Building a pangenome reference for a population

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 8394 LNBI, Issue , 2014, Pages 207-221

  Nguyen, Ngan ^a   Hickey, Glenn ^a   Zerbino, Daniel R ^b   Raney, Brian ^a   Earl, Dent ^a   Armstrong, Joel ^a   Haussler, David ^a,c   Paten, Benedict ^a  

^a University of California Santa Cruz   (United States)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HEURISTIC ALGORITHMS; MOLECULAR BIOLOGY; SOFTWARE TESTING;

CACTUS GRAPHS; CO-ORDINATE SYSTEM; GENOME BROWSERS; HIGH QUALITY; MAXIMAL SOLUTION; NP-HARD; WHOLE GENOME ALIGNMENT;

GENES;

EID: 84958551166     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-319-05269-4_17     Document Type: Conference Paper

References (18)

1. Coffey, A.J., Kokocinski, F., Calafato, M.S., Scott, C.E., Palta, P., Drury, E., Joyce, C.J., Leproust, E.M., Harrow, J., Hunt, S., Lehesjoki, A.E., Turner, D.J., Hubbard, T.J., Palotie, A.: The gencode exome: Sequencing the complete human exome. Eur. J. Hum. Genet. 19(7), 827-831 (2011
2. Myers, R.M., Stamatoyannopoulos, J., Snyder, M., Dunham, I., Hardison, R.C., Bernstein, B.E., Gingeras, T.R., Kent,W.J., Birney, E., Wold, B., Crawford, G.E.: A user's guide to the encyclopedia of dna elements (encode). PLoS Biol. 9(4), e1001046 (2011); ENCODE-Project-Consortium 3. 1000-Genomes-Project-Consortium: A map of human genome variation from population-scale sequencing. Nature 467(7319), 1061-1073 (October 2010
3. Paten, B., Earl, D., Nguyen, N., Diekhans, M., Zerbino, D., Haussler, D.: Cactus: Algorithms for genome multiple sequence alignment. Genome Res. 21(9), 1512-1528 (2011
4. Meyer, L.R., et al.: The UCSC Genome Browser database: Extensions and updates 2013. Nucleic Acids Research, 64-69 (2013
5. Tannier, E., Zheng, C., Sankoff, D.: Multichromosomal median and halving problems under different genomic distances. BMC Bioinformatics 10, 120 (2009
6. Kirkpatrick, M.: How and why chromosome inversions evolve. PLoS Biol. 8(9) (January 2010
7. Berard, S., Chateau, A., Chauve, C., Paul, C., Tannier, E.: Computation of perfect dcj rearrangement scenarios with linear and circular chromosomes. Journal of Computational Biology 16(10), 1287-1309 (2009
8. Fagin, R., Kumar, R., Sivakumar, D.: Comparing Top k Lists. SIAMJ. Discrete Math. 17(1), 134-160 (2002
9. Kendall, M.: A new measure of rank correlation. Biometrika 30(1/2), 81-93 (1938
10. Bertrand, D., Blanchette, M., El-Mabrouk, N.: Genetic map refinement using a comparative genomic approach. J. Comput. Biol. 16(10), 1475-1486 (2009
11. Paten, B., Diekhans, M., Earl, D., John, J.S., Ma, J., Suh, B., Haussler, D.: Cactus graphs for genome comparisons. J. Comput. Biol. 18(3), 469-481 (2011
12. Medvedev, P., Brudno, M.: Maximum likelihood genome assembly. J. Comput. Biol. 16(8), 1101-1116 (2009
13. Griffiths, A.J.F., Miller, J.H., Suzuki, D.T.: An introduction to genetic analysis (January 1999
14. Karp, R.: Reducibility among combinatorial problems. Plenum (Complexity of Computer Computations), 85-103 (January 1972
15. Newman, A.: Max-cut. Encyclopedia of Algorithms 1, 489-492 (2008
16. Erdos, P., Ŕenyi, A.: On the evolution of random graphs. Publications of the Mathematical Institute of the Hungarian Academy of Sciences 5, 17-61 (1960
17. Xu, A.W.: A fast and exact algorithm for the median of three problem: A graph decomposition approach. J. Comput. Biol. 16(10), 1369-1381 (2009
18. Hickey, G., Paten, B., Earl, D., Zerbino, D., Haussler, D.: HAL: A hierarchical format for storing and analyzing multiple genome alignments. Bioinformatics 29(10), 1341-1342 (2013