World Health Organization. Global tuberculosis report. WHO Report. Geneva: World Health Organization; 2015.
Google Scholar
Dye C, Watt CJ, Bleed DM, Hosseini SM, Raviglione MC. Evolution of tuberculosis control and prospects for reducing tuberculosis incidence, prevalence, and deaths globally. JAMA. 2005;293:2767–75.
Article
CAS
PubMed
Google Scholar
Gomez JE, McKinney JD. M. tuberculosis persistence, latency, and drug tolerance. Tuberculosis. 2004;84(1):29–44.
Article
PubMed
Google Scholar
Comas I, Gagneux S. The Past and Future of Tuberculosis Research. PLoS Pathog. 2009;5(10):e1000600.
Article
PubMed
PubMed Central
Google Scholar
Russell DG. Mycobacterium tuberculosis: here today, and here tomorrow. Nat Rev Mol Cell Biol. 2001;2:569–86.
Article
CAS
PubMed
Google Scholar
Cole S, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry C3, Tekaia F. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 1998;393:6685.
Article
Google Scholar
Huynh KK, Joshi SA, Brown EJ. A delicate dance: host response to mycobacteria. Curr Opin Immunol. 2011;23(4):464–72.
Article
CAS
PubMed
Google Scholar
Flannagan RS, Cosío G, Grinstein S. Antimicrobial mechanisms of phagocytes and bacterial evasion strategies. Nat Rev Microbiol. 2009;7:355–66.
Article
CAS
PubMed
Google Scholar
Schnappinger D, Ehrt S, Voskuil MI, Liu Y, Mangan JA, Monahan IM, Dolganov G, Efron B, Butcher PD, Nathan C, Schoolnik GK. Transcriptional adaptation of Mycobacterium tuberculosis within macrophages: insights into the phagosomal environment. J Expt Med. 2003;198(5):693–704.
Article
CAS
Google Scholar
Gutierrez MG, Master SS, Singh SB, Taylor GA, Colombo MI, Deretic V. Autophagy is a defense mechanism inhibiting BCG and Mycobacterium tuberculosis survival in infected macrophages. Cell. 2004;119(6):753–66.
Article
CAS
PubMed
Google Scholar
Keane J, Remold HG, Kornfeld H. Virulent Mycobacterium tuberculosis strains evade apoptosis of infected alveolar macrophages. J Immunol. 2000;164:2016–20.
Article
CAS
PubMed
Google Scholar
Velmurugan K, Chen B, Miller JL, Azogue S, Gurses S, Hsu T, et al. Mycobacterium tuberculosis nuoG Is a Virulence Gene That Inhibits Apoptosis of Infected Host Cells. PLoS Pathog. 2007;3(7):e110.
Article
PubMed
PubMed Central
Google Scholar
Jamwal S, Midha MK, Verma HN, Basu A, Rao KV, Manivel V. Characterizing virulence-specific perturbations in the mitochondrial function of macrophages infected with Mycobacterium tuberculosis. Sci Rep. 2013;3:1328.
Seimon TA, Kim MJ, Blumenthal A, Koo J, Ehrt S, Wainwright H, Bekker LG, Kaplan G, Nathan C, Tabas I, Russell DG. Induction of ER stress in macrophages of tuberculosis granulomas. PLoS One. 2010;5(9):e12772.
Article
PubMed
PubMed Central
Google Scholar
Russell DG, Cardona PJ, Kim MJ, Allain S, Altare F. Foamy macrophages and the progression of the human tuberculosis granuloma. Nat Immunol. 2009;10(9):943–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Singh V, Jamwal S, Jain R, Verma P, Gokhale R, Rao KV. Mycobacterium tuberculosis-driven targeted recalibration of macrophage lipid homeostasis promotes the foamy phenotype. Cell Host Microbe. 2012;12(5):669–81.
Article
CAS
PubMed
Google Scholar
Co DO, Hogan LH, Kim SI, Sandor M. Mycobacterial granulomas: keys to a long-lasting host–pathogen relationship. Clin Immunol. 2004;113(2):130–6.
Article
CAS
PubMed
Google Scholar
Silva Miranda M, Breiman A, Allain S, Deknuydt F, Altare F. The Tuberculous Granuloma: An Unsuccessful Host Defence Mechanism Providing a Safety Shelter for the Bacteria? Clin Dev Immunol. 2012;2012:139127.
Article
PubMed
PubMed Central
Google Scholar
Simeone R, Bobard A, Lippmann J, Bitter W, Majlessi L, Brosch R, et al. Phagosomal Rupture by Mycobacterium tuberculosis Results in Toxicity and Host Cell Death. PLoS Pathog. 2012;8(2):e1002507.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rapanoel HA, Mazandu GK, Mulder NJ. Predicting and Analyzing Interactions between Mycobacterium tuberculosis and Its Human Host. PLoS One. 2013;8(7):e67472.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mehra A, Zahra A, Thompson V, Sirisaengtaksin N, Wells A, et al. Mycobacterium tuberculosis Type VII Secreted Effector EsxH Targets Host ESCRT to Impair Trafficking. PLoS Pathog. 2013;9(10):e1003734.
Article
PubMed
PubMed Central
Google Scholar
Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, et al. High-quality binary protein interaction map of the yeast interactome network. Science. 2008;322:104–10.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhou H, Jin J, Wong L. Progress in computational studies of host-pathogen interactions. J Bioinform Comput Biol. 2013;11:1230001.
Article
PubMed
Google Scholar
Nourani E, Khunjush F, Durmuş S. Computational approaches for prediction of pathogen-host protein-protein interactions. Front Microbiol. 2015;6:94.
Article
PubMed
PubMed Central
Google Scholar
Lee SA, Chan CH, Tsai CH, Lai JM, Wang FS, Kao CY, Huang CY. Ortholog-based protein-protein interaction prediction and its application to inter-species interactions. BMC Bioinf. 2008;9(12):1.
Google Scholar
Garcia-Garcia J, Schleker S, Klein-Seetharaman J, Oliva B. BIPS: BIANA Interolog Prediction Server. A tool for protein–protein interaction inference. Nucleic Acids Res. 2012;40(Web Server issue):W147–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Michaut M, Kerrien S, Montecchi-Palazzi L, Chauvat F, Cassier-Chauvat C, Aude JC, Legrain P, Hermjakob H. InteroPORC: Automated Inference of Highly Conserved Protein Interaction Networks. Bioinformatics. 2008;24(14):1625–31.
Article
CAS
PubMed
Google Scholar
Davis FP, Barkan DT, Eswar N, McKerrow JH, Sali A. Host pathogen protein interactions predicted by comparative modeling. Protein Sci. 2007;16:2585–96.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang QC, Petrey D, Deng L, et al. Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature. 2012;490(7421):556–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yu H, Luscombe NM, Lu HX, Zhu X, Xia Y, Han JD, Bertin N, Chung S, Vidal M, Gerstein M. Annotation transfer between genomes: Protein–protein interologs and protein-DNA regulogs. Genome Res. 2004;14:1107–18.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wuchty S. Computational Prediction of Host-Parasite Protein Interactions between P. falciparum and H. sapiens. PLoS One. 2011;6(11):e26960.
Article
CAS
PubMed
PubMed Central
Google Scholar
Krishnadev O, Srinivasan N. Prediction of protein-protein interactions between human host and a pathogen and its application to three pathogenic bacteria. Int J Biol Macromol. 2011;48:613–9.
Article
CAS
PubMed
Google Scholar
Huo T, Liu W, Guo Y, Yang C, Lin J, Rao Z. Prediction of host - pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs. BMC Bioinf. 2015;16:100.
Article
Google Scholar
Zhou H, Gao S, Nguyen NN, et al. Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions. Biol Direct. 2014;9:5.
Article
PubMed
PubMed Central
Google Scholar
Cui T, Zhang L, Wang X, He ZG. Uncovering new signaling proteins and potential drug targets through the interactome analysis of Mycobacterium tuberculosis. BMC Genomics. 2009;10(1):118.
Article
CAS
PubMed
PubMed Central
Google Scholar
Altschul S, Gish W, Miller W, Myers E, Lipman D. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–10.
Article
CAS
PubMed
Google Scholar
Berman HM, Westbrook J, Feng Z, et al. The Protein Data Bank. Nucleic Acids Res. 2000;28(1):235–42.
Article
CAS
PubMed
PubMed Central
Google Scholar
Reddy TBK, Riley R, Wymore F, et al. TB database: an integrated platform for tuberculosis research. Nucleic Acids Res. 2009;37(Database issue):D499–508.
Article
CAS
PubMed
Google Scholar
de Souza GA, Leversen NA, Malen H, Wiker HG. Bacterial proteins with cleaved or uncleaved signal peptides of the general secretory pathway. J Proteomics. 2011;75(2):502–10.
Article
PubMed
Google Scholar
Yu NY, Wagner JR, Laird MR, et al. PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics. 2010;26(13):1608–15.
Article
CAS
PubMed
PubMed Central
Google Scholar
Finn RD, Miller BL, Clements J, Bateman A. iPfam: a database of protein family and domain interactions found in the Protein Data Bank. Nucleic Acids Res. 2014;42(D1):D364–73.
Article
CAS
PubMed
Google Scholar
Mosca R, Ceol A, Stein A, Olivella R, Aloy P. 3did: a catalogue of domain-based interactions of known three-dimensional structure. Nucleic Acids Res. 2014;42(D1):D374–9.
Article
CAS
PubMed
Google Scholar
Punta M, Coggill PC, Eberhardt RY, et al. The Pfam protein families database. Nucleic Acids Res. 2012;40(Database issue):D290–301.
Article
CAS
PubMed
Google Scholar
Ward N, Moreno-Hagelsieb G. Quickly Finding Orthologs as Reciprocal Best Hits with BLAT, LAST, and UBLAST: How Much Do We Miss? PLoS One. 2014;9(7):e101850.
Article
PubMed
PubMed Central
Google Scholar
Altenhoff AM, Dessimoz C. Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comp Biol. 2009;5:e1000262.
Article
Google Scholar
Salichos L, Rokas A. Evaluating Ortholog Prediction Algorithms in a Yeast Model Clade. PLoS One. 2011;6:e18755.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kersey PJ, Morris L, Hermjakob H, Apweiler R. Integr8: Enhanced Inter-Operability of European Molecular Biology Databases. Methods Inf Med. 2003;42:154–60.
CAS
PubMed
Google Scholar
Powell S, Forslund K, Szklarczyk D, et al. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res. 2014;42(Database issue):D231–9.
Article
CAS
PubMed
Google Scholar
Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular datasets. Nucleic Acids Res. 2012;40:D109–14.
Article
CAS
PubMed
Google Scholar
Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000;16(6):276–7.
Article
CAS
PubMed
Google Scholar
Kerrien S, Aranda B, Breuza L, et al. The IntAct molecular interaction database in 2012. Nucleic Acids Res. 2012;40(Database issue):D841–6.
Article
CAS
PubMed
Google Scholar
Licata L, Briganti L, Peluso D, et al. MINT, the molecular interaction database: 2012 update. Nucleic Acids Res. 2012;40(Database issue):D857–61.
Article
CAS
PubMed
Google Scholar
Chatr-aryamontri A, Breitkreutz B-J, Oughtred R, et al. The BioGRID interaction database: 2015 update. Nucleic Acids Res. 2015;43(Database issue):D470–8.
Article
PubMed
Google Scholar
Xenarios I, Salwínski Ł, Duan XJ, Higney P, Kim S-M, Eisenberg D. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res. 2002;30(1):303–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Keshava Prasad TS, Goel R, Kandasamy K, et al. Human Protein Reference Database—2009 update. Nucleic Acids Res. 2009;37(Database issue):D767–72.
Article
CAS
PubMed
Google Scholar
Kumar R, Nanduri B. HPIDB – a unified resource for host-pathogen interactions. BMC Bioinf. 2010;11 Suppl 6:S16.
Article
Google Scholar
Sonnhammer ELL, Östlund G. InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic. Nucleic Acids Res. 2015;43(Database issue):D234–9.
Article
PubMed
Google Scholar
Ta HX, Holm L. Evaluation of different domain-based methods in protein interaction prediction. Biochem Biophys Res Commun. 2009;390:357–62.
Article
CAS
PubMed
Google Scholar
Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, et al. Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles. PLoS Biol. 2007;5(1):e8.
Article
PubMed
PubMed Central
Google Scholar
Blohm P, Frishman G, Smialowski P, Goebels F, Wachinger B, Ruepp A, Frishman D. Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis. Nucleic Acids Res. 2013;42(D1):D396–D400.
Article
PubMed
PubMed Central
Google Scholar
Kumar D, Nath L, Kamal MA, Varshney A, Jain A, Singh S, Rao KV. Genome-wide analysis of the host intracellular network that regulates survival of Mycobacterium tuberculosis. Cell. 2010;140(5):731–43.
Article
CAS
PubMed
Google Scholar
Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 2005;33(Database Issue):D514–7.
Article
CAS
PubMed
Google Scholar
Borsani G, Rugarli EI, Taglialatela M, Wong C, Ballabio A. Characterization of a human and murine gene (CLCN3) sharing similarities to voltage-gated chloride channels and to a yeast integral membrane protein. Genomics. 1995;27(1):131–41.
Article
CAS
PubMed
Google Scholar
von Schwedler UK, Stuchell M, Müller B, Ward DM, Chung HY, Morita E, Wang HE, Davis T, He GP, Cimbora DM, Scott A, Kräusslich HG, Kaplan J, Morham SG, Sundquist WI. The protein network of HIV budding. Cell. 2003;114(6):701–13.
Article
Google Scholar
Bach H, Papavinasasundaram KG, Wong D, Hmama Z, Av-Gay Y. Mycobacterium tuberculosis virulence is mediated by PtpA dephosphorylation of human vacuolar protein sorting 33B. Cell Host Microbe. 2008;3:316–22.
Article
CAS
PubMed
Google Scholar
Sprinzak E, Margalit H. Correlated sequence-signatures as markers of protein–protein interaction. J Mol Biol. 2001;311:681–92.
Article
CAS
PubMed
Google Scholar
Dyer MD, Murali TM, Sobral BW. Computational prediction of host-pathogen protein-protein interactions. Bioinformatics. 2007;23:i159–66.
Article
CAS
PubMed
Google Scholar
Kim WK, Park J, Suh JK. Large scale statistical prediction of protein-protein interaction by potentially interacting domain (PID) pair. Genome Inform. 2002;13:42–50.
CAS
PubMed
Google Scholar
Guimaraes KS, Jothi R, Zotenko E, Przytycka TM. Predicting domain–domain interactions using a parsimony approach. Genome Biol. 2006;7:R104.
Article
PubMed
PubMed Central
Google Scholar
Zhou H, Rezaei J, Hugo W, et al. Stringent DDI-based Prediction of H. sapiens-M. tuberculosis H37Rv Protein-Protein Interactions. BMC Syst Biol. 2013;7 Suppl 6:S6.
Article
PubMed
PubMed Central
Google Scholar
Chindelevitch L, Ziemek D, Enayetellah A, Randhawa R, Sidders B, Brockel C, et al. Causal reasoning on biological networks: interpreting transcriptional changes. Bioinformatics. 2012;28(8):1114–21.
Article
CAS
PubMed
Google Scholar
Mahajan G, Mande SC. From System-Wide Differential Gene Expression to Perturbed Regulatory Factors: A Combinatorial Approach. PLoS One. 2015;10(11):e0142147.
Article
PubMed
PubMed Central
Google Scholar
Lachmann A, Xu H, Krishnan J, Berger SI, Mazloom AR, Ma'ayan A. ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinformatics. 2010;26(19):2438–44.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vinayagam A, Stelzl U, Foulle R, Plassmann S, Zenkner M, Timm J, Assmus HE, Andrade-Navarro MA, Wanker EE. A directed protein interaction network for investigating intracellular signal transduction. Sci Signal. 2011;4(189):rs8.
Article
PubMed
Google Scholar