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Efficient experimental design for uncertainty reduction in gene regulatory networks.

BMC bioinformatics

Dehghannasiri R, Yoon BJ, Dougherty ER.
PMID: 26423515
BMC Bioinformatics. 2015;16:S2. doi: 10.1186/1471-2105-16-S13-S2. Epub 2015 Sep 25.

BACKGROUND: An accurate understanding of interactions among genes plays a major role in developing therapeutic intervention methods. Gene regulatory networks often contain a significant amount of uncertainty. The process of prioritizing biological experiments to reduce the uncertainty of gene...

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Dehghannasiri R, Yoon BJ, Dougherty ER. Efficient experimental design for uncertainty reduction in gene regulatory networks. BMC Bioinformatics. 2015;16:S2doi: 10.1186/1471-2105-16-S13-S2.
Dehghannasiri, R., Yoon, B. J., & Dougherty, E. R. (2015). Efficient experimental design for uncertainty reduction in gene regulatory networks. BMC bioinformatics, 16S2. https://doi.org/10.1186/1471-2105-16-S13-S2
Dehghannasiri, Roozbeh, et al. "Efficient experimental design for uncertainty reduction in gene regulatory networks." BMC bioinformatics vol. 16 (2015): S2. doi: https://doi.org/10.1186/1471-2105-16-S13-S2
Dehghannasiri R, Yoon BJ, Dougherty ER. Efficient experimental design for uncertainty reduction in gene regulatory networks. BMC Bioinformatics. 2015;16:S2. doi: 10.1186/1471-2105-16-S13-S2. Epub 2015 Sep 25. PMID: 26423515; PMCID: PMC4597030.
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Dynamical modeling of uncertain interaction-based genomic networks.

BMC bioinformatics

Mohsenizadeh DN, Hua J, Bittner M, Dougherty ER.
PMID: 26423606
BMC Bioinformatics. 2015;16:S3. doi: 10.1186/1471-2105-16-S13-S3. Epub 2015 Sep 25.

BACKGROUND: Most dynamical models for genomic networks are built upon two current methodologies, one process-based and the other based on Boolean-type networks. Both are problematic when it comes to experimental design purposes in the laboratory. The first approach requires...

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Mohsenizadeh DN, Hua J, Bittner M, et al. Dynamical modeling of uncertain interaction-based genomic networks. BMC Bioinformatics. 2015;16:S3doi: 10.1186/1471-2105-16-S13-S3.
Mohsenizadeh, D. N., Hua, J., Bittner, M., & Dougherty, E. R. (2015). Dynamical modeling of uncertain interaction-based genomic networks. BMC bioinformatics, 16S3. https://doi.org/10.1186/1471-2105-16-S13-S3
Mohsenizadeh, Daniel N, et al. "Dynamical modeling of uncertain interaction-based genomic networks." BMC bioinformatics vol. 16 (2015): S3. doi: https://doi.org/10.1186/1471-2105-16-S13-S3
Mohsenizadeh DN, Hua J, Bittner M, Dougherty ER. Dynamical modeling of uncertain interaction-based genomic networks. BMC Bioinformatics. 2015;16:S3. doi: 10.1186/1471-2105-16-S13-S3. Epub 2015 Sep 25. PMID: 26423606; PMCID: PMC4596957.
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Proceedings of the 2015 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.

BMC bioinformatics

Wren JD, Thakkar S, Homayouni R, Johann DJ, Dozmorov MG.
PMID: 26424691
BMC Bioinformatics. 2015;16:S1. doi: 10.1186/1471-2105-16-S13-S1. Epub 2015 Sep 25.

No abstract available.

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Wren JD, Thakkar S, Homayouni R, et al. Proceedings of the 2015 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC Bioinformatics. 2015;16:S1doi: 10.1186/1471-2105-16-S13-S1.
Wren, J. D., Thakkar, S., Homayouni, R., Johann, D. J., & Dozmorov, M. G. (2015). Proceedings of the 2015 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC bioinformatics, 16S1. https://doi.org/10.1186/1471-2105-16-S13-S1
Wren, Jonathan D, et al. "Proceedings of the 2015 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference." BMC bioinformatics vol. 16 (2015): S1. doi: https://doi.org/10.1186/1471-2105-16-S13-S1
Wren JD, Thakkar S, Homayouni R, Johann DJ, Dozmorov MG. Proceedings of the 2015 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC Bioinformatics. 2015;16:S1. doi: 10.1186/1471-2105-16-S13-S1. Epub 2015 Sep 25. PMID: 26424691; PMCID: PMC4596983.
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A heuristic approach to determine an appropriate number of topics in topic modeling.

BMC bioinformatics

Zhao W, Chen JJ, Perkins R, Liu Z, Ge W, Ding Y, Zou W.
PMID: 26424364
BMC Bioinformatics. 2015;16:S8. doi: 10.1186/1471-2105-16-S13-S8. Epub 2015 Sep 25.

BACKGROUND: Topic modelling is an active research field in machine learning. While mainly used to build models from unstructured textual data, it offers an effective means of data mining where samples represent documents, and different biological endpoints or omics...

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Zhao W, Chen JJ, Perkins R, et al. A heuristic approach to determine an appropriate number of topics in topic modeling. BMC Bioinformatics. 2015;16:S8doi: 10.1186/1471-2105-16-S13-S8.
Zhao, W., Chen, J. J., Perkins, R., Liu, Z., Ge, W., Ding, Y., & Zou, W. (2015). A heuristic approach to determine an appropriate number of topics in topic modeling. BMC bioinformatics, 16S8. https://doi.org/10.1186/1471-2105-16-S13-S8
Zhao, Weizhong, et al. "A heuristic approach to determine an appropriate number of topics in topic modeling." BMC bioinformatics vol. 16 (2015): S8. doi: https://doi.org/10.1186/1471-2105-16-S13-S8
Zhao W, Chen JJ, Perkins R, Liu Z, Ge W, Ding Y, Zou W. A heuristic approach to determine an appropriate number of topics in topic modeling. BMC Bioinformatics. 2015;16:S8. doi: 10.1186/1471-2105-16-S13-S8. Epub 2015 Sep 25. PMID: 26424364; PMCID: PMC4597325.
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Pathogen metadata platform: software for accessing and analyzing pathogen strain information.

BMC bioinformatics

Chang WE, Peterson MW, Garay CD, Korves T.
PMID: 27634291
BMC Bioinformatics. 2016 Sep 15;17(1):379. doi: 10.1186/s12859-016-1231-2.

BACKGROUND: Pathogen metadata includes information about where and when a pathogen was collected and the type of environment it came from. Along with genomic nucleotide sequence data, this metadata is growing rapidly and becoming a valuable resource not only...

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Chang WE, Peterson MW, Garay CD, et al. Pathogen metadata platform: software for accessing and analyzing pathogen strain information. BMC Bioinformatics. 2016;17(1):379doi: 10.1186/s12859-016-1231-2.
Chang, W. E., Peterson, M. W., Garay, C. D., & Korves, T. (2016). Pathogen metadata platform: software for accessing and analyzing pathogen strain information. BMC bioinformatics, 17(1), 379. https://doi.org/10.1186/s12859-016-1231-2
Chang, Wenling E, et al. "Pathogen metadata platform: software for accessing and analyzing pathogen strain information." BMC bioinformatics vol. 17,1 (2016): 379. doi: https://doi.org/10.1186/s12859-016-1231-2
Chang WE, Peterson MW, Garay CD, Korves T. Pathogen metadata platform: software for accessing and analyzing pathogen strain information. BMC Bioinformatics. 2016 Sep 15;17(1):379. doi: 10.1186/s12859-016-1231-2. PMID: 27634291; PMCID: PMC5025631.
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Erratum to: BayesFlow: latent modeling of flow cytometry cell populations.

BMC bioinformatics

Johnsson K, Wallin J, Fontes M.
PMID: 27036556
BMC Bioinformatics. 2016 Mar 31;17:149. doi: 10.1186/s12859-016-0973-1.

No abstract available.

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Johnsson K, Wallin J, Fontes M. Erratum to: BayesFlow: latent modeling of flow cytometry cell populations. BMC Bioinformatics. 2016;17:149doi: 10.1186/s12859-016-0973-1.
Johnsson, K., Wallin, J., & Fontes, M. (2016). Erratum to: BayesFlow: latent modeling of flow cytometry cell populations. BMC bioinformatics, 17149. https://doi.org/10.1186/s12859-016-0973-1
Johnsson, Kerstin, et al. "Erratum to: BayesFlow: latent modeling of flow cytometry cell populations." BMC bioinformatics vol. 17 (2016): 149. doi: https://doi.org/10.1186/s12859-016-0973-1
Johnsson K, Wallin J, Fontes M. Erratum to: BayesFlow: latent modeling of flow cytometry cell populations. BMC Bioinformatics. 2016 Mar 31;17:149. doi: 10.1186/s12859-016-0973-1. PMID: 27036556; PMCID: PMC4818415.
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Erratum to: How can functional annotations be derived from profiles of phenotypic annotations?.

BMC bioinformatics

Serrano-Solano B, Ramos AD, Hériché JK, Ranea JA.
PMID: 28347274
BMC Bioinformatics. 2017 Mar 27;18(1):194. doi: 10.1186/s12859-017-1607-y.

No abstract available.

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Serrano-Solano B, Ramos AD, Hériché JK, et al. Erratum to: How can functional annotations be derived from profiles of phenotypic annotations?. BMC Bioinformatics. 2017;18(1):194doi: 10.1186/s12859-017-1607-y.
Serrano-Solano, B., Ramos, A. D., Hériché, J. K., & Ranea, J. A. (2017). Erratum to: How can functional annotations be derived from profiles of phenotypic annotations?. BMC bioinformatics, 18(1), 194. https://doi.org/10.1186/s12859-017-1607-y
Serrano-Solano, Beatriz, et al. "Erratum to: How can functional annotations be derived from profiles of phenotypic annotations?." BMC bioinformatics vol. 18,1 (2017): 194. doi: https://doi.org/10.1186/s12859-017-1607-y
Serrano-Solano B, Ramos AD, Hériché JK, Ranea JA. Erratum to: How can functional annotations be derived from profiles of phenotypic annotations?. BMC Bioinformatics. 2017 Mar 27;18(1):194. doi: 10.1186/s12859-017-1607-y. PMID: 28347274; PMCID: PMC5368993.
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SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases.

BMC bioinformatics

Chiba H, Uchiyama I.
PMID: 28178937
BMC Bioinformatics. 2017 Feb 08;18(1):93. doi: 10.1186/s12859-017-1531-1.

BACKGROUND: Toward improved interoperability of distributed biological databases, an increasing number of datasets have been published in the standardized Resource Description Framework (RDF). Although the powerful SPARQL Protocol and RDF Query Language (SPARQL) provides a basis for exploiting RDF...

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Chiba H, Uchiyama I. SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases. BMC Bioinformatics. 2017;18(1):93doi: 10.1186/s12859-017-1531-1.
Chiba, H., & Uchiyama, I. (2017). SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases. BMC bioinformatics, 18(1), 93. https://doi.org/10.1186/s12859-017-1531-1
Chiba, Hirokazu, and Uchiyama, Ikuo. "SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases." BMC bioinformatics vol. 18,1 (2017): 93. doi: https://doi.org/10.1186/s12859-017-1531-1
Chiba H, Uchiyama I. SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases. BMC Bioinformatics. 2017 Feb 08;18(1):93. doi: 10.1186/s12859-017-1531-1. PMID: 28178937; PMCID: PMC5299738.
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OntoGene web services for biomedical text mining.

BMC bioinformatics

Rinaldi F, Clematide S, Marques H, Ellendorff T, Romacker M, Rodriguez-Esteban R.
PMID: 25472638
BMC Bioinformatics. 2014;15:S6. doi: 10.1186/1471-2105-15-S14-S6. Epub 2014 Nov 27.

Text mining services are rapidly becoming a crucial component of various knowledge management pipelines, for example in the process of database curation, or for exploration and enrichment of biomedical data within the pharmaceutical industry. Traditional architectures, based on monolithic...

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Rinaldi F, Clematide S, Marques H, et al. OntoGene web services for biomedical text mining. BMC Bioinformatics. 2014;15:S6doi: 10.1186/1471-2105-15-S14-S6.
Rinaldi, F., Clematide, S., Marques, H., Ellendorff, T., Romacker, M., & Rodriguez-Esteban, R. (2014). OntoGene web services for biomedical text mining. BMC bioinformatics, 15S6. https://doi.org/10.1186/1471-2105-15-S14-S6
Rinaldi, Fabio, et al. "OntoGene web services for biomedical text mining." BMC bioinformatics vol. 15 (2014): S6. doi: https://doi.org/10.1186/1471-2105-15-S14-S6
Rinaldi F, Clematide S, Marques H, Ellendorff T, Romacker M, Rodriguez-Esteban R. OntoGene web services for biomedical text mining. BMC Bioinformatics. 2014;15:S6. doi: 10.1186/1471-2105-15-S14-S6. Epub 2014 Nov 27. PMID: 25472638; PMCID: PMC4255746.
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A web-based protein interaction network visualizer.

BMC bioinformatics

Salazar GA, Meintjes A, Mazandu GK, Rapanoël HA, Akinola RO, Mulder NJ.
PMID: 24885165
BMC Bioinformatics. 2014 May 06;15:129. doi: 10.1186/1471-2105-15-129.

BACKGROUND: Interaction between proteins is one of the most important mechanisms in the execution of cellular functions. The study of these interactions has provided insight into the functioning of an organism's processes. As of October 2013, Homo sapiens had...

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Salazar GA, Meintjes A, Mazandu GK, et al. A web-based protein interaction network visualizer. BMC Bioinformatics. 2014;15:129doi: 10.1186/1471-2105-15-129.
Salazar, G. A., Meintjes, A., Mazandu, G. K., Rapanoël, H. A., Akinola, R. O., & Mulder, N. J. (2014). A web-based protein interaction network visualizer. BMC bioinformatics, 15129. https://doi.org/10.1186/1471-2105-15-129
Salazar, Gustavo A, et al. "A web-based protein interaction network visualizer." BMC bioinformatics vol. 15 (2014): 129. doi: https://doi.org/10.1186/1471-2105-15-129
Salazar GA, Meintjes A, Mazandu GK, Rapanoël HA, Akinola RO, Mulder NJ. A web-based protein interaction network visualizer. BMC Bioinformatics. 2014 May 06;15:129. doi: 10.1186/1471-2105-15-129. PMID: 24885165; PMCID: PMC4029974.
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Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics.

BMC bioinformatics

Facchiano A, Angelini C, Bosotti R, Guffanti A, Marabotti A, Marangoni R, Pascarella S, Romano P, Zanzoni A, Helmer-Citterich M.
PMID: 26050789
BMC Bioinformatics. 2015;16:S1. doi: 10.1186/1471-2105-16-S9-S1. Epub 2015 Jun 01.

This Preface introduces the content of the BioMed Central journal Supplements related to BITS2014 meeting, held in Rome, Italy, from the 26th to the 28th of February, 2014.

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Facchiano A, Angelini C, Bosotti R, et al. Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics. BMC Bioinformatics. 2015;16:S1doi: 10.1186/1471-2105-16-S9-S1.
Facchiano, A., Angelini, C., Bosotti, R., Guffanti, A., Marabotti, A., Marangoni, R., Pascarella, S., Romano, P., Zanzoni, A., & Helmer-Citterich, M. (2015). Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics. BMC bioinformatics, 16S1. https://doi.org/10.1186/1471-2105-16-S9-S1
Facchiano, Angelo, et al. "Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics." BMC bioinformatics vol. 16 (2015): S1. doi: https://doi.org/10.1186/1471-2105-16-S9-S1
Facchiano A, Angelini C, Bosotti R, Guffanti A, Marabotti A, Marangoni R, Pascarella S, Romano P, Zanzoni A, Helmer-Citterich M. Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics. BMC Bioinformatics. 2015;16:S1. doi: 10.1186/1471-2105-16-S9-S1. Epub 2015 Jun 01. PMID: 26050789; PMCID: PMC4464032.
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Highlights from the 11th ISCB Student Council Symposium 2015. Dublin, Ireland. 10 July 2015.

BMC bioinformatics

[No authors listed]
PMID: 26986007
BMC Bioinformatics. 2016 Feb 25;17:95. doi: 10.1186/s12859-016-0901-4.

No abstract available.

Cite
Highlights from the 11th ISCB Student Council Symposium 2015. Dublin, Ireland. 10 July 2015. BMC Bioinformatics. 2016;17:95doi: 10.1186/s12859-016-0901-4.
(2016). Highlights from the 11th ISCB Student Council Symposium 2015. Dublin, Ireland. 10 July 2015. BMC bioinformatics, 1795. https://doi.org/10.1186/s12859-016-0901-4
"Highlights from the 11th ISCB Student Council Symposium 2015. Dublin, Ireland. 10 July 2015." BMC bioinformatics vol. 17 (2016): 95. doi: https://doi.org/10.1186/s12859-016-0901-4
Highlights from the 11th ISCB Student Council Symposium 2015. Dublin, Ireland. 10 July 2015. BMC Bioinformatics. 2016 Feb 25;17:95. doi: 10.1186/s12859-016-0901-4. PMID: 26986007; PMCID: PMC4895264.
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Showing 1 to 12 of 517 entries