TY - JOUR AU - Barabasi, A. -. L. AU - Oltvai, Z. N. PY - 2004 DA - 2004// TI - Network biology: understanding the cell's functional organization JO - Nat Rev Genet VL - 5 UR - https://doi.org/10.1038/nrg1272 DO - 10.1038/nrg1272 ID - Barabasi2004 ER - TY - JOUR AU - Rolland, T. AU - Taşan, M. AU - Charloteaux, B. AU - Pevzner Samuel, J. AU - Zhong, Q. AU - Sahni, N. PY - 2014 DA - 2014// TI - A proteome-scale Map of the human interactome network JO - Cell VL - 159 UR - https://doi.org/10.1016/j.cell.2014.10.050 DO - 10.1016/j.cell.2014.10.050 ID - Rolland2014 ER - TY - JOUR AU - Carninci, P. AU - Kasukawa, T. AU - Katayama, S. AU - Gough, J. AU - Frith, M. AU - Maeda, N. PY - 2005 DA - 2005// TI - The transcriptional landscape of the mammalian genome JO - Science VL - 309 UR - https://doi.org/10.1126/science.1112014 DO - 10.1126/science.1112014 ID - Carninci2005 ER - TY - JOUR AU - Minguez, P. AU - Letunic, I. AU - Parca, L. AU - Bork, P. PY - 2013 DA - 2013// TI - PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins JO - Nucleic Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gks1230 DO - 10.1093/nar/gks1230 ID - Minguez2013 ER - TY - JOUR AU - Minguez, P. AU - Parca, L. AU - Diella, F. AU - Mende, D. R. AU - Kumar, R. AU - Helmer‐Citterich, M. PY - 2012 DA - 2012// TI - Deciphering a global network of functionally associated post‐translational modifications JO - Mol Syst Biol VL - 8 ID - Minguez2012 ER - TY - JOUR AU - Liu, Z. P. AU - Wu, H. AU - Zhu, J. AU - Miao, H. PY - 2014 DA - 2014// TI - Systematic identification of transcriptional and post-transcriptional regulations in human respiratory epithelial cells during influenza A virus infection JO - BMC Bioinformatics VL - 15 UR - https://doi.org/10.1186/1471-2105-15-336 DO - 10.1186/1471-2105-15-336 ID - Liu2014 ER - TY - JOUR AU - Lewis, B. P. AU - Burge, C. B. AU - Bartel, D. P. PY - 2005 DA - 2005// TI - Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets JO - Cell VL - 120 UR - https://doi.org/10.1016/j.cell.2004.12.035 DO - 10.1016/j.cell.2004.12.035 ID - Lewis2005 ER - TY - JOUR AU - Reynolds, A. AU - Leake, D. AU - Boese, Q. AU - Scaringe, S. AU - Marshall, W. S. AU - Khvorova, A. PY - 2004 DA - 2004// TI - Rational siRNA design for RNA interference JO - Nat Biotechnol VL - 22 UR - https://doi.org/10.1038/nbt936 DO - 10.1038/nbt936 ID - Reynolds2004 ER - TY - JOUR AU - Ponting, C. P. AU - Oliver, P. L. AU - Reik, W. PY - 2009 DA - 2009// TI - Evolution and functions of long noncoding RNAs JO - Cell VL - 136 UR - https://doi.org/10.1016/j.cell.2009.02.006 DO - 10.1016/j.cell.2009.02.006 ID - Ponting2009 ER - TY - JOUR AU - Stelzl, U. AU - Worm, U. AU - Lalowski, M. AU - Haenig, C. AU - Brembeck, F. H. AU - Goehler, H. PY - 2005 DA - 2005// TI - A human protein-protein interaction network: a resource for annotating the proteome JO - Cell VL - 122 UR - https://doi.org/10.1016/j.cell.2005.08.029 DO - 10.1016/j.cell.2005.08.029 ID - Stelzl2005 ER - TY - JOUR AU - Rual, J. F. AU - Venkatesan, K. AU - Hao, T. AU - Hirozane-Kishikawa, T. AU - Dricot, A. AU - Li, N. PY - 2005 DA - 2005// TI - Towards a proteome-scale map of the human protein-protein interaction network JO - Nature VL - 437 UR - https://doi.org/10.1038/nature04209 DO - 10.1038/nature04209 ID - Rual2005 ER - TY - JOUR AU - Jeong, H. AU - Tombor, B. AU - Albert, R. AU - Oltvai, Z. N. AU - Barabási, A. L. PY - 2000 DA - 2000// TI - The large-scale organization of metabolic networks JO - Nature VL - 407 UR - https://doi.org/10.1038/35036627 DO - 10.1038/35036627 ID - Jeong2000 ER - TY - JOUR AU - Duarte, N. C. AU - Becker, S. A. AU - Jamshidi, N. AU - Thiele, I. AU - Mo, M. L. AU - Vo, T. D. PY - 2007 DA - 2007// TI - Global reconstruction of the human metabolic network based on genomic and bibliomic data JO - Proc Natl Acad Sci VL - 104 UR - https://doi.org/10.1073/pnas.0610772104 DO - 10.1073/pnas.0610772104 ID - Duarte2007 ER - TY - JOUR AU - Greene, C. S. AU - Krishnan, A. AU - Wong, A. K. AU - Ricciotti, E. AU - Zelaya, R. A. AU - Himmelstein, D. S. PY - 2015 DA - 2015// TI - Understanding multicellular function and disease with human tissue-specific networks JO - Nat Genet VL - 47 UR - https://doi.org/10.1038/ng.3259 DO - 10.1038/ng.3259 ID - Greene2015 ER - TY - JOUR AU - Kidd, B. A. AU - Peters, L. A. AU - Schadt, E. E. AU - Dudley, J. T. PY - 2014 DA - 2014// TI - Unifying immunology with informatics and multiscale biology JO - Nat Immunol VL - 15 UR - https://doi.org/10.1038/ni.2787 DO - 10.1038/ni.2787 ID - Kidd2014 ER - TY - JOUR AU - Pujana, M. A. AU - Han, J. D. J. AU - Starita, L. M. AU - Stevens, K. N. AU - Tewari, M. AU - Ahn, J. S. PY - 2007 DA - 2007// TI - Network modeling links breast cancer susceptibility and centrosome dysfunction JO - Nat Genet VL - 39 UR - https://doi.org/10.1038/ng.2007.2 DO - 10.1038/ng.2007.2 ID - Pujana2007 ER - TY - JOUR AU - Butcher, E. C. AU - Berg, E. L. AU - Kunkel, E. J. PY - 2004 DA - 2004// TI - Systems biology in drug discovery JO - Nat Biotech VL - 22 UR - https://doi.org/10.1038/nbt1017 DO - 10.1038/nbt1017 ID - Butcher2004 ER - TY - JOUR AU - Barabasi, A. L. AU - Gulbahce, N. AU - Loscalzo, J. PY - 2011 DA - 2011// TI - Network medicine: a network-based approach to human disease JO - Nat Rev Genet VL - 12 UR - https://doi.org/10.1038/nrg2918 DO - 10.1038/nrg2918 ID - Barabasi2011 ER - TY - JOUR AU - Domke, J. PY - 2013 DA - 2013// TI - Learning graphical model parameters with approximate marginal inference JO - IEEE Trans Pattern Anal Mach Intell VL - 35 UR - https://doi.org/10.1109/TPAMI.2013.31 DO - 10.1109/TPAMI.2013.31 ID - Domke2013 ER - TY - JOUR AU - Miao, H. AU - Xia, X. AU - Perelson, A. S. AU - Wu, H. PY - 2011 DA - 2011// TI - On identifiability of nonlinear ODE models and applications in viral dynamics JO - SIAM Rev VL - 53 UR - https://doi.org/10.1137/090757009 DO - 10.1137/090757009 ID - Miao2011 ER - TY - JOUR AU - Giraud, C. AU - Tsybakov, A. PY - 2012 DA - 2012// TI - Discussion: Latent variable graphical model selection via convex optimization JO - Ann Stat VL - 40 UR - https://doi.org/10.1214/12-AOS984 DO - 10.1214/12-AOS984 ID - Giraud2012 ER - TY - JOUR AU - Mincheva, M. AU - Roussel, M. R. PY - 2007 DA - 2007// TI - Graph-theoretic methods for the analysis of chemical and biochemical networks. I. Multistability and oscillations in ordinary differential equation models JO - J Math Biol VL - 55 UR - https://doi.org/10.1007/s00285-007-0099-1 DO - 10.1007/s00285-007-0099-1 ID - Mincheva2007 ER - TY - BOOK AU - Kline, R. B. PY - 2005 DA - 2005// TI - Principles and practice of structural equation modeling PB - Guilford Press CY - New York ID - Kline2005 ER - TY - BOOK AU - Pearl, J. PY - 2009 DA - 2009// TI - Causality: models, reasoning, and inference (2nd Edition) PB - Cambridge University Press CY - Cambridge UR - https://doi.org/10.1017/CBO9780511803161 DO - 10.1017/CBO9780511803161 ID - Pearl2009 ER - TY - JOUR AU - Shamaiah, M. AU - Lee, S. H. AU - Vikalo, H. PY - 2012 DA - 2012// TI - Graphical models and inference on graphs in genomics: challenges of high-throughput data analysis JO - IEEE Signal Process Mag VL - 29 UR - https://doi.org/10.1109/MSP.2011.943012 DO - 10.1109/MSP.2011.943012 ID - Shamaiah2012 ER - TY - JOUR AU - Cai, X. B. J. AU - Giannakis, G. B. PY - 2013 DA - 2013// TI - Inference of gene regulatory networks with sparse structural equation models exploiting genetic perturbations JO - PLoS Comput Biol VL - 9 UR - https://doi.org/10.1371/journal.pcbi.1003068 DO - 10.1371/journal.pcbi.1003068 ID - Cai2013 ER - TY - JOUR AU - Dong, Z. S. T. AU - Yuan, C. PY - 2013 DA - 2013// TI - Inference of gene regulatory networks from genetic perturbations with linear regression model JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0083263 DO - 10.1371/journal.pone.0083263 ID - Dong2013 ER - TY - JOUR AU - Brito, C. AU - Pearl, J. PY - 2002 DA - 2002// TI - A new identification condition for recursive models with correlated errors JO - Struct Equ Model VL - 9 UR - https://doi.org/10.1207/S15328007SEM0904_1 DO - 10.1207/S15328007SEM0904_1 ID - Brito2002 ER - TY - STD TI - Brito C, Pearl J. A graphical criterion for the identification of causal effects in linear models. 18th National Conference on Artificial Intelligence. Edmonton, Alberta, Canada, Amerian Association for Artificial Intelligence: 533-538. ID - ref29 ER - TY - BOOK AU - Brito, C. AU - Pearl, J. PY - 2002 DA - 2002// TI - Generalized instrumental variables ID - Brito2002 ER - TY - JOUR AU - Shimizu, S. AU - Hoyer, P. O. AU - Hyvärinen, A. AU - Kerminen, A. PY - 2006 DA - 2006// TI - A linear non-Gaussian acyclic model for causal discovery JO - J Mach Learn Res VL - 7 ID - Shimizu2006 ER - TY - BOOK PY - 2009 DA - 2009// TI - Parameter identification in a class of linear structural equation models ID - ref32 ER - TY - BOOK AU - Hyttinen, A. AU - Eberhardt, F. AU - Hoyer, P. O. PY - 2010 DA - 2010// TI - Causal discovery for linear cyclic models with latent variables on Probabilistic Graphical Models ID - Hyttinen2010 ER - TY - BOOK PY - 2010 DA - 2010// TI - Identifying causal effects with computer algebra PB - AUAI Press CY - Corvallis ID - ref34 ER - TY - JOUR AU - Drton, M. AU - Foygel, R. AU - Sullivant, S. PY - 2011 DA - 2011// TI - Global identifiability of linear structural equation models JO - Ann Stat VL - 39 UR - https://doi.org/10.1214/10-AOS859 DO - 10.1214/10-AOS859 ID - Drton2011 ER - TY - STD TI - Brito C, Pearl J. Graphical condition for identification in recursive SEM. arXiv:1206. 6821. 2012. ID - ref36 ER - TY - JOUR AU - Foygel, R. AU - Draisma, J. AU - Drton, M. PY - 2012 DA - 2012// TI - Half-trek criterion for generic identifiability of linear structural equation models JO - Ann Stat VL - 40 UR - https://doi.org/10.1214/12-AOS1012 DO - 10.1214/12-AOS1012 ID - Foygel2012 ER - TY - STD TI - Hoyer PO, Hyvarinen A, Scheines R, Spirtes PL, Ramsey J, Lacerda G, et al. Causal discovery of linear acyclic models with arbitrary distributions. Uncertainty in Artificial Intelligence - UAI. 2008;282-289. ID - ref38 ER - TY - JOUR AU - Hyttinen, A. AU - Eberhardt, F. AU - Hoyer, P. O. PY - 2012 DA - 2012// TI - Learning linear cyclic causal models with latent variables JO - J Mach Learn Res VL - 13 ID - Hyttinen2012 ER - TY - BOOK AU - Pearl, J. PY - 2012 DA - 2012// TI - The causal foundations of structural equation modeling ID - Pearl2012 ER - TY - STD TI - Tian J. A criterion for parameter identification in structural equation models. arXiv:12065289. 2012. ID - ref41 ER - TY - JOUR AU - Peters, J. AU - Bühlmann, P. PY - 2013 DA - 2013// TI - Identifiability of Gaussian structural equation models with equal error variances JO - Biometrika ID - Peters2013 ER - TY - BOOK AU - Chen, B. AU - Tian, J. PY - 2014 DA - 2014// TI - Pearl J, editors ID - Chen2014 ER - TY - STD TI - Tian J, editor Identifying linear causal effects. AAAI; 2004. ID - ref44 ER - TY - JOUR AU - Wright, S. PY - 1960 DA - 1960// TI - Path coefficients and path regressions: alternative or complementary concepts? JO - Biometrics VL - 16 UR - https://doi.org/10.2307/2527551 DO - 10.2307/2527551 ID - Wright1960 ER - TY - JOUR AU - Wright, S. PY - 1934 DA - 1934// TI - The method of path coefficients JO - Ann Math Stat VL - 5 UR - https://doi.org/10.1214/aoms/1177732676 DO - 10.1214/aoms/1177732676 ID - Wright1934 ER - TY - STD TI - Garcia C, Li T. On the number of solutions to polynomial systems of equations. SIAM J Numer Anal. 1979. ID - ref47 ER - TY - JOUR AU - Bellu, G. AU - Saccomani, M. AU - Audoly, S. AU - Angio, L. PY - 2007 DA - 2007// TI - DAISY: A new software tool to test global identifiability of biological and physiological systems JO - Comput Methods Programs Biomed VL - 88 UR - https://doi.org/10.1016/j.cmpb.2007.07.002 DO - 10.1016/j.cmpb.2007.07.002 ID - Bellu2007 ER - TY - STD TI - Chis OT, Banga J, Balsa-Canto E. Structural identifiability of systems biology models: a critical comparison of methods. PLoS One. 2011;6(11):e27755. doi:10.1371/journal.pone.0027755. ID - ref49 ER - TY - JOUR AU - Gerstein, M. B. AU - Kundaje, A. AU - Hariharan, M. AU - Landt, S. G. AU - Yan, K. -. K. AU - Cheng, C. PY - 2012 DA - 2012// TI - Architecture of the human regulatory network derived from ENCODE data JO - Nature VL - 489 UR - https://doi.org/10.1038/nature11245 DO - 10.1038/nature11245 ID - Gerstein2012 ER - TY - JOUR AU - Kanehisa, M. AU - Goto, S. AU - Sato, Y. AU - Kawashima, M. AU - Furumichi, M. AU - Tanabe, M. PY - 2014 DA - 2014// TI - Data, information, knowledge and principle: back to metabolism in KEGG JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt1076 DO - 10.1093/nar/gkt1076 ID - Kanehisa2014 ER - TY - JOUR AU - Lakdawala, S. S. AU - Jayaraman, A. AU - Halpin, R. A. AU - Lamirande, E. W. AU - Shih, A. R. AU - Stockwell, T. B. PY - 2015 DA - 2015// TI - The soft palate is an important site of adaptation for transmissible influenza viruses JO - Nature VL - 526 UR - https://doi.org/10.1038/nature15379 DO - 10.1038/nature15379 ID - Lakdawala2015 ER - TY - JOUR AU - Matsuoka, Y. AU - Matsumae, H. AU - Katoh, M. AU - Eisfeld, A. J. AU - Neumann, G. AU - Hase, T. PY - 2013 DA - 2013// TI - A comprehensive map of the influenza A virus replication cycle JO - BMC Syst Biol VL - 7 UR - https://doi.org/10.1186/1752-0509-7-97 DO - 10.1186/1752-0509-7-97 ID - Matsuoka2013 ER - TY - JOUR AU - Watanabe, T. AU - Kiso, M. AU - Fukuyama, S. AU - Nakajima, N. AU - Imai, M. AU - Yamada, S. PY - 2013 DA - 2013// TI - Characterization of H7N9 influenza A viruses isolated from humans JO - Nature VL - 501 UR - https://doi.org/10.1038/nature12392 DO - 10.1038/nature12392 ID - Watanabe2013 ER - TY - JOUR AU - Konig, R. AU - Stertz, S. AU - Zhou, Y. AU - Inoue, A. AU - Hoffmann, H. H. AU - Bhattacharyya, S. PY - 2010 DA - 2010// TI - Human host factors required for influenza virus replication JO - Nature VL - 463 UR - https://doi.org/10.1038/nature08699 DO - 10.1038/nature08699 ID - Konig2010 ER - TY - JOUR AU - York, A. AU - Hutchinson, E. AU - Fodor, E. PY - 2014 DA - 2014// TI - Interactome analysis of the influenza A virus transcription/replication machinery identifies protein phosphatase 6 as a cellular factor required for efficient virus replication JO - J Virol VL - 88 UR - https://doi.org/10.1128/JVI.01813-14 DO - 10.1128/JVI.01813-14 ID - York2014 ER - TY - JOUR AU - Honda, A. AU - Mizumoto, K. AU - Ishihama, A. PY - 2002 DA - 2002// TI - Minimum molecular architectures for transcription and replication of the influenza virus JO - Proc Natl Acad Sci U S A VL - 99 UR - https://doi.org/10.1073/pnas.152456799 DO - 10.1073/pnas.152456799 ID - Honda2002 ER -