Quaid Morris: Publications

The Quaid Morris Lab

Quaid Morris: Publications


View a full listing of Quaid Morris: Publications’ journal articles.

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