Martin C Frith

Summary

Affiliation: Computational Biology Research Center
Country: Japan

Publications

  1. pmc An approximate Bayesian approach for mapping paired-end DNA reads to a reference genome
    Anish Man Singh Shrestha
    Computational Biology Research Center, National Institute for Advanced Industrial Science and Technology AIST, Koto ku, Tokyo, Japan
    Bioinformatics 29:965-72. 2013
  2. pmc A mostly traditional approach improves alignment of bisulfite-converted DNA
    Martin C Frith
    Computational Biology Research Center, National Institute for Advanced Industrial Science and Technology AIST, 2 4 7 Aomi, Koto ku, Tokyo 135 0064, Japan
    Nucleic Acids Res 40:e100. 2012
  3. pmc Gentle masking of low-complexity sequences improves homology search
    Martin C Frith
    Computational Biology Research Center, Institute for Advanced Industrial Science and Technology, Koto ku, Tokyo, Japan
    PLoS ONE 6:e28819. 2011
  4. pmc Parameters for accurate genome alignment
    Martin C Frith
    Computational Biology Research Center, Institute for Advanced Industrial Science and Technology, Tokyo 135 0064, Japan
    BMC Bioinformatics 11:80. 2010
  5. pmc A new repeat-masking method enables specific detection of homologous sequences
    Martin C Frith
    Computational Biology Research Center, Institute for Advanced Industrial Science and Technology, Sequence Analysis Team, 2 4 7 Aomi, Koto ku, Tokyo 135 0064, Japan
    Nucleic Acids Res 39:e23. 2011
  6. pmc Incorporating sequence quality data into alignment improves DNA read mapping
    Martin C Frith
    Computational Biology Research Center, Institute for Advanced Industrial Science and Technology, Koto ku, Tokyo 135 0064, Japan
    Nucleic Acids Res 38:e100. 2010
  7. pmc Discovering sequence motifs with arbitrary insertions and deletions
    Martin C Frith
    Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology AIST, Tokyo, Japan
    PLoS Comput Biol 4:e1000071. 2008
  8. pmc A code for transcription initiation in mammalian genomes
    Martin C Frith
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045, Japan
    Genome Res 18:1-12. 2008
  9. pmc Dynamic usage of transcription start sites within core promoters
    Hideya Kawaji
    NTT Software Corporation, 209 Yamashita cho Nakak ku, Yokohama, Kanagawa, 231 8551, Japan
    Genome Biol 7:R118. 2006
  10. pmc Evolutionary turnover of mammalian transcription start sites
    Martin C Frith
    Genome Exploration Research Group, RIKEN Genomic Sciences Centre GSC, RIKEN Yokohama Institute, Tsurumi ku, Yokohama, Kanagawa, 230 0045, Japan
    Genome Res 16:713-22. 2006

Detail Information

Publications24

  1. pmc An approximate Bayesian approach for mapping paired-end DNA reads to a reference genome
    Anish Man Singh Shrestha
    Computational Biology Research Center, National Institute for Advanced Industrial Science and Technology AIST, Koto ku, Tokyo, Japan
    Bioinformatics 29:965-72. 2013
    ..An open-source implementation of our method is available as part of Last, a multi-purpose alignment program freely available at http://last.cbrc.jp...
  2. pmc A mostly traditional approach improves alignment of bisulfite-converted DNA
    Martin C Frith
    Computational Biology Research Center, National Institute for Advanced Industrial Science and Technology AIST, 2 4 7 Aomi, Koto ku, Tokyo 135 0064, Japan
    Nucleic Acids Res 40:e100. 2012
    ..It also illustrates how to adapt general-purpose alignment methods to a special case with distorted base patterns: this should be informative for other special cases such as ancient DNA and AT-rich genomes...
  3. pmc Gentle masking of low-complexity sequences improves homology search
    Martin C Frith
    Computational Biology Research Center, Institute for Advanced Industrial Science and Technology, Koto ku, Tokyo, Japan
    PLoS ONE 6:e28819. 2011
    ..Gentle masking is currently the best way to treat low-complexity tracts during homology search...
  4. pmc Parameters for accurate genome alignment
    Martin C Frith
    Computational Biology Research Center, Institute for Advanced Industrial Science and Technology, Tokyo 135 0064, Japan
    BMC Bioinformatics 11:80. 2010
    ..Surprisingly, there has been no large-scale assessment of these choices using real genomic data. Moreover, rigorous procedures to control the rate of spurious alignment have not been employed...
  5. pmc A new repeat-masking method enables specific detection of homologous sequences
    Martin C Frith
    Computational Biology Research Center, Institute for Advanced Industrial Science and Technology, Sequence Analysis Team, 2 4 7 Aomi, Koto ku, Tokyo 135 0064, Japan
    Nucleic Acids Res 39:e23. 2011
    ..This method thoroughly eliminates spurious homology predictions for DNA-DNA, protein-protein and DNA-protein comparisons. Moreover, it enables accurate homology search for non-coding DNA with extreme A + T composition...
  6. pmc Incorporating sequence quality data into alignment improves DNA read mapping
    Martin C Frith
    Computational Biology Research Center, Institute for Advanced Industrial Science and Technology, Koto ku, Tokyo 135 0064, Japan
    Nucleic Acids Res 38:e100. 2010
    ..This approach enables more effective use of DNA reads from organisms that lack reference genomes, are extinct or are highly polymorphic...
  7. pmc Discovering sequence motifs with arbitrary insertions and deletions
    Martin C Frith
    Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology AIST, Tokyo, Japan
    PLoS Comput Biol 4:e1000071. 2008
    ..It may be equally useful for arbitrarily gapped motifs in DNA and RNA, although fewer examples of such motifs are known at present. GLAM2 is public domain software, available for download at http://bioinformatics.org.au/glam2...
  8. pmc A code for transcription initiation in mammalian genomes
    Martin C Frith
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045, Japan
    Genome Res 18:1-12. 2008
    ....
  9. pmc Dynamic usage of transcription start sites within core promoters
    Hideya Kawaji
    NTT Software Corporation, 209 Yamashita cho Nakak ku, Yokohama, Kanagawa, 231 8551, Japan
    Genome Biol 7:R118. 2006
    ..We previously characterized the static structures of transcription start site usage within promoters at the base pair level, based on large-scale sequencing of transcript 5' ends...
  10. pmc Evolutionary turnover of mammalian transcription start sites
    Martin C Frith
    Genome Exploration Research Group, RIKEN Genomic Sciences Centre GSC, RIKEN Yokohama Institute, Tsurumi ku, Yokohama, Kanagawa, 230 0045, Japan
    Genome Res 16:713-22. 2006
    ..These findings suggest that the signals encoding transcription start sites are highly flexible and evolvable, and have cautionary implications for the use of sequence-level conservation to detect gene regulatory elements...
  11. pmc Large-scale clustering of CAGE tag expression data
    Kazuro Shimokawa
    Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, Japan
    BMC Bioinformatics 8:161. 2007
    ..The standard hierarchical clustering algorithm, which gives us easily understandable graphical tree images, has difficulties in processing such huge amounts of TSS data and a better method to calculate and display the results is needed...
  12. ncbi request reprint Splicing bypasses 3' end formation signals to allow complex gene architectures
    Martin C Frith
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Centre GSC, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045, Japan
    Gene 403:188-93. 2007
    ..This bypassing mechanism permits nested and interleaved gene architectures, as well as fusion transcripts that combine exons from adjacent genes...
  13. pmc The abundance of short proteins in the mammalian proteome
    Martin C Frith
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan
    PLoS Genet 2:e52. 2006
    ..Translation assays confirm that some of these novel proteins can be translated and localised to the secretory pathway...
  14. pmc Pseudo-messenger RNA: phantoms of the transcriptome
    Martin C Frith
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan
    PLoS Genet 2:e23. 2006
    ..Many of these transcripts do not correspond cleanly to any identifiable object in the genome, implying fundamental limits to the goal of annotating all functional elements at the genome sequence level...
  15. ncbi request reprint Discrimination of non-protein-coding transcripts from protein-coding mRNA
    Martin C Frith
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, Kanagawa, Japan
    RNA Biol 3:40-8. 2006
    ..Conversely and surprisingly, our analyses also provide evidence that as much as approximately 10% of entries in the manually curated protein database Swiss-Prot are erroneous translations of actually non-coding transcripts...
  16. doi request reprint Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection
    Michiaki Hamada
    Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277 8562, Japan
    Bioinformatics 27:3085-92. 2011
    ....
  17. ncbi request reprint Recount: expectation maximization based error correction tool for next generation sequencing data
    Edward Wijaya
    AIST, Computational Biology Research Center, 2 42 Aomi, Koutou ku, Tokyo 135 0064, Japan
    Genome Inform 23:189-201. 2009
    ..RECOUNT is an open-source C++ program available at http://seq.cbrc.jp/recount...
  18. pmc The whole alignment and nothing but the alignment: the problem of spurious alignment flanks
    Martin C Frith
    Computational Biology Research Center, Institute for Advanced Industrial Science and Technology, Tokyo 135 0064, Japan
    Nucleic Acids Res 36:5863-71. 2008
    ..Moreover, by explicitly demonstrating the tradeoff between over- and under-alignment, our methods guide the rational choice of scoring schemes for various alignment tasks...
  19. pmc Improved search heuristics find 20,000 new alignments between human and mouse genomes
    Martin C Frith
    Computational Biology Research Center, AIST, 2 4 7 Aomi, Koto ku, Tokyo 135 0064, Japan and LIFL UMR 8022 INRIA Lille Nord Europe, bat M3 Ext, Université Lille1 59655 Villeneuve d Ascq Cedex, France
    Nucleic Acids Res 42:e59. 2014
    ..Our optimized heuristics find ∼20,000 new human-mouse alignments that are missing from the standard UCSC alignments. We tabulate seed patterns and parameters that work well so they can be used in future research...
  20. pmc Finding protein-coding genes through human polymorphisms
    Edward Wijaya
    Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
    PLoS ONE 8:e54210. 2013
    ..On average 10% of these genes are located in the genomic regions devoid of annotated genes in 12 other catalogs. Our statistical analysis showed that these ORFs are unlikely to occur by chance...
  21. ncbi request reprint Genome-wide analysis of mammalian promoter architecture and evolution
    Piero Carninci
    Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045, Japan
    Nat Genet 38:626-35. 2006
    ..These data permit genome-scale identification of tissue-specific promoters and analysis of the cis-acting elements associated with them...
  22. pmc A bioinformatician's guide to the forefront of suffix array construction algorithms
    Anish Man Singh Shrestha
    Computational Biology Research Center, AIST, Tokyo, Japan
    Brief Bioinform 15:138-54. 2014
    ....
  23. pmc RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE)
    Hiroko Ohmiya
    RIKEN Center for Life Science Technologies CLST, Division of Genomic Technologies, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, 230 0045 Yokohama, Japan
    BMC Genomics 15:269. 2014
    ..After mapping the sequenced reads back to a reference genome CAGE data highlights the transcriptional start sites (TSSs) and their usage at a single nucleotide resolution...
  24. pmc RecountDB: a database of mapped and count corrected transcribed sequences
    Edward Wijaya
    Graduate School of Frontier Sciences, University of Tokyo, 5 1 5 Kashiwanoha, Kashiwa 277 8562, Japan
    Nucleic Acids Res 40:D1089-92. 2012
    ..The database is currently populated with 2265 entries from 45 organisms and continuously growing. RecountDB is publicly available at: http://recountdb.cbrc.jp...