Below is a selection of abstracts, past seminars, workshops, and presentations given by CCBB’s analysts.



  1. Focal Adhesion Kinase (FAK) Regulation of Programmed Death-1 (PD-1)/Programmed Death Ligand-1 (PD-L1) checkpoint signaling in a mouse model of epithelial ovarian cancer. K. Taylor, X. Chen, I. Tancioni, E. Kleinschmidt, A. Barrie, C. Diaz-Osterman, G. Fu, A Mark, G. Xu, K. Fisch, C. Xiao, D. Schlaepfer. DOI:

  2. Inflammatory Cytokine Responsive Enzymatic Mutagenesis Fuels Myeloproliferative Neoplasm Pre-Leukemia Stem Cell Evolution. Catriona Jamieson, Qingfei Jiang, Frida Holm, Jane Isquith, Adam Mark,Cayla Mason, Wenxue Ma, Raymond H Diep, Jessica Pham, Eduardo Reynoso Moreno, Chanond A Nasamran, Guorong Xu, Amanda Birmingham, Leslie A Crews, Ludmil Alexandrov, Gabriel Pineda, Thomas Whisenant, Kathleen M Fisch. Blood (2019) 134 (Supplement_1): 3780.
  3. Mechanisms of Iron Clearance from the Joint in FVIII-Deficient Mice after Induced Hemarthrosis. Esther J Cooke, Chanond Nasamran, Kathleen M Fisch, Annette von Drygalski. Blood (2019) 134 (Supplement_1): 157.

Past events:


  1. Reproducible Genomic Interpretation Tools for Translational Medicine: Application to an N of 1 Case Study by Katie Fisch (ISMB Translational Medicine SIG in Orlando, Florida – July 2016)
  2. Choosing the Right Strategy for Conducting a Microbiome Study by Amanda Birmingham (Symposium on the Human Microbiome at the University of Costa Rica – November 2016)


  1. Enabling Reproducible Analysis of NGS Experiments through Automated Jupyter Pipelines by Amanda Birmingham (NGS Data Analysis & Informatics Conference in San Diego, CA – February 2017)
  2. Microbiome 16S Analysis: A Quick-Start Guide by Amanda Birmingham (Host-microbe symbioses: from functional to ecological perspectives at the Gulbenkian Institute of Science, Oeiras, Portugal – July 2017)


  1. Can Jupyter Notebooks Serve Two Masters? by Amanda Birmingham (Reproducible Research and Interactive Education: Application of Jupyter Notebooks in San Diego, CA – April 2018)
  2. Cirrus-NGS: Cloud-optimized next generation sequencing primary analysis pipeline by Guorong Xu (BOSC 2018 in Portland, Oregon – June 2018)
  3. Choosing the Right Strategy for Conducting a Microbiome Study and Microbiome Analysis with QIIME2: A Hands-On Tutorial by Amanda Birmingham (Oslo University, Norway – June 2018)
  4. A network landscape of autism spectrum and other developmental disorders reveals shared molecular mechanism by Brin Rosenthal (ISMB 2018 in Chicago, Illinois – July 2018)
  5. QIIMP: Microbiome Metadata Made Easy and Microbiome Analysis with QIIME2: A Hands-On Tutorial by Amanda Birmingham (Bioinformatics: from Algorithms to Applications 2018 in St. Petersburg, Russia – July 2018)


  1. Abstract 2247: Platinoid-induced MHCI antigen presentation enables checkpoint inhibitor responsiveness by Katie Fisch (AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA)




Past courses:

  1. Winter 2018 – Dr. Katie Fisch is course co-director for SOMI229: Introduction to Genomics and Precision Medicine
  2. Winter 2018 – Dr. Katie Fisch is a guest lecturer for MED263 Bioinformatics Applications to Human Disease
  3. Winter 2018 – Dr. Katie Fisch is a guest lecturer for SPPS263A: Principles of Pharmaceutical Sciences and Drug Development

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