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<citation key="chen2020gppial"> | ||
<article_title>GPPIAL: A new global PPI network aligner | ||
based on orthologs</article_title> | ||
<author>Chen</author> | ||
<journal_title>2020 IEEE international conference on | ||
bioinformatics and biomedicine (BIBM)</journal_title> | ||
<doi>10.1109/bibm49941.2020.9313552</doi> | ||
<cYear>2020</cYear> | ||
<unstructured_citation>Chen, Y., Zhu, Y., Zhong, M., Peng, | ||
R., & Liu, J. (2020). GPPIAL: A new global PPI network aligner based | ||
on orthologs. 2020 IEEE International Conference on Bioinformatics and | ||
Biomedicine (BIBM), 100–107. | ||
https://doi.org/10.1109/bibm49941.2020.9313552</unstructured_citation> | ||
</citation> | ||
<citation key="hovcevar2016computation"> | ||
<article_title>Computation of graphlet orbits for nodes and | ||
edges in sparse graphs</article_title> | ||
<author>Hočevar</author> | ||
<journal_title>Journal of Statistical | ||
Software</journal_title> | ||
<volume>71</volume> | ||
<doi>10.18637/jss.v071.i10</doi> | ||
<cYear>2016</cYear> | ||
<unstructured_citation>Hočevar, T., & Demšar, J. (2016). | ||
Computation of graphlet orbits for nodes and edges in sparse graphs. | ||
Journal of Statistical Software, 71, 1–24. | ||
https://doi.org/10.18637/jss.v071.i10</unstructured_citation> | ||
</citation> | ||
<citation key="kuchaiev2010topological"> | ||
<article_title>Topological network alignment uncovers | ||
biological function and phylogeny</article_title> | ||
<author>Kuchaiev</author> | ||
<journal_title>Journal of the Royal Society | ||
Interface</journal_title> | ||
<issue>50</issue> | ||
<volume>7</volume> | ||
<doi>10.1098/rsif.2010.0063</doi> | ||
<cYear>2010</cYear> | ||
<unstructured_citation>Kuchaiev, O., Milenković, T., | ||
Memišević, V., Hayes, W., & Pržulj, N. (2010). Topological network | ||
alignment uncovers biological function and phylogeny. Journal of the | ||
Royal Society Interface, 7(50), 1341–1354. | ||
https://doi.org/10.1098/rsif.2010.0063</unstructured_citation> | ||
</citation> | ||
<citation key="kuchaiev2011graphcrunch"> | ||
<article_title>GraphCrunch 2: Software tool for network | ||
modeling, alignment and clustering</article_title> | ||
<author>Kuchaiev</author> | ||
<journal_title>BMC bioinformatics</journal_title> | ||
<issue>1</issue> | ||
<volume>12</volume> | ||
<doi>10.1186/1471-2105-12-24</doi> | ||
<cYear>2011</cYear> | ||
<unstructured_citation>Kuchaiev, O., Stevanović, A., Hayes, | ||
W., & Pržulj, N. (2011). GraphCrunch 2: Software tool for network | ||
modeling, alignment and clustering. BMC Bioinformatics, 12(1), 1–13. | ||
https://doi.org/10.1186/1471-2105-12-24</unstructured_citation> | ||
</citation> | ||
<citation key="kuhn1955hungarian"> | ||
<article_title>The hungarian method for the assignment | ||
problem</article_title> | ||
<author>Kuhn</author> | ||
<journal_title>Naval research logistics | ||
quarterly</journal_title> | ||
<issue>1-2</issue> | ||
<volume>2</volume> | ||
<doi>10.1002/nav.20053</doi> | ||
<cYear>1955</cYear> | ||
<unstructured_citation>Kuhn, H. W. (1955). The hungarian | ||
method for the assignment problem. Naval Research Logistics Quarterly, | ||
2(1-2), 83–97. https://doi.org/10.1002/nav.20053</unstructured_citation> | ||
</citation> | ||
<citation key="kurtz2015sparse"> | ||
<article_title>Sparse and compositionally robust inference | ||
of microbial ecological networks</article_title> | ||
<author>Kurtz</author> | ||
<journal_title>PLOS Computational Biology</journal_title> | ||
<issue>5</issue> | ||
<volume>11</volume> | ||
<doi>10.1371/journal.pcbi.1004226</doi> | ||
<cYear>2015</cYear> | ||
<unstructured_citation>Kurtz, Z. D., Muller, C. L., Miraldi, | ||
E. R., Littman, D. R., Blaser, M. J., & Bonneau, R. A. (2015). | ||
Sparse and compositionally robust inference of microbial ecological | ||
networks. PLOS Computational Biology, 11(5), 1–25. | ||
https://doi.org/10.1371/journal.pcbi.1004226</unstructured_citation> | ||
</citation> | ||
<citation key="ma2020review"> | ||
<article_title>A review of protein–protein interaction | ||
network alignment: From pathway comparison to global | ||
alignment</article_title> | ||
<author>Ma</author> | ||
<journal_title>Computational and Structural Biotechnology | ||
Journal</journal_title> | ||
<volume>18</volume> | ||
<doi>10.1016/j.csbj.2020.09.011</doi> | ||
<cYear>2020</cYear> | ||
<unstructured_citation>Ma, C.-Y., & Liao, C.-S. (2020). | ||
A review of protein–protein interaction network alignment: From pathway | ||
comparison to global alignment. Computational and Structural | ||
Biotechnology Journal, 18, 2647–2656. | ||
https://doi.org/10.1016/j.csbj.2020.09.011</unstructured_citation> | ||
</citation> | ||
<citation key="malod2015graal"> | ||
<article_title>L-GRAAL: Lagrangian graphlet-based network | ||
aligner</article_title> | ||
<author>Malod-Dognin</author> | ||
<journal_title>Bioinformatics</journal_title> | ||
<issue>13</issue> | ||
<volume>31</volume> | ||
<doi>10.1093/bioinformatics/btv130</doi> | ||
<cYear>2015</cYear> | ||
<unstructured_citation>Malod-Dognin, N., & Pržulj, N. | ||
(2015). L-GRAAL: Lagrangian graphlet-based network aligner. | ||
Bioinformatics, 31(13), 2182–2189. | ||
https://doi.org/10.1093/bioinformatics/btv130</unstructured_citation> | ||
</citation> | ||
<citation key="milenkovic2008uncovering"> | ||
<article_title>Uncovering biological network function via | ||
graphlet degree signatures</article_title> | ||
<author>Milenković</author> | ||
<journal_title>Cancer informatics</journal_title> | ||
<volume>6</volume> | ||
<doi>10.4137/cin.s680</doi> | ||
<cYear>2008</cYear> | ||
<unstructured_citation>Milenković, T., & Pržulj, N. | ||
(2008). Uncovering biological network function via graphlet degree | ||
signatures. Cancer Informatics, 6, CIN–S680. | ||
https://doi.org/10.4137/cin.s680</unstructured_citation> | ||
</citation> | ||
<citation key="neyshabur2013netal"> | ||
<article_title>NETAL: A new graph-based method for global | ||
alignment of protein–protein interaction networks</article_title> | ||
<author>Neyshabur</author> | ||
<journal_title>Bioinformatics</journal_title> | ||
<issue>13</issue> | ||
<volume>29</volume> | ||
<doi>10.1093/bioinformatics/btt202</doi> | ||
<cYear>2013</cYear> | ||
<unstructured_citation>Neyshabur, B., Khadem, A., | ||
Hashemifar, S., & Arab, S. S. (2013). NETAL: A new graph-based | ||
method for global alignment of protein–protein interaction networks. | ||
Bioinformatics, 29(13), 1654–1662. | ||
https://doi.org/10.1093/bioinformatics/btt202</unstructured_citation> | ||
</citation> | ||
<citation key="peschel2021netcomi"> | ||
<article_title>NetCoMi: Network construction and comparison | ||
for microbiome data in r</article_title> | ||
<author>Peschel</author> | ||
<journal_title>Briefings in bioinformatics</journal_title> | ||
<issue>4</issue> | ||
<volume>22</volume> | ||
<doi>10.1101/2020.07.15.195248</doi> | ||
<cYear>2021</cYear> | ||
<unstructured_citation>Peschel, S., Müller, C. L., Mutius, | ||
E. von, Boulesteix, A.-L., & Depner, M. (2021). NetCoMi: Network | ||
construction and comparison for microbiome data in r. Briefings in | ||
Bioinformatics, 22(4), bbaa290. | ||
https://doi.org/10.1101/2020.07.15.195248</unstructured_citation> | ||
</citation> | ||
<citation key="pilgrim1995"> | ||
<article_title>Tutorial on implementation of munkres’ | ||
assignment algorithm</article_title> | ||
<author>Pilgrim</author> | ||
<journal_title>Lecture notes</journal_title> | ||
<doi>10.13140/RG.2.1.3572.3287</doi> | ||
<cYear>1995</cYear> | ||
<unstructured_citation>Pilgrim, R. (1995). Tutorial on | ||
implementation of munkres’ assignment algorithm. Lecture Notes. | ||
https://doi.org/10.13140/RG.2.1.3572.3287</unstructured_citation> | ||
</citation> | ||
<citation key="prvzulj2007biological"> | ||
<article_title>Biological network comparison using graphlet | ||
degree distribution</article_title> | ||
<author>Pržulj</author> | ||
<journal_title>Bioinformatics</journal_title> | ||
<issue>2</issue> | ||
<volume>23</volume> | ||
<doi>10.1093/bioinformatics/btq091</doi> | ||
<cYear>2007</cYear> | ||
<unstructured_citation>Pržulj, N. (2007). Biological network | ||
comparison using graphlet degree distribution. Bioinformatics, 23(2), | ||
e177–e183. | ||
https://doi.org/10.1093/bioinformatics/btq091</unstructured_citation> | ||
</citation> | ||
<citation key="yang2019meta"> | ||
<article_title>Meta-network: Optimized species-species | ||
network analysis for microbial communities</article_title> | ||
<author>Yang</author> | ||
<journal_title>BMC genomics</journal_title> | ||
<issue>2</issue> | ||
<volume>20</volume> | ||
<doi>10.1186/s12864-019-5471-1</doi> | ||
<cYear>2019</cYear> | ||
<unstructured_citation>Yang, P., Yu, S., Cheng, L., & | ||
Ning, K. (2019). Meta-network: Optimized species-species network | ||
analysis for microbial communities. BMC Genomics, 20(2), 143–151. | ||
https://doi.org/10.1186/s12864-019-5471-1</unstructured_citation> | ||
</citation> | ||
</citation_list> | ||
</journal_article> | ||
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