| Validating genome-wide CRISPR-Cas9 function improves screening in the oleaginous yeast Yarrowia lipolytica C Schwartz, JF Cheng, R Evans, CA Schwartz, JM Wagner, S Anglin, ... Metabolic engineering 55, 102-110, 2019 | 92 | 2019 |
| A complete assembly of the rice Nipponbare reference genome L Shang, W He, T Wang, Y Yang, Q Xu, X Zhao, L Yang, H Zhang, X Li, ... Molecular plant 16 (8), 1232-1236, 2023 | 83 | 2023 |
| GFAP: ultrafast and accurate gene functional annotation software for plants D Xu, Y Yang, D Gong, X Chen, K Jin, H Jiang, W Yu, J Li, J Zhang, ... Plant Physiology 193 (3), 1745-1748, 2023 | 19 | 2023 |
| OMGS: optical map-based genome scaffolding W Pan, T Jiang, S Lonardi Journal of Computational Biology 27 (4), 519-533, 2020 | 19 | 2020 |
| Novo&Stitch: accurate reconciliation of genome assemblies via optical maps W Pan, SI Wanamaker, AMV Ah-Fong, HS Judelson, S Lonardi Bioinformatics 34 (13), i43-i51, 2018 | 19 | 2018 |
| Accurate detection of chimeric contigs via Bionano optical maps W Pan, S Lonardi Bioinformatics 35 (10), 1760-1762, 2019 | 18 | 2019 |
| Improving error-correcting capability in DNA digital storage via soft-decision decoding L Ding, S Wu, Z Hou, A Li, Y Xu, H Feng, W Pan, J Ruan National Science Review 11 (2), nwad229, 2024 | 9 | 2024 |
| CentIER: Accurate centromere identification for plant genomes D Xu, J Yang, H Wen, W Feng, X Zhang, X Hui, J Yue, Y Xu, F Chen, ... Plant Communications 5 (10), 2024 | 8 | 2024 |
| Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes W Yu, H Luo, J Yang, S Zhang, H Jiang, X Zhao, X Hui, D Sun, L Li, X Wei, ... Genome Research 34 (2), 326-340, 2024 | 6 | 2024 |
| Validating genome-wide CRISPR-Cas9 function in the non-conventional yeast Yarrowia lipolytica C Schwartz, JF Cheng, R Evans, CA Schwartz, JM Wagner, S Anglin, ... BioRxiv, 358630, 2018 | 5 | 2018 |
| Novo&stitch: accurate reconciliation of genome assemblies via optical maps. Bioinformatics 34: i43–i51 W Pan, SI Wanamaker, AMV Ah-Fong, HS Judelson, S Lonardi | 5 | 2018 |
| Comparison of hi-c-based scaffolding tools on plant genomes Y Hou, L Wang, W Pan Genes 14 (12), 2147, 2023 | 4 | 2023 |
| Melon ripeness detection by an improved object detection algorithm for resource constrained environments X Jing, Y Wang, D Li, W Pan Plant Methods 20 (1), 127, 2024 | 3 | 2024 |
| Comprehensive Assessment of Eleven de novo HiFi Assemblers on Complex Eukaryotic Genomes and Metagenomes W Yu, H Luo, J Yang, S Zhang, H Jiang, X Zhao, X Hui, D Sun, L Li, X Wei, ... bioRxiv, 2023.06. 29.546998, 2023 | 2 | 2023 |
| RAfilter: an algorithm for detecting and filtering false-positive alignments in repetitive genomic regions J Yang, X Zhao, H Jiang, Y Yang, Y Hou, W Pan Horticulture Research 10 (1), uhac288, 2023 | 2 | 2023 |
| RAviz: a visualization tool for detecting false-positive alignments in repetitive genomic regions D Xu, Y Song, X Zhao, D Gong, Y Yang, W Pan Horticulture Research 9, uhac161, 2022 | 2 | 2022 |
| Improving the completeness of chromosome-level assembly by recalling sequences from lost Contigs J Liu, F Liu, W Pan Genes 14 (10), 1926, 2023 | 1 | 2023 |
| CIDP: A multi-functional platform for designing CRISPR sgRNAs D Xu, J Zhang, X Zhao, Y Hou, H Jiang, W He, X Ma, W Pan Horticulture Research 10 (7), uhad092, 2023 | 1 | 2023 |
| HiCancer: accurate and complete cancer genome phasing with Hi-C reads W Pan, D Gong, D Sun, H Luo Scientific Reports 11 (1), 6609, 2021 | 1 | 2021 |
| ThIEF: Finding genome-wide trajectories of epigenetics marks A Polishko, MA Hasan, W Pan, EM Bunnik, K Le Roch, S Lonardi 17th International Workshop on Algorithms in Bioinformatics (WABI 2017), 19 …, 2017 | 1 | 2017 |
