| Petabase-scale sequence alignment catalyses viral discovery RC Edgar, B Taylor, V Lin, T Altman, P Barbera, D Meleshko, D Lohr, ... Nature 602 (7895), 142-147, 2022 | 273 | 2022 |
| Endogenous retroviral promoter exaptation in human cancer A Babaian, DL Mager Mobile DNA 7, 1-21, 2016 | 199 | 2016 |
| Onco-exaptation of an endogenous retroviral LTR drives IRF5 expression in Hodgkin lymphoma A Babaian, MT Romanish, L Gagnier, LY Kuo, MM Karimi, C Steidl, ... Oncogene 35 (19), 2542-2546, 2016 | 96 | 2016 |
| Length of dsRNA (poly I: C) drives distinct innate immune responses, depending on the cell type MF Mian, AN Ahmed, M Rad, A Babaian, D Bowdish, AA Ashkar Journal of leukocyte biology 94 (5), 1025-1036, 2013 | 90 | 2013 |
| Distinct isoform of FABP7 revealed by screening for retroelement-activated genes in diffuse large B-cell lymphoma FE Lock, R Rebollo, K Miceli-Royer, L Gagnier, S Kuah, A Babaian, ... Proceedings of the National Academy of Sciences 111 (34), E3534-E3543, 2014 | 76 | 2014 |
| Loss of m1acp3Ψ ribosomal RNA modification is a major feature of cancer A Babaian, K Rothe, D Girodat, I Minia, S Djondovic, M Milek, SES Miko, ... Cell reports 31 (5), 2020 | 68 | 2020 |
| The absence or overexpression of IL-15 drastically alters breast cancer metastasis via effects on NK cells, CD4 T cells, and macrophages A Gillgrass, N Gill, A Babaian, AA Ashkar The Journal of Immunology 193 (12), 6184-6191, 2014 | 47 | 2014 |
| The miR-185/PAK6 axis predicts therapy response and regulates survival of drug-resistant leukemic stem cells in CML H Lin, K Rothe, M Chen, A Wu, A Babaian, R Yen, J Zeng, J Ruschmann, ... Blood, The Journal of the American Society of Hematology 136 (5), 596-609, 2020 | 38 | 2020 |
| Ribovirus classification by a polymerase barcode sequence A Babaian, R Edgar PeerJ 10, e14055, 2022 | 37 | 2022 |
| Integrin-linked kinase mediates therapeutic resistance of quiescent CML stem cells to tyrosine kinase inhibitors K Rothe, A Babaian, N Nakamichi, M Chen, SC Chafe, A Watanabe, ... Cell Stem Cell 27 (1), 110-124. e9, 2020 | 37 | 2020 |
| Hybrids of RNA viruses and viroid-like elements replicate in fungi M Forgia, B Navarro, S Daghino, A Cervera, A Gisel, S Perotto, ... Nature Communications 14 (1), 2591, 2023 | 30* | 2023 |
| LIONS: analysis suite for detecting and quantifying transposable element initiated transcription from RNA-seq A Babaian, IR Thompson, J Lever, L Gagnier, MM Karimi, DL Mager Bioinformatics 35 (19), 3839-3841, 2019 | 30 | 2019 |
| A novel isoform of IL-33 revealed by screening for transposable element promoted genes in human colorectal cancer FE Lock, A Babaian, Y Zhang, L Gagnier, S Kuah, A Weberling, ... PLoS One 12 (7), e0180659, 2017 | 26 | 2017 |
| Synthetic modeling reveals HOXB genes are critical for the initiation and maintenance of human leukemia M Kusakabe, AC Sun, K Tyshchenko, R Wong, A Nanda, C Shanna, ... Nature communications 10 (1), 2913, 2019 | 14 | 2019 |
| hackseq: Catalyzing collaboration between biological and computational scientists via hackathon hackseq Organizing Committee F1000Research 6, 2017 | 13 | 2017 |
| Visualized computational predictions of transcriptional effects by intronic endogenous retroviruses Y Zhang, A Babaian, L Gagnier, DL Mager PLoS One 8 (8), e71971, 2013 | 9 | 2013 |
| Intra-and Inter-individual genetic variation in human ribosomal RNAs A Babaian BioRxiv, 118760, 2017 | 6 | 2017 |
| Petabase-Scale Homology Search for Structure Prediction S Lee, G Kim, EL Karin, M Mirdita, S Park, R Chikhi, A Babaian, ... Cold Spring Harbor Perspectives in Biology, a041465, 2024 | 5* | 2024 |
| bioSyntax: syntax highlighting for computational biology A Babaian, A Ebou, A Fegen, HY Kam, GE Novakovsky, J Wong, D Aīssi, ... BMC bioinformatics 19, 1-6, 2018 | 4 | 2018 |
| Viroid-like colonists of human microbiomes IN Zheludev, RC Edgar, MJL Galiano, M De la Peņa, A Babaian, AS Bhatt, ... bioRxiv, 2024.01. 20.576352, 2024 | 2 | 2024 |
