Searching journal content for articles similar to Alexandersson et al. 13 (3): 496.

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  1. Methods: Græmlin: General and robust alignment of multiple large interaction networks
    • Jason Flannick,
    • Antal Novak,
    • Balaji S. Srinivasan,
    • Harley H. McAdams,
    • and Serafim Batzoglou
    Genome Res. September 2006 16: 1169-1181; Published in Advance August 9, 2006, doi:10.1101/gr.5235706
    ...previous methods while improving sensitivity. The publication of the second complete sequence in 1995 ( Kaneko et al. 1995 ) ushered in the era of computational comparative genomics. The years that followed saw the application of cross-species genomic comparisons to problems ranging from gene prediction...
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  2. RESOURCE: Iterative gene prediction and pseudogene removal improves genome annotation
    • Marijke J. van Baren and
    • Michael R. Brent
    Genome Res. May 2006 16: 678-685; doi:10.1101/gr.4766206
    ...with a generalized pair hidden Markov model. Genome Res. 13 : 496 – 502 . ↵ Ashurst J.L. , Chen C.K. , Gilbert J.G. , Jekosch K. , Keenan S. , Meidl P. , Searle S.M. , Stalker J. , Storey R. , Trevanion S. , et al. ( 2005 ) The Vertebrate Genome Annotation (Vega) database. Nucleic Acids Res. 33 : D459 – D465...
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  3. Methods: Human–Mouse Gene Identification by Comparative Evidence Integration and Evolutionary Analysis
    • Lingang Zhang,
    • Vladimir Pavlovic,
    • Charles R Cantor,
    • and Simon Kasif
    Genome Res. June 2003 13: 1190-1202; Published in Advance May 12, 2003, doi:10.1101/gr.703903
    ...Networks ( Pavlovic et al. 2002 ), Product-HMMs (Hidden Markov Model) ( Walker et al. 2002 ), Generalized HMMs ( Korf et al. 2001 ; Yeh et al. 2001 ), and Pair-HMMs/Generalized Pair-HMMs ( Pachter et al. 2002 ). Here, we demonstrate the integration of different sources of evidence with the Bayesian network...
  4. Method: A unified model for yeast transcript definition
    • Carl G. de Boer,
    • Harm van Bakel,
    • Kyle Tsui,
    • Joyce Li,
    • Quaid D. Morris,
    • Corey Nislow,
    • Jack F. Greenblatt,
    • and Timothy R. Hughes
    Genome Res. January 2014 24: 154-166; Published in Advance October 29, 2013, doi:10.1101/gr.164327.113
    ...of the genome using a hidden Markov model whose emissions are the outputs of the initiation and termination classifiers. We validated the novel predictions of the UM with available RNA-seq data and tested it further by directly comparing the transcript structure predicted by the model to the transcription...
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  5. ENSEMBL Special: GeneWise and Genomewise
    • Ewan Birney,
    • Michele Clamp,
    • and Richard Durbin
    Genome Res. May 2004 14: 988-995; doi:10.1101/gr.1865504
    ...gene finding and alignment with a generalized pair hidden Markov model. Genome Res. 13 : 496 -502. ↵ Aparicio, S., Chapman, J., Stupka, E., Putnam, N., Chia, J.-M., Dehal, P., Christoffels, A., Rash, S., Hoon, S., Smit, A., et al. 2002 . Whole- shotgun assembly and analysis of the of Fugu rubripes...
  6. COMMENTARY: Confidence in comparative genomics
    • Elliott H. Margulies
    Genome Res. February 2008 18: 199-200; doi:10.1101/gr.7228008
    ...↵ Alexandersson, M. , Cawley, S. , Pachter, L. ( 2003 ) SLAM: Cross-species gene finding and alignment with a generalized pair hidden Markov model . Genome Res. 13 : 496 – 502 . ↵ Blanchette, M. , Tompa, M. ( 2002 ) Discovery of regulatory elements by a computational method for phylogenetic footprinting . Genome...
  7. RESOURCE: Visualization of Multiple Genome Annotations and Alignments With the K-BROWSER
    • Kushal Chakrabarti and
    • Lior Pachter
    Genome Res. April 2004 14: 716-720; doi:10.1101/gr.1957004
    ...-MAIL lpachter@math.berkeley.edu ; FAX (510) 642-8204. Accepted November 17, 2003. Received September 10, 2003. Cold Spring Harbor Laboratory Press References ↵ Alexandersson, M., Cawley, S., and Pachter, L. 2003 . SLAM: Cross-species gene finding and alignment with a generalized pair hidden Markov model. Genome...
  8. Methods: Genome-wide nucleotide-level mammalian ancestor reconstruction
    • Benedict Paten,
    • Javier Herrero,
    • Stephen Fitzgerald,
    • Kathryn Beal,
    • Paul Flicek,
    • Ian Holmes,
    • and Ewan Birney
    Genome Res. November 2008 18: 1829-1843; Published in Advance October 10, 2008, doi:10.1101/gr.076521.108
    ...in turn. To define the σ function, we use the intuitive theory of evolutionary transducers, a subclass of hidden Markov model (HMM) recently introduced within biological sequence analysis ( Holmes 2003 ). We start by briefly and informally describing a probabilistic branch transducer, which models...
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  9. PERSPECTIVE: Genome annotation past, present, and future: How to define an ORF at each locus
    • Michael R. Brent
    Genome Res. December 2005 15: 1777-1786; doi:10.1101/gr.3866105
    ...De novo gene prediction, in its modern form, also appeared in the mid-1990s. Stormo and Haussler ( 1994 ) described the first Generalized Hidden Markov model (GHMM) for gene prediction. GHMMs are mathematical models that can be used to define probabilities for all possible exon-intron annotations...
  10. LETTER: Comparison of Human Chromosome 21 Conserved Nongenic Sequences (CNGs) With the Mouse and Dog Genomes Shows That Their Selective Constraint Is Independent of Their Genic Environment
    • Emmanouil T. Dermitzakis,
    • Ewen Kirkness,
    • Scott Schwarz,
    • Ewan Birney,
    • Alexandre Reymond,
    • and Stylianos E. Antonarakis
    Genome Res. May 2004 14: 852-859; Published in Advance April 12, 2004, doi:10.1101/gr.1934904
    ...., Cawley, S., and Pachter, L. 2003 . SLAM: Cross-species gene finding and alignment with a generalized pair Hidden Markov Model. Genome Res. 13 : 496 -502. ↵ Boffelli, D., McAuliffe, J., Ovcharenko, D., Lewis, K.D., Ovcharenko, I., Pachter, L., and Rubin, E.M. 2003 . Phylogenetic shadowing of primate...
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