TY - CHAP AU - Akutsu, T. AU - Miyano, S. AU - Kuhara, S. PY - 1999 DA - 1999// TI - Identification of genetic networks from a small number of gene expression patterns under the Boolean network model BT - Pac Symp Biocomput ID - Akutsu1999 ER - TY - CHAP AU - Bernard, A. AU - Hartemink, A. PY - 2005 DA - 2005// TI - Informative structure priors: joint learning of dynamic regulatory networks from multiple types of data BT - Pac Symp Biocomput ID - Bernard2005 ER - TY - CHAP AU - Chen, T. AU - He, H. AU - Church, G. PY - 1999 DA - 1999// TI - Modeling gene expression with differential equations BT - Pac Symp Biocomput ID - Chen1999 ER - TY - CHAP AU - De Hoon, M. AU - Imoto, S. AU - Kobayashi, K. AU - Ogasawara, N. AU - Miyano, S. PY - 2003 DA - 2003// TI - Inferring gene regulatory networks from time-ordered gene expression data of Bacillus subtilis using differential equations BT - Pac Symp Biocomput ID - De Hoon2003 ER - TY - JOUR AU - Hu, X. AU - Ng, M. AU - Wu, F. AU - Sokhansanj, B. PY - 2009 DA - 2009// TI - Mining, modeling, and evaluation of subnetworks from large biomolecular networks and its comparison study JO - IEEE Trans Inf Technol Biomed VL - 13 UR - https://doi.org/10.1109/TITB.2008.2007649 DO - 10.1109/TITB.2008.2007649 ID - Hu2009 ER - TY - JOUR AU - Huang, Y. AU - Tienda-Luna, I. AU - Wang, Y. PY - 2009 DA - 2009// TI - A survey of statistical models for reverse engineering gene regulatory networks JO - IEEE Signal Process Mag VL - 26 UR - https://doi.org/10.1109/MSP.2008.930647 DO - 10.1109/MSP.2008.930647 ID - Huang2009 ER - TY - JOUR AU - Wu, F. PY - 2007 DA - 2007// TI - Inference of gene regulatory networks and its validation JO - Current Bioinformatics VL - 2 UR - https://doi.org/10.2174/157489307780618240 DO - 10.2174/157489307780618240 ID - Wu2007 ER - TY - JOUR AU - Yuan, Y. AU - Li, C. AU - Windram, O. PY - 2011 DA - 2011// TI - Directed partial correlation: inferring large-scale gene regulatory network through induced topology disruptions JO - PLoS One VL - 6 UR - https://doi.org/10.1371/journal.pone.0016835 DO - 10.1371/journal.pone.0016835 ID - Yuan2011 ER - TY - JOUR AU - Newman, M. PY - 2004 DA - 2004// TI - Fast algorithm for detecting community structure in networks JO - Phys Rev E Stat Nonlin Soft Matter Phys VL - 69 UR - https://doi.org/10.1103/PhysRevE.69.066133 DO - 10.1103/PhysRevE.69.066133 ID - Newman2004 ER - TY - JOUR AU - Pothen, A. AU - Simon, H. AU - Liou, K. PY - 1990 DA - 1990// TI - Partitioning sparse matrices with eigenvectors of graphs JO - SIAM J Matrix Anal Applic VL - 11 UR - https://doi.org/10.1137/0611030 DO - 10.1137/0611030 ID - Pothen1990 ER - TY - JOUR AU - Kernighan, B. AU - Lin, S. PY - 1970 DA - 1970// TI - An efficient heuristic procedure for partitioning graphs JO - Bell System Technical Journal VL - 49 UR - https://doi.org/10.1002/j.1538-7305.1970.tb01770.x DO - 10.1002/j.1538-7305.1970.tb01770.x ID - Kernighan1970 ER - TY - JOUR AU - Girvan, M. AU - Newman, M. PY - 2002 DA - 2002// TI - Community structure in social and biological networks JO - Proc Natl Acad Sci USA VL - 99 UR - https://doi.org/10.1073/pnas.122653799 DO - 10.1073/pnas.122653799 ID - Girvan2002 ER - TY - JOUR AU - Radicchi, F. AU - Castellano, C. AU - Cecconi, F. AU - Loreto, V. AU - Parisi, D. PY - 2004 DA - 2004// TI - Defining and identifying communities in networks JO - Proc Natl Acad Sci USA VL - 101 UR - https://doi.org/10.1073/pnas.0400054101 DO - 10.1073/pnas.0400054101 ID - Radicchi2004 ER - TY - JOUR AU - Palla, G. AU - Derényi, I. AU - Farkas, I. AU - Vicsek, T. PY - 2005 DA - 2005// TI - Uncovering the overlapping community structure of complex networks in nature and society JO - Nature VL - 435 UR - https://doi.org/10.1038/nature03607 DO - 10.1038/nature03607 ID - Palla2005 ER - TY - JOUR AU - Newman, M. PY - 2004 DA - 2004// TI - Detecting community structure in networks JO - The European Physical Journal B-Condensed Matter and Complex Systems VL - 38 UR - https://doi.org/10.1140/epjb/e2004-00124-y DO - 10.1140/epjb/e2004-00124-y ID - Newman2004 ER - TY - CHAP AU - Wu, F. AU - Liu, L. AU - Xia, Z. PY - 2010 DA - 2010// TI - Identification of gene regulatory networks from time course gene expression data BT - Conf Proc IEEE Eng Med Biol Soc ID - Wu2010 ER - TY - JOUR AU - Lee, M. AU - Shen, H. AU - Huang, J. AU - Marron, J. PY - 2010 DA - 2010// TI - Biclustering via sparse singular value decomposition JO - Biometrics VL - 66 UR - https://doi.org/10.1111/j.1541-0420.2010.01392.x DO - 10.1111/j.1541-0420.2010.01392.x ID - Lee2010 ER - TY - STD TI - Grant M, Boyd S: CVX: Matlab software for disciplined convex programming, version 1.21 (2010). ID - ref18 ER - TY - STD TI - Candés E, Li X, Ma Y, Wright J: Robust principal component analysis?. ArXiv:0912.3599. ID - ref19 ER - TY - JOUR AU - Chandrasekaran, V. AU - Sanghavi, S. AU - Parrilo, P. AU - Willsky, A. PY - 2011 DA - 2011// TI - Rank-sparsity incoherence for matrix decomposition JO - SIAM J Optim VL - 21 UR - https://doi.org/10.1137/090761793 DO - 10.1137/090761793 ID - Chandrasekaran2011 ER - TY - CHAP AU - He, B. AU - Tao, M. AU - Yuan, X. PY - 2010 DA - 2010// TI - A splitting method for separate convex programming with linking linear constraints BT - Tech rep ID - He2010 ER - TY - JOUR AU - Cai, J. AU - Candés, E. AU - Shen, Z. PY - 2010 DA - 2010// TI - A singular value thresholding algorithm for matrix completion JO - SIAM J Optim VL - 20 UR - https://doi.org/10.1137/080738970 DO - 10.1137/080738970 ID - Cai2010 ER - TY - STD TI - Lin Z, Chen M, Wu L, Ma Y: The augmented lagrange multiplier method for exact recovery of corrupted low-rank matrices. ArXiv:1009.5055. ID - ref23 ER - TY - JOUR AU - Boyd, S. AU - Parikh, N. AU - Chu, E. AU - Peleato, B. AU - Eckstein, J. PY - 2010 DA - 2010// TI - Distributed optimization and statistical learning via the alternating direction method of multipliers JO - Foundations and Trends in Machine Learning VL - 3 UR - https://doi.org/10.1561/2200000016 DO - 10.1561/2200000016 ID - Boyd2010 ER - TY - STD TI - AGN. [http://www.comp-sys-bio.org/AGN/index.html] UR - http://www.comp-sys-bio.org/AGN/index.html ID - ref25 ER - TY - JOUR AU - Zhao, X. AU - Sun, D. AU - Toh, K. PY - 2010 DA - 2010// TI - A Newton-CG augmented Lagrangian method for semidefinite programming JO - SIAM J Optim VL - 20 UR - https://doi.org/10.1137/080718206 DO - 10.1137/080718206 ID - Zhao2010 ER - TY - STD TI - web100-023. [http://www.comp-sys-bio.org/AGN/Web/Web100-023.html] UR - http://www.comp-sys-bio.org/AGN/Web/Web100-023.html ID - ref27 ER - TY - STD TI - SDPNAL. [http://www.math.nus.edu.sg/~matsundf/] UR - http://www.math.nus.edu.sg/~matsundf/ ID - ref28 ER - TY - STD TI - CVX. [http://cvxr.com/cvx/] UR - http://cvxr.com/cvx/ ID - ref29 ER -