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Citations

 

Papers that cite EXPANDER:

  1. Wu, K., Fang, H., Lyu, L.-D., Lowrie, D.B., Wong, K.-W., Fan, X.-Y. A derived network-based interferon-related signature of human macrophages responding to mycobacterium tuberculosis. BioMed Research International, art. no. 713071, 2014.
     
  2. Ronen, D., Benvenisty, N. Sex-dependent gene expression in human pluripotent stem cells. Cell Reports, 8 ( 4 ) pp. 923 - 932, 2014.
     
  3. Camargo, E.L.O., Nascimento, L.C., Soler, M., Salazar, M.M., Lepikson-Neto, J., Marques, W.L., Alves, A., Teixeira, P.J.P.L., Mieczkowski, P., Carazzolle, M.F., Martinez, Y., Deckmann, A.C., Rodrigues, J.C., Grima-Pettenati, J., Pereira, G.A.G. Contrasting nitrogen fertilization treatments impact xylem gene expression and secondary cell wall lignification in Eucalyptus. BMC Plant Biology, 14 ( 1 ) , art. no. 256, 2014.
     
  4. Degu, A., Hochberg, U., Sikron, N., Venturini, L., Buson, G., Ghan, R., Plaschkes, I., Batushansky, A., Chalifa-Caspi, V., Mattivi, F., Delledonne, M., Pezzotti, M., Rachmilevitch, S., Cramer, G.R., Fait, A. Metabolite and transcript profiling of berry skin during fruit development elucidates differential regulation between Cabernet Sauvignon and Shiraz cultivars at branching points in the polyphenol pathway. BMC Plant Biology, 14 ( 1 ), art. no. 188, 2014.
     
  5. Jia, X., Li, J., Shi, D., Zhao, Y., Dong, Y., Ju, H., Yang, J., Sun, J., Li, X., Ren, H. Grouping annotations on the subcellular layered interactome demonstrates enhanced autophagy activity in a recurrent experimental autoimmune uveitis T cell line. PLoS ONE, 9 ( 8 ), art. no. e104404, 2014.
     
  6. Campos, G., Schmidt-Heck, W., Ghallab, A., Rochlitz, K., Pütter, L., Medinas, D.B., Hetz, C., Widera, A., Cadenas, C., Begher-Tibbe, B., Reif, R., Günther, G., Sachinidis, A., Hengstler, J.G., Godoy, P. The transcription factor CHOP, a central component of the transcriptional regulatory network induced upon CCl4 intoxication in mouse liver, is not a critical mediator of hepatotoxicity. Archives of Toxicology, 88 ( 6 ) pp. 1267 - 1280, 2014.
     
  7. Lim, Y., Lee, D., Kalichamy, K., Hong, S.-E., Michalak, M., Ahnn, J., Kim, D.H., Lee, S.-K. Sumoylation regulates ER stress response by modulating calreticulin gene expression in XBP-1-dependent mode in Caenorhabditis elegans. International Journal of Biochemistry and Cell Biology, 53 pp. 399 - 408, 2014.
     
  8. Freiman, Z.E., Doron-Faigenboim, A., Dasmohapatra, R., Yablovitz, Z., Flaishman, M.A. High-throughput sequencing analysis of common fig (Ficus carica L.) transcriptome during fruit ripening. Tree Genetics and Genomes, 10 ( 4 ) pp. 923 - 935, 2014.
     
  9. Xie, W., Wang, H., Wu, J. Similar morphological and molecular signatures shared by female and male germline stem cells. Scientific Reports, 4 , art. no. 5580, 2014.
     
  10. Ben-David, U., Benvenisty, N. Chemical ablation of tumor-initiating human pluripotent stem cells. Nature Protocols, 9 ( 3 ) pp. 729 - 740, 2014.
     
  11. Santamaría, R., Therón, R., Quintales, L. BicOverlapper 2.0: Visual analysis for gene expression. Bioinformatics, 30 ( 12 ) pp. 1785 - 1786, 2014.
     
  12. Hu, H., Lu, X., Cen, X., Chen, X., Li, F., Zhong, S. RNA-seq identifies key reproductive gene expression alterations in response to cadmium exposure. BioMed Research International, 2014 , art. no. 529271, 2014.
     
  13. Rashi-Elkeles, S., Warnatz, H.-J., Elkon, R., Kupershtein, A., Chobod, Y., Paz, A., Amstislavskiy, V., Sultan, M., Safer, H., Nietfeld, W., Lehrach, H., Shamir, R., Yaspo, M.-L., Shiloh, Y. Parallel profiling of the transcriptome, cistrome, and epigenome in the cellular response to ionizing radiation. Science Signaling, 7 ( 325 ) , art. no. rs3, 2014.
     
  14. Altaf-Ul-Amin, M., Katsuragi, T., Sato, T., Ono, N., Kanaya, S. An unsupervised approach to predict functional relations between genes based on expression data. BioMed Research International, 2014 , art. no. 154594, 2014.
     
  15. Asif, M.T., Dauwels, J., Goh, C.Y., Oran, A., Fathi, E., Xu, M., Dhanya, M.M., Mitrovic, N., Jaillet, P. Spatiotemporal patterns in large-scale traffic speed prediction. IEEE Transactions on Intelligent Transportation Systems, 15 ( 2 ) , art. no. 6678316 , pp. 794 - 804, 2014.
     
  16. Cea, M.G., Claverol, S., Castillo, C.A., Pinilla, C.R., Ramírez, L.B. Desiccation tolerance of Hymenophyllacea filmy ferns is mediated by constitutive and non-inducible cellular mechanisms. Comptes Rendus - Biologies, 337 ( 4 ) pp. 235 - 243, 2014.
     
  17. Lee, S., Huang, J.Z. A biclustering algorithm for binary matrices based on penalized Bernoulli likelihood. Statistics and Computing, 24 ( 3 ) pp. 429 - 441, 2014.
     
  18. Luzzatto-Knaan, T., Kerem, Z., Doron-Faigenboim, A., Yedidia, I. Priming of protein expression in the defence response of Zantedeschia aethiopica to Pectobacterium carotovorum. Molecular Plant Pathology, 15 ( 4 ) pp. 364 - 378, 2014.
     
  19. Gharib, S.A., Seiger, A.N., Hayes, A.L., Mehra, R., Patel, S.R. Treatment of obstructive sleep apnea alters cancer-associated transcriptional signatures in circulating leukocytes. Sleep, 37 ( 4 ) pp. 709 - 714, 2014.
     
  20. Amar, D., Shamir, R. Constructing module maps for integrated analysis of heterogeneous biological networks. Nucleic Acids Research, 42 ( 7 ) pp. 4208 - 4219, 2014.
     
  21. Waldmann, T., Rempel, E., Balmer, N.V., König, A., Kolde, R., Gaspar, J.A., Henry, M., Hescheler, J., Sachinidis, A., Rahnenführer, J., Hengstler, J.G., Leist, M. Design principles of concentration-dependent transcriptome deviations in drug-exposed differentiating stem cells. Chemical Research in Toxicology, 27 ( 3 ) pp. 408 - 420, 2014.
     
  22. Dabir, S., Kluge, A., McColl, K., Liu, Y., Lam, M., Halmos, B., Wildey, G., Dowlati, A. PIAS3 activates the intrinsic apoptotic pathway in non-small cell lung cancer cells independent of p53 status. International Journal of Cancer, 134 ( 5 ) pp. 1045 - 1054, 2014.
     
  23. Nuruzzaman, M., Sharoni, A.M., Satoh, K., Kumar, A., Leung, H., Kikuchi, S. Comparative transcriptome profiles of the WRKY gene family under control, hormone-treated, and drought conditions in near-isogenic rice lines reveal differential, tissue specific gene activation. Journal of Plant Physiology, 171 ( 1 ) pp. 2 - 13, 2014.
     
  24. Wu, C., Bakshi, A., Aronow, B., Jegga, A., Bhatnagar, R. A biclustering algorithm to discover functional modules from ENCODE ChIP-seq data. Proceedings - IEEE 13th International Conference on Data Mining Workshops, ICDMW 2013 , art. no. 6753908 , pp. 96 - 103, 2013.
     
  25. Marei, H.E.S., Althani, A., Afifi, N., Abd-Elmaksoud, A., Bernardini, C., Michetti, F., Barba, M., Pescatori, M., Maira, G., Paldino, E., Manni, L., Casalbore, P., Cenciarelli, C. Over-expression of hNGF in adult human olfactory bulb neural stem cells promotes cell growth and oligodendrocytic differentiation. PLoS ONE, 8 ( 12 ) , art. no. e82206, 2013.
     
  26. Geifman, N., Cohen, R., Rubin, E. Redefining meaningful age groups in the context of disease. Age, 35 ( 6 ) pp. 2357 - 2366, 2013.
     
  27. Geifman, N., Rubin, E. The mouse age phenome knowledgebase and disease-specific inter-species age mapping. PLoS ONE, 8 ( 12 ), art. no. e81114, 2013.
     
  28. Jaskowiak, P.A., Campello, R.J.G.B., Costa, I.G. Proximity measures for clustering gene expression microarray data: A validation methodology and a comparative analysis. IEEE/ACM Transactions on Computational Biology and Bioinformatics , 10 ( 4 ) , art. no. 6461019 , pp. 845 - 857, 2013.
     
  29. Kim, T., Song, H.K., Hong, S.-E., Kim, D.H. Meta-analysis of interspecies microarray sets of cardiac diseases revealed common and disease-specific signatures. Animal Cells and Systems, 17 ( 6 ) pp. 388 - 396, 2013.
     
  30. Gill, S.E., Gharib, S.A., Bench, E.M., Sussman, S.W., Wang, R.T., Rims, C., Birkland, T.P., Wang, Y., Manicone, A.M., McGuire, J.K., Parks, W.C. Tissue inhibitor of metalloproteinases-3 moderates the proinflammatory status of macrophages. American Journal of Respiratory Cell and Molecular Biology, 49 ( 5 ) pp. 768 - 777, 2013.
     
  31. Liu, C.-G., Lin, Y.-H., Bai, F.-W. Global gene expression analysis of Saccharomyces cerevisiae grown under redox potential-controlled very-high-gravity conditions. Biotechnology Journal, 8 ( 11 ) pp. 1332 - 1340, 2013.
     
  32. Bruno, G., Fiori, A. MicroClAn: Microarray clustering analysis. Journal of Parallel and Distributed Computing, 73 ( 3 ) pp. 360 - 370, 2013.
     
  33. Yin, D., Wang, Y., Zhang, X., Li, H., Lu, X., Zhang, J., Zhang, W., Chen, S. De Novo Assembly of the Peanut (Arachis hypogaea L.) Seed Transcriptome Revealed Candidate Unigenes for Oil Accumulation Pathways. PLoS ONE, 8 ( 9 ) , art. no. e73767, 2013.
     
  34. Dicken, J., Mildner, A., Leshkowitz, D., Touw, I.P., Hantisteanu, S., Jung, S., Groner, Y. Transcriptional Reprogramming of CD11b+Esamhi Dendritic Cell Identity and Function by Loss of Runx3. PLoS ONE, 8 ( 10 ) , art. no. e77490, 2013.
     
  35. Tripoliti, E.E., Fotiadis, D.I., Manis, G. Modifications of the construction and voting mechanisms of the Random Forests Algorithm. Data and Knowledge Engineering, 87 pp. 41 - 65, 2013.
     
  36. Tripoliti, E.E., Fotiadis, D.I., Manis, G. Modifications of the construction and voting mechanisms of the Random Forests Algorithm. Data and Knowledge Engineering, 87 pp. 41 - 65, 2013.
     
  37. Kaissi, O., Moussa, A., Vannier, B., Ghacham, A. Comparative analysis between soft and tools in microarray data processing. Proceedings of the IASTED International Conference on Biomedical Engineering, BioMed 2013, pp. 504 - 509 , 2013.
     
  38. Saha, S., Ekbal, A., Gupta, K., Bandyopadhyay, S. Gene expression data clustering using a multiobjective symmetry based clustering technique. Computers in Biology and Medicine, 43 ( 11 ) pp. 1965 - 1977, 2013.
     
  39. Yin, D., Wang, Y., Zhang, X., Li, H., Lu, X., Zhang, J., Zhang, W., Chen, S. De Novo Assembly of the Peanut (Arachis hypogaea L.) Seed Transcriptome Revealed Candidate Unigenes for Oil Accumulation Pathways. PLoS ONE, 8 ( 9 ) , art. no. e73767, 2013.
     
  40. Pavlopoulos, G.A., Iacucci, E., Iliopoulos, I., Bagos, P. Interpreting the Omics 'era' Data. Smart Innovation, Systems and Technologies, 25 pp. 79 - 100, 2013.
     
  41. Eran, A., Li, J.B., Vatalaro, K., McCarthy, J., Rahimov, F., Collins, C., Markianos, K., Margulies, D.M., Brown, E.N., Calvo, S.E., Kohane, I.S., Kunkel, L.M. Comparative RNA editing in autistic and neurotypical cerebella. Molecular Psychiatry, 18 ( 9 ) pp. 1041 - 1048, 2013.
     
  42. Kaissi, O., Moussa, A., Vannier, B., Ghacham, A. Comparative analysis between soft and tools in microarray data processing. Proceedings of the IASTED International Conference on Biomedical Engineering, BioMed 2013, pp. 504 - 509, 2013.
     
  43. Kratsch, S., Wahlström, M. Two edge modification problems without polynomial kernels. Discrete Optimization, 10 ( 3 ) pp. 193 - 199, 2013.
     
  44. Silva, A., Sampaio-Marques, B., Fernandes, Â., Carreto, L., Rodrigues, F., Holcik, M., Santos, M.A.S., Ludovico, P. Involvement of Yeast HSP90 Isoforms in Response to Stress and Cell Death Induced by Acetic Acid. PLoS ONE, 8 ( 8 ), art. no. e71294, 2013.
     
  45. Guven Maiorov, E., Keskin, O., Hatirnaz Ng, O., Ozbek, U., Gursoy, A. Identification of interconnected markers for T-cell acute lymphoblastic leukemia. BioMed Research International, art. no. 210253, 2013.
     
  46. Cui, J., Xu, Y., Puett, D. Microarray-based transcriptome profiling of ovarian cancer cells. Methods in Molecular Biology, 1049 pp. 119 - 137, 2013.
     
  47. Bruck, T., Yanuka, O., Benvenisty, N. Human pluripotent stem cells with distinct X inactivation status show molecular and cellular differences controlled by the X-Linked ELK-1 gene. Cell Reports, 4 ( 2 ) pp. 262 - 270, 2013.
     
  48. Bochner, R., Ziv, Y., Zeevi, D., Donyo, M., Abraham, L., Ashery-Padan, R., Ast, G. Phosphatidylserine increases IKBKAP levels in a humanized knock-in IKBKAP mouse model. Human Molecular Genetics , 22 ( 14 ) , art. no. ddt126 , pp. 2785 - 2794 , 2013.
     
  49. Feala, J.D., Abdulhameed, M.D.M., Yu, C., Dutta, B., Yu, X., Schmid, K., Dave, J., Tortella, F., Reifman, J. Systems biology approaches for discovering biomarkers for traumatic brain injury. Journal of Neurotrauma , 30 ( 13 ) pp. 1101 - 1116 , 2013.
     
  50. Böcker, S., Baumbach, J. Cluster editing. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 7921 LNCS pp. 33 - 44 , 2013.
     
  51. de la Iglesia, D., García-Remesal, M., de la Calle, G., Kulikowski, C., Sanz, F., Maojo, V. The impact of computer science in molecular medicine: Enabling high-throughput research. Current Topics in Medicinal Chemistry, 13 ( 5 ) pp. 526 - 575, 2013.
     
  52. Cheng, J.-S., Liang, Y.-Q., Ding, M.-Z., Cui, S.-F., Lv, X.-M., Yuan, Y.-J. Metabolic analysis reveals the amino acid responses of Streptomyces lydicus to pitching ratios during improving streptolydigin production. Applied Microbiology and Biotechnology, 97 ( 13 ) pp. 5943 - 5954, 2013.
     
  53. Mukherjee, S., Sambarey, A., Prashanthi, K., Chandra, N. Current trends in modeling host-pathogen interactions. Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery, 3 ( 2 ) pp. 109 - 128, 2013.
     
  54. Fréalle, E., Aliouat-Denis, C.-M., Delhaes, L., Hot, D., Dei-Cas, E. Transcriptomic insights into the oxidative response of stress-exposed Aspergillus fumigatus. Current Pharmaceutical Design, 19 ( 20 ) pp. 3713 - 3737, 2013.
     
  55. Gat-Viks, I., Chevrier, N., Wilentzik, R., Eisenhaure, T., Raychowdhury, R., Steuerman, Y., Shalek, A.K., Hacohen, N., Amit, I., Regev, A. Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli. Nature Biotechnology, 31 ( 4 ) pp. 342 - 349, 2013.
     
  56. Csermely, P., Korcsmáros, T., Kiss, H.J.M., London, G., Nussinov, R. Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review. Pharmacology and Therapeutics, 138 ( 3 ) pp. 333 - 408, 2013.
     
  57. Shaham, O., Gueta, K., Mor, E., Oren-Giladi, P., Grinberg, D., Xie, Q., Cvekl, A., Shomron, N., Davis, N., Keydar-Prizant, M., Raviv, S., Pasmanik-Chor, M., Bell, R.E., Levy, C., Avellino, R., Banfi, S., Conte, I., Ashery-Padan, R. Pax6 Regulates Gene Expression in the Vertebrate Lens through miR-204. PLoS Genetics, 9 ( 3 ) , art. no. e1003357, 2013.
     
  58. Chen, K.-D., Goto, S., Hsu, L.-W., Lin, T.-Y., Nakano, T., Lai, C.-Y., Chang, Y.-C., Weng, W.-T., Kuo, Y.-R., Wang, C.-C., Cheng, Y.-F., Ma, Y.-Y., Lin, C.-C., Chen, C.-L. Identification of miR-27b as a Novel Signature from the mRNA Profiles of Adipose-Derived Mesenchymal Stem Cells Involved in the Tolerogenic Response. PLoS ONE,8 ( 4 ) , art. no. e60492, 2013.
     
  59. Amar, D., Safer, H., Shamir, R. Dissection of Regulatory Networks that Are Altered in Disease via Differential Co-expression. PLoS Computational Biology, 9 ( 3 ) , art. no. e1002955, 2013.
     
  60. Madar, S., Harel, E., Goldstein, I., Stein, Y., Kogan-Sakin, I., Kamer, I., Solomon, H., Dekel, E., Tal, P., Goldfinger, N., Friedlander, G., Rotter, V. Mutant p53 Attenuates the Anti-Tumorigenic Activity of Fibroblasts-Secreted Interferon Beta. PLoS ONE, 8 ( 4 ) , art. no. e61353, 2013.
     
  61. Suzuki, H.I., Mihira, H., Watabe, T., Sugimoto, K., Miyazono, K. Widespread inference of weighted microRNA-mediated gene regulation in cancer transcriptome analysis. Nucleic Acids Research, 41 ( 5 ) 2013.
     
  62. Fan, M., Pfeffer, S.R., Lynch, H.T., Cassidy, P., Leachman, S., Pfeffer, L.M., Kopelovich, L. Altered transcriptome signature of phenotypically normal skin fibroblasts heterozygous for CDKN2A in familial melanoma: Relevance to early intervention. Oncotarget, 4 ( 1 ) pp. 128 - 141, 2013.
     
  63. Amar, D., Safer, H., Shamir, R. Dissection of Regulatory Networks that Are Altered in Disease via Differential Co-expression. PLoS Computational Biology, 9 ( 3 ) , art. no. e1002955, 2013.
     
  64. Henig, N., Avidan, N., Mandel, I., Staun-Ram, E., Ginzburg, E., Paperna, T., Pinter, R.Y., Miller, A. Interferon-Beta Induces Distinct Gene Expression Response Patterns in Human Monocytes versus T cells. PLoS ONE, 8 ( 4 ) , art. no. e62366, 2013.
     
  65. Huang, S.-S.C., Clarke, D.C., Gosline, S.J.C., Labadorf, A., Chouinard, C.R., Gordon, W., Lauffenburger, D.A., Fraenkel, E. Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling. PLoS Computational Biology, 9 ( 2 ) , art. no. e1002887 , 2013.
     
  66. Frangini, M., Franzolin, E., Chemello, F., Laveder, P., Romualdi, C., Bianchi, V., Rampazzo, C. Synthesis of mitochondrial DNA precursors during myogenesis, an analysis in purified C2C12 myotubes. Journal of Biological Chemistry, 288 ( 8 ) pp. 5624 - 5635 , 2013.
     
  67. Aure, M.R., Steinfeld, I., Baumbusch, L.O., Liestøl, K., Lipson, D., Nyberg, S., Naume, B., Sahlberg, K.K., Kristensen, V.N., Børresen-Dale, A.-L., Lingjærde, O.C., Yakhini, Z. Identifying In-Trans Process Associated Genes in Breast Cancer by Integrated Analysis of Copy Number and Expression Data. PLoS ONE, 8 ( 1 ) , art. no. e53014 , 2013.
     
  68. Xu, X. Enhancing gene expression clustering analysis using tangent transformation. International Journal of Machine Learning and Cybernetics , 4 ( 1 ) pp. 31 - 40 , 2013.
     
  69. Paredes, J.A., Zhou, X., Höglund, S., Karlsson, A. Gene Expression Deregulation in Postnatal Skeletal Muscle of TK2 Deficient Mice Reveals a Lower Pool of Proliferating Myogenic Progenitor Cells. PLoS ONE , 8 ( 1 ) , art. no. e53698, 2013.
     
  70. Krug, A.K., Kolde, R., Gaspar, J.A., Rempel, E., Balmer, N.V., Meganathan, K., Vojnits, K., Baquié, M., Waldmann, T., Ensenat-Waser, R., Jagtap, S., Evans, R.M., Julien, S., Peterson, H., Zagoura, D., Kadereit, S., Gerhard, D., Sotiriadou, I., Heke, M., Natarajan, K., Henry, M., Winkler, J., Marchan, R., Stoppini, L., Bosgra, S., Westerhout, J., Verwei, M., Vilo, J., Kortenkamp, A., Hescheler, J., Hothorn, L., Bremer, S., Van Thriel, C., Krause, K.-H., Hengstler, J.G., Rahnenführer, J., Leist, M., Sachinidis, A. Human embryonic stem cell-derived test systems for developmental neurotoxicity: A transcriptomics approach. Archives of Toxicology , 87 ( 1 ) pp. 123 - 143 , 2013.
     
  71. Satoh, K., Kondoh, H., De Leon, T.B., Macalalad, R.J.A., Cabunagan, R.C., Cabauatan, P.Q., Mauleon, R., Kikuchi, S., Choi, I.-R. Gene expression responses to Rice tungro spherical virus in susceptible and resistant near-isogenic rice plants. Virus Research, 171 ( 1 ) pp. 111 - 120, 2013.
     
  72. Brosh, R., Assia-Alroy, Y., Molchadsky, A., Bornstein, C., Dekel, E., Madar, S., Shetzer, Y., Rivlin, N., Goldfinger, N., Sarig, R., Rotter, V. P53 Counteracts reprogramming by inhibiting mesenchymal-to-epithelial transition. Cell Death and Differentiation, 20 ( 2 ) pp. 312 - 320, 2013.
     
  73. Castro-Melchor, M., Le, H., Hu, W.-S. Transcriptome data analysis for cell culture processes. Advances in Biochemical Engineering/Biotechnology, 127 pp. 27 - 70, 2012.
     
  74. Geifman, N., Rubin, E. The age-phenome database. SpringerPlus, 1 ( 1 ) pp. 1 - 8, 2012.
     
  75. Tzfadia, O., Amar, D., Bradbury, L.M.T., Wurtzel, E.T., Shamir, R. The MORPH algorithm: Ranking candidate genes for membership in arabidopsis and tomato pathwaysC W. Plant Cell, 24 ( 11 ) pp. 4389 - 4406, 2012.
     
  76. Cheng, J.-S., Lv, X.-M., Yuan, Y.-J. Investigation of proteomic responses of streptomyces lydicus to pitching ratios for improving streptolydigin production. Biotechnology and Bioprocess Engineering, 17 ( 5 ) pp. 997 - 1007, 2012.
     
  77. Nam, J.-W., Bartel, D.P. Long noncoding RNAs in C. elegans. Genome Research, 22 ( 12 ) pp. 2529 - 2540, 2012.
     
  78. Mäder, U., Nicolas, P. Array-based approaches to bacterial transcriptome analysis. Methods in Microbiology, 39 pp. 151 - 182 , 2012.
     
  79. Zhou, H., Cheng, J.-S., Wang, B.L., Fink, G.R., Stephanopoulos, G. Xylose isomerase overexpression along with engineering of the pentose phosphate pathway and evolutionary engineering enable rapid xylose utilization and ethanol production by Saccharomyces cerevisiae. Metabolic Engineering, 14 ( 6 ) pp. 611 - 622, 2012.
     
  80. Landau, G., Ran, A., Bercovich, Z., Feldmesser, E., Horn-Saban, S., Korkotian, E., Jacob-Hirsh, J., Rechavi, G., Ron, D., Kahana, C. Expression profiling and biochemical analysis suggest stress response as a potential mechanism inhibiting proliferation of polyamine-depleted cells. Journal of Biological Chemistry, 287 ( 43 ) pp. 35825 - 35837, 2012.
     
  81. Ding, M.-Z., Wang, X., Liu, W., Cheng, J.-S., Yang, Y., Yuan, Y.-J. Proteomic research reveals the stress response and detoxification of yeast to combined inhibitors. PLoS ONE, 7 ( 8 ) , art. no. e43474, 2012.
     
  82. Krupp, D.R., Xu, P.-T., Thomas, S., Dellinger, A., Etchevers, H.C., Vekemans, M., Gilbert, J.R., Speer, M.C., Ashley-Koch, A.E., Gregory, S.G. Transcriptome profiling of genes involved in neural tube closure during human embryonic development using long serial analysis of gene expression (long-SAGE). PBirth Defects Research Part A - Clinical and Molecular Teratology, 94 ( 9 ) pp. 683 - 692, 2012.
     
  83. Katzir, Y., Stolovicki, E., Stern, S., Braun, E. Cellular Plasticity Enables Adaptation to Unforeseen Cell-Cycle Rewiring Challenges. PLoS ONE, 7 ( 9 ) , art. no. e45184, 2012.
     
  84. Li, L., Guo, Y., Wu, W., Shi, Y., Cheng, J., Tao, S. A comparison and evaluation of five biclustering algorithms by quantifying goodness of biclusters for gene expression data. BioData Mining, 5 ( 1 ) , art. no. 8, 2012.
     
  85. Ahmed, H.A., Mahanta, P., Bhattacharyya, D.K. Finding gene coherent patterns using PATSUB+. ACM International Conference Proceeding Series, pp. 38-44, 2012.
     
  86. Huang, Q., Tao, D., Li, X., Liew, A. Parallelized evolutionary learning for detection of biclusters in gene expression data. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9 (2), art. no. 5728798, pp. 560-570, 2012.
     
  87. Stiubea-Cohen, R., David, R., Neumann, Y., Krief, G., Deutsch, O., Zacks, B., Aframian, D.J., Palmon, A. Effect of irradiation on cell transcriptome and proteome of rat submandibular salivary glands. PLoS ONE, 7 (7), art. no. e40636, 2012.
     
  88. Nicol-Benoît, F., Le-Goff, P., Le-Dréan, Y., Demay, F., Pakdel, F., Flouriot, G., Michel, D. Epigenetic memories: Structural marks or active circuits? Cellular and Molecular Life Sciences, 69 (13) pp. 2189-2203, 2012.
     
  89. Wittkop, T., Berman, A.E., Fleisch, K.M., Mooney, S.D. DEFOG: Discrete enrichment of functionally organized genes. Integrative Biology (United Kingdom), 4 (7) pp. 795-804, 2012.
     
  90. Wu, K., Dong, D., Fang, H., Levillain, F., Jin, W., Mei, J., Gicquel, B., Du, Y., Wang, K., Gao, Q., Neyrolles, O., Zhang, J. An interferon-related signature in the transcriptional core response of human macrophages to mycobacterium tuberculosis infection . PLoS ONE, 7 (6), art. no. e38367, 2012.
     
  91. States, J.C., Singh, A.V., Knudsen, T.B., Rouchka, E.C., Ngalame, N.O., Arteel, G.E., Piao, Y., Ko, M.S.H. Prenatal arsenic exposure alters gene expression in the adult liver to a proinflammatory state contributing to accelerated atherosclerosis . PLoS ONE, 7 (6), art. no. e38713, 2012.
     
  92. Balch, C., Naegeli, K., Nam, S., Ballard, B., Hyslop, A., Melki, C., Reilly, E., Hur, M.-W., Nephew, K.P. A unique histone deacetylase inhibitor alters microRNA expression and signal transduction in chemoresistant ovarian cancer cells . Cancer Biology and Therapy, 13 (8) pp. 682-694, 2012.
     
  93. Hertzano, R., Elkon, R. High throughput gene expression analysis of the inner ear . Hearing Research, 288 (1-2) pp. 77-88, 2012.
     
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