| Comprehensive molecular characterization of gastric adenocarcinoma. TCGA Nature 513 (7517), 202–209, 2014 | 5335 | 2014 |
| Comprehensive genomic characterization of squamous cell lung cancers. TCGA Nature 489 (7423), 519–525, 2012 | 3731 | 2012 |
| Subgroup-specific structural variation across 1,000 medulloblastoma genomes PA Northcott, DJH Shih, J Peacock, L Garzia, A Sorana Morrissy, ... Nature 488 (7409), 49-56, 2012 | 982 | 2012 |
| Reduced adenosine-to-inosine miR-455-5p editing promotes melanoma growth and metastasis E Shoshan, AK Mobley, RR Braeuer, T Kamiya, L Huang, ME Vasquez, ... Nature Cell Biology 17 (3), 311, 2015 | 239 | 2015 |
| BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters J Chu, S Sadeghi, A Raymond, SD Jackman, KM Nip, R Mar, ... Bioinformatics 30 (23), 3402-3404, 2014 | 120 | 2014 |
| Complete genomic landscape of a recurring sporadic parathyroid carcinoma K Kasaian, SM Wiseman, N Thiessen, KL Mungall, RD Corbett, JQ Qian, ... The Journal of Pathology 230 (3), 249-260, 2013 | 76 | 2013 |
| A clinical transcriptome approach to patient stratification and therapy selection in acute myeloid leukemia TR Docking, JDK Parker, M Jädersten, G Duns, L Chang, J Jiang, ... Nature Communications 12 (1), 2474, 2021 | 75 | 2021 |
| RNA-Bloom enables reference-free and reference-guided sequence assembly for single-cell transcriptomes KM Nip, R Chiu, C Yang, J Chu, H Mohamadi, RL Warren, I Birol Genome research 30 (8), 1191-1200, 2020 | 53* | 2020 |
| Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection AY Lee, AD Ewing, K Ellrott, Y Hu, KE Houlahan, JC Bare, SMG Espiritu, ... Genome Biology 19 (1), 188, 2018 | 50 | 2018 |
| Systematic assessment of long-read RNA-seq methods for transcript identification and quantification FJ Pardo-Palacios, D Wang, F Reese, M Diekhans, S Carbonell-Sala, ... Nature methods, 1-15, 2024 | 46 | 2024 |
| Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes Z Xue, RL Warren, EA Gibb, D MacMillan, J Wong, R Chiu, SA Hammond, ... BMC Genomics 19 (1), 536, 2018 | 31 | 2018 |
| Kleat: cleavage site analysis of transcriptomes I Birol, A Raymond, R Chiu, KM Nip, SD Jackman, M Kreitzman, ... Pacific Symposium on Biocomputing 2015, 347-358, 2014 | 28 | 2014 |
| Spruce giga‐genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes KK Gagalova, RL Warren, L Coombe, J Wong, KM Nip, MMS Yuen, ... The Plant Journal 111 (5), 1469-1485, 2022 | 21 | 2022 |
| Trans-NanoSim characterizes and simulates nanopore RNA-sequencing data S Hafezqorani, C Yang, T Lo, KM Nip, RL Warren, I Birol Gigascience 9 (6), giaa061, 2020 | 21 | 2020 |
| Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies L Swanson, G Robertson, KL Mungall, YS Butterfield, R Chiu, RD Corbett, ... BMC Genomics 14 (1), 550, 2013 | 18 | 2013 |
| TAP: A targeted clinical genomics pipeline for detecting transcript variants using RNA-seq data R Chiu, KM Nip, J Chu, I Birol BMC Medical Genomics 11 (1), 79, 2018 | 17 | 2018 |
| Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2 KM Nip, S Hafezqorani, KK Gagalova, R Chiu, C Yang, RL Warren, I Birol Nature Communications 14 (1), 2940, 2023 | 16 | 2023 |
| Mining amphibian and insect transcriptomes for antimicrobial peptide sequences with rAMPage D Lin, D Sutherland, SI Aninta, N Louie, KM Nip, C Li, A Yanai, L Coombe, ... Antibiotics 11 (7), 952, 2022 | 14 | 2022 |
| Linear time complexity de novo long read genome assembly with GoldRush J Wong, L Coombe, V Nikolić, E Zhang, KM Nip, P Sidhu, RL Warren, ... Nature Communications 14 (1), 2906, 2023 | 13 | 2023 |
| Fusion-Bloom: fusion detection in assembled transcriptomes R Chiu, KM Nip, I Birol Bioinformatics 36 (7), 2256-2257, 2020 | 13 | 2020 |