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Bioinformatics Tool-Related Papers of Note, April 1- 24 2003


Lee K., Kohane I.S., Butte A.J. PGAGENE: integrating quantitative gene-specific results from the NHLBI Programs for Genomic Applications. [Bioinformatics 2003 Apr 12;19(6):778-9]: A gene-specific genomic data search engine for genetic and genomic data from the NHLBI, including microarray measurements, SNPs, and mutations. Available at:


Coin L., Bateman A., Durbin R. Enhanced protein domain discovery by using language modeling techniques from speech recognition. [Proc. Natl. Acad. Sci. USA, Vol. 100, Issue 8, 4516-4520, April 15, 2003]: The application of context-based speech recognition technology to protein domain discovery.


Abe T., Kanaya S., Kinouchi M., Ichiba Y., Kozuki T., Ikemura T. Informatics for unveiling hidden genome signatures. [Genome Res 2003 Apr;13(4):693-702]: Demonstrates how self-organizing maps can be used to classify genomic sequence.


Lin J.C., Xu J.L., Luo J.H., Li Y.X. Prediction of prokaryotic promoters based on prediction of transcriptional units. [Acta Biochimica et Biophysica Sinica 2003, 35(4):317-324]: A method to predict transcription units and promoters using a hidden Markov model.


Sadovsky M.G. The method to compare nucleotide sequences based on the minimum entropy principle. [Bull Math Biol 2003 Mar;65(2):309-22]. A method to compare symbol sequences based on the comparison of the frequencies of the small fragments of the compared sequences. Applications of the developed method in the fields of genetics and bioinformatics are discussed.


Thornton T.A., Haines JL. PowerTrim: An automated decision support algorithm for preprocessing family- based genetic data. [Am J Hum Genet 2003 Apr 3;72(5)]: Interactive algorithm to automate the task of reducing pedigree size to fit the computational constraints of statistical genetics software packages for linkage analysis.


Lu B., Chen T. A suboptimal algorithm for de novo peptide sequencing via tandem mass spectrometry. [J Comput Biol 2003;10(1):1-12]: Algorithm transforms spectral data into a matrix spectrum graph for de novo peptide sequencing using tandem mass spectrometry. Available at:


Meyer F., Goesmann A., McHardy A.C., Bartels D., Bekel T., Clausen J., Kalinowski J., Linke B., Rupp O., Giegerich R., Puhler A. GenDB - an open source genome annotation system for prokaryote genomes. [Nucl. Acids. Res. 2003 31: 2187-2195]: A modular genome annotation system for prokaryote genomes. Available at:


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The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.