Coupled transcriptome and proteome analysis of human lymphotropic tumor viruses: insights on the detection and discovery of viral genes

[1]  T. Schulz,et al.  Kaposi's Sarcoma-Associated Herpesvirus Bacterial Artificial Chromosome Contains a Duplication of a Long Unique-Region Fragment within the Terminal Repeat Region , 2011, Journal of Virology.

[2]  D. Elgui de Oliveira,et al.  KSHV genotypes A and C are more frequent in Kaposi sarcoma lesions from Brazilian patients with and without HIV infection, respectively. , 2011, Cancer letters.

[3]  P. Lieberman,et al.  Initiation of Epstein-Barr Virus Lytic Replication Requires Transcription and the Formation of a Stable RNA-DNA Hybrid Molecule at OriLyt , 2010, Journal of Virology.

[4]  Leigh-Ann MacFarlane,et al.  MicroRNA: Biogenesis, Function and Role in Cancer , 2010, Current genomics.

[5]  E. Gotuzzo,et al.  Human Herpesvirus 8 Genotype E in Patients with Kaposi Sarcoma, Peru , 2010, Emerging infectious diseases.

[6]  Samuel H. Payne,et al.  A proteogenomic update to Yersinia: enhancing genome annotation , 2010, BMC Genomics.

[7]  D. Lukac,et al.  Convergence of Kaposi's Sarcoma-Associated Herpesvirus Reactivation with Epstein-Barr Virus Latency and Cellular Growth Mediated by the Notch Signaling Pathway in Coinfected Cells , 2010, Journal of Virology.

[8]  Juliane C. Dohm,et al.  Strand-specific deep sequencing of the transcriptome. , 2010, Genome research.

[9]  D. Ganem,et al.  The Lytic Transcriptome of Kaposi's Sarcoma-Associated Herpesvirus Reveals Extensive Transcription of Noncoding Regions, Including Regions Antisense to Important Genes , 2010, Journal of Virology.

[10]  D. Ganem,et al.  Making Sense of Antisense: Seemingly Noncoding RNAs Antisense to the Master Regulator of Kaposi's Sarcoma-Associated Herpesvirus Lytic Replication Do Not Regulate That Transcript but Serve as mRNAs Encoding Small Peptides , 2010, Journal of Virology.

[11]  D. Ganem,et al.  Array-Based Transcript Profiling and Limiting-Dilution Reverse Transcription-PCR Analysis Identify Additional Latent Genes in Kaposi's Sarcoma-Associated Herpesvirus , 2010, Journal of Virology.

[12]  M. Rowe,et al.  Burkitt's lymphoma: The Rosetta Stone deciphering Epstein-Barr virus biology , 2009, Seminars in cancer biology.

[13]  D. Vereide,et al.  Proof for EBV's sustaining role in Burkitt's lymphomas. , 2009, Seminars in cancer biology.

[14]  Mark Craven,et al.  EDGE3: A web-based solution for management and analysis of Agilent two color microarray experiments , 2009, BMC Bioinformatics.

[15]  P. Pevzner,et al.  Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. , 2008, Journal of proteome research.

[16]  M. Bates,et al.  Diverse genotypes of Kaposi's sarcoma associated herpesvirus (KSHV) identified in infant blood infections in African childhood-KS and HIV/AIDS endemic region , 2007, Journal of medical virology.

[17]  P. Benos,et al.  Human Transcriptome Subtraction by Using Short Sequence Tags To Search for Tumor Viruses in Conjunctival Carcinoma , 2007, Journal of Virology.

[18]  M. Ressing,et al.  The nested open reading frame in the Epstein-Barr virus nuclear antigen-1 mRNA encodes a protein capable of inhibiting antigen presentation in cis. , 2007, Molecular immunology.

[19]  D. McGeoch,et al.  The genome of Epstein-Barr virus type 2 strain AG876. , 2006, Virology.

[20]  P. Moore,et al.  Transcriptional Analysis of Latent and Inducible Kaposi's Sarcoma-Associated Herpesvirus Transcripts in the K4 to K7 Region , 2005, Journal of Virology.

[21]  Mark S Friedrichs,et al.  Guidelines for the Routine Application of the Peptide Hits Technique , 2005, Journal of the American Society for Mass Spectrometry.

[22]  Rafael A. Irizarry,et al.  Bioinformatics and Computational Biology Solutions using R and Bioconductor , 2005 .

[23]  Michael G. Katze,et al.  Proteome Analysis of Liver Cells Expressing a Full-Length Hepatitis C Virus (HCV) Replicon and Biopsy Specimens of Posttransplantation Liver from HCV-Infected Patients , 2005, Journal of Virology.

[24]  Ronald J Moore,et al.  Comparative proteome analyses of human plasma following in vivo lipopolysaccharide administration using multidimensional separations coupled with tandem mass spectrometry , 2005, Proteomics.

[25]  Matthew E Monroe,et al.  Probability-based evaluation of peptide and protein identifications from tandem mass spectrometry and SEQUEST analysis: the human proteome. , 2005, Journal of proteome research.

[26]  Gordon K. Smyth,et al.  limma: Linear Models for Microarray Data , 2005 .

[27]  M. Chase,et al.  Proteins of purified Epstein-Barr virus. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

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

[29]  J. Yates,et al.  A model for random sampling and estimation of relative protein abundance in shotgun proteomics. , 2004, Analytical chemistry.

[30]  P. Athanassiadou,et al.  Primary Effusion Lymphoma , 2004, Acta Cytologica.

[31]  Gordon K Smyth,et al.  Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2004, Statistical applications in genetics and molecular biology.

[32]  P. Moore,et al.  Kaposi's sarcoma-associated herpesvirus immunoevasion and tumorigenesis: two sides of the same coin? , 2003, Annual review of microbiology.

[33]  K. Kaye,et al.  The Kaposi's Sarcoma-Associated Herpesvirus K12 Transcript from a Primary Effusion Lymphoma Contains Complex Repeat Elements, Is Spliced, and Initiates from a Novel Promoter , 2002, Journal of Virology.

[34]  P. Moore,et al.  Molecular virology of Kaposi's sarcoma-associated herpesvirus. , 2001, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[35]  M. Borowitz,et al.  A New Primary Effusion Lymphoma-Derived Cell Line Yields a Highly Infectious Kaposi's Sarcoma Herpesvirus-Containing Supernatant , 2000, Journal of Virology.

[36]  M. Corbellino,et al.  Differential viral protein expression in Kaposi's sarcoma-associated herpesvirus-infected diseases: Kaposi's sarcoma, primary effusion lymphoma, and multicentric Castleman's disease. , 2000, The American journal of pathology.

[37]  A. Aguirre,et al.  Characterization of intertypic recombinants of the Epstein-Barr virus from the body-cavity-based lymphomas cell lines BC-1 and BC-2. , 1999, Virology.

[38]  Lijun Wu,et al.  A Complex Translational Program Generates Multiple Novel Proteins from the Latently Expressed Kaposin (K12) Locus of Kaposi’s Sarcoma-Associated Herpesvirus , 1999, Journal of Virology.

[39]  G. Gaidano,et al.  HHV-8 infection is specific for cell lines derived from primary effusion (body cavity-based) lymphomas , 1998, Leukemia.

[40]  A. Haase,et al.  A Cluster of Latently Expressed Genes in Kaposi’s Sarcoma-Associated Herpesvirus , 1998, Journal of Virology.

[41]  M. Reitz,et al.  Novel organizational features, captured cellular genes, and strain variability within the genome of KSHV/HHV8. , 1998, Journal of the National Cancer Institute. Monographs.

[42]  P. Moore,et al.  Transcription Mapping of the Kaposi’s Sarcoma-Associated Herpesvirus (Human Herpesvirus 8) Genome in a Body Cavity-Based Lymphoma Cell Line (BC-1) , 1998, Journal of Virology.

[43]  E. Cesarman,et al.  Epstein-Barr virus latent gene expression in primary effusion lymphomas containing Kaposi's sarcoma-associated herpesvirus/human herpesvirus-8. , 1997, Blood.

[44]  L. Rainbow,et al.  The 222- to 234-kilodalton latent nuclear protein (LNA) of Kaposi's sarcoma-associated herpesvirus (human herpesvirus 8) is encoded by orf73 and is a component of the latency-associated nuclear antigen , 1997, Journal of virology.

[45]  G. Gerard,et al.  Reverse Transcriptase , 1997, Molecular biotechnology.

[46]  R. Sun,et al.  Selective switch between latency and lytic replication of Kaposi's sarcoma herpesvirus and Epstein-Barr virus in dually infected body cavity lymphoma cells , 1997, Journal of virology.

[47]  J. Russo,et al.  Nucleotide sequence of the Kaposi sarcoma-associated herpesvirus (HHV8). , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[48]  C. Boshoff,et al.  Molecular Mimicry of Human Cytokine and Cytokine Response Pathway Genes by KSHV , 1996, Science.

[49]  R. Sun,et al.  Polyadenylylated nuclear RNA encoded by Kaposi sarcoma-associated herpesvirus. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[50]  M. McGrath,et al.  Lytic growth of Kaposi's sarcoma–associated herpesvirus (human herpesvirus 8) in culture , 1996, Nature Medicine.

[51]  E. Cesarman,et al.  In vitro establishment and characterization of two acquired immunodeficiency syndrome-related lymphoma cell lines (BC-1 and BC-2) containing Kaposi's sarcoma-associated herpesvirus-like (KSHV) DNA sequences. , 1995, Blood.

[52]  E. Cesarman,et al.  Kaposi's sarcoma-associated herpesvirus-like DNA sequences in AIDS-related body-cavity-based lymphomas. , 1995, The New England journal of medicine.

[53]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[54]  E. Cesarman,et al.  Identification of herpesvirus-like DNA sequences in AIDS-associated Kaposi's sarcoma. , 1994, Science.

[55]  J. Yates,et al.  An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database , 1994, Journal of the American Society for Mass Spectrometry.

[56]  J. Epstein,et al.  Abundant expression of EBER1 small nuclear RNA in nasopharyngeal carcinoma. A morphologically distinctive target for detection of Epstein-Barr virus in formalin-fixed paraffin-embedded carcinoma specimens. , 1991, The American journal of pathology.

[57]  M. Rowe,et al.  Different Epstein-Barr virus-B cell interactions in phenotypically distinct clones of a Burkitt's lymphoma cell line. , 1990, The Journal of general virology.

[58]  C. Gaillard,et al.  Ethanol precipitation of DNA with linear polyacrylamide as carrier. , 1990, Nucleic acids research.

[59]  P. Chomczyński,et al.  Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. , 1987, Analytical biochemistry.

[60]  P. L. Deininger,et al.  DNA sequence and expression of the B95-8 Epstein—Barr virus genome , 1984, Nature.

[61]  J. Robinson,et al.  Identification of Epstein-Barr nuclear antigen polypeptide in mouse and monkey cells after gene transfer with a cloned 2.9-kilobase-pair subfragment of the genome. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[62]  E. Kieff,et al.  One of two Epstein-Barr virus nuclear antigens contains a glycine-alanine copolymer domain. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[63]  J. Steitz,et al.  Two small RNAs encoded by Epstein-Barr virus and complexed with protein are precipitated by antibodies from patients with systemic lupus erythematosus. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[64]  G. Klein,et al.  Establishment and characterization of an Epstein-Barr virus (EBC)-negative lymphoblastoid B cell line (BJA-B) from an exceptional, EBV-genome-negative African Burkitt's lymphoma. , 1975, Biomedicine / [publiee pour l'A.A.I.C.I.G.].

[65]  G. Klein,et al.  Relationship between Epstein‐Barr virus (EBV) DNA and the EBV‐determined nuclear antigen (EBNA) in Burkitt lymphoma biopsies and other lymphoproliferative malignancies , 1974, International journal of cancer.

[66]  G. Klein,et al.  DNA of Epstein-Barr virus detected in tissue of Burkitt's lymphoma and nasopharyngeal carcinoma. , 1973, Proceedings of the National Academy of Sciences of the United States of America.

[67]  G. Klein,et al.  Epstein–Barr Virus in Burkitt's Lymphoma and Nasopharyngeal Carcinoma: EBV DNA in Biopsies of Burkitt Tumours and Anaplastic Carcinomas of the Nasopharynx , 1970, Nature.

[68]  M. Epstein,et al.  VIRUS PARTICLES IN CULTURED LYMPHOBLASTS FROM BURKITT'S LYMPHOMA. , 1964, Lancet.