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

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1. DNA-Based Diagnostic Approaches for Identification of Burkholderia cepacia Complex, Burkholderia vietnamiensis, Burkholderia multivorans,Burkholderia stabilis, and Burkholderia cepacia Genomovars I and III
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2. High-Throughput Sequencing Reveals the Incomplete, Short-Term Recovery of Infant Gut Microbiota following Parenteral Antibiotic Treatment with Ampicillin and Gentamicin
   Fiona Fouhy, Caitriona M. Guinane, Séamus Hussey, Rebecca Wall, C. Anthony Ryan, Eugene Michael Dempsey, Brendan Paul Murphy, R. Paul Ross, Gerald F. Fitzgerald, Catherine Stanton et al. · 2012 · Antimicrobial Agents and Chemotherapy
3. An In silico approach for the evaluation of DNA barcodes
   Gentile Francesco Ficetola, Éric Coissac, Stéphanie Zundel, Tiayyba Riaz, Wasim Shehzad, Julien Bessière, Pierre Taberlet, François Pompanon · 2010 · BMC Genomics
4. The Chondroitin Sulfate Proteoglycans Neurocan and Phosphacan Are Expressed by Reactive Astrocytes in the Chronic CNS Glial Scar
   McKeon, Robert J., Jurynec, Michael J., Buck, Charles R. · 1999 · The Journal of Neuroscience
5. Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga Nannochloropsis oceanica CCMP1779
   Vieler, Astrid, Wu, Guangxi, Tsai, Chia-Hong, Bullard, Blair, Cornish, Adam J., Harvey, Christopher, Reca, Ida-Barbara, Thornburg, Chelsea, Achawanantakun, Rujira, Buehl, Christopher J. et al. · 2012 · PLoS Genetics
6. Prevalence of Molecular Mechanisms of Resistance to Azole Antifungal Agents in <i>Candida albicans</i> Strains Displaying High-Level Fluconazole Resistance Isolated from Human Immunodeficiency Virus-Infected Patients
   Perea, Sofia, López-Ribot, José L., Kirkpatrick, William R., McAtee, Robert K., Santillán, Rebecca A., Martı́nez, Marcos, Calabrese, David, Sanglard, Dominique, Patterson, Thomas F. · 2001 · Antimicrobial Agents and Chemotherapy
7. CAMP: a useful resource for research on antimicrobial peptides.
   Thomas, Shaini, Karnik, Shreyas, Barai, Ram Shankar, Jayaraman, V. K., Idicula-Thomas, Susan · 2010 · Nucleic Acids Research
8. The Transporter Classification Database (TCDB): 2021 update
   Saier, Milton H, Reddy, Vamsee S, Moreno-Hagelsieb, Gabriel, Hendargo, Kevin J, Zhang, Yichi, Iddamsetty, Vasu, Lam, Katie Jing Kay, Tian, Nuo, Russum, Steven, Wang, Jianing et al. · 2021 · Nucleic Acids Research
9. Paircoil2: improved prediction of coiled coils from sequence.
   McDonnell, A. V., Jiang, T., Keating, A. E., Berger, B. · 2006 · Bioinformatics
10. Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery
    Parchman, Thomas L, Geist, Katherine S, Grahnen, Johan A, Benkman, Craig W, Buerkle, C ALEX · 2010 · BMC Genomics
11. Signal peptidases.
    Paetzel, Mark, Karla, Andrew, Strynadka, Natalie C. J., Dalbey, Ross E. · 2002 · Chemical Reviews
12. De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas)
    Wang, Zhangying, Fang, Boping, Chen, Jingyi, Zhang, Xiongjian, Luo, Zhongxia, Huang, Lifei, Chen, Xinliang, Li, Yujun · 2010 · BMC Genomics
13. A model for carbohydrate metabolism in the diatom Phaeodactylum tricornutum deduced from comparative whole genome analysis
    Kroth, Peter G., Chiovitti, Anthony, Gruber, Ansgar, Martin-Jezequel, Veronique, Mock, Thomas, Parker, Micaela Schnitzler, Stanley, Michele S., Kaplan, Aaron, Caron, Lise, Weber, Till et al. · 2008 · PLoS ONE
14. Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits
    Chen, Lei, Qiu, Qiang, Jiang, Yu, Wang, Kun, Lin, Zeshan, Li, Zhipeng, Bibi, Faysal, Yang, Yongzhi, Wang, Jinhuan, Nie, Wenhui et al. · 2019 · Science
15. Molecular characterization of mucosal adherent bacteria and associations with colorectal adenomas
    Shen, Xiang Jun, Rawls, John F., Randall, Thomas A., Burcall, Lauren, Mpande, Caroline, Jenkins, Natascha, Jovov, Biljana, Abdo, Zaid, Sandler, Robert S., Keku, Temitope O. · 2010 · Gut Microbes
16. ECOD: an evolutionary classification of protein domains
    Cheng, Hua, Schaeffer, R. Dustin, Liao, Yuxing, Kinch, Lisa N., Pei, Jimin, Shi, Shuoyong, Kim, Bong-Hyun, Grishin, Nick V. · 2014 · PLoS Computational Biology
17. The HIrisPlex system for simultaneous prediction of hair and eye colour from DNA
    Walsh, Susan, Liu, Fan, Wollstein, Andreas, Kovatsi, Leda, Ralf, Arwin, Kosiniak-Kamysz, Agnieszka, Branicki, Wojciech, Kayser, Manfred · 2013 · Forensic Science International Genetics
18. Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein
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19. Anillin is a scaffold protein that links RhoA, actin, and myosin during cytokinesis
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20. Updates to the integrated protein-protein interaction benchmarks: docking benchmark version 5 and affinity benchmark version 2
    Vreven, Thom, Moal, Iain H., Vangone, Anna, Pierce, Brian G., Kastritis, Panagiotis L., Torchala, Mieczyslaw, Chaleil, Raphael, Jiménez-García, Brian, Bates, Paul A., Fernandez-Recio, Juan et al. · 2015 · Journal of Molecular Biology
21. Evolution of Aminoacyl-tRNA Synthetases—Analysis of Unique Domain Architectures and Phylogenetic Trees Reveals a Complex History of Horizontal Gene Transfer Events
    Wolf, Yuri I., Aravind, L., Grishin, Nick V., Koonin, Eugene V. · 1999 · Genome Research
22. Complete Nucleotide Sequence of a 43-Kilobase Genomic Island Associated with the Multidrug Resistance Region of<i>Salmonella enterica</i>Serovar Typhimurium DT104 and Its Identification in Phage Type DT120 and Serovar Agona
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23. Mutations in the Human Sterol Δ7-Reductase Gene at 11q12-13 Cause Smith-Lemli-Opitz Syndrome
    Wassif, Christopher A., Maslen, Cheryl, Kachilele-Linjewile, Stivelia, Lin, Don, Linck, Leesa M., Connor, William E., Steiner, Robert D., Porter, Forbes D. · 1998 · The American Journal of Human Genetics
24. Ancient gene linkages support ctenophores as sister to other animals
    Schultz, Darrin T., Haddock, Steven H. D., Bredeson, Jessen V., Green, Richard E., Simakov, Oleg, Rokhsar, Daniel S. · 2023 · Nature
25. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis
    Dalloul, Rami A., Long, Julie A., Zimin, Aleksey V., Aslam, Luqman, Beal, Kathryn, Ann Blomberg, Le, Bouffard, Pascal, Burt, David W., Crasta, Oswald, Crooijmans, Richard P. M. A. et al. · 2010 · PLoS Biology
26. The HAMP Domain Structure Implies Helix Rotation in Transmembrane Signaling
    Hulko, Michael, Berndt, Franziska, Gruber, Markus, Linder, Jürgen U., Truffault, Vincent, Schultz, Anita, Martin, Jörg, Schultz, Joachim E., Lupas, Andrei N., Coles, Murray · 2006 · Cell
27. Deep mitochondrial origin outside the sampled alphaproteobacteria
    Martijn, Joran, Vosseberg, Julian, Guy, Lionel, Offre, Pierre, Ettema, Thijs J. G. · 2018 · Nature
28. The <i>NPH4</i> Locus Encodes the Auxin Response Factor ARF7, a Conditional Regulator of Differential Growth in Aerial Arabidopsis Tissue
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29. Gut microbiota richness promotes its stability upon increased dietary fibre intake in healthy adults
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30. The Ensembl Automatic Gene Annotation System
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31. Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease
    Erickson, Alison R., Cantarel, Brandi L., Lamendella, Regina, Darzi, Youssef, Mongodin, Emmanuel F., Pan, Chongle, Shah, Manesh, Halfvarson, Jonas, Tysk, Curt, Henrissat, Bernard et al. · 2012 · PLoS ONE
32. START: a lipid-binding domain in StAR, HD-ZIP and signalling proteins
    Ponting, Chris P., Aravind, L. · 1999 · Trends in Biochemical Sciences
33. Microbial genomic analysis reveals the essential role of inflammation in bacteria-induced colorectal cancer
    Arthur, Janelle C., Gharaibeh, Raad Z., Mühlbauer, Marcus, Perez-Chanona, Ernesto, Uronis, Joshua M., McCafferty, Jonathan, Fodor, Anthony A., Jobin, Christian · 2014 · Nature Communications
34. Effect of broad- and narrow-spectrum antimicrobials on <i>Clostridium difficile</i> and microbial diversity in a model of the distal colon
    Rea, Mary C., Dobson, Alleson, O'Sullivan, Orla, Crispie, Fiona, Fouhy, Fiona, Cotter, Paul D., Shanahan, Fergus, Kiely, Barry, Hill, Colin, Ross, R. Paul · 2011 · Proceedings of the National Academy of Sciences
35. A new clustering of antibody CDR loop conformations
    North, Benjamin, Lehmann, Andreas, Dunbrack, Roland L. · 2011 · Journal of Molecular Biology
36. Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA
    Baek, Minkyung, McHugh, Ryan, Anishchenko, Ivan, Jiang, Hanlun, Baker, David, DiMaio, Frank · 2024 · Nature Methods
37. CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise
    Pertea, Mihaela, Shumate, Alaina, Pertea, Geo, Varabyou, Ales, Breitwieser, Florian P., Chang, Yu-Chi, Madugundu, Anil K., Pandey, Akhilesh, Salzberg, Steven L. · 2018 · Genome Biology
38. Purification, Characterization, and Sequence Analysis of a Potential Virulence Factor from <i>Porphyromonas gingivalis</i> , Peptidylarginine Deiminase
    McGraw, Walker T., Potempa, Jan, Farley, David, Travis, James · 1999 · Infection and Immunity
39. Steroids, triterpenoids and molecular oxygen
    Summons, Roger E, Bradley, Alexander S, Jahnke, Linda L, Waldbauer, Jacob R · 2006 · Philosophical Transactions of the Royal Society B: Biological Sciences
40. The ESAT-6/WXG100 superfamily – and a new Gram-positive secretion system?
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41. An evolution-based model for designing chorismate mutase enzymes
    Russ, William P., Figliuzzi, Matteo, Stocker, Christian, Barrat-Charlaix, Pierre, Socolich, Michael, Kast, Peter, Hilvert, Donald, Monasson, Remi, Cocco, Simona, Weigt, Martin et al. · 2020 · Science
42. Systematic Discovery of New Recognition Peptides Mediating Protein Interaction Networks
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43. Defining a new nomenclature for the structures of active and inactive kinases
    Modi, Vivek, Dunbrack, Roland L. · 2019 · Proceedings of the National Academy of Sciences
44. Evolutionary history, structural features and biochemical diversity of the NlpC/P60 superfamily of enzymes
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45. Mutations in a newly identified GTPase gene cause autosomal dominant hereditary spastic paraplegia
    Zhao, Xinping, Alvarado, David, Rainier, Shirley, Lemons, Rosemary, Hedera, Peter, Weber, Christian H., Tukel, Turgut, Apak, Memnune, Heiman-Patterson, Terry, Ming, Lei et al. · 2001 · Nature Genetics
46. Linear motifs: Evolutionary interaction switches
    Neduva, Victor, Russell, Robert B. · 2005 · FEBS Letters
47. SOCKET: a program for identifying and analysing coiled-coil motifs within protein structures11Edited by J. Thornton
    Walshaw, John, Woolfson, Derek N · 2001 · Journal of Molecular Biology
48. Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2-mRNA-vaccinated individuals
    Kustin, Talia, Harel, Noam, Finkel, Uriah, Perchik, Shay, Harari, Sheri, Tahor, Maayan, Caspi, Itamar, Levy, Rachel, Leshchinsky, Michael, Ken Dror, Shifra et al. · 2021 · Nature Medicine
49. EST Analysis of the Cnidarian Acropora millepora Reveals Extensive Gene Loss and Rapid Sequence Divergence in the Model Invertebrates
    Kortschak, R.Daniel, Samuel, Gabrielle, Saint, Robert, Miller, David J · 2003 · Current Biology
50. Did DNA replication evolve twice independently?
    Leipe, D. D., Aravind, L., Koonin, E. V. · 1999 · Nucleic Acids Research
51. Severe neural tube defects in the loop-tail mouse result from mutation of Lpp1, a novel gene involved in floor plate specification
    Murdoch, J. N. · 2001 · Human Molecular Genetics
52. Elevated expression of metal transporter genes in three accessions of the metal hyperaccumulator<i>Thlaspi caerulescens</i>
    Assunção, A. G. L., Martins, P. Da Costa, De Folter, S., Vooijs, R., Schat, H., Aarts, M. G. M. · 2001 · Plant, Cell &amp; Environment
53. The structural and functional signatures of proteins that undergo multiple events of post‐translational modification
    Pejaver, Vikas, Hsu, Wei‐Lun, Xin, Fuxiao, Dunker, A. Keith, Uversky, Vladimir N., Radivojac, Predrag · 2014 · Protein Science
54. Evolutionary Origins of Genomic Repertoires in Bacteria
    Lerat, Emmanuelle, Daubin, Vincent, Ochman, Howard, Moran, Nancy A · 2005 · PLoS Biology
55. Protein structure prediction using multiple deep neural networks in the 13th critical assessment of protein structure prediction (CASP13)
    Senior, Andrew W., Evans, Richard, Jumper, John, Kirkpatrick, James, Sifre, Laurent, Green, Tim, Qin, Chongli, Žídek, Augustin, Nelson, Alexander W. R., Bridgland, Alex et al. · 2019 · Proteins: Structure, Function, and Bioinformatics
56. The origin and early evolution of eukaryotes in the light of phylogenomics
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57. Intestinal microbiota associated with differential feed conversion efficiency in chickens
    Stanley, Dragana, Denman, Stuart E., Hughes, Robert J., Geier, Mark S., Crowley, Tamsyn M., Chen, Honglei, Haring, Volker R., Moore, Robert J. · 2012 · Applied Microbiology and Biotechnology
58. Binding MOAD (Mother Of All Databases)
    Hu, Liegi, Benson, Mark L., Smith, Richard D., Lerner, Michael G., Carlson, Heather A. · 2005 · Proteins: Structure, Function, and Bioinformatics
59. Optimization of de novo transcriptome assembly from next-generation sequencing data
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60. Critical assessment of protein intrinsic disorder prediction
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61. β-Lactamases of <i>Kluyvera ascorbata</i> , Probable Progenitors of Some Plasmid-Encoded CTX-M Types
    Humeniuk, Christel, Arlet, Guillaume, Gautier, Valerie, Grimont, Patrick, Labia, Roger, Philippon, Alain · 2002 · Antimicrobial Agents and Chemotherapy
62. Using deep learning to annotate the protein universe
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63. N- and C-Terminal Flanking Regions Modulate Light-Induced Signal Transduction in the LOV2 Domain of the Blue Light Sensor Phototropin 1 from <i>Avena sativa</i> ^,
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64. Identification and Characterization of Novel Human Endogenous Retrovirus Families by Phylogenetic Screening of the Human Genome Mapping Project Database
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65. Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products
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66. Emergence and pathogenicity of highly virulent Cryptococcus gattii genotypes in the northwest United States
    Byrnes, Edmond J., Li, Wenjun, Lewit, Yonathan, Ma, Hansong, Voelz, Kerstin, Ren, Ping, Carter, Dee A., Chaturvedi, Vishnu, Bildfell, Robert J., May, Robin C. et al. · 2010 · PLoS Pathogens
67. The product of C9orf72, a gene strongly implicated in neurodegeneration, is structurally related to DENN Rab-GEFs
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68. Engineering an allosteric transcription factor to respond to new ligands
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69. mRNA up-regulation of MHC II and pivotal pro-inflammatory genes in normal brain aging
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70. The microbiome-derived metabolite TMAO drives immune activation and boosts responses to immune checkpoint blockade in pancreatic cancer
    Mirji, Gauri, Worth, Alison, Bhat, Sajad Ahmad, El Sayed, Mohamed, Kannan, Toshitha, Goldman, Aaron R., Tang, Hsin-Yao, Liu, Qin, Auslander, Noam, Dang, Chi V. et al. · 2022 · Science Immunology
71. Inventory, evolution and expression profiling diversity of the LEA (late embryogenesis abundant) protein gene family in Arabidopsis thaliana
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72. Molecular Analysis of Antibiotic Resistance Gene Clusters in <i>Vibrio cholerae</i> O139 and O1 SXT Constins
    Hochhut, Bianca, Lotfi, Yasmin, Mazel, Didier, Faruque, Shah M., Woodgate, Roger, Waldor, Matthew K. · 2001 · Antimicrobial Agents and Chemotherapy
73. <i>Arabidopsis</i> NPH3: A NPH1 Photoreceptor-Interacting Protein Essential for Phototropism
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74. Clostridium scindens: a human gut microbe with a high potential to convert glucocorticoids into androgens
    Ridlon, Jason M., Ikegawa, Shigeo, Alves, João M.P., Zhou, Biao, Kobayashi, Akiko, Iida, Takashi, Mitamura, Kuniko, Tanabe, Genzoh, Serrano, Myrna, De Guzman, Ainee et al. · 2013 · Journal of Lipid Research
75. Prokaryotic Genetic Diversity throughout the Salinity Gradient of a Coastal Solar Saltern
    Benlloch, Susana, López‐López, Arantxa, Casamayor, Emilio O., Øvreås, Lise, Goddard, Victoria, Daae, Frida Lise, Smerdon, Gary, Massana, Ramón, Joint, Ian, Thingstad, Frede et al. · 2002 · Environmental Microbiology
76. An iron homeostasis regulatory circuit with reciprocal roles in Candida albicans commensalism and pathogenesis
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77. Emergence of Young Human Genes after a Burst of Retroposition in Primates
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78. Glucocorticoids mediate stress-induced priming of microglial pro-inflammatory responses
    Frank, Matthew G., Thompson, Brittany M., Watkins, Linda R., Maier, Steven F. · 2012 · Brain, Behavior, and Immunity
79. Prior exposure to glucocorticoids sensitizes the neuroinflammatory and peripheral inflammatory responses to E. coli lipopolysaccharide
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80. Structure and Evolution of Neurexin Genes: Insight into the Mechanism of Alternative Splicing
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81. Early bioenergetic evolution
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82. Ctenophore relationships and their placement as the sister group to all other animals
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83. An eight cysteine-containing CFEM domain unique to a group of fungal membrane proteins
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84. Human Scc4 is required for cohesin binding to chromatin, sister-chromatid cohesion, and mitotic progression
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85. Human Transcription Factors Contain a High Fraction of Intrinsically Disordered Regions Essential for Transcriptional Regulation
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86. Comparative modeling for protein structure prediction
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87. Progress in Modeling of Protein Structures and Interactions.
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88. HDAC4, a Human Histone Deacetylase Related to Yeast HDA1, Is a Transcriptional Corepressor
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89. Comprehensive benchmarking and ensemble approaches for metagenomic classifiers
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90. A Post-Synaptic Scaffold at the Origin of the Animal Kingdom
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91. Molecular Cloning of the Human Gene, PNKP, Encoding a Polynucleotide Kinase 3′-Phosphatase and Evidence for Its Role in Repair of DNA Strand Breaks Caused by Oxidative Damage
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92. Identification and Characterization of a Sphingolipid Δ4-Desaturase Family
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93. Molecular paleontology of transposable elements in the <i>Drosophila melanogaster</i> genome
    Kapitonov, Vladimir V., Jurka, Jerzy · 2003 · Proceedings of the National Academy of Sciences
94. HaMStR: Profile hidden markov model based search for orthologs in ESTs
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95. Genomic insights into the evolutionary origin of Myxozoa within Cnidaria
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96. VI. Genome structure and cognitive map of Williams syndrome
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97. The Analysis of Eight Transcriptomes from All Poriferan Classes Reveals Surprising Genetic Complexity in Sponges
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98. Real-Time PCR for Detection and Identification of <i>Plasmodium</i> spp
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99. Complete Genomic Structure of the Bloom-forming Toxic Cyanobacterium Microcystis aeruginosa NIES-843
    Kaneko, Takakazu, Nakajima, Nobuyoshi, Okamoto, Shinobu, Suzuki, Iwane, Tanabe, Yuuhiko, Tamaoki, Masanori, Nakamura, Yasukazu, Kasai, Fumie, Watanabe, Akiko, Kawashima, Kumiko et al. · 2007 · DNA Research
100. Unique amino acid composition of proteins in halophilic bacteria
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