Application of the Transcriptional Disease Signature (TDSs) to Screen Melanoma-Effective Compounds in a Small Fish Model

[1]  Takashi Suzuki,et al.  OLFM4, LY6D and S100A7 as potent markers for distant metastasis in estrogen receptor‐positive breast carcinoma , 2018, Cancer science.

[2]  Lei Wang,et al.  BNPMDA: Bipartite Network Projection for MiRNA–Disease Association prediction , 2018, Bioinform..

[3]  Xuan Liu,et al.  RHCG suppresses cervical cancer progression through inhibiting migration and inducing apoptosis regulated by TGF-β1. , 2018, Biochemical and biophysical research communications.

[4]  Xing Chen,et al.  MDHGI: Matrix Decomposition and Heterogeneous Graph Inference for miRNA-disease association prediction , 2018, PLoS Comput. Biol..

[5]  A. Amores,et al.  Comparison of Xiphophorus and human melanoma transcriptomes reveals conserved pathway interactions , 2018, Pigment cell & melanoma research.

[6]  Na-Na Guan,et al.  Predicting miRNA‐disease association based on inductive matrix completion , 2018, Bioinform..

[7]  J. Postlethwait,et al.  Expression signatures of early-stage and advanced medaka melanomas. , 2018, Comparative biochemistry and physiology. Toxicology & pharmacology : CBP.

[8]  R. Walter,et al.  Waveband specific transcriptional control of select genetic pathways in vertebrate skin (Xiphophorus maculatus) , 2018, BMC Genomics.

[9]  A. Gore,et al.  The zebrafish: A fintastic model for hematopoietic development and disease , 2018, Wiley interdisciplinary reviews. Developmental biology.

[10]  Robert L. Tanguay,et al.  Transcriptomic and phenotypic profiling in developing zebrafish exposed to thyroid hormone receptor agonists. , 2018, Reproductive toxicology.

[11]  V. Scaria,et al.  Chemical and genetic rescue of an ep300 knockdown model for Rubinstein Taybi Syndrome in zebrafish. , 2018, Biochimica et biophysica acta. Molecular basis of disease.

[12]  R. Kleta,et al.  Zebrafish as a model for kidney function and disease , 2018, Pediatric Nephrology.

[13]  W. Norton,et al.  Automatic quantification of juvenile zebrafish aggression , 2018, Journal of Neuroscience Methods.

[14]  J. Rho,et al.  A novel metabolism-based phenotypic drug discovery platform in zebrafish uncovers HDACs 1 and 3 as a potential combined anti-seizure drug target , 2018, Brain : a journal of neurology.

[15]  X. Guan,et al.  RHCG Suppresses Tumorigenicity and Metastasis in Esophageal Squamous Cell Carcinoma via Inhibiting NF-κB Signaling and MMP1 Expression , 2018, Theranostics.

[16]  Ramon Grima,et al.  Single-cell variability in multicellular organisms , 2018, Nature Communications.

[17]  J. Skolnick,et al.  Brain activity patterns in high-throughput electrophysiology screen predict both drug efficacies and side effects , 2018, Nature Communications.

[18]  Xing Chen,et al.  LRSSLMDA: Laplacian Regularized Sparse Subspace Learning for MiRNA-Disease Association prediction , 2017, PLoS Comput. Biol..

[19]  Yu-Heng Lai,et al.  Live Fluorescent Staining Platform for Drug-Screening and Mechanism-Analysis in Zebrafish for Bone Mineralization , 2017, Molecules.

[20]  L. Kwong,et al.  miRNAs, Melanoma and Microenvironment: An Intricate Network , 2017, International journal of molecular sciences.

[21]  R. Longuespée,et al.  OLFM4, KNG1 and Sec24C identified by proteomics and immunohistochemistry as potential markers of early colorectal cancer stages , 2017, Clinical Proteomics.

[22]  J. Iovanna L’autophagie contribue à l’initiation du cancer pancréatique , 2017 .

[23]  C. Croce,et al.  MicroRNAs in melanoma development and resistance to target therapy , 2017, Oncotarget.

[24]  Michal P. Switnicki,et al.  RHCG and TCAF1 promoter hypermethylation predicts biochemical recurrence in prostate cancer patients treated by radical prostatectomy , 2016, Oncotarget.

[25]  J. Iovanna [Autophagy contributes to the initiation of pancreatic cancer]. , 2017, Medecine sciences : M/S.

[26]  H. Jono,et al.  Indoxyl Sulfate as a Mediator Involved in Dysregulation of Pulmonary Aquaporin-5 in Acute Lung Injury Caused by Acute Kidney Injury , 2016, International journal of molecular sciences.

[27]  T. Ramesh,et al.  ZNStress: a high-throughput drug screening protocol for identification of compounds modulating neuronal stress in the transgenic mutant sod1G93R zebrafish model of amyotrophic lateral sclerosis , 2016, Molecular Neurodegeneration.

[28]  J. Postlethwait,et al.  Germ cell and tumor associated piRNAs in the medaka and Xiphophorus melanoma models , 2016, BMC Genomics.

[29]  Manfred Schartl,et al.  Xiphophorus and Medaka Cancer Models. , 2016, Advances in experimental medicine and biology.

[30]  Sanyuan Hu,et al.  Downregulation of betaine homocysteine methyltransferase (BHMT) in hepatocellular carcinoma associates with poor prognosis , 2016, Tumor Biology.

[31]  R. Wilson,et al.  Whole Body Melanoma Transcriptome Response in Medaka , 2015, PloS one.

[32]  M. Schartl,et al.  Molecular genetic response of Xiphophorus maculatus-X. couchianus interspecies hybrid skin to UVB exposure. , 2015, Comparative biochemistry and physiology. Toxicology & pharmacology : CBP.

[33]  R. Walter,et al.  Sex-specific molecular genetic response to UVB exposure in Xiphophorus maculatus skin. , 2015, Comparative biochemistry and physiology. Toxicology & pharmacology : CBP.

[34]  R. Walter,et al.  Exposure to fluorescent light triggers down regulation of genes involved with mitotic progression in Xiphophorus skin. , 2015, Comparative biochemistry and physiology. Toxicology & pharmacology : CBP.

[35]  R. Walter,et al.  Molecular genetic response to varied wavelengths of light in Xiphophorus maculatus skin. , 2015, Comparative biochemistry and physiology. Toxicology & pharmacology : CBP.

[36]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[37]  M. Schartl,et al.  Comparative analysis of melanoma deregulated miRNAs in the medaka and Xiphophorus pigment cell cancer models. , 2014, Comparative biochemistry and physiology. Toxicology & pharmacology : CBP.

[38]  H. Koon,et al.  What Is the Role of Chemotherapy in the Treatment of Melanoma? , 2014, Current Treatment Options in Oncology.

[39]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[40]  Xing Chen,et al.  Novel human lncRNA-disease association inference based on lncRNA expression profiles , 2013, Bioinform..

[41]  Scott C. Baraban,et al.  Drug screening in Scn1a zebrafish mutant identifies clemizole as a potential Dravet Syndrome treatment , 2013, Nature Communications.

[42]  R. Gerszten,et al.  Chemical and metabolomic screens identify novel biomarkers and antidotes for cyanide exposure , 2013, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[43]  Davis J. McCarthy,et al.  Count-based differential expression analysis of RNA sequencing data using R and Bioconductor , 2013, Nature Protocols.

[44]  R. Gerszten,et al.  An In Vivo Zebrafish Screen Identifies Organophosphate Antidotes with Diverse Mechanisms of Action , 2013, Journal of biomolecular screening.

[45]  D. Stainier,et al.  Whole-organism screening for gluconeogenesis identifies activators of fasting metabolism , 2012, Nature chemical biology.

[46]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[47]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[48]  J. Utikal,et al.  Improved survival with MEK inhibition in BRAF-mutated melanoma. , 2012, The New England journal of medicine.

[49]  Dirk Schadendorf,et al.  Improved survival with MEK Inhibition in BRAF-mutated melanoma for the METRIC Study Group , 2012 .

[50]  Archana Agarwal,et al.  Zebrafish screen identifies novel compound with selective toxicity against leukemia. , 2012, Blood.

[51]  Su Guo,et al.  Zebrafish Chemical Screening Reveals the Impairment of Dopaminergic Neuronal Survival by Cardiac Glycosides , 2012, PloS one.

[52]  A. Amores,et al.  Effects of short read quality and quantity on a de novo vertebrate transcriptome assembly. , 2012, Comparative biochemistry and physiology. Toxicology & pharmacology : CBP.

[53]  Terri T. Ni,et al.  Discovering small molecules that promote cardiomyocyte generation by modulating Wnt signaling. , 2011, Chemistry & biology.

[54]  Nicole E. Bodycombe,et al.  A small-molecule screening strategy to identify suppressors of statin myopathy. , 2011, ACS chemical biology.

[55]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[56]  D. Swinney,et al.  How were new medicines discovered? , 2011, Nature Reviews Drug Discovery.

[57]  Charles Y. Lin,et al.  DHODH modulates transcriptional elongation in the neural crest and melanoma , 2011, Nature.

[58]  Francesca Zappacosta,et al.  GSK1120212 (JTP-74057) Is an Inhibitor of MEK Activity and Activation with Favorable Pharmacokinetic Properties for Sustained In Vivo Pathway Inhibition , 2011, Clinical Cancer Research.

[59]  Robert W. Mills,et al.  Novel Chemical Suppressors of Long QT Syndrome Identified by an In Vivo Functional Screen , 2011, Circulation.

[60]  Shuo Lin,et al.  Chemical screening with zebrafish embryos. , 2011, Methods in molecular biology.

[61]  H. Boezen,et al.  Association of PAI‐1 gene polymorphism with survival and chemotherapy‐related vascular toxicity in testicular cancer , 2010, Cancer.

[62]  Peter G. Schultz,et al.  High-Throughput Chemical Screen Identifies a Novel Potent Modulator of Cellular Circadian Rhythms and Reveals CKIα as a Clock Regulatory Kinase , 2010, PLoS biology.

[63]  Michael C. Myers,et al.  Identification of Novel Inhibitors of Dietary Lipid Absorption Using Zebrafish , 2010, PloS one.

[64]  B. Silber,et al.  Driving Drug Discovery: The Fundamental Role of Academic Labs , 2010, Science Translational Medicine.

[65]  R. Peterson,et al.  A Forward Chemical Screen in Zebrafish Identifies a Retinoic Acid Derivative with Receptor Specificity , 2010, PloS one.

[66]  C. Lindsley,et al.  In vivo structure-activity relationship study of dorsomorphin analogues identifies selective VEGF and BMP inhibitors. , 2010, ACS chemical biology.

[67]  Christian Laggner,et al.  Rapid behavior—based identification of neuroactive small molecules in the zebrafish , 2009, Nature chemical biology.

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

[69]  M. Schartl,et al.  A mutated EGFR is sufficient to induce malignant melanoma with genetic background-dependent histopathologies. , 2010, The Journal of investigative dermatology.

[70]  R. Nairn,et al.  Xmrk in medaka: a new genetic melanoma model. , 2010, The Journal of investigative dermatology.

[71]  B. Munos Lessons from 60 years of pharmaceutical innovation , 2009, Nature Reviews Drug Discovery.

[72]  Dan M Roden,et al.  Drug-Sensitized Zebrafish Screen Identifies Multiple Genes, Including GINS3, as Regulators of Myocardial Repolarization , 2009, Circulation.

[73]  Robert Gerlai,et al.  Zebrafish (Danio rerio) responds to the animated image of a predator: Towards the development of an automated aversive task , 2009, Behavioural Brain Research.

[74]  Ivet Bahar,et al.  Zebrafish chemical screening reveals an inhibitor of Dusp6 that expands cardiac cell lineages , 2009, Nature chemical biology.

[75]  Kyle J. McCulloch,et al.  Small molecule screen for compounds that affect vascular development in the zebrafish retina , 2009, Mechanisms of Development.

[76]  D. Raible,et al.  Identification of FDA-Approved Drugs and Bioactives that Protect Hair Cells in the Zebrafish (Danio rerio) Lateral Line and Mouse (Mus musculus) Utricle , 2009, Journal of the Association for Research in Otolaryngology.

[77]  Stephen L. Johnson,et al.  Small molecule modifier screen for kit-dependent functions in zebrafish embryonic melanocytes. , 2008, Zebrafish.

[78]  R. Milner,et al.  Cisplatin: a review of toxicities and therapeutic applications. , 2008, Veterinary and comparative oncology.

[79]  Jennifer L. Osborn,et al.  Direct multiplexed measurement of gene expression with color-coded probe pairs , 2008, Nature Biotechnology.

[80]  D. Richardson,et al.  The function of melanotransferrin: a role in melanoma cell proliferation and tumorigenesis. , 2006, Carcinogenesis.

[81]  L. Zon,et al.  A Chemical Genetic Screen for Cell Cycle Inhibitors in Zebrafish Embryos , 2006, Chemical biology & drug design.

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

[83]  A. Manolis,et al.  Rethinking target discovery in polygenic diseases. , 2006, Current topics in medicinal chemistry.

[84]  Michael Williams,et al.  Systems and integrative biology as alternative guises for pharmacology: prime time for an iPharm concept? , 2005, Biochemical pharmacology.

[85]  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.

[86]  M. Fielden,et al.  Development of a large-scale chemogenomics database to improve drug candidate selection and to understand mechanisms of chemical toxicity and action. , 2005, Journal of biotechnology.

[87]  Shuo Lin,et al.  Induction of reversible hemolytic anemia in living zebrafish using a novel small molecule. , 2004, Comparative biochemistry and physiology. Toxicology & pharmacology : CBP.

[88]  M. Daly,et al.  PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes , 2003, Nature Genetics.

[89]  M. Lindsay Target discovery , 2003, Nature Reviews Drug Discovery.

[90]  M. Schartl,et al.  Autocrine stimulation by osteopontin contributes to antiapoptotic signalling of melanocytes in dermal collagen. , 2002, Cancer research.

[91]  M. Schartl,et al.  Activation of STAT5 triggers proliferation and contributes to anti-apoptotic signalling mediated by the oncogenic Xmrk kinase , 2002, Oncogene.

[92]  M. Schartl,et al.  Activation of p59Fyn Leads to Melanocyte Dedifferentiation by Influencing MKP-1-regulated Mitogen-activated Protein Kinase Signaling* , 2002, The Journal of Biological Chemistry.

[93]  M. Schartl,et al.  Activation of p59(Fyn) leads to melanocyte dedifferentiation by influencing MKP-1-regulated mitogen-activated protein kinase signaling. , 2002, The Journal of biological chemistry.

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

[95]  M. Schartl,et al.  Activation of phosphatidylinositol 3-kinase by a complex of p59fyn and the receptor tyrosine kinase Xmrk is involved in malignant transformation of pigment cells. , 2000, European journal of biochemistry.

[96]  R. Tukey,et al.  Human UDP-glucuronosyltransferases: metabolism, expression, and disease. , 2000, Annual review of pharmacology and toxicology.

[97]  M. Schartl,et al.  Multiple binding sites in the growth factor receptor Xmrk mediate binding to p59fyn, GRB2 and Shc. , 1999, European journal of biochemistry.

[98]  M. Schartl,et al.  Novel putative receptor tyrosine kinase encoded by the melanoma-inducing Tu locus in Xiphophorus , 1989, Nature.