Genomics and transcriptomics in drug discovery.

[1]  Urs A Meyer,et al.  Omics and drug response. , 2013, Annual review of pharmacology and toxicology.

[2]  N. Lennon,et al.  Characterizing and measuring bias in sequence data , 2013, Genome Biology.

[3]  C. Tyler-Smith,et al.  Deleterious- and disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing. , 2012, American journal of human genetics.

[4]  Nuno A. Fonseca,et al.  Tools for mapping high-throughput sequencing data , 2012, Bioinform..

[5]  M. Schwab,et al.  Pharmacogenomics: a key component of personalized therapy , 2012, Genome Medicine.

[6]  Rune Linding,et al.  Navigating cancer network attractors for tumor-specific therapy , 2012, Nature Biotechnology.

[7]  Raymond K. Auerbach,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[8]  Joaquín Dopazo,et al.  A map of human microRNA variation uncovers unexpectedly high levels of variability , 2012, Genome Medicine.

[9]  Y. Moreau,et al.  Computational tools for prioritizing candidate genes: boosting disease gene discovery , 2012, Nature Reviews Genetics.

[10]  ENCODEConsortium,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[11]  Cristina Y. González,et al.  VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing , 2012, Nucleic Acids Res..

[12]  P. Turnbaugh,et al.  Is It Time for a Metagenomic Basis of Therapeutics? , 2012, Science.

[13]  Elhanan Borenstein,et al.  Computational systems biology and in silico modeling of the human microbiome , 2012, Briefings Bioinform..

[14]  T. Dallman,et al.  Performance comparison of benchtop high-throughput sequencing platforms , 2012, Nature Biotechnology.

[15]  P. A. Futreal,et al.  Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. , 2012, The New England journal of medicine.

[16]  A. Conesa,et al.  Differential expression in RNA-seq: a matter of depth. , 2011, Genome research.

[17]  J. Shendure,et al.  Exome sequencing as a tool for Mendelian disease gene discovery , 2011, Nature Reviews Genetics.

[18]  John A. Todd,et al.  Metagenomics and Personalized Medicine , 2011, Cell.

[19]  J. Benítez,et al.  Exome sequencing identifies MAX mutations as a cause of hereditary pheochromocytoma , 2011, Nature Genetics.

[20]  Joel Dudley,et al.  Exploiting drug-disease relationships for computational drug repositioning , 2011, Briefings Bioinform..

[21]  Peter M Woollard,et al.  The application of next-generation sequencing technologies to drug discovery and development. , 2011, Drug discovery today.

[22]  Cole Trapnell,et al.  Computational methods for transcriptome annotation and quantification using RNA-seq , 2011, Nature Methods.

[23]  Benjamin J. Raphael,et al.  Integrated Genomic Analyses of Ovarian Carcinoma , 2011, Nature.

[24]  M. Stratton.  Exploring the Genomes of Cancer Cells: Progress and Promise , 2011, Science.

[25]  D. MacArthur,et al.  Loss-of-function variants in the genomes of healthy humans. , 2010, Human molecular genetics.

[26]  D. Altshuler,et al.  A map of human genome variation from population-scale sequencing , 2010, Nature.

[27]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[28]  G. Nolan,et al.  Computational solutions to large-scale data management and analysis , 2010, Nature Reviews Genetics.

[29]  B. Langmead,et al.  Cloud-scale RNA-sequencing differential expression analysis with Myrna , 2010, Genome Biology.

[30]  R. Tagliaferri,et al.  Discovery of drug mode of action and drug repositioning from transcriptional responses , 2010, Proceedings of the National Academy of Sciences.

[31]  Kevin C. Dorff,et al.  The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models , 2010, Nature Biotechnology.

[32]  G. Hon,et al.  Next-generation genomics: an integrative approach , 2010, Nature Reviews Genetics.

[33]  F. Collins,et al.  Genomic medicine--an updated primer. , 2010, The New England journal of medicine.

[34]  L. Stein.  The case for cloud computing in genome informatics , 2010, Genome Biology.

[35]  Joel Dudley,et al.  Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets , 2010, PLoS Comput. Biol..

[36]  John C. Wooley,et al.  A Primer on Metagenomics , 2010, PLoS Comput. Biol..

[37]  J. C. Pastor-Pareja,et al.  Interaction between RasV12 and scribble clones induces tumour growth and invasion , 2009, Nature.

[38]  J. Jansson,et al.  Changes in the Composition of the Human Fecal Microbiome After Bacteriotherapy for Recurrent Clostridium difficile-associated Diarrhea , 2009, Journal of clinical gastroenterology.

[39]  L. Biesecker.  Exome sequencing makes medical genomics a reality , 2010, Nature Genetics.

[40]  M. Metzker.  Sequencing technologies — the next generation , 2010, Nature Reviews Genetics.

[41]  A. Barabasi,et al.  Network medicine : a network-based approach to human disease , 2010 .

[42]  S. Coons.  The FDA's critical path initiative: a brief introduction. , 2009, Clinical therapeutics.

[43]  Judy H. Cho,et al.  Finding the missing heritability of complex diseases , 2009, Nature.

[44]  Kevin Dieckhaus,et al.  Low-Abundance HIV Drug-Resistant Viral Variants in Treatment-Experienced Persons Correlate with Historical Antiretroviral Use , 2009, PloS one.

[45]  F. Collins,et al.  Potential etiologic and functional implications of genome-wide association loci for human diseases and traits , 2009, Proceedings of the National Academy of Sciences.

[46]  R. Sharan,et al.  Metabolic-network-driven analysis of bacterial ecological strategies , 2009, Genome Biology.

[47]  Xia Yang,et al.  Validation of Candidate Causal Genes for Abdominal Obesity Which Affect Shared Metabolic Pathways and Networks , 2009, Nature Genetics.

[48]  L. Hood,et al.  Systems medicine: the future of medical genomics and healthcare , 2009, Genome Medicine.

[49]  Abdul W Basit,et al.  The gastrointestinal microbiota as a site for the biotransformation of drugs. , 2008, International journal of pharmaceutics.

[50]  P. Bork,et al.  Drug Target Identification Using Side-Effect Similarity , 2008, Science.

[51]  R. Bernards,et al.  Enabling personalized cancer medicine through analysis of gene-expression patterns , 2008, Nature.

[52]  S. Ekins,et al.  In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling , 2007, British journal of pharmacology.

[53]  C. Sotiriou,et al.  Taking gene-expression profiling to the clinic: when will molecular signatures become relevant to patient care? , 2007, Nature Reviews Cancer.

[54]  G. Schneider,et al.  Predicting Compound Selectivity by Self‐Organizing Maps: Cross‐Activities of Metabotropic Glutamate Receptor Antagonists , 2006, ChemMedChem.

[55]  Paul A Clemons,et al.  The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease , 2006, Science.

[56]  K. Bush,et al.  Infrequent occurrence of single mutations in topoisomerase IV and DNA gyrase genes among US levofloxacin-susceptible clinical isolates of Streptococcus pneumoniae from nine institutions (1999-2003). , 2006, The Journal of antimicrobial chemotherapy.

[57]  Daniel J. Blankenberg,et al.  Galaxy: a platform for interactive large-scale genome analysis. , 2005, Genome research.

[58]  I. Kola,et al.  Can the pharmaceutical industry reduce attrition rates? , 2004, Nature Reviews Drug Discovery.

[59]  A. Barabasi,et al.  Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.

[60]  Syed Rizwanuddin Ahmad,et al.  Adverse drug event monitoring at the food and drug administration , 2003, Journal of general internal medicine.

[61]  J. Hopfield,et al.  From molecular to modular cell biology , 1999, Nature.

[62]  G R Gibson,et al.  Probiotics, prebiotics, and synbiotics: approaches for modulating the microbial ecology of the gut. , 1999, The American journal of clinical nutrition.

[63]  D. Falconer,et al.  Introduction to Quantitative Genetics. , 1961 .