Constructing gene regulatory networks using epigenetic data

by DeMeo, D.L, Glass, K., Quackenbush, J., Sonawane, A.R
Published 2021

Optimizing network propagation for multi-omics data integration

by Beyer, A., Charmpi, K., Chokkalingam, M., Johnen, R.
Published 2021

Data-driven biological network alignment that uses topological, sequence, and functional information

by Gu, S., Milenković, T.
Published 2021

Extended graphical lasso for multiple interaction networks for high dimensional omics data

by Jiang, H., Jiang, W., Xu, Y.
Published 2021

Modeling transcriptional regulation using gene regulatory networks based on multi-omics data sources

by Bush, W.S, Patel, N.
Published 2021

DFHiC: a dilated full convolution model to enhance the resolution of Hi-C data

by Li, Y., Liu, K., Wang, B., Wang, J.
Published 2023

Multi-dimensional data integration algorithm based on random walk with restart

by Bo, X., He, S., Leng, D., Song, X., Wen, Y., Wu, L., Yan, B., Yang, X.
Published 2021

A machine learning framework that integrates multi-omics data predicts cancer-related LncRNAs

by Shen, Z., Sun, T., Yuan, L., Zhao, J.
Published 2021

Inference of a Dynamic Aging-related Biological Subnetwork via Network Propagation

by Milenkovic, T., Newaz, K.
Published 2022

Sparsely-connected autoencoder (SCA) for single cell RNAseq data mining

by Alessandri, L., Arigoni, M., Beccuti, M., Calogero, R., Cordero, F., Di Renzo, M.F, Licheri, N., Olivero, M., Sapino, A.
Published 2021

The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data

by Abdennur, N., Alver, B.H, Bakker, C., Balashov, A.K, Çamoğlu, U., Cosolo, A., Ehmsen, S.R, Gehlenborg, N., Imakaev, M., Johnson, J., Kerpedjiev, P., Kırlı, K., Lee, S., Mirny, L.A, Öztürk, S.U, Park, P.J, Pitman, K.M, Reiff, S.B, Ronchetti, W., Schroeder, A.J, Veit, A.D, Vitzthum, C.
Published 2022

Factor graph-aggregated heterogeneous network embedding for disease-gene association prediction

by He, M., Huang, C., Li, J., Liu, B., Wang, Y.
Published 2021

MethylSPWNet and MethylCapsNet: Biologically Motivated Organization of DNAm Neural Networks, Inspired by Capsule Networks

by Azizgolshani, N., Chen, Y., Christensen, B.C, Levy, J.J, Moen, E.L, Petersen, C.L, Salas, L.A, Titus, A.J, Vaickus, L.J
Published 2021

Meta-analysis of transcriptomic data reveals clusters of consistently deregulated gene and disease ontologies in down syndrome

by de Toma, I., Dierssen, M., Sierra, C.
Published 2021

Predicting genotype-specific gene regulatory networks

by Glass, K., Guebila, M.B, Platig, J., Quackenbush, J., Weighill, D.
Published 2022

Reconstructing contact network structure and cross-immunity patterns from multiple infection histories

by Alizon, S., Selinger, C.
Published 2021

Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data

by Le, T.D, Li, J., Li, S., Liu, L., Rao, N., Xu, T., Zhang, J., Zhang, W., Zhao, C.
Published 2021

Prediction and analysis of multiple protein lysine modified sites based on conditional wasserstein generative adversarial networks

by Li, W., Liu, Y., Wang, H., Wang, X., Wei, S., Xu, Y., Yang, Y.
Published 2021

Harmonizing model organism data in the Alliance of Genome Resources

by Alliance of Genome Resources Consortium
Published 2022

Zebrafish information network, the knowledgebase for Danio rerio research

by Bradford, Y.M, Eagle, A., Fashena, D., Frazer, K., Howe, D.G, Martin, R., Paddock, H., Pich, C., Ramachandran, S., Ruzicka, L., Singer, A., Van Slyke, C.E, Westerfield, M.
Published 2022