Murakami, Katsuhiko, Imanishi, Tadashi, Gojobori, Takashi, Nakai, Kenta
Abstract Background It is essential in modern biology to understand how transcriptional regulatory regions are composed of cis -elements, yet we have limited knowledge of, for example, the...
Genome Informatics 14: 408--409 (2003) Detection of Tissue Specific Genes by Putative (2004)
Katsuhiko Murakami, Toshio Kojima, Yoshiyuki Sakaki
Introduction Gene expression of multi-cellular organisms is regulated by transcription factors (TFs) that interact with regulatory cis-elements on DNA sequences. To find the functional regulatory...
Murakami, Katsuhiko, Kojima, Toshio, Sakaki, Yoshiyuki
Abstract Background Gene expression is regulated mainly by transcription factors (TFs) that interact with regulatory cis -elements on DNA sequences. To identify functional regulatory elements,...
A Transcription Regulatory Region Analysis System (2001)
Katsuhiko Murakami, Yohinori Ohta, Koji Tanikawa, Hiroki Nakae, Shigeo Ihara, Toshihisa Takagi
Introduction Despite the enormous growthof genomic sequence data, computational analysisof regulatory sequences remains a relatively marginal domain. Pol II Promoter prediction programs were assessed...
A Database System for cDNA Expression Profile Using ESTs of Oligo-Capping Clones and UniGene (2001)
Naoyuki Harada, Katsuhiko Murakami, Tetsuo Nishikawa, Tomoyasu Sugiyama, Toshio Ota, Ryotaro Irie, ...
Introduction With progress of the human genome pro ect, thewhol sequences of the human genomewil be determined complnedj in a few years. Functional analona of genes of human genome is now being...
An Integrated Analysis and Database System for Full-Length cDNA (2001)
Tetsuo Nishikawa, Katsuhiko Murakami, Naoyuki Harada, Toshio Ota, Tomoyasu Sugiyama, Keiichi Nagai, ...
Annotation and databasesystem of full-length cDNA sequences was developed. As the com ponents of thesystem ORF annotationsystem functional annotationsystem based on database search results,msults...
Clustering and Detection of 5' Splice Sites of mRNA by (1998)
Katsuhiko Murakami, Toshihisa Takagi
Introduction Biological signals on DNA sequences such as TATA box, GC box, CAAT box, the Shine-Dalgarno sequence in the promoter regions, and splice sites (donor/acceptor sites) in eukaryotic mRNA...
Clustering and Detection of 5' Splice Sites of mRNA by k Weight Matrix Model (1998)
Katsuhiko Murakami, Toshihisa Takagi
Introduction Biological signals on DNA sequences such as TATA box, GC box, CAAT box, the Shine-Dalgarno sequence in the promoter regions, and splice sites (donor/acceptor sites) in eukaryotic mRNA...
Gene Recognition Using Multiple Gene-Finding Programs (1997)
Katsuhiko Murakami, Toshihisa Takagi
This paper demonstrates how effective re-analysis of the results of multiple gene-finding programs is. Four simple algorithms to integrate the results of some programs are proposed and tested. Our...
Katsuhiko Murakami, Toshihisa Takagi
We have developed a coding region prediction system. It is constructed from several measures that indicate exonness of a region in DNA sequence. The system includes a new statistical measure called...
Evaluation of exon prediction tools using a long DNA sequence data (1997)
Katsuhiko Murakami, Shiho Tsukuni, Toshihisa Takagi, Masahira Hattori
We have evaluated the ability to locate coding regions of two exon prediction software, GRAIL and FEX, using a long (about 301k bases) genomic DNA sequence. We performed an experiment to check the...
Katsuhiko Murakami, Toshihisa Takagi
We have developed a coding region prediction system. It is constructed from several measures that indicate exonness of a region in DNA sequence. The system includes a new statistical measure called...
Evaluation of exon prediction tools using a long DNA sequence data (1995)
Katsuhiko Murakami, Shiho Tsukuni, Toshihisa Takagi, Masahira Hattori
We have evaluated the ability to locate coding regions of two exon prediction software, GRAIL and FEX, using a long (about 301k bases) genomic DNA sequence. We performed an experiment to check the...
Evaluation of exon prediction tools using a long DNA sequence data (1995)
Katsuhiko Murakami, Shiho Tsukuni, Toshihisa Takagi, Masahira Hattori
We have evaluated the ability to locate coding regions of two exon prediction software, GRAIL and FEX, using a long (about 301k bases) genomic DNA sequence. We performed an experiment to check the...
Evaluation of exon prediction tools using a long DNA sequence data (1995)
Katsuhiko Murakami, Shiho Tsukuni, Toshihisa Takagi, Masahira Hattori
We have evaluated the ability to locate coding regions of two exon prediction software, GRAIL and FEX, using a long (about 301k bases) genomic DNA sequence. We performed an experiment to check the...
Tungsten/Carbon Multilayers Prepared by Ion-Beam Sputtering, (1992)
Murakami, Katsuhiko, Nakamura, Hiroshi, Oshino, Tetsuya, Nikaido, Hideo
Tungsten/carbon(W/C) multilayers were prepared by ion beam sputtering. The properties of the multilayers were studied by low-angle x-ray diffraction, transmission electron microscopy (TEM)...
Murakami, Katsuhiko, Kimura, Makoto, Owens, Jeffrey T., Meares, Claude F., Ishihama, Akira
RNA polymerase core enzyme of Escherichia coli is composed of two α subunits and one each of the β and β′ subunits. The C-terminal domain of the RNA polymerase α subunit plays a key role in...
Murakami, Katsuhiko, Owens, Jeffrey T., Belyaeva, Tamara A., Meares, Claude F., Busby, Stephen J. W., Ishihama, Akira
Interactions between the cAMP receptor protein (CRP) and the carboxy-terminal regulatory domain (CTD) of Escherichia coli RNA polymerase α subunit were analyzed at promoters carrying tandem DNA...
Owens, Jeffrey T., Miyake, Reiko, Murakami, Katsuhiko, Chmura, Albert J., Fujita, Nobuyuki, Ishihama, Akira, ...
The core enzyme of Escherichia coli RNA polymerase acquires essential promoter recognition and transcription initiation activities by binding one of several σ subunits. To characterize the proximity...
Cra-Dependent Transcriptional Activation of the icd Gene of Escherichia coli
Prost, Jean-François, Nègre, Didier, Oudot, Christelle, Murakami, Katsuhiko, Ishihama, Akira, Cozzone, Alain J., ...
The icd gene of Escherichia coli, encoding isocitrate dehydrogenase, was shown to be expressed from two different promoters: the previously identified icd P1 and a newly detected second promoter, icd...
Finney, Angela H., Blick, Robert J., Murakami, Katsuhiko, Ishihama, Akira, Stevens, Ann M.
During quorum sensing in Vibrio fischeri, the luminescence, or lux, operon is regulated in a cell density-dependent manner by the activator LuxR in the presence of an acylated homoserine lactone...
Murakami, Katsuhiko, Kimura, Makoto, Owens, Jeffrey T., Meares, Claude F., Ishihama, Akira
RNA polymerase core enzyme of Escherichia coli is composed of two α subunits and one each of the β and β′ subunits. The C-terminal domain of the RNA polymerase α subunit plays a key role in...
Murakami, Katsuhiko, Owens, Jeffrey T., Belyaeva, Tamara A., Meares, Claude F., Busby, Stephen J. W., Ishihama, Akira
Interactions between the cAMP receptor protein (CRP) and the carboxy-terminal regulatory domain (CTD) of Escherichia coli RNA polymerase α subunit were analyzed at promoters carrying tandem DNA...
Owens, Jeffrey T., Miyake, Reiko, Murakami, Katsuhiko, Chmura, Albert J., Fujita, Nobuyuki, Ishihama, Akira, ...
The core enzyme of Escherichia coli RNA polymerase acquires essential promoter recognition and transcription initiation activities by binding one of several σ subunits. To characterize the proximity...
Cra-Dependent Transcriptional Activation of the icd Gene of Escherichia coli
Prost, Jean-François, Nègre, Didier, Oudot, Christelle, Murakami, Katsuhiko, Ishihama, Akira, Cozzone, Alain J., ...
The icd gene of Escherichia coli, encoding isocitrate dehydrogenase, was shown to be expressed from two different promoters: the previously identified icd P1 and a newly detected second promoter, icd...
Finney, Angela H., Blick, Robert J., Murakami, Katsuhiko, Ishihama, Akira, Stevens, Ann M.
During quorum sensing in Vibrio fischeri, the luminescence, or lux, operon is regulated in a cell density-dependent manner by the activator LuxR in the presence of an acylated homoserine lactone...
Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees
Matsuya, Akihiro, Sakate, Ryuichi, Kawahara, Yoshihiro, Koyanagi, Kanako O., Sato, Yoshiharu, Fujii, Yasuyuki, ...
Orthologs are genes in different species that evolved from a common ancestral gene by speciation. Currently, with the rapid growth of transcriptome data of various species, more reliable orthology...