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WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction

R. Overbeek
2000 Nucleic Acids Research  
The WIT (What Is There) (http://wit.mcs.anl.gov/WIT2/ ) system has been designed to support comparative analysis of sequenced genomes and to generate metabolic reconstructions based on chromosomal sequences  ...  of gene functions and for development of overviews of genomes within WIT.  ...  Using the WIT genome analysis system, a major part of the central metabolism of an organism can be reconstructed entirely in silico (16) .  ... 
doi:10.1093/nar/28.1.123 pmid:10592199 pmcid:PMC102471 fatcat:nb5kgeksafhsrilrgpgm7l3yfq

Systems metabolic engineering: Genome-scale models and beyond

John Blazeck, Hal Alper
2010 Biotechnology Journal  
The most pragmatic systems-based tool for metabolic engineering to arise is the in silico genome-scale metabolic reconstruction.  ...  The advent of high throughput genome-scale bioinformatics has led to an exponential increase in available cellular system data.  ...  Acknowledgments We acknowledge support from NIH (Grant number: 1R01GM090221-01) and the Camille and Henry Dreyfus New Faculty Award.  ... 
doi:10.1002/biot.200900247 pmid:20151446 pmcid:PMC2911524 fatcat:kcqqwagubfgavpoh65u2xy7g3y

MAGMA: inference of sparse microbial association networks [article]

Arnaud Pierre Cougoul, Xavier Bailly, Ernst C. Wit
2019 bioRxiv   pre-print
Microorganisms often live in symbiotic relationship with their environment and they play a central role in many biological processes. They form a complex system of interacting species.  ...  Until now correlation-based network analysis and graphical modelling have been used to identify the putative interaction networks formed by the species of microorganisms, but these methods do not take  ...  Acknowledgments The work was funded by two INRA metaprogrammes: Meta-omics of microbial ecosystems (MEM) and Integrated management of animal health (GISA) and by the European Cooperation for Statistics  ... 
doi:10.1101/538579 fatcat:c5fwm3fk7ja3tc3ixlsyuae4se

Networks and Graphs Discovery in Metabolomics Data Analysis and Interpretation

Adam Amara, Clément Frainay, Fabien Jourdan, Thomas Naake, Steffen Neumann, Elva María Novoa-del-Toro, Reza M Salek, Liesa Salzer, Sarah Scharfenberg, Michael Witting
2022 Frontiers in Molecular Biosciences  
Then, we present the state of the art of network-based methods for mass spectrometry-based metabolomics data analysis, as well as future developments expected in this area.  ...  Untargeted approaches allow to detect as many metabolites as possible at once, identify unexpected metabolic changes, and characterize novel metabolites in biological samples.  ...  ., and Palsson, B. Ø. (2010). A Protocol for Generating a High-Quality Genome-Scale Metabolic Reconstruction. Nat.  ... 
doi:10.3389/fmolb.2022.841373 pmid:35350714 pmcid:PMC8957799 fatcat:7teponhsdvhezny25s5mvrpioy

Automatic Generation of Cell-Wide Pathway Model from Complete Genome

Kazuharu Arakawa, Yohei Yamada, Hiromi Komai, Kosaku Shinoda, Yoichi Nakayama, Masaru Tomita
2003 Genome Informatics Series  
The Genome-based E-cell Modeling System (GEM System) developed upon the generic bioinformatics workbench G-language Genome Analysis Environment [1] realizes a fully automatic conversion of genome sequence  ...  Therefore a large scale modeling of cell in silico demands for a novel high-throughput approach.  ... 
doi:10.11234/gi1990.14.639 fatcat:qynlgeg2lnab3jlwl5rvht7ueu

Integration of expression data in genome-scale metabolic network reconstructions

Anna S. Blazier, Jason A. Papin
2012 Frontiers in Physiology  
In this review, we summarize such FBA-based methods for integrating expression data into genome-scale metabolic network reconstructions, highlighting their advantages as well as their limitations.  ...  Several recent studies have successfully demonstrated how flux balance analysis (FBA), a constraint-based modeling approach, can be used to integrate transcriptomic data into genome-scale metabolic network  ...  ACKNOWLEDGMENTS The authors would like to thank Arvind Chavali, Kevin D'Auria, and Paul Jensen for reading the manuscript and for providing valuable feedback.  ... 
doi:10.3389/fphys.2012.00299 pmid:22934050 pmcid:PMC3429070 fatcat:ayxykl6vvfhv7c7zqk3xfxmpre

Metabolic modeling of microbial strains in silico

Markus W. Covert, Christophe H. Schilling, Iman Famili, Jeremy S. Edwards, Igor I. Goryanin, Evgeni Selkov, Bernhard O. Palsson
2001 TIBS -Trends in Biochemical Sciences. Regular ed  
Many high-throughput experimental technologies have been developed in recent years that have enabled full genomic sequences to be obtained, genome-wide expression assessment to be performed and the protein  ...  Several high-quality genomic database and metabolic network reconstruction web sites that provide access to the annotated genome sequences of many organisms can be found online 5, 6 .  ... 
doi:10.1016/s0968-0004(00)01754-0 pmid:11246024 fatcat:hjkbmt6uence5cqci25ujim7uy

The ERGOTM genome analysis and discovery system

R. Overbeek
2003 Nucleic Acids Research  
The ERGO TM (http://ergo.integratedgenomics.com/ ERGO/) genome analysis and discovery suite is an integration of biological data from genomics, biochemistry, high-throughput expression profiling, genetics  ...  The current version of the system integrates 500 genomes from all domains of life in various levels of completion, 403 of which are available for subscription.  ...  Lihua Zhu, as well as the Sequencing, Assembly, Microarray and Applications groups of Integrated Genomics for their contribution to the ERGO development.  ... 
doi:10.1093/nar/gkg148 pmid:12519973 pmcid:PMC165577 fatcat:w77bcjopvjfvjow3ua7zpsn5ge

Unpredictability of metabolism—the key role of metabolomics science in combination with next-generation genome sequencing

Wolfram Weckwerth
2011 Analytical and Bioanalytical Chemistry  
and RNA sequencing for transcriptome studies.  ...  Strategies for genome-scale measurement, modelling and predicting of dynamic metabolic networks need to be applied.  ...  Acknowledgments I thank Anke Bellaire and Xiaoliang Sun for all our fruitful discussions. I apologize to all colleagues who have been cited incompletely due to space problems.  ... 
doi:10.1007/s00216-011-4948-9 pmid:21556754 pmcid:PMC3098350 fatcat:pykytnqi65hm3iybb6cs6h6v6u

Conquering computational challenges of omics data and post-ENCODE paradigms

Yves A Lussier, Haiquan Li, Mark Maienschein-Cline
2013 Genome Biology  
Tools for effi cient and accurate analysis of newly generated high-throughput data are continuing to be developed.  ...  Th e past few years have witnessed an unprecedented development of high-throughput technologies, particularly in next-generation sequencing, that measure nearly every molecule of life and its modifi cations  ...  Acknowledgements This work has been supported in part by the University of Illinois Cancer Center, the University of Illinois CCTS (UL1TR000050) and The Institute for Interventional Health Informatics.  ... 
doi:10.1186/gb-2013-14-8-310 pmid:23998801 pmcid:PMC4053832 fatcat:csdndkvprrf7fea2ybljmgezfe

Building Biofoundry India: Challenges and Path Forward

Binay Panda, Pawan K Dhar
2021 Synthetic Biology  
We describe three key areas of our focus, harnessing the potential of non-expressing parts of the sequenced genomes, using deep learning in pathway reconstruction, and synthesis of enzymes and metabolites  ...  In this perspective, we describe our efforts to build Biofoundry India (BI) and where we see the facility add substantial value in supporting research, innovation, and entrepreneurship.  ...  ACKNOWLEDGEMENTS We thank Paul Freemont and Neeraja M Krishnan for critically reading the manuscript and NMK for helping us with Figure 2 .  ... 
doi:10.1093/synbio/ysab015 pmid:34712840 pmcid:PMC8546612 fatcat:j5tj7wosrndotezhkbjknm6dju

Microbial Metabolomics

Jane Tang
2011 Current Genomics  
Recent advancement of technologies and post-genomic developments enable the study and analysis of metabolome.  ...  Microbial metabolomics constitutes an integrated component of systems biology.  ...  Availability of Genomic Sequences The last decade witnessed a profound increase in capability to perform low-cost, high-throughput sequencing.  ... 
doi:10.2174/138920211797248619 pmid:22379393 pmcid:PMC3178908 fatcat:s255k7dstvgz3ggftszg3svzwq

Gnare: Automated System For High-Throughput Genome Analysis With Grid Computational Backend

Dinanath Sulakhe, Alex Rodriguez, Mark D'Souza, Michael Wilde, Veronika Nefedova, Ian Foster, Natalia Maltsev
2005 Journal of clinical monitoring and computing  
To leverage this we have developed the Genome Analysis Research Environment (GNARE) -a scalable computational system for the highthroughput analysis of genomes, which provides an integrated database and  ...  The Grid, with its aggregated and distributed computational and storage infrastructure, offers an ideal platform for high-throughput bioinformatics analysis.  ...  and the systems support groups of MCS, GRID2003, Globus, Condor, and iVDGL VDT.  ... 
doi:10.1007/s10877-005-3463-y pmid:16328950 fatcat:224zf24f45gaxon67rpctoadi4

GNARE: an environment for grid-based high-throughput genome analysis

D. Sulakhe, A. Rodriguez, M. D'Souza, M. Wilde, V. Nefedova, I. Foster, N. Maltsev
2005 CCGrid 2005. IEEE International Symposium on Cluster Computing and the Grid, 2005.  
To leverage this we have developed the Genome Analysis Research Environment (GNARE) -a scalable computational system for the highthroughput analysis of genomes, which provides an integrated database and  ...  The Grid, with its aggregated and distributed computational and storage infrastructure, offers an ideal platform for high-throughput bioinformatics analysis.  ...  , and the systems support groups of MCS, GRID2003, Globus, Condor, and iVDGL VDT.  ... 
doi:10.1109/ccgrid.2005.1558590 dblp:conf/ccgrid/SulakheRDWNFM05 fatcat:ieavcecyjvcnhpwh5cpztu4n5q

Building biological foundries for next-generation synthetic biology

Ran Chao, YongBo Yuan, HuiMin Zhao
2015 Science China Life Sciences  
design, DNA assembly, DNA sequencing, metabolite analysis Citation: Chao R, Yuan YB, Zhao HM.  ...  This review summarizes the state-of-the-art technologies for synthetic biology and discusses the challenges to establish such biological foundries. biofabrication, automation, metabolic engineering, biosystems  ...  Based on 9-AA matrix, a MALDI-MSbased approach was reported by Yukihira and co-workers which enables high sensitivity and high throughput metabolite analysis for intracellular metabolic dynamics [75]  ... 
doi:10.1007/s11427-015-4866-8 pmid:25985756 fatcat:l7irzybvhzaslewlvnicjkp2oi
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