System-wide coordinates of higher order functions in host-pathogen environment upon Mycobacterium tuberculosis infection

[1]  S. Mande,et al.  Using structural knowledge in the protein data bank to inform the search for potential host-microbe protein interactions in sequence space: application to Mycobacterium tuberculosis , 2017, BMC Bioinformatics.

[2]  S. Sreevatsan,et al.  The role of IL-10 in Mycobacterium avium subsp. paratuberculosis infection , 2016, Cell Communication and Signaling.

[3]  J. Li,et al.  The ubiquitin system: a critical regulator of innate immunity and pathogen–host interactions , 2016, Cellular & Molecular Immunology.

[4]  Sailu Yellaboina,et al.  Identification and functional analysis of essential, conserved, housekeeping and duplicated genes , 2016, FEBS letters.

[5]  J. Mesirov,et al.  The Molecular Signatures Database Hallmark Gene Set Collection , 2015 .

[6]  M. Savitskaya,et al.  Mechanisms of apoptosis , 2015, Biochemistry (Moscow).

[7]  Y. Akhter,et al.  Proteome-scale identification and characterization of mitochondria targeting proteins of Mycobacterium avium subspecies paratuberculosis: Potential virulence factors modulating host mitochondrial function. , 2015, Mitochondrion.

[8]  Y. Akhter,et al.  A tug-of-war between the host and the pathogen generates strategic hotspots for the development of novel therapeutic interventions against infectious diseases , 2015, Virulence.

[9]  Balvinder Singh,et al.  Rv2031c of Mycobacterium tuberculosis: a master regulator of Rv2028–Rv2031 (HspX) operon , 2015, Front. Microbiol..

[10]  T. Arnould,et al.  Mitochondria: a target for bacteria. , 2015, Biochemical pharmacology.

[11]  S. Weinberg,et al.  Mitochondria in the regulation of innate and adaptive immunity. , 2015, Immunity.

[12]  M. Kopylov,et al.  Biosynthesis of Cell Envelope-Associated Phenolic Glycolipids in Mycobacterium marinum , 2015, Journal of bacteriology.

[13]  Yu-Rong Fu,et al.  Differential Transcriptional Response in Macrophages Infected with Cell Wall Deficient versus Normal Mycobacterium Tuberculosis , 2015, International journal of biological sciences.

[14]  M. García-Díaz,et al.  A Distinct MaoC-like Enoyl-CoA Hydratase Architecture Mediates Cholesterol Catabolism in Mycobacterium tuberculosis , 2014, ACS chemical biology.

[15]  Sailu Yellaboina,et al.  Integrative framework for identification of key cell identity genes uncovers determinants of ES cell identity and homeostasis , 2014, Proceedings of the National Academy of Sciences.

[16]  Ning Jiang,et al.  Network portal: a database for storage, analysis and visualization of biological networks , 2013, Nucleic Acids Res..

[17]  J. García,et al.  A highly conserved mycobacterial cholesterol catabolic pathway. , 2013, Environmental microbiology.

[18]  B. Py,et al.  Iron/sulfur proteins biogenesis in prokaryotes: formation, regulation and diversity. , 2013, Biochimica et biophysica acta.

[19]  Fatih Erdogan Sevilgen,et al.  PHISTO: pathogen-host interaction search tool , 2013, Bioinform..

[20]  Thomas R. Ioerger,et al.  Global Assessment of Genomic Regions Required for Growth in Mycobacterium tuberculosis , 2012, PLoS pathogens.

[21]  S. Kaufmann,et al.  Mycobacterium tuberculosis: success through dormancy. , 2012, FEMS microbiology reviews.

[22]  M. Fallahi-Sichani,et al.  NF-κB Signaling Dynamics Play a Key Role in Infection Control in Tuberculosis , 2012, Front. Physio..

[23]  Ashley M. Sherrid,et al.  The Polyketide Pks1 Contributes to Biofilm Formation in Mycobacterium tuberculosis , 2011, Journal of bacteriology.

[24]  Jonathan B. Johnston,et al.  Cholesterol catabolism as a therapeutic target in Mycobacterium tuberculosis. , 2011, Trends in microbiology.

[25]  Damian Smedley,et al.  BioMart Central Portal: an open database network for the biological community , 2011, Database J. Biol. Databases Curation.

[26]  Thomas R. Ioerger,et al.  High-Resolution Phenotypic Profiling Defines Genes Essential for Mycobacterial Growth and Cholesterol Catabolism , 2011, PLoS pathogens.

[27]  Yamir Moreno,et al.  The Transcriptional Regulatory Network of Mycobacterium tuberculosis , 2011, PloS one.

[28]  Hannah P. Gideon,et al.  Latent tuberculosis: what the host “sees”? , 2011, Immunologic research.

[29]  Helga Thorvaldsdóttir,et al.  Molecular signatures database (MSigDB) 3.0 , 2011, Bioinform..

[30]  Gary K. Schoolnik,et al.  The Response of Mycobacterium Tuberculosis to Reactive Oxygen and Nitrogen Species , 2011, Front. Microbio..

[31]  Joo-Ho Chung,et al.  Association of IL10, IL10RA, and IL10RB Polymorphisms with Benign Prostate Hyperplasia in Korean Population , 2011, Journal of Korean medical science.

[32]  J. Torrelles,et al.  Mycobacterium Tuberculosis Infection and Inflammation: what is Beneficial for the Host and for the Bacterium? , 2010, Front. Microbio..

[33]  Lincoln Stein,et al.  Reactome: a database of reactions, pathways and biological processes , 2010, Nucleic Acids Res..

[34]  Bindu Nanduri,et al.  HPIDB - a unified resource for host-pathogen interactions , 2010, BMC Bioinformatics.

[35]  Stefan Niemann,et al.  Functional Genetic Diversity among Mycobacterium tuberculosis Complex Clinical Isolates: Delineation of Conserved Core and Lineage-Specific Transcriptomes during Intracellular Survival , 2010, PLoS pathogens.

[36]  G. Hur,et al.  Endoplasmic reticulum stress response is involved in Mycobacterium tuberculosis protein ESAT‐6‐mediated apoptosis , 2010, FEBS letters.

[37]  E. Tocheva,et al.  A Flavin-dependent Monooxygenase from Mycobacterium tuberculosis Involved in Cholesterol Catabolism* , 2010, The Journal of Biological Chemistry.

[38]  Sarman Singh,et al.  Genome-wide Analysis of the Host Intracellular Network that Regulates Survival of Mycobacterium tuberculosis , 2010, Cell.

[39]  W. Jacobs,et al.  Mycobacterial Cytochrome P450 125 (Cyp125) Catalyzes the Terminal Hydroxylation of C27 Steroids* , 2009, The Journal of Biological Chemistry.

[40]  Junjun Zhang,et al.  BioMart Central Portal—unified access to biological data , 2009, Nucleic Acids Res..

[41]  N. Warner,et al.  Function of Nod‐like receptors in microbial recognition and host defense , 2009, Immunological reviews.

[42]  Vesteinn Thorsson,et al.  Identification of Tuberculosis Susceptibility Genes with Human Macrophage Gene Expression Profiles , 2008, PLoS pathogens.

[43]  J. Edwards,et al.  Exploring the full spectrum of macrophage activation , 2008, Nature Reviews Immunology.

[44]  D. Philpott,et al.  The microbial and danger signals that activate Nod-like receptors. , 2008, Cytokine.

[45]  Douglas G Altman,et al.  Key Issues in Conducting a Meta-Analysis of Gene Expression Microarray Datasets , 2008, PLoS medicine.

[46]  B. Mishra,et al.  NF-κB Activation Controls Phagolysosome Fusion-Mediated Killing of Mycobacteria by Macrophages1 , 2008, The Journal of Immunology.

[47]  Osamu Takeuchi,et al.  MDA5/RIG-I and virus recognition. , 2008, Current opinion in immunology.

[48]  Tige R. Rustad,et al.  The Enduring Hypoxic Response of Mycobacterium tuberculosis , 2008, PloS one.

[49]  Philip D. Butcher,et al.  Probing Host Pathogen Cross-Talk by Transcriptional Profiling of Both Mycobacterium tuberculosis and Infected Human Dendritic Cells and Macrophages , 2008, PloS one.

[50]  Yao-Zhong Liu,et al.  Bivariate Whole Genome Linkage Analyses for Total Body Lean Mass and BMD , 2007, Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research.

[51]  L. A. Basso,et al.  The Two Chorismate Mutases from both Mycobacterium tuberculosis and Mycobacterium smegmatis: Biochemical Analysis and Limited Regulation of Promoter Activity by Aromatic Amino Acids , 2007, Journal of bacteriology.

[52]  D. Sherman,et al.  Identification of Mycobacterial genes that alter growth and pathology in macrophages and in mice. , 2007, The Journal of infectious diseases.

[53]  S. Elmore.  Apoptosis: A Review of Programmed Cell Death , 2007, Toxicologic pathology.

[54]  S. Johnston,et al.  Mycobacterial Bacilli Are Metabolically Active during Chronic Tuberculosis in Murine Lungs: Insights from Genome-Wide Transcriptional Profiling , 2007, Journal of bacteriology.

[55]  L. Dijkhuizen,et al.  A gene cluster encoding cholesterol catabolism in a soil actinomycete provides insight into Mycobacterium tuberculosis survival in macrophages , 2007, Proceedings of the National Academy of Sciences.

[56]  Rainer Breitling,et al.  RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis , 2006, Bioinform..

[57]  K. Mdluli,et al.  Novel targets for tuberculosis drug discovery. , 2006, Current opinion in pharmacology.

[58]  Angelo Martino,et al.  Gene expression profiling of human macrophages at late time of infection with Mycobacterium tuberculosis , 2006, Immunology.

[59]  Sailu Yellaboina,et al.  Comparative analysis of iron regulated genes in mycobacteria , 2006, FEBS letters.

[60]  Irina Kolesnikova,et al.  The Mycobacterium tuberculosis PhoPR two‐component system regulates genes essential for virulence and complex lipid biosynthesis , 2006, Molecular microbiology.

[61]  C. Ouzounis,et al.  Expansion of the BioCyc collection of pathway/genome databases to 160 genomes , 2005, Nucleic acids research.

[62]  M. Daffé,et al.  Identification of the Mycobacterium tuberculosis SUF Machinery as the Exclusive Mycobacterial System of [Fe-S] Cluster Assembly: Evidence for Its Implication in the Pathogen's Survival , 2005, Journal of bacteriology.

[63]  E. Rubin,et al.  Genome-wide requirements for Mycobacterium tuberculosis adaptation and survival in macrophages. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[64]  Mahavir Singh,et al.  Mycobacterium Tuberculosis Heat Shock Proteins Use Diverse Toll-like Receptor Pathways to Activate Pro-inflammatory Signals* , 2005, Journal of Biological Chemistry.

[65]  N. Pathak,et al.  pheA (Rv3838c) of Mycobacterium tuberculosis Encodes an Allosterically Regulated Monofunctional Prephenate Dehydratase That Requires Both Catalytic and Regulatory Domains for Optimum Activity* , 2005, Journal of Biological Chemistry.

[66]  Alexei A. Sharov,et al.  Gene expression A web-based tool for principal component and significance analysis of microarray data , 2005 .

[67]  W. El-Deiry,et al.  Overview of cell death signaling pathways , 2005, Cancer biology & therapy.

[68]  Farahnaz Movahedzadeh,et al.  What do microarrays really tell us about M. tuberculosis? , 2004, Trends in microbiology.

[69]  Rainer Breitling,et al.  Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments , 2004, FEBS letters.

[70]  Shizuo Akira,et al.  The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses , 2004, Nature Immunology.

[71]  John Chan,et al.  TNF Influences Chemokine Expression of Macrophages In Vitro and That of CD11b+ Cells In Vivo during Mycobacterium tuberculosis Infection1 , 2004, The Journal of Immunology.

[72]  L. Ferguson,et al.  External validity, generalizability, and knowledge utilization. , 2004, Journal of nursing scholarship : an official publication of Sigma Theta Tau International Honor Society of Nursing.

[73]  R. Mondragón-Flores,et al.  Mycobacterium tuberculosis Virulence Correlates with Mitochondrial Cytochrome c Release in Infected Macrophages , 2003, Scandinavian journal of immunology.

[74]  Yang Liu,et al.  Transcriptional Adaptation of Mycobacterium tuberculosis within Macrophages , 2003, The Journal of experimental medicine.

[75]  R. Tapping,et al.  Mycobacterial lipoarabinomannan mediates physical interactions between TLR1 and TLR2 to induce signaling. , 2003, Journal of endotoxin research.

[76]  I. Smith,et al.  Mycobacterium tuberculosis gene expression in macrophages. , 2003, Microbes and infection.

[77]  E. Rubin,et al.  Genes required for mycobacterial growth defined by high density mutagenesis , 2003, Molecular microbiology.

[78]  E. Fish,et al.  Chemokines: attractive mediators of the immune response. , 2003, Seminars in immunology.

[79]  M. Daffé,et al.  Role of the pks15/1 gene in the biosynthesis of phenolglycolipids in the Mycobacterium tuberculosis complex. Evidence that all strains synthesize glycosylated p-hydroxybenzoic methyl esters and that strains devoid of phenolglycolipids harbor a frameshift mutation in the pks15/1 gene. , 2002, The Journal of biological chemistry.

[80]  J. Basu,et al.  Overexpression and functional characterization of an ABC (ATP-binding cassette) transporter encoded by the genes drrA and drrB of Mycobacterium tuberculosis. , 2002, The Biochemical journal.

[81]  Tanya Parish,et al.  The common aromatic amino acid biosynthesis pathway is essential in Mycobacterium tuberculosis. , 2002, Microbiology.

[82]  T. Barrette,et al.  Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. , 2002, Cancer research.

[83]  S. Howell,et al.  Changes in gene expression in macrophages infected with Mycobacterium tuberculosis: a combined transcriptomic and proteomic approach , 2001, Immunology.

[84]  Dirk Schnappinger,et al.  Regulation of the Mycobacterium tuberculosis hypoxic response gene encoding α-crystallin , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[85]  V. Deretic,et al.  Mycobacterial FurA is a negative regulator of catalase–peroxidase gene katG , 2001, Molecular microbiology.

[86]  J. Vanderleyden,et al.  A Metabolic Node in Action: Chorismate-Utilizing Enzymes in Microorganisms , 2001, Critical reviews in microbiology.

[87]  James C. Sacchettini,et al.  Persistence of Mycobacterium tuberculosis in macrophages and mice requires the glyoxylate shunt enzyme isocitrate lyase , 2000, Nature.

[88]  D. Golenbock,et al.  Human toll-like receptors mediate cellular activation by Mycobacterium tuberculosis. , 1999, Journal of immunology.

[89]  S L Normand,et al.  Meta-analysis: formulating, evaluating, combining, and reporting. , 1999, Statistics in medicine.

[90]  S. Churchill,et al.  Isolation and Characterization of aMycobacterium Species Capable of Degrading Three- and Four-Ring Aromatic and Aliphatic Hydrocarbons , 1999, Applied and Environmental Microbiology.

[91]  Gupta Ud,et al.  Understanding the phenomenon of persistence in mycobacterial infections. , 1997 .

[92]  David Baltimore,et al.  An Essential Role for NF-κB in Preventing TNF-α-Induced Cell Death , 1996, Science.

[93]  D. Crane,et al.  Stationary phase-associated protein expression in Mycobacterium tuberculosis: function of the mycobacterial alpha-crystallin homolog , 1996, Journal of bacteriology.

[94]  L. Wayne,et al.  An in vitro model for sequential study of shiftdown of Mycobacterium tuberculosis through two stages of nonreplicating persistence , 1996, Infection and immunity.

[95]  Karpov Lm.  The role of Na K ATPase in thiamine and lipoic acid interrelations during their absorption in the gastrointestinal tract of mice , 1989 .

[96]  Z LEVNTAL,et al.  [History of tuberculosis]. , 1957, Medicinski glasnik.

[97]  J. Mesirov,et al.  The Molecular Signatures Database (MSigDB) hallmark gene set collection. , 2015, Cell systems.

[98]  J. Kagan,et al.  Intracellular pathogen detection by RIG-I-like receptors. , 2013, Advances in immunology.

[99]  D. Radzioch,et al.  Role of TLR2- and TLR4-mediated signaling in Mycobacterium tuberculosis-induced macrophage death. , 2010, Cellular immunology.

[100]  G. Schoolnik,et al.  Mycobacterium tuberculosis gene expression during adaptation to stationary phase and low-oxygen dormancy. , 2004, Tuberculosis.

[101]  S. Nass.  FIBERS WITH DNA CHARACTERISTICS II . Enzymatic and Other Hydrolytic Treatments , 2003 .

[102]  Minoru Kanehisa,et al.  The KEGG database. , 2002, Novartis Foundation symposium.

[103]  D. Sherman,et al.  Regulation of the Mycobacterium tuberculosis hypoxic response gene encoding alpha -crystallin. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[104]  V. Katoch,et al.  Understanding the phenomenon of persistence in mycobacterial infections. , 1997, Indian journal of leprosy.

[105]  D. Baltimore,et al.  An essential role for NF-kappaB in preventing TNF-alpha-induced cell death. , 1996, Science.

[106]  Matthias Abend,et al.  Tuberculosis: Pathogenesis, Protection and Control , 1996, Nature Medicine.

[107]  R. Bentley,et al.  The shikimate pathway--a metabolic tree with many branches. , 1990, Critical reviews in biochemistry and molecular biology.

[108]  L. Karpov.  [The role of Na K ATPase in thiamine and lipoic acid interrelations during their absorption in the gastrointestinal tract of mice]. , 1989, Fiziolohichnyĭ zhurnal.