PubMed

GraphCrunch: a tool for large network analyses.

Milenković T, Lai J, Przulj N.

BMC Bioinformatics. 2008 Jan 30;9:70.PMID: 18230190 [PubMed - indexed for MEDLINE]Related articlesFree article

Biological network comparison using graphlet degree distribution.

Przulj N.

Bioinformatics. 2007 Jan 15;23(2):e177-83.PMID: 17237089 [PubMed - indexed for MEDLINE]Related articlesFree article

ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining.

Huan T, Sivachenko AY, Harrison SH, Chen JY.

BMC Bioinformatics. 2008 Aug 12;9 Suppl 9:S5.PMID: 18793469 [PubMed - indexed for MEDLINE]Related articlesFree article

Exploration of biological network centralities with CentiBiN.

Junker BH, Koschützki D, Schreiber F.

BMC Bioinformatics. 2006 Apr 21;7:219.PMID: 16630347 [PubMed - indexed for MEDLINE]Related articlesFree article

Efficient estimation of graphlet frequency distributions in protein-protein interaction networks.

Przulj N, Corneil DG, Jurisica I.

Bioinformatics. 2006 Apr 15;22(8):974-80. Epub 2006 Feb 1.PMID: 16452112 [PubMed - indexed for MEDLINE]Related articlesFree article

Modeling interactome: scale-free or geometric?

Przulj N, Corneil DG, Jurisica I.

Bioinformatics. 2004 Dec 12;20(18):3508-15. Epub 2004 Jul 29.PMID: 15284103 [PubMed - indexed for MEDLINE]Related articlesFree article

Fitting a geometric graph to a protein-protein interaction network.

Higham DJ, Rasajski M, Przulj N.

Bioinformatics. 2008 Apr 15;24(8):1093-9. Epub 2008 Mar 14.PMID: 18344248 [PubMed - indexed for MEDLINE]Related articlesFree article

Cytoscape ESP: simple search of complex biological networks.

Ashkenazi M, Bader GD, Kuchinsky A, Moshelion M, States DJ.

Bioinformatics. 2008 Jun 15;24(12):1465-6. Epub 2008 Apr 28.PMID: 18445605 [PubMed - indexed for MEDLINE]Related articlesFree article

Exploring biological network structure using exponential random graph models.

Saul ZM, Filkov V.

Bioinformatics. 2007 Oct 1;23(19):2604-11. Epub 2007 Jul 20.PMID: 17644557 [PubMed - indexed for MEDLINE]Related articlesFree article

SAGA: a subgraph matching tool for biological graphs.

Tian Y, McEachin RC, Santos C, States DJ, Patel JM.

Bioinformatics. 2007 Jan 15;23(2):232-9. Epub 2006 Nov 16.PMID: 17110368 [PubMed - indexed for MEDLINE]Related articlesFree article

Modularization of biochemical networks based on classification of Petri net t-invariants.

Grafahrend-Belau E, Schreiber F, Heiner M, Sackmann A, Junker BH, Grunwald S, Speer A, Winder K, Koch I.

BMC Bioinformatics. 2008 Feb 8;9:90.PMID: 18257938 [PubMed - indexed for MEDLINE]Related articlesFree article

COPASI--a COmplex PAthway SImulator.

Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, Kummer U.

Bioinformatics. 2006 Dec 15;22(24):3067-74. Epub 2006 Oct 10.PMID: 17032683 [PubMed - indexed for MEDLINE]Related articlesFree article

Graph theoretic modeling of large-scale semantic networks.

Bales ME, Johnson SB.

J Biomed Inform. 2006 Aug;39(4):451-64. Epub 2005 Dec 15. Review.PMID: 16442849 [PubMed - indexed for MEDLINE]Related articles

Modeling biochemical transformation processes and information processing with Narrator.

Mandel JJ, Fuss H, Palfreyman NM, Dubitzky W.

BMC Bioinformatics. 2007 Mar 27;8:103.PMID: 17389034 [PubMed - indexed for MEDLINE]Related articlesFree article

FANMOD: a tool for fast network motif detection.

Wernicke S, Rasche F.

Bioinformatics. 2006 May 1;22(9):1152-3. Epub 2006 Feb 2.PMID: 16455747 [PubMed - indexed for MEDLINE]Related articlesFree article

BioNetBuilder: automatic integration of biological networks.

Avila-Campillo I, Drew K, Lin J, Reiss DJ, Bonneau R.

Bioinformatics. 2007 Feb 1;23(3):392-3. Epub 2006 Nov 30.PMID: 17138585 [PubMed - indexed for MEDLINE]Related articlesFree article

Hierarchical modularity of nested bow-ties in metabolic networks.

Zhao J, Yu H, Luo JH, Cao ZW, Li YX.

BMC Bioinformatics. 2006 Aug 18;7:386.PMID: 16916470 [PubMed - indexed for MEDLINE]Related articlesFree article

AVIS: AJAX viewer of interactive signaling networks.

Berger SI, Iyengar R, Ma'ayan A.

Bioinformatics. 2007 Oct 15;23(20):2803-5. Epub 2007 Sep 12.PMID: 17855420 [PubMed - indexed for MEDLINE]Related articlesFree article

CAGER: classification analysis of gene expression regulation using multiple information sources.

Ruan J, Zhang W.

BMC Bioinformatics. 2005 May 12;6:114.PMID: 15890068 [PubMed - indexed for MEDLINE]Related articlesFree article

MannDB - a microbial database of automated protein sequence analyses and evidence integration for protein characterization.

Zhou CL, Lam MW, Smith JR, Zemla AT, Dyer MD, Kuczmarski TA, Vitalis EA, Slezak TR.

BMC Bioinformatics. 2006 Oct 17;7:459.PMID: 17044936 [PubMed - indexed for MEDLINE]Related articlesFree article