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Items: 17

1.

Enumeration of minimal stoichiometric precursor sets in metabolic networks.

Andrade R, Wannagat M, Klein CC, Acuña V, Marchetti-Spaccamela A, Milreu PV, Stougie L, Sagot MF.

Algorithms Mol Biol. 2016 Sep 19;11:25. doi: 10.1186/s13015-016-0087-3. eCollection 2016.

2.

A Combinatorial Algorithm for Microbial Consortia Synthetic Design.

Julien-Laferrière A, Bulteau L, Parrot D, Marchetti-Spaccamela A, Stougie L, Vinga S, Mary A, Sagot MF.

Sci Rep. 2016 Jul 4;6:29182. doi: 10.1038/srep29182.

3.

WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads.

Patterson M, Marschall T, Pisanti N, van Iersel L, Stougie L, Klau GW, Schönhuth A.

J Comput Biol. 2015 Jun;22(6):498-509. doi: 10.1089/cmb.2014.0157. Epub 2015 Feb 6.

4.

Fast flux module detection using matroid theory.

Reimers AC, Bruggeman FJ, Olivier BG, Stougie L.

J Comput Biol. 2015 May;22(5):414-24. doi: 10.1089/cmb.2014.0141. Epub 2015 Jan 7.

PMID:
25565150
5.

Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure.

Milreu PV, Klein CC, Cottret L, Acuña V, Birmelé E, Borassi M, Junot C, Marchetti-Spaccamela A, Marino A, Stougie L, Jourdan F, Crescenzi P, Lacroix V, Sagot MF.

Bioinformatics. 2014 Jan 1;30(1):61-70. doi: 10.1093/bioinformatics/btt597. Epub 2013 Oct 27.

6.

Ancient dispersal of the human fungal pathogen Cryptococcus gattii from the Amazon rainforest.

Hagen F, Ceresini PC, Polacheck I, Ma H, van Nieuwerburgh F, Gabaldón T, Kagan S, Pursall ER, Hoogveld HL, van Iersel LJ, Klau GW, Kelk SM, Stougie L, Bartlett KH, Voelz K, Pryszcz LP, Castañeda E, Lazera M, Meyer W, Deforce D, Meis JF, May RC, Klaassen CH, Boekhout T.

PLoS One. 2013 Aug 7;8(8):e71148. doi: 10.1371/journal.pone.0071148. Print 2013.

7.

A realistic model under which the genetic code is optimal.

Buhrman H, van der Gulik PT, Klau GW, Schaffner C, Speijer D, Stougie L.

J Mol Evol. 2013 Oct;77(4):170-84. doi: 10.1007/s00239-013-9571-2. Epub 2013 Jul 23.

PMID:
23877342
8.

Networks: expanding evolutionary thinking.

Bapteste E, van Iersel L, Janke A, Kelchner S, Kelk S, McInerney JO, Morrison DA, Nakhleh L, Steel M, Stougie L, Whitfield J.

Trends Genet. 2013 Aug;29(8):439-41. doi: 10.1016/j.tig.2013.05.007. Epub 2013 Jun 11.

PMID:
23764187
9.

Charge group partitioning in biomolecular simulation.

Canzar S, El-Kebir M, Pool R, Elbassioni K, Mark AE, Geerke DP, Stougie L, Klau GW.

J Comput Biol. 2013 Mar;20(3):188-98. doi: 10.1089/cmb.2012.0239.

10.

Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks.

Kelk SM, Olivier BG, Stougie L, Bruggeman FJ.

Sci Rep. 2012;2:580. doi: 10.1038/srep00580. Epub 2012 Aug 15.

11.

Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks.

Acuña V, Milreu PV, Cottret L, Marchetti-Spaccamela A, Stougie L, Sagot MF.

Bioinformatics. 2012 Oct 1;28(19):2474-83. Epub 2012 Jul 10.

PMID:
22782547
12.

Some mathematical refinements concerning error minimization in the genetic code.

Buhrman H, van der Gulik PT, Kelk SM, Koolen WM, Stougie L.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Sep-Oct;8(5):1358-72. doi: 10.1109/TCBB.2011.40.

PMID:
21358008
13.

Graph-based analysis of the metabolic exchanges between two co-resident intracellular symbionts, Baumannia cicadellinicola and Sulcia muelleri, with their insect host, Homalodisca coagulata.

Cottret L, Milreu PV, Acuña V, Marchetti-Spaccamela A, Stougie L, Charles H, Sagot MF.

PLoS Comput Biol. 2010 Sep 2;6(9). pii: e1000904. doi: 10.1371/journal.pcbi.1000904.

14.

A note on the complexity of finding and enumerating elementary modes.

Acuña V, Marchetti-Spaccamela A, Sagot MF, Stougie L.

Biosystems. 2010 Mar;99(3):210-4. doi: 10.1016/j.biosystems.2009.11.004. Epub 2009 Dec 3.

PMID:
19962421
15.

Constructing level-2 phylogenetic networks from triplets.

van Iersel L, Keijsper J, Kelk S, Stougie L, Hagen F, Boekhout T.

IEEE/ACM Trans Comput Biol Bioinform. 2009 Oct-Dec;6(4):667-81. doi: 10.1109/TCBB.2009.22.

PMID:
19875864
16.

Modes and cuts in metabolic networks: complexity and algorithms.

Acuña V, Chierichetti F, Lacroix V, Marchetti-Spaccamela A, Sagot MF, Stougie L.

Biosystems. 2009 Jan;95(1):51-60. doi: 10.1016/j.biosystems.2008.06.015. Epub 2008 Aug 3. Review.

PMID:
18722501
17.

Shorelines of islands of tractability: algorithms for parsimony and minimum perfect phylogeny haplotyping problems.

van Iersel L, Keijsper J, Kelk S, Stougie L.

IEEE/ACM Trans Comput Biol Bioinform. 2008 Apr-Jun;5(2):301-12. doi: 10.1109/TCBB.2007.70232.

PMID:
18451439

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