic regions and structural variations using mutagenesis and next generation sequencing. Plos One. 7: e43359. PMID 22912860 DOI: 10.1371/Journal.Pone.0043359 |
0.824 |
|
| 2012 |
Massingham T, Goldman N. Error-correcting properties of the SOLiD Exact Call Chemistry. Bmc Bioinformatics. 13: 145. PMID 22726842 DOI: 10.1186/1471-2105-13-145 |
0.811 |
|
| 2012 |
Löytynoja A, Vilella AJ, Goldman N. Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm. Bioinformatics (Oxford, England). 28: 1684-91. PMID 22531217 DOI: 10.1093/Bioinformatics/Bts198 |
0.77 |
|
| 2012 |
Zhai W, Nielsen R, Goldman N, Yang Z. Looking for Darwin in genomic sequences--validity and success of statistical methods. Molecular Biology and Evolution. 29: 2889-93. PMID 22490825 DOI: 10.1093/Molbev/Mss104 |
0.713 |
|
| 2012 |
Schroder K, Irvine KM, Taylor MS, Bokil NJ, Le Cao KA, Masterman KA, Labzin LI, Semple CA, Kapetanovic R, Fairbairn L, Akalin A, Faulkner GJ, Baillie JK, Gongora M, Daub CO, ... ... Goldman N, et al. Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages. Proceedings of the National Academy of Sciences of the United States of America. 109: E944-53. PMID 22451944 DOI: 10.1073/Pnas.1110156109 |
0.468 |
|
| 2012 |
Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, ... ... Goldman N, et al. Insights into hominid evolution from the gorilla genome sequence. Nature. 483: 169-75. PMID 22398555 DOI: 10.1038/Nature10842 |
0.644 |
|
| 2012 |
Massingham T, Goldman N. All Your Base: a fast and accurate probabilistic approach to base calling. Genome Biology. 13: R13. PMID 22377270 DOI: 10.1186/Gb-2012-13-2-R13 |
0.799 |
|
| 2012 |
Jordan G, Goldman N. The effects of alignment error and alignment filtering on the sitewise detection of positive selection. Molecular Biology and Evolution. 29: 1125-39. PMID 22049066 DOI: 10.1093/Molbev/Msr272 |
0.548 |
|
| 2012 |
Yang Z, Goldman N. Are big trees indeed easy? Trends in Ecology & Evolution. 12: 357. PMID 21238103 DOI: 10.1016/S0169-5347(97)83196-5 |
0.642 |
|
| 2011 |
Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, ... ... Goldman N, et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 478: 476-82. PMID 21993624 DOI: 10.1038/Nature10530 |
0.808 |
|
| 2011 |
Hess J, Goldman N. Addressing inter-gene heterogeneity in maximum likelihood phylogenomic analysis: yeasts revisited. Plos One. 6: e22783. PMID 21850235 DOI: 10.1371/Journal.Pone.0022783 |
0.629 |
|
| 2011 |
Kosiol C, Goldman N. Markovian and non-Markovian protein sequence evolution: aggregated Markov process models. Journal of Molecular Biology. 411: 910-23. PMID 21718704 DOI: 10.1016/J.Jmb.2011.06.005 |
0.733 |
|
| 2011 |
Sipos B, Massingham T, Jordan GE, Goldman N. PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment. Bmc Bioinformatics. 12: 104. PMID 21504561 DOI: 10.1186/1471-2105-12-104 |
0.796 |
|
| 2011 |
Washietl S, Findeiss S, Müller SA, Kalkhof S, von Bergen M, Hofacker IL, Stadler PF, Goldman N. RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. Rna (New York, N.Y.). 17: 578-94. PMID 21357752 DOI: 10.1261/Rna.2536111 |
0.431 |
|
| 2011 |
Lakner C, Holder MT, Goldman N, Naylor GJ. What's in a likelihood? Simple models of protein evolution and the contribution of structurally viable reconstructions to the likelihood. Systematic Biology. 60: 161-74. PMID 21233085 DOI: 10.1093/Sysbio/Syq088 |
0.467 |
|
| 2010 |
Löytynoja A, Goldman N. webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser. Bmc Bioinformatics. 11: 579. PMID 21110866 DOI: 10.1186/1471-2105-11-579 |
0.76 |
|
| 2009 |
Chor B, Horn D, Goldman N, Levy Y, Massingham T. Genomic DNA k-mer spectra: models and modalities. Genome Biology. 10: R108. PMID 19814784 DOI: 10.1186/Gb-2009-10-10-R108 |
0.8 |
|
| 2009 |
Yang Z, Nielsen R, Goldman N. In defense of statistical methods for detecting positive selection. Proceedings of the National Academy of Sciences of the United States of America. 106: E95; author reply E9. PMID 19805241 DOI: 10.1073/Pnas.0904550106 |
0.682 |
|
| 2009 |
Löytynoja A, Goldman N. Evolution. Uniting alignments and trees. Science (New York, N.Y.). 324: 1528-9. PMID 19541988 DOI: 10.1126/Science.1175949 |
0.743 |
|
| 2008 |
Taylor MS, Massingham T, Hayashizaki Y, Carninci P, Goldman N, Semple CA. Rapidly evolving human promoter regions. Nature Genetics. 40: 1262-3; author reply. PMID 18957975 DOI: 10.1038/Ng1108-1262 |
0.755 |
|
| 2008 |
Washietl S, Machné R, Goldman N. Evolutionary footprints of nucleosome positions in yeast. Trends in Genetics : Tig. 24: 583-7. PMID 18951646 DOI: 10.1016/J.Tig.2008.09.003 |
0.368 |
|
| 2008 |
Löytynoja A, Goldman N. A model of evolution and structure for multiple sequence alignment. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 363: 3913-9. PMID 18852103 DOI: 10.1098/Rstb.2008.0170 |
0.767 |
|
| 2008 |
Goldman N, Yang Z. Introduction. Statistical and computational challenges in molecular phylogenetics and evolution. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 363: 3889-92. PMID 18852095 DOI: 10.1098/Rstb.2008.0182 |
0.668 |
|
| 2008 |
Löytynoja A, Goldman N. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science (New York, N.Y.). 320: 1632-5. PMID 18566285 DOI: 10.1126/Science.1158395 |
0.759 |
|
| 2008 |
Tress ML, Wesselink JJ, Frankish A, López G, Goldman N, Löytynoja A, Massingham T, Pardi F, Whelan S, Harrow J, Valencia A. Determination and validation of principal gene products. Bioinformatics (Oxford, England). 24: 11-7. PMID 18006548 DOI: 10.1093/Bioinformatics/Btm547 |
0.776 |
|
| 2007 |
Massingham T, Goldman N. Statistics of the log-det estimator. Molecular Biology and Evolution. 24: 2277-85. PMID 17703055 DOI: 10.1093/Molbev/Msm160 |
0.785 |
|
| 2007 |
Geuten K, Massingham T, Darius P, Smets E, Goldman N. Experimental design criteria in phylogenetics: where to add taxa. Systematic Biology. 56: 609-22. PMID 17654365 DOI: 10.1080/10635150701499563 |
0.787 |
|
| 2007 |
Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Goldman N, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874 |
0.795 |
|
| 2007 |
Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, ... ... Goldman N, et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research. 17: 760-74. PMID 17567995 DOI: 10.1101/Gr.6034307 |
0.82 |
|
| 2007 |
Pardi F, Goldman N. Resource-aware taxon selection for maximizing phylogenetic diversity. Systematic Biology. 56: 431-44. PMID 17558965 DOI: 10.1080/10635150701411279 |
0.703 |
|
| 2007 |
Kosiol C, Holmes I, Goldman N. An empirical codon model for protein sequence evolution. Molecular Biology and Evolution. 24: 1464-79. PMID 17400572 DOI: 10.1093/Molbev/Msm064 |
0.738 |
|
| 2007 |
Bofkin L, Goldman N. Variation in evolutionary processes at different codon positions. Molecular Biology and Evolution. 24: 513-21. PMID 17119011 DOI: 10.1093/Molbev/Msl178 |
0.828 |
|
| 2006 |
Klosterman PS, Uzilov AV, Bendaña YR, Bradley RK, Chao S, Kosiol C, Goldman N, Holmes I. XRate: a fast prototyping, training and annotation tool for phylo-grammars. Bmc Bioinformatics. 7: 428. PMID 17018148 DOI: 10.1186/1471-2105-7-428 |
0.735 |
|
| 2006 |
Whelan S, de Bakker PI, Quevillon E, Rodriguez N, Goldman N. PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees. Nucleic Acids Research. 34: D327-31. PMID 16381879 DOI: 10.1093/Nar/Gkj087 |
0.662 |
|
| 2005 |
Pardi F, Goldman N. Species choice for comparative genomics: being greedy works. Plos Genetics. 1: e71. PMID 16327885 DOI: 10.1371/Journal.Pgen.0010071 |
0.747 |
|
| 2005 |
Löytynoja A, Goldman N. An algorithm for progressive multiple alignment of sequences with insertions. Proceedings of the National Academy of Sciences of the United States of America. 102: 10557-62. PMID 16000407 DOI: 10.1073/Pnas.0409137102 |
0.709 |
|
| 2005 |
Massingham T, Goldman N. Detecting amino acid sites under positive selection and purifying selection. Genetics. 169: 1753-62. PMID 15654091 DOI: 10.1534/Genetics.104.032144 |
0.8 |
|
| 2005 |
Kosiol C, Goldman N. Different versions of the Dayhoff rate matrix. Molecular Biology and Evolution. 22: 193-9. PMID 15483331 DOI: 10.1093/Molbev/Msi005 |
0.703 |
|
| 2005 |
Pardi F, Goldman N. Species choice for comparative genomics: Being greedy works Plos Genetics. 1: 0672-0675. DOI: 10.1371 /journal.pgen.0010071 |
0.688 |
|
| 2004 |
Wong WS, Yang Z, Goldman N, Nielsen R. Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics. 168: 1041-51. PMID 15514074 DOI: 10.1534/Genetics.104.031153 |
0.709 |
|
| 2004 |
Whelan S, Goldman N. Estimating the frequency of events that cause multiple-nucleotide changes. Genetics. 167: 2027-43. PMID 15342538 DOI: 10.1534/Genetics.103.023226 |
0.649 |
|
| 2004 |
Kosiol C, Goldman N, Buttimore NH. A new criterion and method for amino acid classification. Journal of Theoretical Biology. 228: 97-106. PMID 15064085 DOI: 10.1016/J.Jtbi.2003.12.010 |
0.725 |
|
| 2004 |
Liò P, Goldman N. Phylogenomics and bioinformatics of SARS-CoV. Trends in Microbiology. 12: 106-11. PMID 15058277 DOI: 10.1016/J.Tim.2004.01.005 |
0.572 |
|
| 2003 |
Whelan S, de Bakker PI, Goldman N. Pandit: a database of protein and associated nucleotide domains with inferred trees. Bioinformatics (Oxford, England). 19: 1556-63. PMID 12912837 DOI: 10.1093/Bioinformatics/Btg188 |
0.689 |
|
| 2003 |
Robinson DM, Jones DT, Kishino H, Goldman N, Thorne JL. Protein evolution with dependence among codons due to tertiary structure. Molecular Biology and Evolution. 20: 1692-704. PMID 12885968 DOI: 10.1093/Molbev/Msg184 |
0.452 |
|
| 2003 |
Hardison RC, Roskin KM, Yang S, Diekhans M, Kent WJ, Weber R, Elnitski L, Li J, O'Connor M, Kolbe D, Schwartz S, Furey TS, Whelan S, Goldman N, Smit A, et al. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Research. 13: 13-26. PMID 12529302 DOI: 10.1101/Gr.844103 |
0.63 |
|
| 2002 |
Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, ... ... Goldman N, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420: 520-62. PMID 12466850 DOI: 10.1038/Nature01262 |
0.748 |
|
| 2002 |
Goldman N, Whelan S. A novel use of equilibrium frequencies in models of sequence evolution. Molecular Biology and Evolution. 19: 1821-31. PMID 12411592 DOI: 10.1093/Oxfordjournals.Molbev.A004007 |
0.652 |
|
| 2002 |
Liò P, Goldman N. Modeling mitochondrial protein evolution using structural information. Journal of Molecular Evolution. 54: 519-29. PMID 11956690 DOI: 10.1007/S00239001-0052-7 |
0.545 |
|
| 2001 |
Whelan S, Liò P, Goldman N. Molecular phylogenetics: state-of-the-art methods for looking into the past. Trends in Genetics : Tig. 17: 262-72. PMID 11335036 DOI: 10.1016/S0168-9525(01)02272-7 |
0.725 |
|
| 2001 |
Whelan S, Goldman N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Molecular Biology and Evolution. 18: 691-9. PMID 11319253 DOI: 10.1093/Oxfordjournals.Molbev.A003851 |
0.681 |
|
| 2000 |
Massingham T, Goldman N. EDIBLE: experimental design and information calculations in phylogenetics. Bioinformatics (Oxford, England). 16: 294-5. PMID 10869025 DOI: 10.1093/Bioinformatics/16.3.294 |
0.788 |
|
| 2000 |
Goldman N, Whelan S. Statistical tests of gamma-distributed rate heterogeneity in models of sequence evolution in phylogenetics. Molecular Biology and Evolution. 17: 975-8. PMID 10833204 DOI: 10.1093/Oxfordjournals.Molbev.A026378 |
0.625 |
|
| 2000 |
Hagelberg E, Goldman N, Lio P, Whelan S, Schiefenhovel W, Clegg JB, Bowden DK. Evidence for mitochondrial DNA recombination in a human population of island Melanesia: Correction Proceedings of the Royal Society B: Biological Sciences. 267: 1595-1596. DOI: 10.1098/Rspb.2000.1183 |
0.666 |
|
| 1999 |
Liò P, Goldman N. Using protein structural information in evolutionary inference: transmembrane proteins. Molecular Biology and Evolution. 16: 1696-710. PMID 10605112 DOI: 10.1093/Oxfordjournals.Molbev.A026083 |
0.644 |
|
| 1999 |
Hagelberg E, Goldman N, Lió P, Whelan S, Schiefenhövel W, Clegg JB, Bowden DK. Evidence for mitochondrial DNA recombination in a human population of island Melanesia. Proceedings. Biological Sciences / the Royal Society. 266: 485-92. PMID 10189712 DOI: 10.1098/Rspb.1999.0663 |
0.678 |
|
| 1999 |
Pollock DD, Taylor WR, Goldman N. Coevolving protein residues: maximum likelihood identification and relationship to structure. Journal of Molecular Biology. 287: 187-98. PMID 10074416 DOI: 10.1006/Jmbi.1998.2601 |
0.373 |
|
| 1999 |
Whelan S, Goldman N. Distributions of statistics used for the comparison of models of sequence evolution in phylogenetics Molecular Biology and Evolution. 16: 1292-1299. DOI: 10.1093/Oxfordjournals.Molbev.A026219 |
0.65 |
|
| 1998 |
Liò P, Goldman N. Models of molecular evolution and phylogeny. Genome Research. 8: 1233-44. PMID 9872979 DOI: 10.1101/Gr.8.12.1233 |
0.589 |
|
| 1998 |
Liò P, Goldman N, Thorne JL, Jones3 DT. PASSML: combining evolutionary inference and protein secondary structure prediction. Bioinformatics (Oxford, England). 14: 726-33. PMID 9789098 DOI: 10.1093/Bioinformatics/14.8.726 |
0.609 |
|
| 1998 |
Goldman N. Phylogenetic information and experimental design in molecular systematics Proceedings of the Royal Society B: Biological Sciences. 265: 1779-1786. PMID 9787470 DOI: 10.1098/Rspb.1998.0502 |
0.479 |
|
| 1998 |
Liò P, Goldman N. Review: Models of molecular evolution and phylogeny Genome Research. 8: 1233-1244. DOI: 10.1101/gr.8.12.1233 |
0.435 |
|
| 1998 |
Goldman N. Effects of sequence alignment procedures on estimates of phylogeny Bioessays. 20: 287-290. DOI: 10.1002/(Sici)1521-1878(199804)20:4<287::Aid-Bies4>3.0.Co;2-N |
0.393 |
|
| 1996 |
Goldman N, Thorne JL, Jones DT. Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses. Journal of Molecular Biology. 263: 196-208. PMID 8913301 DOI: 10.1006/Jmbi.1996.0569 |
0.456 |
|
| 1996 |
Thorne JL, Goldman N, Jones DT. Combining protein evolution and secondary structure. Molecular Biology and Evolution. 13: 666-73. PMID 8676741 DOI: 10.1093/Oxfordjournals.Molbev.A025627 |
0.433 |
|
| 1995 |
Yang Z, Goldman N, Friday A. Maximum likelihood trees from DNA sequences: A peculiar statistical estimation problem Systematic Biology. 44: 384-399. DOI: 10.1093/Sysbio/44.3.384 |
0.773 |
|
| 1994 |
Yang Z, Goldman N, Friday A. Comparison of models for nucleotide substitution used in maximum- likelihood phylogenetic estimation Molecular Biology and Evolution. 11: 316-324. PMID 8170371 DOI: 10.1093/Oxfordjournals.Molbev.A040112 |
0.796 |
|
| 1994 |
Goldman N, Yang Z. A codon-based model of nucleotide substitution for protein-coding DNA sequences Molecular Biology and Evolution. 11: 725-736. PMID 7968486 DOI: 10.1093/Oxfordjournals.Molbev.A040153 |
0.733 |
|
| 1994 |
Goldman N. Variance to Mean Ratio, R(t), for Poisson Processes on Phylogenetic Trees Molecular Phylogenetics and Evolution. 3: 230-239. PMID 7820287 DOI: 10.1006/Mpev.1994.1025 |
0.342 |
|
| 1994 |
Gardner MJ, Goldman N, Barnett P, Moore PW, Rangachari K, Strath M, Whyte A, Williamson DH, Wilson RJ. Phylogenetic analysis of the rpoB gene from the plastid-like DNA of Plasmodium falciparum. Molecular and Biochemical Parasitology. 66: 221-31. PMID 7808472 DOI: 10.1016/0166-6851(94)90149-X |
0.374 |
|
| 1993 |
Goldman N. Nucleotide, dinucleotide and trinucleotide frequencies explain patterns observed in chaos game representations of DNA sequences Nucleic Acids Research. 21: 2487-2491. PMID 8506142 DOI: 10.1093/Nar/21.10.2487 |
0.396 |
|
| 1993 |
Goldman N. Statistical tests of models of DNA substitution Journal of Molecular Evolution. 36: 182-198. PMID 7679448 DOI: 10.1007/Bf00166252 |
0.366 |
|
| 1993 |
Goldman N. Simple diagnostic statistical tests of models for DNA substitution Journal of Molecular Evolution. 37: 661. DOI: 10.1007/Bf00182751 |
0.459 |
|
| 1990 |
Goldman N. Maximum likelihood inference of phylogenetic trees, with special reference to a poisson process model of dna substitution and to parsimony analyses Systematic Zoology. 39: 345-361. DOI: 10.2307/2992355 |
0.369 |
|
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