Optimal transport analysis reveals trajectories in steady-state systems

by Afanassiev, A., Greenstreet, L., Matsumoto, T., Schiebinger, G., Zhang, 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

Simpler and Faster Development of Tumor Phylogeny Pipelines

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

Origami: Single-cell 3D shape dynamics oriented along the apico-basal axis of folding epithelia from fluorescence microscopy data

by Baxendale, S., Frangi, A.F, Jones, A.A, Mendonca, T., Pozo, J.M, Whitfield, T.T
Published 2021

Using Galaxy to Perform Large-Scale Interactive Data Analyses—An Update

by Afgan, E., Blankenberg, D., Bouvier, D., Clements, D., Hillman-Jackson, J., Lariviere, D., Nekrutenko, A., Ostrovsky, A., Schatz, M.C, Taylor, J., Team, T.G
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

CytoTree: an R/Bioconductor package for analysis and visualization of flow and mass cytometry data

by Chen, J., Dai, Y., Huang, J., Li, J., Sun, X.-J, Wu, L., Xu, A., Yu, S., Zhao, W.
Published 2021

CDSeqR: fast complete deconvolution for gene expression data from bulk tissues

by Huang, C., Kang, K., Li, L., Li, Y., Umbach, D.M
Published 2021

Hybrid computational modeling demonstrates the utility of simulating complex cellular networks in type 1 diabetes

by Jaberi-Douraki, M., Li, Y., Shi, Z.
Published 2021

ISOTOPE: ISOform-guided prediction of epiTOPEs in cancer

by Eyras, E., Fugmann, T., Pérez-Granado, J., Reixachs-Solé, M., Sanz, F., Trincado, J.L, Yokota, J.
Published 2021

Inference of phenotype-relevant transcriptional regulatory networks elucidates cancer type-specific regulatory mechanisms in a pan-cancer study

by Emad, A., Sinha, S.
Published 2021

dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design

by Maranas, C.D, Upadhyay, V., Wang, L.
Published 2021

Performance evaluation of pipelines for mapping, variant calling and interval padding, for the analysis of NGS germline panels

by Christodoulou, K., Hadjisavvas, A., Kyriacou, K., Loizidou, M.A, Machattou, C., Michailidou, K., Pirpa, P., Spyrou, G.M, Zanti, M.
Published 2021

IsomiR_Window: a system for analyzing small-RNA-seq data in an integrative and user-friendly manner

by Amaral, A.J, Carmo, M.B, Ferreira, A., Ferreira, B., Gama-Carvalho, M., Vasconcelos, A.M, Viegas, I.
Published 2021

RNA editing regulates lncRNA splicing in human early embryo development

by Ma, X., Qiu, J., Yan, J., Zeng, F.
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

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

by Acencio, M.L, Ackerman, E.E, Aghamiri, S.S, Auffray, C., Augé, F., Babur, O., Bachman, J.A, Ballereau, S., Balling, R., Barillot, E., Bauch, A., Beckmann, J.S, Bocskei, Z., Borlinghaus, H., Börnigen, D., Brauner, B., Calzone, L., Conti, M., Coort, S., Czauderna, T., De Meulder, B., de Waard, A., Demir, E., D'Eustachio, P., Dopazo, J., Dräger, A., Dugourd, A., Ehrhart, F., Eijssen, L., Esteban-Medina, M., Evelo, C.T, Fergusson, L., Fobo, G., Fraser, R., Freeman, T.C, Frishman, G., Funahashi, A., Gawron, P., Gillespie, M.E, Glaab, E., Goble, C., Golebiewski, M., Grouès, V., Gyori, B.M, Hanspers, K., Hasenauer, J., Haw, R., Heirendt, L., Helikar, T., Hermjakob, H., Hiki, Y., Hiroi, N., Hoch, M., Hu, X., Iannuccelli, M., Jassal, B., Kitano, H., Kocakaya, E., Korcsmaros, T., Kumar Gupta, S., Kuperstein, I., Kutmon, M., Licata, L., Luna, A., Maier, D., Marchesi, S., Martens, M., Matthews, L., Mazein, A., Messina, F., Modos, D., Monraz Gómez, L.C, Montagud, A., Montrone, C., Nakonecnij, V., Naldi, A., Naveez, M., Nesterova, A., Niarakis, A., Noël, V., Olbei, M., Orlic-Milacic, M., Orta-Resendiz, A., Ortseifen, V., Ostaszewski, M., Overall, R.W, Owen, S., Oxford, K., Peña-Chilet, M., Phair, R., Pham, N., Pico, A.R, Ponce de Leon, M., Porras, P., Puniya, B.L, Rameil, M., Ravel, J.-M, Renz, A., Rex, D.A.B, Rian, K., Riutta, A., Rothfels, K., Ruepp, A., Sacco, F., Saez-Rodriguez, J., Sander, C., Satagopam, V., Scheel, J., Schmiester, L., Schneider, R., Schreiber, F., Senff Ribeiro, A., Sevilla, C., Shamovsky, V., Shoemaker, J.E, Singh, V., Slenter, D., Smula, E., Soliman, S., Somers, J., Stein, L.D, Stephan, R., Summak, G.Y, Teuton, J., the COVID-19 Disease Map Community, Treveil, A., Turei, D., Valdeolivas, A., Valencia, A., Vanhoefer, J., Varusai, T., Vazquez, M., Vega, C., Wang, M., Wilighagen, E.L, Wolkenhauer, O., Wu, G., Yamada, T.G, Yuryev, A., Zucker, J.
Published 2021

Gene Set Knowledge Discovery with Enrichr

by Bailey, A., Clarke, D.J.B, Evangelista, J.E, Jagodnik, K.M, Jenkins, S.L, Jeon, M., Kropiwnicki, E., Kuleshov, M.V, Lachmann, A., Ma'ayan, A., Wojciechowicz, M.L, Xie, Z.
Published 2021

Computational redesign of a fluorogen activating protein with Rosetta

by Baranov, M.S, Bender, B.J, Bozhanova, N.G, Gavrikov, A.S, Gorbachev, D.A, Harp, J.M, Lukyanov, K.A, Meiler, J., Mercado, C.B, Mishin, A.S, Zhang, X.
Published 2021

Systematic evaluation of NIPT aneuploidy detection software tools with clinically validated NIPT samples

by Ardeshirdavani, A., Bayindir, B., Krjutškov, K., Palta, P., Paluoja, P., Salumets, A., Teder, H., Vermeesch, J.
Published 2021