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

Harmonizing model organism data in the Alliance of Genome Resources

by Alliance of Genome Resources Consortium
Published 2022

WormBase in 2022-data, processes, and tools for analyzing Caenorhabditis elegans

by Arnaboldi, V., Becerra, A., Berriman, M., Cain, S., Chan, J., Chen, W.J, Cho, J., da Veiga Beltrame, E., Davis, P., Diamantakis, S., Gao, S., Grigoriadis, D., Grove, C.A, Harris, T.W, Howe, K.L, Kishore, R., Le, T., Lee, R.Y.N, Luypaert, M., Müller, H.-M, Nakamura, C., Nuin, P., Paulini, M., Quinton-Tulloch, M., Raciti, D., Rodgers, F.H, Russell, M., Schedl, T., Schindelman, G., Singh, A., Stein, L., Sternberg, P.W, Stickland, T., Van Auken, K., Wang, Q., Williams, G., Wright, A.J, Yook, K., Zarowiecki, M.
Published 2022

GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction

by Damiani, C., Filippo, M.D, Pescini, D.
Published 2021

Pooling and expanding registries of familial hypercholesterolaemia to assess gaps in care and improve disease management and outcomes: Rationale and design of the global EAS Famili...

by Abifadel, M., Aguilar-Salinas, C.A, Akram, A., Alnouri, F., Alonso, R., Al-Rasadi, K., Banach, M., Bogsrud, M.P, Bourbon, M., Bruckert, E., Car, J., Catapano, A.L, Ceska, R., Cole, D., Corral, P., Descamps, O., Dieplinger, H., Do, C.T, Durst, R., Ezhov, M.V, Fras, Z., Freiberger, T., Gaita, D., Gaspar, I.M, Genest, J., Harada-Shiba, M., Hovingh, G.K, Jiang, L., Kastelein, J.J.P, Kayikcioglu, M., Kondapally Seshasai, S.R, Lam, C.S.P, Latkovskis, G., Laufs, U., Liberopoulos, E., Lin, J., Lin, N., Maher, V., Majano, N., Marais, A.D, März, W., Mata, P., Mirrakhimov, E., Miserez, A.R, Mitchenko, O., Nawawi, H., Nilsson, L., Nordestgaard, B.G, Paragh, G., Petrulioniene, Z., Pojskic, B., Raal, F.J, Ray, K.K, Reiner, Ž, Sahebkar, A., Santos, L.E, Santos, R.D, Schunkert, H., Shehab, A., Slimane, M.N, Soran, H., Stoll, M., Su, T.-C, Susekov, A., Tilney, M., Tomlinson, B., Tselepis, A.D, Vallejo-Vaz, A.J, Vohnout, B., Watts, G.F, Widén, E., Yamashita, S.
Published 2016

A new algorithm to train hidden Markov models for biological sequences with partial labels

by Lee, J.-Y, Li, J., Liao, L.
Published 2021

airpg: automatically accessing the inverted repeats of archived plastid genomes

by Gruenstaeudl, M., Mehl, T.
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

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

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

The analysis on the human protein domain targets and host-like interacting motifs for the MERS-CoV and SARS-CoV/CoV-2 infers the molecular mimicry of coronavirus

by Castañeda-Delgado, J.E, Enciso-Moreno, J.A, García-Pérez, C.A, Guo, X., Lara-Ramírez, E.E, Martínez, Y.A, Portales-Pérez, D.P, Rivera, G.
Published 2021

FunOrder: A robust and semi-automated method for the identification of essential biosynthetic genes through computational molecular co-evolution

by Derntl, C., Mach, R.L, Mach-Aigner, A.R, Schaffer, D., Vignolle, G.A, Zehetner, L.
Published 2021

A representation and deep learning model for annotating ubiquitylation sentences stating E3 ligase - substrate interaction

by Lee, T.-Y, Li, S., Li, Z., Luo, M.
Published 2021

Assembly and Exploration of a Single Cell Atlas of the Drosophila Larval Ventral Cord. Identification of Rare Cell Types

by Brody, T., Choudhury, S.D, Nguyen, T.H, Serpe, M., Vicidomini, R.
Published 2021

ggComp enables dissection of germplasm resources and construction of a multiscale germplasm network in wheat

by Chai, L., Feng, X., Guo, W., Hu, Z., Li, J., Liang, R., Liu, J., Ni, Z., Peng, H., Su, Z., Sun, Q., Wang, W., Wang, X., Wang, Z., Xie, X., Xin, M., Yang, Z., Yao, Y., You, M.
Published 2022

An integrated strategy for target SSR genotyping with toleration of nucleotide variations in the SSRs and flanking regions

by Huo, Y., Jia, X., Wang, F., Xu, L., Yi, H., Zhang, Y., Zhao, H., Zhao, J., Zhao, Y.
Published 2021

A functional analysis of omic network embedding spaces reveals key altered functions in cancer

by Ceddia, G., Doria-Belenguer, S., Malod-Dognin, N., Pržulj, N., Xenos, A.
Published 2023

A learning-based method to predict LncRNA-disease associations by combining CNN and ELM

by Chen, Z.-H, Guo, Z.-H, Wang, M.-N, Wang, Y.-B, Yi, H.-C, You, Z.-H
Published 2021

Simulation study and comparative evaluation of viral contiguous sequence identification tools

by Glickman, C., Hendrix, J., Strong, M.
Published 2021