View a full listing of Quaid Morris: Publications’ journal articles.
Sasse, A., Ray, D., Laverty, K.U., Tam, C.L., Albu, M., Zheng, H., Levdansky, Y., et al. (2025). A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function. Nature Biotechnology, 1-11.
Shi, R., Dalal, T., Fradkin, P., Koyyalagunta, D., Chhabria, S., Jung, A., Tam, C., et al. (2025). mRNABench: A curated benchmark for mature mRNA property and function prediction. bioRxiv, 2025.07.05.662870.
Köster, T., Venhuizen, P., Lewinski, M., Petrillo, E., Marquez, Y., Fuchs, A., Ray, D., et al. (2025). At‐RS31 orchestrates hierarchical cross‐regulation of splicing factors and integrates alternative splicing with TOR‐ABA pathways. New Phytologist.
Hess, J., & Morris, Q. (2025). Associative Memory and Generative Diffusion in the Zero-noise Limit. arXiv preprint arXiv:2506.05178.
Mohsen, H., Blenman, K., Emani, P.S., Morris, Q., Carrot-Zhang, J., & Pusztai, L. (2025). Dynamic clustering of genomics cohorts beyond race, ethnicity—and ancestry. BMC Medical Genomics, 18(1), 87.
Fu, C., Droop, P., Wang, X., Zhang, H., Fernandez, N., Lu, C., Anand, A., Ayub, U., et al. (2025). OncoTagger, a novel tool for accelerated and accurate literature-based curation of cancer related genes and variants. Cancer Research, 85(8_Supplement_1), 5041-5041.
Jiang, Q., Raghavan, M., Forsyth, B., Rodriguez, A., Tam, C., Balkaran, S., et al. (2025). ZFP36L2 orchestrates stress adaptive plasticity during injury repair and metastasis. Cancer Research, 85(8_Supplement_1), 2648-2648.
Chebanov, D., & Morris, Q. (2025). Transformer-based foundation model for clinically relevant DNA alterations: Filling gene status gaps and enhancing classification of rare cancer types. Cancer Research, 85(8_Supplement_1), 5040-5040.
Koyyalagunta, D., Ganesh, K., & Morris, Q. (2025). Inferring cancer type-specific patterns of metastatic spread using Metient. bioRxiv, 2024.07.09.602790.
Harrigan, C.F., Campbell, K., Morris, Q., & Funnell, T. (2025). Damage and Misrepair Signatures: Compact Representations of Pan-cancer Mutational Processes. bioRxiv, 2025.05.29.656360.
Kulman, E., Kuang, R., & Morris, Q. (2024). Orchard: building large cancer phylogenies using stochastic combinatorial search. PLoS Computational Biology, 20(12), e1012653.
Fradkin, P., Shi, R., Isaev, K., Frey, B.J., Morris, Q., Lee, L.J., & Wang, B. (2024). Orthrus: towards evolutionary and functional RNA foundation models. bioRxiv.
Razavi, R., Fathi, A., Yellan, I., Brechalov, A., Laverty, K.U., Jolma, A., et al. (2024). Extensive binding of uncharacterized human transcription factors to genomic dark matter. bioRxiv.
Xie, X., Chavez, F.H., Baali, I., Chu, E.L., Evans, C., Yang, X., Wei, W., Luo, H., et al. (2024). Uncovering the HOXA9 Translational Regulatory Complex That Promotes AML Leukemic Stem Cells. Blood, 144, 4106.
Kang, J.R.W., Kim, J., Skead, K., Bruat, V., Harwood, M., Soave, D., Morris, Q.D., et al. (2024). Mosaic Chromosomal Alterations Driving Clonal Hematopoiesis Show Shared and Divergent Patterns of Accumulation Among Humans of Diverse Ancestries. Blood, 144, 4053.
Sasse, A., Ray, D., Laverty, K.U., Tam, C.L., Albu, M., Zheng, H., Lyudovyk, O., et al. (2024). Reconstructing the sequence specificities of RNA-binding proteins across eukaryotes. bioRxiv.
Salcedo, A., Tarabichi, M., Buchanan, A., Espiritu, S.M.G., Zhang, H., Zhu, K., et al. (2024). Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction. Nature Biotechnology, 1-12.
Darmofal, M., Suman, S., Atwal, G., Toomey, M., Chen, J.F., Chang, J.C., et al. (2024). Deep-learning model for tumor-type prediction using targeted clinical genomic sequencing data. Cancer Discovery, 14(6), 1064-1081.
Kuzmin, E., Baker, T.M., Lesluyes, T., Monlong, J., Abe, K.T., Coelho, P.P., et al. (2024). Evolution of chromosome-arm aberrations in breast cancer through genetic network rewiring. Cell Reports, 43(4).
Luo, H., Cortés-López, M., Tam, C.L., Xiao, M., Wakiro, I., Chu, K.L., Pierson, A., et al. (2023). SON is an essential m6A target for hematopoietic stem cell fate. Cell Stem Cell, 30(12), 1658-1673.e10.
Luo, H., Cortés-López, M., Tam, C.L., Xiao, M., Wakiro, I., Chu, K.L., Pierson, A., et al. (2023). m6a-Son-CCL5 Axis Controls HSC Fate and Inflammation. Blood, 142, 1297.
S Sharma, S Kajjo, Z Harra, B Hasaj, V Delisle, D Ray, RL Gutierrez, …Uncovering a mammalian neural-specific poly (A) binding protein with unique properties. Genes & Development 2023
E Kuzmin, TM Baker, T Lesluyes, J Monlong, KT Abe, PP Coelho, … Evolution of chromosome arm aberrations in breast cancer through genetic network rewiring. bioRxiv, 2023.06. 10.544434
M Darmofal, S Suman, G Atwal, JF Chen, A Varghese, JC Chang, … Deep-learning model for tumor type classification enables enhanced clinical decision support in cancer diagnosis. Cancer Research 83 (7_Supplement), 5440-5440 2023
O Lyudovyk, Y Elhanati, A Streltsov, Q Morris, S Vardhana, B Greenbaum T-cell mediated response to emerging COVID-19 strains in patients with cancer studied via deep learning. Cancer Research 83 (7_Supplement), 795-795 2023
D Ray, KU Laverty, A Jolma, K Nie, R Samson, SE Pour, CL Tam, … RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific. Scientific Reports 13 (1), 5238 2023
Author Correction: Pan-cancer analysis of whole genomes. Nature 614 (7948), E39-E39 2023
M Gerstung, C Jolly, I Leshchiner, SC Dentro, S Gonzalez, D Rosebrock, … Author Correction: The evolutionary history of 2,658 cancers. Nature 614 (7948), E42-E42 2023
A Elbasir, Y Ye, DE Schäffer, X Hao, J Wickramasinghe, K Tsingas, … A deep learning approach reveals unexplored landscape of viral expression in cancer. Nature communications 14 (1), 785 2023
M Gerstung, C Jolly, I Leshchiner, SC Dentro, S Gonzalez, D Rosebrock, … The evolutionary history of 2,658 cancers (vol 578, pg 122, 2020). NATURE 2023
M Darmofal, S Suman, G Atwal, JF Chen, JC Chang, M Toomey, … Deep Learning Model for Tumor Type Prediction using Targeted Clinical Genomic Sequencing Data. medRxiv, 2023.09. 08.23295131
H Mohsen, K Blenman, PS Emani, Q Morris, J Carrot-Zhang, L Pusztai Dynamic clustering of genomics cohorts beyond race, ethnicity—and ancestry. bioRxiv, 2023.08. 04.552035
E Kulman, J Wintersinger, Q Morris Reconstructing cancer phylogenies using Pairtree, a clone tree reconstruction algorithm. STAR protocols 3 (4), 101706. 2022
Y Rubanova, R Shi, CF Harrigan, R Li, J Wintersinger, N Sahin, … Author Correction: Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig. nature communications 13 (1), 7567. 2022
W Jiao, G Atwal, P Polak, R Karlic, E Cuppen, A Danyi, J de Ridder, … Author Correction: A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns. nature communications 13 (1), 7573. 2022
A Elbasir, Y Ye, DE Schäffer, J Wickramasinghe, X Hao, PM Lieberman, … Characterizing the landscape of viral expression in cancer by deep learning. 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM …
C Timmons, Q Morris, CF Harrigan Regional mutational signature activities in cancer genomes. PLOS Computational Biology 18 (12), e1010733 2022
R Shi, H Zhang, Q Morris PAN-cODE: COVID-19 forecasting using conditional latent ODEs. Journal of the American Medical Informatics Association 29 (12), 2089-2095. 2022
A Pillai, C Valero, D Zanoni, K Navas, Q Morris, I Ganly, SG Patel Prognostic impact of autoimmune disease in oral cavity squamous cell carcinoma. Journal of Surgical Oncology 126 (7), 1183-1190. 2022
KU Laverty, A Jolma, SE Pour, H Zheng, D Ray, Q Morris, TR Hughes PRIESSTESS: interpretable, high-performing models of the sequence and structure preferences of RNA-binding proteins. Nucleic Acids Research 50 (19), e111-e111. 2022
AA Bielska, CF Harrigan, YJ Kyung, Q Morris, W Palm, CB Thompson Activating mTOR mutations are detrimental in nutrient-poor conditions. Cancer Research 82 (18), 3263-3274. 2022
E Kuzmin, J Monlong, M Bourgey, J Barber, T Lesluyes, T Baker, G Morin, … Evolution of large copy number variants in breast cancer through genetic network rewiring. Cancer Research 82 (12_Supplement), 44-44. 2022
A Salcedo, M Tarabichi, A Buchanan, SMG Espiritu, H Zhang, K Zhu, … Crowd-sourced benchmarking of single-sample tumour subclonal reconstruction. bioRxiv, 2022.06. 14.495937
LD Stein, W Jiao, G Atwal, Q Morris DeepTumour: Identify tumor origin from whole genome sequences. Cancer Research 82 (12_Supplement), 5046-5046. 2022
K Skead, D Soave, MJ Fave, V Bruat, Q Morris, P Awadalla A multi-omic perspective of how selection shapes blood cancer risk phenotypes in aging populations. Cancer Research 82 (12_Supplement), 2228-2228. 2022
JA Wintersinger, SM Dobson, E Kulman, LD Stein, JE Dick, Q Morris Reconstructing complex cancer evolutionary histories from multiple bulk DNA samples using Pairtree. Blood Cancer Discovery 3 (3), 208-219. 2022
T Spruce, M Plass, A Gohr, D Ray, M Martínez de Lagrán, G Rot, A Nóvoa, … The X-linked splicing regulator MBNL3 has been co-opted to restrict placental growth in eutherians. Plos Biology 20 (4), e3001615. 2022
RJ Vanner, SM Dobson, OI Gan, J McLeod, EM Schoof, I Grandal, … Multiomic profiling of central nervous system leukemia identifies mRNA translation as a therapeutic target. Blood cancer discovery 3 (1), 16-31. 2022
H Zhang, Q Morris, B Ustun, M Ghassemi Learning optimal predictive checklists. Advances in Neural Information Processing Systems 34, 1215-1229. 2021
A Pillai, C Valero, K Navas, Q Morris, SG Patel Peripheral blood values as predictors of autoimmune status in oral cavity squamous cell carcinoma. Translational Oncology 14 (12), 101220. 2021
K Skead, A Ang Houle, S Abelson, M Agbessi, V Bruat, B Lin, D Soave, … Interacting evolutionary pressures drive mutation dynamics and health outcomes in aging blood. Nature communications 12 (1), 4921. 2021
J Bayani, QM Trinh, MA Quintayo, C Crozier, M Hopkins, J Qiao, … Tumour spatial heterogeneity in breast cancer and the impact on clinical management. Cancer Research 81 (13_Supplement), 3131-3131. 2021
R Shi, Q Morris Segmenting hybrid trajectories using latent odes. International Conference on Machine Learning, 9569-9579. 2021