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

Single cell biology—a Keystone Symposia report

by Alon, U., Arbel-Goren, R., Arekatla, G., Balzer, M.S, Cable, J., Cai, L., Domingos, A.I, Elowitz, M.B, Fan, J., Gaiti, F., Galloway, K.E, Garcia, H.G, Greenwald, N.F, Guilliams, M., Habib, N., Hamel, R., Hamidzada, H., Hong, C.K.Y, Itzkovitz, S., Junker, J.P, Keren, L., Klein, A.M, Liberali, P., Morris, S.A, Murray, J.I, Pfau, S.J, Quake, S.R, Raj, A., Ratz, M., Romeike, M., Rulands, S., Santos, S.D.M, Shalek, A.K, Spencer, S.L, Stergachis, A.B, Streets, A., Trapnell, C., Vento-Tormo, R., Wang, B., Whited, J., Yanai, I., Zhang, N.R
Published 2021

Shared genetic and epigenetic mechanisms between chronic periodontitis and oral squamous cell carcinoma

by Acharya, A., Deng, Y., Haak, R., Hu, X., Li, H., Li, S., Liu, X., Pan, H., Savkovic, V., Schmalz, G., Schmidt, J., Shang, R., Shang, W., Wu, N., Xu, C., Yu, Y., Zhou, Y., Ziebolz, D.
Published 2018

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

by Bandyopadhyay, S., Lall, S., Ray, S.
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

Programming cell growth into different cluster shapes using diffusible signals

by Brenner, M.P, Guo, Y., Nitzan, M.
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

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

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

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

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

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

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

Simpler and Faster Development of Tumor Phylogeny Pipelines

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

Frequent contiguous pattern mining over biological sequences of protein misfolded diseases

by Arefin, M.S, Dhar, P.K, Islam, M.S, Koshiba, T., Mia, M.A.K, Rahman, M.S
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

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

RESEARCH ARTICLE Multilevel selection favors fragmentation modes that maintain cooperative interactions in multispecies communities

by Doebeli, M., Henriques, G.J.B, Vliet, S.V
Published 2021

A data-driven approach for constructing mutation categories for mutational signature analysis

by Gilad, G., Leiserson, M.D.M, Sharan, R.
Published 2021