Combinatorial reconstruction of half-sibling groups from microsatellite data

Journal of Bioinformatics and Computational Biology

Volumn 8, Issue 2, 2010, Pages 337-356

  Sheikh, Saad I ^a   Berger Wolf, Tanya Y ^a   Khokhar, Ashfaq A ^a   Caballero, Isabel C ^b   Ashley, Mary V ^b   Chaovalitwongse, Wanpracha ^c   Chou, Chun An ^c   Dasgupta, Bhaskar ^a  

^a 1120 Science and Engineering Offices   (United States)

^b UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

^c DEPARTMENT OF INDUSTRIAL AND SYSTEMS ENGINEERING   (United States)

Author keywords

Combinatorial optimization; Genetics; Kinship analysis; Mating systems; Microsatellite markers; Molecular ecology; Parsimony; Population genetics; Wild populations

Indexed keywords

MICROSATELLITE DNA;

ALGORITHM; ALLELE; ANIMAL; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; COMPUTER PROGRAM; FEMALE; FISH; GENETIC DATABASE; GENETICS; GRYLLIDAE; MALE; SIBLING; STATISTICAL MODEL;

ALGORITHMS; ALLELES; ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; FEMALE; FISHES; GRYLLIDAE; MALE; MICROSATELLITE REPEATS; MODELS, GENETIC; MODELS, STATISTICAL; SIBLINGS; SOFTWARE;

EID: 77951607501     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720010004793     Document Type: Article

References (26)

1. Queller DC, Goodnight KF, Estimating relatedness using genetic markers, Evolution 43(2):258-275, 1989.
2. Blouin MS, DNA-based methods for pedigree reconstruction and kinship analysis in natural populations, TRENDS in Ecology and Evolution 18:503-511, 2003.
3. Queller DC, Goodnight KF, Computer software for performing likelihood tests of pedigree relationship using genetic markers, Mol Ecol 8(7):1231-1234, 1999.
4. Beyer J, May B, A graph-theoretic approach to the partition of individuals into full-sib families, Mol Ecol 12:2243-2250, 2003.
5. Wang J, Sibship reconstruction from genetic data with typing errors, Genetics 166:1968-1979, 2004.
6. Almudevar A, Field C, Estimation of single generation sibling relationships based on DNA markers, Journal of Agricultural, Biological, and Environmental Statistics 4:136-165, 1999.
7. Almudevar A, A simulated annealing algorithm for maximum likelihood pedigree reconstruction, Theoretical Population Biology 63, 2003.
8. Thomas SC and Hill WG, Sibship reconstruction in hierarchical population structures using markov chain monte carlo techniques, Genetics Res 79:227-234, 2002.
9. Chaovalitwongse W, Berger-Wolf TY, Dasgupta B, Ashley MV, Set covering approach for reconstruction of sibling relationships, Optimization Methods and Software 22(1):11-24, 2007.
10. Berger-Wolf TY, DasGupta B, Chaovalitwongse W, Ashley MV, Combinatorial reconstruction of sibling relationships, in Proceedings of the 6th International Symposium on Computational Biology and Genome Informatics (CBGI 05), pp. 1252-1255, Utah, 2005.
11. Chaovalitwongse WA, Chou C-A, Berger-Wolf TY, Dasgupta B, Sheikh S, Ashley MV, Caballero IC, New optimization model and algorithm for sibling reconstruction from genetic markers, INFORMS Journal On Computing, (to appear), 2009.
12. Berger-Wolf TY, Sheikh SI, Dasgupta B, Ashley MV, Caballero IC, Chaovalitwongse W, Lahari SP, Reconstructing sibling relationships in wild populations, Bioinformatics 23(13):49-56, 2007.
13. Sheikh SI, Berger-Wolf TY, Ashley MV, Caballero IC, Chaovalitwongse W, DasGupta B, Error-tolerant sibship reconstruction in wild populations, in Proc 7th Ann Int Conf Computat Systems Bioinformatics (CSB), 2008.
14. Sheikh SI, Berger-Wolf TT, Chaovalitwongse W, Ashley MV, Reconstructing sibling relationships from microsatellite data, in Proc European Conf Computat Biol (ECCB), 2007.
15. Casteele V DE T, Matthysen E, Natal dispersal and parental escorting predict relatedness between mates in a passerine bird, Mol Ecol 15:2557-2565, 2006.
16. Wang J, Santure AW, Parentage and sibship inference from multi-locus genotype data under polygamy, Genetics 181:1579-1594, 2009.
17. Konovalov DA, Manning C, Henshaw MT, KINGROUP: A program for pedigree relationship reconstruction and kin group assignments using genetic markers, Mol Ecol Notes 4(4):779-782, 2004.
18. Herbinger CM, O'Reilly PT, Doyle RW, Wright JM, O'Flynn F, Early growth performance of atlantic salmon full-sib families reared in single family tanks versus in mixed family tanks, Aquaculture 173(1-4):105-116, 1999.
19. Wilson AJ, McDonald G, Moghadam HK, Herbinger CM, Ferguson MM, Marker-assisted estimation of quantitative genetic parameters in rainbow trout, Oncorhynchus mykiss, Genetics Res 81:145-156, 2003.
20. Thomas SC, Hill WG, Estimating Quantitative Genetic Parameters Using Sibships Reconstructed From Marker Data, Genetics 155:1961-1972, 2000.
21. Ashley M, Berger-Wolf T, Berman P, Chaovalitwongse W, DasGupta B, Kao MY, On approximating four covering and packing problems, J Computer System Sci 75:287-302, 2009.
22. Karp RM, Reducibility among combinatorial problems, in Miller RE, Thatcher JW (eds.), Complexity of Computer Computations, pp. 85-103, Plenum Press, 1972.
23. Bretman A, Tregenza T, Measuring polyandry in wild populations: A case study using promiscuous crickets, Mol Ecol 14:2169-2179, 2005.
24. Sogard SM, Gilbert-Horvath E, Anderson EC, Fisher R, Berkeley SA, Carlos Garza J, Multiple paternity in viviparous kelp rockfish, Sebastes Atrovirens, Environmental Biology of Fishes 81:7-13, 2008.
25. Gusfield D, Partition-distance: A problem and class of perfect graphs arising in clustering, Inf Process Lett 82(3):159-164, 2002.
26. Sheikh SI, Khokhar AA, Berger-Wolf TY, Efficient and scalable parallel reconstruction of sibling relationships from genetic data in wild-populations, in Proceedings of the Ninth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2010), 2010.