A review on computational systems biology of pathogen-host interactions

Frontiers in Microbiology

Volumn 6, Issue APR, 2015, Pages

  Durmus, Saliha ^a   Çakir, Tunahan ^a   Özgür, Arzucan ^b   Guthke, Reinhard ^c  

^a GEBZE TECHNICAL UNIVERSITY   (Turkey)

^b BOGAZICI UNIVERSITY   (Turkey)

^c HANS KNÖLL INSTITUTE   (Germany)

Author keywords

Bioinformatics; Computational systems biology; Drug target; Gene regulatory network; Metabolic interaction; Omics data; Pathogen host interaction; Protein protein interaction

Indexed keywords

ALGORITHM; BIOINFORMATICS; BIOLOGY; COMPUTER NETWORK; COMPUTER PROGRAM; GENOMICS; HOST PATHOGEN INTERACTION; HUMAN; INFECTION; MATHEMATICAL MODEL; METABOLOME; NONHUMAN; PROTEIN DATABASE; PROTEIN INTERACTION; PROTEOMICS; REVIEW; SYSTEMS BIOLOGY; TRANSCRIPTOMICS;

EID: 84930932707     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2015.00235     Document Type: Review

References (236)

1. Ahmad, F., Babalola, O. O., and Tak, H. I. (2012). Potential of MALDI-TOF mass spectrometry as a rapid detection technique in plant pathology: identification of plant-associated microorganisms. Anal. Bioanal. Chem. 404, 1247-1255. doi: 10.1007/s00216-012-6091-7.
2. Airola, A., Pyysalo, S., Björne, J., Pahikkala, T., Ginter, F., and Salakoski, T. (2008). All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning. BMC Bioinform. 9(Suppl. 11):S2. doi: 10.1186/1471-2105-9-S11-S2.
3. Ako-Adjei, D., Fu, W., Wallin, C., Katz, K. S., Song, G., Darji, D., et al. (2015). HIV-1, human interaction database: current status and new features. Nucleic Acids Res. 43, D566-D570. doi: 10.1093/nar/gku1126.
4. Albà, M. M., Lee, D., Pearl, F. M., Shepherd, A. J., Martin, N., Orengo, C. A., et al. (2001). VIDA: a virus database system for the organization of animal virus genome open reading frames. Nucleic Acids Res. 29, 133-136. doi: 10.1093/nar/29.1.133.
5. Albrecht, D., Guthke, R., Brakhage, A. A., and Kniemeyer, O. (2010). Integrative analysis of the heat shock response in Aspergillus fumigatus. BMC Genomics 11:32. doi: 10.1186/1471-2164-11-32.
6. Albrecht, D., Kniemeyer, O., Brakhage, A. A., Berth, M., and Guthke, R. (2007). Integration of transcriptome and proteome data from human-pathogenic fungi by using a data warehouse. J. Integr. Bioinform 4, 52.
7. Albrecht, D., Kniemeyer, O., Mech, F., Gunzer, M., Brakhage, A., and Guthke, R. (2011). On the way toward systems biology of Aspergillus fumigatus infection. Int. J. Med. Microbiol. 301, 453-459. doi: 10.1016/j.ijmm.2011.04.014.
8. Alfarano, C., Andrade, C. E., Anthony, K., Bahroos, N., Bajec, M., Bantoft, K., et al. (2005). The biomolecular interaction network database and related tools 2005 update. Nucleic Acids Res. 33, D418-D424. doi: 10.1093/nar/gki051.
9. Altwasser, R., Linde, J., Buyko, E., Hahn, U., and Guthke, R. (2012). Genome-wide scale-free network inference for Candida albicans. Front. Microbiol. 3:51. doi: 10.3389/fmicb.2012.00051.
10. Anthony, S., Sintchenko, V., and Coiera, E. (2010). Text mining for discovery of host-pathogen interactions. Infect. Dis. Inform. 2010, 149-165. doi: 10.1007/978-1-4419-1327-2_7.
11. Antunes, L. C. M., Arena, E. T., Menendez, A., Han, J., Ferreira, R. B., Buckner, M. M., et al. (2011). Impact of salmonella infection on host hormone metabolism revealed by metabolomics. Infect. Immun. 79, 1759-1769. doi: 10.1128/IAI.01373-10.
12. Aranda, B., Blankenburg, H., Kerrien, S., Brinkman, F. S. L., Ceol, A., Chautard, E., et al. (2011). PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat. Methods 8, 528-529. doi: 10.1038/nmeth.1637.
13. Arighi, C. N., Lu, Z., Krallinger, M., Cohen, K. B., Wilbur, W. J., Valencia, A., et al. (2011). Overview of the biocreative III workshop. BMC Bioinform. 12(Suppl. 8):S1. doi: 10.1186/1471-2105-12-S8-S1.
14. Baccam, P., Beauchemin, C., Macken, C. A., Hayden, F. G., and Perelson, A. S. (2009). Kineticsof influenza a virus infection in human. J. Virol. 80, 7509-7590.
15. Bansal, M., Belcastro, V., Ambesi-Impiombato, A., and Di Bernardo, D. (2007). How to infer gene networks from expression profiles. Mol. Syst. Biol. 122, 78.
16. Bartel, P. L., Roecklein, J. A., Sen Gupta, D., and Fields, S. (1996). A protein linkage map of Escherichia coli bacteriophage T7. Nat. Genet. 12, 72-77. doi: 10.1038/ng0196-72.
17. Baumgartner, W. A., Cohen, K. B., Fox, L. M., Acquaah-Mensah, G., and Hunter, L. (2007). Manual curation is not sufficient for annotation of genomic databases. Bioinformatics 23, i41-i48. doi: 10.1093/bioinformatics/btm229.
18. Bazzani, S., Hoppe, A., and Holzhütter, H.-G. (2012). Network-based assessment of the selectivity of metabolic drug targets in Plasmodium falciparum with respect to human liver metabolism. BMC Syst. Biol. 6:118. doi: 10.1186/1752-0509-6-118.
19. Berglund, E. C., Nystedt, B., and Andersson, S. G. (2009). Computational resources in infectious disease: limitations and challenges. PLoS Comput. Biol. 5:e1000481. doi: 10.1371/journal.pcbi.1000481.
20. Beste, D. J. V., Nöh, K., Niedenführ, S., Mendum, T. A., Hawkins, N. D., Ward, J. L., et al. (2013). 13C-flux spectral analysis of host-pathogen metabolism reveals a mixed diet for intracellular Mycobacterium tuberculosis. Chem. Biol. 20, 1012-1021. doi: 10.1016/j.chembiol.2013.06.012.
21. Björne, J., Heimonen, J., Ginter, F., Airola, A., Pahikkala, T., and Salakoski, T. (2009). "Extracting complex biological events with rich graph-based feature sets," in Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task, Stroudsburg, PA, 10-18.
22. Blaschke, C., and Valencia, A. (2002). The frame-based module of the SUISEKI information extraction system. IEEE Intell. Syst. 17, 14-20.
23. Bleves, S., Dunger, I., Walter, M. C., Frangoulidis, D., Kastenmüller, G., Voulhoux, R., et al. (2014). HoPaCI-DB: host-Pseudomonas and Coxiella interaction database. Nucleic Acids Res. 42, D671-D676. doi: 10.1093/nar/gkt925.
24. BonHomme, M., Wong, S., Carter, C., and Scarlata, S. (2003). The pH dependence of HIV-1 capsid assembly and its interaction with cyclophilin A. Biophys. Chem. 105, 67-77. doi: 10.1016/S0301-4622(03)00063-2.
25. Bordbar, A., Lewis, N. E., Schellenberger, J., Palsson, B.Ø., and Jamshidi, N. (2010). Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. Mol. Syst. Biol. 6, 422. doi: 10.1038/msb.2010.68.
26. Bordbar, A., and Palsson, B. O. (2012). Using the reconstructed genome-scale human metabolic network to study physiology and pathology. J. Intern. Med. 271, 131-141. doi: 10.1111/j.1365-2796.2011.02494.x.
27. Brass, A. L., Dykxhoorn, D. M., Benita, Y., Yan, N., Engelman, A., Xavier, R. J., et al. (2008). Identification of host proteins required for HIV infection through a functional genomic screen. Science 319, 921-926. doi: 10.1126/science.1152725.
28. Brazma, A., Krestyaninova, M., and Sarkans, U. (2006). Standards for systems biology. Nat. Rev. Genet. 7, 593-605. doi: 10.1038/nrg1922.
29. Brown, J. R., Magid-Slav, M., Sanseau, P., and Rajpal, D. K. (2011). Computational biology approaches for selecting host-pathogen drug targets. Drug Discov. Today 16, 229-236. doi: 10.1016/j.drudis.2011.01.008.
30. Brown, S. A., Palmer, K. L., and Whiteley, M. (2008). Revisiting the host as a growth medium. Nat. Rev. Microbiol. 6, 657-666. doi: 10.1038/nrmicro1955.
31. Bröker, B. M., and van Belkum, A. (2011). Immune proteomics of Staphylococcus aureus. Proteomics 11, 3221-3231. doi: 10.1002/pmic.201100010.
32. Bumann, D. (2009). System-level analysis of Salmonella metabolism during infection. Curr. Opin. Microbiol. 12, 559-567. doi: 10.1016/j.mib.2009.08.004.
33. Bushman, F. D., Malani, N., Fernandes, J., D'Orso, I., Cagney, G., Diamond, T. L., et al. (2009). Host cell factors in HIV replication: meta-analysis of genome-wide studies. PLoS Pathog. 5:e1000437. doi: 10.1371/journal.ppat.1000437.
34. Cakir, T., and Khatibipour, M. J. (2014). Metabolic network discovery by top-down and bottom-up approaches and paths for reconciliation. Front. Bioeng. Biotechnol. 2:62. doi: 10.3389/fbioe.2014.00062.
35. Calderone, A., Licata, L., and Cesareni, G. (2015). VirusMentha: a new resource for virus-host protein interactions. Nucleic Acids Res. 43, D588-D592. doi: 10.1093/nar/gku830.
36. Calderwood, M. A., Venkatesan, K., Xing, L., Chase, M. R., Vazquez, A., Holthaus, A. M., et al. (2007). Epstein-Barr virus and virus human protein interaction maps. Proc. Natl. Acad. Sci. U.S.A. 104, 7606-7611. doi: 10.1073/pnas.0702332104.
37. Camilios-Neto, D., Bonato, P., Wassem, R., Tadra-Sfeir, M. Z., Brusamarello-Santos, L. C., Valdameri, G., et al. (2014). Dual RNA-seq transcriptional analysis of wheat roots colonized by Azospirillum brasilense reveals up-regulation of nutrient acquisition and cell cycle genes. BMC Genomics 15:378. doi: 10.1186/1471-2164-15-378.
38. Cash, P. (2011). Investigating pathogen biology at the level of the proteome. Proteomics 11, 3190-3202. doi: 10.1002/pmic.201100029.
39. Chang, S., Zhang, J., Liao, X., Zhu, X., Wang, D., Zhu, J., et al. (2007). Influenza virus database (IVDB): an integrated information resource and analysis platform for influenza virus research. Nucleic Acids Res. 35, D376-D380. doi: 10.1093/nar/gkl779.
40. Chatr-Aryamontri, A., Breitkreutz, B.-J., Heinicke, S., Boucher, L., Winter, A., Stark, C., et al. (2013). The BioGRID interaction database: 2013 update. Nucleic Acids Res. 41, D816-D823. doi: 10.1093/nar/gks1158.
41. Chatr-Aryamontri, A., Ceol, A., Peluso, D., Nardozza, A., Panni, S., Sacco, F., et al. (2009). VirusMINT: a viral protein interaction database. Nucleic Acids Res. 37, D669-D673. doi: 10.1093/nar/gkn739.
42. Chavali, A. K., D'Auria, K. M., Hewlett, E. L., Pearson, R. D., and Papin, J. A. (2012). A metabolic network approach for the identification and prioritization of antimicrobial drug targets. Trends Microbiol. 20, 113-123. doi: 10.1016/j.tim.2011.12.004.
43. Chen, L., Xiong, Z., Sun, L., Yang, J., and Jin, Q. (2011). VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. Nucleic Acids Res. 40, D641-D645. doi: 10.1093/nar/gkr989.
44. Chen, R., Mias, G. I., Li-Pook-Than, J., Jiang, L., Lam, H. Y., Chen, R., et al. (2012). Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell 148, 1293-1307. doi: 10.1016/j.cell.2012.02.009.
45. Cortes, C., and Vapnik, V. (1995). Support-vector networks. Mach. Learn. 20, 273-297. doi: 10.1007/BF00994018.
46. Croft, D., Mundo, A. F., Haw, R., Milacic, M., Weiser, J., Wu, G., et al. (2014). The Reactome pathway knowledgebase. Nucleic Acids Res. 42, D472-D477. doi: 10.1093/nar/gkt1102.
47. Cujec, T. P., Cho, H., Maldonado, E., Meyer, J., Reinberg, D., and Peterlin, B. M. (1997). The human immunodeficiency virus transactivator Tat interacts with the RNA polymerase II holoenzyme. Mol. Cell. Biol. 17, 1817-1823.
48. Daraselia, N., Yuryev, A., Egorov, S., Novichkova, S., Nikitin, A., and Mazo, I. (2004). Extracting human protein interactions from MEDLINE using a full-sentence parser. Bioinformatics 20, 604-611. doi: 10.1093/bioinformatics/btg452.
49. De Chassey, B., Navratil, V., Tafforeau, L., Hiet, M. S., Aublin-Gex, A., Agaugue, S., et al. (2008). Hepatitis C virus infection protein network. Mol. Syst. Biol. 4, 230. doi: 10.1038/msb.2008.66.
50. De Jong, H. (2002). Modeling and simulation of genetic regulatory systems: a literature review. J. Comput. Biol. 9, 67-103. doi: 10.1089/10665270252833208.
51. Del Chierico, F., Petrucca, A., Vernocchi, P., Bracaglia, G., Fiscarelli, E., Bernaschi, P., et al. (2014). Proteomics boosts translational and clinical microbiology. J. proteomics 97, 69-87. doi: 10.1016/j.jprot.2013.10.013.
52. Di Carli, M., Benvenuto, E., and Donini, M. (2012). Recent Insights into plant-virus interactions through proteomic analysis. J. Proteome Res. 11, 4765-4780. doi: 10.1021/pr300494e.
53. Dolan, P. T., Zhang, C., Khadka, S., Arumugaswami, V., Vangeloff, A. D., Heaton, N. S., et al. (2013). Identification and comparative analysis of hepatitis C virus-host cell protein interactions. Mol. Biosyst. 9, 3199-3209. doi: 10.1039/c3mb70343f.
54. Durmus Tekir, S., Çakir, T., Ardiç, E., Sayilirbas, A. S., Konuk, G., Konuk, M., et al. (2013). PHISTO: pathogen-host interaction search tool. Bioinformatics 29, 1357-1358. doi: 10.1093/bioinformatics/btt137.
55. Durmus Tekir, S., Çakir, T., and Ülgen, K.Ö. (2012). Infection strategies of bacterial and viral pathogens through pathogen-human protein-protein interactions. Front. Microbiol. 3:46. doi: 10.3389/fmicb.2012.00046.
56. Durmus Tekir, S., and Ülgen, K.Ö. (2013). Systems biology of pathogen-host interaction: networks of protein-protein interaction within pathogens and pathogen-human interactions in the post-genomic era. Biotechnol. J. 8, 85-96. doi: 10.1002/biot.201200110.
57. Dyer, M. D., Murali, T. M., and Sobral, B. W. (2008). The landscape of human proteins interacting with viruses and other pathogens. PLoS Pathog. 4:e32. doi: 10.1371/journal.ppat.0040032.
58. Dyer, M. D., Neff, C., Dufford, M., Rivera, C. G., Shattuck, D., Bassaganya-Riera, J., et al. (2010). The human-bacterial pathogen protein interaction networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis. PLoS ONE 5:e12089. doi: 10.1371/journal.pone.0012089.
59. Eisenreich, W., Heesemann, J., Rudel, T., and Goebel, W. (2013). Metabolic host responses to infection by intracellular bacterial pathogens. Front. Cell. Infect. Microbiol. 3:24. doi: 10.3389/fcimb.2013.00024.
60. Emmert-Streib, F., Dehmer, M., and Haibe-Kains, B. (2014). Gene regulatory networks and their applications: understanding biological and medical problems in terms of networks. Front. Cell Dev. Biol. 2:38. doi: 10.3389/fcell.2014.00038.
61. Erkan, G., Özgür, A., and Radev, D. R. (2007). "Semi-supervised classification for extracting protein interaction sentences using dependency parsing," in Proceedings of the 2007 Joint Conference on Empirical Methods in Natural Language Processing and Computational Natural Language Learning, Prague, 228-237.
62. Feist, A. M., Herrgård, M. J., Thiele, I., Reed, J. L., and Palsson, B.Ø. (2008). Reconstruction of biochemical networks in microorganisms. Nat. Rev. Microbiol. 7, 129-143. doi: 10.1038/nrmicro1949.
63. Fields, S., and Song, O. (1989). A novel genetic system to detect protein protein interactions. Nature 340, 245-246. doi: 10.1038/340245a0.
64. Finley, R. L., and Brent, R. (1994). Interaction mating reveals binary and ternary connections between Drosophila cell cycle regulators. Proc. Natl. Acad. Sci. U.S.A. 91, 12980-12984. doi: 10.1073/pnas.91.26.12980.
65. Fisher, S. K., Novak, J. E., and Agranoff, B. W. (2002). Inositol and higher inositol phosphates in neural tissues: homeostasis, metabolism and functional significance. J. Neurochem. 82, 736-754. doi: 10.1046/j.1471-4159.2002.01041.x.
66. Flajolet, M., Rotondo, G., Daviet, L., Bergametti, F., Inchauspé, G., Tiollais, P., et al. (2000). A genomic approach of the hepatitis C virus generates a protein interaction map. Gene 242, 369-379. doi: 10.1016/S0378-1119(99)00511-9.
67. Forsman, A., Rüetschi, U., Ekholm, J., and Rymo, L. (2008). Identification of intracellular proteins associated with the EBV-encoded nuclear antigen 5 using an efficient tap procedure and FT-ICR mass spectrometry. J. Proteome Res. 7, 2309-2319. doi: 10.1021/pr700769e.
68. Franceschini, A., Szklarczyk, D., Frankild, S., Kuhn, M., Simonovic, M., Roth, A., et al. (2013). STRING v9. 1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 41, D808-D815. doi: 10.1093/nar/gks1094.
69. Fromont-Racine, M., Rain, J.-C., and Legrain, P. (1997). Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nat. Genet. 16, 277-282. doi: 10.1038/ng0797-277.
70. Fukuda, K., Tamura, A., Tsunoda, T., and Takagi, T. (1998). "Toward information extraction: identifying protein names from biological papers," in proceedings of the Pacific Symposium on Biocomputing, Hawaii, 707-718.
71. Fundel, K., Küffner, R., and Zimmer, R. (2007). RelEx-Relation extraction using dependency parse trees. Bioinformatics 23, 365-371. doi: 10.1093/bioinformatics/btl616.
72. Gardiner, D. M., and Howlett, B. J. (2005). Bioinformatic and expression analysis of the putative gliotoxin biosynthetic gene cluster of Aspergillus fumigatus. FEMS Microbiol. Lett. 248, 241-248. doi: 10.1016/j.femsle.2005.05.046.
73. Gardner, T. S., and Faith, J. J. (2005). Reverse-engineering transcription control networks. Phys. Life Rev. 2, 65-88. doi: 10.1016/j.plrev.2005.01.001.
74. Gautier, V. W., Gu, L., O'Donoghue, N., Pennington, S., Sheehy, N., and Hall, W. W. (2009). In vitro nuclear interactome of the HIV-1 Tat protein. Retrovirology 6, 47. doi: 10.1186/1742-4690-6-47.
75. Gavin, A.-C., Bösche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., et al. (2002). Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147. doi: 10.1038/415141a.
76. Gerner, M., Nenadic, G., and Bergman, C. M. (2010). LINNAEUS: a species name identification system for biomedical literature. BMC Bioinform. 11:85. doi: 10.1186/1471-2105-11-85.
77. Goll, J., Rajagopala, S. V., Shiau, S. C., Wu, H., Lamb, B. T., and Uetz, P. (2008). MPIDB: the microbial protein interaction database. Bioinformatics 24, 1743-1744. doi: 10.1093/bioinformatics/btn285.
78. Gottschalk, R. A., Martins, A. J., Sjoelund, V. H., Angermann, B. R., Lin, B., and Germain, R. N. (2013). Recent progress using systems biology approaches to better understand molecular mechanisms of immunity. Semin. Immunol. 25, 201-208. doi: 10.1016/j.smim.2012.11.002.
79. Gottwein, E., and Cullen, B. R. (2008). Viral and cellular microRNAs as determinants of viral pathogenesis and immunity. Cell host Microbe 3, 375-387. doi: 10.1016/j.chom.2008.05.002.
80. Gouzy, A., Poquet, Y., and Neyrolles, O. (2014). Nitrogen metabolism in Mycobacterium tuberculosis physiology and virulence. Nat. Rev. Microbiol. 12, 729-737. doi: 10.1038/nrmicro3349.
81. Greenfield, A., Madar, A., Ostrer, H., and Bonneau, R. (2010). DREAM4: combining genetic and dynamic information to identify biological networks and dynamical models. PLoS ONE 5:e13397. doi: 10.1371/journal.pone.0013397.
82. Guillet, J., Hallier, M., and Felden, B. (2013). Emerging functions for the Staphylococcus aureus RNome. PLoS Pathog. 9:e1003767. doi: 10.1371/journal.ppat.1003767.
83. Guirimand, T., Delmotte, S., and Navratil, V. (2015). VirHostNet 2.0: surfing on the web of virus/host molecular interactions data. Nucleic Acids Res. 43, D583-D587. doi: 10.1093/nar/gku1121.
84. Guo, Y., Luo, J., Wang, J., Wang, Y., and Wu, R. (2011). How to compute which genes control drug resistance dynamics. Drug Discov. Today 16, 339-344. doi: 10.1016/j.drudis.2011.02.004.
85. Guthke, R., Linde, J., Mech, F., and Figge, M. T. (2012). Systems biology of microbial infection. Front. Microbiol. 3:328. doi: 10.3389/fmicb.2012.00328.
86. Guthke, R., Möller, U., Hoffmann, M., Thies, F., and Töpfer, S. (2005). Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection. Bioinformatics 21, 1626-1634. doi: 10.1093/bioinformatics/bti226.
87. Guttman, D. S., McHardy, A. C., and Schulze-Lefert, P. (2014). Microbial genome-enabled insights into plant-microorganism interactions. Nat. Rev. Genet. 15, 797-813. doi: 10.1038/nrg3748.
88. Hao, L., Sakurai, A., Watanabe, T., Sorensen, E., Nidom, C. A., Newton, M. A., et al. (2008). Drosophila RNAi screen identifies host genes important for influenza virus replication. Nature 454, 890-893. doi: 10.1038/nature07151.
89. Hartlova, A., Krocova, Z., Cerveny, L., and Stulik, J. (2011). A proteomic view of the host-pathogen interaction: the host perspective. Proteomics 11, 3212-3220. doi: 10.1002/pmic.201000767.
90. Hecker, M., Lambeck, S., Toepfer, S., van Someren, E., and Guthke, R. (2009). Gene regulatory network inference: data integration in dynamic models-a review. Biosystems 96, 86-103. doi: 10.1016/j.biosystems.2008.12.004.
91. Heilmann, C. J., Sorgo, A. G., and Klis, F. M. (2012). News from the fungal front: wall proteome dynamics and host-pathogen interplay. PLoS Pathog. 8:e1003050. doi: 10.1371/journal.ppat.1003050.
92. Heroven, A. K., and Dersch, P. (2014). Coregulation of host-adapted metabolism and virulence by pathogenic yersiniae. Front. Cell. Infect. Microbiol. 4:146. doi: 10.3389/fcimb.2014.00146.
93. Heyl, K. A., Klassert, T. E., Heinrich, A., Müller, M. M., Klaile, E., Dienemann, H., et al. (2014). Dectin-1 is expressed in human lung and mediates the proinflammatory immune response to nontypeable Haemophilus influenzae. mBio 5, e01492-e01414. doi: 10.1128/mBio.01492-14.
94. Ho, Y., Gruhler, A., Heilbut, A., Bader, G. D., Moore, L., Adams, S.-L., et al. (2002). Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183. doi: 10.1038/415180a.
95. Hobbs, J. R. (1978). Resolving pronoun references. Lingua 44, 311-338. doi: 10.1016/0024-3841(78)90006-2.
96. Horn, F., Heinekamp, T., Kniemeyer, O., Pollmächer, J., Valiante, V., and Brakhage, A. A. (2012). Systems biology of fungal infection. Front. Microbiol. 3:108. doi: 10.3389/fmicb.2012.00108.
97. Horn, F., Rittweger, M., Taubert, J., Lysenko, A., Rawlings, C., and Guthke, R. (2014). Interactive exploration of integrated biological datasets using context-sensitive workflows. Front. Genet. 5:21. doi: 10.3389/fgene.2014.00021.
98. Hsieh, T. Y., Matsumoto, M., Chou, H. C., Schneider, R., Hwang, S. B., Lee, A. S., et al. (1998). Hepatitis C virus core protein interacts with heterogeneous nuclear ribonucleoprotein K. J. Biol. Chem. 273, 17651-17659. doi: 10.1074/jbc.273.28.17651.
99. Hsu, C.-N., Chang, Y.-M., Kuo, C.-J., Lin, Y.-S., Huang, H.-S., and Chung, I.-F. (2008). Integrating high dimensional bi-directional parsing models for gene mention tagging. Bioinformatics 24, i286-i294. doi: 10.1093/bioinformatics/btn183.
100. Hünniger, K., Lehnert, T., Bieber, K., Martin, R., Figge, M. T., and Kurzai, O. (2014). A virtual infection model quantifies innate effector mechanisms and Candida albicans immune escape in human blood. PLoS Comput. Biol. 10:e1003479. doi: 10.1371/journal.pcbi.1003479.
101. Huthmacher, C., Hoppe, A., Bulik, S., and Holzhütter, H.-G. (2010). Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis. BMC Syst. Biol. 4:120. doi: 10.1186/1752-0509-4-120.
102. Isci, S., Dogan, H., Ozturk, C., and Otu, H. H. (2014). Bayesian network prior: network analysis of biological data using external knowledge. Bioinformatics 30, 860-867. doi: 10.1093/bioinformatics/btt643.
103. Ito, T., Tashiro, K., Muta, S., Ozawa, R., Chiba, T., Nishizawa, M., et al. (2000). Toward a protein-protein interaction map of the budding yeast: a comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc. Natl. Acad. Sci. U.S.A. 97, 1143-1147. doi: 10.1073/pnas.97.3.1143.
104. Jäger, S., Cimermancic, P., Gulbahce, N., Johnson, J. R., McGovern, K. E., Clarke, S. C., et al. (2012). Global landscape of HIV-human protein complexes. Nature 481, 365-370.
105. Jelier, R., Jenster, G., Dorssers, L. C. J., van der Eijk, C. C., van Mulligen, E. M., Mons, B., et al. (2005). Co-occurrence based meta-analysis of scientific texts: retrieving biological relationships between genes. Bioinformatics 21, 2049-2058. doi: 10.1093/bioinformatics/bti268.
106. Kafsack, B. F., and Llinás, M. (2010). Eating at the table of another: metabolomics of host-parasite interactions. Cell host Microbe 7, 90-99. doi: 10.1016/j.chom.2010.01.008.
107. Karlas, A., Machuy, N., Shin, Y., Pleissner, K.-P., Artarini, A., Heuer, D., et al. (2010). Genome-wide RNAi screen identifies human host factors crucial for influenza virus replication. Nature 463, 818-822. doi: 10.1038/nature08760.
108. Kauffman, K. J., Prakash, P., and Edwards, J. S. (2003). Advances in flux balance analysis. Curr. Opin. Biotechnol. 14, 491-496. doi: 10.1016/j.copbio.2003.08.001.
109. Kentner, D., Martano, G., Callon, M., Chiquet, P., Brodmann, M., Burton, O., et al. (2014). Shigella reroutes host cell central metabolism to obtain high-flux nutrient supply for vigorous intracellular growth. Proc. Natl. Acad. Sci. U.S.A. 111, 9929-9934. doi: 10.1073/pnas.1406694111.
110. Keshava Prasad, T. S., Goel, R., Kandasamy, K., Keerthikumar, S., Kumar, S., Mathivanan, S., et al. (2009). Human protein reference database-2009 update. Nucleic Acids Res. 37, D767-D772. doi: 10.1093/nar/gkn892.
111. Khadka, S., Vangeloff, A. D., Zhang, C., Siddavatam, P., Heaton, N. S., Wang, L., et al. (2011). A physical interaction network of dengue virus and human proteins. Mol. Cell. Proteomics 10:M111.012187. doi: 10.1074/mcp.M111.012187.
112. Kim, J.-D., Ohta, T., Pyysalo, S., Kano, Y., and Tsujii, J. (2009). "Overview of BioNLP'09 shared task on event extraction," in Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Tas, Stroudsburg, PA, 1-9.
113. Kim, J.-D., Pyysalo, S., Ohta, T., Bossy, R., Nguyen, N., and Tsujii, J. (2011). "Overview of BioNLP shared task 2011," in Proceedings of the BioNLP Shared Task 2011 Workshop, Portland, OR, 1-6.
114. Kim, S., Shin, S.-Y., Lee, I.-H., Kim, S.-J., Sriram, R., and Zhang, B.-T. (2008). PIE: an online prediction system for protein-protein interactions from text. Nucleic Acids Res. 36, W411-W415. doi: 10.1093/nar/gkn281.
115. Kitano, H. (2002). Systems biology: a brief overview. Science 295, 1662-1664. doi: 10.1126/science.1069492.
116. Komarova, A. V., Combredet, C., Meyniel-Schicklin, L., Chapelle, M., Caignard, G., Camadro, J.-M., et al. (2011). Proteomic analysis of virus-host interactions in an infectious context using recombinant viruses. Mol. Cell. Proteomics 10:M110.007443. doi: 10.1074/mcp.M110.007443.
117. König, R., Stertz, S., Zhou, Y., Inoue, A., Hoffmann, H.-H., Bhattacharyya, S., et al. (2010). Human host factors required for influenza virus replication. Nature 463, 813-817. doi: 10.1038/nature08699.
118. König, R., Zhou, Y., Elleder, D., Diamond, T. L., Bonamy, G. M. C., Irelan, J. T., et al. (2008). Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell 135, 49-60. doi: 10.1016/j.cell.2008.07.032.
119. Korkin, D., Thieu, T., Joshi, S., and Warren, S. (2011). "Mining host-pathogen interactions," in Systems and Computational Biology-Molecular and Cellular Experimental Systems, ed. N.-S. Yang (Rijeka: InTech), 163-184. doi: 10.5772/22016.
120. Kraibooj, K., Park, H.-R., Dahse, H.-M., Skerka, C., Voigt, K., and Figge, M. T. (2014). Virulent strain of Lichtheimia corymbifera shows increased phagocytosis by macrophages as revealed by automated microscopy image analysis. Mycoses 57(Suppl. 3), 56-66. doi: 10.1111/myc.12237.
121. Krallinger, M., Leitner, F., Rodriguez-Penagos, C., and Valencia, A. (2008). Overview ofthe protein-protein interaction annotation extraction task of BioCreative II. Genome Biol. 9(Suppl. 2), S4. doi: 10.1186/gb-2008-9-s2-s4.
122. Krishnan, M. N., Ng, A., Sukumaran, B., Gilfoy, F. D., Uchil, P. D., Sultana, H., et al. (2008). RNA interference screen for human genes associated with West Nile virus infection. Nature 455, 242-245. doi: 10.1038/nature07207.
123. Kumar, D., Nath, L., Kamal, M. A., Varshney, A., Jain, A., Singh, S., et al. (2010). Genome-wide analysis of the host intracellular network that regulates survival of Mycobacterium tuberculosis. Cell 140, 731-743. doi: 10.1016/j.cell.2010.02.012.
124. Kumar, R., and Nanduri, B. (2010). HPIDB-a unified resource for host-pathogen interactions. BMC Bioinform. 11(Suppl. 6):S16. doi: 10.1186/1471-2105-11-S6-S16.
125. Kwofie, S. K., Schaefer, U., Sundararajan, V. S., Bajic, V. B., and Christoffels, A. (2011). HCVpro: hepatitis C virus protein interaction database. Infect. Genet. Evol. 11, 1971-1977. doi: 10.1016/j.meegid.2011.09.001.
126. Law, G. L., Korth, M. J., Benecke, A. G., and Katze, M. G. (2013). Systems virology: host-directed approaches to viral pathogenesis and drug targeting. Nat. Rev. Microbiol. 11, 455-466. doi: 10.1038/nrmicro3036.
127. Leaman, R., and Gonzalez, G. (2008). "BANNER: an executable survey of advances in biomedical named entity recognition," in Proceedings of the Pacific Symposium on Biocomputing, Kohala Coast, 652-663.
128. Lee, A. S.-Y., Burdeinick-Kerr, R., and Whelan, S. P. J. (2014). A genome-wide small interfering RNA screen identifies host factors required for vesicular stomatitis virus infection. J. Virol. 88, 8355-8360. doi: 10.1128/JVI.00642-14.
129. Leitner, F., Mardis, S. A., Krallinger, M., Cesareni, G., Hirschman, L. A., and Valencia, A. (2010). An overview of BioCreative II. 5. IEEE/ACM Trans. Comput. Biol. Bioinform. 7, 385-399. doi: 10.1109/TCBB.2010.61.
130. Le Rouzic, E., Mousnier, A., Rustum, C., Stutz, F., Hallberg, E., Dargemont, C., et al. (2002). Docking of HIV-1 Vpr to the nuclear envelope is mediated by the interaction with the nucleoporin hCG1. J. Biol. Chem. 277, 45091-45098. doi: 10.1074/jbc.M207439200.
131. Licata, L., Briganti, L., Peluso, D., Perfetto, L., Iannuccelli, M., Galeota, E., et al. (2012). MINT, the molecular interaction database: 2012 update. Nucleic Acids Res. 40, D857-D861. doi: 10.1093/nar/gkr930.
132. Lima, T. B., Pinto, M. F. S., Ribeiro, S. M., de Lima, L. A., Viana, J. C., Gomes Júnior, N., et al. (2013). Bacterial resistance mechanism: what proteomics can elucidate. FASEB J. 7, 1291-1303. doi: 10.1096/fj.12-221127.
133. Linde, J., Hortschansky, P., Fazius, E., Brakhage, A. A., Guthke, R., and Haas, H. (2012). Regulatory interactions for iron homeostasis in Aspergillus fumigatus inferred by a systems biology approach. BMC Syst. Biol. 6:6. doi: 10.1186/1752-0509-6-6.
134. Linde, J., Schulze, S., Henkel, S. G., and Guthke, R. (2015). Data-and knowledge-based modeling of gene regulatory networks: an update. EXCLI J. 14, 346-378.
135. Linde, J., Wilson, D., Hube, B., and Guthke, R. (2010). Regulatory network modelling of iron acquisition by a fungal pathogen in contact with epithelial cells. BMC Syst. Biol. 4:148. doi: 10.1186/1752-0509-4-148.
136. Li, Q., Brass, A. L., Ng, A., Hu, Z., Xavier, R. J., Liang, T. J., et al. (2009). A genome-wide genetic screen for host factors required for hepatitis C virus propagation. Proc. Natl. Acad. Sci. U.S.A. 106, 16410-16415. doi: 10.1073/pnas.0907439106.
137. Li, Y., Wang, C., Miao, Z., Bi, X., Wu, D., Jin, N., et al. (2015). ViRBase: a resource for virus-host ncRNA-associated interactions. Nucleic Acids Res. 43, D578-D582. doi: 10.1093/nar/gku903.
138. Li-Pook-Than, J., and Snyder, M. (2013). iPOP goes the world: integrated personalized Omics profiling and the road toward improved health care. Chem. Biol. 20, 660-666. doi: 10.1016/j.chembiol.2013.05.001.
139. Liu, B., and Pop, M. (2009). ARDB-antibiotic resistance genes database. Nucleic Acids Res. 37, D443-D447. doi: 10.1093/nar/gkn656.
140. Longo, A. V., Burrowes, P. A., and Zamudio, K. R. (2014). Genomic studies of disease-outcome in host-pathogen dynamics. Integr. Comp. Biol. 54, 427-438. doi: 10.1093/icb/icu073.
141. Lu, W., Lo, S. Y., Chen, M., Wu, K. J., Fung, Y. K., and Ou, J. H. (1999). Activation of p53 tumor suppressor by hepatitis C virus core protein. Virology 264, 134-141. doi: 10.1006/viro.1999.9979.
142. Lusic, M., Marcello, A., Cereseto, A., and Giacca, M. (2003). Regulation of HIV-1 gene expression by histone acetylation and factor recruitment at the LTR promoter. EMBO J. 22, 6550-6561. doi: 10.1093/emboj/cdg631.
143. Ma, H., and Goryanin, I. (2008). Human metabolic network reconstruction and its impact on drug discovery and development. Drug Discov. Today 13, 402-408. doi: 10.1016/j.drudis.2008.02.002.
144. Manchanda, H., Seidel, N., Krumbholz, A., Sauerbrei, A., Schmidtke, M., and Guthke, R. (2014). Within-host influenza dynamics: a small-scale mathematical modeling approach. Biosystems 118, 51-59. doi: 10.1016/j.biosystems.2014.02.004.
145. Marbach, D., Costello, J. C., Küffner, R., Vega, N. M., Prill, R. J., Camacho, D. M., et al. (2012). Wisdom of crowds for robust gene network inference. Nat. Methods 9, 796-804. doi: 10.1038/nmeth.2016.
146. Matsumoto, M., Hsieh, T., Zhu, N., Van Arsdale, T., Hwang, S. B., Jeng, K.-S., et al. (1997). Hepatitis C virus core protein interacts with the cytoplasmic tail of lymphotoxin-beta receptor. J. Virol. 71, 1301-1309.
147. McCraith, S., Holtzman, T., Moss, B., and Fields, S. (2000). Genome-wide analysis of vaccinia virus protein-protein interactions. Proc. Natl. Acad. Sci. U.S.A. 97, 4879-4884. doi: 10.1073/pnas.080078197.
148. McDonald, R., and Pereira, F. (2005). Identifying gene and protein mentions in text using conditional random fields. BMC Bioinform. 6(Suppl. 1):S6. doi: 10.1186/1471-2105-6-S1-S6.
149. Mech, F., Thywissen, A., Guthke, R., Brakhage, A. A., and Figge, M. T. (2011). Automated image analysis of the host-pathogen interaction between phagocytes and Aspergillus fumigatus. PLoS ONE 6:e19591. doi: 10.1371/journal.pone.0019591.
150. Mika, S., and Rost, B. (2004). Protein names precisely peeled off free text. Bioinformatics 20, i241-i247. doi: 10.1093/bioinformatics/bth904.
151. Milenbachs, A. A., Brown, D. P., Moors, M., and Youngman, P. (1997). Carbon-source regulation of virulence gene expression in Listeria monocytogenes. Mol. Microbiol. 23, 1075-1085. doi: 10.1046/j.1365-2958.1997.2711634.x.
152. Mooney, M., McWeeney, S., Canderan, G., and Sékaly, R.-P. (2013). A systems framework for vaccine design. Curr. Opin. Immunol. 25, 551-555. doi: 10.1016/j.coi.2013.09.014.
153. Morens, D. M., Folkers, G. K., and Fauci, A. S. (2004). The challenge of emerging and re-emerging infectious diseases. Nature 430, 242-249. doi: 10.1038/nature02759.
154. Moser, L. A., Pollard, A. M., and Knoll, L. J. (2013). A Genome-wide siRNA screen to identify host factors necessary for growth of the parasite Toxoplasma gondii. PLoS ONE 8:e68129. doi: 10.1371/journal.pone.0068129.
155. Mulder, N. J., Akinola, R. O., Mazandu, G. K., and Rapanoel, H. (2014). Using biological networks to improve our understanding of infectious diseases. Comput. Struct. Biotechnol. J. 11, 1-10. doi: 10.1016/j.csbj.2014.08.006.
156. Murali, T. M., Dyer, M. D., Badger, D., Tyler, B. M., and Katze, M. G. (2011). Network-based prediction and analysis of HIV dependency factors. PLoS Comput. Biol. 7:e1002164. doi: 10.1371/journal.pcbi.1002164.
157. Naderi, N., Kappler, T., Baker, C. J. O., and Witte, R. (2011). Organism tagger: detection, normalization and grounding of organism entities in biomedical documents. Bioinformatics 27, 2721-2729. doi: 10.1093/bioinformatics/btr452.
158. Naji, S., Ambrus, G., Cimermančič, P., Reyes, J. R., Johnson, J. R., Filbrandt, R., et al. (2012). Host cell interactome of HIV-1 Rev includes RNA helicases involved in multiple facets of virus production. Mol. Cell. Proteomics 11:M111.015313. doi: 10.1074/mcp.M111.015313.
159. Nakajima, N., and Akutsu, T. (2014). Network completion for static gene expression data. Adv. Bioinform. 2014, 382452. doi: 10.1155/2014/382452.
160. Nédellec, C., Bossy, R., Kim, J.-D., Kim, J., Ohta, T., Pyysalo, S., et al. (2013). "Overview of bionlp shared task 2013," in Proceedings of the BioNLP Shared Task 2013 Workshop, Sofia, 1-7.
161. Ngo, H. T. T., Pham, L. V., Kim, J.-W., Lim, Y.-S., and Hwang, S. B. (2013). Modulation of mitogen-activated protein kinase-activated protein kinase 3 by hepatitis C virus core protein. J. Virol. 87, 5718-5731. doi: 10.1128/JVI.03353-12.
162. Ng, T. I., Mo, H., Pilot-Matias, T., He, Y., Koev, G., Krishnan, P., et al. (2007). Identification of host genes involved in hepatitis C virus replication by small interfering RNA technology. Hepatology 45, 1413-1421. doi: 10.1002/hep.21608.
163. Oberhardt, M. A., Palsson, B.Ø., and Papin, J. A. (2009). Applications of genome-scale metabolic reconstructions. Mol. Syst. Biol. 5, 320. doi: 10.1038/msb.2009.77.
164. Olszewski, K. L., Morrisey, J. M., Wilinski, D., Burns, J. M., Vaidya, A. B., Rabinowitz, J. D., et al. (2009). Host-parasite interactions revealed by Plasmodium falciparum metabolomics. Cell Host Microbe 5, 191-199. doi: 10.1016/j.chom.2009.01.004.
165. Ono, T., Hishigaki, H., Tanigami, A., and Takagi, T. (2001). Automated extraction of information on protein-protein interactions from the biological literature. Bioinformatics 17, 155-161. doi: 10.1093/bioinformatics/17.2.155.
166. Orchard, S., Ammari, M., Aranda, B., Breuza, L., Briganti, L., Broackes-Carter, F., et al. (2013). The MIntAct project-IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res. 42, D358-D363. doi: 10.1093/nar/gkt1115.
167. Orth, J. D., Thiele, I., and Palsson, B.Ø. (2010). What is flux balance analysis? Nat. Biotechnol. 28, 245-248. doi: 10.1038/nbt.1614.
168. Otto, A., van Dijl, J. M., Hecker, M., and Becher, D. (2014). The Staphylococcus aureus proteome. Int. J. Med. Microbiol. 304, 110-120. doi: 10.1016/j.ijmm.2013.11.007.
169. Owsianka, A. M., and Patel, A. H. (1999). Hepatitis C virus core protein interacts with a human DEAD box protein DDX3. Virology 257, 330-340. doi: 10.1006/viro.1999.9659.
170. Palmer, A. C., and Kishony, R. (2013). Understanding, predicting and manipulating the genotypic evolution of antibiotic resistance. Nat. Rev. Genet. 14, 243-248. doi: 10.1038/nrg3351.
171. Panayidou, S., Ioannidou, E., and Apidianakis, Y. (2014). Human pathogenic bacteria, fungi, and viruses in Drosophila: disease modeling, lessons, and shortcomings. Virulence 5, 253-269. doi: 10.4161/viru.27524.
172. Perelson, A. S. (2002). Modelling viral and immune system dynamics. Nat. Rev. Immunol. 2, 28-36. doi: 10.1038/nri700.
173. Pichlmair, A., Kandasamy, K., Alvisi, G., Mulhern, O., Sacco, R., Habjan, M., et al. (2012). Viral immune modulators perturb the human molecular network by common and unique strategies. Nature 487, 486-490. doi: 10.1038/nature11289.
174. Pickett, B. E., Sadat, E. L., Zhang, Y., Noronha, J. M., Squires, R. B., Hunt, V., et al. (2012). ViPR: an open bioinformatics database and analysis resource for virology research. Nucleic Acids Res. 40, D593-D598. doi: 10.1093/nar/gkr859.
175. Pittman, K. J., Aliota, M. T., and Knoll, L. J. (2014). Dual transcriptional profiling of mice and Toxoplasma gondii during acute and chronic infection. BMC Genomics 15:806. doi: 10.1186/1471-2164-15-806.
176. Pollmächer, J., and Figge, M. T. (2014). Agent-Based model of human alveoli predicts chemotactic signaling by epithelial cells during early Aspergillus fumigatus infection. PLoS ONE 9:e111630. doi: 10.1371/journal.pone.0111630.
177. Prieto, C., and De Las Rivas, J. (2006). APID: agile protein interaction dataanalyzer. Nucleic Acids Res. 34, W298-W302. doi: 10.1093/nar/gkl128.
178. Prill, R. J., Marbach, D., Saez-Rodriguez, J., Sorger, P. K., Alexopoulos, L. G., Xue, X., et al. (2010). Towards a rigorous assessment of systems biology models: the DREAM3 challenges. PLoS ONE 5:e9202. doi: 10.1371/journal.pone.0009202.
179. Qian, C., and Cao, X. (2013). Regulation of Toll-like receptor signaling pathways in innate immune responses. Ann. N. Y. Acad. Sci. 1283, 67-74. doi: 10.1111/j.1749-6632.2012.06786.x.
180. Raghunathan, A., Reed, J., Shin, S., Palsson, B., and Daefler, S. (2009). Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction. BMC Syst. Biol. 3:38. doi: 10.1186/1752-0509-3-38.
181. Rain, J.-C., Selig, L., De Reuse, H., Battaglia, V., Reverdy, C., Simon, S., et al. (2001). The protein-protein interaction map of Helicobacter pylori. Nature 409, 211-215. doi: 10.1038/35051615.
182. Ramachandra, S., Linde, J., Brock, M., Guthke, R., Hube, B., and Brunke, S. (2014). Regulatory networks controlling nitrogen sensing and uptake in Candida albicans. PLoS ONE 9:e92734. doi: 10.1371/journal.pone.0092734.
183. Razick, S., Magklaras, G., and Donaldson, I. M. (2008). iRefIndex: a consolidated protein interaction database with provenance. BMC Bioinform. 9:405. doi: 10.1186/1471-2105-9-405.
184. Rienksma, R. A., Suarez-Diez, M., Spina, L., Schaap, P. J., and Martins Dos Santos, V. A. P. (2014). Systems-level modeling of mycobacterial metabolism for the identification of new (multi-) drug targets. Semin. Immunol. 26, 610-622. doi: 10.1016/j.smim.2014.09.013.
185. Rohmer, L., Hocquet, D., and Miller, S. I. (2011). Are pathogenic bacteria just looking for food? Metabolism and microbial pathogenesis. Trends Microbiol. 19, 341-348. doi: 10.1016/j.tim.2011.04.003.
186. Ruppin, E., Papin, J. A., de Figueiredo, L. F., and Schuster, S. (2010). Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks. Curr. Opin. Biotechnol. 21, 502-510. doi: 10.1016/j.copbio.2010.07.002.
187. Saayman, S., Ackley, A., Turner, A.-M. W., Famiglietti, M., Bosque, A., Clemson, M., et al. (2014). An HIV-encoded antisense long noncoding RNA epigenetically regulates viral transcription. Mol. Ther. 22, 1164-1175. doi: 10.1038/mt.2014.29.
188. Saenz, R. A., Quinlivan, M., Elton, D., Macrae, S., Blunden, A. S., Mumford, J. A., et al. (2010). Dynamics of influenza virus infection and pathology. J. Virol. 84, 3974-3983. doi: 10.1128/JVI.02078-09.
189. Salwinski, L., Miller, C. S., Smith, A. J., Pettit, F. K., Bowie, J. U., and Eisenberg, D. (2004). The database of interacting proteins: 2004 update. Nucleic Acids Res. 32, D449-D451. doi: 10.1093/nar/gkh086.
190. Sarker, M., Talcott, C., and Galande, A. K. (2013). In silico systems biology approaches for the identification of antimicrobial targets. Methods Mol. Biol. 993, 13-30. doi: 10.1007/978-1-62703-342-8_2.
191. Sasikaran, J., Ziemski, M., Zadora, P. K., Fleig, A., and Berg, I. A. (2014). Bacterial itaconate degradation promotes pathogenicity. Nat. Chem. Biol. 10, 371-377. doi: 10.1038/nchembio.1482.
192. Scharf, D. H., Heinekamp, T., Remme, N., Hortschansky, P., Brakhage, A. A., and Hertweck, C. (2012). Biosynthesis and function of gliotoxin in Aspergillus fumigatus. Appl. Microbiol. Biotechnol. 93, 467-472. doi: 10.1007/s00253-011-3689-1.
193. Schmidt, F., and Völker, U. (2011). Proteome analysis of host-pathogen interactions: investigation of pathogen responses to the host cell environment. Proteomics 11, 3203-3211. doi: 10.1002/pmic.201100158.
194. Schulze, S., Henkel, S. G., Driesch, D., Guthke, R., and Linde, J. (2015). Computationalprediction of molecular pathogen-host interactions based on dual transcriptome data. Front. Microbiol. 6:65. doi: 10.3389/fmicb.2015.00065.
195. Sessions, O. M., Barrows, N. J., Souza-Neto, J. A., Robinson, T. J., Hershey, C. L., Rodgers, M. A., et al. (2009). Discovery of insect and human dengue virus host factors. Nature 458, 1047-1050. doi: 10.1038/nature07967.
196. Settles, B. (2005). ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text. Bioinformatics 21, 3191-3192. doi: 10.1093/bioinformatics/bti475.
197. Shapira, S. D., Gat-Viks, I., Shum, B. O. V., Dricot, A., de Grace, M. M., Wu, L., et al. (2009). A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection. Cell 139, 1255-1267. doi: 10.1016/j.cell.2009.12.018.
198. Simon, S., Guthke, R., Kamradt, T., and Frey, O. (2012). Multivariate analysis of flow cytometric data using decision trees. Front. Microbiol. 3:114. doi: 10.3389/fmicb.2012.00114.
199. Singh, H., Khan, A. A., and Dinner, A. R. (2014). Gene regulatory networks in the immune system. Trends Immunol. 35, 211-218. doi: 10.1016/j.it.2014.03.006.
200. Singh, I., Tastan, O., and Klein-Seetharaman, J. (2010). "Comparison of virus interactions with human signal transduction pathways," in Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, Niagara Falls, NY, 17-24. doi: 10.1145/1854776.1854785.
201. Six, A., Mariotti-Ferrandiz, M. E., Chaara, W., Magadan, S., Pham, H.-P., Lefranc, M.-P., et al. (2013). The past, present, and future of immune repertoire biology-the rise of next-generation repertoire analysis. Front. Immunol. 4:413. doi: 10.3389/fimmu.2013.00413.
202. Skalsky, R. L., and Cullen, B. R. (2010). Viruses, microRNAs, and host interactions. Annu. Rev. Microbiol. 64, 123-141. doi: 10.1146/annurev.micro.112408.134243.
203. Sleator, D. D., and Temperley, D. (1995). Parsing English with a link grammar. ArXiv Prepr. Cmp-lg/9508004.
204. Smith, L., Tanabe, L. K., Nee Ando, R. J., Kuo, C.-J., Chung, I.-F., Hsu, C.-N., et al. (2008). Overview of BioCreative II gene mention recognition. Genome Biol. 9(Suppl. 2):S2. doi: 10.1186/gb-2008-9-s2-s2.
205. Stanberry, L., Mias, G. I., Haynes, W., Higdon, R., Snyder, M., and Kolker, E. (2013). Integrative analysis of longitudinal metabolomics data from a personal multi-omics profile. Metabolites 3, 741-760. doi: 10.3390/metabo3030741.
206. Stebbins, C. E. (2005). Structural microbiology at the pathogen-host interface. Cell. Microbiol. 7, 1227-1236. doi: 10.1111/j.1462-5822.2005.00564.x.
207. Tai, A. W., Benita, Y., Peng, L. F., Kim, S.-S., Sakamoto, N., Xavier, R. J., et al. (2009). A functional genomic screen identifies cellular cofactors of hepatitis C virus replication. Cell Host Microbe 5, 298-307. doi: 10.1016/j.chom.2009.02.001.
208. Temkin, J. M., and Gilder, M. R. (2003). Extraction of protein interaction information from unstructured text using a context-free grammar. Bioinformatics 19, 2046-2053. doi: 10.1093/bioinformatics/btg279.
209. Thieu, T., Joshi, S., Warren, S., and Korkin, D. (2012). Literature mining of host-pathogen interactions: comparing feature-based supervised learning and language-based approaches. Bioinformatics 28, 867-875. doi: 10.1093/bioinformatics/bts042.
210. Tierney, L., Kuchler, K., Rizzetto, L., and Cavalieri, D. (2012a). Systems biology of host-fungus interactions: turning complexity into simplicity. Curr. Opin. Microbiol. 15, 440-446. doi: 10.1016/j.mib.2012.05.001.
211. Tierney, L., Linde, J., Müller, S., Brunke, S., Molina, J. C., Hube, B., et al. (2012b). An interspecies regulatory network inferred from simultaneous RNA-seq of Candida albicans invading innate immune cells. Front. Microbiol. 3:85. doi: 10.3389/fmicb.2012.00085.
212. Tikk, D., Thomas, P., Palaga, P., Hakenberg, J., and Leser, U. (2010). A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature. PLoS Comput. Biol. 6:e1000837. doi: 10.1371/journal.pcbi.1000837.
213. Tripathi, L. P., Kataoka, C., Taguwa, S., Moriishi, K., Mori, Y., Matsuura, Y., et al. (2010). Network based analysis of hepatitis C virus core and NS4B protein interactions. Mol. Biosyst. 6, 2539-2553. doi: 10.1039/c0mb00103a.
214. Tsai, R. T.-H., Sung, C.-L., Dai, H.-J., Hung, H.-C., Sung, T.-Y., and Hsu, W.-L. (2006). NERBio: using selected word conjunctions, term normalization, and global patterns to improve biomedical named entity recognition. BMC Bioinform. 7(Suppl. 5):S11. doi: 10.1186/1471-2105-7-S5-S11.
215. Tsuruoka, Y., Tateishi, Y., Kim, J.-D., Ohta, T., McNaught, J., Ananiadou, S., et al. (2005). "Developing a robust part-of-speech tagger for biomedical text," in Advances in Informatics-10th Panhellenic Conference on Informatics, LNCS, Vol. 3746, eds P. Bozanis and E. N. Houstis (Berlin: Springer-Verlag), 382-392.
216. Ud-Dean, S. M. M., and Gunawan, R. (2014). Ensemble inference and inferability of gene regulatory networks. PLoS ONE 9:e103812. doi: 10.1371/journal.pone.0103812.
217. Urban, M., Pant, R., Raghunath, A., Irvine, A. G., Pedro, H., and Hammond-Kosack, K. E. (2015). The Pathogen-host interactions database (PHI-base): additions and future developments. Nucleic Acids Res. 43, D645-D655. doi: 10.1093/nar/gku1165.
218. van Someren, E. P., Wessels, L. F. A., Backer, E., and Reinders, M. J. T. (2002). Genetic network modeling. Pharmacogenomics 3, 507-525. doi: 10.1517/14622416.3.4.507.
219. Vialás, V., Nogales-Cadenas, R., Nombela, C., Pascual-Montano, A., and Gil, C. (2009). Proteopathogen, a protein database for studying Candida albicans-host interaction. Proteomics 9, 4664-4668. doi: 10.1002/pmic.200900023.
220. von Mentzer, A., Connor, T. R., Wieler, L. H., Semmler, T., Iguchi, A., Thomson, N. R., et al. (2014). Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution. Nat. Genet. 46, 1321-1326. doi: 10.1038/ng.3145.
221. Walhout, A. J., Sordella, R., Lu, X., Hartley, J. L., Temple, G. F., Brasch, M. A., et al. (2000). Protein interaction mapping in C. elegans using proteins involved in vulval development. Science 287, 116-122. doi: 10.1126/science.287.5450.116.
222. Wattam, A. R., Abraham, D., Dalay, O., Disz, T. L., Driscoll, T., Gabbard, J. L., et al. (2014). PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res. 42, D581-D591. doi: 10.1093/nar/gkt1099.
223. Weber, M., Henkel, S. G., Vlaic, S., Guthke, R., van Zoelen, E. J., and Driesch, D. (2013). Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0. BMC Syst. Biol. 7:1. doi: 10.1186/1752-0509-7-1.
224. Wenk, M. R. (2006). Lipidomics of host-pathogen interactions. FEBS Lett. 580, 5541-5551. doi: 10.1016/j.febslet.2006.07.007.
225. Westermann, A. J., Gorski, S. A., and Vogel, J. (2012). Dual RNA-seq of pathogen and host. Nat. Rev. Microbiol. 10, 618-630. doi: 10.1038/nrmicro2852.
226. Wolstencroft, K., Owen, S., du Preez, F., Krebs, O., Mueller, W., Goble, C., et al. (2011). The SEEK: a platform for sharing data and models in systems biology. Methods Enzymol. 500, 629-655. doi: 10.1016/B978-0-12-385118-5.00029-3.
227. Wu, W., Tran, K. C., Teng, M. N., Heesom, K. J., Matthews, D. A., Barr, J. N., et al. (2012). The interactome of the human respiratory syncytial virus NS1 protein highlights multiple effects on host cell biology. J. Virol. 86, 7777-7789. doi: 10.1128/JVI.00460-12.
228. Xiang, Z., Tian, Y., and He, Y. (2007). PHIDIAS: a pathogen-host interaction data integration and analysis system. Genome Biol. 8, R150 doi: 10.1186/gb-2007-8-7-r150.
229. Xu, G., Strong, M. J., Lacey, M. R., Baribault, C., Flemington, E. K., and Taylor, C. M. (2014). RNA CoMPASS: a dual approach for pathogen and host transcriptome analysis of RNA-seq datasets. PLoS ONE 9:e89445. doi: 10.1371/journal.pone.0089445.
230. Yang, H., Ke, Y., Wang, J., Tan, Y., Myeni, S. K., Li, D., et al. (2011). Insight into bacterial virulence mechanisms against host immune response via the Yersinia pestis-human protein-protein interaction network. Infection Immun. 79, 4413-4424. doi: 10.1128/IAI.05622-11.
231. Yin, L., Xu, G., Torii, M., Niu, Z., Maisog, J. M., Wu, C., et al. (2010). Document classification for mining host pathogen protein-protein interactions. Artif. Intell. Med. 49, 155-160. doi: 10.1016/j.artmed.2010.04.003.
232. Zheng, J., Sugrue, R. J., and Tang, K. (2011). Mass spectrometry based proteomic studies on viruses and hosts-a review. Anal. Chim. Acta 702, 149-159. doi: 10.1016/j.aca.2011.06.045.
233. Zhou, C. E., Smith, J., Lam, M., Zemla, A., Dyer, M. D., and Slezak, T. (2007). MvirDB-a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications. Nucleic Acids Res. 35, D391-D394. doi: 10.1093/nar/gkl791.
234. Zhou, H., Jin, J., and Wong, L. (2013). Progress in computational studies of host-pathogen interactions. J. Bioinform. Comput. Biol. 11, 1230001. doi: 10.1142/S0219720012300018.
235. Zhou, H., Xu, M., Huang, Q., Gates, A. T., Zhang, X. D., Castle, J. C., et al. (2008). Genome-scale RNAi screen for host factors required for HIV replication. Cell Host Microbe 4, 495-504. doi: 10.1016/j.chom.2008.10.004.
236. Zoraghi, R., and Reiner, N. E. (2013). Protein interaction networks as starting points to identify novel antimicrobial drug targets. Curr. Opin. Microbiol. 16, 566-572. doi: 10.1016/j.mib.2013.07.010.