Popularity and performance of bioinformatics software: the case of gene set analysis

by Jauhari, S., Mora, A., Xie, C.
Published 2021

pyGOMoDo: GPCRs modeling and docking with python

by Giorgetti, A., Ribeiro, R.P
Published 2023

FAS: assessing the similarity between proteins using multi-layered feature architectures

by Bergmann, H., Dosch, J., Ebersberger, I., Tran, V.
Published 2023

Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service

by Alessandri, L., Antonacci, M., Bianchi, D.M, Bianco, A., Bonetti, E., Calogero, R.A, Cangelosi, D., Chiara, M., Donvito, G., Mandreoli, P., Molineris, I., Mordenti, M., Nosi, V., Parisi, A., Pedrini, E., Pesole, G., Romano, A., Sangiorgi, L., Tangaro, M.A, Uva, P., Zambelli, F.
Published 2021

A framework for high-throughput sequence alignment using real processing-in-memory systems

by Alser, M., Diab, S., El Hajj, I., Gómez Luna, J., Mutlu, O., Nassereldine, A.
Published 2023

A flexible ChIP-sequencing simulation toolkit

by Goren, A., Gymrek, M., Lamkin, M., Qiu, Y., Ren, K., Zheng, A.
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

Exploring the Genomic Landscape of Cancer Patient Cohorts with GenVisR

by Campbell, K.M, Cotto, K.C, Griffith, M., Griffith, O.L, Skidmore, Z.L
Published 2021

Fast and exact quantification of motif occurrences in biological sequences

by Boucher, C., Marini, S., Prosperi, M.
Published 2021

VPMBench: a test bench for variant prioritization methods

by Ewald, R., Reimler, A.L, Ruscheinski, A., Uhrmacher, A.M
Published 2021

TSEBRA: transcript selector for BRAKER

by Borodovsky, M., Brůna, T., Gabriel, L., Hoff, K.J, Stanke, M.
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

Effective Clustering for Single Cell Sequencing Cancer Data

by Bonizzoni, P., Ciccolella, S., Della Vedova, G., Patterson, M.
Published 2021

Identifying proximal RNA interactions from cDNA-encoded crosslinks with ShapeJumper

by Christy, T.W, Giannetti, C.A, Laederach, A., Weeks, K.M
Published 2021

Impact of concurrency on the performance of a whole exome sequencing pipeline

by Castellani, G., Curti, N., Dall’Olio, D., Fonzi, E., Giampieri, E., Remondini, D., Sala, C.
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

MSA: reproducible mutational signature attribution with confidence based on simulations

by Senkin, S.
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

CrossTalkeR: analysis and visualization of ligand-receptorne tworks

by Costa, I.G, Leimkühler, N.B, Nagai, J.S, Schaub, M.T, Schneider, R.K
Published 2021

DEGGs: an R package with shiny app for the identification of differentially expressed gene-gene interactions in high-throughput sequencing data

by Alaimo, S., Ferro, A., Latora, V., Lewis, M.J, Pitzalis, C., Pulvirenti, A., Sciacca, E., Silluzio, G.
Published 2023