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Items: 1 to 20 of 105

1.

The State of Software for Evolutionary Biology.

Darriba D, Flouri T, Stamatakis A.

Mol Biol Evol. 2018 May 1;35(5):1037-1046. doi: 10.1093/molbev/msy014. Review.

2.

Biology Needs Evolutionary Software Tools: Let's Build Them Right.

Nekrutenko A, Team G, Goecks J, Taylor J, Blankenberg D.

Mol Biol Evol. 2018 Jun 1;35(6):1372-1375. doi: 10.1093/molbev/msy084.

3.

Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).

Foffi G, Pastore A, Piazza F, Temussi PA.

Phys Biol. 2013 Aug;10(4):040301. Epub 2013 Aug 2.

PMID:
23912807
4.

Proceedings of the Second Workshop on Theory meets Industry (Erwin-Schrödinger-Institute (ESI), Vienna, Austria, 12-14 June 2007).

Hafner J.

J Phys Condens Matter. 2008 Feb 13;20(6):060301. doi: 10.1088/0953-8984/20/06/060301. Epub 2008 Jan 24.

PMID:
21693862
5.
6.

SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines.

Audoux J, Salson M, Grosset CF, Beaumeunier S, Holder JM, Commes T, Philippe N.

BMC Bioinformatics. 2017 Sep 29;18(1):428. doi: 10.1186/s12859-017-1831-5.

7.

Web Resources for Metagenomics Studies.

Dudhagara P, Bhavsar S, Bhagat C, Ghelani A, Bhatt S, Patel R.

Genomics Proteomics Bioinformatics. 2015 Oct;13(5):296-303. doi: 10.1016/j.gpb.2015.10.003. Epub 2015 Nov 18. Review.

8.

Current practice in software development for computational neuroscience and how to improve it.

Gewaltig MO, Cannon R.

PLoS Comput Biol. 2014 Jan;10(1):e1003376. doi: 10.1371/journal.pcbi.1003376. Epub 2014 Jan 23.

9.

BEAST: Bayesian evolutionary analysis by sampling trees.

Drummond AJ, Rambaut A.

BMC Evol Biol. 2007 Nov 8;7:214.

10.

Scalable computing for evolutionary genomics.

Prins P, Belhachemi D, Möller S, Smant G.

Methods Mol Biol. 2012;856:529-45. doi: 10.1007/978-1-61779-585-5_22.

PMID:
22399474
11.

compomics-utilities: an open-source Java library for computational proteomics.

Barsnes H, Vaudel M, Colaert N, Helsens K, Sickmann A, Berven FS, Martens L.

BMC Bioinformatics. 2011 Mar 8;12:70. doi: 10.1186/1471-2105-12-70.

12.

A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway.

Miller MA, Schwartz T, Pickett BE, He S, Klem EB, Scheuermann RH, Passarotti M, Kaufman S, O'Leary MA.

Evol Bioinform Online. 2015 Mar 16;11:43-8. doi: 10.4137/EBO.S21501. eCollection 2015. Review.

13.

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button.

Swertz MA, Dijkstra M, Adamusiak T, van der Velde JK, Kanterakis A, Roos ET, Lops J, Thorisson GA, Arends D, Byelas G, Muilu J, Brookes AJ, de Brock EO, Jansen RC, Parkinson H.

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S12. doi: 10.1186/1471-2105-11-S12-S12.

14.

An integrated SNP mining and utilization (ISMU) pipeline for next generation sequencing data.

Azam S, Rathore A, Shah TM, Telluri M, Amindala B, Ruperao P, Katta MA, Varshney RK.

PLoS One. 2014 Jul 8;9(7):e101754. doi: 10.1371/journal.pone.0101754. eCollection 2014.

15.

PoPLAR: Portal for Petascale Lifescience Applications and Research.

Rekapalli B, Giblock P, Reardon C.

BMC Bioinformatics. 2013;14 Suppl 9:S3. doi: 10.1186/1471-2105-14-S9-S3. Epub 2013 Jun 28.

16.

Software support for SBGN maps: SBGN-ML and LibSBGN.

van Iersel MP, Villéger AC, Czauderna T, Boyd SE, Bergmann FT, Luna A, Demir E, Sorokin A, Dogrusoz U, Matsuoka Y, Funahashi A, Aladjem MI, Mi H, Moodie SL, Kitano H, Le Novère N, Schreiber F.

Bioinformatics. 2012 Aug 1;28(15):2016-21. Epub 2012 May 10.

17.

Constructing computational pipelines.

Halling-Brown M, Shepherd AJ.

Methods Mol Biol. 2008;453:451-70. doi: 10.1007/978-1-60327-429-6_24.

PMID:
18712319
18.

Clinical code set engineering for reusing EHR data for research: A review.

Williams R, Kontopantelis E, Buchan I, Peek N.

J Biomed Inform. 2017 Jun;70:1-13. doi: 10.1016/j.jbi.2017.04.010. Epub 2017 Apr 22. Review.

19.

BEAST 2: a software platform for Bayesian evolutionary analysis.

Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ.

PLoS Comput Biol. 2014 Apr 10;10(4):e1003537. doi: 10.1371/journal.pcbi.1003537. eCollection 2014 Apr.

20.

HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking.

Lazaris C, Kelly S, Ntziachristos P, Aifantis I, Tsirigos A.

BMC Genomics. 2017 Jan 5;18(1):22. doi: 10.1186/s12864-016-3387-6.

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