TY - JOUR AU - Laplante, M. AU - Sabatini, D. M. PY - 2012 DA - 2012// TI - mTOR signaling in growth control and disease JO - Cell VL - 149 UR - https://doi.org/10.1016/j.cell.2012.03.017 DO - 10.1016/j.cell.2012.03.017 ID - Laplante2012 ER - TY - JOUR AU - MacDonald, B. T. PY - 2009 DA - 2009// TI - Wnt/β-catenin signaling: components, mechanisms, and diseases JO - Developmental cell VL - 17 UR - https://doi.org/10.1016/j.devcel.2009.06.016 DO - 10.1016/j.devcel.2009.06.016 ID - MacDonald2009 ER - TY - JOUR AU - Mizuno, S. PY - 2012 DA - 2012// TI - Alzpathway: a comprehensive map of signaling pathways of alzheimer's disease JO - BMC systems biology VL - 6 UR - https://doi.org/10.1186/1752-0509-6-52 DO - 10.1186/1752-0509-6-52 ID - Mizuno2012 ER - TY - JOUR AU - Yook, S. PY - 2004 DA - 2004// TI - Functional and topological characterization of protein interaction networks JO - PROTEOMICS VL - 4 UR - https://doi.org/10.1002/pmic.200300636 DO - 10.1002/pmic.200300636 ID - Yook2004 ER - TY - JOUR AU - Jeong, H. 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 - Wagner, A. PY - 2001 DA - 2001// TI - The small world inside large metabolic networks JO - Proceedings of the Royal Society of London Series B: Biological Sciences VL - 268 UR - https://doi.org/10.1098/rspb.2001.1711 DO - 10.1098/rspb.2001.1711 ID - Wagner2001 ER - TY - CHAP AU - Todor, A. AU - Dobra, A. AU - Kahveci, T. PY - 2012 DA - 2012// TI - Uncertain interactions affect degree distribution of biological networks BT - Bioinformatics and Biomedicine (BIBM), 2012 IEEE International Conference UR - https://doi.org/10.1109/BIBM.2012.6392723 DO - 10.1109/BIBM.2012.6392723 ID - Todor2012 ER - TY - JOUR AU - Hahn, M. W. AU - Kern, A. D. PY - 2005 DA - 2005// TI - Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks JO - Molecular Biology and Evolution VL - 22 UR - https://doi.org/10.1093/molbev/msi072 DO - 10.1093/molbev/msi072 ID - Hahn2005 ER - TY - JOUR AU - Jeong, H. PY - 2001 DA - 2001// TI - Lethality and centrality in protein networks JO - Nature VL - 411 UR - https://doi.org/10.1038/35075138 DO - 10.1038/35075138 ID - Jeong2001 ER - TY - BOOK AU - Tasa, T. PY - 2011 DA - 2011// TI - Centrality in biological networks ID - Tasa2011 ER - TY - JOUR AU - Alon, U. PY - 2003 DA - 2003// TI - Biological networks: the tinkerer as an engineer JO - Science VL - 301 UR - https://doi.org/10.1126/science.1089072 DO - 10.1126/science.1089072 ID - Alon2003 ER - TY - JOUR AU - Kwon, Y. AU - Cho, K. PY - 2008 DA - 2008// TI - Quantitative analysis of robustness and fragility in biological networks based on feedback dynamics JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn060 DO - 10.1093/bioinformatics/btn060 ID - Kwon2008 ER - TY - JOUR AU - Ryba, T. PY - 2001 DA - 2001// TI - Replication timing: a fingerprint for cell identity and pluripotency JO - PLoS computational biology VL - 7 UR - https://doi.org/10.1371/journal.pcbi.1002225 DO - 10.1371/journal.pcbi.1002225 ID - Ryba2001 ER - TY - JOUR AU - Sch¨ubeler, D. PY - 2002 DA - 2002// TI - Genome-wide dna replication profile for drosophila melanogaster: a link between transcription and replication timing JO - Nature genetics VL - 32 UR - https://doi.org/10.1038/ng1005 DO - 10.1038/ng1005 ID - Sch¨ubeler2002 ER - TY - JOUR AU - Todor, A. PY - 2012 DA - 2012// TI - Probabilistic biological network alignment JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics VL - 99 ID - Todor2012 ER - TY - JOUR AU - Szklarczyk, D. PY - 2011 DA - 2011// TI - The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored JO - Nucleic acids research VL - 39 UR - https://doi.org/10.1093/nar/gkq973 DO - 10.1093/nar/gkq973 ID - Szklarczyk2011 ER - TY - CHAP AU - Ceol, A. PY - 2009 DA - 2009// TI - MINT, the Molecular INTeraction database: 2009 update BT - Nucleic acids research ID - Ceol2009 ER - TY - JOUR AU - Bader, J. S. PY - 2003 DA - 2003// TI - Gaining confidence in high-throughput protein interaction networks JO - Nature biotechnology VL - 22 UR - https://doi.org/10.1038/nbt924 DO - 10.1038/nbt924 ID - Bader2003 ER - TY - JOUR AU - von Mering, C. PY - 2002 DA - 2002// TI - Comparative assessment of large-scale data sets of protein-protein interactions JO - Nature VL - 417 UR - https://doi.org/10.1038/nature750 DO - 10.1038/nature750 ID - von Mering2002 ER - TY - JOUR AU - Barabási, A. AU - Oltvai, Z. N. PY - 2004 DA - 2004// TI - Network biology: understanding the cell's functional organization JO - Nature Reviews Genetics VL - 5 UR - https://doi.org/10.1038/nrg1272 DO - 10.1038/nrg1272 ID - Barabási2004 ER - TY - JOUR AU - Ravasz, E. PY - 2002 DA - 2002// TI - Hierarchical Organization of Modularity in Metabolic Networks JO - Science VL - 297 UR - https://doi.org/10.1126/science.1073374 DO - 10.1126/science.1073374 ID - Ravasz2002 ER - TY - JOUR AU - Oxley, J. AU - Welsh, D. PY - 2002 DA - 2002// TI - Chromatic, flow, and reliability polynomials: the complexity of their coefficients JO - Combinatorics, Probability & Computing VL - 11 UR - https://doi.org/10.1017/S0963548302005175 DO - 10.1017/S0963548302005175 ID - Oxley2002 ER - TY - JOUR AU - Brown, D. B. PY - 2971 DA - 2971// TI - A computerized algorithm for determining the reliability of redundant configurations JO - Reliability, IEEE Transactions VL - 20 ID - Brown2971 ER - TY - JOUR AU - Sokal, A. D. PY - 2005 DA - 2005// TI - The multivariate tutte polynomial (alias potts model) for graphs and matroids JO - Surveys in combinatorics VL - 327 ID - Sokal2005 ER - TY - CHAP AU - Gabr, H. AU - Todor, A. AU - Zandi, H. AU - Dobra, A. AU - Kahveci, T. PY - 2013 DA - 2013// TI - Preach: Reachability in probabilistic signaling networks BT - Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics BCB'13 PB - ACM CY - Wshington DC, USA ID - Gabr2013 ER - TY - CHAP AU - Gabr, H. AU - Kahveci, T. PY - 2014 DA - 2014// TI - Characterization of probabilistic signaling networks through signal propagation BT - Computational Advances in Bio and Medical Sciences (ICCABS), 2014 IEEE 4th International Conference ID - Gabr2014 ER - TY - JOUR AU - Ashburner, M. PY - 2000 DA - 2000// TI - Gene ontology: tool for the unification of biology JO - Nature genetics VL - 25 UR - https://doi.org/10.1038/75556 DO - 10.1038/75556 ID - Ashburner2000 ER - TY - JOUR AU - Kanehisa, M. PY - 2004 DA - 2004// TI - The KEGG resource for deciphering the genome JO - Nucleic acids research VL - 32 UR - https://doi.org/10.1093/nar/gkh063 DO - 10.1093/nar/gkh063 ID - Kanehisa2004 ER - TY - JOUR AU - Gulsoy, G. PY - 2012 DA - 2012// TI - HIDEN: Hierarchical decomposition of regulatory networks JO - BMC bioinformatics VL - 13 UR - https://doi.org/10.1186/1471-2105-13-250 DO - 10.1186/1471-2105-13-250 ID - Gulsoy2012 ER - TY - JOUR AU - Yoon, J. PY - 2006 DA - 2006// TI - An algorithm for modularity analysis of directed and weighted biological networks based on edge-betweenness centrality JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl533 DO - 10.1093/bioinformatics/btl533 ID - Yoon2006 ER - TY - JOUR AU - Joy, M. P. PY - 2005 DA - 2005// TI - High-betweenness proteins in the yeast protein interaction network JO - BioMed Research International VL - 2005 ID - Joy2005 ER - TY - JOUR AU - Yu, H. PY - 2007 DA - 2007// TI - The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics JO - PLoS computational biology VL - 3 UR - https://doi.org/10.1371/journal.pcbi.0030059 DO - 10.1371/journal.pcbi.0030059 ID - Yu2007 ER - TY - JOUR AU - Bar-Joseph, Z. PY - 2001 DA - 2001// TI - Fast optimal leaf ordering for hierarchical clustering JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.suppl_1.S22 DO - 10.1093/bioinformatics/17.suppl_1.S22 ID - Bar-Joseph2001 ER - TY - JOUR AU - Bazley, L. A. AU - Gullick, W. J. PY - 2005 DA - 2005// TI - The epidermal growth factor receptor family JO - Endocrine-Related Cancer VL - 12 UR - https://doi.org/10.1677/erc.1.01032 DO - 10.1677/erc.1.01032 ID - Bazley2005 ER - TY - JOUR AU - Gorgoulis, V. PY - 1992 DA - 1992// TI - Expression of egf, tgf-alpha and egfr in squamous cell lung carcinomas JO - Anticancer research VL - 12 ID - Gorgoulis1992 ER - TY - JOUR AU - Jackson, L. F. PY - 2003 DA - 2003// TI - Defective valvulogenesis in hb-egf and tace-null mice is associated with aberrant bmp signaling JO - The EMBO journal VL - 22 UR - https://doi.org/10.1093/emboj/cdg264 DO - 10.1093/emboj/cdg264 ID - Jackson2003 ER - TY - JOUR AU - Pathak, B. PY - 1995 DA - 1995// TI - Mouse chromosomal location of three egf receptor ligands: amphiregulin (areg), betacellulin (btc), and heparin-binding egf (hegfl) JO - Genomics VL - 28 UR - https://doi.org/10.1006/geno.1995.1116 DO - 10.1006/geno.1995.1116 ID - Pathak1995 ER -