|Petabase-scale sequence alignment catalyses viral discovery|
RC Edgar, J Taylor, V Lin, T Altman, P Barbera, D Meleshko, D Lohr, ...
Nature 602 (7895), 142-147, 2022
|Endogenous retroviral promoter exaptation in human cancer|
A Babaian, DL Mager
Mobile DNA 7 (1), 1-21, 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
|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
|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
|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
|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
|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
|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
|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
|Ribovirus classification by a polymerase barcode sequence|
A Babaian, R Edgar
PeerJ 10, e14055, 2022
|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
|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
|hackseq: Catalyzing collaboration between biological and computational scientists via hackathon|
hackseq Organizing Committee
F1000Research 6, 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
|Visualized computational predictions of transcriptional effects by intronic endogenous retroviruses|
Y Zhang, A Babaian, L Gagnier, DL Mager
PLoS One 8 (8), e71971, 2013
|Intra-and Inter-individual genetic variation in human ribosomal RNAs|
BioRxiv, 118760, 2017
|bioSyntax: syntax highlighting for computational biology|
A Babaian, A Ebou, A Fegen, HY Kam, GE Novakovsky, J Wong, D A´ssi, ...
BMC bioinformatics 19, 1-6, 2018
|Petascale Homology Search for Structure Prediction|
S Lee, G Kim, EL Karin, M Mirdita, S Park, R Chikhi, A Babaian, ...
|The Focal Adhesion Complex Ilk-Pinch-Parvin Is Key to Niche Interactions and Survival of Quiescent Stem Cells in Chronic Myeloid Leukemia In Vitro and In Vivo|
K Rothe, A Babaian, N Nakamichi, M Chen, A Watanabe, D Mager, ...
Blood, The Journal of the American Society of Hematology 128 (22), 936-936, 2016