Genomic Data Analysis for Personalized Medicine

[1]  Howard L McLeod,et al.  Carbamazepine, HLA-B*1502 and risk of Stevens-Johnson syndrome and toxic epidermal necrolysis: US FDA recommendations. , 2008, Pharmacogenomics.

[2]  M. King,et al.  Genetic Heterogeneity in Human Disease , 2010, Cell.

[3]  Roded Sharan,et al.  Associating Genes and Protein Complexes with Disease via Network Propagation , 2010, PLoS Comput. Biol..

[4]  J. C. Hinshaw,et al.  Discovering Modes of Action for Therapeutic Compounds Using a Genome-Wide Screen of Yeast Heterozygotes , 2004, Cell.

[5]  Francine E. Garrett-Bakelman,et al.  methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles , 2012, Genome Biology.

[6]  Emmanuel Barillot,et al.  Spatial normalization of array-CGH data , 2006, BMC Bioinformatics.

[7]  V. Thorsson,et al.  Discovery of regulatory interactions through perturbation: inference and experimental design. , 1999, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[8]  M. Gerstein,et al.  RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.

[9]  K. Kinzler,et al.  Cancer Genome Landscapes , 2013, Science.

[10]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[11]  J. Ross,et al.  MammaPrint™ 70-gene signature: another milestone in personalized medical care for breast cancer patients , 2009, Expert review of molecular diagnostics.

[12]  Rafael A Irizarry,et al.  Comprehensive high-throughput arrays for relative methylation (CHARM). , 2008, Genome research.

[13]  Alan R. Powell,et al.  Integration of text- and data-mining using ontologies successfully selects disease gene candidates , 2005, Nucleic acids research.

[14]  C. Harris,et al.  The IARC TP53 database: New online mutation analysis and recommendations to users , 2002, Human mutation.

[15]  I. Amit,et al.  Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .

[16]  Staffan Persson,et al.  GeneCAT—novel webtools that combine BLAST and co-expression analyses , 2008, Nucleic Acids Res..

[17]  Michael Krawczak,et al.  The human gene mutation database , 1998, Nucleic Acids Res..

[18]  Robert B Livingston,et al.  Prognostic and predictive value of the 21-gene recurrence score assay in postmenopausal women with node-positive, oestrogen-receptor-positive breast cancer on chemotherapy: a retrospective analysis of a randomised trial. , 2010, The Lancet. Oncology.

[19]  Lior Pachter,et al.  Identification of novel transcripts in annotated genomes using RNA-Seq , 2011, Bioinform..

[20]  Igor Jurisica,et al.  Gene expression–based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study , 2008, Nature Medicine.

[21]  Joshua M. Stuart,et al.  The Cancer Genome Atlas Pan-Cancer analysis project , 2013, Nature Genetics.

[22]  N. Schork,et al.  Utility of network integrity methods in therapeutic target identification , 2013, Front. Genet..

[23]  D. Matthews,et al.  De novo derivation of proteomes from transcriptomes for transcript and protein identification , 2012, Nature Methods.

[24]  Juan Cui,et al.  Regulation of gene expression in ovarian cancer cells by luteinizing hormone receptor expression and activation , 2011, BMC Cancer.

[25]  Robert P. St.Onge,et al.  The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes , 2008, Science.

[26]  Dexter T. Duncan,et al.  CanProVar: a human cancer proteome variation database , 2010, Human mutation.

[27]  Daniel R. Richards,et al.  Predictive Systems Biology Approach to Broad-Spectrum, Host-Directed Drug Target Discovery in Infectious Diseases , 2012, Pacific Symposium on Biocomputing.

[28]  Tijl De Bie,et al.  Kernel-based data fusion for gene prioritization , 2007, ISMB/ECCB.

[29]  J. Fostel,et al.  Genome-Wide Expression Patterns inSaccharomyces cerevisiae: Comparison of Drug Treatments and Genetic Alterations Affecting Biosynthesis of Ergosterol , 2000, Antimicrobial Agents and Chemotherapy.

[30]  Ken Chen,et al.  VarScan: variant detection in massively parallel sequencing of individual and pooled samples , 2009, Bioinform..

[31]  S A Forbes,et al.  The Catalogue of Somatic Mutations in Cancer (COSMIC) , 2008, Current protocols in human genetics.

[32]  Hsien-Da Huang,et al.  miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions , 2013, Nucleic Acids Res..

[33]  A. Nekrutenko,et al.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences , 2010, Genome Biology.

[34]  A. Shilatifard,et al.  An operational definition of epigenetics. , 2009, Genes & development.

[35]  Tim Becker,et al.  INTERSNP: genome-wide interaction analysis guided by a priori information , 2009, Bioinform..

[36]  C. Croce Causes and consequences of microRNA dysregulation in cancer , 2009, Nature Reviews Genetics.

[37]  Suzette J. Bielinski,et al.  Use of diverse electronic medical record systems to identify genetic risk for type 2 diabetes within a genome-wide association study , 2012, J. Am. Medical Informatics Assoc..

[38]  Jason Weston,et al.  Gene Selection for Cancer Classification using Support Vector Machines , 2002, Machine Learning.

[39]  J. Collins,et al.  A network biology approach to prostate cancer , 2007, Molecular systems biology.

[40]  K. Guegler,et al.  Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation , 2004, Nature Biotechnology.

[41]  Steve Horvath,et al.  WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.

[42]  Corinna Cortes,et al.  Support-Vector Networks , 1995, Machine Learning.

[43]  Eleazar Eskin,et al.  Efficient algorithms for tandem copy number variation reconstruction in repeat-rich regions , 2011, Bioinform..

[44]  Mihai Pop,et al.  Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies , 2011, BMC Bioinformatics.

[45]  Martin Vingron,et al.  Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads , 2012, Bioinform..

[46]  P. Khatri,et al.  A systems biology approach for pathway level analysis. , 2007, Genome research.

[47]  John Quackenbush,et al.  Computational genetics: Computational analysis of microarray data , 2001, Nature Reviews Genetics.

[48]  Graziano Pesole,et al.  Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes , 2009, Nucleic Acids Res..

[49]  R. Stephens,et al.  Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer. , 2008, Cancer research.

[50]  Jiajie Zhang,et al.  MethyCancer: the database of human DNA methylation and cancer , 2007, Nucleic Acids Res..

[51]  Melissa A. Basford,et al.  Variants near FOXE1 are associated with hypothyroidism and other thyroid conditions: using electronic medical records for genome- and phenome-wide studies. , 2011, American journal of human genetics.

[52]  Richard T. Barfield,et al.  CpGassoc: an R function for analysis of DNA methylation microarray data , 2012, Bioinform..

[53]  Steven J. M. Jones,et al.  Comprehensive molecular characterization of human colon and rectal cancer , 2012, Nature.

[54]  R. Nielsen,et al.  Population genetic inference from genomic sequence variation. , 2010, Genome research.

[55]  I. Cascorbi,et al.  Clozapine-induced agranulocytosis in schizophrenic Caucasians: confirming clues for associations with human leukocyte class I and II antigens , 2007, The Pharmacogenomics Journal.

[56]  Pedro Larrañaga,et al.  Filter versus wrapper gene selection approaches in DNA microarray domains , 2004, Artif. Intell. Medicine.

[57]  R. Tibshirani,et al.  Significance analysis of microarrays applied to the ionizing radiation response , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[58]  Huanming Yang,et al.  SNP detection for massively parallel whole-genome resequencing. , 2009, Genome research.

[59]  Wenyi Wang,et al.  DeMix: deconvolution for mixed cancer transcriptomes using raw measured data , 2013, Bioinform..

[60]  C. Ball,et al.  Repeatability of published microarray gene expression analyses , 2009, Nature Genetics.

[61]  Seon-Young Kim,et al.  Gene-set approach for expression pattern analysis , 2008, Briefings Bioinform..

[62]  J. Gilbert,et al.  Complement Factor H Variant Increases the Risk of Age-Related Macular Degeneration , 2005, Science.

[63]  Shah Ebrahim,et al.  Common variants in the GDF5-UQCC region are associated with variation in human height , 2008, Nature Genetics.

[64]  T. Barrette,et al.  Mining for regulatory programs in the cancer transcriptome , 2005, Nature Genetics.

[65]  Bruce Gottlieb,et al.  The androgen receptor gene mutations database , 1996, Nucleic Acids Res..

[66]  Monica L. Mo,et al.  Global reconstruction of the human metabolic network based on genomic and bibliomic data , 2007, Proceedings of the National Academy of Sciences.

[67]  Marylyn D. Ritchie,et al.  Pacific Symposium on Biocomputing 14:368-379 (2009) BIOFILTER: A KNOWLEDGE-INTEGRATION SYSTEM FOR THE MULTI-LOCUS ANALYSIS OF GENOME-WIDE ASSOCIATION STUDIES * , 2022 .

[68]  Richard Simon,et al.  A random variance model for detection of differential gene expression in small microarray experiments , 2003, Bioinform..

[69]  Phillip Stafford,et al.  Methods in Microarray Normalization , 2008 .

[70]  David A. Rasko,et al.  Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions , 2013, Nature Reviews Genetics.

[71]  Lin Chen,et al.  Importance of multi-modal approaches to effectively identify cataract cases from electronic health records , 2012, J. Am. Medical Informatics Assoc..

[72]  Anil K. Jain,et al.  Data clustering: a review , 1999, CSUR.

[73]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[74]  Emmanuel Barillot,et al.  ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays , 2008, Bioinform..

[75]  Clive E. Bowman,et al.  Genetic variations in HLA-B region and hypersensitivity reactions to abacavir , 2002, The Lancet.

[76]  S. Kasif,et al.  Network-Based Analysis of Affected Biological Processes in Type 2 Diabetes Models , 2007, PLoS genetics.

[77]  S. Salzberg,et al.  Repetitive DNA and next-generation sequencing: computational challenges and solutions , 2011, Nature Reviews Genetics.

[78]  S. Wyman,et al.  Repertoire of microRNAs in Epithelial Ovarian Cancer as Determined by Next Generation Sequencing of Small RNA cDNA Libraries , 2009, PloS one.

[79]  Thomas Lengauer,et al.  EpiExplorer: live exploration and global analysis of large epigenomic datasets , 2012, Genome Biology.

[80]  R. Stephens,et al.  Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. , 2006, Cancer cell.

[81]  Jason H. Moore,et al.  STUDENTJAMA. The challenges of whole-genome approaches to common diseases. , 2004, JAMA.

[82]  D. Allison,et al.  Microarray data analysis: from disarray to consolidation and consensus , 2006, Nature Reviews Genetics.

[83]  Yvonne Tay,et al.  A Pattern-Based Method for the Identification of MicroRNA Binding Sites and Their Corresponding Heteroduplexes , 2006, Cell.

[84]  Thomas J. Hardcastle,et al.  baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data , 2010, BMC Bioinformatics.

[85]  D. Bartel MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.

[86]  Michael C. Rusch,et al.  CREST maps somatic structural variation in cancer genomes with base-pair resolution , 2011, Nature Methods.

[87]  E. Eichler,et al.  Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. , 2009, Genome research.

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

[89]  Carlo Gambacorti-Passerini,et al.  Part I: Milestones in personalised medicine--imatinib. , 2008, The Lancet. Oncology.

[90]  Gong-Hua Li,et al.  Inferring therapeutic targets from heterogeneous data: HKDC1 is a novel potential therapeutic target for cancer , 2014, Bioinform..

[91]  Peer Bork,et al.  iPath2.0: interactive pathway explorer , 2011, Nucleic Acids Res..

[92]  M. Schatz,et al.  Genome assembly forensics: finding the elusive mis-assembly , 2008, Genome Biology.

[93]  S. Knudsen,et al.  A 71-Gene Signature of TRAIL Sensitivity in Cancer Cells , 2011, Molecular Cancer Therapeutics.

[94]  J. Bond,et al.  The CDKN2A database: Integrating allelic variants with evolution, structure, function, and disease association , 2004, Human mutation.

[95]  Gerben Menschaert,et al.  PubMeth: a cancer methylation database combining text-mining and expert annotation , 2007, Nucleic Acids Res..

[96]  Elizabeth M. Smigielski,et al.  dbSNP: a database of single nucleotide polymorphisms , 2000, Nucleic Acids Res..

[97]  Junhyong Kim,et al.  Sniper: improved SNP discovery by multiply mapping deep sequenced reads , 2011, Genome Biology.

[98]  George A Calin,et al.  MicroRNA signatures associated with cytogenetics and prognosis in acute myeloid leukemia. , 2008, Blood.

[99]  Casey Lynnette Overby,et al.  Personalized medicine: challenges and opportunities for translational bioinformatics. , 2013, Personalized medicine.

[100]  Sean R. Davis,et al.  NCBI GEO: archive for functional genomics data sets—update , 2012, Nucleic Acids Res..

[101]  T. Ideker,et al.  Network-based classification of breast cancer metastasis , 2007, Molecular systems biology.

[102]  Christian Gilissen,et al.  Unlocking Mendelian disease using exome sequencing , 2011, Genome Biology.

[103]  Gordon K Smyth,et al.  Statistical Applications in Genetics and Molecular Biology Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2011 .

[104]  David J. Arenillas,et al.  JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles , 2009, Nucleic Acids Res..

[105]  R. Fisher 014: On the "Probable Error" of a Coefficient of Correlation Deduced from a Small Sample. , 1921 .

[106]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[107]  Kevin Dobbin,et al.  Statistical Design of Reverse Dye Microarrays , 2003, Bioinform..

[108]  P. Bork,et al.  Association of genes to genetically inherited diseases using data mining , 2002, Nature Genetics.

[109]  R. Durbin,et al.  Mapping Quality Scores Mapping Short Dna Sequencing Reads and Calling Variants Using P

, 2022 .

[110]  R. Collins,et al.  Newly identified loci that influence lipid concentrations and risk of coronary artery disease , 2008, Nature Genetics.

[111]  A. Mortazavi,et al.  Computation for ChIP-seq and RNA-seq studies , 2009, Nature Methods.

[112]  Weijun Luo,et al.  Pathview: an R/Bioconductor package for pathway-based data integration and visualization , 2013, Bioinform..

[113]  T. Hubbard,et al.  A census of human cancer genes , 2004, Nature Reviews Cancer.

[114]  R. Altman,et al.  Estimation of the warfarin dose with clinical and pharmacogenetic data. , 2009, The New England journal of medicine.

[115]  V. Ambros The functions of animal microRNAs , 2004, Nature.

[116]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[117]  Russ B. Altman,et al.  Bioinformatics challenges for personalized medicine , 2011, Bioinform..

[118]  Muller Fabbri,et al.  A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. , 2005, The New England journal of medicine.

[119]  Ron Shamir,et al.  Allegro: Analyzing expression and sequence in concert to discover regulatory programs , 2009, Nucleic acids research.

[120]  M. Rieder,et al.  A genome-wide scan for common genetic variants with a large influence on warfarin maintenance dose. , 2008, Blood.

[121]  Yudong D. He,et al.  Functional Discovery via a Compendium of Expression Profiles , 2000, Cell.

[122]  M. DePristo,et al.  A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.

[123]  C. Burge,et al.  Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets , 2005, Cell.

[124]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[125]  Ying Xu,et al.  QUBIC: a qualitative biclustering algorithm for analyses of gene expression data , 2009, Nucleic acids research.

[126]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[127]  Daniel Hanisch,et al.  New methods for joint analysis of biological networks and expression data , 2004, German Conference on Bioinformatics.

[128]  George A Calin,et al.  MicroRNA expression profiles associated with prognosis and therapeutic outcome in colon adenocarcinoma. , 2008, JAMA.