Using predictive machine learning models for drug response simulation by calibrating patient-specific pathway signatures

by Bharadhwaj, V.S, Domingo-Fernández, D., Golriz Khatami, S., Hofmann-Apitius, M., Kodamullil, A.T, Mubeen, S.
Published 2021

A systems genomics approach uncovers molecular associates of RSV severity

by Benoodt, L., Caserta, M.T, Chu, C.-Y, Corbett, A., Falsey, A.R, Gill, S.R, Grier, A., Holden-Wiltse, J., Mariani, T.J, McCall, M.N, Qiu, X., Slaunwhite, C., Thakar, J., Topham, D.J, Walsh, E.E, Wang, L.
Published 2021

FiCoS: A fine-grained and coarse-grained GPU-powered deterministic simulator for biochemical networks

by Besozzi, D., Capitoli, G., Cazzaniga, P., Mauri, G., Nobile, M.S, Rundo, L., Spolaor, S., Tangherloni, A.
Published 2021

SMILE: systems metabolomics using interpretable learning and evolution

by Cuperlovic-Culf, M., Hu, T., Sha, C.
Published 2021

Predicting chemotherapy response using a variational autoencoder approach

by Ramsey, S.A, Wei, Q.
Published 2021

Learned Embeddings from Deep Learning to Visualize and Predict Protein Sets

by Dallago, C., Heinzinger, M., Littmann, M., Lu, A.X, Min, S., Morton, J.T, Olenyi, T., Rost, B., Schütze, K., Yang, K.K, Yoon, S.
Published 2021

Identification of Potential Biomarkers for Group I Pulmonary Hypertension Based on Machine Learning and Bioinformatics Analysis

by Bajpai, A.K, Cai, J., Hu, H., Huang, X., Li, B., Liu, J., Lu, L., Qi, D., Wang, C., Yu, L., Zhang, X., Zheng, F.
Published 2023

Exploring Promising Biomarkers for Alzheimer’s Disease through the Computational Analysis of Peripheral Blood Single-Cell RNA Sequencing Data

by Krokidis, M.G, Lazaros, K., Vlamos, P., Vrahatis, A.G
Published 2023

Identification of lncRNA Signature Associated with Pan-Cancer Prognosis

by Bao, G., Chen, A., Huang, B., Ji, J., Kong, B., Li, W., Li, X., Wang, J., Wang, L., Wang, X., Wang, X., Xu, R., Yang, Q., Yuan, C., Zhang, D., Zhang, Q.
Published 2021

Protein domain-based prediction of drug/ compound-target interactions and experimental validation on LIM kinases

by Atas, H., Baumann, M., Baxendale, I.R, Cetin-Atalay, R., Doǧan, T., Güzelcan, E.A, Koyas, A., Martin, M.
Published 2021

Deep protein representations enable recombinant protein expression prediction

by Armenteros, J.J.A, Johansen, A.R, Martiny, H.-M, Nielsen, H., Salomon, J.
Published 2021

Predicting environmentally responsive transgenerational differential DNA methylated regions (epimutations) in the genome using a hybrid deep-machine learning approach

by Beck, D., Holder, L., Mavaie, P., Skinner, M.K
Published 2021

Integration of human cell lines gene expression and chemical properties of drugs for Drug Induced Liver Injury prediction

by Golińska, A.K, Lesiński, W., Mnich, K., Rudnicki, W.R
Published 2021

Cell-to-cell and type-to-type heterogeneity of signaling networks: insights from the crowd

by Bodenmiller, B., Cao, W., Chung, V., Driessen, A., Gabor, A., Guo, B., Saez-Rodriguez, J., Shen, H., Single Cell Signaling in Breast Cancer DREAM Consortium members, Tanevski, J., Tognetti, M., Yu, T.
Published 2021

Crowdsourced identification of multi-target kinase inhibitors for RET- And TAU- based disease- And Multi-Targeting Drug DREAM Challenge

by Abagyan, R., Allaway, R.J, Cagan, R., Carlson, H.A, Dang, K.K, Das, T.K, Guinney, J., Guo, X., Hecht, C., Jeon, H., Jeon, M., Jiang, H., Kang, J., Ko, M., Lee, J., Park, D., Schlessinger, A., Tan, A.C, Tropsha, A., Xiong, Z., Zheng, M.
Published 2021

Comprehensive understanding of Tn5 insertion preference improves transcription regulatory element identification

by Chen, F., Cheng, T., Liu, S., Lu, T., Sun, G., Xu, J., Yang, J., Yen, K., Zhang, H.
Published 2021