Filters








29,624 Hits in 7.3 sec

Experimental Construction of Very Large Scale DNA Databases with Associative Search Capability [chapter]

John H. Reif, Thomas H. LaBean, Michael Pirrung, Vipul S. Rana, Bo Guo, Carl Kingsford, Gene S. Wickham
2002 Lecture Notes in Computer Science  
We describe the experimental creation of very large databases of artificially synthesized DNA sequences designed for encoding digital data.  ...  DNA has the theoretical capability of storing vast databases in a very compact volume, for example, a gram of DNA can store 4.2 x 10 21 bits of information.  ...  We are currently adapting our database system for construction of large cDNA libraries with synthetic DNA tags on both ends of each element for more complex associative search procedures.  ... 
doi:10.1007/3-540-48017-x_22 fatcat:lttgtsmgx5gdlefbbuwvvtlp4e

A Content-Addressable DNA Database with Learned Sequence Encodings [chapter]

Kendall Stewart, Yuan-Jyue Chen, David Ward, Xiaomeng Liu, Georg Seelig, Karin Strauss, Luis Ceze
2018 Lecture Notes in Computer Science  
We present strand and codeword design schemes for a DNA database capable of approximate similarity search over a multidimensional dataset of content-rich media.  ...  Our strand designs address crosstalk in associative DNA databases, and we demonstrate a novel method for learning DNA sequence encodings from data, applying it to a dataset of tens of thousands of images  ...  Acknowledgements We would like to thank the anonymous reviewers for their input, which were very helpful to improve the manuscript.  ... 
doi:10.1007/978-3-030-00030-1_4 fatcat:53747qnwe5alnlw2nil7gjlmsu

Alternative Computational Models: A Comparison of Biomolecular and Quantum Computation [chapter]

John H. Reif
1998 Lecture Notes in Computer Science  
., NP search problems), if solved with polynomial time bounds, requires exponentially large volume for BMC, so BMC does not scale well to solve very large NP search problems.  ...  In addition to NP search problems and database search problems, we enumerate a wide variety of further potential practical applications of BMC and QC.  ...  Brassard for his clear explanation of numerous results in the field of QC. Also, I would like to thank P. Shor and U.  ... 
doi:10.1007/978-3-540-49382-2_10 fatcat:icfyjfvgejdznldkvarhgtdypm

CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle

H. Kurata
2003 Nucleic Acids Research  
We have developed the software suite, CADLIVE (Computer-Aided Design of LIVing systEms), which features a graphical user interface (GUI) to edit large-scale maps of complicated signal transduction pathways  ...  We propose the regulator±reaction equations combined with detailed attributes including the associated cellular component, molecular function, and biological process and present the simulation-directed  ...  ACKNOWLEDGEMENTS This study was carried out as a part of The Project for Development of a Technological Infrastructure for Industrial Bioprocesses on R&D of New Industrial Science and Technology Frontiers  ... 
doi:10.1093/nar/gkg461 pmid:12853624 pmcid:PMC165976 fatcat:w7c4grk5jzghdapp5qyswsav5e

cerebra: A tool for fast and accurate summarizing of variant calling format (VCF) files

Lincoln Harris, Rohan Vanheusden, Olga Botvinnik, Spyros Darmanis
2020 Zenodo  
Conclusions RNA/DNA sequencing paired with fast and accurate summarizing of variants is often crucial to understanding the biology of an experimental system.  ...  VCF files encode: i) the genomic position, ii) reference vs. observed DNA sequence, and iii) quality associated with each observed variant. Shown below are the first 4 lines of a sample VCF file.  ... 
doi:10.5281/zenodo.4037272 fatcat:zhubc2kogvfsrmgsihmzbo2awa

Prediction, Annotation, and Analysis of Human Promoters

M.Q. ZHANG
2003 Cold Spring Harbor Symposia on Quantitative Biology  
Acknowledgements I would like to thank all (including previous) members of Zhang lab and my collaborators for contributing most of the data and the figures, many before publications.  ...  With only the primary DNA sequences, one would have to use large-scale statistical features of those length characteristics.  ...  These experimental exercises have demonstrated the validity of the large-scale computational prediction plus experimental verification approach for accurate genome annotation.  ... 
doi:10.1101/sqb.2003.68.217 pmid:15338621 fatcat:cnnsldcc7jeirm6yg2gz6kcwwe

Genomic Mapping and Mapping Databases [chapter]

Peter S. White, Tara C. Matise
2002 Methods of biochemical analysis  
With the pending availability of a finished human sequence, most efforts to construct genomic maps will come to a halt; however, integrated maps, genome catalogues, and comprehensive databases linking  ...  By taking advantage of the available maps and DNA sequence, a researcher can, in many cases, focus in on a candidate region by searching public mapping databases in a matter of hours rather than by performing  ...  For chromosomes with complete DNA sequence available, the Mb estimates are very precise.  ... 
doi:10.1002/0471223921.ch6 fatcat:x4v2e6gl7vc7dn5esov7sanque

Bioinformatics and genomic medicine

Ju Han Kim
2002 Genetics in Medicine  
A flood of large-scale genomic and postgenomic data means that many of the challenges in biomedical research are now challenges in computational science.  ...  , and the integrated management of biomolecular databases, are also discussed.  ...  Acknowledgment This study was supported by a grant from the Korea Health 21 R&D Project, Ministry of Health & Welfare, Republic of Korea (01-PJ10-PG6-01GM01-0004).  ... 
doi:10.1097/00125817-200211001-00013 pmid:12544491 fatcat:mjvvr4xg7rdz3o7bumqdex6onu

Soft computing data mining

Sankar K Pal, Ashish Ghosh
2004 Information Sciences  
While the next four articles deal with classificatory rule analysis, the sixth one concerns with association rule mining.  ...  and understandable patterns from large data bases, where the data is frequently ambiguous, incomplete, noisy, redundant and changes with time.  ...  Based on experimentation, the algorithm has been found suitable for large databases.  ... 
doi:10.1016/j.ins.2003.03.012 fatcat:76s2jvritzedfb6wfjiquqql7u

Soft computing data mining

S PAL
2004 Information Sciences  
While the next four articles deal with classificatory rule analysis, the sixth one concerns with association rule mining.  ...  and understandable patterns from large data bases, where the data is frequently ambiguous, incomplete, noisy, redundant and changes with time.  ...  Based on experimentation, the algorithm has been found suitable for large databases.  ... 
doi:10.1016/s0020-0255(03)00412-2 fatcat:flcop34blzeajivwiug5dhzpyq

Computational tools for metabolic engineering

Wilbert B. Copeland, Bryan A. Bartley, Deepak Chandran, Michal Galdzicki, Kyung H. Kim, Sean C. Sleight, Costas D. Maranas, Herbert M. Sauro
2012 Metabolic Engineering  
A great variety of software applications are now employed in the metabolic engineering field. These applications have been created to support a wide range of experimental and analysis techniques.  ...  Computational tools are utilized throughout the metabolic engineering workflow to extract and interpret relevant information from large data sets, to present complex models in a more manageable form, and  ...  The funders had no role in the decision to publish, or in the preparation of the manuscript.  ... 
doi:10.1016/j.ymben.2012.03.001 pmid:22629572 pmcid:PMC3361690 fatcat:xqnmydnnejcupp2ujup45krwnm

Building with a scaffold: emerging strategies for high- to low-level cellular modeling

Trey Ideker, Douglas Lauffenburger
2003 Trends in Biotechnology  
Large-scale experimental measurements validate high-level models, whereas targeted experimental manipulations and measurements test low-level models.  ...  We review the important trends that make this approach feasible and describe how they are spurring the development of models at multiple levels of abstraction.  ...  Ozier for inspiring discussions and for very helpful comments on the manuscript. T.I. was generously supported by a research fellowship from Pfizer; D.L. was supported by grants from DARPA and NIGMS.  ... 
doi:10.1016/s0167-7799(03)00115-x pmid:12788545 fatcat:anguqrphzfa7pkbfvn5mf6mf7q

Functional modules integrating essential cellular functions are predictive of the response of leukaemia cells to DNA damage

Katrin Sameith, Philipp Antczak, Elliot Marston, Nil Turan, Dieter Maier, Tanja Stankovic, Francesco Falciani
2008 Computer applications in the biosciences : CABIOS  
Availability: Supplementary material including R code, additional results, experimental datasets, as well as a detailed description of the methodology are available at  ...  We have discovered that the overall activity of functional modules integrating protein degradation and mRNA processing is predictive of response to DNA damage.  ...  With the development of integrated databases combining several public repositories it is therefore likely that module-based analysis will become a standard tool in Bioinformatics for mining large-scale  ... 
doi:10.1093/bioinformatics/btn489 pmid:18801750 fatcat:ckv44p73pvdejlnjwa4n73kjce

cerebra: A tool for fast and accurate summarizing of variant calling format (VCF) files

Lincoln Harris, Rohan Vanheusden, Olga Botvinnik, Spyros Darmanis
2020 Journal of Open Source Software  
Conclusions RNA/DNA sequencing paired with fast and accurate summarizing of variants is often crucial to understanding the biology of an experimental system.  ...  VCF files encode: i) the genomic position, ii) reference vs. observed DNA sequence, and iii) quality associated with each observed variant. Shown below are the first 4 lines of a sample VCF file.  ... 
doi:10.21105/joss.02432 fatcat:ihkdnk64fjaivaywejb5znm2bi

Annotation, comparison and databases for hundreds of bacterial genomes

Claudine Médigue, Ivan Moszer
2007 Research in Microbiology  
sites in protein sequences Comparative genomic tools Mauve http://gel.ahabs.wisc.edu/mauve/ Multiple genome alignments in the presence of large-scale evolutionary events MOSAIC Define the set of backbones  ...  This paper reviews advances in the development of bacterial annotation and comparative analysis tools, and progress in the design of novel database structures for the integration of heterogeneous biological  ...  We need to improve the quality and the speed of annotation, and to combine computational analysis with results of experimental studies (both large-scale investigations and focused assays), especially to  ... 
doi:10.1016/j.resmic.2007.09.009 pmid:18031997 fatcat:bfw4zslyw5bgrdtrxhozk2uc7e
« Previous Showing results 1 — 15 out of 29,624 results