Maximum Sequence Alignment Fails to Predict Off-targeted Gene Regulation by RNAi. - Amanda Birmingham; Emily M. Anderson; William S. Marshall; Anastasia Khvorova (CSB Workshops, 2005)

NoiseMaker: simulated screens for statistical assessment. - Phoenix Kwan; Amanda Birmingham (Bioinform., 2010)

Efficient population-scale variant analysis and prioritization with VAPr. - Amanda Birmingham; Adam M. Mark; Carlo Mazzaferro; Guorong Xu; Kathleen M. Fisch (Bioinform., 2018)

Interactive network visualization in Jupyter notebooks: visJS2jupyter. - Sara Brin Rosenthal; Julia Len; Mikayla Webster; Aaron Gary; Amanda Birmingham; Kathleen M. Fisch (Bioinform., 2018)

Ten Simple Rules for Reproducible Research in Jupyter Notebooks. - Adam Rule; Amanda Birmingham; Cristal Zuñiga; Ilkay Altintas; Shih-Cheng Huang; Rob Knight 001; Niema Moshiri; Mai H. Nguyen; Sara Brin Rosenthal; Fernando Pérez; Peter W. Rose (CoRR, 2018)

Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks. - Adam Rule; Amanda Birmingham; Cristal Zuñiga; Ilkay Altintas; Shih-Cheng Huang; Rob Knight 001; Niema Moshiri; Mai H. Nguyen; Sara Brin Rosenthal; Fernando Pérez; Peter W. Rose (PLoS Comput. Biol., 2019)