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Items: 9

1.

Benchmarking time-series data discretization on inference methods.

Li Y, Jann T, Vera-Licona P.

Bioinformatics. 2019 Sep 1;35(17):3102-3109. doi: 10.1093/bioinformatics/btz036.

PMID:
30657860
2.

Chromatin interaction networks revealed unique connectivity patterns of broad H3K4me3 domains and super enhancers in 3D chromatin.

Thibodeau A, Márquez EJ, Shin DG, Vera-Licona P, Ucar D.

Sci Rep. 2017 Oct 31;7(1):14466. doi: 10.1038/s41598-017-14389-7.

3.

CD169+ macrophages orchestrate innate immune responses by regulating bacterial localization in the spleen.

Perez OA, Yeung ST, Vera-Licona P, Romagnoli PA, Samji T, Ural BB, Maher L, Tanaka M, Khanna KM.

Sci Immunol. 2017 Oct 6;2(16). pii: eaah5520. doi: 10.1126/sciimmunol.aah5520.

4.

QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks.

Thibodeau A, Márquez EJ, Luo O, Ruan Y, Menghi F, Shin DG, Stitzel ML, Vera-Licona P, Ucar D.

PLoS Comput Biol. 2016 Jun 23;12(6):e1004809. doi: 10.1371/journal.pcbi.1004809. eCollection 2016 Jun.

5.

AlgoRun: a Docker-based packaging system for platform-agnostic implemented algorithms.

Hosny A, Vera-Licona P, Laubenbacher R, Favre T.

Bioinformatics. 2016 Aug 1;32(15):2396-8. doi: 10.1093/bioinformatics/btw120. Epub 2016 Mar 2.

6.

An algebra-based method for inferring gene regulatory networks.

Vera-Licona P, Jarrah A, Garcia-Puente LD, McGee J, Laubenbacher R.

BMC Syst Biol. 2014 Mar 26;8:37. doi: 10.1186/1752-0509-8-37.

7.

OCSANA: optimal combinations of interventions from network analysis.

Vera-Licona P, Bonnet E, Barillot E, Zinovyev A.

Bioinformatics. 2013 Jun 15;29(12):1571-3. doi: 10.1093/bioinformatics/btt195. Epub 2013 Apr 26.

PMID:
23626000
8.

TIGRESS: Trustful Inference of Gene REgulation using Stability Selection.

Haury AC, Mordelet F, Vera-Licona P, Vert JP.

BMC Syst Biol. 2012 Nov 22;6:145. doi: 10.1186/1752-0509-6-145.

9.

Comparison of reverse-engineering methods using an in silico network.

Camacho D, Vera Licona P, Mendes P, Laubenbacher R.

Ann N Y Acad Sci. 2007 Dec;1115:73-89. Epub 2007 Oct 9. Review.

PMID:
17925358

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