Boolean factor graph model for biological systems: the yeast cell-cycle network

by Eslami, A., Kotiang, S.
Published 2021

A systems biology model of junctional localization and downstream signaling of the Ang–Tie signaling pathway

by Annex, B.H, Kontos, C.D, Popel, A.S, Zhang, Y.
Published 2021

Integrative computational approach identifies drug targets in CD4+ T-cell-mediated immune disorders

by Amin, R., Barberis, M., Bennett, S.J, Ciurej, A., Helikar, T., Lichter, B., Moore, R., Puniya, B.L, Shah, A.R
Published 2021

A metric for evaluating biological information in gene sets and its application to identify co-expressed gene clusters in PBMC

by Bennett, J., Peters, B., Pomaznoy, M., Singhania, A.
Published 2021

DeepCellState: An autoencoder-based framework for predicting cell type specific transcriptional states induced by drug treatment

by Arner, E., Li, Y., Umarov, R.
Published 2021

RgCop-A regularized copula based method for gene selection in single cell rna-seq data

by Bandyopadhyay, S., Lall, S., Ray, S.
Published 2021

SwarmTCR: a computational approach to predict the specificity of T cell receptors

by Ehrlich, R., Ghersi, D., Gil, A., Kamga, L., Luzuriaga, K., Selin, L.K
Published 2021

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

Transcriptomic profiling in canines and humans reveals cancer specific gene modules and biological mechanisms common to both species

by Braisted, J., Breen, M., Gerhold, D., Grewal, G., LeBlanc, A.K, Mazcko, C., Sittampalam, G., Tawa, G.J
Published 2021

Generic self-stabilization mechanism for biomolecular adhesions under load

by Braeutigam, A., Gompper, G., Sabass, B., Simsek, A.N
Published 2022

Studying the History of Tumor Evolution from Single-Cell Sequencing Data by Exploring the Space of Binary Matrices

by Azer, E.S, Ebrahimabadi, M.H, Malikić, S., Mehrabadi, F.R, Sahinalp, S.C
Published 2021

CoRE-ATAC: A deep learning model for the functional classification of regulatory elements from single cell and bulk ATAC-seq data

by Eroglu, A., Khetan, S., Stitzel, M.L, Tewhey, R., Thibodeau, A., Ucar, D.
Published 2021

Simpler and Faster Development of Tumor Phylogeny Pipelines

by Ali, S., Ciccolella, S., Lucarella, L., Patterson, M., Vedova, G.D
Published 2021

A detailed map of coupled circadian clock and cell cycle with qualitative dynamics validation

by Delaunay, F., Paulevé, L., Rougny, A., Teboul, M.
Published 2021

Fission stories: using PomBase to understand Schizosaccharomyces pombe biology

by Bähler, J., Harris, M.A, Hayles, J., Lock, A., Mata, J., Oliver, S.G, Rutherford, K.M, Wood, V.
Published 2022

A highly multiplexed quantitative phosphosite assay for biology and preclinical studies

by Babur, O., Burgess, M., Carr, S.A, Forestier, D., Gillette, M.A, Golji, J., Jane-Valbuena, J., Jean Beltran, P.M, Keshishian, H., Krug, K., Kuhn, E., MacMullan, M.A, Mani, D.R, Marlow, S.E, McDonald, E.R., III, Melanson, R., Mundt, F., Olive, M.E, Porter, D.A, Rabasha, B., Rejtar, T., Robinson, M.L, Satpathy, S., Sellers, W.R, Specht, H., Todres, E., Wallace, L., Wang, K.
Published 2021

Integrated genetic and metabolic landscapes predict vulnerabilities of temozolomide resistant glioblastoma cells

by Ghanate, A.D, Immanuel, S.R.C, Panchagnula, V., Parmar, D.S, Raghunathan, A., Uthup, R., Yadav, R.
Published 2021

Comparative Analysis of T-Cell Spatial Proteomics and the Influence of HIV Expression

by Gonzalez, D.J, Guatelli, J., Krogan, N.J, Lewinski, M.K, Oom, A.L, Richards, A., Shams-Ud-Doha, K., Stoneham, C.A, Wozniak, J.M
Published 2022

DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks

by Birchler, J.A, Chen, C., Cheng, J., Hou, J., Shi, X., Yang, H.
Published 2021

Differential contribution to gene expression prediction of histone modifications at enhancers or promoters

by Ballaré, C., Beringer, M., Blanco, E., Di Croce, L., González-Ramírez, M., Mugianesi, F., Santanach, A.
Published 2021