A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium. - Denis Kazakiewicz; Jonathan R. Karr; Karol M. Langner; Dariusz Plewczynski (Comput. Biol. Chem., 2015)

Toward Community Standards and Software for Whole-Cell Modeling. - Dagmar Waltemath; Jonathan R. Karr; Frank T. Bergmann; Vijayalakshmi Chelliah; Michael Hucka; Marcus Krantz; Wolfram Liebermeister; Pedro Mendes 001; Chris J. Myers; Pinar Pir; Begum Alaybeyoglu; Naveen K. Aranganathan; et al. (IEEE Trans. Biomed. Eng., 2016)

A Multivariate Negative-Binomial Model with Random Effects for Differential Gene-Expression Analysis of Correlated mRNA Sequencing Data. - Denis Kazakiewicz; Jürgen Claesen; Katarzyna Górczak; Dariusz Plewczynski; Tomasz Burzykowski (J. Comput. Biol., 2019)