publication . Other literature type . Article . 2015

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future

Pavlopoulos, Georgios A; Malliarakis, Dimitris; Papanikolaou, Nikolas; Theodosiou, Theodosis; Enright, Anton; Iliopoulos, Ioannis;
Open Access
  • Published: 25 Aug 2015
  • Publisher: (:unav)
  • Country: United Kingdom
Abstract
“Α picture is worth a thousand words.” This widely used adage sums up in a few words the notion that a successful visual representation of a concept should enable easy and rapid absorption of large amounts of information. Although, in general, the notion of capturing complex ideas using images is very appealing, would 1000 words be enough to describe the unknown in a research field such as the life sciences? Life sciences is one of the biggest generators of enormous datasets, mainly as a result of recent and rapid technological advances; their complexity can make these datasets incomprehensible without effective visualization methods. Here we discuss the past, p...
Subjects
free text keywords: Genome, Review, Biological data visualization, Network biology, Genomics, Systems biology, Multivariate analysis
Funded by
WT
Project
  • Funder: Wellcome Trust (WT)
,
EC| TRANSPOT
Project
TRANSPOT
Enhancing University of Crete Medical School Scientific Excellence and Translational Research Potential in Human Diseases
  • Funder: European Commission (EC)
  • Project Code: 285948
  • Funding stream: FP7 | SP4 | REGPOT
,
EC| INFLA-CARE
Project
INFLA-CARE
Understanding inflammation-associated tumorigenesis for the rational design of novel anti-cancer therapeutic strategies.
  • Funder: European Commission (EC)
  • Project Code: 223151
  • Funding stream: FP7 | SP1 | HEALTH
317 references, page 1 of 22

Howe, D, Costanzo, M, Fey, P, Gojobori, T, Hannick, L, Hide, W. Big data: the future of biocuration. Nature. 2008; 455: 47-50 [OpenAIRE] [PubMed] [DOI]

Liolios, K, Mavromatis, K, Tavernarakis, N, Kyrpides, NC. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 2008; 36: D475-9 [OpenAIRE] [PubMed] [DOI]

3.Census of Marine Life. How many species on Earth? About 8.7 million, new estimate says. ScienceDaily. 24 August 2011. ht tp://www.sciencedaily.com/releases/2011/08/110823180459.htm. Accessed 27 July 2015.

4.May M. Life Science Technologies: Big biological impacts from big data. Science. 2014; doi:10.1126/science.opms.p1400086.

Reddy, TB, Thomas, AD, Stamatis, D, Bertsch, J, Isbandi, M, Jansson, J. The Genomes OnLine Database (GOLD) v. 5: a metadata management system based on a four level (meta)genome project classification. Nucleic Acids Res. 2015; 43: D1099-1106 [OpenAIRE] [PubMed] [DOI]

Finishing the euchromatic sequence of the human genome. Nature. 2004; 431: 931-45 [OpenAIRE] [PubMed] [DOI]

Ezkurdia, I, Juan, D, Rodriguez, JM, Frankish, A, Diekhans, M, Harrow, J. Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes. Hum Mol Genet. 2014; 23: 5866-78 [OpenAIRE] [PubMed] [DOI]

Berman, H, Henrick, K, Nakamura, H. Announcing the worldwide Protein Data Bank. Nat Struct Biol. 2003; 10: 980 [OpenAIRE] [PubMed] [DOI]

Pavlopoulos, GA, Iacucci, E, Iliopoulos, I, Bagos, PG. Interpreting the Omics 'era' data. Multimedia Services in Intelligent Environments vol. 25. 2013: 79-100

Pavlopoulos, GA, Secrier, M, Moschopoulos, CN, Soldatos, TG, Kossida, S, Aerts, J. Using graph theory to analyze biological networks. BioData Min. 2011; 4: 10 [OpenAIRE] [PubMed] [DOI]

Moschopoulos, CN, Pavlopoulos, GA, Likothanassis, SD, Kossida, S. Analyzing protein-protein interaction networks with web tools. Curr Bioinform.. 2011; 6: 389-97 [OpenAIRE] [DOI]

Papanikolaou, N, Pavlopoulos, GA, Theodosiou, T, Iliopoulos, I. Protein-protein interaction predictions using text mining methods. Methods. 2015; 74: 47-53 [OpenAIRE] [PubMed] [DOI]

Pavlopoulos, GA, Promponas, VJ, Ouzounis, CA, Iliopoulos, I. Biological information extraction and co-occurrence analysis. Methods Mol Biol.. 2014; 1159: 77-92 [OpenAIRE] [PubMed] [DOI]

Puig, O, Caspary, F, Rigaut, G, Rutz, B, Bouveret, E, Bragado-Nilsson, E. The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods.. 2001; 24: 218-29 [OpenAIRE] [PubMed] [DOI]

Ito, T, Chiba, T, Ozawa, R, Yoshida, M, Hattori, M, Sakaki, Y. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA. 2001; 98: 4569-74 [OpenAIRE] [PubMed] [DOI]

317 references, page 1 of 22
Abstract
“Α picture is worth a thousand words.” This widely used adage sums up in a few words the notion that a successful visual representation of a concept should enable easy and rapid absorption of large amounts of information. Although, in general, the notion of capturing complex ideas using images is very appealing, would 1000 words be enough to describe the unknown in a research field such as the life sciences? Life sciences is one of the biggest generators of enormous datasets, mainly as a result of recent and rapid technological advances; their complexity can make these datasets incomprehensible without effective visualization methods. Here we discuss the past, p...
Subjects
free text keywords: Genome, Review, Biological data visualization, Network biology, Genomics, Systems biology, Multivariate analysis
Funded by
WT
Project
  • Funder: Wellcome Trust (WT)
,
EC| TRANSPOT
Project
TRANSPOT
Enhancing University of Crete Medical School Scientific Excellence and Translational Research Potential in Human Diseases
  • Funder: European Commission (EC)
  • Project Code: 285948
  • Funding stream: FP7 | SP4 | REGPOT
,
EC| INFLA-CARE
Project
INFLA-CARE
Understanding inflammation-associated tumorigenesis for the rational design of novel anti-cancer therapeutic strategies.
  • Funder: European Commission (EC)
  • Project Code: 223151
  • Funding stream: FP7 | SP1 | HEALTH
317 references, page 1 of 22

Howe, D, Costanzo, M, Fey, P, Gojobori, T, Hannick, L, Hide, W. Big data: the future of biocuration. Nature. 2008; 455: 47-50 [OpenAIRE] [PubMed] [DOI]

Liolios, K, Mavromatis, K, Tavernarakis, N, Kyrpides, NC. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 2008; 36: D475-9 [OpenAIRE] [PubMed] [DOI]

3.Census of Marine Life. How many species on Earth? About 8.7 million, new estimate says. ScienceDaily. 24 August 2011. ht tp://www.sciencedaily.com/releases/2011/08/110823180459.htm. Accessed 27 July 2015.

4.May M. Life Science Technologies: Big biological impacts from big data. Science. 2014; doi:10.1126/science.opms.p1400086.

Reddy, TB, Thomas, AD, Stamatis, D, Bertsch, J, Isbandi, M, Jansson, J. The Genomes OnLine Database (GOLD) v. 5: a metadata management system based on a four level (meta)genome project classification. Nucleic Acids Res. 2015; 43: D1099-1106 [OpenAIRE] [PubMed] [DOI]

Finishing the euchromatic sequence of the human genome. Nature. 2004; 431: 931-45 [OpenAIRE] [PubMed] [DOI]

Ezkurdia, I, Juan, D, Rodriguez, JM, Frankish, A, Diekhans, M, Harrow, J. Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes. Hum Mol Genet. 2014; 23: 5866-78 [OpenAIRE] [PubMed] [DOI]

Berman, H, Henrick, K, Nakamura, H. Announcing the worldwide Protein Data Bank. Nat Struct Biol. 2003; 10: 980 [OpenAIRE] [PubMed] [DOI]

Pavlopoulos, GA, Iacucci, E, Iliopoulos, I, Bagos, PG. Interpreting the Omics 'era' data. Multimedia Services in Intelligent Environments vol. 25. 2013: 79-100

Pavlopoulos, GA, Secrier, M, Moschopoulos, CN, Soldatos, TG, Kossida, S, Aerts, J. Using graph theory to analyze biological networks. BioData Min. 2011; 4: 10 [OpenAIRE] [PubMed] [DOI]

Moschopoulos, CN, Pavlopoulos, GA, Likothanassis, SD, Kossida, S. Analyzing protein-protein interaction networks with web tools. Curr Bioinform.. 2011; 6: 389-97 [OpenAIRE] [DOI]

Papanikolaou, N, Pavlopoulos, GA, Theodosiou, T, Iliopoulos, I. Protein-protein interaction predictions using text mining methods. Methods. 2015; 74: 47-53 [OpenAIRE] [PubMed] [DOI]

Pavlopoulos, GA, Promponas, VJ, Ouzounis, CA, Iliopoulos, I. Biological information extraction and co-occurrence analysis. Methods Mol Biol.. 2014; 1159: 77-92 [OpenAIRE] [PubMed] [DOI]

Puig, O, Caspary, F, Rigaut, G, Rutz, B, Bouveret, E, Bragado-Nilsson, E. The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods.. 2001; 24: 218-29 [OpenAIRE] [PubMed] [DOI]

Ito, T, Chiba, T, Ozawa, R, Yoshida, M, Hattori, M, Sakaki, Y. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA. 2001; 98: 4569-74 [OpenAIRE] [PubMed] [DOI]

317 references, page 1 of 22
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