A simple greedy algorithm for reconstructing pedigrees

Theoretical Population Biology

Volumn 83, Issue 1, 2013, Pages 55-63

  Cowell, Robert G ^a  

^a CITY UNIVERSITY   (United Kingdom)

Author keywords

Greedy search; Maximum likelihood pedigree; Pedigree reconstruction

Indexed keywords

MICROSATELLITE DNA;

ALGORITHM; GENETIC ANALYSIS; GENETIC MARKER; MAXIMUM LIKELIHOOD ANALYSIS; RECONSTRUCTION;

ALGORITHM; ARTICLE; GENETICS; STATISTICAL MODEL;

ALGORITHMS; LIKELIHOOD FUNCTIONS; MICROSATELLITE REPEATS;

EID: 84873464244     PISSN: 00405809     EISSN: 10960325     Source Type: Journal    
DOI: 10.1016/j.tpb.2012.11.002     Document Type: Article

References (24)

1. Achterberg T. SCIP: Solving constraint integer programs. Mathematical Programming Computation 2009, 1:1-41.
2. Almudevar A. A simulated annealing algorithm for maximum likelihood pedigree reconstruction. Theoretical Population Biology 2003, 63:63-75.
3. Almudevar A., LaCombe J. On the choice of prior density for the Bayesian analysis of pedigree structure. Theoretical Population Biology 2012, 81:131-143.
4. Blouin M.S. DNA-based methods for pedigree reconstruction and kinship analysis in natural populations. TRENDS in Ecology and Evolution 2003, 18(10):503-511.
5. Cowell R.G. Efficient maximum likelihood pedigree reconstruction. Theoretical Population Biology 2009, 76:285-291.
6. Cussens, J., 2010. Maximum likelihood pedigree reconstruction using integer programming. in: Proceedings of the Workshop on Constraint Based Methods for Bioinformatics (WCB-10) Edinburgh.
7. Cussens, J., Bartlett, M., Jones, E.M., Sheehan, N.A., 2012. Maximum likelihood pedigree reconstruction using integer linear programming. Genetic Epidemiology, in press (). http://dx.doi.org/10.1002/gepi.21686.
8. Egeland T., Mostad P.F., Mevåg B., Stenersen M. Beyond traditional paternity and identification cases: Selecting the most probable pedigree. Forensic Science International 2000, 110:47-59.
9. Gill P., Ivanov P.L., Kimpton C., Piercy R., Benson N., Tully G., Evett I., Hagelberg E., Sullivan K. Identification of the remains of the Romanov family by DNA analysis. Nature Genetics 1994, 6:130-135.
10. Hadfield J.D., Richardson D.S., Burke T. Towards unbiased parentage assignment: combining genetic, behavioural and spatial data in a Bayesian framework. Molecular Ecology 2006, 15(12):3715-3730. URL http://dx.doi.org/10.1111/j.1365-294X.2006.03050.x.
11. Jerry D.R., Evansa B.S., Kenway M., Wilson K. Development of a microsatellite DNA parentage marker suite for black tiger shrimp penaeus monodon. Aquaculture 2005, 255:1-4.
12. Jones A.G., Ardren W.R. Methods of parentage analysis in natural populations. Molecular Ecology 2003, 12:2511-2523.
13. Kruskal J.B. On the shortest spanning subtree of a graph and the traveling salesman problem. Proceedings of the American Mathematical Society 1956, 7(1):48-50.
14. Lawler E. A procedure for computing the K best solutions to discrete optimization problems and its application to the shortest path. Management Science 1972, 7:401-405.
15. Murty K.G. An algorithm for ranking all the assignments in order of increasing cost. Operations Research 1968, 16(3):682-687.
16. Nilsson D. An efficient algorithm for finding the M most probable configurations in a probabilistic expert system. Statistics and Computing 1998, 8:159-173.
17. Pemberton J.M. Wild pedigrees: the way forward. Proceedings of the Royal Society, Series B 2008, 275:613-621.
18. Riester M., Stadler P.F., Klemm K. FRANz: fast reconstruction of wild pedigrees. Bioinformatics 2009, 25:2134-2139.
19. Sheehan N.A., Egeland T. Structured incorporation of prior information in relationship identification problems. Annals of Human Genetics 2007, 71(Pt 4):501-518. URL http://dx.doi.org/10.1111/j.1469-1809.2006.00345.x.
20. Silander T., Myllymäkki P. A simple approach to finding the globally optimal Bayesian network structure. Proceedings of the 22nd Conference on Artificial intelligence 2006, 445-452. AUAI Press. R. Dechter, T. Richardson (Eds.).
21. Sörensen K., Janssens G.K. An algorithm to generate all spanning trees of a graph in order of increasing cost. Pesquisa Operacional 2005, 25(2):219-229.
22. Thompson E.A. Inference of genealogical structure. Social Science Information sur les Sciences Social 1976, 15:477-526.
23. Thompson E.A. Pedigree Analysis in Human Genetics 1986, John Hopkins University Press, Baltimore.
24. Tian J., He R., Ram L. Bayesian model averaging using the k-best Bayesian network structures. Proceedings of the 26th Conference on Uncertainty in Artificial Intelligence 2010, AUAI Press. P. Grünwald, P. Spirtes (Eds.).