-
T. Nepusz, R. Sasidharan, and A. Paccanaro
BMC Bioinformatics, vol. 11, iss. 1, p. 120, 2010.
@article{citeulike:6780423,
author = {Nepusz, Tam\'{a}s and Sasidharan, Rajkumar and Paccanaro, Alberto},
citeulike-article-id = {6780423},
citeulike-linkout-0 = {http://dx.doi.org/10.1186/1471-2105-11-120},
citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20214776},
citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20214776},
day = {9},
doi = {10.1186/1471-2105-11-120},
issn = {1471-2105},
journal = {BMC Bioinformatics},
keywords = {clustering, connected\_component\_analysis, hierarchical\_clustering, protein\_families, protein\_sequences, proteins, scop\_database, spectral\_clustering},
month = {March},
number = {1},
pages = {120+},
title = {SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale.},
url = {http://dx.doi.org/10.1186/1471-2105-11-120},
volume = {11},
year = {2010}
}
-
T. A. Gianoulis, J. Raes, P. V. Patel, R. Bjornson, J. O. Korbel, I. Letunic, T. Yamada, A. Paccanaro, L. J. Jensen, M. Snyder, P. Bork, and M. B. Gerstein
Proceedings of the National Academy of Sciences, vol. 106, iss. 5, pp. 1374-1379, 2009.
@article{citeulike:3969446,
author = {Gianoulis, Tara A. and Raes, Jeroen and Patel, Prianka V. and Bjornson, Robert and Korbel, Jan O. and Letunic, Ivica and Yamada, Takuji and Paccanaro, Alberto and Jensen, Lars J. and Snyder, Michael and Bork, Peer and Gerstein, Mark B.},
citeulike-article-id = {3969446},
citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0808022106},
citeulike-linkout-1 = {http://www.pnas.org/content/106/5/1374.abstract},
citeulike-linkout-2 = {http://www.pnas.org/content/106/5/1374.full.pdf},
citeulike-linkout-3 = {http://www.pnas.org/cgi/content/abstract/106/5/1374},
citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/19164758},
citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=19164758},
day = {3},
doi = {10.1073/pnas.0808022106},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences},
month = {February},
number = {5},
pages = {1374--1379},
title = {Quantifying environmental adaptation of metabolic pathways in metagenomics},
url = {http://dx.doi.org/10.1073/pnas.0808022106},
volume = {106},
year = {2009}
}
-
P. Hu, S. C. Janga, M. Babu, J. J. D’iaz-Mej’ia, G. Butland, W. Yang, O. Pogoutse, X. Guo, S. Phanse, P. Wong, S. Chandran, C. Christopoulos, A. Nazarians-Armavil, N. K. Nasseri, G. Musso, M. Ali, N. Nazemof, V. Eroukova, A. Golshani, A. Paccanaro, J. F. Greenblatt, G. Moreno-Hagelsieb, and A. Emili
PLoS biology, vol. 7, iss. 4, p. 1000096, 2009.
@article{citeulike:4462926,
author = {Hu, Pingzhao and Janga, Sarath C. and Babu, Mohan and D\'{\i}az-Mej\'{\i}a, Javier J. and Butland, Gareth and Yang, Wenhong and Pogoutse, Oxana and Guo, Xinghua and Phanse, Sadhna and Wong, Peter and Chandran, Shamanta and Christopoulos, Constantine and Nazarians-Armavil, Anaies and Nasseri, Negin K. and Musso, Gabriel and Ali, Mehrab and Nazemof, Nazila and Eroukova, Veronika and Golshani, Ashkan and Paccanaro, Alberto and Greenblatt, Jack F. and Moreno-Hagelsieb, Gabriel and Emili, Andrew},
citeulike-article-id = {4462926},
citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pbio.1000096},
citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19402753},
citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19402753},
day = {28},
doi = {10.1371/journal.pbio.1000096},
issn = {1545-7885},
journal = {PLoS biology},
month = {April},
number = {4},
pages = {e1000096+},
publisher = {Public Library of Science},
title = {Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins.},
url = {http://dx.doi.org/10.1371/journal.pbio.1000096},
volume = {7},
year = {2009}
}
-
A. Devoto and A. Paccanaro
2008, pp. 331-350.
@incollection{citeulike:5847015,
author = {Devoto, Alessandra and Paccanaro, Alberto},
booktitle = {Plant Growth Signaling},
citeulike-article-id = {5847015},
citeulike-linkout-0 = {http://dx.doi.org/10.1007/7089\_2007\_152},
citeulike-linkout-1 = {http://www.springerlink.com/content/j441164615213g34},
doi = {10.1007/7089\_2007\_152},
journal = {-},
pages = {331--350},
title = {Signal Transduction Networks During Stress Responses in Arabidopsis: High-Throughput Analysis and Modelling},
url = {http://dx.doi.org/10.1007/7089\_2007\_152},
year = {2008}
}
-
H. Yang, P. Bhat, H. Shanahan, and A. Paccanaro
A maximal eigenvalue method for detecting process representative genes by integrating data from multiple sources
in NIPS Workshop on Learning from Multiple Sources, 2008.
@inproceedings{citeulike:5847191, author = {Yang, Haixuan and Bhat, Prajwal and Shanahan, Hugh and Paccanaro, Alberto},
booktitle = {NIPS Workshop on Learning from Multiple Sources},
citeulike-article-id = {5847191},
title = {A maximal eigenvalue method for detecting process representative genes by integrating data from multiple sources},
year = {2008}
}
-
Z. D. Zhang, A. Paccanaro, Y. Fu, S. Weissman, Z. Weng, J. Chang, M. Snyder, and M. B. Gerstein
Genome Research, vol. 17, iss. 6, pp. 787-797, 2007.
@article{citeulike:1390187,
author = {Zhang, Zhengdong D. and Paccanaro, Alberto and Fu, Yutao and Weissman, Sherman and Weng, Zhiping and Chang, Joseph and Snyder, Michael and Gerstein, Mark B.},
citeulike-article-id = {1390187},
citeulike-linkout-0 = {http://dx.doi.org/10.1101/gr.5573107},
citeulike-linkout-1 = {http://www.genome.org/cgi/content/abstract/17/6/787},
citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/17567997},
citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=17567997},
day = {1},
doi = {10.1101/gr.5573107},
issn = {1088-9051},
journal = {Genome Research},
month = {June},
number = {6},
pages = {787--797},
title = {Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions.},
url = {http://dx.doi.org/10.1101/gr.5573107},
volume = {17},
year = {2007}
}
-
N. J. Krogan, G. Cagney, H. Yu, G. Zhong, X. Guo, A. Ignatchenko, J. Li, S. Pu, N. Datta, A. P. Tikuisis, T. Punna, J. M. PeregrÃn-Alvarez, M. Shales, X. Zhang, M. Davey, M. D. Robinson, A. Paccanaro, J. E. Bray, A. Sheung, B. Beattie, D. P. Richards, V. Canadien, A. Lalev, F. Mena, P. Wong, A. Starostine, M. M. Canete, J. Vlasblom, S. Wu, C. Orsi, S. R. Collins, S. Chandran, R. Haw, J. J. Rilstone, K. Gandi, N. J. Thompson, G. Musso, P. St Onge, S. Ghanny, M. H. Y. Lam, G. Butland, A. M. Altaf-Ul, S. Kanaya, A. Shilatifard, E. O’Shea, J. S. Weissman, J. C. Ingles, T. R. Hughes, J. Parkinson, M. Gerstein, S. J. Wodak, A. Emili, and J. F. Greenblatt
Nature, vol. 440, iss. 7084, pp. 637-643, 2006.
@article{citeulike:560813,
author = {Krogan, Nevan J. and Cagney, Gerard and Yu, Haiyuan and Zhong, Gouqing and Guo, Xinghua and Ignatchenko, Alexandr and Li, Joyce and Pu, Shuye and Datta, Nira and Tikuisis, Aaron P. and Punna, Thanuja and Peregr\~{A}n-Alvarez, Jos\~{A}{\copyright} M. and Shales, Michael and Zhang, Xin and Davey, Michael and Robinson, Mark D. and Paccanaro, Alberto and Bray, James E. and Sheung, Anthony and Beattie, Bryan and Richards, Dawn P. and Canadien, Veronica and Lalev, Atanas and Mena, Frank and Wong, Peter and Starostine, Andrei and Canete, Myra M. and Vlasblom, James and Wu, Samuel and Orsi, Chris and Collins, Sean R. and Chandran, Shamanta and Haw, Robin and Rilstone, Jennifer J. and Gandi, Kiran and Thompson, Natalie J. and Musso, Gabe and St Onge, Peter and Ghanny, Shaun and Lam, Mandy H. Y. and Butland, Gareth and Altaf-Ul, Amin M. and Kanaya, Shigehiko and Shilatifard, Ali and O'Shea, Erin and Weissman, Jonathan S. and Ingles, C. James and Hughes, Timothy R. and Parkinson, John and Gerstein, Mark and Wodak, Shoshana J. and Emili, Andrew and Greenblatt, Jack F.},
citeulike-article-id = {560813},
citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature04670},
citeulike-linkout-1 = {http://dx.doi.org/10.1038/nature04670},
citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/16554755},
citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=16554755},
day = {22},
doi = {10.1038/nature04670},
issn = {0028-0836},
journal = {Nature},
month = {March},
number = {7084},
pages = {637--643},
publisher = {Nature Publishing Group},
title = {Global landscape of protein complexes in the yeast Saccharomyces cerevisiae},
url = {http://dx.doi.org/10.1038/nature04670},
volume = {440},
year = {2006}
}
-
R. Sasidharan, M. Gerstein, and A. Paccanaro
Spectral clustering of protein sequences using sequence-profile scores
in Proceedings of ICNPSC 2006 – 3rd International Conference on Neural Parallel and Scientific Computations, 2006.
@inproceedings{citeulike:5847201, author = {Sasidharan, Rajkumar and Gerstein, Mark and Paccanaro, Alberto},
booktitle = {Proceedings of ICNPSC 2006 - 3rd International Conference on Neural Parallel and Scientific Computations},
citeulike-article-id = {5847201},
title = {Spectral clustering of protein sequences using sequence-profile scores},
year = {2006}
}
-
M. Seringhaus, A. Paccanaro, A. Borneman, M. Snyder, and M. Gerstein
Genome research, vol. 16, iss. 9, pp. 1126-1135, 2006.
@article{citeulike:1286363,
author = {Seringhaus, Michael and Paccanaro, Alberto and Borneman, Anthony and Snyder, Michael and Gerstein, Mark},
citeulike-article-id = {1286363},
citeulike-linkout-0 = {http://dx.doi.org/10.1101/gr.5144106},
citeulike-linkout-1 = {http://www.genome.org/cgi/content/abstract/16/9/1126},
citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/16899653},
citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=16899653},
day = {1},
doi = {10.1101/gr.5144106},
issn = {1088-9051},
journal = {Genome research},
month = {September},
number = {9},
pages = {1126--1135},
title = {Predicting essential genes in fungal genomes.},
url = {http://dx.doi.org/10.1101/gr.5144106},
volume = {16},
year = {2006}
}
-
A. Paccanaro, J. A. Casbon, and M. A. Saqi
Nucleic Acids Research, vol. 34, iss. 5, pp. 1571-1580, 2006.
@article{citeulike:575333,
author = {Paccanaro, Alberto and Casbon, James A. and Saqi, Mansoor A.},
citeulike-article-id = {575333},
citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkj515},
citeulike-linkout-1 = {http://nar.oxfordjournals.org/cgi/content/abstract/34/5/1571},
citeulike-linkout-2 = {http://www.ingentaconnect.com/content/oup/nar/2006/00000034/00000005/art01571},
citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/16547200},
citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=16547200},
doi = {10.1093/nar/gkj515},
issn = {1362-4962},
journal = {Nucleic Acids Research},
number = {5},
pages = {1571--1580},
publisher = {Oxford University Press},
title = {Spectral clustering of protein sequences.},
url = {http://dx.doi.org/10.1093/nar/gkj515},
volume = {34},
year = {2006}
}
-
R. D. Waite, A. Paccanaro, A. Papakonstantinopoulou, J. M. Hurst, M. Saqi, E. Littler, and M. A. Curtis
BMC Genomics, vol. 7, p. 162, 2006.
@article{citeulike:711774,
author = {Waite, Richard D. and Paccanaro, Alberto and Papakonstantinopoulou, Anastasia and Hurst, Jacob M. and Saqi, Mansoor and Littler, Eddie and Curtis, Michael A.},
citeulike-article-id = {711774},
citeulike-linkout-0 = {http://dx.doi.org/10.1186/1471-2164-7-162},
citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/16800888},
citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=16800888},
day = {26},
doi = {10.1186/1471-2164-7-162},
issn = {1471-2164},
journal = {BMC Genomics},
month = {June},
pages = {162+},
title = {Clustering of Pseudomonas aeruginosa transcriptomes from planktonic cultures, developing and mature biofilms reveals distinct expression profiles.},
url = {http://dx.doi.org/10.1186/1471-2164-7-162},
volume = {7},
year = {2006}
}
-
C. S. Goh, T. A. Gianoulis, Y. Liu, J. Li, A. Paccanaro, Y. A. Lussier, and M. Gerstein
BMC Genomics, vol. 7, p. 257, 2006.
@article{citeulike:894945,
author = {Goh, Chern-Sing S. and Gianoulis, Tara A. and Liu, Yang and Li, Jianrong and Paccanaro, Alberto and Lussier, Yves A. and Gerstein, Mark},
citeulike-article-id = {894945},
citeulike-linkout-0 = {http://dx.doi.org/10.1186/1471-2164-7-257},
citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17038185},
citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17038185},
day = {12},
doi = {10.1186/1471-2164-7-257},
issn = {1471-2164},
journal = {BMC Genomics},
month = {October},
pages = {257+},
title = {Integration of curated databases to identify genotype-phenotype associations.},
url = {http://dx.doi.org/10.1186/1471-2164-7-257},
volume = {7},
year = {2006}
}
-
H. Yu, A. Paccanaro, V. Trifonov, and M. Gerstein
Bioinformatics (Oxford, England), vol. 22, iss. 7, pp. 823-829, 2006.
@article{citeulike:561194,
author = {Yu, Haiyuan and Paccanaro, Alberto and Trifonov, Valery and Gerstein, Mark},
citeulike-article-id = {561194},
citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btl014},
citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/7/823},
citeulike-linkout-2 = {http://www.ingentaconnect.com/content/oup/cabios/2006/00000022/00000007/art00823},
citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/16455753},
citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=16455753},
day = {1},
doi = {10.1093/bioinformatics/btl014},
issn = {1367-4803},
journal = {Bioinformatics (Oxford, England)},
month = {April},
number = {7},
pages = {823--829},
publisher = {Oxford University Press},
title = {Predicting interactions in protein networks by completing defective cliques},
url = {http://dx.doi.org/10.1093/bioinformatics/btl014},
volume = {22},
year = {2006}
}
-
L. J. Lu, Y. Xia, A. Paccanaro, H. Yu, and M. Gerstein
Genome Research, vol. 15, iss. 7, pp. 945-953, 2005.
@article{citeulike:334796, abstract = {10.1101/gr.3610305 Genomic data integration\^{a}the process of statistically combining diverse sources of information from functional genomics experiments to make large-scale predictions\^{a}is becoming increasingly prevalent. One might expect that this process should become progressively more powerful with the integration of more evidence. Here, we explore the limits of genomic data integration, assessing the degree to which predictive power increases with the addition of more features. We focus on a predictive context that has been extensively investigated and benchmarked in the past\^{a}the prediction of protein\^{a}protein interactions in yeast. We start by using a simple Naive Bayes classifier for integrating diverse sources of genomic evidence, ranging from coexpression relationships to similar phylogenetic profiles. We expand the number of features considered for prediction to 16, significantly more than previous studies. Overall, we observe a small, but measurable improvement in prediction performance over previous benchmarks, based on four strong features. This allows us to identify new yeast interactions with high confidence. It also allows us to quantitatively assess the inter-relations amongst different genomic features. It is known that subtle correlations and dependencies between features can confound the strength of interaction predictions. We investigate this issue in detail through calculating mutual information. To our surprise, we find no appreciable statistical dependence between the many possible pairs of features. We further explore feature dependencies by comparing the performance of our simple Naive Bayes classifier with a boosted version of the same classifier, which is fairly resistant to feature dependence. We find that boosting does not improve performance, indicating that, at least for prediction purposes, our genomic features are essentially independent. In summary, by integrating a few (i.e., four) good features, we approach the maximal predictive power of current genomic data integration; moreover, this limitation does not reflect (potentially removable) inter-relationships between the features.},
address = {Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.},
author = {Lu, Long J. and Xia, Yu and Paccanaro, Alberto and Yu, Haiyuan and Gerstein, Mark},
citeulike-article-id = {334796},
citeulike-linkout-0 = {http://dx.doi.org/10.1101/gr.3610305},
citeulike-linkout-1 = {http://genome.cshlp.org/content/15/7/945.long.abstract},
citeulike-linkout-2 = {http://genome.cshlp.org/content/15/7/945.long.full.pdf},
citeulike-linkout-3 = {http://www.genome.org/cgi/content/abstract/15/7/945},
citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/15998909},
citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=15998909},
doi = {10.1101/gr.3610305},
issn = {1088-9051},
journal = {Genome Research},
month = {July},
number = {7},
pages = {945--953},
title = {Assessing the limits of genomic data integration for predicting protein networks},
url = {http://dx.doi.org/10.1101/gr.3610305},
volume = {15},
year = {2005}
}
-
A. Paccanaro, V. Trifonov, Y. Haiyuan, and M. Gerstein
in Proceedings of the International Joint Conference on Neural Networks, 2005, pp. 161-166.
@inproceedings{citeulike:5847188,
author = {Paccanaro, A. and Trifonov, V. and Haiyuan, Y. and Gerstein, M.},
booktitle = {Proceedings of the International Joint Conference on Neural Networks},
citeulike-article-id = {5847188},
citeulike-linkout-0 = {http://dx.doi.org/10.1109/IJCNN.2005.1555823},
citeulike-linkout-1 = {http://ieeexplore.ieee.org/xpls/abs\_all.jsp?arnumber=1555823},
day = {27},
doi = {10.1109/IJCNN.2005.1555823},
isbn = {0-7803-9048-2},
journal = {-},
location = {Montreal, Quebec, Canada},
month = {December},
pages = {161--166},
publisher = {IEEE},
title = {Inferring protein-protein interactions using interaction network topologies},
url = {http://dx.doi.org/10.1109/IJCNN.2005.1555823},
volume = {2},
year = {2005}
}
-
C. Chennubhotla and A. Paccanaro
Markov analysis of protein sequence similarities
Springer, 2003, vol. 2859, pp. 278-286.
@inbook{citeulike:5847004,
author = {Chennubhotla, Chakra and Paccanaro, Alberto},
citeulike-article-id = {5847004},
isbn = {978-3-540-20227-1},
issn = {0302-9743},
pages = {278--286},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
title = {Markov analysis of protein sequence similarities},
volume = {2859},
year = {2003}
}
-
A. Paccanaro, C. Chennubhotla, J. A. Casbon, and M. A. S. Saqi
in Proceedings of the International Joint Conference on Neural Networks, 2003, pp. 3083-3088.
@inproceedings{citeulike:694514,
author = {Paccanaro, A. and Chennubhotla, C. and Casbon, J. A. and Saqi, M. A. S.},
booktitle = {Proceedings of the International Joint Conference on Neural Networks},
citeulike-article-id = {694514},
citeulike-linkout-0 = {http://dx.doi.org/10.1109/IJCNN.2003.1224064},
citeulike-linkout-1 = {http://ieeexplore.ieee.org/xpls/abs\_all.jsp?arnumber=1224064},
day = {26},
doi = {10.1109/IJCNN.2003.1224064},
isbn = {0-7803-7898-9},
journal = {-},
location = {Portland, Oregon, USA},
month = {August},
pages = {3083--3088},
publisher = {IEEE},
title = {Spectral clustering of protein sequences},
url = {http://dx.doi.org/10.1109/IJCNN.2003.1224064},
volume = {4},
year = {2003}
}
