Systems and Synthetic Biology
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[1] Timothy B. Stockwell,et al. The Diploid Genome Sequence of an Individual Human , 2007, PLoS biology.
[2] Kellen L. Olszewski,et al. Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network , 2010, Molecular systems biology.
[3] John R Yates,et al. A Comprehensive Survey of the Plasmodium Life Cycle by Genomic, Transcriptomic, and Proteomic Analyses , 2005, Science.
[4] Ruiqi Wang,et al. MicroRNA-mediated regulation in the mammalian circadian rhythm. , 2012, Journal of theoretical biology.
[5] A. Papachristodoulou,et al. Engineering and ethical perspectives in synthetic biology , 2012, EMBO reports.
[6] T. Bestor,et al. Cytosine methylation targetted to pre-determined sequences , 1997, Nature Genetics.
[7] S. Rees,et al. Principles of early drug discovery , 2011, British journal of pharmacology.
[8] Emmanuel Barillot,et al. Continuous time boolean modeling for biological signaling: application of Gillespie algorithm , 2012, BMC Systems Biology.
[9] Kira J. Weissman,et al. Combinatorial biosynthesis of reduced polyketides , 2005, Nature Reviews Microbiology.
[10] Francisco Azuaje,et al. Systems-Based Approaches to Cardiovascular Biomarker Discovery , 2012, Circulation. Cardiovascular genetics.
[11] Heather L. Van Epps. René Dubos: unearthing antibiotics. , 2006 .
[12] Oliver Sawodny,et al. ON/OFF and Beyond - A Boolean Model of Apoptosis , 2009, PLoS Comput. Biol..
[13] R. Beerli,et al. Engineering polydactyl zinc-finger transcription factors , 2002, Nature Biotechnology.
[14] Elizabeth M. Smigielski,et al. dbSNP: the NCBI database of genetic variation , 2001, Nucleic Acids Res..
[15] H. Lichtenthaler,et al. Inhibitors of the nonmevalonate pathway of isoprenoid biosynthesis as antimalarial drugs. , 1999, Science.
[16] Yun Liu,et al. LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures , 2009, Bioinform..
[17] John R Carney,et al. Combinatorial polyketide biosynthesis by de novo design and rearrangement of modular polyketide synthase genes , 2005, Nature Biotechnology.
[18] Yongjin Li,et al. Discovering disease-genes by topological features in human protein-protein interaction network , 2006, Bioinform..
[19] P. Sorger,et al. Dissecting Variability in Responses to Cancer Chemotherapy Through Systems Pharmacology , 2010, Clinical pharmacology and therapeutics.
[20] B. Brüne,et al. Nitric oxide (NO): an effector of apoptosis , 1999, Cell Death and Differentiation.
[21] Elo Leung,et al. Targeted Genome Editing Across Species Using ZFNs and TALENs , 2011, Science.
[22] Andaaronklug. Synergy between adjacent zinc fingers in sequence-specific DNA recognition , 1997 .
[23] Sandhya Rani,et al. Human Protein Reference Database—2009 update , 2008, Nucleic Acids Res..
[24] Joachim Henkel,et al. The economics of synthetic biology , 2007, Molecular systems biology.
[25] D. Givol,et al. The gene for human p53 cellular tumor antigen is located on chromosome 17 short arm (17p13). , 1986, Proceedings of the National Academy of Sciences of the United States of America.
[26] Andrea Crisanti,et al. A synthetic homing endonuclease-based gene drive system in the human malaria mosquito , 2011, Nature.
[27] J. Mekalanos,et al. MetR-Regulated Vibrio cholerae Metabolism Is Required for Virulence , 2012, mBio.
[28] Keshab K. Parhi,et al. Synchronous sequential computation with molecular reactions , 2011, 2011 48th ACM/EDAC/IEEE Design Automation Conference (DAC).
[29] A Goldbeter,et al. Bursting, chaos and birhythmicity originating from self-modulation of the inositol 1,4,5-trisphosphate signal in a model for intracellular Ca2+ oscillations , 1999, Bulletin of mathematical biology.
[30] T. Myers,et al. The Transcriptional Responses of Mycobacterium tuberculosis to Inhibitors of Metabolism , 2004, Journal of Biological Chemistry.
[31] Alessandro Antonelli,et al. Cytokines (interferon-γ and tumor necrosis factor-α)-induced nuclear factor-κB activation and chemokine (C-X-C motif) ligand 10 release in Graves disease and ophthalmopathy are modulated by pioglitazone. , 2011, Metabolism: Clinical and Experimental.
[32] D Bhattacharya,et al. A general procedure for generation of curved DNA molecules. , 1988, Journal of biomolecular structure & dynamics.
[33] M. Oren,et al. Mdm2 promotes the rapid degradation of p53 , 1997, Nature.
[34] A. Barabasi,et al. Hierarchical Organization of Modularity in Metabolic Networks , 2002, Science.
[35] M. J. Pilling. Mathematical Models of Chemical Reactions. Theory and Applications of Deterministic and Stochastic Models : by P. Érdi and J. Tóth; published by Manchester University Press, 1989; xxiv + 259 pp.; price £37.50 , 1989 .
[36] P. Baldi,et al. DNA structure in human RNA polymerase II promoters. , 1998, Journal of molecular biology.
[37] P. Bork,et al. Network Neighbors of Drug Targets Contribute to Drug Side-Effect Similarity , 2011, PloS one.
[38] Farren J. Isaacs,et al. Engineered riboregulators enable post-transcriptional control of gene expression , 2004, Nature Biotechnology.
[39] W. Deen,et al. Analysis of the effects of cell spacing and liquid depth on nitric oxide and its oxidation products in cell cultures. , 2001, Chemical research in toxicology.
[40] I. Brukner,et al. Sequence‐dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides. , 1995, The EMBO journal.
[41] Yi Li,et al. The Genetic Map of Artemisia annua L. Identifies Loci Affecting Yield of the Antimalarial Drug Artemisinin , 2010, Science.
[42] B. Snel,et al. Conservation of gene order: a fingerprint of proteins that physically interact. , 1998, Trends in biochemical sciences.
[43] Søren Brunak,et al. Deciphering Diseases and Biological Targets for Environmental Chemicals using Toxicogenomics Networks , 2010, PLoS Comput. Biol..
[44] Kellen L. Olszewski,et al. Host-parasite interactions revealed by Plasmodium falciparum metabolomics. , 2009, Cell host & microbe.
[45] C. Hertweck,et al. Biosynthesis of cervimycin C, an aromatic polyketide antibiotic bearing an unusual dimethylmalonyl moiety. , 2004, Organic & biomolecular chemistry.
[46] Mario Cannataro,et al. Visualization of protein interaction networks: problems and solutions , 2013, BMC Bioinformatics.
[47] P. Bork,et al. A side effect resource to capture phenotypic effects of drugs , 2010, Molecular systems biology.
[48] Benjamin M. Good,et al. DataBiNS: a BioMoby-based data-mining workflow for biological pathways and non-synonymous SNPs , 2007, Bioinform..
[49] Stephen Naylor,et al. Status of systems biology - does it have a future? , 2004 .
[50] Eung-Soo Kim,et al. Biotechnological doxorubicin production: pathway and regulation engineering of strains for enhanced production , 2010, Applied Microbiology and Biotechnology.
[51] David John Adams,et al. Ion channels and regulation of intracellular calcium in vascular endothelial cells , 1989, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.
[52] L. Hood,et al. A personal view of molecular technology and how it has changed biology. , 2002, Journal of proteome research.
[53] Yi Wang,et al. Global protein-protein interaction network in the human pathogen Mycobacterium tuberculosis H37Rv. , 2010, Journal of proteome research.
[54] D. Swerdlow,et al. Host-pathogen interactions in emerging and re-emerging infectious diseases: a genomic perspective of tuberculosis, malaria, human immunodeficiency virus infection, hepatitis B, and cholera. , 2000, Annual review of public health.
[55] L. Tanoue. Cancer Statistics, 2011: The Impact of Eliminating Socioeconomic and Racial Disparities on Premature Cancer Deaths , 2012 .
[56] Daniel F. Voytas,et al. Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool , 2007, Nucleic Acids Res..
[57] D. Endy,et al. Refinement and standardization of synthetic biological parts and devices , 2008, Nature Biotechnology.
[58] M. Iorio,et al. Breast cancer and microRNAs: therapeutic impact. , 2011, Breast.
[59] Shankar Balasubramanian,et al. G-quadruplexes in promoters throughout the human genome , 2006, Nucleic acids research.
[60] E. Werner,et al. Tetrahydrobiopterin and Nitric Oxide: Mechanistic and Pharmacological Aspects , 2003, Experimental biology and medicine.
[61] I. Kola,et al. Can the pharmaceutical industry reduce attrition rates? , 2004, Nature Reviews Drug Discovery.
[62] Kristian M Müller,et al. Standardization in synthetic biology. , 2012, Methods in molecular biology.
[63] R. Patt,et al. Sequential therapy with JX-594, a targeted oncolytic poxvirus, followed by sorafenib in hepatocellular carcinoma: preclinical and clinical demonstration of combination efficacy. , 2011, Molecular therapy : the journal of the American Society of Gene Therapy.
[64] Richard C Trembath,et al. A synonymous SNP of the corneodesmosin gene leads to increased mRNA stability and demonstrates association with psoriasis across diverse ethnic groups. , 2004, Human molecular genetics.
[65] Andrew C. R. Martin,et al. Mapping SNPs to protein sequence and structure data , 2005, Bioinform..
[66] Young-Joon Kim,et al. Intrinsic variability of gene expression encoded in nucleosome positioning sequences , 2009, Nature Genetics.
[67] David Alderton,et al. A versatile ligation-independent cloning method suitable for high-throughput expression screening applications , 2007, Nucleic acids research.
[68] N. Chandra,et al. A systems perspective of host-pathogen interactions: predicting disease outcome in tuberculosis. , 2010, Molecular bioSystems.
[69] Z. Deng,et al. Engineering of an industrial polyoxin producer for the rational production of hybrid peptidyl nucleoside antibiotics. , 2012, Metabolic Engineering.
[70] C. Bashor,et al. Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems. , 2010, Annual review of biophysics.
[71] Dylan Alexander,et al. Combinatorial biosynthesis of novel antibiotics related to daptomycin , 2006, Proceedings of the National Academy of Sciences.
[72] R. Ranjan,et al. Development and Functional Analysis of Novel Genetic Promoters Using DNA Shuffling, Hybridization and a Combination Thereof , 2012, PloS one.
[73] G. D. Gatta,et al. Systems and Synthetic biology: tackling genetic networks and complex diseases , 2009, Heredity.
[74] F. He,et al. KRAB-type zinc-finger protein Apak specifically regulates p53-dependent apoptosis , 2009, Nature Cell Biology.
[75] Laura Inés Furlong,et al. From SNPs to pathways: integration of functional effect of sequence variations on models of cell signalling pathways , 2009, BMC Bioinformatics.
[76] G. Church,et al. Analysis of optimality in natural and perturbed metabolic networks , 2002 .
[77] J. Hopfield,et al. From molecular to modular cell biology , 1999, Nature.
[78] A. Barabasi,et al. Network medicine : a network-based approach to human disease , 2010 .
[79] Won Seok Jung,et al. Heterologous expression of tylosin polyketide synthase and production of a hybrid bioactive macrolide in Streptomyces venezuelae , 2006, Applied Microbiology and Biotechnology.
[80] J. Tyagi,et al. Signal transduction systems of mycobacteria with special reference to M. tuberculosis , 2004 .
[81] Lourdes Cucurull-Sanchez,et al. Relevance of systems pharmacology in drug discovery. , 2012, Drug discovery today.
[82] D. Sundar,et al. Prediction of DNA-binding specificity in zinc finger proteins , 2012, Journal of Biosciences.
[83] J. Lancaster,et al. Simulation of the diffusion and reaction of endogenously produced nitric oxide. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[84] J. T. Kadonaga,et al. The RNA polymerase II core promoter. , 2003, Annual review of biochemistry.
[85] Howard L McLeod,et al. Pharmacogenomics--drug disposition, drug targets, and side effects. , 2003, The New England journal of medicine.
[86] Rafael C. Jimenez,et al. The IntAct molecular interaction database in 2012 , 2011, Nucleic Acids Res..
[87] Peter D. Karp,et al. Construction and completion of flux balance models from pathway databases , 2012, Bioinform..
[88] Pilar Blancafort,et al. Development of Zinc Finger Domains for Recognition of the 5′-CNN-3′ Family DNA Sequences and Their Use in the Construction of Artificial Transcription Factors* , 2005, Journal of Biological Chemistry.
[89] James R Faeder,et al. The Complexity of Cell Signaling and the Need for a New Mechanics , 2009, Science Signaling.
[90] B. Ravi,et al. NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures , 1995, Comput. Appl. Biosci..
[91] William S. Hlavacek,et al. BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains , 2004, Bioinform..
[92] R. Zamora,et al. The regulatory role of nitric oxide in apoptosis. , 2001, International immunopharmacology.
[93] W. Witte. International dissemination of antibiotic resistant strains of bacterial pathogens. , 2004, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.
[94] Jennifer N Cha,et al. Large-area spatially ordered arrays of gold nanoparticles directed by lithographically confined DNA origami. , 2010, Nature nanotechnology.
[95] Rongfeng Li,et al. Rational strain improvement for enhanced clavulanic acid production by genetic engineering of the glycolytic pathway in Streptomyces clavuligerus. , 2006, Metabolic engineering.
[96] B. Reinhart,et al. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans , 2000, Nature.
[97] Vito Porcelli,et al. Computational approaches for protein function prediction: a combined strategy from multiple sequence alignment to molecular docking-based virtual screening. , 2010, Biochimica et biophysica acta.
[98] D. Gillespie. The chemical Langevin equation , 2000 .
[99] Jens Preben Morth,et al. Two-component systems of Mycobacterium tuberculosis: structure-based approaches. , 2007, Methods in enzymology.
[100] Philip E. Bourne,et al. Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis , 2009, PLoS Comput. Biol..
[101] Timothy K Lu,et al. Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy , 2009, Proceedings of the National Academy of Sciences.
[102] Martin Fussenegger,et al. A novel hybrid dual-channel catalytic-biological sensor system for assessment of fruit quality. , 2009, Journal of biotechnology.
[103] William S. Hlavacek,et al. RuleMonkey: software for stochastic simulation of rule-based models , 2010, BMC Bioinformatics.
[104] V. Singh,et al. Kinetic modeling of tricarboxylic acid cycle and glyoxylate bypass in Mycobacterium tuberculosis, and its application to assessment of drug targets , 2006, Theoretical Biology and Medical Modelling.
[105] Qiong Shao,et al. MicroRNA miR-21 overexpression in human breast cancer is associated with advanced clinical stage, lymph node metastasis and patient poor prognosis. , 2008, RNA.
[106] A. Aderem,et al. A 2020 vision for vaccines against HIV, tuberculosis and malaria , 2011, Nature.
[107] D. Eisenberg,et al. Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps. , 2003, Nucleic acids research.
[108] J. Pieters,et al. Mycobacterium tuberculosis and the macrophage: maintaining a balance. , 2008, Cell host & microbe.
[109] F. Sato,et al. Microbial production of plant benzylisoquinoline alkaloids , 2008, Proceedings of the National Academy of Sciences.
[110] D. Faller,et al. DNA-damaging Aryl Hydrocarbons Induce Mdm2 Expression via p53-independent Post-transcriptional Mechanisms* , 2000, The Journal of Biological Chemistry.
[111] D. Baker,et al. A simple physical model for the prediction and design of protein-DNA interactions. , 2004, Journal of molecular biology.
[112] J. Bailey,et al. Toward a science of metabolic engineering , 1991, Science.
[113] A. Y. Lu,et al. Pharmacogenetics, Pharmacogenomics, and Individualized Medicine , 2011, Pharmacological Reviews.
[114] Pall I. Olason,et al. A human phenome-interactome network of protein complexes implicated in genetic disorders , 2007, Nature Biotechnology.
[115] W. Weckwerth. Metabolomics in systems biology. , 2003, Annual review of plant biology.
[116] Shawn M. Douglas,et al. Self-assembly of DNA into nanoscale three-dimensional shapes , 2009, Nature.
[117] Eileen Kraemer,et al. PlasmoDB: a functional genomic database for malaria parasites , 2008, Nucleic Acids Res..
[118] J. Collins,et al. Construction of a genetic toggle switch in Escherichia coli , 2000, Nature.
[119] Archana Chugh,et al. Microbial synthetic biology for human therapeutics , 2012, Systems and Synthetic Biology.
[120] F. Bosch,et al. The Contributions of Paul Ehrlich to Pharmacology: A Tribute on the Occasion of the Centenary of His Nobel Prize , 2008, Pharmacology.
[121] Alex J. Brown,et al. inflammatory cell apoptosis autoimmune encephalomyelitis by stimulating reverses experimental 3 1,25-dihydroxyvitamin D Gene expression analysis suggests that , 2005 .
[122] J. Clemens,et al. Oral vaccines against cholera. , 2011, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.
[123] M. Elowitz,et al. Reconstruction of genetic circuits , 2005, Nature.
[124] J. Pronk,et al. Resolving Phenylalanine Metabolism Sheds Light on Natural Synthesis of Penicillin G in Penicillium chrysogenum , 2011, Eukaryotic Cell.
[125] Saraswathi Vishveshwara,et al. Rule-based modelling of iron homeostasis in tuberculosis. , 2011, Molecular bioSystems.
[126] J. Keasling,et al. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids , 2003, Nature Biotechnology.
[127] T. Billiar,et al. Nitric Oxide Protects PC12 Cells from Serum Deprivation-Induced Apoptosis by cGMP-Dependent Inhibition of Caspase Signaling , 1999, The Journal of Neuroscience.
[128] B A Pfeifer,et al. Biosynthesis of Complex Polyketides in a Metabolically Engineered Strain of E. coli , 2001, Science.
[129] M. Chopp,et al. MiR-146b-5p Suppresses EGFR Expression and Reduces In Vitro Migration and Invasion of Glioma , 2010, Cancer investigation.
[130] Wenjun Zhang,et al. Engineered Biosynthesis of a Novel Amidated Polyketide, Using the Malonamyl-Specific Initiation Module from the Oxytetracycline Polyketide Synthase , 2006, Applied and Environmental Microbiology.
[131] N. Rajewsky,et al. Natural selection on human microRNA binding sites inferred from SNP data , 2006, Nature Genetics.
[132] Scott T. Weiss,et al. Creating and evaluating genetic tests predictive of drug response , 2008, Nature Reviews Drug Discovery.
[133] N. White,et al. Assessment of the pharmacodynamic properties of antimalarial drugs in vivo , 1997, Antimicrobial agents and chemotherapy.
[134] D J Segal,et al. Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5'-GNN-3' DNA target sequences. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[135] Yan V. Sun,et al. Integration of biological networks and pathways with genetic association studies , 2012, Human Genetics.
[136] Philip Ball,et al. Synthetic biology for nanotechnology , 2004 .
[137] R. Albert. Network Inference, Analysis, and Modeling in Systems Biology , 2007, The Plant Cell Online.
[138] C. Lowenstein,et al. iNOS (NOS2) at a glance , 2004, Journal of Cell Science.
[139] Sean Ekins,et al. In silico repositioning of approved drugs for rare and neglected diseases. , 2011, Drug discovery today.
[140] F. Slack,et al. The let-7 family of microRNAs. , 2008, Trends in cell biology.
[141] Réka Albert,et al. Elementary signaling modes predict the essentiality of signal transduction network components , 2011, BMC Systems Biology.
[142] S. Levy. Balancing the drug-resistance equation. , 1994, Trends in microbiology.
[143] Yu-Ping Wang,et al. MiRTif: a support vector machine-based microRNA target interaction filter , 2008, BMC Bioinformatics.
[144] N. Forbes. Engineering the perfect (bacterial) cancer therapy , 2010, Nature Reviews Cancer.
[145] F. Eisenhaber,et al. Synthesizing non-natural parts from natural genomic template , 2009, Journal of biological engineering.
[146] W. Rom,et al. The host immune response to tuberculosis. , 1998, American journal of respiratory and critical care medicine.
[147] J. Chen,et al. Predicting adverse side effects of drugs , 2011, BMC Genomics.
[148] Marco F. Ramoni,et al. A Systems Biology Approach To Modeling Vibrio cholerae Gene Expression under Virulence-Inducing Conditions , 2010, Journal of bacteriology.
[149] Ann Richard,et al. ACToR--Aggregated Computational Toxicology Resource. , 2008, Toxicology and applied pharmacology.
[150] E. Rubin,et al. Genes required for mycobacterial growth defined by high density mutagenesis , 2003, Molecular microbiology.
[151] D. Sundar,et al. ZifBASE: a database of zinc finger proteins and associated resources , 2009, BMC Genomics.
[152] Manju Bansal,et al. Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes , 2005, Nucleic acids research.
[153] G. Wogan,et al. Nitric oxide as a modulator of apoptosis. , 2005, Cancer letters.
[154] Eric J Kunkel,et al. Systems biology in drug discovery. , 2006, Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference.
[155] V. Grantcharova,et al. Therapeutically Targeting ErbB3: A Key Node in Ligand-Induced Activation of the ErbB Receptor–PI3K Axis , 2009, Science Signaling.
[156] M. L. Simpson,et al. Frequency domain analysis of noise in autoregulated gene circuits , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[157] Sherry L. Jenkins,et al. Network analysis of FDA approved drugs and their targets. , 2007, The Mount Sinai journal of medicine, New York.
[158] A. Butte,et al. Predicting Adverse Drug Reactions Using Publicly Available PubChem BioAssay Data , 2011, Clinical pharmacology and therapeutics.
[159] J. Swanson,et al. Live cell fluorescence microscopy to study microbial pathogenesis , 2009, Cellular microbiology.
[160] Keshab K. Parhi,et al. VLSI digital signal processing systems , 1999 .
[161] D. Zack,et al. Analysis of regulatory network topology reveals functionally distinct classes of microRNAs , 2008, Nucleic acids research.
[162] Kathleen Marchal,et al. DNA Structural Properties in the Classification of Genomic Transcription Regulation Elements , 2012, Bioinformatics and biology insights.
[163] R. Iyengar,et al. Systems pharmacology: network analysis to identify multiscale mechanisms of drug action. , 2012, Annual review of pharmacology and toxicology.
[164] J. Sohng,et al. Metabolic Engineering of Nocardia sp. CS682 for Enhanced Production of Nargenicin A1 , 2012, Applied Biochemistry and Biotechnology.
[165] Ron Weiss,et al. Toward in vivo Digital Circuits , 2002 .
[166] Elizabeth A. Winzeler,et al. Applied systems biology and malaria , 2006, Nature Reviews Microbiology.
[167] Christopher D Reeves,et al. Combinatorial biosynthesis for drug development. , 2007, Current opinion in microbiology.
[168] Hisashi Kashima,et al. Side Effect Prediction Using Cooperative Pathways , 2009, 2009 IEEE International Conference on Bioinformatics and Biomedicine.
[169] P. Hotez,et al. Combating tropical infectious diseases: report of the Disease Control Priorities in Developing Countries Project. , 2004, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.
[170] R. Jackson,et al. General mass action kinetics , 1972 .
[171] Ralf Jungmann,et al. DNA origami as a nanoscopic ruler for super-resolution microscopy. , 2009, Angewandte Chemie.
[172] D. Gillespie. Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .
[173] Mads Kærn,et al. Noise in eukaryotic gene expression , 2003, Nature.
[174] M. Bennett,et al. A fast, robust, and tunable synthetic gene oscillator , 2008, Nature.
[175] Mark J. Miller,et al. Two‐photon microscopy of host–pathogen interactions: acquiring a dynamic picture of infection in vivo , 2009, Cellular microbiology.
[176] V. Kim,et al. MicroRNA precursors in motion: exportin-5 mediates their nuclear export. , 2004, Trends in cell biology.
[177] J. SantaLucia,et al. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[178] T. Lu,et al. Synthetic biology: an emerging engineering discipline. , 2012, Annual review of biomedical engineering.
[179] S. Quake,et al. Long-Term Monitoring of Bacteria Undergoing Programmed Population Control in a Microchemostat , 2005, Science.
[180] I. Serventi,et al. Rapid, reliable ligation-independent cloning of PCR products using modified plasmid vectors. , 1992, BioTechniques.
[181] Z. Yakhini,et al. Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters , 2012, Nature Biotechnology.
[182] J. Arrowsmith. Trial watch: Phase II failures: 2008–2010 , 2011, Nature Reviews Drug Discovery.
[183] Aaron Klug,et al. The discovery of zinc fingers and their applications in gene regulation and genome manipulation. , 2010, Annual review of biochemistry.
[184] D. Bonatto,et al. Transcriptomics and systems biology analysis in identification of specific pathways involved in cacao resistance and susceptibility to witches' broom disease. , 2012, Molecular bioSystems.
[185] A. Bonvin,et al. The HADDOCK web server for data-driven biomolecular docking , 2010, Nature Protocols.
[186] C. Donnelly,et al. Field performance of engineered male mosquitoes , 2011, Nature Biotechnology.
[187] J. Mekalanos,et al. Small-Molecule Inhibitor of Vibrio cholerae Virulence and Intestinal Colonization , 2005, Science.
[188] Ravi Iyengar,et al. Quantitative and Systems Pharmacology in the Post-genomic Era : New Approaches to Discovering Drugs and Understanding Therapeutic , 2011 .
[189] K. Ocorr,et al. ZNF418, a novel human KRAB/C2H2 zinc finger protein, suppresses MAPK signaling pathway , 2008, Molecular and Cellular Biochemistry.
[190] Thomas H Segall-Shapiro,et al. Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome , 2010, Science.
[191] J. Ross,et al. Computational functions in biochemical reaction networks. , 1994, Biophysical journal.
[192] Irving R. Epstein,et al. An Introduction to Nonlinear Chemical Dynamics: Oscillations, Waves, Patterns, and Chaos , 1998 .
[193] Desmond S. Lun,et al. Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production , 2009, PLoS Comput. Biol..
[194] Sonu Kumar,et al. ZiF-Predict: A Web Tool for Predicting DNA-Binding Specificity in C2H2 Zinc Finger Proteins , 2010, Genom. Proteom. Bioinform..
[195] Manuel C Peitsch,et al. From proteomics to systems biology of bacterial pathogens: Approaches, tools, and applications , 2007, Proteomics.
[196] Jie Li,et al. The architecture of the gene regulatory networks of different tissues , 2012, Bioinform..
[197] M. Vihinen,et al. Performance of mutation pathogenicity prediction methods on missense variants , 2011, Human mutation.
[198] R. Altman,et al. Pharmacogenomics Knowledge for Personalized Medicine , 2012, Clinical pharmacology and therapeutics.
[199] E. Winzeler,et al. Genomics and systems biology in malaria drug discovery. , 2010, Current opinion in investigational drugs.
[200] S. Elledge,et al. Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC , 2007, Nature Methods.
[201] A. Krainer,et al. Listening to silence and understanding nonsense: exonic mutations that affect splicing , 2002, Nature Reviews Genetics.
[202] Iris Hunger,et al. Dual-Use Research and Technological Diffusion: Reconsidering the Bioterrorism Threat Spectrum , 2011, PLoS pathogens.
[203] B. Pugh,et al. Identification and Distinct Regulation of Yeast TATA Box-Containing Genes , 2004, Cell.
[204] T. Billiar,et al. Nitric oxide as a bioregulator of apoptosis. , 2001, Biochemical and biophysical research communications.
[205] G. Kaatz,et al. Multidrug Resistance in Staphylococcus aureus Due to Overexpression of a Novel Multidrug and Toxin Extrusion (MATE) Transport Protein , 2005, Antimicrobial Agents and Chemotherapy.
[206] P. Gubbins,et al. Population Mobility, Globalization, and Antimicrobial Drug Resistance , 2009, Emerging infectious diseases.
[207] Travis S. Bayer,et al. Programmable ligand-controlled riboregulators of eukaryotic gene expression , 2005, Nature Biotechnology.
[208] C. Finlay,et al. The mdm-2 oncogene can overcome wild-type p53 suppression of transformed cell growth , 1993, Molecular and cellular biology.
[209] E. A. Boucher. Stochastic approach to reaction and physico-chemical kinetics , 1974 .
[210] Tudor I. Oprea,et al. Associating Drugs, Targets and Clinical Outcomes into an Integrated Network Affords a New Platform for Computer‐Aided Drug Repurposing , 2011, Molecular informatics.
[211] Kalidas Yeturu,et al. targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis , 2008, BMC Systems Biology.
[212] Erik Winfree,et al. Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates. , 2010, Nature nanotechnology.
[213] Li Jin,et al. Female-specific flightless phenotype for mosquito control , 2010, Proceedings of the National Academy of Sciences.
[214] Hsien-Da Huang,et al. miRTar: an integrated system for identifying miRNA-target interactions in human , 2011, BMC Bioinformatics.
[215] Vesselin Baev,et al. MicroInspector: a web tool for detection of miRNA binding sites in an RNA sequence , 2005, Nucleic Acids Res..
[216] Y. Vodovotz,et al. Mechanisms of Hepatoprotection by Nitric Oxide , 2002, Annals of the New York Academy of Sciences.
[217] Bernhard O. Palsson,et al. Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets , 2007 .
[218] S. Waksman. What is an antibiotic or an antibiotic substance? , 1947, Mycologia.
[219] Joost Boele,et al. FAME, the Flux Analysis and Modeling Environment , 2012, BMC Systems Biology.
[220] M. Katze,et al. A Systems Biology Approach to Infectious Disease Research: Innovating the Pathogen-Host Research Paradigm , 2011, mBio.
[221] J. Wood,et al. Models of the diffusional spread of nitric oxide: Implications for neural nitric oxide signalling and its pharmacological properties , 1994, Neuropharmacology.
[222] C. Rao,et al. Control, exploitation and tolerance of intracellular noise , 2002, Nature.
[223] Cizhong Jiang,et al. Nucleosome positioning and gene regulation: advances through genomics , 2009, Nature Reviews Genetics.
[224] P. Rothemund. Folding DNA to create nanoscale shapes and patterns , 2006, Nature.
[225] M. DePamphilis,et al. HUMAN DISEASE , 1957, The Ulster Medical Journal.
[226] J. Sambrook,et al. Molecular Cloning: A Laboratory Manual , 2001 .
[227] B. Pfeifer,et al. Improved E. coli erythromycin a production through the application of metabolic and bioprocess engineering , 2012, Biotechnology progress.
[228] Feng Zhang,et al. Selection-Free Zinc-Finger Nuclease Engineering by Context-Dependent Assembly (CoDA) , 2010, Nature Methods.
[229] A. Izzo,et al. Portrait of a Pathogen: The Mycobacterium tuberculosis Proteome In Vivo , 2010, PloS one.
[230] A. Arkin,et al. Stochastic mechanisms in gene expression. , 1997, Proceedings of the National Academy of Sciences of the United States of America.
[231] Ioannis Xenarios,et al. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions , 2002, Nucleic Acids Res..
[232] Yusuke Nakamura,et al. Pharmacogenomics and Patient Care: One Size Does Not Fit All , 2012, Science Translational Medicine.
[233] E. Brown,et al. Calcium-sensing receptor activation induces nitric oxide production in H-500 Leydig cancer cells. , 2005, American journal of physiology. Endocrinology and metabolism.
[234] Robert M. Dirks,et al. Selective cell death mediated by small conditional RNAs , 2010, Proceedings of the National Academy of Sciences.
[235] R. Nussinov,et al. Protein-protein interaction networks: how can a hub protein bind so many different partners? , 2009, Trends in biochemical sciences.
[236] S. Pastorino,et al. MicroRNAs in cerebrospinal fluid identify glioblastoma and metastatic brain cancers and reflect disease activity. , 2012, Neuro-oncology.
[237] M. Murphy,et al. Nitric oxide and cell death. , 1999, Biochimica et biophysica acta.
[238] Timothy S. Ham,et al. Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools , 2012, Nucleic acids research.
[239] Y. Pawitan,et al. Human genetics and genomics a decade after the release of the draft sequence of the human genome , 2011, Human Genomics.
[240] A Klug,et al. Repetitive zinc‐binding domains in the protein transcription factor IIIA from Xenopus oocytes. , 1985, The EMBO journal.
[241] D. Burgess. Technology: A CRISPR genome-editing tool , 2013, Nature Reviews Genetics.
[242] M. di Bernardo,et al. A comparative analysis of synthetic genetic oscillators , 2010, Journal of The Royal Society Interface.
[243] H. Bujard,et al. Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. , 1997, Nucleic acids research.
[244] N. Kelleher,et al. Heterologous production of fosfomycin and identification of the minimal biosynthetic gene cluster. , 2006, Chemistry & biology.
[245] Vip Viprakasit,et al. A Regulatory SNP Causes a Human Genetic Disease by Creating a New Transcriptional Promoter , 2006, Science.
[246] D. Eisenberg,et al. Detecting protein function and protein-protein interactions from genome sequences. , 1999, Science.
[247] John A. Robinson,et al. Insertional Inactivation of Methylmalonyl Coenzyme A (CoA) Mutase and Isobutyryl-CoA Mutase Genes in Streptomyces cinnamonensis: Influence on Polyketide Antibiotic Biosynthesis , 1999, Journal of bacteriology.
[248] Varda Rotter,et al. Nitric oxide-induced cellular stress and p53 activation in chronic inflammation , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[249] Christopher M. Overall,et al. Deciphering complex mechanisms in neurodegenerative diseases: the advent of systems biology , 2009, Trends in Neurosciences.
[250] A. Levine,et al. Regulation of Transcription Functions of the p53 Tumor Suppressor by the mdm-2 Oncogene , 1995, Molecular medicine.
[251] Soo Young Cho,et al. ZIFIBI: Prediction of DNA binding sites for zinc finger proteins. , 2008, Biochemical and biophysical research communications.
[252] Y. Zhuang,et al. Improved oxytetracycline production in Streptomyces rimosus M4018 by metabolic engineering of the G6PDH gene in the pentose phosphate pathway. , 2011, Enzyme and microbial technology.
[253] Joy Y. Zhang,et al. The art of trans-boundary governance: the case of synthetic biology , 2013, Systems and Synthetic Biology.
[254] Nagasuma R. Chandra,et al. Flux Balance Analysis of Mycolic Acid Pathway: Targets for Anti-Tubercular Drugs , 2005, PLoS Comput. Biol..
[255] Stephen N. Jones,et al. Regulation of p53 stability by Mdm2 , 1997, Nature.
[256] R. Overbeek,et al. Characterization of the Staphylococcus aureus Heat Shock, Cold Shock, Stringent, and SOS Responses and Their Effects on Log-Phase mRNA Turnover , 2006, Journal of bacteriology.
[257] Eran Segal,et al. Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast , 2012, Nature Genetics.
[258] Andreas Hoppe,et al. FASIMU: flexible software for flux-balance computation series in large metabolic networks , 2011, BMC Bioinformatics.
[259] Xiaoyan Zhu,et al. Building Disease-Specific Drug-Protein Connectivity Maps from Molecular Interaction Networks and PubMed Abstracts , 2009, PLoS Comput. Biol..
[260] C. Gualerzi,et al. The virF promoter in Shigella: more than just a curved DNA stretch , 2004, Molecular microbiology.
[261] Andreas Hoppe,et al. Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis , 2010, BMC Systems Biology.
[262] Gurumayum Reenaroy Devi,et al. Intercellular synchronization of diffusively coupled Ca2+ oscillators , 2012, Journal of chemical biology.
[263] Bruno O Villoutreix,et al. Structural bioinformatics: methods, concepts and applications to blood coagulation proteins. , 2002, Current protein & peptide science.
[264] M. Noordewier,et al. Stress-induced DNA duplex destabilization (SIDD) in the E. coli genome: SIDD sites are closely associated with promoters. , 2004, Genome research.
[265] M. McClain,et al. Microfluidic devices for the high-throughput chemical analysis of cells. , 2003, Analytical chemistry.
[266] Benno Schwikowski,et al. Discovering regulatory and signalling circuits in molecular interaction networks , 2002, ISMB.
[267] William H. Cernota,et al. An erythromycin process improvement using the diethyl methylmalonate-responsive (Dmr) phenotype of the Saccharopolyspora erythraea mutB strain , 2011, Applied Microbiology and Biotechnology.
[268] B. Spitzer-Rimon,et al. Generation of the potent anti-malarial drug artemisinin in tobacco , 2011, Nature Biotechnology.
[269] T. Haran,et al. The unique structure of A-tracts and intrinsic DNA bending , 2009, Quarterly Reviews of Biophysics.
[270] Jing Chen,et al. PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease , 2006, Nucleic Acids Res..
[271] H. Drew,et al. Sequence periodicities in chicken nucleosome core DNA. , 1986, Journal of molecular biology.
[272] C. Gualerzi,et al. Thermoregulation of Shigella and Escherichia coli EIEC pathogenicity. A temperature‐dependent structural transition of DNA modulates accessibility of virF promoter to transcriptional repressor H‐NS , 1998, The EMBO journal.
[273] Adelinde M. Uhrmacher,et al. Rule-based multi-level modeling of cell biological systems , 2011, BMC Systems Biology.
[274] Christopher A. Voigt,et al. Environmental signal integration by a modular AND gate , 2007, Molecular systems biology.
[275] A. Friedman,et al. Tuberculosis research: going forward with a powerful "translational systems biology" approach. , 2010, Tuberculosis.
[276] J. Kjems,et al. Self-assembly of a nanoscale DNA box with a controllable lid , 2009, Nature.
[277] C. Ball,et al. TB database 2010: overview and update. , 2010, Tuberculosis.
[278] J. Padiadpu,et al. Protein–protein interaction networks suggest different targets have different propensities for triggering drug resistance , 2010, Systems and Synthetic Biology.
[279] L. Tsimring,et al. A synchronized quorum of genetic clocks , 2009, Nature.
[280] Gary D. Bader,et al. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function , 2010, Nucleic Acids Res..
[281] Manju Bansal,et al. A glossary of DNA structures from A to Z. , 2003, Acta crystallographica. Section D, Biological crystallography.
[282] Ron Weiss,et al. Cellular computation and communications using engineered genetic regulatory networks , 2001, Cellular Computing.
[283] Subramaniam Pennathur,et al. Analytical approaches to metabolomics and applications to systems biology. , 2010, Seminars in nephrology.
[284] Brian F. Pfleger,et al. Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes , 2006, Nature Biotechnology.
[285] Yvonne Tay,et al. A Pattern-Based Method for the Identification of MicroRNA Binding Sites and Their Corresponding Heteroduplexes , 2006, Cell.
[286] Elo Leung,et al. A TALE nuclease architecture for efficient genome editing , 2011, Nature Biotechnology.
[287] K. Friehs. Plasmid copy number and plasmid stability. , 2004, Advances in biochemical engineering/biotechnology.
[288] C. Forst. Host-pathogen systems biology. , 2006, Drug discovery today.
[289] D. Ralt. Intercellular communication, NO and the biology of Chinese medicine , 2005, Cell Communication and Signaling.
[290] S Moncada,et al. Nitric oxide synthases in mammals. , 1994, The Biochemical journal.
[291] S. Way,et al. Regulatory T Cell Suppressive Potency Dictates the Balance between Bacterial Proliferation and Clearance during Persistent Salmonella Infection , 2010, PLoS pathogens.
[292] Martin S. Taylor,et al. Genome-wide analysis of mammalian promoter architecture and evolution , 2006, Nature Genetics.
[293] B. Honig,et al. Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry , 2007, Nucleic acids research.
[294] C. Burge,et al. Prediction of Mammalian MicroRNA Targets , 2003, Cell.
[295] L. Bracco,et al. Synthetic curved DNA sequences can act as transcriptional activators in Escherichia coli. , 1989, The EMBO journal.
[296] Ronan M. T. Fleming,et al. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 , 2007, Nature Protocols.
[297] Yan P. Yuan,et al. HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources , 2002, Nucleic Acids Res..
[298] Gregory M. Goldgof,et al. Direct transfer of whole genomes from bacteria to yeast , 2013, Nature Methods.
[299] S. Srinivasula,et al. Cell Stress and Cell Death , 2010, International journal of cell biology.
[300] Wei Zheng,et al. dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks , 2011, Bioinform..
[301] Nagasuma R. Chandra,et al. Flux balance analysis of biological systems: applications and challenges , 2009, Briefings Bioinform..
[302] Jens Nielsen,et al. Production of plant sesquiterpenes in Saccharomyces cerevisiae: Effect of ERG9 repression on sesquiterpene biosynthesis , 2008, Biotechnology and bioengineering.
[303] J. Sohng,et al. Heterologous production of ribostamycin derivatives in engineered Escherichia coli. , 2010, Research in microbiology.
[304] Axel Kowald,et al. Systems Biology in Practice: Concepts, Implementation and Application , 2005 .
[305] J. Arrowsmith. Trial watch: Phase III and submission failures: 2007–2010 , 2011, Nature Reviews Drug Discovery.
[306] James T. L. Mah,et al. In silico SNP analysis and bioinformatics tools: a review of the state of the art to aid drug discovery. , 2011, Drug discovery today.
[307] Timothy S. Ham,et al. Production of the antimalarial drug precursor artemisinic acid in engineered yeast , 2006, Nature.
[308] Mudita Singhal,et al. Bioinformatics Original Paper Copasi—a Complex Pathway Simulator , 2022 .
[309] Christopher A. Voigt,et al. Environmentally controlled invasion of cancer cells by engineered bacteria. , 2006, Journal of molecular biology.
[310] Peter M Woollard,et al. The application of next-generation sequencing technologies to drug discovery and development. , 2011, Drug discovery today.
[311] M. Fussenegger,et al. A synthetic mammalian gene circuit reveals antituberculosis compounds , 2008, Proceedings of the National Academy of Sciences of the United States of America.
[312] Hyun Uk Kim,et al. Metabolic engineering of microorganisms: general strategies and drug production. , 2009, Drug discovery today.
[313] E. Shapiro,et al. An autonomous molecular computer for logical control of gene expression , 2004, Nature.
[314] Ravi Iyengar,et al. Network analyses in systems pharmacology , 2009, Bioinform..
[315] Chengpeng Bi,et al. WebSIDD: server for predicting stress-induced duplex destabilized (SIDD) sites in superhelical DNA. , 2004, Bioinformatics.
[316] A. Levine,et al. p53-Mdm2 loop controlled by a balance of its feedback strength and effective dampening using ATM and delayed feedback. , 2005, Systems biology.
[317] Maung Nyan Win,et al. Frameworks for programming biological function through RNA parts and devices. , 2009, Chemistry & biology.
[318] Lei Xie,et al. Structure-based systems biology for analyzing off-target binding. , 2011, Current opinion in structural biology.
[319] Stephen N. Jones,et al. Nitric oxide-mediated inhibition of Hdm2-p53 binding. , 2002, Biochemistry.
[320] Albert-László Barabási,et al. Systems biology. Life's complexity pyramid. , 2002, Science.
[321] N. Pavletich,et al. Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A , 1991, Science.
[322] Ho Young Lee,et al. Bioassay-Guided Evolution of Glycosylated Macrolide Antibiotics in Escherichia coli , 2007, PLoS biology.
[323] D. Kirn,et al. Targeted and armed oncolytic poxviruses: a novel multi-mechanistic therapeutic class for cancer , 2009, Nature Reviews Cancer.
[324] Manju Bansal,et al. High-quality annotation of promoter regions for 913 bacterial genomes , 2010, Bioinform..
[325] Hanah Margalit,et al. A Structure-Based Approach for Prediction of Protein Binding Sites in Gene-Upstream Regions , 2000, Pacific Symposium on Biocomputing.
[326] Keshab K. Parhi,et al. Writing and Compiling Code into Biochemistry , 2010, Pacific Symposium on Biocomputing.
[327] U. Förstermann,et al. Regulation of endothelial-type NO synthase expression in pathophysiology and in response to drugs. , 2002, Nitric oxide : biology and chemistry.
[328] R. Iyengar,et al. Toward predictive models of mammalian cells. , 2005, Annual review of biophysics and biomolecular structure.
[329] Y. Jang,et al. Engineering of microorganisms for the production of biofuels and perspectives based on systems metabolic engineering approaches. , 2012, Biotechnology advances.
[330] J. R. Lancaster. A tutorial on the diffusibility and reactivity of free nitric oxide. , 1997, Nitric oxide : biology and chemistry.
[331] L. Blatter,et al. Mitochondrial calcium uptake stimulates nitric oxide production in mitochondria of bovine vascular endothelial cells. , 2004, American journal of physiology. Cell physiology.
[332] B. Williams,et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.
[333] Dmitrij Frishman,et al. The MIPS mammalian protein?Cprotein interaction database , 2005, Bioinform..
[334] C C Case,et al. Synthetic Zinc Finger Transcription Factor Action at an Endogenous Chromosomal Site , 2000, The Journal of Biological Chemistry.
[335] P. Bork,et al. Drug Target Identification Using Side-Effect Similarity , 2008, Science.
[336] Yitzhak Pilpel,et al. Global and Local Architecture of the Mammalian microRNA–Transcription Factor Regulatory Network , 2007, PLoS Comput. Biol..
[337] A. Levine,et al. The mdm-2 oncogene product forms a complex with the p53 protein and inhibits p53-mediated transactivation , 1992, Cell.
[338] A. Jemal,et al. Global Patterns of Cancer Incidence and Mortality Rates and Trends , 2010, Cancer Epidemiology, Biomarkers & Prevention.
[339] Herbert M. Sauro,et al. In-Fusion BioBrick assembly and re-engineering , 2010, Nucleic acids research.
[340] P Rhodes,et al. Roles of nitric oxide in tumor growth. , 1995, Proceedings of the National Academy of Sciences of the United States of America.
[341] Jong Bhak,et al. SNP@Promoter: a database of human SNPs (Single Nucleotide Polymorphisms) within the putative promoter regions , 2008, BMC Bioinformatics.
[342] D T Chiu,et al. Using three-dimensional microfluidic networks for solving computationally hard problems , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[343] A Klug,et al. Towards therapeutic applications of engineered zinc finger proteins , 2005, FEBS letters.
[344] Lippincott-Schwartz,et al. Supporting Online Material Materials and Methods Som Text Figs. S1 to S8 Table S1 Movies S1 to S3 a " Silent " Polymorphism in the Mdr1 Gene Changes Substrate Specificity Corrected 30 November 2007; See Last Page , 2022 .
[345] A. Hopkins. Network pharmacology: the next paradigm in drug discovery. , 2008, Nature chemical biology.
[346] G. Seelig,et al. Enzyme-Free Nucleic Acid Logic Circuits , 2022 .
[347] Adam H. Marblestone,et al. Rapid prototyping of 3D DNA-origami shapes with caDNAno , 2009, Nucleic acids research.
[348] Joost Schymkowitz,et al. Bioinformatics Applications Note Snpeffect V2.0: a New Step in Investigating the Molecular Phenotypic Effects of Human Non-synonymous Snps , 2022 .
[349] Jeremy G. Siek,et al. The Boost Graph Library - User Guide and Reference Manual , 2001, C++ in-depth series.
[350] Panayiotis V. Benos,et al. HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models , 2009, BMC Bioinformatics.
[351] Irving R. Epstein,et al. A systematically designed homogeneous oscillating reaction: the arsenite-iodate-chlorite system , 1981 .
[352] S. E. Eklund,et al. Multianalyte microphysiometry as a tool in metabolomics and systems biology , 2006 .
[353] Carole J. Proctor,et al. Explaining oscillations and variability in the p53-Mdm2 system , 2008, BMC Systems Biology.
[354] Mark Bathe,et al. A primer to scaffolded DNA origami , 2011, Nature Methods.
[355] R E Harrington,et al. Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. , 1991, Proceedings of the National Academy of Sciences of the United States of America.
[356] X. Jia,et al. Metabolic Flux Analysis and Principal Nodes Identification for Daptomycin Production Improvement by Streptomyces roseosporus , 2011, Applied biochemistry and biotechnology.
[357] Ruth Nussinov,et al. Structure and dynamics of molecular networks: A novel paradigm of drug discovery. A comprehensive review , 2012, Pharmacology & therapeutics.
[358] M. Clarke,et al. A Bipartite Nuclear Localization Signal Is Required for p53 Nuclear Import Regulated by a Carboxyl-terminal Domain* , 1999, The Journal of Biological Chemistry.
[359] H. Mori,et al. Two‐component system VraSR positively modulates the regulation of cell‐wall biosynthesis pathway in Staphylococcus aureus , 2003, Molecular microbiology.
[360] Frederick K. Balagaddé,et al. Biology by design: reduction and synthesis of cellular components and behaviour , 2007, Journal of The Royal Society Interface.
[361] Alexander Kelle,et al. SYNBIOSAFE e-conference: online community discussion on the societal aspects of synthetic biology , 2008, Systems and Synthetic Biology.
[362] M. Fussenegger,et al. A Synthetic Optogenetic Transcription Device Enhances Blood-Glucose Homeostasis in Mice , 2011, Science.
[363] R. Iyengar,et al. From components to regulatory motifs in signalling networks. , 2006, Briefings in functional genomics & proteomics.
[364] J. SantaLucia,et al. Thermodynamics and NMR of internal G.T mismatches in DNA. , 1997, Biochemistry.
[365] Christopher J. Silva,et al. Heterologous production of daptomycin in Streptomyces lividans , 2006, Journal of Industrial Microbiology and Biotechnology.
[366] R. Milo,et al. Oscillations and variability in the p53 system , 2006, Molecular systems biology.
[367] Nan Xiao,et al. Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli , 2008, Bioinform..
[368] J. Collins,et al. How antibiotics kill bacteria: from targets to networks , 2010, Nature Reviews Microbiology.
[369] S. Klamt,et al. GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism , 2007, Genome Biology.
[370] Ronnie J Winfrey,et al. Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification. , 2008, Molecular cell.
[371] Hiroaki Kitano,et al. CellDesigner: a process diagram editor for gene-regulatory and biochemical networks , 2003 .
[372] Jonathan E. Allen,et al. Genome sequence of the human malaria parasite Plasmodium falciparum , 2002, Nature.
[373] Ryo Takeuchi,et al. Tapping natural reservoirs of homing endonucleases for targeted gene modification , 2011, Proceedings of the National Academy of Sciences.
[374] J. Doyle,et al. Reverse Engineering of Biological Complexity , 2002, Science.
[375] L. Trautmann,et al. Solving vaccine mysteries: a systems biology perspective , 2011, Nature Immunology.
[376] Ronald R. Breaker,et al. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression , 2002, Nature.
[377] J. Chen,et al. Unraveling human complexity and disease with systems biology and personalized medicine. , 2010, Personalized medicine.
[378] M. Win,et al. A modular and extensible RNA-based gene-regulatory platform for engineering cellular function , 2007, Proceedings of the National Academy of Sciences.
[379] J. Martín,et al. CefR modulates transporters of beta-lactam intermediates preventing the loss of penicillins to the broth and increases cephalosporin production in Acremonium chrysogenum. , 2011, Metabolic engineering.
[380] Damian Szklarczyk,et al. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored , 2010, Nucleic Acids Res..
[381] A. Turberfield,et al. A DNA-fuelled molecular machine made of DNA , 2022 .
[382] P. Shannon,et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.
[383] R. Giegerich,et al. Fast and effective prediction of microRNA/target duplexes. , 2004, RNA.
[384] D. Crothers,et al. Synthetic DNA bending sequences increase the rate of in vitro transcription initiation at the Escherichia coli lac promoter. , 1991, Journal of molecular biology.
[385] Steffen Klamt,et al. Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling , 2009, BMC Systems Biology.
[386] L. Esteva,et al. A mathematical model for cellular immunology of tuberculosis. , 2011, Mathematical biosciences and engineering : MBE.
[387] Andrew W. Torrance,et al. Synthesizing Law for Synthetic Biology , 2010 .
[388] J. Stern. Nitric oxide and homeostatic control: an intercellular signalling molecule contributing to autonomic and neuroendocrine integration? , 2004, Progress in biophysics and molecular biology.
[389] J. LaBaer,et al. Many paths to many clones: a comparative look at high-throughput cloning methods. , 2004, Genome research.
[390] Vincent Danos,et al. Rule-Based Modelling, Symmetries, Refinements , 2008, FMSB.
[391] S. Roche,et al. Point-mutation effects on charge-transport properties of the tumor-suppressor gene p53. , 2007, Physical review letters.
[392] Michael J. Campolongo,et al. Novel DNA materials and their applications , 2010, Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnology.
[393] D. Kirschner,et al. A hybrid multi-compartment model of granuloma formation and T cell priming in tuberculosis. , 2011, Journal of theoretical biology.
[394] T. Oh,et al. Efficient Production of Polymyxin in the Surrogate Host Bacillus subtilis by Introducing a Foreign ectB Gene and Disrupting the abrB Gene , 2012, Applied and Environmental Microbiology.
[395] D. Eisenberg,et al. Mycobacterium tuberculosis gene expression profiling within the context of protein networks. , 2006, Microbes and infection.
[396] Leroy Hood,et al. The impact of systems approaches on biological problems in drug discovery , 2004, Nature Biotechnology.
[397] L M Adleman,et al. Molecular computation of solutions to combinatorial problems. , 1994, Science.
[398] C. Guha,et al. Systemic administration of reovirus (Reolysin) inhibits growth of human sarcoma xenografts , 2011, Cancer.
[399] E. Andrianantoandro,et al. Synthetic biology: new engineering rules for an emerging discipline , 2006, Molecular systems biology.
[400] Leroy Hood,et al. Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized medicine. , 2004, Journal of proteome research.
[401] J. Glenn Morris,et al. Cholera transmission: the host, pathogen and bacteriophage dynamic , 2009, Nature Reviews Microbiology.
[402] Jeffrey G. Mandell,et al. Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases , 2006, Nucleic Acids Res..
[403] Russ B. Altman,et al. Bioinformatics challenges for personalized medicine , 2011, Bioinform..
[404] Peter M Woollard. Asking complex questions of the genome without programming. , 2010, Methods in molecular biology.
[405] M. Tyers,et al. From genomics to proteomics , 2003, Nature.
[406] G. Wright,et al. Glycopeptide Antibiotic Resistance Genes in Glycopeptide-Producing Organisms , 1998, Antimicrobial Agents and Chemotherapy.
[407] Gary An,et al. Translational Systems Biology of Inflammation , 2008, PLoS Comput. Biol..
[408] J. Bartlett,et al. The epidemic of antibiotic-resistant infections: a call to action for the medical community from the Infectious Diseases Society of America. , 2008, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.
[409] Steven R Tannenbaum,et al. Reactive nitrogen species in the chemical biology of inflammation. , 2004, Archives of biochemistry and biophysics.
[410] J. Berg. Zinc finger domains: hypotheses and current knowledge. , 1990, Annual review of biophysics and biophysical chemistry.
[411] Nagiza F. Samatova,et al. Gene network shaping of inherent noise spectra , 2006 .
[412] L. Ghibelli,et al. Cytosolic and Endoplasmic Reticulum Ca2+ Concentrations Determine the Extent and the Morphological Type of Apoptosis, Respectively , 2003, Annals of the New York Academy of Sciences.
[413] H. Florey. The Use of Micro-organisms for Therapeutic Purposes * , 1946, The Yale journal of biology and medicine.
[414] Shuanglin Xiang,et al. Short hairpin RNA–expressing bacteria elicit RNA interference in mammals , 2006, Nature Biotechnology.
[415] Hidde de Jong,et al. Modeling and Simulation of Genetic Regulatory Systems: A Literature Review , 2002, J. Comput. Biol..
[416] Erik Winfree,et al. DNA as a universal substrate for chemical kinetics , 2009, Proceedings of the National Academy of Sciences.
[417] Y. Zhuang,et al. Genetic Modulation of the Overexpression of Tailoring Genes eryK and eryG Leading to the Improvement of Erythromycin A Purity and Production in Saccharopolyspora erythraea Fermentation , 2008, Applied and Environmental Microbiology.
[418] Karthik Raman,et al. Principles and Practices of Pathway Modelling , 2006 .
[419] Jing Zhou,et al. Systems biology approach to identify transcriptome reprogramming and candidate microRNA targets during the progression of polycystic kidney disease , 2011, BMC Systems Biology.
[420] P. Swain,et al. Stochastic Gene Expression in a Single Cell , 2002, Science.
[421] R. Garg,et al. Investigations of valanimycin biosynthesis: Elucidation of the role of seryl-tRNA , 2008, Proceedings of the National Academy of Sciences.
[422] H. Kitano. Systems Biology: A Brief Overview , 2002, Science.
[423] Fang Yang,et al. Biosynthesis of phloroglucinol compounds in microorganisms—review , 2011, Applied Microbiology and Biotechnology.
[424] L. Steinmetz,et al. Bidirectional promoters generate pervasive transcription in yeast , 2009, Nature.
[425] C. Barbas,et al. Positive and negative regulation of endogenous genes by designed transcription factors. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[426] M. Daly,et al. Proteins Encoded in Genomic Regions Associated with Immune-Mediated Disease Physically Interact and Suggest Underlying Biology , 2011, PLoS genetics.
[427] H. Pelham,et al. A specific transcription factor that can bind either the 5S RNA gene or 5S RNA. , 1980, Proceedings of the National Academy of Sciences of the United States of America.
[428] D. Kirschner,et al. A model for Vibrio cholerae colonization of the human intestine. , 2011, Journal of theoretical biology.
[429] Mona Singh,et al. Predicting DNA recognition by Cys2His2 zinc finger proteins , 2009, Bioinform..
[430] E. Hsu. Reflections on the 'discovery' of the antimalarial qinghao. , 2006, British journal of clinical pharmacology.
[431] Mike Tyers,et al. BioGRID: a general repository for interaction datasets , 2005, Nucleic Acids Res..
[432] Michael Balls,et al. Translation of new technologies: from basic research to drug discovery and development. , 2008, Current drug discovery technologies.
[433] D. Lalloo,et al. Oral cholera vaccines: use in clinical practice. , 2006, The Lancet. Infectious diseases.
[434] Sean Ekins,et al. Techniques: application of systems biology to absorption, distribution, metabolism, excretion and toxicity. , 2005, Trends in pharmacological sciences.
[435] D. Nebert,et al. Pharmacogenetics and pharmacogenomics: why is this relevant to the clinical geneticist? , 1999, Clinical genetics.
[436] Ruedi Aebersold,et al. Complementary Analysis of the Mycobacterium tuberculosis Proteome by Two-dimensional Electrophoresis and Isotope-coded Affinity Tag Technology * , 2004, Molecular & Cellular Proteomics.
[437] John W. R. Schwabe,et al. The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/DNA recognition , 1993, Nature.
[438] R. Coombes,et al. A Phase I Study of OncoVEXGM-CSF, a Second-Generation Oncolytic Herpes Simplex Virus Expressing Granulocyte Macrophage Colony-Stimulating Factor , 2006, Clinical Cancer Research.
[439] M. Asaduzzaman,et al. The Major Subunit of the Toxin-Coregulated Pilus TcpA Induces Mucosal and Systemic Immunoglobulin A Immune Responses in Patients with Cholera Caused by Vibrio cholerae O1 and O139 , 2004, Infection and Immunity.
[440] D R Westhead,et al. Petri Net representations in systems biology. , 2003, Biochemical Society transactions.
[441] Jason H. Moore,et al. Systems genetics for drug target discovery. , 2011, Trends in pharmacological sciences.
[442] B. Palsson,et al. Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions , 2010, Molecular systems biology.
[443] Ozlem Keskin,et al. Prediction of protein–protein interactions: unifying evolution and structure at protein interfaces , 2011, Physical biology.
[444] Timothy B. Stockwell,et al. The Sequence of the Human Genome , 2001, Science.
[445] Anup D. Shah,et al. Crowd Sourcing a New Paradigm for Interactome Driven Drug Target Identification in Mycobacterium tuberculosis , 2012, PloS one.
[446] E. Silverman,et al. Heterogeneity of therapeutic responses in asthma. , 2000, British medical bulletin.
[447] Drew Endy,et al. Engineering BioBrick vectors from BioBrick parts , 2008, Journal of Biological Engineering.
[448] Ryan J. Kershner,et al. Placement and orientation of individual DNA shapes on lithographically patterned surfaces. , 2009, Nature nanotechnology.
[449] M. Delbrück,et al. Mutations of Bacteria from Virus Sensitivity to Virus Resistance. , 1943, Genetics.
[450] Richard M. Karp,et al. Genome-Wide Association Data Reveal a Global Map of Genetic Interactions among Protein Complexes , 2009, PLoS genetics.
[451] H. Sauro,et al. Standard Biological Parts Knowledgebase , 2011, PloS one.
[452] G. Stephanopoulos,et al. Metabolic Engineering: Principles And Methodologies , 1998 .
[453] Fariza Tahi,et al. A fast ab-initio method for predicting miRNA precursors in genomes , 2012, Nucleic acids research.
[454] Ravi Iyengar,et al. Systems pharmacology. , 2010, The Mount Sinai journal of medicine, New York.
[455] H. Nikaido. Multidrug resistance in bacteria. , 2009, Annual review of biochemistry.
[456] James R Faeder,et al. Detailed qualitative dynamic knowledge representation using a BioNetGen model of TLR-4 signaling and preconditioning. , 2009, Mathematical biosciences.
[457] P. Swain,et al. Intrinsic and extrinsic contributions to stochasticity in gene expression , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[458] C. Wijmenga,et al. Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. , 2006, American journal of human genetics.
[459] Kenta Nakai,et al. DBTSS: database of transcription start sites, progress report 2008 , 2007, Nucleic Acids Res..