Joseph Coco
Masters of Science in Computer...
Savannah College of Art and Design · Interactive Services

Topics (69) View all

Skills (84)

Research experience

  • May 2010–
    May 2011
    Research: Joseph Coco
    University of New Orleans · Computer Science · University of New Orleans
    USA · New Orleans
    Bioinformatics, Exogenous Agent Extraction from Tumor RNA-Seq, Integration Site Prediction, Non-mapped DNA.
  • Aug 2009–
    May 2010
    Teaching: Beginner Java Labs
    University of New Orleans · Department of Computer Science
    USA · New Orleans
    Software Development I-II Lab Applications, exercises, and explorations in methodologies for Object-Oriented development.

Education

  • Aug 2009–
    May 2011
    University of New Orleans
    Bioinformatics · Masters of Science
    United States of America (USA) · New Orleans
  • Aug 2005–
    May 2009
    University of New Orleans
    Computer Science · Bachelor of Sciences
    United States of America (USA) · New Orleans

Awards & achievements

  • May 2010
    Scholarship: Research Assistantship
  • Aug 2009
    Scholarship: Teaching Assistantship

Other

  • Other Interests
    Reading, Music, Tennis, Racquetball, Rock Climbing, Weight-lifting, Running, Table Tennis, Playing Music., PLoS Computational Biology, BMC Bioinformatics., ArsTechnica, Abhishek Tiwari, Bitesize Bio, Manuel Corpas, ScienceOss, 88 Proof Synth Bio Blog, YOKOFAKUN.

Questions and Answers (31) View all

Publications (4) View all

  • Article: Differences in Gastric Carcinoma Microenvironment Stratify According to EBV Infection Intensity: Implications for Possible Immune Adjuvant Therapy.
    Michael J Strong, Guorong Xu, Joseph Coco, Carl Baribault, Dass S Vinay, Michelle R Lacey, Amy L Strong, Teresa A Lehman, Michael B Seddon, Zhen Lin, Monica Concha, Melody Baddoo, Marybeth Ferris, Kenneth F Swan, Deborah E Sullivan, Matthew E Burow, Christopher M Taylor, Erik K Flemington
    [show abstract] [hide abstract]
    ABSTRACT: Epstein-Barr virus (EBV) is associated with roughly 10% of gastric carcinomas worldwide (EBVaGC). Although previous investigations provide a strong link between EBV and gastric carcinomas, these studies were performed using selected EBV gene probes. Using a cohort of gastric carcinoma RNA-seq data sets from The Cancer Genome Atlas (TCGA), we performed a quantitative and global assessment of EBV gene expression in gastric carcinomas and assessed EBV associated cellular pathway alterations. EBV transcripts were detected in 17% of samples but these samples varied significantly in EBV coverage depth. In four samples with the highest EBV coverage (hiEBVaGC - high EBV associated gastric carcinoma), transcripts from the BamHI A region comprised the majority of EBV reads. Expression of LMP2, and to a lesser extent, LMP1 were also observed as was evidence of abortive lytic replication. Analysis of cellular gene expression indicated significant immune cell infiltration and a predominant IFNG response in samples expressing high levels of EBV transcripts relative to samples expressing low or no EBV transcripts. Despite the apparent immune cell infiltration, high levels of the cytotoxic T-cell (CTL) and natural killer (NK) cell inhibitor, IDO1, was observed in the hiEBVaGCs samples suggesting an active tolerance inducing pathway in this subgroup. These results were confirmed in a separate cohort of 21 Vietnamese gastric carcinoma samples using qRT-PCR and on tissue samples using in situ hybridization and immunohistochemistry. Lastly, a panel of tumor suppressors and candidate oncogenes were expressed at lower levels in hiEBVaGC versus EBV-low and EBV-negative gastric cancers suggesting the direct regulation of tumor pathways by EBV.
    PLoS Pathogens 05/2013; 9(5):e1003341. · 9.13 Impact Factor
  • Source
    Article: Detection of murine leukemia virus in the Epstein-Barr virus-positive human B-cell line JY, using a computational RNA-Seq-based exogenous agent detection pipeline, PARSES.
    Zhen Lin, Adriane Puetter, Joseph Coco, Guorong Xu, Michael J Strong, Xia Wang, Claire Fewell, Melody Baddoo, Christopher Taylor, Erik K Flemington
    [show abstract] [hide abstract]
    ABSTRACT: Many cell lines commonly used for biological studies have been found to harbor exogenous agents such as the human tumor viruses Epstein-Barr virus (EBV) and human papillomavirus. Nevertheless, broad-based, unbiased approaches to globally assess the presence of ectopic organisms within cell model systems have not previously been available. We reasoned that high-throughput sequencing should provide unparalleled insights into the microbiomes of tissue culture cell systems. Here we have used our RNA-seq analysis pipeline, PARSES (Pipeline for Analysis of RNA-Seq Exogenous Sequences), to investigate the presence of ectopic organisms within two EBV-positive B-cell lines commonly used by EBV researchers. Sequencing data sets from both the Akata and JY B-cell lines were found to contain reads for EBV, and the JY data set was found to also contain reads from the murine leukemia virus (MuLV). Further investigation revealed that MuLV transcription in JY cells is highly active. We also identified a number of MuLV alternative splicing events, and we uncovered evidence of APOBEC3G (apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G)-dependent DNA editing. Finally, reverse transcription-PCR analysis showed the presence of MuLV in three other human B-cell lines (DG75, Ramos, and P3HR1 Cl.13) commonly used by investigators in the Epstein-Barr virus field. We believe that a thorough examination of tissue culture microbiomes using RNA-seq/PARSES-like approaches is critical for the appropriate utilization of these systems in biological studies.
    Journal of Virology 03/2012; 86(6):2970-7. · 5.40 Impact Factor
  • Source
    Article: PARSES: A Pipeline for Analysis of RNA-Seq Exogenous Sequences
    Joseph R. Coco, Erik K. Flemington, Christopher M. Taylor
    [show abstract] [hide abstract]
    ABSTRACT: RNA-Sequencing (RNA-Seq) has become one of the most widely used techniques to interrogate the transcriptome of an organism since the advent of next generation sequencing technologies. A plethora of tools have been developed to analyze and visualize the transcriptome data from RNA-Seq experiments solving the problem of mapping reads back to the host organism's genome. This allows for the analysis of the majority of reads produced by the experiments but these tools typically discard reads that do not match well to the reference genome. This additional information that is being discarded could reveal important insight into the experiment and possible contributing factors to the condition under consideration. We introduce PARSES, a pipeline constructed from existing sequence analysis tools that allows the user to interrogate RNA-Sequencing experiments for possible biological contamination or the presence of exogenous sequences that may shed light on other factors infuencing an organism's condition.
    Bioinformatics and Computational Biology. 01/2011; 3:196-200.
  • Source
    Thesis: PARSES: A Pipeline for Analysis of RNA-Seq Exogenous Sequences
    Joseph R. Coco
    01/2011, Degree: Masters of Science, Supervisor: Christopher Taylor

Following (19) See all

Followers (78) See all

Browse more researchers