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Items: 1 to 20 of 226

1.

SIApopr: a computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution.

McDonald TO, Michor F.

Bioinformatics. 2017 Jul 15;33(14):2221-2223. doi: 10.1093/bioinformatics/btx146.

2.

DIFFpop: a stochastic computational approach to simulate differentiation hierarchies with single cell barcoding.

Ferlic J, Shi J, McDonald TO, Michor F.

Bioinformatics. 2019 Oct 1;35(19):3849-3851. doi: 10.1093/bioinformatics/btz074.

PMID:
30816920
3.

Rust-Bio: a fast and safe bioinformatics library.

Köster J.

Bioinformatics. 2016 Feb 1;32(3):444-6. doi: 10.1093/bioinformatics/btv573. Epub 2015 Oct 6.

PMID:
26446134
4.

Discoal: flexible coalescent simulations with selection.

Kern AD, Schrider DR.

Bioinformatics. 2016 Dec 15;32(24):3839-3841. Epub 2016 Aug 24.

5.

A computational strategy to adjust for copy number in tumor Hi-C data.

Wu HJ, Michor F.

Bioinformatics. 2016 Dec 15;32(24):3695-3701. Epub 2016 Aug 16.

6.

Inferring clonal evolution of tumors from single nucleotide somatic mutations.

Jiao W, Vembu S, Deshwar AG, Stein L, Morris Q.

BMC Bioinformatics. 2014 Feb 1;15:35. doi: 10.1186/1471-2105-15-35.

7.

A scalable moment-closure approximation for large-scale biochemical reaction networks.

Kazeroonian A, Theis FJ, Hasenauer J.

Bioinformatics. 2017 Jul 15;33(14):i293-i300. doi: 10.1093/bioinformatics/btx249.

8.

UpSetR: an R package for the visualization of intersecting sets and their properties.

Conway JR, Lex A, Gehlenborg N.

Bioinformatics. 2017 Sep 15;33(18):2938-2940. doi: 10.1093/bioinformatics/btx364.

9.

MEANS: python package for Moment Expansion Approximation, iNference and Simulation.

Fan S, Geissmann Q, Lakatos E, Lukauskas S, Ale A, Babtie AC, Kirk PD, Stumpf MP.

Bioinformatics. 2016 Sep 15;32(18):2863-5. doi: 10.1093/bioinformatics/btw229. Epub 2016 May 5.

10.

geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees.

Pennell MW, Eastman JM, Slater GJ, Brown JW, Uyeda JC, FitzJohn RG, Alfaro ME, Harmon LJ.

Bioinformatics. 2014 Aug 1;30(15):2216-8. doi: 10.1093/bioinformatics/btu181. Epub 2014 Apr 10.

PMID:
24728855
11.

OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations.

Diaz-Uriarte R.

Bioinformatics. 2017 Jun 15;33(12):1898-1899. doi: 10.1093/bioinformatics/btx077.

12.

STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB.

Klingbeil G, Erban R, Giles M, Maini PK.

Bioinformatics. 2011 Apr 15;27(8):1170-1. doi: 10.1093/bioinformatics/btr068. Epub 2011 Feb 25.

PMID:
21357575
13.

Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity.

Li Y, Xie X.

Bioinformatics. 2014 Aug 1;30(15):2121-9. doi: 10.1093/bioinformatics/btu174. Epub 2014 Apr 2. Erratum in: Bioinformatics. 2015 Feb 15;31(4):618.

14.

Coala: an R framework for coalescent simulation.

Staab PR, Metzler D.

Bioinformatics. 2016 Jun 15;32(12):1903-4. doi: 10.1093/bioinformatics/btw098. Epub 2016 Feb 18.

PMID:
27153679
15.

libSRES: a C library for stochastic ranking evolution strategy for parameter estimation.

Ji X, Xu Y.

Bioinformatics. 2006 Jan 1;22(1):124-6. Epub 2005 Nov 2.

PMID:
16267082
16.

MulRF: a software package for phylogenetic analysis using multi-copy gene trees.

Chaudhary R, Fernández-Baca D, Burleigh JG.

Bioinformatics. 2015 Feb 1;31(3):432-3. doi: 10.1093/bioinformatics/btu648. Epub 2014 Oct 1.

PMID:
25273112
17.

Tumor phylogeny inference using tree-constrained importance sampling.

Satas G, Raphael BJ.

Bioinformatics. 2017 Jul 15;33(14):i152-i160. doi: 10.1093/bioinformatics/btx270.

18.

DiffGraph: an R package for identifying gene network rewiring using differential graphical models.

Zhang XF, Ou-Yang L, Yang S, Hu X, Yan H.

Bioinformatics. 2018 May 1;34(9):1571-1573. doi: 10.1093/bioinformatics/btx836.

PMID:
29309511
19.

QuantumClone: clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction.

Deveau P, Colmet Daage L, Oldridge D, Bernard V, Bellini A, Chicard M, Clement N, Lapouble E, Combaret V, Boland A, Meyer V, Deleuze JF, Janoueix-Lerosey I, Barillot E, Delattre O, Maris JM, Schleiermacher G, Boeva V.

Bioinformatics. 2018 Jun 1;34(11):1808-1816. doi: 10.1093/bioinformatics/bty016.

20.

Rcupcake: an R package for querying and analyzing biomedical data through the BD2K PIC-SURE RESTful API.

Gutiérrez-Sacristán A, Guedj R, Korodi G, Stedman J, Furlong LI, Patel CJ, Kohane IS, Avillach P.

Bioinformatics. 2018 Apr 15;34(8):1431-1432. doi: 10.1093/bioinformatics/btx788.

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