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{userid:"asai", "refid":"33","repocollections":"","attachment":"","_thumb":"","articletype":"inproceedings","sectionheading":"","title":"Finding Precursor Compounds in Secondary Metabolism.","year":"1999","author":" M. Arita, K. Asai, T. Nishioka","booktitle":"Genome Informatics Vol.10","editor":"","pages":"113-120","organization":"","address":"","publisher":"","doi":"","pubmed":"11072348","pdflink":"","urllink":"","abstract":"A precursor is a compound which is transformed to a class of functional molecules within short steps. It is an important process in the production of natural drugs to decide whether a given compound is a precursor or not. We present two strategies to select precursor compounds in the secondary metabolism of terpenoids: one is to find the packing of basic molecules in the given cyclic structure, and the other is to find the synthetic map of the given set of compounds. Both strategies play important roles in reproducing tracer experiments on a computer.","note":"","tags":"","month":"","journal":"Genome Inform Ser Workshop Genome Inform","volume":"10","number":"","school":"","issn":"0919-9454","key":"Arita1999","howpublished":""}
,

{userid:"asai", "articletype":"article","pages":"317-325","author":"T Yada, Y Totoki, M Ishikawa, K Asai, K Nakai","year":"1998","title":"Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences.","month":"","journal":"Bioinformatics","publisher":"","volume":"14","number":"4","note":"","tags":"Algorithms,Base Sequence,Benchmarking,Binding Sites,Chi-Square Distribution,Gene Library,Humans,Information Storage and Retrieval,Markov Chains,Models, Genetic,Models, Statistical,Promoter Regions (Genetics),Software,Software Design,Transcription, Genetic","booktitle":"","editor":"","abstract":"MOTIVATION: Automatic extraction of motifs that occur frequently on a set of unaligned DNA sequences is useful for predicting the binding sites of unknown transcription factors. Several programs for this purpose have been released. However, in our opinion, they are not practical enough to be applied to a large number of upstream sequences. RESULTS: We propose a new program called YEBIS (Yet another Environment for the analysis of BIopolymer Sequences) which is capable of extracting a set of motifs, without any a priori knowledge, from a number of functionally related DNA sequences. Using the hidden Markov model, these motifs are represented in a more general form than other conventional methods, such as the weight matrix method. When applied to several sets of benchmark data, it was found that YEBIS had comparable capability to the existing methods, but was much faster. Moreover, it could extract all known motifs from the LTR sequences (long terminal repeat sequences) in a single run. Finally, it could be successfully applied to approximately 400 human promoter sequences and some of the extracted motifs turned out to be known cis-elements. Therefore, YEBIS could be a practical tool for exploring the upstream sequences of genomic ORFs, some of which are regulated in a similar fashion. AVAILABILITY: YEBIS will be distributed to academic users free of charge. All requests should be sent to the address below. CONTACT: E-MAIL: yada@tokyo.jst.go.jp","address":"","school":"","issn":"1367-4803","doi":"","pubmed":"9632826","key":"Yada1998","howpublished":"","urllink":"","refid":37}
,

{userid:"asai", "refid":"38","repocollections":"","attachment":"","_thumb":"","articletype":"inproceedings","sectionheading":"","title":"Extraction of hidden Markov model representations of signal patterns in DNA sequences.","year":"1996","author":"T Yada, M Ishikawa, H Tanaka, K Asai","booktitle":"Proceedings of Pacific Symposium on Biocomputing (PSB96)","editor":"","pages":"686-696","organization":"","address":"","publisher":"","doi":"","pubmed":"9390268","pdflink":"","urllink":"","abstract":"We have developed a method to extract the signal patterns in DNA sequences. In this method, the Genetic Algorithm (GA) and Baum-Welch algorithm are used to obtain the best Hidden Markov Model (HMM) representations of the signal patterns in DNA sequences. The GA is used to search the best network shapes and the initial parameters of the HMMs. Baum-Welch algorithm is used to optimize the HMM parameters for the given network shapes. Akaike Information Criterion (AIC), which gives a criterion for the balance of adaptation and complexity of a model, is applied in the HMM evaluation. We have applied the method to the extraction of the signal patterns in human promoters and 5' ends of yeast introns. As a result, we obtained HMM representations of characteristic features in these sequences. To validate the efficiency of the method, we have performed promoter recognition using obtained HMMs. Two entries including nine promoters are selected from GenBank 76.0, and it is observed that the HMM can predicts eight promoters correctly. These results imply that the method is efficient to design preferable HMM networks, and provides reliable models for the recognition of the signal patterns.","note":"","tags":"Algorithms,Base Sequence,Computational Biology,Computer Simulation,DNA,Humans,Introns,Markov Chains,Models, Genetic,Mutation,Point Mutation,Promoter Regions (Genetics),Saccharomyces cerevisiae,Sequence Alignment","month":"","journal":"Pac Symp Biocomput","volume":"","number":"","school":"","issn":"1793-5091","key":"Yada1996","howpublished":""}
,

{userid:"asai", "refid":"43","repocollections":"","attachment":"","_thumb":"","articletype":"inproceedings","sectionheading":"","title":"A multi-level description scheme of protein conformation.","year":"1993","author":"K Onizuka, M Ishikawa, S T Wong, K Asai","booktitle":"Proceedings of International Conference on Intelligent Systems for Molecular Biology (ISMB93)","editor":"","pages":"301-309","organization":"","address":"","publisher":"","doi":"","pubmed":"7584351","pdflink":"","urllink":"","abstract":"We propose a novel description scheme of protein backbone conformation that can model the important factors of protein structure formation, such as global interaction and geometric constraints. This description scheme represents a protein conformation with several symbolic sequences of multiple levels of abstraction. Each symbol in the sequence denotes the class of abstracted topology of subconformation with the size specific to the level. Low level sequences of this description represent fine structures of high resolution, and high level sequences represent the abstracted topologies of large scale. The classification of protein backbone subconformations of various sizes is the most important base for this description scheme. This has never been tried so far due to the complexity in dealing with the number of degrees of freedom in subconformations. However, the proposed technique solved this problem by abstracting the topology of middle and large scale subconformations. This linear expansion technique extracts a fixed number of parameters as the expansion coefficients from the co-ordinate representation of subconformations. In this case, the simple reverse-transformation from the expansion coefficients reconstructs the three-dimensional topology of a subconformation. The analysis of the relation between primary structure of a region and the subconformation of that region at each level in this description helps to model both local and global interactions of protein structure formation. Further, the statistic analysis of overlapping patterns of two subconformations models the geometric constraints important for a structure prediction system in generating a conformation which is geometrically sound.","note":"","tags":"Amino Acid Sequence,Computer Simulation,Databases, Factual,Flavodoxin,Models, Chemical,Molecular Sequence Data,Myoglobin,Protein Conformation,Triose-Phosphate Isomerase","month":"","journal":"Proc Int Conf Intell Syst Mol Biol","volume":"1","number":"","school":"","issn":"1553-0833","key":"Onizuka1993","howpublished":""}
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{userid:"chikara.ohtsuki", "refid":69,"attachment":"","articletype":"article","sectionheading":"","title":"Synthesis of Poly(isobutyl methacrylate-co-2,2,2-trifluoroethyl methacrylate) having Tetraphenylporphinato Platinum(II) Moiety as an Oxygen-Sensing Dye for Pressure Sensitive Paint (PSP)","year":"2005","author":"M Obata, Y Tanaka, N Araki, S Yano, M Harada, K Mitsuo, K Asai, T Kakuchi, C Ohtsuki","journal":"Journal of Polymer Science Part A: Polymer Chemistry","volume":"43","number":"14","pages":"2997-3006","month":"July","doi":"10.1002\/pola.20776","pubmed":"","pdflink":"","urllink":"","abstract":"","note":"","tags":""}
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{userid:"chikara.ohtsuki", "refid":162,"repocollections":"","attachment":"","_thumb":"","articletype":"article","sectionheading":"","title":"Optical oxygen-sensing properties of porphyrin derivatives anchored on ordered porous aluminium oxide plates","year":"2007","author":"N. Araki, Y. Amao, T. Funabiki, M. Kamitakahara, C. Ohtsuki, K. Mitsuo, K. Asai, M. Obata and S. Yano","journal":"Photochemical & Photobiological Sciences","volume":"6","number":"7","pages":"794-803","month":"July","doi":"10.1039\/B618030B","pubmed":"17609774","pdflink":"","urllink":"","abstract":"","note":"","tags":""}
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{userid:"asai", "articletype":"article","pages":"991-996","author":"Yasnory T F Sasaki, Miho Sano, Takashi Ideue, Taishin Kin, Kiyoshi Asai, Tetsuro Hirose","year":"2007","title":"Identification and characterization of human non-coding RNAs with tissue-specific expression.","month":"Jun","journal":"Biochem Biophys Res Commun","publisher":"","volume":"357","number":"4","note":"","tags":"Animals,Base Sequence,Humans,Mice,Molecular Sequence Data,Organ Specificity,RNA, Untranslated,Sequence Analysis, RNA,Sequence Homology, Nucleic Acid,Tissue Distribution,Transcription Factors","booktitle":"","editor":"","abstract":"We have examined the expression profile of selected non-coding RNAs (ncRNAs) in 11 human tissues. Among 5489 full-length cDNA clones annotated as non-protein-coding transcripts in the H-Invitational database, we chose 150 clones for further analysis based on their gene structure and EST information. Expression profiling using quantitative RT-PCR and Northern blot hybridization revealed that the majority of the selected ncRNAs exhibited tissue specificity: 67% are predominantly expressed in a restricted subset of tissues. The absolute quantification of representative ncRNAs revealed that the majority of ncRNAs are expressed as low abundance transcripts. A comparative genomic analysis revealed that only 27% of the selected ncRNAs have mouse counterparts. Since the expression patterns of the human ncRNAs having no mouse counterparts remain to be similar to those of the mouse ncRNAs, the expression patterns of the selected ncRNAs may be conserved between human and mouse.","address":"","school":"","issn":"0006-291X","doi":"10.1016\/j.bbrc.2007.04.034","pubmed":"17451645","key":"Sasaki2007","howpublished":"","urllink":"","refid":7}
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{userid:"asai", "articletype":"article","pages":"724-730","author":"Yasnory T F Sasaki, Miho Sano, Taishin Kin, Kiyoshi Asai, Tetsuro Hirose","year":"2007","title":"Coordinated expression of ncRNAs and HOX mRNAs in the human HOXA locus.","month":"Jun","journal":"Biochem Biophys Res Commun","publisher":"","volume":"357","number":"3","note":"","tags":"Animals,Base Sequence,Cell Line,Cell Line, Tumor,Female,Gene Expression Profiling,HL-60 Cells,Hela Cells,Homeodomain Proteins,Humans,Jurkat Cells,K562 Cells,Mice,Molecular Sequence Data,Nucleic Acid Conformation,RNA, Messenger,RNA, Untranslated,Reverse Transcriptase Polymerase Chain Reaction,Sequence Homology, Nucleic Acid","booktitle":"","editor":"","abstract":"In the human HOXA locus a number of ncRNAs are transcribed from the intergenic regions in the opposite direction to HOXA mRNAs. We observed that the genomic organization of genes for the ncRNAs and HOXA proteins is highly conserved between human and mouse. We examined the expression profiles of these ncRNAs and HOXA mRNAs in various human tissues. The expression patterns of ncRNAs in human tissues coincide with those of the adjacent HOXA mRNAs that are collinearly expressed along the anteroposterior axis. This coordinated expression was observed even in transformed tumors and cancer cell lines, suggesting that the expression of ncRNAs is prerequisite for the regulated expression of HOXA genes. HIT18844 ncRNA transcribed from the most upstream position of the HOXA cluster possesses an ultra-conserved short stretch which potentially forms an evolutionarily conserved secondary structure. Our data suggest a critical role for ncRNAs in the regulation of HOXA gene expression.","address":"","school":"","issn":"0006-291X","doi":"10.1016\/j.bbrc.2007.03.200","pubmed":"17445766","key":"Sasaki2007","howpublished":"","urllink":"","refid":8}
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{userid:"masashi.tanaka", "articletype":"article","pages":"1735-1742","author":"K Hattori, M Tanaka, S Sugiyama, T Obayashi, T Ito, T Satake, Y Hanaki, J Asai, M Nagano, T Ozawa","year":"1991","title":"Age-dependent increase in deleted mitochondrial DNA in the human heart: possible contributory factor to presbycardia.","month":"Jun","journal":"Am Heart J","publisher":"","volume":"121","number":"6 Pt 1","note":"","tags":"Adolescent,Adult,Aged,Aged, 80 and over,Aging,Base Sequence,Blotting, Southern,Child,Child, Preschool,Chromosome Deletion,DNA,Female,Heart Diseases,Humans,Male,Middle Aged,Mitochondria, Heart,Molecular Sequence Data,Polymerase Chain Reaction","booktitle":"","editor":"","abstract":"Cardiac function deteriorates with age, and endogenous damage to mitochondrial DNA (mt DNA) is believed to be a major contributory factor to aging. Mitochondria occupy a pivotal position in energy metabolism, and mitochondria have their own DNA, which encodes 13 subunits of the mitochondrial energy transducing system. Other subunits are encoded by nuclear DNA. DNA has been shown to have a high mutation rate, and genetic mutation might primarily be ascribed to mtDNA mutation in the energy transducing system. Recent advances in gene technology, especially in polymerase chain reactions (PCR), permit us to analyze mtDNA mutations in a small quantity of tissue. We devised rapid and accurate methods to detect mitochondrial mutations--the primer shift PCR method, PCR-Southern method, the modified primer shift PCR method, and the asymmetric PCR method. With these methods, we analyzed myocardia mtDNA in human cadavers of various ages (from 3 years old to 97 years old, mean 57 years old). The 7.4 kb deletion of mtDNA was commonly detected in elderly subjects, and the proportion of deleted mtDNA to normal mtDNA increased with age. Deleted mtDNA was observed in all subjects that were over 70 years old. The mutation was based on the directly repeated sequence: 5'-CATCAA-CAACCG-3', which exists in both the adenosine triphosphatase 6 gene and the displacement loop (D-loop) region. Replication impairment occurred at that directly repeated sequence, which caused the elimination of genomes between the adenosine triphosphatase 6 gene and the D-loop region and resulted in a 7.4 kb deletion.(ABSTRACT TRUNCATED AT 250 WORDS)","address":"","school":"","issn":"0002-8703","doi":"","isi":"","pubmed":"2035386","key":"Hattori1991","howpublished":"","urllink":"","refid":132}
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{userid:"nicolas.karakatsanis", "refid":"35","repocollections":"","attachment":"","_thumb":"","articletype":"article","sectionheading":"","title":"Recent developments in Geant4","year":"2016","author":"J Allison, K Amako, J Apostolakis, Pedro Arce, M Asai, T Aso, E Bagli, A Bagulya, S Banerjee, G Barrand, ..., N A Karakatsanis, ..., H. Yoshida","journal":"Nuclear Instruments and Methods in Physics Research Section A : Accelerators, Spectrometers, Detectors and Associated Equipment","volume":"835","number":"","pages":"186-225","month":"","doi":"https:\/\/doi.org\/10.1016\/j.nima.2016.06.125","pubmed":"","pdflink":"","urllink":"https:\/\/doi.org\/10.1016\/j.nima.2016.06.125","abstract":"Geant4 is a software toolkit for the simulation of the passage of particles through matter. It is used by a large number of experiments and projects in a variety of application domains, including high energy physics, astrophysics and space science, medical physics and radiation protection. Over the past several years, major changes have been made to the toolkit in order to accommodate the needs of these user communities, and to efficiently exploit the growth of computing power made available by advances in technology. The adaptation of Geant4 to multithreading, advances in physics, detector modeling and visualization, extensions to the toolkit, including biasing and reverse Monte Carlo, and tools for physics and release validation are discussed here.","note":"","tags":"","weight":35,"publisher":"Elsevier","booktitle":"","editor":"","address":"","school":"","issn":"0168-9002","isi":"","key":"Allison2016","howpublished":""}
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