Papers and Other Reference Materials |
The best tutorial on HMMs
A Tutorial on Hidden Markov Models and Selected Applications in Speech Recognition (PDF)
Gene Finding
- Genscan: Prediction of Complete Gene Structures in Human Genomic DNA (PDF)
- EasyGene - a prokaryotic gene finder that ranks ORFs by statistical significance (PDF)
- SLAM - Cross-species Gene Finding and Alignment with a Generalized Pair Hidden Markov Model (PDF)
- Prediction of Complete Gene Structures in Human Genomic DNA (PDF)
- Integrating Genomic Homology into Gene Structure Prediction (PDF)
- Christopher Burge's PhD Thesis (PS) (PDF)
Sequence Alignment
- LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA (PDF)
- Glocal Alignment: Finding Rearrangements During Alignment (PDF)
- AVID: A Global Alignment Program (PDF)
- BLAT: The BLAST-Like Local Alignment Tool (PDF)
- Gapped BLAST and PHI-BLAST (PDF)
- Pattern Hunter: Faster and more sensitive homology search (PDF)
- The estimation of statistical parameters for local alignment score distributions (PDF)
- T-Coffee: A Novel Method for Fast and Accurate Multiple Sequence Alignment (PDF)
- BWA (PDF)
- BOWTIE (PDF)
Fragment Assembly
- Genome Sizes (HTML)
- Transposons (HTML)
- Genomic mapping, mathematical analysis (PDF, PDF)
- ARACHNE: A Whole-Genome Shotgun Assembler (PDF)
- ARACHNE 2: Whole-genome sequence assembly for Mammalian Genomes (PDF)
- The Eulerian path approach to DNA fragment assembly (PDF)
Gene Regulation and Motif Finding
- Transcriptional Regulation of the Stem Cell Leukemia Gene (PDF)
- Exploring the conditional co-regulation of yeast gene expression through fuzzy k-means clustering (PDF)
- Systematic determination of genetic network architecture (PDF)
- Identifying DNA and Protein Patterns with Statistically Significant Alignments of Multiple Sequences (PDF)
- Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment (PDF)
Conditional Random Fields
Genomics
- The Genome Project: What Will It Do as a Teenager? (PDF)
- Will Computers Crash Genomics? (PDF)
- On the Future of Genomic Data (PDF)
- The sequence and de novo assembly of the giant panda genome (PDF)
- Comparative and demographic analysis of orang-utan genomes (PDF)
Ancestry Inference
- Genes mirror geography within Europe (PDF)
- The human Y chromosome: an evolutionary marker comes of age (PDF)