The 2017 Network Tools and Applications in Biology (NETTAB) workshop: Aims, topics and outcomes: BMC Bioinformatics

P. Romano; A. Céol; A. Dräger; A. Fiannaca; R. Giugno; M. La Rosa; L. Milanesi; U. Pfeffer; R. Rizzo; S.-Y. Shin; J. Xia; A. Urso

doi:10.1186/s12859-019-2681-0

The 2017 Network Tools and Applications in Biology (NETTAB) workshop: Aims, topics and outcomes: BMC Bioinformatics

P. Romano, A. Céol, A. Dräger, A. Fiannaca, R. Giugno, M. La Rosa, L. Milanesi, U. Pfeffer, R. Rizzo, S.-Y. Shin, J. Xia, A. Urso

Research output: Contribution to journal › Article › peer-review

Abstract

The 17th International NETTAB workshop was held in Palermo, Italy, on October 16-18, 2017. The special topic for the meeting was "Methods, tools and platforms for Personalised Medicine in the Big Data Era", but the traditional topics of the meeting series were also included in the event. About 40 scientific contributions were presented, including four keynote lectures, five guest lectures, and many oral communications and posters. Also, three tutorials were organised before and after the workshop. Full papers from some of the best works presented in Palermo were submitted for this Supplement of BMC Bioinformatics. Here, we provide an overview of meeting aims and scope. We also shortly introduce selected papers that have been accepted for publication in this Supplement, for a complete presentation of the outcomes of the meeting. © 2019 The Author(s).

Original language	English
Journal	BMC Bioinform.
Volume	20
DOIs	https://doi.org/10.1186/s12859-019-2681-0
Publication status	Published - 2019

Keywords

Network tools
Oral communication
Personalised medicines
Scientific contributions
bioinformatics
biology
publication
review
genetics
genomics
health care delivery
human
Italy
neoplasm
personalized medicine
procedures
Computational Biology
Delivery of Health Care
Genomics
Humans
Neoplasms
Precision Medicine

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@article{2ae5705b49d44926946774b0e505c9f5,

title = "The 2017 Network Tools and Applications in Biology (NETTAB) workshop: Aims, topics and outcomes: BMC Bioinformatics",

abstract = "The 17th International NETTAB workshop was held in Palermo, Italy, on October 16-18, 2017. The special topic for the meeting was {"}Methods, tools and platforms for Personalised Medicine in the Big Data Era{"}, but the traditional topics of the meeting series were also included in the event. About 40 scientific contributions were presented, including four keynote lectures, five guest lectures, and many oral communications and posters. Also, three tutorials were organised before and after the workshop. Full papers from some of the best works presented in Palermo were submitted for this Supplement of BMC Bioinformatics. Here, we provide an overview of meeting aims and scope. We also shortly introduce selected papers that have been accepted for publication in this Supplement, for a complete presentation of the outcomes of the meeting. {\textcopyright} 2019 The Author(s).",

keywords = "Network tools, Oral communication, Personalised medicines, Scientific contributions, bioinformatics, biology, publication, review, genetics, genomics, health care delivery, human, Italy, neoplasm, personalized medicine, procedures, Computational Biology, Delivery of Health Care, Genomics, Humans, Neoplasms, Precision Medicine",

author = "P. Romano and A. C{\'e}ol and A. Dr{\"a}ger and A. Fiannaca and R. Giugno and {La Rosa}, M. and L. Milanesi and U. Pfeffer and R. Rizzo and S.-Y. Shin and J. Xia and A. Urso",

note = "Export Date: 2 March 2020 CODEN: BBMIC Correspondence Address: Romano, P.; IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, Italy; email: paolo.romano@hsanmartino.it Funding details: National Research Council Funding details: National Council for Scientific Research Funding text 1: The last guest lecture was given by Luana Licata, ELIXIR-IIB, Italy. The lecture, titled “ELIXIR-IIB: the Italian Infrastructure for Bioinformatics: a growing support to national and international research in life sciences”, gave an overview on the ELIXIR Italian node and infrastructure for bioinformatics. The node is coordinated by the National Research Council and currently includes 17 centers of excellence among which are research institutes, universities and technological institutions. The infrastructure supports the exchange and development of skills, and the integration of publicly available and internationally recognised Italian bioinformatics resources within the European infrastructure. Funding text 2: The second tutorial was offered by the CNR InterOmics Flagship project. The tutorial, titled “Biological network-based analysis of omics for precision medicine: overview, interaction databases and network diffusion approaches”, was given by Ettore Mosca, Institute of Biomedical Technologies, National Research Council of Italy, Milan, Italy. The tutorial illustrated how the known molecular interactions can be useful in the interpretation of “omics” data for precision medicine, with a main focus on data referable to genes. The first part introduced broad objectives and principles of biological network-based analyses of “omics” data. Then, an overview of the state-of-the art of current datasets from which networks can be defined was given, also in term of their completeness in relation to the coverage of high-throughput technologies and the issues in mapping “omics” data to biological networks. The second part focused on network diffusion-based approaches and illustrated how the principles behind this class of methods have been recently applied to several problems, including patient stratification and gene module extraction. Throughout the tutorial, benefits, limitations and open issues in the field of network-based analysis were underlined, including also software availability and computational cost. References: NETTAB Workshops, , http://www.nettab.org/, Accessed 26 Feb 2019; NETTAB 2017 Workshop, , http://www.igst.it/nettab/2017/, Accessed 26 Feb 2019; Barab{\'a}si, A.L., Oltvai, Z.N., Network biology: Understanding the cell's functional organization (2004) Nat Rev Genet, 5, p. 101. , https://doi.org/10.1038/nrg1272; Mast, F.D., Ratushny, A.V., Aitchison, J.D., Systems cell biology (2014) J Cell Biol, 206 (6), pp. 695-706. , https://doi.org/10.1083/jcb.201405027; Sompairac, N., Modamio, J., Rmt, F., Barillot, E., Zinovyev, A., Kuperstein, I., Metabolic and signalling network map integration: Application to cross-talk studies and omics data analysis in cancer BMC Bioinformatics, , https://doi.org/10.1186/s12859-019-2682-z; Kuperstein, I., Bonnet, E., Nguyen, H.A., Cohen, D., Viara, E., Grieco, L., Atlas of Cancer Signalling Network: A systems biology resource for integrative analysis of cancer data with Google Maps (2015) Oncogenesis, 4 (7), p. e160. , https://doi.org/10.1038/oncsis.2015.19; Noronha A, D., ReconMap: An interactive visualization of human metabolism (2017) Bioinformatics, 33 (4), pp. 605-607. , https://doi.org/10.1093/bioinformatics/btw667; Burgoon, L.D., The need for standards, not guidelines, in biological data reporting and sharing (2006) Nat Biotechnol, 24, p. 1369. , https://doi.org/10.1038/nbt1106-1369; Saito, R., Smoot, M.E., Ono, K., Ruscheinski, J., Wang, P.L., Lotia, S., A travel guide to Cytoscape plugins (2012) Nat Methods, 9, p. 1069. , https://doi.org/10.1038/nmeth.2212; Wilkinson, M.D., Dumontier, M., Aalbersberg, I.J., Appleton, G., Axton, M., Baak, A., The FAIR Guiding Principles for scientific data management and stewardship (2016) Sci Data, 3, p. 160018. , https://doi.org/10.1038/sdata.2016.18; Kuperstein, I., Cohen, D.P., Pook, S., Viara, E., Calzone, L., Barillot, E., NaviCell: A web-based environment for navigation, curation and maintenance of large molecular interaction maps (2013) BMC Syst Biol, 7 (1), p. 100. , https://doi.org/10.1186/1752-0509-7-100; Kuperstein, I., Cohen, D.P., Pook, S., Viara, E., Calzone, L., Barillot, E., NaviCell: A web-based environment for navigation, curation and maintenance of large molecular interaction maps (2013) BMC Syst Biol, 7 (1), p. 100. , https://doi.org/10.1186/1752-0509-7-100; Zhou, Q., Su, X., Wang, A., Xu, J., Ning, K., QC-Chain: Fast and holistic quality control method for next-generation sequencing data (2013) PloS ONE, 8 (4), p. e60234. , https://doi.org/10.1371/journal.pone.0060234; Sangiovannni, M., Granata, I., Shing Thind, A., Guarracino, M., From trash to treasure: Detecting unexpected contamination in unmapped NGS data BMC Bioinformatics, , https://doi.org/10.1186/s12859-019-2684-x; Kostic, A.D., Gevers, D., Pedamallu, C.S., Michaud, M., Duke, F., Earl, A.M., Genomic analysis identifies association of Fusobacterium with colorectal carcinoma (2012) Genome Res, 22 (2), pp. 292-298. , http://www.genome.org/cgi/doi/10.1101/gr.126573.111; Lin, Z., Puetter, A., Coco, J., Xu, G., Strong, M.J., Wang, X., Detection of Murine Leukemia Virus in the Epstein-Barr virus-positive human B-cell line JY using a computational RNA-seq based exogenous agent detection pipeline, PARSES (2012) J Virol, pp. JVI-06717. , https://jvi.asm.org/content/86/6/2970; Strong, M.J., O'Grady, T., Lin, Z., Xu, G., Baddoo, M., Parsons, C., Epstein-Barr virus and human herpesvirus 6 detection in a non-Hodgkin's diffuse large B-cell lymphoma cohort by using RNA sequencing (2013) J Virol, 87 (23), pp. 13059-13062. , https://jvi.asm.org/content/87/23/13059; Amadou, A., Hainaut, P., Romieu, I., Role of Obesity in the Risk of Breast Cancer: Lessons from Anthropometry (2013) J Oncol, 2013, p. 19. , http://doi.org/10.1155/2013/906495; Goodwin, P.J., Obesity and Breast Cancer Outcomes: How Much Evidence Is Needed to Change Practice? 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INSTICC. SciTePress",

year = "2019",

doi = "10.1186/s12859-019-2681-0",

language = "English",

volume = "20",

journal = "BMC Bioinform.",

issn = "1471-2105",

publisher = "BioMed Central Ltd.",

}

TY - JOUR

T1 - The 2017 Network Tools and Applications in Biology (NETTAB) workshop: Aims, topics and outcomes

T2 - BMC Bioinformatics

AU - Romano, P.

AU - Céol, A.

AU - Dräger, A.

AU - Fiannaca, A.

AU - Giugno, R.

AU - La Rosa, M.

AU - Milanesi, L.

AU - Pfeffer, U.

AU - Rizzo, R.

AU - Shin, S.-Y.

AU - Xia, J.

AU - Urso, A.

N1 - Export Date: 2 March 2020 CODEN: BBMIC Correspondence Address: Romano, P.; IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, Italy; email: paolo.romano@hsanmartino.it Funding details: National Research Council Funding details: National Council for Scientific Research Funding text 1: The last guest lecture was given by Luana Licata, ELIXIR-IIB, Italy. The lecture, titled “ELIXIR-IIB: the Italian Infrastructure for Bioinformatics: a growing support to national and international research in life sciences”, gave an overview on the ELIXIR Italian node and infrastructure for bioinformatics. The node is coordinated by the National Research Council and currently includes 17 centers of excellence among which are research institutes, universities and technological institutions. The infrastructure supports the exchange and development of skills, and the integration of publicly available and internationally recognised Italian bioinformatics resources within the European infrastructure. Funding text 2: The second tutorial was offered by the CNR InterOmics Flagship project. The tutorial, titled “Biological network-based analysis of omics for precision medicine: overview, interaction databases and network diffusion approaches”, was given by Ettore Mosca, Institute of Biomedical Technologies, National Research Council of Italy, Milan, Italy. The tutorial illustrated how the known molecular interactions can be useful in the interpretation of “omics” data for precision medicine, with a main focus on data referable to genes. The first part introduced broad objectives and principles of biological network-based analyses of “omics” data. Then, an overview of the state-of-the art of current datasets from which networks can be defined was given, also in term of their completeness in relation to the coverage of high-throughput technologies and the issues in mapping “omics” data to biological networks. The second part focused on network diffusion-based approaches and illustrated how the principles behind this class of methods have been recently applied to several problems, including patient stratification and gene module extraction. Throughout the tutorial, benefits, limitations and open issues in the field of network-based analysis were underlined, including also software availability and computational cost. References: NETTAB Workshops, , http://www.nettab.org/, Accessed 26 Feb 2019; NETTAB 2017 Workshop, , http://www.igst.it/nettab/2017/, Accessed 26 Feb 2019; Barabási, A.L., Oltvai, Z.N., Network biology: Understanding the cell's functional organization (2004) Nat Rev Genet, 5, p. 101. , https://doi.org/10.1038/nrg1272; Mast, F.D., Ratushny, A.V., Aitchison, J.D., Systems cell biology (2014) J Cell Biol, 206 (6), pp. 695-706. , https://doi.org/10.1083/jcb.201405027; Sompairac, N., Modamio, J., Rmt, F., Barillot, E., Zinovyev, A., Kuperstein, I., Metabolic and signalling network map integration: Application to cross-talk studies and omics data analysis in cancer BMC Bioinformatics, , https://doi.org/10.1186/s12859-019-2682-z; Kuperstein, I., Bonnet, E., Nguyen, H.A., Cohen, D., Viara, E., Grieco, L., Atlas of Cancer Signalling Network: A systems biology resource for integrative analysis of cancer data with Google Maps (2015) Oncogenesis, 4 (7), p. e160. , https://doi.org/10.1038/oncsis.2015.19; Noronha A, D., ReconMap: An interactive visualization of human metabolism (2017) Bioinformatics, 33 (4), pp. 605-607. , https://doi.org/10.1093/bioinformatics/btw667; Burgoon, L.D., The need for standards, not guidelines, in biological data reporting and sharing (2006) Nat Biotechnol, 24, p. 1369. , https://doi.org/10.1038/nbt1106-1369; Saito, R., Smoot, M.E., Ono, K., Ruscheinski, J., Wang, P.L., Lotia, S., A travel guide to Cytoscape plugins (2012) Nat Methods, 9, p. 1069. , https://doi.org/10.1038/nmeth.2212; Wilkinson, M.D., Dumontier, M., Aalbersberg, I.J., Appleton, G., Axton, M., Baak, A., The FAIR Guiding Principles for scientific data management and stewardship (2016) Sci Data, 3, p. 160018. , https://doi.org/10.1038/sdata.2016.18; Kuperstein, I., Cohen, D.P., Pook, S., Viara, E., Calzone, L., Barillot, E., NaviCell: A web-based environment for navigation, curation and maintenance of large molecular interaction maps (2013) BMC Syst Biol, 7 (1), p. 100. , https://doi.org/10.1186/1752-0509-7-100; Kuperstein, I., Cohen, D.P., Pook, S., Viara, E., Calzone, L., Barillot, E., NaviCell: A web-based environment for navigation, curation and maintenance of large molecular interaction maps (2013) BMC Syst Biol, 7 (1), p. 100. , https://doi.org/10.1186/1752-0509-7-100; Zhou, Q., Su, X., Wang, A., Xu, J., Ning, K., QC-Chain: Fast and holistic quality control method for next-generation sequencing data (2013) PloS ONE, 8 (4), p. e60234. , https://doi.org/10.1371/journal.pone.0060234; Sangiovannni, M., Granata, I., Shing Thind, A., Guarracino, M., From trash to treasure: Detecting unexpected contamination in unmapped NGS data BMC Bioinformatics, , https://doi.org/10.1186/s12859-019-2684-x; Kostic, A.D., Gevers, D., Pedamallu, C.S., Michaud, M., Duke, F., Earl, A.M., Genomic analysis identifies association of Fusobacterium with colorectal carcinoma (2012) Genome Res, 22 (2), pp. 292-298. , http://www.genome.org/cgi/doi/10.1101/gr.126573.111; Lin, Z., Puetter, A., Coco, J., Xu, G., Strong, M.J., Wang, X., Detection of Murine Leukemia Virus in the Epstein-Barr virus-positive human B-cell line JY using a computational RNA-seq based exogenous agent detection pipeline, PARSES (2012) J Virol, pp. JVI-06717. , https://jvi.asm.org/content/86/6/2970; Strong, M.J., O'Grady, T., Lin, Z., Xu, G., Baddoo, M., Parsons, C., Epstein-Barr virus and human herpesvirus 6 detection in a non-Hodgkin's diffuse large B-cell lymphoma cohort by using RNA sequencing (2013) J Virol, 87 (23), pp. 13059-13062. , https://jvi.asm.org/content/87/23/13059; Amadou, A., Hainaut, P., Romieu, I., Role of Obesity in the Risk of Breast Cancer: Lessons from Anthropometry (2013) J Oncol, 2013, p. 19. , http://doi.org/10.1155/2013/906495; Goodwin, P.J., Obesity and Breast Cancer Outcomes: How Much Evidence Is Needed to Change Practice? 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INSTICC. SciTePress

PY - 2019

Y1 - 2019

N2 - The 17th International NETTAB workshop was held in Palermo, Italy, on October 16-18, 2017. The special topic for the meeting was "Methods, tools and platforms for Personalised Medicine in the Big Data Era", but the traditional topics of the meeting series were also included in the event. About 40 scientific contributions were presented, including four keynote lectures, five guest lectures, and many oral communications and posters. Also, three tutorials were organised before and after the workshop. Full papers from some of the best works presented in Palermo were submitted for this Supplement of BMC Bioinformatics. Here, we provide an overview of meeting aims and scope. We also shortly introduce selected papers that have been accepted for publication in this Supplement, for a complete presentation of the outcomes of the meeting. © 2019 The Author(s).

AB - The 17th International NETTAB workshop was held in Palermo, Italy, on October 16-18, 2017. The special topic for the meeting was "Methods, tools and platforms for Personalised Medicine in the Big Data Era", but the traditional topics of the meeting series were also included in the event. About 40 scientific contributions were presented, including four keynote lectures, five guest lectures, and many oral communications and posters. Also, three tutorials were organised before and after the workshop. Full papers from some of the best works presented in Palermo were submitted for this Supplement of BMC Bioinformatics. Here, we provide an overview of meeting aims and scope. We also shortly introduce selected papers that have been accepted for publication in this Supplement, for a complete presentation of the outcomes of the meeting. © 2019 The Author(s).

KW - Network tools

KW - Oral communication

KW - Personalised medicines

KW - Scientific contributions

KW - bioinformatics

KW - biology

KW - publication

KW - review

KW - genetics

KW - genomics

KW - health care delivery

KW - human

KW - Italy

KW - neoplasm

KW - personalized medicine

KW - procedures

KW - Computational Biology

KW - Delivery of Health Care

KW - Genomics

KW - Humans

KW - Neoplasms

KW - Precision Medicine

U2 - 10.1186/s12859-019-2681-0

DO - 10.1186/s12859-019-2681-0

M3 - Article

VL - 20

JO - BMC Bioinform.

JF - BMC Bioinform.

SN - 1471-2105

ER -