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Papers that cite EXPANDER:

  1. Jha, M., Guzzi, P.H., Roy, S. Qualitative assessment of functional module detectors on microarray and RNASeq data. Network Modeling Analysis in Health Informatics and Bioinformatics, 8(1), art. no. 1, 2019.
  2. Fogelman, E., Oren-Shamir, M., Hirschberg, J., (...), Faigenboim, A., Ginzberg, I. ENutritional value of potato (Solanum tuberosum) in hot climates: anthocyanins, carotenoids, and steroidal glycoalkaloids. 2019, Planta. Article in Press, 2019.
  3. Jha, M., Roy, S. Extracting functional modules from RNASeq counts using ensemble of clustering based module detection methods. Journal of Computational and Theoretical Nanoscience, 15(6-7), pp. 2359-2363, 2018.
  4. Perry, R.B.-T., Hezroni, H., Goldrich, M.J., Ulitsky, I. Regulation of Neuroregeneration by Long Noncoding RNAs. Molecular Cell, 72(3), pp. 553-567.e5, 2018.
  5. Kolberg, L., Kuzmin, I., Adler, P., Vilo, J., Peterson, H. FuncExplorer: A tool for fast data-driven functional characterisation of high-throughput expression data. BMC Genomics, 19(1), art. no. 817, 2018.
  6. Wang, H., Zhao, H., Huang, X., Sun, K., Feng, J. Comparative cochlear transcriptomics of echolocating bats provides new insights into different nervous activities of CF bat species. Scientific Reports, 8(1), art. no. 15934, 2018.
  7. Kosel, J., Raspor, P., Cadez, N. Maximum residue limit of fungicides inhibits the viability and growth of desirable non-Saccharomyces wine yeasts. Australian Journal of Grape and Wine Research, Article in Press, 2018.
  8. Aouabed, H., Santamaría, R., Elloumi, M. Suitable overlapping set visualization techniques and their application to visualize biclustering results on gene expression data. Communications in Computer and Information Science, 903, pp. 191-201, 2018.
  9. Fox, H., Doron-Faigenboim, A., Kelly, G., (...), Moshelion, M., David-Schwartz, R. Transcriptome analysis of Pinus halepensis under drought stress and during recovery. Tree Physiology, 38(3), pp. 423-441, 2018.
  10. Braverman-Gross, C., Nudel, N., Ronen, D., (...), McCarty, M.I., Benvenisty, N. Derivation and molecular characterization of pancreatic differentiated MODY1-iPSCs. Stem Cell Research, 31, pp. 16-26, 2018.
  11. Bhowmick, S.S., Saha, I., Bhattacharjee, D., Genovese, L.M., Geraci, F. Genome-wide analysis of NGS data to compile cancer-specific panels of miRNA biomarkers. PLoS ONE, 13(7), art. no. e0200353, 2018.
  12. Ke, M., Gao, Z., Chen, J., (...), Zhang, L., Chen, X. Auxin controls circadian flower opening and closure in the waterlily. BMC Plant Biology, 18(1), art. no. 143, 2018.
  13. Dykes, I.M., Szumska, D., Kuncheria, L., (...), Collignon, J., Bhattacharya, S. A Requirement for Zic2 in the regulation of nodal expression underlies the establishment of left-sided identity. Scientific Reports, 8(1), art. no. 104392018, 2018.
  14. Roy, S., Manners, H.N., Jha, M., Guzzi, P.H., Kalita, J.K. Soft computing approaches to extract biologically significant gene network modules. Soft Computing for Biological Systems, pp. 23-37, 2018.
  15. Perner, J., Kropácková, S., Kopácek, P., Ribeiro, J.M.C. Sialome diversity of ticks revealed by RNAseq of single tick salivary glands. PLoS Neglected Tropical Diseases, 12(4), art. no. e0006410, 2018.
  16. Byron, A. Proteomic profiling of integrin adhesion complex assembly. Methods in Molecular Biology, 1764, pp. 193-236, 2018.
  17. Biechonski, S., Olender, L., Zipin-Roitman, A., (...), Nagler, A., Milyavsky, M. Attenuated DNA damage responses and increased apoptosis characterize human hematopoietic stem cells exposed to irradiation. Scientific Reports, 8(1), art. no. 6071, 2018.
  18. Yao, X., Yan, J., Kim, S., (...), Saykin, A.J., Shen, L. Two-dimensional enrichment analysis for mining high-level imaging genetic associations . Brain Informatics, 4(1), pp. 27-37, 2018.
  19. Meyer, B.M., Adhikari, P.L., Olson, G.M., Overton, E.B., Miles, M.S. Louisiana Coastal Marsh Environments and MC252 Oil Biomarker Chemistry . Oil Spill Environmental Forensics Case Studies, pp. 737-756, 2018.
  20. Huang, L., Yang, M., Li, L., (...), Shi, T., Yang, P. Whole genome re-sequencing reveals evolutionary patterns of sacred lotus (Nelumbo nucifera) . Journal of Integrative Plant Biology, 60(1), pp. 2-15, 2018.
  21. Tanr, D., Nuriyeva, F. An effective method determining the initial cluster centers for k-means for clustering gene expression data. 2nd International Conference on Computer Science and Engineering, UBMK 2017, art. no. 8093520, pp. 751-754, 2017.
  22. Ray, S., Maulik, U. Identifying differentially coexpressed module during HIV disease progression: A multiobjective approach. Scientific Reports, 7(1), art. no. 86, 2017.
  23. Jin, D., Lee, H. FGMD: A novel approach for functional gene module detection in cancer. PLoS ONE, 12(12), art. no. e0188900, 2017.
  24. Qiu, J.-J., Liu, Y.-N., Ren, Z.-R., Yan, J.-B. Dysfunctions of mitochondria in close association with strong perturbation of long noncoding RNAs expression in down syndrome. International Journal of Biochemistry and Cell Biology, 92 pp. 115 - 120, 2017.
  25. Ziv, T., Chalifa-Caspi, V., Denekamp, N., Plaschkes, I., Kierszniowska, S., Blais, I., Admon, A., Lubzens, E. Dormancy in embryos: Insight from hydrated encysted embryos of an aquatic invertebrate. Molecular and Cellular Proteomics, 16 ( 10 ) pp. 1746 - 1769, 2017.
  26. García-Calderón, M., Pérez-Delgado, C.M., Credali, A., Vega, J.M., Betti, M., Márquez, A.J. Genes for asparagine metabolism in Lotus japonicus: Differential expression and interconnection with photorespiration. BMC Genomics, 18 ( 1 ), art. no. 781, 2017.
  27. Shamir, R., Klein, C., Amar, D., Vollstedt, E.-J., Bonin, M., Usenovic, M., Wong, Y.C., Maver, A., Poths, S., Safer, H., Corvol, J.-C., Lesage, S., Lavi, O., Deuschl, G., Kuhlenbaeumer, G., Pawlack, H., Ulitsky, I., Kasten, M., Riess, O., Brice, A., Peterlin, B., Krainc, D. Analysis of blood-based gene expression in idiopathic Parkinson disease. Neurology, 89 ( 16 ) pp. 1676 - 1683, 2017.
  28. Chen, W., Xu, Q., Zhong, Y., Yu, H., Shu, J., Ma, T., Li, Z. Genetic variation and co-evolutionary relationship of RNA polymerase complex segments in influenza A viruses. Virology, 511 pp. 193 - 206, 2017.
  29. Lan, C., Yang, Y., Li, X., Luo, B., Huan, J. Learning Social Circles in Ego-Networks Based on Multi-View Network Structure. IEEE Transactions on Knowledge and Data Engineering, 29 ( 8 ) , art. no. 7883882 , pp. 1681 - 1694, 2017.
  30. Misra, S., Ray, S.S. Finding optimum width of discretization for gene expressions using functional annotations. Computers in Biology and Medicine, 90 pp. 59 - 67, 2017.
  31. Dutta, P., Saha, S. Fusion of expression values and protein interaction information using multi-objective optimization for improving gene clustering. Computers in Biology and Medicine, 89 pp. 31 - 43, 2017.
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  34. Monsanto, M.M., White, K.S., Kim, T., Wang, B.J., Fisher, K., Ilves, K., Khalafalla, F.G., Casillas, A., Broughton, K., Mohsin, S., Dembitsky, W.P., Sussman, M.A. Concurrent Isolation of 3 Distinct Cardiac Stem Cell Populations from a Single Human Heart Biopsy. Circulation Research, 121 ( 2 ) pp. 113 - 124, 2017.
  35. Dangwal, S., Schimmel, K., Foinquinos, A., Xiao, K., Thum, T. Noncoding RNAs in heart failure. Handbook of Experimental Pharmacology, 243 pp. 423 - 445, 2017.
  36. Bhattacharya, A., Cui, Y. A GPU-accelerated algorithm for biclustering analysis and detection of condition-dependent coexpression network modules. Scientific Reports, 7 ( 1 ) , art. no. 4162, 2017.
  37. Diament, A., Tuller, T. Tracking the evolution of 3D gene organization demonstrates its connection to phenotypic divergence. Nucleic Acids Research, 45 ( 8 ) pp. 4330 - 4343, 2017.
  38. Oliva, M., Bar, E., Ovadia, R., Perl, A., Galili, G., Lewinsohn, E., Oren-Shamir, M. Phenylpyruvate contributes to the synthesis of fragrant benzenoid-phenylpropanoids in petunia × hybrida flowers. Frontiers in Plant Science, 8 , art. no. 769, 2017.
  39. Oliva, M., Bar, E., Ovadia, R., Perl, A., Galili, G., Lewinsohn, E., Oren-Shamir, M. Phenylpyruvate contributes to the synthesis of fragrant benzenoid-phenylpropanoids in petunia × hybrida flowers. Frontiers in Plant Science, 8 , art. no. 769, 2017.
  40. Perl, K., Ushakov, K., Pozniak, Y., Yizhar-Barnea, O., Bhonker, Y., Shivatzki, S., Geiger, T., Avraham, K.B., Shamir, R. Reduced changes in protein compared to mRNA levels across non-proliferating tissues. BMC Genomics, 18 ( 1 ) , art. no. 305, 2017.
  41. Pal, S.K., Ray, S.S., Ganivada, A. Gene function analysis. Studies in Computational Intelligence, 712 pp. 163 - 193, 2017.
  42. van Hagen, M., Piebes, D.G.E., de Leeuw, W.C., Vuist, I.M., van Roon-Mom, W.M.C., Moerland, P.D., Verschure, P.J. The dynamics of early-state transcriptional changes and aggregate formation in a Huntington's disease cell model. BMC Genomics, 18 ( 1 ) , art. no. 373, 2017.
  43. Byron, A. Clustering and network analysis of reverse phase protein array data. Methods in Molecular Biology, 1606 pp. 171 - 191, 2017.
  44. Hur, W., Ryu, J.Y., Kim, H.U., Hong, S.W., Lee, E.B., Lee, S.Y., Yoon, S.K. Systems approach to characterize the metabolism of liver cancer stem cells expressing CD133. Scientific Reports, 7 , art. no. 45557, 2017.
  45. Slobodin, B., Han, R., Calderone, V., Vrielink, J.A.F.O., Loayza-Puch, F., Elkon, R., Agami, R. Transcription Impacts the Efficiency of mRNA Translation via Co-transcriptional N6-adenosine Methylation. Cell, 169 ( 2 ) pp. 326 - 337.e12, 2017.
  46. Luo, J., Song, D., Liang, C., Li, G., Cao, B. Detecting co-regulatory modules from human regulatory network by randomly walking between regulator and gene modules. Journal of Computational and Theoretical Nanoscience, 14 ( 1 ) pp. 384 - 388, 2017.
  47. Choo, D.W., Goh, S.H., Cho, Y.W., Baek, H.J., Park, E.J., Motoyama, N., Kim, T.H., Kim, J.Y., Kim, S.S. CHK2 is involved in the p53-independent radiosensitizing effects of valproic acid. Oncology Letters, 13 ( 4 ) pp. 2591 - 2598, 2017.
  48. Mahata, K., Das, R., Das, S., Sarkar, A. Indian river watershed image analysis using fuzzy- CA hybrid approach. Intelligent Analysis of Multimedia Information, pp. 232 - 246, 2017.
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  51. Shi, T., Wang, K., Yang, P. The evolution of plant microRNAs: insights from a basal eudicot sacred lotus. Plant Journal, 89 ( 3 ) pp. 442 - 457, 2017.
  52. Shamir, R., Zehavi, M., Zeira, R. A linear-time algorithm for the copy number transformation problem. Leibniz International Proceedings in Informatics, LIPIcs, 54 pp. 16.1 - 16.13, 2017.
  53. Zeira, R., Shamir, R. Sorting by Cuts, Joins, and Whole Chromosome Duplications. Journal of Computational Biology, 24 ( 2 ) pp. 127 - 137, 2017.
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  55. Sumazin, P., Chen, Y., Treviño, L.R., Sarabia, S.F., Hampton, O.A., Patel, K., Mistretta, T.-A., Zorman, B., Thompson, P., Heczey, A., Comerford, S., Wheeler, D.A., Chintagumpala, M., Meyers, R., Rakheja, D., Finegold, M.J., Tomlinson, G., Parsons, D.W., López-Terrada, D. Genomic analysis of hepatoblastoma identifies distinct molecular and prognostic subgroups. Hepatology, 65 ( 1 ) pp. 104 - 121, 2017.
  56. Yin, L., Liu, Y. Biclustering analysis and comparison for gene expression data. Revista de la Facultad de Ingenieria, 31 ( 12 ) pp. 183 - 198, 2016.
  57. Bar-Lavan, Y., Shemesh, N., Dror, S., Ofir, R., Yeger-Lotem, E., Ben-Zvi, A. A Differentiation Transcription Factor Establishes Muscle-Specific Proteostasis in Caenorhabditis elegans. PLoS Genetics, 12 ( 12 ) , art. no. e1006531, 2016.
  58. Itkin, M., Davidovich-Rikanati, R., Cohen, S., Portnoy, V., Doron-Faigenboim, A., Oren, E., Freilich, S., Tzuri, G., Baranes, N., Shen, S., Petreikov, M., Sertchook, R., Ben-Dor, S., Gottlieb, H., Hernandez, A., Nelson, D.R., Paris, H.S., Tadmor, Y., Burger, Y., Lewinsohn, E., Katzir, N., Schaffer, A. The biosynthetic pathway of the nonsugar, high-intensity sweetener mogroside V from Siraitia grosvenorii. Proceedings of the National Academy of Sciences of the United States of America, 113 ( 47 ) pp. E7619 - E7628, 2016.
  59. Xie, Y., Liu, Y., Valdar, W. Joint estimation of multiple dependent Gaussian graphical models with applications to mouse genomics. Biometrika, 103 ( 3 ) pp. 493 - 511, 2016.
  60. Pourreza-Shahri, M., Kahani, M., Ekbia, H.-R. Providing FAQ lists based on ontology. 2016 24th Iranian Conference on Electrical Engineering, ICEE 2016 , art. no. 7585537 , pp. 305 - 310, 2016.
  61. Horie, M., Yamaguchi, Y., Saito, A., Nagase, T., Lizio, M., Itoh, M., Kawaji, H., Lassmann, T., Carninci, P., Forrest, A.R.R., Hayashizaki, Y., Suzutani, T., Kappert, K., Micke, P., Ohshima, M. Transcriptome analysis of periodontitis-associated fibroblasts by CAGE sequencing identified DLX5 and RUNX2 long variant as novel regulators involved in periodontitis. Scientific Reports, 6 , art. no. 33666, 2016.
  62. Maron-Katz, A., Amar, D., Simon, E.B., Hendler, T., Shamir, R. RichMind: A tool for improved inference from large-scale neuroimaging results. PLoS ONE, 11 ( 7 ), art. no. e0159643, 2016.
  63. Mhenni, R.B., Mhamdi, A., Naanaa, W. La classification des gènes basée sur les csp pondérés. Douziemes Journees Francophones de Programmation par Contraintes, JFPC 2016, pp. 173 - 182, 2016.
  64. Ray, S., Chakraborty, S., Mukhopadhyay, A. DCoSpect: A novel differentially coexpressed gene module detection algorithm using spectral clustering. Advances in Intelligent Systems and Computing, 404 pp. 69 - 77, 2016.
  65. Alvarez, J.I., Prat, A., Sobel, R.A., Kobzik, L., Lassmann, H., Quintana, F.J., Weiner, H.L. Integrated Genomic and Network-Based Analyses of Complex Diseases and Human Disease Network. Journal of Genetics and Genomics, 43 ( 6 ) pp. 349 - 367, 2016.
  66. Mayo, L., Cunha, A.P.D., Madi, A., Beynon, V., Yang, Z., Alvarez, J.I., Prat, A., Sobel, R.A., Kobzik, L., Lassmann, H., Quintana, F.J., Weiner, H.L. IL-10-dependent Tr1 cells attenuate astrocyte activation and ameliorate chronic central nervous system inflammation. Brain, 139 ( 7 ) pp. 1939 - 1957, 2016.
  67. Tichon, A., Gil, N., Lubelsky, Y., Solomon, T.H., Lemze, D., Itzkovitz, S., Stern-Ginossar, N., Ulitsky, I. A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells. Nature Communications, 7 , art. no. 12209, 2016.
  68. Hayamizu, K., Manji, A. Application of Genomics and Bioinformatics Analysis in Exploratory Study of Functional Foods. Genomics, Proteomics and Metabolomics in Nutraceuticals and Functional Foods: Second Edition, pp. 140 - 149, 2016.
  69. Bar-Lev, Y., Moshitch-Moshkovitz, S., Tsarfaty, G., Kaufman, D., Horev, J., Resau, J.H., Tsarfaty, I. Mimp/Mtch2, an obesity susceptibility gene, induces alteration of fatty acid metabolism in transgenic mice. PLoS ONE, 11 ( 6 ) , art. no. e0157850, 2016.
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  71. Netanely, D., Avraham, A., Ben-Baruch, A., Evron, E., Shamir, R. Expression and methylation patterns partition luminal-A breast tumors into distinct prognostic subgroups. Breast Cancer Research, 18 ( 1 ) , art. no. 74, 2016.
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  74. Chitforoushzadeh, Z., Ye, Z., Sheng, Z., La Rue, S., Fry, R.C., Lauffenburger, D.A., Janes, K.A. TNF-insulin crosstalk at the transcription factor GATA6 is revealed by a model that links signaling and transcriptomic data tensors. Science Signaling, 9 ( 431 ) , art. no. ra59, 2016.
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  77. Greulich, F., Trowe, M.-O., Leffler, A., Stoetzer, C., Farin, H.F., Kispert, A. Misexpression of Tbx18 in cardiac chambers of fetal mice interferes with chamber-specific developmental programs but does not induce a pacemaker-like gene signature. Journal of Molecular and Cellular Cardiology, 97 pp. 140 - 149, 2016.
  78. Salazar, G., Bellocchi, C., Todoerti, K., Saporiti, F., Piacentini, L., Scorza, R., Colombo, G.I. Gene expression profiling reveals novel protective effects of Aminaphtone on ECV304 endothelial cells. European Journal of Pharmacology, 782 pp. 59 - 69, 2016.
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  81. Maron-Katz, A., Vaisvaser, S., Lin, T., Hendler, T., Shamir, R. A large-scale perspective on stress-induced alterations in resting-state networks. Scientific Reports, 6 , art. no. 21503, 2016.
  82. Sala, V., Gallo, S., Gatti, S., Medico, E., Vigna, E., Cantarella, D., Fontani, L., Natale, M., Cimino, J., Morello, M., Comoglio, P.M., Ponzetto, A., Crepaldi, T. Cardiac concentric hypertrophy promoted by activated Met receptor is mitigated in vivo by inhibition of Erk1,2 signalling with Pimasertib. Journal of Molecular and Cellular Cardiology, 93 pp. 84 - 97, 2016.
  83. Young, P.R., Eyeghe-Bickong, H.A., du Plessis, K., Alexandersson, E., Jacobson, D.A., Coetzee, Z., Deloire, A., Vivier, M.A. Grapevine plasticity in response to an altered microclimate: Sauvignon Blanc modulates specific metabolites in response to increased berry exposure. Plant Physiology, 170 ( 3 ) pp. 1235 - 1254, 2016.
  84. Palomares-Rius, J.E., Hedley, P., Cock, P.J., Morris, J.A., Jones, J.T., Blok, V.C. Gene expression changes in diapause or quiescent potato cyst nematode, Globodera pallida, eggs after hydration or exposure to tomato root diffusate. PeerJ, ( 2 ) , art. no. 1654, 2016.
  85. Günther, J., Koy, M., Berthold, A., Schuberth, H.-J., Seyfert, H.-M. Comparison of the pathogen species-specific immune response in udder derived cell types and their models. Veterinary Research, 47 ( 1 ) , art. no. 22, 2016.
  86. Friedman-Mazursky, O., Elkon, R., Efrat, S. Redifferentiation of expanded human islet ? cells by inhibition of ARX. Scientific Reports, 6 , art. no. 20698, 2016.
  87. Bastos, L., Ochi, L.S., Protti, F., Subramanian, A., Martins, I.C., Pinheiro, R.G.S. Efficient algorithms for cluster editing. Journal of Combinatorial Optimization, 31 ( 1 ) pp. 347 - 371, 2016.
  88. Sarkar, A., Das, R. Remote sensing image classification using fuzzy- pso hybrid approach. Handbook of Research on Swarm Intelligence in Engineering, pp. 435 - 468, 2015.
  89. Mahata, K., Sarkar, A. Cancer pathway network analysis using cellular automata. Improving Knowledge Discovery through the Integration of Data Mining Techniques, pp. 145 - 159, 2015.
  90. Elkon, R., Loayza-Puch, F., Korkmaz, G., Lopes, R., Van Breugel, P.C., Bleijerveld, O.B., Altelaar, A.F.M., Wolf, E., Lorenzin, F., Eilers, M., Agami, R. Myc coordinates transcription and translation to enhance transformation and suppress invasiveness. EMBO Reports, 16 ( 12 ) pp. 1723 - 1736, 2015.
  91. Pappa, K.I., Polyzos, A., Jacob-Hirsch, J., Amariglio, N., Vlachos, G.D., Loutradis, D., Anagnou, N.P. Profiling of discrete gynecological cancers reveals novel transcriptional modules and common features shared by other cancer types and embryonic stem cells. PLoS ONE, 10 ( 11 ) , art. no. e0142229, 2015.
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