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Computational Biology

PyCellBase, an efficient python package for easy retrieval of biological data from heterogeneous sources.

Submitted by iguillen on Tue, 06/25/2019 - 10:00
Perez-Gil D, Lopez FJ, Dopazo J, Marin-Garcia P, Rendon A, Medina I. PyCellBase, an efficient python package for easy retrieval of biological data from heterogeneous sources. BMC Bioinformatics. 2019;20(1):159. doi:10.1186/s12859-019-2726-4.

Using GPUs for the exact alignment of short-read genetic sequences by means of the Burrows-Wheeler transform.

Submitted by iguillen on Tue, 06/18/2019 - 10:48
Torres JSalavert, Espert IBlanquer, Domínguez ATomás, et al. Using GPUs for the exact alignment of short-read genetic sequences by means of the Burrows-Wheeler transform. IEEE/ACM Trans Comput Biol Bioinform. 2012;9(4):1245-56. doi:10.1109/TCBB.2012.49.

The protease MT1-MMP drives a combinatorial proteolytic program in activated endothelial cells.

Submitted by iguillen on Tue, 06/18/2019 - 10:47
Koziol A, Gonzalo P, Mota A, et al. The protease MT1-MMP drives a combinatorial proteolytic program in activated endothelial cells. FASEB J. 2012;26(11):4481-94. doi:10.1096/fj.12-205906.

High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes.

Submitted by iguillen on Mon, 06/10/2019 - 12:01
Hidalgo MR, Cubuk C, Amadoz A, Salavert F, Carbonell-Caballero J, Dopazo J. High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes. Oncotarget. 2017;8(3):5160-5178. doi:10.18632/oncotarget.14107.

Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models.

Submitted by iguillen on Thu, 06/06/2019 - 12:49
Cubuk C, Hidalgo MR, Amadoz A, et al. Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models. NPJ Syst Biol Appl. 2019;5:7. doi:10.1038/s41540-019-0087-2.

Models of cell signaling uncover molecular mechanisms of high-risk neuroblastoma and predict disease outcome.

Submitted by jdopazo on Fri, 11/02/2018 - 11:02
Hidalgo MR, Amadoz A, Cubuk C, Carbonell-Caballero J, Dopazo J. Models of cell signaling uncover molecular mechanisms of high-risk neuroblastoma and predict disease outcome. Biol Direct. 2018;13(1):16. doi:10.1186/s13062-018-0219-4.