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.
  4. Cooper, Kim & Saxena, Aditya & Sharma, Virag & Neufeld, Stanley & Tran, Mai & Gutierrez, Haydee & Erberich, Joel & Birmingham, Amanda & Cobb, John & Hiller, Michael. (2020). Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion. The FASEB Journal. 34. 1-1. 10.1096/fasebj.2020.34.s1.00363.
  5. Selective Targeting of Alternative Splicing Deregulation in Pediatric Acute Myeloid Stem and Progenitor Cells. Inge Van Der Werf, MSc, Phoebe Mondala, BS, Raymond Diep, BS, Larissa Balaian, PhD, Cayla Mason, BS, Jacqueline Cloos, PhD, Gertjan J.L. Kaspers, Prof. MD PhD, Jim La Clair, Peggy Wentworth, Leslie A Crews, PhD, Thomas Whisenant, PhD, Kathleen Fisch, PhD, Michael Burkart, PhD, Catriona Jamieson, MD PhD.  Blood (2020) 136 (Supplement 1): 8. DOI:
  6. Imetelstat Inhibits Telomerase and Prevents Propagation of ADAR1-Activated Myeloproliferative Neoplasm and Leukemia Stem Cells. Wenxue Ma, MD PhD, Larissa Balaian, PhD, Phoebe Mondala, BS, Yudou He, BS, Cayla Mason, BS, Jessica Pham, B.S., Jeremy Lee, BS, Raymond Diep, BS, Sanja Coso, PhD, Kathleen Fisch, PhD, Adam Mark, MS, Sheldon Morris, MD MPH, Qingfei Jiang, PhD, Thomas Whisenant, PhD, Aleksandra Rizo, MD PhD, Fei Huang, PhD, Mary Donohoe, PhD, Ludmil Alexandrov, PhD, Catriona Jamieson, MD PhD. Blood (2020) 136 (Supplement 1): 18. DOI:
  7. Lymphatic Remodeling Associated with Hemophilic Joint Bleeding in FVIII-Deficient Mice. Esther J Cooke, PhD, Chanond A Nasamran, Kathleen Fisch, PhD, Annette von Drygalski, MD PharmD, RMSK. Blood (2020) 136 (Supplement 1): 20. DOI:

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)
  3. Enabling Reproducible Analysis of NGS Experiments through Automated Jupyter Pipelines by Amanda Birmingham (NGS Data Analysis & Informatics Conference in San Diego, CA – February 2017)
  4. 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)
  5. Can Jupyter Notebooks Serve Two Masters? by Amanda Birmingham (Reproducible Research and Interactive Education: Application of Jupyter Notebooks in San Diego, CA – April 2018)
  6. Cirrus-NGS: Cloud-optimized next generation sequencing primary analysis pipeline by Guorong Xu (BOSC 2018 in Portland, Oregon – June 2018)
  7. 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)
  8. A network landscape of autism spectrum and other developmental disorders reveals shared molecular mechanism by Brin Rosenthal (ISMB 2018 in Chicago, Illinois – July 2018)
  9. 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)
  10. 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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