Maximum likelihood estimation of incomplete genomic spectrum from HTS data

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

Volumn 6833 LNBI, Issue , 2011, Pages 213-224

  Mangul, Serghei ^a   Astrovskaya, Irina ^a   Nicolae, Marius ^b   Tork, Bassam ^a   Mandoiu, Ion ^b   Zelikovsky, Alex ^a  

^a GEORGIA STATE UNIVERSITY   (United States)

^b University of Connecticut   (United States)

Author keywords

expectation maximization; high throughput sequencing; RNA Sequencing; viral quasispecies

Indexed keywords

EXPECTATION MAXIMIZATION; EXPECTATION-MAXIMIZATION METHOD; GENOMIC SEQUENCE; HIGH-THROUGHPUT; ISOFORMS; QUASISPECIES; RNA-SEQUENCING;

ALGORITHMS; BIOINFORMATICS; ESTIMATION; FREQUENCY ESTIMATION; GENES; MAXIMUM PRINCIPLE; RNA;

MAXIMUM LIKELIHOOD ESTIMATION;

EID: 80052996140     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-23038-7_19     Document Type: Conference Paper

References (10)

1. Astrovskaya, I., Tork, B., Mangul, S., Westbrooks, K., Mandoiu, I., Balfe, P., Zelikovsky, A.: Inferring viral spectrum from 454 pyrosequencing reads. BMC Bioinformatics (to appear), http://dna.engr.uconn.edu/bibtexmngr/ upload/Aal.11a.pdf
2. Balser, S., Malde, K., Lanzen, A., Sharma, A., Jonassen, I.: Characteristics of 454 pyrosequencing data-enabling realistic simulation with flowsim. Bioinformatics 26, i420-i425 (2010)
3. Zaitlen, N., Pasaniuc, B., Halperin, E.: Accurate estimation of expression levels of homologous genes in RNA-seq experiments. Journal of Computational Biology 18(3), 459-468 (2011)
4. Eriksson, N., Pachter, L., Mitsuya, Y., Rhee, S.Y., Wang, C.: et al. Viral population estimation using pyrosequencing. PLoS Comput. Biol. 4, e1000074 (2008)
5. Von Hahn, T., Yoon, J.C., Alter, H., Rice, C.M., Rehermann, B., Balfe, P., Mckeating, J.A.: Hepatitis c virus continuously escapes from neutralizing antibody and t-cell responses during chronic infection in vivo. Gastroenterology 132, 667-678 (2007)
6. Hoffmann, S., Otto, C., Kurtz, S., Sharma, C.M., Khaitovich, P., Vogel, J., Stadler, P.F., Hackermüller, J.: Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comput. Biol. 5(9), e1000502 (2009)
7. Li, B., Ruotti, V., Stewart, R.M., Thomson, J.A., Dewey, C.N.: RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics 26(4), 493-500 (2010)
8. Nicolae, M., Mangul, S., Mandoiu, I.I., Zelikovsky, A.: Estimation of alternative splicing isoform frequencies from RNA-seq data. Algorithms for Molecular Biology 6, 9 (2011)
9. Mortazavi, A., Williams, B.A.A., McCue, K., Schaeffer, L., Wold, B.: Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature methods (2008)
10. Zagordi, O., Geyrhofer, L., Roth, V., Beerenwinkel, N.: Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction. Journal of Computational Biology: A Journal of ComputationalMolecular Cell Biology 17(3), 417-428 (2010)