Publications and Presentations

IMAC
Inter- and Intra-Metabolite Atom-level Connectivity Database

Jun Ohta:
Single-atom tracing in a model network of carbohydrate metabolism and pathway selection
IPSJ Transactions on Bioinformatics Vol.11, 1-13 (2018)
doi: 10.2197/ipsjtbio.11.1 Supplemental information

Jun Ohta:
Connectivity matrix method for analyses of biological networks and its application to atom-level analysis of a model network of carbohydrate metabolism
IEE Proceedings Systems Biology 153(5), 372-374 (2006)
PMID: 16986320 Supplemental information

Several presentations below include data, slides, or sheets made using Octave, Marvin, or the LIGAND database. Octave is a software distributed under the terms of the GNU General Public License (www.octave.org). Marvin is a product of ChemAxon Ltd., Máramaros köz 3/a, Budapest, 1037 Hungary (www.chemaxon.com). As for the LIGAND database, please see the following article: Goto, S., Nishioka, T., and Kanehisa, M., "LIGAND: Chemical Database for Enzyme Reactions", Bioinformatics, 14:591-599 (1998).

Jun Ohta:
Metabolic networks: Investigation of relationship between topological position of individual nodes in a given network and the function assigned to each of them [The original title is written in Japanese.]
Program and Abstracts 21-21 (2008)
The 2nd Annual Meeting of the Society of Genome Microbiology, Japan (Osaka, Japan) March 6-8, 2008

Jun Ohta:
A Strategy for Metabolic Pathway Prediction: Generation of Metabolic Networks by Network Expansion
The Proceedings of the 2007 Annual Conference of the Japanese Society for Bioinformatics, P018-1 & P018-2 (2007)
JSBi2007, The 2007 Annual Conference of the Japanese Society for Bioinformatics (Tokyo, Japan) December 17-19, 2007

Jun Ohta:
Metabolic networks as atom networks and balanced reaction pattern
Abstracs 328-328 (2007)
BMB2007, The 30th Annual Meeting of the Molecular Biology Society of Japan, The 80th Annual Meeting of the Japanese Biochemical Society (Yokohama, Japan) December 11-15, 2007

Jun Ohta:
Concept of metabolic networks as atom networks
Program and Abstracs 96-96 (2007)
Nishinomiya-Yukawa International & Interdisciplinary Symposium 2007, What is Life? Yukawa Institute for Theoretical Physics, Kyoto University (Kyoto, Japan) October 15-20, 2007

Jun Ohta:
Visualization of atom network structure of metabolic networks by Pajek
CBI2007 Proceedings, Quantum Chemistry & Computational Chemistry to Life, Chem-Bio Informatics Society, 119-119 (2007)
CBI2007 (Hiroshima, Japan) October 3-5, 2007

Jun Ohta:
A Strategy for Metabolic Pathway Prediction: Generation of Metabolic Networks Using Balanced Reaction Pattern
Program and Abstracts 37-38 (2007)
The Seventh International Workshop on Bioinformatics and Systems Biology (Tokyo, Japan) July 31 – August 2, 2007

Jun Ohta:
Connectivity matrix method and atom mapping matrices
Course Book, Program and Abstracts, 186-186 (2007)
Second FEBS Advanced Course on Systems Biology: From Molecules To Life (Gosau, Austria, EU) March 10- 16, 2007

Jun Ohta:
Matrix expression of biological network information and its application to metabolic networks [The original title is written in Japanese.]
Program and Abstracts 48-48 (2007)
The 1st Annual Meeting of the Society of Genome Microbiology, Japan (Kisaradzu, Japan) March 1-3, 2007

Jun Ohta:
Visualization of Metabolic Networks as Networks of Atoms by Pajek: An Application of Connectivity Matrix Method
Genome Informatics, Volume 17 Poster and Software demonstrations, P146 (2006)
GIW2006 (Yokohama, Japan) December 18-20, 2006
Please see the abstract at http://www.jsbi.org/pdfs/journal1/GIW06/GIW06P146.pdf

Jun Ohta:
Attempt to express topological position of individual metabolites in the whole metabolic network of Escherichia coli.
Program and Abstracts 106-106, 2006
IECA2006, 3rd International E.Coli Alliance Conference on Systems Biology 2006 (Jeju, Korea) October 30-November 3, 2006

Jun Ohta:
Metabolic Networks: Connectivity Matrix-Based Isotopomer Analysis on Matlab/Octave
ICSB2006, The 7th International Conference on Systems Biology (Yokohama, Japan) October 9-13, 2006

Jun Ohta:
Similarity of metabolic networks as networks of atoms to social networks: Assuming that an atom is a person [The original title is written in Japanese. The original English translation has been corrected.]
2nd Workshop, SIG on Emergent Intelligence on Network, Japan Society for Software Science and Technology (Akanko, Japan) September 27-29, 2006

Jun Ohta:
Connectivity matrix method for analyses of biological networks and its application to atom-level analysis of a model network of carbohydrate metabolism
12th BTK meeting, Systems Biology: Redefining Biothermokinetics, International Study Group on Systems Biology (Trakai, Lithuania) September 14-17, 2006

Jun Ohta:
Topological position of each node in a given network: Toward investigation of its relationship with the function assigned to each node [The original title is written in Japanese.]
Satellite Meeting of SIG on Systems Biology in Akita, Japanese Society for Bioinformatics (Akita, Japan) August 31, 2006

Jun Ohta:
IMAC, Inter- And Intra-Metabolite Atom-Level Connectivity Database
IFMBE Volume 14, 4131-4131, 2006 (ISSN 1727-1983, ISBN 3-540-36839-6 Springer Berlin Heidelberg New York)
World Congress on Medical Physics and Biomedical Engineering 2006 (Seoul, Korea) August 27-September 1, 2006

Jun Ohta:
Network analysis by connectivity matrix method: Its application to atom-level analysis of metabolic networks [The original title is written in Japanese.]
Summer School 2006, Japanese Society for Bioinformatics (Kyoto, Japan) August 21-23, 2006

Jun Ohta:
Application of Connectivity Matrix Method to Atom-level Analysis of Metabolic Networks: Calculation of Paths Connecting Two Metabolites
CBI2006 Proceedings, Integration of Chem-Bio-Pharma Informatics for Rational Drug Development and e-ADMET, Chem-Bio Informatics Society, 85-85 (2006)
CBI2006 (Tokyo, Japan) July 24-26, 2006

Jun Ohta:
Atom-level and Metabolite-level Analyses of Metabolic Networks using Matlab and Octave
Abstracts, 568-568 (2006)
20th IUBMB International Congress of Biochemistry and Molecular Biology and 11th FAOBMB Congress in conjugation with 79th Annual Meeting of the Japanese Biochemical Society and 29th Annual Meeting of the Molecular Biology Society of Japan (Kyoto, Japan) June 18-23, 2006

Jun Ohta:
Description and analysis of atom-level metabolic network structure including chemical structure [The original title is written in Japanese.]
Frontier of Microbe Genome Research, The 8th Workshop on Genome Science, The Ministry of Education, Culture, Sports, Science and Technology specific area research (Kisaradzu, Japan) March 3-4, 2006

Jun Ohta:
Study of metabolic networks using Octave or Matlab [The original title is written in Japanese.]
The 9th Meeting of SIG on Systems Biology, Japanese Society for Bioinformatics (Fukuoka, Japan) January 18, 2006

Jun Ohta:
Theoretical Analysis of Metabolic Networks: Attempt to Express Topological Position of Individual Atoms in a Given Network
Genome Informatics, Volume 16 Poster and Software demonstrations, P163 (2005)
GIW2005 (Yokohama, Japan) December 19-21, 2005
Please see the abstract at http://www.jsbi.org/pdfs/journal1/GIW05/GIW05P163.pdf

Jun Ohta:
Development of "connectivity matrix" method for theoretical analyses of metabolic networks
Seikagaku 77(8), 1036-1036 (2005)
The 78th Annual Meeting of the Japanese Biochemical Society (Kobe, Japan) October 19-22, 2005

Jun Ohta:
Atom-level study of metabolic networks using numerical computation softwares, Octave and Matlab
First Protein Informatics Workshop in Kyushu, Kyushu Branch, Japanese Society for Bioinformatics (Fukuoka, Japan) October 9-10, 2005

Jun Ohta:
"Connectivity Matrix" Method: Analysis of Metabolic Networks on GNU Octave/Matlab
SYMBIONIC 2005, Course Book, 31-31 (2005)
SYMBIONIC COURSE 2005: Methods, Data Handling and Standards in Neuronal Systems Biology (Trieste, Italy) August 31-September 3, 2005

Jun Ohta:
Matlab/GNU Octave as a Platform for Analyses of Metabolic Networks
CBI2005 Proceedings, Chem-Bio Informatics in the Post-Genome Era, Chem-Bio Informatics Society, 105-105 (2005)
CBI2005 (Yokohama, Japan) August 24-26, 2005

Jun Ohta:
Development of general format for describing network structure
Summer School 2005, Japanese Society for Bioinformatics (Fukuoka, Japan) August 1-3, 2005

Jun Ohta:
"Connectivity matrix" method for theoretical analyses of metabolic networks
Program & Abstracts, 73-73 (2005)
Metabolomics 2005, The First Annual Meeting of the Metabolomics Society (Tsuruoka, Japan) June 20-23, 2005

Jun Ohta:
Connectivity matrix for describing all the atom-level connectivities in a given metabolic network and its use for analysis of the network structure
Course Book, Program and Abstracts, 140-140 (2005)
First FEBS Advanced Course on Systems Biology: From Molecules & Modeling To Cells (Gosau, Austria, EU) March 12-18, 2005

Jun Ohta:
Metabolic Networks: Use of Matrix Expression for Structural Analyses
Program and Abstracts, The 27th Annual Meeting of the Molecular Biology Society of Japan, 2PB-415 (2004)
The 27th Annual Meeting of the Molecular Biology Society of Japan (Kobe, Japan) December 8-11, 2004

Jun Ohta:
Atom-level Analysis of Metabolic Networks Consisting of Multiple Compartments
Seikagaku 76(8), 978-978 (2004)
The 77th Annual Meeting of the Japanese Biochemical Society (Yokohama, Japan) October 13-16, 2004

Jun Ohta:
Toward Complete Structural Analyses of Metabolic Networks:
Prototype Data Format for Describing Both Inter- and Intra-Metabolite Atom-level Connectivities
Proceedings for 5th International Conference on Systems Biology, 141-141 (2004)
ICSB2004 (Heidelberg, Germany) October 9-13, 2004

Jun Ohta:
Structural analyses of metabolic networks using GNU Octave
Proceedings for 2004 Meeting, New Technologies for Drug Design and Discovery in the Post-Genome Era, Chem-Bio Informatics Society, 132-133 (2004)
CBI2004 (Tokyo, Japan) July 28-30, 2004

Jun Ohta:
Atom-level Analysis of Metabolic Networks using GNU Octave and IMAC, A Database of Inter-Metabolite Atom-level Connectivity
Proceedings for 2nd International E.Coli Alliance Conference on Systems Biology, XLI (2004)
IECA2004, 2nd International E.Coli Alliance Conference on Systems Biology (Banff, Alberta, Canada), June 18-22, 2004

Jun Ohta:
Intermetabolite atom-level connectivity in metabolic network
Pathways from 6 carbon atoms of D-Glucose to CO2 in a model network of carbohydrate metabolism
Seikagaku 75(8), 1102-1102 (2003)
The 76th Annual Meeting of the Japanese Biochemical Society (Yokohama, Japan) October 15-18, 2003

Jun Ohta:
Data Format for Computational Analysis of Intermetabolite Atom-level Connectivity in Metabolic Networks
Molecular & Cellular Proteomics 2(9), 830-830 (2003)
HUPO 2nd Annual & IUBMB XIX World Congress (Montreal, Canada), October 8-11, 2003

Jun Ohta:
Structural Analysis of Metabolic Networks: Format Describing Intermetabolite Atom-Level Connectivity
Proceedings for 2003 Meeting, New Frontiers for Chem-Bio Informatics, Chem-Bio Informatics Society, 227-228 (2003)
CBI2003 (Tokyo, Japan) September 17-19, 2003

Jun Ohta:
Intermetabolite atom-level connectivity in a model metabolic network of carbohydrate metabolism
Programs and Abstracts, First IECA Conference on Systems Biology of E. coli, 112-112 (2003)
IECA2003, First IECA Conference on Systems Biology of E. Coli (Tsuruoka, Yamagata, Japan), June 23-25, 2003

This page is maintained by Jun Ohta, M.D.& Ph.D., Metabolism Group.
E-mail: jo25@md.okayama-u.ac.jp
Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences
Okayama University Medical School