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Incorporating Machine Learning into Established Bioinformatics Frameworks

Noam Auslander, Ayal B. Gussow, Eugene V. Koonin
2021 International Journal of Molecular Sciences  
The exponential growth of biomedical data in recent years has urged the application of numerous machine learning techniques to address emerging problems in biology and clinical research.  ...  Machine learning techniques are frequently integrated with bioinformatic methods, as well as curated databases and biological networks, to enhance training and validation, identify the best interpretable  ...  The bioinformatics approaches include sequence analysis, comparative genomics, molecular evolution studies and phylogenetics, protein and RNA structure prediction, gene expression and regulation analysis  ... 
doi:10.3390/ijms22062903 pmid:33809353 pmcid:PMC8000113 fatcat:ssfoobbtcjhidbaffbkakqbwfe

XML-based approaches for the integration of heterogeneous bio-molecular data

Marco Mesiti, Ernesto Jiménez-Ruiz, Ismael Sanz, Rafael Berlanga-Llavori, Paolo Perlasca, Giorgio Valentini, David Manset
2009 BMC Bioinformatics  
In this paper we survey the most interesting and novel approaches for the representation, integration and management of different kinds of biological data by exploiting XML and the related recommendations  ...  The today's public database infrastructure spans a very large collection of heterogeneous biological data, opening new opportunities for molecular biology, bio-medical and bioinformatics research, but  ...  This article has been published as part of BMC Bioinformatics Volume 10 Supplement 12, 2009: Bioinformatics Methods for Biomedical Complex System Applications.  ... 
doi:10.1186/1471-2105-10-s12-s7 pmid:19828083 pmcid:PMC2762072 fatcat:n4tvxjx3ifadjbo4x7jbpx5zfa

From Sequence to Biology: The Impact on Bioinformatics

R. Fuchs
2002 Bioinformatics  
data representation, database integration, knowledge management, and simulations.  ...  Considerable headway has been made in the last decade to improve the quality of structure prediction approaches, however, the chasm between protein structure and precise molecular function is still wide  ... 
doi:10.1093/bioinformatics/18.4.505 pmid:12016047 fatcat:g3mrcgyodnbgnjtsoac4dwyri4

XML-Based Approaches for the Integration of Heterogeneous Bio-Molecular Data [chapter]

Marco Mesiti, Ernesto Jiménez-Ruiz, Ismael Sanz, Rafael Berlanga-Llavori, Paolo Perlasca, Giorgio Valentini, David Manset
2011 Recent Advances in Biochemistry  
Results: In this paper we survey the most interesting and novel approaches for the representation, integration and management of different kinds of biological data by exploiting XML and the related recommendations  ...  Abstract Background: The today's public database infrastructure spans a very large collection of heterogeneous biological data, opening new opportunities for molecular biology, bio-medical and bioinformatics  ...  This article has been published as part of BMC Bioinformatics Volume 10 Supplement 12, 2009: Bioinformatics Methods for Biomedical Complex System Applications.  ... 
doi:10.1201/b13131-13 fatcat:ytu7u4pcbzgbflpblij6x3wwky

XML in Motion from Genome to Drug

C. Gopi Mohan, C. Gopi Mohan
2007 Nature Precedings  
Researchers involved in genomics, proteomics, transcriptional profiling, high throughput structure determination, and in other sub-disciplines of bioinformatics have direct impact on this IT revolution  ...  As the full genome sequences of many species, data from structural genomics, micro-arrays, and proteomics became available, integration of these data to a common platform require sophisticated bioinformatics  ...  Nowdays, in structural genomics, XML representation of sequence and structure is developing, to accelerate the data representation, storage, retrieval and exchange through internet, and is presented in  ... 
doi:10.1038/npre.2007.287.1 fatcat:3c5nn4v4fbbqrgkgz5eculwylm

XML in Motion from Genome to Drug

C. Gopi Mohan, C. Gopi Mohan
2007 Nature Precedings  
Researchers involved in genomics, proteomics, transcriptional profiling, high throughput structure determination, and in other sub-disciplines of bioinformatics have direct impact on this IT revolution  ...  As the full genome sequences of many species, data from structural genomics, micro-arrays, and proteomics became available, integration of these data to a common platform require sophisticated bioinformatics  ...  Nowdays, in structural genomics, XML representation of sequence and structure is developing, to accelerate the data representation, storage, retrieval and exchange through internet, and is presented in  ... 
doi:10.1038/npre.2007.287 fatcat:x2uxyxnleva7ra53jgjecojolm

Toolboxes for a standardised and systematic study of glycans

Matthew P Campbell, René Ranzinger, Thomas Lütteke, Julien Mariethoz, Catherine A Hayes, Jingyu Zhang, Yukie Akune, Kiyoko F Aoki-Kinoshita, David Damerell, Giorgio Carta, Will S York, Stuart M Haslam (+5 others)
2014 BMC Bioinformatics  
Automation of structure analysis then calls for software development since adding meaning to large data collections in reasonable time requires corresponding bioinformatics methods and tools.  ...  Recent progress in method development for characterising the branched structures of complex carbohydrates has now enabled higher throughput technology.  ...  Acknowledgements RR and WSY are supported by NIH/NIGMS funding the National Center for Glycomics and Glycoproteomics (8P41GM103490) and the Beilstein-Institut, a non-profit foundation located in Frankfurt  ... 
doi:10.1186/1471-2105-15-s1-s9 pmid:24564482 pmcid:PMC4016020 fatcat:yklyisg7lfdxrb4cpgldufvrve

Mining Substructures in Protein Data

Fedja Hadzic, Tharam S. Dillon, Amandeep S. Sidhu, Elizabeth Chang, Henry Tan
2006 Sixth IEEE International Conference on Data Mining - Workshops (ICDMW'06)  
This has given rise to the development of many tree mining algorithms which can aid in structural comparisons, association rule discovery and in general mining of tree structured knowledge representations  ...  This approach is shown to be a viable technique for mining protein data.  ...  Run-Time Biological Interpretation In bioinformatics, the discovery of structural patterns by matching data representation structures is essential for analysis and understanding of biological data.  ... 
doi:10.1109/icdmw.2006.114 dblp:conf/icdm/HadzicDSCT06 fatcat:7ebzkdbbnvg2pd7uiqhxhbbqai

Ontologies in Bioinformatics [chapter]

Robert Stevens, Chris Wroe, Phillip Lord, Carole Goble
2004 Handbook on Ontologies  
Ontologies in bioinformatics cover a wide range of usages and representation styles.  ...  Given the exponential growth of already large quantities of data and associated knowledge, this is an unsustainable form of representation.  ...  An informatics ontology captures the key concepts of data, data structures, databases, metadata and so forth.  ... 
doi:10.1007/978-3-540-24750-0_32 fatcat:uq7ieianz5bijcvyvxyh7z2o7u

The role of bioinformatics in pathway curation

A. S. Waagmeester, T. Kelder, C. T. A. Evelo
2008 Genes & Nutrition  
We describe the role of bioinformatics in facilitating the creation and curation of pathway.  ...  Pathway models are used in the analysis of genomic data.  ...  Open Access This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided  ... 
doi:10.1007/s12263-008-0098-x pmid:19034548 pmcid:PMC2593017 fatcat:rzbowrplindixfl3sdtbjrh5ca

Systems chemical biology

Tudor I Oprea, Alexander Tropsha, Jean-Loup Faulon, Mark D Rintoul
2007 Nature Chemical Biology  
The increasing availability of data related to genes, proteins and their modulation by small molecules, paralleled by the emergence of simulation tools in systems biology, has provided a vast amount of  ...  However, there is a critical need to develop cheminformatics tools that can integrate chemical knowledge with these biological databases, with the goal of creating systems chemical biology.  ...  In these databases, all objects are clickable, and lead to additional information related to reactions and pathways (all objects), and to gene and protein data, including links to other on-line databases  ... 
doi:10.1038/nchembio0807-447 pmid:17637771 pmcid:PMC2734506 fatcat:kp7sylazfbcihfvamigtnqplme

VINEdb: a data warehouse for integration and interactive exploration of life science data

Sridhar Hariharaputran, Thoralf Töpel, Björn Brockschmidt, Ralf Hofestädt, Bioinformatics, Medical Informatics Department, Bielefeld University Library, Publikationsdienste.Ub@Uni-Bielefeld.De, BieColl, Bielefeld University
2008 Journal of Integrative Bioinformatics  
The molecular interactions involved in this and other processes are analyzed and annotated by experts and stored as data in different databases.  ...  The key task is to integrate, manage and visualize these data available from different sources and present them in a user-comprehensible manner.  ...  Acknowledgements The work is funded by the DFG Graduate College Bioinformatics at Bielefeld University.  ... 
doi:10.2390/biecoll-jib-2007-63 dblp:journals/jib/HariharaputranTBH07 fatcat:lhysmhjc75hydeituotepr57aa

Bioinformatics and molecular modeling in glycobiology

Martin Frank, Siegfried Schloissnig
2010 Cellular and Molecular Life Sciences (CMLS)  
In this review, the various graphical representations and sequence formats of carbohydrates are introduced, and an overview of newly developed databases, the latest developments in sequence alignment and  ...  Consequently, the availability of databases and tools to store, retrieve and analyze these data in an efficient way is of fundamental importance to progress in glycobiology.  ...  In this respect, bioinformatics provides databases and tools to support glycobiologists in their research.  ... 
doi:10.1007/s00018-010-0352-4 pmid:20364395 pmcid:PMC2912727 fatcat:o6wy4fvsavhgrgo7avdl2cl2sa

Performance Comparison of Five Exact Graph Matching Algorithms on Biological Databases [chapter]

Vincenzo Carletti, Pasquale Foggia, Mario Vento
2013 Lecture Notes in Computer Science  
Graphs are a powerful data structure that can be applied to several problems in bioinformatics.  ...  In this paper we will consider some popular and freely available matching algorithms, and will experimentally compare them on graphs derived from bioinformatics applications, in order to help the researchers  ...  Introduction Graphs are a powerful and flexible data structure that can be used for the representation of several kinds of data in many applicative fields [9] [5] [7] .  ... 
doi:10.1007/978-3-642-41190-8_44 fatcat:5m5uvkeparfbrfkpo5cdui7qfm

MultiSeq: unifying sequence and structure data for evolutionary analysis

Elijah Roberts, John Eargle, Dan Wright, Zaida Luthey-Schulten
2006 BMC Bioinformatics  
Currently, more than 3 million sequences and 35 thousand structures of proteins and nucleic acids are available in public databases.  ...  Here we present MultiSeq, a unified bioinformatics analysis environment that allows one to organize, display, align and analyze both sequence and structure data for proteins and nucleic acids.  ...  All of the authors would also like to specially thank Carl Woese for his suggestions about the software features necessary to analyze and edit sequence data in an evolutionary framework.  ... 
doi:10.1186/1471-2105-7-382 pmid:16914055 pmcid:PMC1586216 fatcat:qdppsxqqazf2vkxe2s2x3kudbm
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