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Items: 1 to 20 of 96

1.

Process-driven inference of biological network structure: feasibility, minimality, and multiplicity.

Wang G, Rong Y, Chen H, Pearson C, Du C, Simha R, Zeng C.

PLoS One. 2012;7(7):e40330. doi: 10.1371/journal.pone.0040330. Epub 2012 Jul 18.

2.

Steady state analysis of Boolean molecular network models via model reduction and computational algebra.

Veliz-Cuba A, Aguilar B, Hinkelmann F, Laubenbacher R.

BMC Bioinformatics. 2014 Jun 26;15:221. doi: 10.1186/1471-2105-15-221.

3.

An algebraic geometry approach to protein structure determination from NMR data.

Wang L, Mettu RR, Donald BR.

Proc IEEE Comput Syst Bioinform Conf. 2005:235-46.

PMID:
16447981
4.

Biological Network Inference from Microarray Data, Current Solutions, and Assessments.

Roy S, Guzzi PH.

Methods Mol Biol. 2016;1375:155-67. doi: 10.1007/7651_2015_284.

PMID:
26507508
5.

Control of Boolean networks: hardness results and algorithms for tree structured networks.

Akutsu T, Hayashida M, Ching WK, Ng MK.

J Theor Biol. 2007 Feb 21;244(4):670-9. Epub 2006 Sep 24.

PMID:
17069859
6.

Reconstruction of ancestral genomic sequences using likelihood.

Elias I, Tuller T.

J Comput Biol. 2007 Mar;14(2):216-37.

PMID:
17456016
7.

Identification of genetic network dynamics with unate structure.

Porreca R, Cinquemani E, Lygeros J, Ferrari-Trecate G.

Bioinformatics. 2010 May 1;26(9):1239-45. doi: 10.1093/bioinformatics/btq120. Epub 2010 Mar 19.

PMID:
20305266
8.

Improving gene regulatory network inference using network topology information.

Nair A, Chetty M, Wangikar PP.

Mol Biosyst. 2015 Sep;11(9):2449-63. doi: 10.1039/c5mb00122f. Epub 2015 Jul 1.

PMID:
26126758
9.

A parallel attractor-finding algorithm based on Boolean satisfiability for genetic regulatory networks.

Guo W, Yang G, Wu W, He L, Sun M.

PLoS One. 2014 Apr 9;9(4):e94258. doi: 10.1371/journal.pone.0094258. eCollection 2014.

10.

CollHaps: a heuristic approach to haplotype inference by parsimony.

Tininini L, Bertolazzi P, Godi A, Lancia G.

IEEE/ACM Trans Comput Biol Bioinform. 2010 Jul-Sep;7(3):511-23. doi: 10.1109/TCBB.2008.130.

PMID:
20671321
11.
12.

Reconstructing ancestral genomic sequences by co-evolution: formal definitions, computational issues, and biological examples.

Tuller T, Birin H, Kupiec M, Ruppin E.

J Comput Biol. 2010 Sep;17(9):1327-44. doi: 10.1089/cmb.2010.0112.

PMID:
20874411
13.

An efficient algorithm for haplotype inference on pedigrees with recombinations and mutations.

Pirola Y, Bonizzoni P, Jiang T.

IEEE/ACM Trans Comput Biol Bioinform. 2012 Jan-Feb;9(1):12-25. doi: 10.1109/TCBB.2011.51. Epub 2011 Mar 3.

PMID:
21383417
14.

Pure parsimony xor haplotyping.

Bonizzoni P, Della Vedova G, Dondi R, Pirola Y, Rizzi R.

IEEE/ACM Trans Comput Biol Bioinform. 2010 Oct-Dec;7(4):598-610. doi: 10.1109/TCBB.2010.52.

PMID:
20498511
15.

Predicting RNA secondary structures with arbitrary pseudoknots by maximizing the number of stacking pairs.

Ieong S, Kao MY, Lam TW, Sung WK, Yiu SM.

J Comput Biol. 2003;10(6):981-95.

PMID:
14980021
16.

Sets2Networks: network inference from repeated observations of sets.

Clark NR, Dannenfelser R, Tan CM, Komosinski ME, Ma'ayan A.

BMC Syst Biol. 2012 Jul 23;6:89. doi: 10.1186/1752-0509-6-89.

17.

Solving satisfiability problems using a novel microarray-based DNA computer.

Lin CH, Cheng HP, Yang CB, Yang CN.

Biosystems. 2007 Jul-Aug;90(1):242-52. Epub 2006 Aug 30.

PMID:
17029765
18.

Hub-centered gene network reconstruction using automatic relevance determination.

Böck M, Ogishima S, Tanaka H, Kramer S, Kaderali L.

PLoS One. 2012;7(5):e35077. doi: 10.1371/journal.pone.0035077. Epub 2012 May 3.

19.

A new fast algorithm for solving the minimum spanning tree problem based on DNA molecules computation.

Wang Z, Huang D, Meng H, Tang C.

Biosystems. 2013 Oct;114(1):1-7. doi: 10.1016/j.biosystems.2013.07.007. Epub 2013 Jul 16.

20.

Computing a smallest multilabeled phylogenetic tree from rooted triplets.

Guillemot S, Jansson J, Sung WK.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Jul-Aug;8(4):1141-7. doi: 10.1109/TCBB.2010.77.

PMID:
20733243

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