Adaptable probabilistic mapping of short reads using position specific scoring matrices. - Peter Kerpedjiev; Jes Frellsen; Stinus Lindgreen; Anders Krogh (BMC Bioinform., 2014)

Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams. - Peter Kerpedjiev; Stefan Hammer; Ivo L. Hofacker (Bioinform., 2015)

HiPiler: Visual Exploration of Large Genome Interaction Matrices with Interactive Small Multiples. - Fritz Lekschas; Benjamin Bach; Peter Kerpedjiev; Nils Gehlenborg; Hanspeter Pfister (IEEE Trans. Vis. Comput. Graph., 2018)

3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements. - Bernhard C. Thiel; Irene K. Beckmann; Peter Kerpedjiev; Ivo L. Hofacker (F1000Research, 2019)

Pattern-Driven Navigation in 2D Multiscale Visualizations with Scalable Insets. - Fritz Lekschas; Michael Behrisch 001; Benjamin Bach; Peter Kerpedjiev; Nils Gehlenborg; Hanspeter Pfister (IEEE Trans. Vis. Comput. Graph., 2020)

StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps. - Mitchell R. Vollger; Peter Kerpedjiev; Adam M. Phillippy; Evan E. Eichler (Bioinform., 2022)

DrForna: visualization of cotranscriptional folding. - Anda Ramona Tanasie; Peter Kerpedjiev; Stefan Hammer; Stefan Badelt (Bioinform., 2023)