| The complete sequence of a human genome S Nurk, S Koren, A Rhie, M Rautiainen, AV Bzikadze, A Mikheenko, ... Science 376 (6588), 44-53, 2022 | 794 | 2022 |
| HiGlass: Web-based Visual Comparison And Exploration Of Genome Interaction Maps P Kerpedjiev, N Abdennur, F Lekschas, C McCallum, K Dinkla, H Strobelt, ... biorXiv, 121889, 2017 | 618* | 2017 |
| The 4D nucleome project J Dekker, AS Belmont, M Guttman, VO Leshyk, JT Lis, S Lomvardas, ... Nature 549 (7671), 219-226, 2017 | 527 | 2017 |
| Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams P Kerpedjiev, S Hammer, IL Hofacker Bioinformatics 31 (20), 3377-3379, 2015 | 311 | 2015 |
| Complete genomic and epigenetic maps of human centromeres N Altemose, GA Logsdon, AV Bzikadze, P Sidhwani, SA Langley, ... Science 376 (6588), eabl4178, 2022 | 106 | 2022 |
| Complete Genome Sequence of the Cystic Fibrosis Pathogen Achromobacter xylosoxidans NH44784-1996 Complies with Important Pathogenic Phenotypes TH Jakobsen, MA Hansen, PØ Jensen, L Hansen, L Riber, A Cockburn, ... PloS one 8 (7), e68484, 2013 | 89 | 2013 |
| RIsearch2: suffix array-based large-scale prediction of RNA–RNA interactions and siRNA off-targets F Alkan, A Wenzel, O Palasca, P Kerpedjiev, AF Rudebeck, PF Stadler, ... Nucleic acids research 45 (8), e60-e60, 2017 | 76 | 2017 |
| Predicting RNA 3D structure using a coarse-grain helix-centered model P Kerpedjiev, CH Zu Siederdissen, IL Hofacker Rna 21 (6), 1110-1121, 2015 | 70 | 2015 |
| Adaptable probabilistic mapping of short reads using position specific scoring matrices P Kerpedjiev, J Frellsen, S Lindgreen, A Krogh BMC bioinformatics 15, 1-17, 2014 | 51 | 2014 |
| HiNT: a computational method for detecting copy number variations and translocations from Hi-C data S Wang, S Lee, C Chu, D Jain, P Kerpedjiev, GM Nelson, JM Walsh, ... Genome biology 21, 1-15, 2020 | 43 | 2020 |
| HiPiler: Visual Exploration Of Large Genome Interaction Matrices With Interactive Small Multiples F Lekschas, B Bach, P Kerpedjiev, N Gehlenborg, H Pfister biorXiv, 123588, 2017 | 38 | 2017 |
| The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data SB Reiff, AJ Schroeder, K Kırlı, A Cosolo, C Bakker, L Mercado, S Lee, ... Nature communications 13 (1), 2365, 2022 | 20 | 2022 |
| Pattern-driven navigation in 2D multiscale visualizations with scalable insets F Lekschas, M Behrisch, B Bach, P Kerpedjiev, N Gehlenborg, H Pfister IEEE transactions on visualization and computer graphics 26 (1), 611-621, 2019 | 20 | 2019 |
| StainedGlass: Interactive visualization of massive tandem repeat structures with identity heatmaps MR Vollger, P Kerpedjiev, AM Phillippy, EE Eichler Bioinformatics 38 (7), 2049-2051, 2022 | 18 | 2022 |
| 3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements. BC Thiel, IK Beckmann, P Kerpedjiev, IL Hofacker F1000Research 8, 2019 | 18 | 2019 |
| The dynseq browser track shows context-specific features at nucleotide resolution S Nair, A Barrett, D Li, BJ Raney, BT Lee, P Kerpedjiev, V Ramalingam, ... Nature Genetics 54 (11), 1581-1583, 2022 | 1 | 2022 |
| The dynseq genome browser track enables visualization of context-specific, dynamic DNA sequence features at single nucleotide resolution S Nair, A Barrett, D Li, BJ Raney, BT Lee, P Kerpedjiev, V Ramalingam, ... bioRxiv, 2022.05. 26.493621, 2022 | 1 | 2022 |
| Pattern-Driven Navigation in 2D Multiscale Visual Spaces with Scalable Insets F Lekschas, M Behrisch, B Bach, P Kerpedjiev, N Gehlenborg, H Pfister bioRxiv, 2018 | 1 | 2018 |
| HiPiler F Lekschas, B Bach, P Kerpedjiev, N Gehlenborg, H Pfister | | 2019 |
| patterns using, an RNA Python library centered on forgi 2.0 secondary structure elements.[version 2; peer review: 2 BC Thiel, IK Beckmann, P Kerpedjiev, IL Hofacker | | 2019 |
