Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

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1. Genome Sequence of the Radioresistant Bacterium Deinococcus radiodurans R1
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2. Mycobiome diversity: high-throughput sequencing and identification of fungi
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3. An Introduction to Sequence Similarity (“Homology”) Searching
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4. SCOP: a Structural Classification of Proteins database
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5. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract
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6. Composition and energy harvesting capacity of the gut microbiota: relationship to diet, obesity and time in mouse models
   Eileen F. Murphy, Paul D. Cotter, S Healy, Tatiana Milena Marques, Órla O’Sullivan, Fiona Fouhy, Siobhan F. Clarke, Paul William O’Toole, Eamonn M.M. Quigley, Catherine Stanton et al. · 2010 · Gut
7. Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information
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8. Whole-genome sequencing of multiple Arabidopsis thaliana populations
   Jun Cao, Korbinian Schneeberger, Stephan Ossowski, Torsten Günther, Sebastian Bender, Joffrey Fitz, Daniel Koenig, Christa Lanz, Oliver Stegle, Christoph Lippert et al. · 2011 · Nature Genetics
9. Regulation of microbial populations by coral surface mucus and mucus-associated bacteria
   KB Ritchie · 2006 · Marine Ecology Progress Series
10. Data growth and its impact on the SCOP database: new developments
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11. THE SPECTRUM KERNEL: A STRING KERNEL FOR SVM PROTEIN CLASSIFICATION
    Christina S. Leslie, Eleazar Eskin, William Stafford Noble · 2001 · Pacific Symposium on Biocomputing (PSB)
12. Mutations in a novel gene lead to kidney tumors, lung wall defects, and benign tumors of the hair follicle in patients with the Birt-Hogg-Dubé syndrome
    Michael L. Nickerson, Michelle B. Warren, Jorge R. Toro, Vera Y. Matrosova, Gladys M. Glenn, Maria L Chanco Turner, Paul H. Duray, Maria J. Merino, Peter L. Choyke, Christian P. Pavlovich et al. · 2002 · Cancer Cell
13. LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA
    Brudno, Michael, Do, Chuong B., Cooper, Gregory M., Kim, Michael F., Davydov, Eugene, Program, NISC Comparative Sequencing, Green, Eric D., Sidow, Arend, Batzoglou, Serafim · 2003 · Genome Research
14. The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics
    Lincoln David Stein, Zhirong Bao, Darin Blasiar, Thomas Blumenthal, Michael R. Brent, Nansheng Chen, Asif Chinwalla, Laura Clarke, Chris M. Clee, Avril Coghlan et al. · 2003 · PLoS Biology
15. Protein Phylogenetic Analysis of Ca2+/cation Antiporters and Insights into their Evolution in Plants
    Laura R. Emery, Simon Whelan, Kendal D. Hirschi, Jon K. Pittman · 2012 · Frontiers in Plant Science
16. The genome sequence of the plant pathogen Xylella fastidiosa
    Andrew J.G. Simpson, Fernando C. Reinach, Paulo Arruda, F. A. Abreu, Márcio Luís Acencio, Renato Alvarenga, Lúcia Maria Carareto Alves, Jorge Enrique Araya, Gilson Soares Baía, Cassio Silva Baptista et al. · 2000 · Nature
17. A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights
    Qi‐Long Qin, Bin-Bin Xie, Xi‐Ying Zhang, Xiu‐Lan Chen, Bai‐Cheng Zhou, Jizhong Z. Zhou, Aharon Oren, Yu‐Zhong Zhang · 2014 · Journal of Bacteriology
18. Towards the human intestinal microbiota phylogenetic core
    Tap, Julien, Mondot, Stanislas, Levenez, Florence, Pelletier, Eric, Caron, Christophe, Furet, Jean‐Pierre, Ugarte, Edgardo, Muñoz‐Tamayo, Rafael, Paslier, Denis L. E., Nalin, Renaud et al. · 2009 · Environmental Microbiology
19. Length-dependent prediction of protein intrinsic disorder
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20. Complete sequencing and characterization of 21,243 full-length human cDNAs
    Ota, Toshio, Suzuki, Yutaka, Nishikawa, Tetsuo, Otsuki, Tetsuji, Sugiyama, Tomoyasu, Irie, Ryotaro, Wakamatsu, Ai, Hayashi, Koji, Sato, Hiroyuki, Nagai, Keiichi et al. · 2004 · Nature Genetics
21. The evolution of sex-biased genes and sex-biased gene expression
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22. Automatic annotation of eukaryotic genes, pseudogenes and promoters
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23. Molecular and Phylogenetic Analyses of the Complete MADS-Box Transcription Factor Family in Arabidopsis
    Lucie Pařenicová, Stefan de Folter, Martin Kieffer, David Stephen Horner, Cristina Favalli, Jacqueline Busscher, Holly E. Cook, Richard M. Ingram, Martin M. Kater, Brendan Davies et al. · 2003 · The Plant Cell
24. Properties of MHC Class I Presented Peptides That Enhance Immunogenicity
    Jorg J. A. Calis, Matt Maybeno, Jason Greenbaum, Daniela Weiskopf, Aruna Dharshan De Silva, Alessandro Sette, Can Keşmir, Bjoern Peters · 2013 · PLoS Computational Biology
25. 3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets
    Birmingham, Amanda, Anderson, Emily M, Reynolds, Angela, Ilsley-Tyree, Diane, Leake, Devin, Fedorov, Yuriy, Baskerville, Scott, Maksimova, Elena, Robinson, Kathryn, Karpilow, Jon et al. · 2006 · Nature Methods
26. Expansion of the Receptor-Like Kinase/Pelle Gene Family and Receptor-Like Proteins in Arabidopsis
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27. The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides
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28. Stimulating the In Situ Activity of Geobacter Species To Remove Uranium from the Groundwater of a Uranium-Contaminated Aquifer
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29. The genome of Eucalyptus grandis
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30. Modeling gene and genome duplications in eukaryotes
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31. Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination
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32. Structural classification of zinc fingers: SURVEY AND SUMMARY
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33. HMMER web server: 2015 update
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34. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks
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35. COG database update: focus on microbial diversity, model organisms, and widespread pathogens
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36. The UCSC genome browser and associated tools
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37. The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families
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38. Anther developmental defects in Arabidopsis thaliana male-sterile mutants
    Paul M. Sanders, Anhthu Q. Bui, Koen Weterings, K. N. McIntire, Yung-Chao Hsu, Pei Yun Lee, Mai Thy Truong, Thomas P. Beals, Robert B. Goldberg · 1999 · Sexual Plant Reproduction
39. A combined algorithm for genome-wide prediction of protein function
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40. Prophages and bacterial genomics: what have we learned so far?
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41. Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor
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42. Detection of antibiotic-resistant bacteria and their resistance genes in wastewater, surface water, and drinking water biofilms
    Thomas Schwartz, Wolfgang Kohnen, Bernd Jansen, Ursula Obst · 2003 · FEMS Microbiology Ecology
43. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences
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44. Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans
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45. GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis
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46. Defining operational taxonomic units using DNA barcode data
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47. Rapid Detection and Quantification of Members of the Archaeal Community by Quantitative PCR Using Fluorogenic Probes
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48. The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered
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49. Isoprenoid biosynthesis: The evolution of two ancient and distinct pathways across genomes
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50. A role for excreted quinones in extracellular electron transfer
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51. Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers
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52. Large-scale prediction and testing of drug activity on side-effect targets
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53. A survey of sequence alignment algorithms for next-generation sequencing
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54. Bap, a Staphylococcus aureus Surface Protein Involved in Biofilm Formation
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55. MEROPS : the database of proteolytic enzymes, their substrates and inhibitors
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56. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes
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57. Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites
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58. The compact Selaginella genome identifies changes in gene content associated with the evolution of vascular plants
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59. Active and total microbial communities in forest soil are largely different and highly stratified during decomposition
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60. The BDGP Gene Disruption Project
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61. SNAP: predict effect of non-synonymous polymorphisms on function
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62. DISOPRED3: precise disordered region predictions with annotated protein-binding activity
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63. Complete Genomic Sequence of Nitrogen-fixing Symbiotic Bacterium Bradyrhizobium japonicum USDA110
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64. Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III
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65. High-Resolution Temporal Profiling of Transcripts during Arabidopsis Leaf Senescence Reveals a Distinct Chronology of Processes and Regulation
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66. On the origins of cells: A hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells
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67. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change
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68. A tale of two clades: monkeypox viruses
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69. Ab initio protein structure assembly using continuous structure fragments and optimized knowledge‐based force field
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70. PROSITE, a protein domain database for functional characterization and annotation
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71. CDD: a conserved domain database for interactive domain family analysis
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72. PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations
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73. Database resources of the National Center for Biotechnology Information
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74. TCDB: the Transporter Classification Database for membrane transport protein analyses and information
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75. Recognition and Degradation of Plant Cell Wall Polysaccharides by Two Human Gut Symbionts
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76. Automated Approach for Ribosomal Intergenic Spacer Analysis of Microbial Diversity and Its Application to Freshwater Bacterial Communities
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77. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China
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78. Structure of von Willebrand Factor-cleaving Protease (ADAMTS13), a Metalloprotease Involved in Thrombotic Thrombocytopenic Purpura
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79. Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation
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80. Biochemistry and Evolution of Anaerobic Energy Metabolism in Eukaryotes
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81. The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants
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82. A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi
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83. Evidence of Increasing Antibiotic Resistance Gene Abundances in Archived Soils since 1940
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84. The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000
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85. Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily
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86. PrDOS: prediction of disordered protein regions from amino acid sequence
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87. Protein Sequence Analysis Using the MPI Bioinformatics Toolkit
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88. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes
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89. GenBank
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90. Metagenomic Analyses of an Uncultured Viral Community from Human Feces
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91. A Functional-Phylogenetic Classification System for Transmembrane Solute Transporters
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92. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria
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93. Genome-Wide Characterization of the Lignification Toolbox in Arabidopsis
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94. PatternHunter: faster and more sensitive homology search
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95. Evolutionarily conserved networks of residues mediate allosteric communication in proteins
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96. Why highly expressed proteins evolve slowly
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97. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia
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98. Deep learning for computational chemistry
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99. Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis , Drosophila , and Arabidopsis
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100. EIR1, a root-specific protein involved in auxin transport, is required for gravitropism inArabidopsis thaliana
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