Papers

The contents of the syringe

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letter to Nature from the GISAID consortium

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over 70 scientists from 34 countries

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letter to the editor of Nature

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It is time to end the patenting of software

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Beware of mis-assembled genomes

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Nature journal club

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letter to the editor of Nature

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The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

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A unified model explaining the offsets of overlapping and near-overlapping prokaryotic genes

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Draft Genome of the Filarial Nematode Parasite Brugia malayi

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Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis

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Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution.

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[Local PDF copy]

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Yeast rises again

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[Local PDF copy]

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Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis.

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Genome sequence of the human malaria parasite Plasmodium falciparum

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The genome sequence of the malaria mosquito Anopheles gambiae

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Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster

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Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii

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(Local PDF copy)

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Evidence for symmetric chromosomal inversions around the replication origin in bacteria.

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Gene Index analysis of the human genome estimates approximately 120,000* genes

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*Estimate corrected to 56,000 genes

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Optimized Multiplex PCR: Efficiently Closing a Whole-Genome Shotgun Sequencing Project

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Bioinformatics challenges of new sequencing technology

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Automated eukaryotic gene structure annotation using EVidenceModeler

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Identifying bacterial genes and endosymbiont DNA with Glimmer

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JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions

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Comparative genome assembly

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Automated correction of genome sequence errors

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Versatile and open software for comparing large genomes

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Hierarchical scaffolding with Bambus

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Computational gene prediction using multiple sources of evidence

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Fast algorithms for large-scale genome alignment and comparison

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Full-length messenger RNA sequences greatly improve genome annotation

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GeneSplicer: a new computational method for splice site prediction

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A probabilistic method for identifying start codons in bacterial genomes

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Prediction of operons in microbial genomes

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A clustering method for repeat analysis in DNA sequences

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Finding genes in Plasmodium falciparum chromosome 3

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An optimized protocol for analysis of EST sequences

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Prediction of transcription terminators in bacterial genomes

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Improved microbial gene identification with GLIMMER

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Interpolated Markov models for eukaryotic gene finding

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Alignment of Whole Genomes

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Click here for the color figure (PDF)

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Microbial gene identification using interpolated Markov models

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Skewed Oligomers and Origins of Replication

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Finding Genes in Human DNA with a Hidden Markov Model

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A Method for Identifying Splice Sites and Translational Start Sites in Eukaryotic mRNA.

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On Comparing Classifiers: Pitfalls to Avoid and a Recommended Approach

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A System for Induction of Oblique Decision Trees

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