The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families
暂无分享,去创建一个
Benjamin J. Raphael | Susan S. Taylor | David A W Soergel | A. Godzik | A. Halpern | G. Sutton | V. Bafna | K. Remington | M. Frazier | R. Strausberg | J. Venter | S. Yooseph | S. Brenner | R. Friedman | J. Eisen | P. Cieplak | J. Dixon | J. Chandonia | Weizhong Li | L. Jaroszewski | D. Rusch | G. Manning | M. Joachimiak | K. Natarajan | K. Heidelberg | S. Williamson | ChristopherA. Miller | Huiying Li | S. T. Mashiyama | Christopher J van Belle | Yufeng Zhai | Shaun Lee | D. Eisenberg | marcin pawel joachimiak | marcin p. joachimiak | Shibu Yooseph
[1] E. Birney,et al. Pfam: the protein families database , 2013, Nucleic Acids Res..
[2] Ncbi. National Center for Biotechnology Information , 2008 .
[3] A. Oskooi. Molecular Evolution and Phylogenetics , 2008 .
[4] A. Halpern,et al. The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific , 2007, PLoS biology.
[5] Gerard Manning,et al. Structural and Functional Diversity of the Microbial Kinome , 2007, PLoS biology.
[6] Maureen L. Coleman,et al. Genomic Islands and the Ecology and Evolution of Prochlorococcus , 2006, Science.
[7] E. Delong,et al. Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior , 2006, Science.
[8] Steven E Brenner,et al. The Impact of Structural Genomics: Expectations and Outcomes , 2005, Science.
[9] Korine S. E. Ung,et al. Evidence of a Large Novel Gene Pool Associated with Prokaryotic Genomic Islands , 2005, PLoS genetics.
[10] Edward M. Rubin,et al. Metagenomics: DNA sequencing of environmental samples , 2005, Nature Reviews Genetics.
[11] M. Noordewier,et al. Genome Streamlining in a Cosmopolitan Oceanic Bacterium , 2005, Science.
[12] D. Field,et al. Orphans as taxonomically restricted and ecologically important genes. , 2005, Microbiology.
[13] S. Brenner,et al. Update on the Pfam5000 Strategy for Selection of Structural Genomics Targets , 2005, 2005 IEEE Engineering in Medicine and Biology 27th Annual Conference.
[14] J. Paul,et al. Marine phage genomics: what have we learned? , 2005, Current opinion in biotechnology.
[15] D. Eisenberg,et al. Crystal structure of a RuBisCO-like protein from the green sulfur bacterium Chlorobium tepidum. , 2005, Structure.
[16] Maureen L. Coleman,et al. Three Prochlorococcus Cyanophage Genomes: Signature Features and Ecological Interpretations , 2005, PLoS biology.
[17] L. Nováková,et al. Characterization of a eukaryotic type serine/threonine protein kinase and protein phosphatase of Streptococcus pneumoniae and identification of kinase substrates , 2005, The FEBS journal.
[18] G. Prendergast,et al. Inhibition of indoleamine 2,3-dioxygenase, an immunoregulatory target of the cancer suppression gene Bin1, potentiates cancer chemotherapy , 2005, Nature Medicine.
[19] Christian von Mering,et al. STRING: known and predicted protein–protein associations, integrated and transferred across organisms , 2004, Nucleic Acids Res..
[20] Cathy H. Wu,et al. InterPro, progress and status in 2005 , 2004, Nucleic Acids Res..
[21] Sébastien Carrère,et al. The ProDom database of protein domain families: more emphasis on 3D , 2004, Nucleic Acids Res..
[22] S. Tringe,et al. Comparative Metagenomics of Microbial Communities , 2004, Science.
[23] S. Brenner,et al. Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches , 2004, Proteins.
[24] R. Edwards,et al. Viral metagenomics , 2005, Nature Reviews Microbiology.
[25] S. Heaphy,et al. Analysis of the Virus Population Present in Equine Faeces Indicates the Presence of Hundreds of Uncharacterized Virus Genomes , 2005, Virus Genes.
[26] Thomas Mailund,et al. QuickJoin - fast neighbour-joining tree reconstruction , 2004, Bioinform..
[27] D. Munn,et al. Ido expression by dendritic cells: tolerance and tryptophan catabolism , 2004, Nature Reviews Immunology.
[28] L. Adorini. Faculty Opinions recommendation of Murine plasmacytoid dendritic cells initiate the immunosuppressive pathway of tryptophan catabolism in response to CD200 receptor engagement. , 2004 .
[29] Daniel Rokhsar,et al. Reverse Methanogenesis: Testing the Hypothesis with Environmental Genomics , 2004, Science.
[30] Andrew C. Tolonen,et al. Transfer of photosynthesis genes to and from Prochlorococcus viruses. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[31] E. Raz,et al. Inhibition of experimental asthma by indoleamine 2,3-dioxygenase. , 2004, The Journal of clinical investigation.
[32] H. Ochman,et al. Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli. , 2004, Genome research.
[33] Simon C. Potter,et al. An overview of Ensembl. , 2004, Genome research.
[34] Heribert Hirt,et al. Plant PP2C phosphatases: emerging functions in stress signaling. , 2004, Trends in plant science.
[35] Matteo Pellegrini,et al. Prolinks: a database of protein functional linkages derived from coevolution , 2004, Genome Biology.
[36] O. White,et al. Environmental Genome Shotgun Sequencing of the Sargasso Sea , 2004, Science.
[37] P. Salamon,et al. Diversity and population structure of a near–shore marine–sediment viral community , 2004, Proceedings of the Royal Society of London. Series B: Biological Sciences.
[38] J. Banfield,et al. Community structure and metabolism through reconstruction of microbial genomes from the environment , 2004, Nature.
[39] Robert C. Edgar,et al. MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.
[40] Ke Fan,et al. PROTEINS: Structure, Function, and Bioinformatics 54:491–499 (2004) The Number of Protein Folds and Their Distribution Over Families in Nature , 2022 .
[41] A. Barabasi,et al. Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.
[42] Julio Collado-Vides,et al. RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12 , 2004, Nucleic Acids Res..
[43] Damian Smedley,et al. Ensembl 2004 , 2004, Nucleic Acids Res..
[44] Cathy H. Wu,et al. UniProt: the Universal Protein knowledgebase , 2004, Nucleic Acids Res..
[45] A. Tyagi,et al. Phosphoprotein phosphatase of Mycobacterium tuberculosis dephosphorylates serine-threonine kinases PknA and PknB. , 2003, Biochemical and biophysical research communications.
[46] P. Salamon,et al. Metagenomic Analyses of an Uncultured Viral Community from Human Feces , 2003, Journal of bacteriology.
[47] N. Ogasawara,et al. A Functional Link Between RuBisCO-like Protein of Bacillus and Photosynthetic RuBisCO , 2003, Science.
[48] O. Gascuel,et al. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.
[49] S. Cole,et al. PknB kinase activity is regulated by phosphorylation in two Thr residues and dephosphorylation by PstP, the cognate phospho‐Ser/Thr phosphatase, in Mycobacterium tuberculosis , 2003, Molecular microbiology.
[50] D. Eisenberg,et al. Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach , 2003, Genome Biology.
[51] J. Denu,et al. Probing the Function of Conserved Residues in the Serine/Threonine Phosphatase PP2Cᆠ, 2003 .
[52] Carole A. Goble,et al. Investigating Semantic Similarity Measures Across the Gene Ontology: The Relationship Between Sequence and Annotation , 2003, Bioinform..
[53] Shlomo Havlin,et al. Scaling law in sizes of protein sequence families: From super‐families to orphan genes , 2003, Proteins.
[54] H. Hirt,et al. Stress-induced Protein Phosphatase 2C Is a Negative Regulator of a Mitogen-activated Protein Kinase* , 2003, Journal of Biological Chemistry.
[55] L. Holm,et al. Exhaustive enumeration of protein domain families. , 2003, Journal of molecular biology.
[56] W. Jacobs,et al. Origins of Highly Mosaic Mycobacteriophage Genomes , 2003, Cell.
[57] Yasufumi Yamamoto,et al. Comparison of the sequences of Turbo and Sulculus indoleamine dioxygenase-like myoglobin genes. , 2003, Gene.
[58] J. Haber,et al. PP2C phosphatases Ptc2 and Ptc3 are required for DNA checkpoint inactivation after a double-strand break. , 2003, Molecular cell.
[59] Victor de Lorenzo,et al. Myriads of protein families, and still counting , 2003, Genome Biology.
[60] Robert S. Ledley,et al. The Protein Information Resource , 2003, Nucleic Acids Res..
[61] Owen White,et al. The TIGRFAMs database of protein families , 2003, Nucleic Acids Res..
[62] J. Denu,et al. Probing the function of conserved residues in the serine/threonine phosphatase PP2Calpha. , 2003, Biochemistry.
[63] Zukang Feng,et al. The Protein Data Bank and structural genomics , 2003, Nucleic Acids Res..
[64] Maria Jesus Martin,et al. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 , 2003, Nucleic Acids Res..
[65] Vincent Lombard,et al. The EMBL Nucleotide Sequence Database: major new developments , 2003, Nucleic Acids Res..
[66] Hideaki Sugawara,et al. DNA Data Bank of Japan (DDBJ) in XML , 2003, Nucleic Acids Res..
[67] Ori Sasson,et al. ProtoNet: hierarchical classification of the protein space , 2003, Nucleic Acids Res..
[68] E. Myers,et al. Finishing a whole-genome shotgun: Release 3 of the Drosophila melanogaster euchromatic genome sequence , 2002, Genome Biology.
[69] Marcin P Joachimiak,et al. JEvTrace: refinement and variations of the evolutionary trace in JAVA , 2002, Genome Biology.
[70] Alex Bateman,et al. QuickTree: building huge Neighbour-Joining trees of protein sequences , 2002, Bioinform..
[71] B. Andresen,et al. Genomic analysis of uncultured marine viral communities , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[72] Alexander Schliep,et al. ProClust: improved clustering of protein sequences with an extended graph-based approach , 2002, ECCB.
[73] H. Takami,et al. Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments. , 2002, Nucleic acids research.
[74] Robert D. Finn,et al. The PASTA domain: a β-lactam-binding domain , 2002 .
[75] Howard Ochman,et al. Distinguishing the ORFs from the ELFs: short bacterial genes and the annotation of genomes. , 2002, Trends in genetics : TIG.
[76] Ingeborg Holt,et al. The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[77] Burkhard Rost,et al. Did evolution leap to create the protein universe? , 2002, Current opinion in structural biology.
[78] D. Juretic,et al. Basic Charge Clusters and Predictions of Membrane Protein Topology , 2002, J. Chem. Inf. Comput. Sci..
[79] M. Vidal,et al. Structural genomics: A pipeline for providing structures for the biologist , 2002, Protein science : a publication of the Protein Society.
[80] Martin Vingron,et al. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing , 2002, Bioinform..
[81] Adam Godzik,et al. Tolerating some redundancy significantly speeds up clustering of large protein databases , 2002, Bioinform..
[82] Alex Bateman,et al. The PASTA domain: a beta-lactam-binding domain. , 2002, Trends in biochemical sciences.
[83] John Moult,et al. A unifold, mesofold, and superfold model of protein fold use , 2002, Proteins.
[84] Wen-Hsiung Li,et al. The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study. , 2002, Genome research.
[85] Gaetano T. Montelione,et al. Structural genomics: An approach to the protein folding problem , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[86] M. Gerstein,et al. Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model. , 2001, Journal of molecular biology.
[87] A. Sali,et al. Protein Structure Prediction and Structural Genomics , 2001, Science.
[88] S. Brenner. A tour of structural genomics , 2001, Nature Reviews Genetics.
[89] A Bairoch,et al. SWISS-PROT: connecting biomolecular knowledge via a protein database. , 2001, Current issues in molecular biology.
[90] P. Kennelly,et al. Protein phosphatases--a phylogenetic perspective. , 2001, Chemical reviews.
[91] J. Bujnicki,et al. Identification of a PD-(D/E)XK-like domain with a novel configuration of the endonuclease active site in the methyl-directed restriction enzyme Mrr and its homologs. , 2001, Gene.
[92] Annabel E. Todd,et al. Evolution of function in protein superfamilies, from a structural perspective. , 2001, Journal of molecular biology.
[93] F. Tabita,et al. A ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO)-like protein from Chlorobium tepidum that is involved with sulfur metabolism and the response to oxidative stress , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[94] Adam Godzik,et al. Clustering of highly homologous sequences to reduce the size of large protein databases , 2001, Bioinform..
[95] A. Krogh,et al. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.
[96] Irene Ota,et al. Ptc1, a Type 2C Ser/Thr Phosphatase, Inactivates the HOG Pathway by Dephosphorylating the Mitogen-Activated Protein Kinase Hog1 , 2001, Molecular and Cellular Biology.
[97] Fan Yang,et al. TIGRFAMs: a protein family resource for the functional identification of proteins , 2001, Nucleic Acids Res..
[98] P. Setlow. Resistance of spores of Bacillus species to ultraviolet light , 2001, Environmental and molecular mutagenesis.
[99] A. Godzik,et al. Comparison of sequence profiles. Strategies for structural predictions using sequence information , 2008, Protein science : a publication of the Protein Society.
[100] S. Séror,et al. Characterization of PrpC from Bacillus subtilis, a Member of the PPM Phosphatase Family , 2000, Journal of bacteriology.
[101] C. DeLisi,et al. Predictions of gene family distributions in microbial genomes: evolution by gene duplication and modification. , 2000, Physical review letters.
[102] G. Sancar,et al. Enzymatic photoreactivation: 50 years and counting. , 2000, Mutation research.
[103] T L Blundell,et al. Structural genomics: an overview. , 2000, Progress in biophysics and molecular biology.
[104] Michael Y. Galperin,et al. Who's your neighbor? New computational approaches for functional genomics , 2000, Nature Biotechnology.
[105] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[106] N. Goldman,et al. Codon-substitution models for heterogeneous selection pressure at amino acid sites. , 2000, Genetics.
[107] D. Eisenberg,et al. Structure-function relationships of glutamine synthetases. , 2000, Biochimica et biophysica acta.
[108] Eugene W. Myers,et al. A whole-genome assembly of Drosophila. , 2000, Science.
[109] John Quackenbush,et al. The TIGR Gene Indices: reconstruction and representation of expressed gene sequences , 2000, Nucleic Acids Res..
[110] A. Halpern,et al. Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction. , 2000, Molecular biology and evolution.
[111] R. Apweiler. Protein sequence databases. , 2000, Advances in protein chemistry.
[112] Michael Y. Galperin,et al. The COG database: a tool for genome-scale analysis of protein functions and evolution , 2000, Nucleic Acids Res..
[113] Stephen K Burley,et al. Structural genomics , 1999, Current Biology.
[114] Frances M. G. Pearl,et al. Protein folds, functions and evolution. , 1999, Journal of molecular biology.
[115] Albert,et al. Emergence of scaling in random networks , 1999, Science.
[116] David S. Eisenberg,et al. Finding families for genomic ORFans , 1999, Bioinform..
[117] Mutsuhiro Takekawa,et al. Protein phosphatase 2Cα inhibits the human stress‐responsive p38 and JNK MAPK pathways , 1998, The EMBO journal.
[118] Sean R. Eddy,et al. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids , 1998 .
[119] M. Huynen,et al. The frequency distribution of gene family sizes in complete genomes. , 1998, Molecular biology and evolution.
[120] D. Lilley,et al. DNA Repair , 1998, Nucleic Acids and Molecular Biology.
[121] Sean R. Eddy,et al. Profile hidden Markov models , 1998, Bioinform..
[122] Sean R. Eddy,et al. Pfam: multiple sequence alignments and HMM-profiles of protein domains , 1998, Nucleic Acids Res..
[123] Jérôme Gouzy,et al. The ProDom database of protein domain families , 1998, Nucleic Acids Res..
[124] David L. Wheeler,et al. GenBank , 2015, Nucleic Acids Res..
[125] Adam Eyre-Walker,et al. Molecular Evolution by Wen-Hsiung Li. Published by Sinauer Associates, Sunderland, MA, USA. ISBN: 0-87893-463-4 (cloth). , 1997 .
[126] Ziheng Yang,et al. PAML: a program package for phylogenetic analysis by maximum likelihood , 1997, Comput. Appl. Biosci..
[127] Thomas L. Madden,et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.
[128] David C. Jones,et al. CATH--a hierarchic classification of protein domain structures. , 1997, Structure.
[129] D. Barford,et al. Crystal structure of the protein serine/threonine phosphatase 2C at 2.0 A resolution. , 1996, The EMBO journal.
[130] P Bork,et al. The protein phosphatase 2C (PP2C) superfamily: Detection of bacterial homologues , 1996, Protein science : a publication of the Protein Society.
[131] R. Lloyd,et al. Purification and Cloning of Micrococcus luteus Ultraviolet Endonuclease, an N-Glycosylase/Abasic Lyase That Proceeds via an Imino Enzyme-DNA Intermediate (*) , 1995, The Journal of Biological Chemistry.
[132] A G Murzin,et al. SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.
[133] T. Hunter,et al. Protein kinases and phosphatases: The Yin and Yang of protein phosphorylation and signaling , 1995, Cell.
[134] J. Thompson,et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.
[135] C. Smith,et al. A new ATP-independent DNA endonuclease from Schizosaccharomyces pombe that recognizes cyclobutane pyrimidine dimers and 6-4 photoproducts. , 1994, Nucleic acids research.
[136] H. Nakamura,et al. Crystal Structure of T4 Endonuclease V: An Excision Repair Enzyme for a Pyrimidine Dimer , 1994, Annals of the New York Academy of Sciences.
[137] D. R. Benson,et al. Close linkage of genes encoding glutamine synthetases I and II in Frankia alni CpI1 , 1993, Journal of bacteriology.
[138] Y Tateno,et al. Evolution of the glutamine synthetase gene, one of the oldest existing and functioning genes. , 1993, Proceedings of the National Academy of Sciences of the United States of America.
[139] S. Henikoff,et al. Amino acid substitution matrices from protein blocks. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[140] D. Labie,et al. Molecular Evolution , 1991, Nature.
[141] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[142] B. K. Chelm,et al. Apparent eukaryotic origin of glutamine synthetase II from the bacterium Bradyrhizobium japonicum , 1986, Nature.
[143] David Eisenberg,et al. Novel subunit—subunit interactions in the structure of glutamine synthetase , 1986, Nature.
[144] S. Fisher,et al. Bacillus subtilis glutamine synthetase mutants pleiotropically altered in glucose catabolite repression , 1984, Journal of bacteriology.
[145] R. Ellis. The most abundant protein in the world , 1979 .
[146] E. Stadtman,et al. Bacillus subtilis glutamine synthetase. Purification and physical characterization. , 1970, The Journal of biological chemistry.
[147] E. Stadtman,et al. Regulation of glutamine synthetase. XII. Electron microscopy of the enzyme from Escherichia coli. , 1968, Biochemistry.
[148] Lvek,et al. Evolution of protein structures and functions , 2022 .