PUBLICATIONS ON HYBSTATION (HS) HYBRIDIZATION SYSTEM. (HYBSTATION & HYB4) (2001 – DEC 2018). 2018. Divergent responses of forest soil microbial communities under elevated CO2 in different depths of upper soil layers. Hao Yu, Zhili He, Aijie Wang, Jianping Xie, Liyou Wu, Joy D. Van Nostrand, Decai Jin, Zhimin Shao, Christopher W. Schadt, Jizhong Zhou and Ye Deng Applied and Environmental Microbiology, January 2018; 84(1): e01694-17. 2017. Determining the fidelity of tRNA aminoacylation via microarrays. Michael H. Schwartz, and Tao Pan. Methods, 15 January 2017; 113: 27-33 (Hyb4/Hyb12) Cell-free methylation markers with diagnostic and prognostic potential in hepatocellular carcinoma. Chang-Yi Lu, Shih-Ya Chen, Hui-Ling Peng, Pu-Yeh Kan, Wan-Chi Chang, and Chia-Jui Yen. Oncotarget, 24 January 2017; 8(4): 640, 13 pp. (HybChamber) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5351641/pdf/oncotarget-08-6406.pdf Microarray-based quantification of cellular tRNAs. Sebastian Kirchner, Robert Rauscher, Andreas Czech, and Zoya Ignatova. Protocols. Io, 29 March 2017; dx.doi.org/10.17504/protocols.io.hfcb3iw, 9 pp. (Hyb4). https://www.researchgate.net/profile/Sebastian_Kirchner/publication/315723193_Microarray-Based_Quantification_of_Cellular_tRNAs/links/58dedcac92851c3695457512/Microarray-Based-Quantification-of-Cellular-tRNAs.pdf Transcriptome dynamics in early zebrafish embryogenesis determined by high-resolution time course analysis of 180 successive, individual zebrafish embryos. Han Rauwerda, Johanna FB Pagano, Wim C. de Leeuw, Wim Ensink, Ulrike Nehrdich, Mark de Jong, Martijs Jonker, Herman P. Spaink, and Timo M. Breit. BMC Genomics, 11 April 2017; 18(1): 287, 15 pp. (HS) https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3672-z Alteration of protein function by a silent polymorphism linked to tRNA abundance. Sebastian Kirchner, Zhiwei Cai, Robert Rauscher, Nicolai Kastelic, Melanie Anding, Andreas Czech, Bertrand Kleizen, Lynda S. Ostedgaard, Ineke Braakman, David N. Sheppard, Zoya Ignatova PLoS Biology, 16 May 2017; 15(5): e2000779, 29 pp. (Hyb4). http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2000779

Growth-Rate Dependent Regulation of tRNA Level and Charging in Bacillus licheniformis. Iolanda Ferro, Klaus Liebeton, and Zoya Ignatova. Journal of Molecular Biology, 13 October 2017; 429(20): 3102-3112. (Hyb4). 2016. A dual fluorescent reporter for the investigation of methionine mistranslation in live cells. Ana Cristina Gomes, Anna J. Kordala, Rita Strack, Xiaoyun Wang, Renaud Geslain, Kamila Delaney, Wesley C. Clark, Robert Keenan, and Tao Pan. RNA, March 2016; 22(3): 467-476. (Hyb4) http://keenanlab.bsd.uchicago.edu/ewExternalFiles/RNA%202016%20Gomes.pdf Identification of novel extracellular protein for PCB/biphenyl metabolism in Rhodococcus jostii RHA1. Yuki Atago, Jun Shimodaira, Naoto Araki, Nor’azizi Bin Othman, Zuriati Zakaria, Masao Fukuda, Junichiro Futami, and Hirofumi Hara. Bioscience, Biotechnology, and Biochemistry, May 2016; 80(5): 1012-1019. (HS) http://biochem.flas.kps.ku.ac.th/02738451/pcb.pdf Discharging tRNAs: a tug of war between translation and detoxification in Escherichia coli. Irem Avcilar-Kucukgoze, Alexander Bartholomäus, Juan A. Cordero Varela, Robert Franz-Xaver Kaml, Peter Neubauer, Nediljko Budisa, and Zoya Ignatova. Nucleic Acids Research, 30 September 2016; 44(17): 8324-8334. (Hyb4) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5041488/pdf/gkw697.pdf Recurrent DNA copy number alterations in intestinal-type sinonasal adenocarcinoma. Jhudit Pérez-Escuredo, Alejandro López-Hernández, María Costales, Fernando López, Sira Potes Ares, Blanca Vivanco, José Luis Llorente, and Mario A. Hermsen. Rhinology, September 2016; 54 (3): 278-286. (HS12) http://www.servicioorlhuca.com/wp-content/uploads/2015/02/Recurrent-DNA-copy-number-alterations-in-intestinal-type-sinonasal-adenocarcinoma.pdf Codon optimality controls differential mRNA translation during amino acid starvation. Mridusmita Saikia, Xiaoyun Wang, Yuanhui Mao, Ji Wan, Tao Pan, and Shu-Bing Qian. RNA, November 2016; 22(11): 1719-1727. (Hyb4) http://rnajournal.cshlp.org/content/22/11/1719.long 2015. Gene expression profile of high-fat diet-fed C57BL/6J mice: in search of potential role of azelaic acid. Shanmugam Muthulakshmi, Alok K. Chakrabarti, and Sanjay Mukherjee. Journal of Physiology and Biochemistry, March 2015; 71(1): 29-42. (HS) Identification of peptidic substrates for the human kinase Myt1 using peptide microarrays. Alexander Rohe, Charlott Platzer, Antonia Masch, Sandra Greiner, Claudia Henze, Christian Ihling, Frank Erdmann, Mike Schutkowski, Wolfgang Sippl, and Matthias Schmidt.

Bioorganic & Medicinal Chemistry, 1 August 2015; 23(15): 4936-4942. (HS) In vitro study of normoxic epidermal growth factor receptor-induced hypoxia-inducible factor-1-alpha, vascular endothelial growth factor, and BNIP3 expression in head and neck squamous cell carcinoma cell lines: Implications for anti-epidermal growth factor receptor therapy. Pablo Secades, Inés Saenz Santa-María, Anna Merlo, Carlos Suarez, and María-Dolores Chiara. Head & Neck, August 2015; 37(8): 1150-1162 (HS12) Biomolecule interaction using atomic force microscope. Inventors: Joon Won Park, Yu Jin Jung, Bong Jin Hong, Saul Tendler, and Stephanie Allen. United States Patent: US 9175335 B2, Publication Date: 3 November 2015; (GeneTAC HS) https://www.google.com/patents/US9175335 Membrane-Associated Glucose-Methanol-Choline Oxidoreductase Family Enzymes PhcC and PhcD Are Essential for Enantioselective Catabolism of Dehydrodiconiferyl Alcohol. Kenji Takahashi, Yusaku Hirose, Naofumi Kamimura, Shojiro Hishiyama, Hirofumi Hara, Takuma Araki, Daisuke Kasai, Shinya Kajita Yoshihiro Katayama Masao Fukuda and Eiji Masai Applied and Environmental Microbiology, December 2015; 81(23): 8022-8036. (HS) http://aem.asm.org/content/81/23/8022.full Size-controlled macromolecule. Inventors: Joon Won Park, Bong Jin Hong, Young Seo Choi, Soon Jin Oh, and Kwan Yong Choi. United States Patent: US 9201067 B2, Publication Date: 1 December 2015; (GeneTAC) https://www.google.com/patents/US9201067 2014. Differential gene expression in Giardia lamblia under oxidative stress: Significance in eukaryotic evolution. Dibyendu Raj, Dibyendu, Esha Ghosh, Avik K. Mukherjee, Tomoyoshi Nozaki, Sandipan Ganguly. Gene, 10 February 2014; 535(2): 131-139. (HS) http://s3.amazonaws.com/academia.edu.documents/35636417/Giardia_microarray.pdf?AWSAccessKeyId=AKIAJ56TQJRTWSMTNPEA&Expires=1474489078&Signature=dueihLoQxqMcXqwsDEODDQEwmqM%3D&response-content-disposition=inline%3B%20filename%3DDifferential_gene_expression_in_Giardia.pdf Biomolecule interaction using atomic force microscope. Inventors: Joon Won Park, Yu Jin Jung, Bong Jin Hong, Saul Tendler, Stephanie Allen United States Patent: 8673621 B2, Publication Date: 18 March 2014 (HS) https://www.google.com/patents/US8673621 Large-scale genetic perturbations reveal regulatory networks and an abundance of gene-specific repressors. Patrick Kemmeren, Katrin Sameith, Loes AL van de Pasch, Joris J. Benschop, Tineke L. Lenstra, Thanasis Margaritis, Eoghan O’Duibhir, Eva Apweiler, Sake van Wageningen, Cheuk W. Ko, Sebastiaan van Heesch, Mehdi M. Kashani, Giannis Ampatziadis-Michailidis, Mariel O. Brok, Nathalie A.C.H. Brabers, Anthony J. Miles, Diane Bouwmeester, Sander R. van Hooff, Harm van Bakel, Erik Sluiters, Linda V. Bakker, Berend Snel, Philip Lijnzaad, Dik van Leenen, Marian J.A. Groot Koerkamp, Frank C.P. Holstege Cell, 24 April 2014; 157(3): 740-752. (HS)

http://www.cell.com/cell/abstract/S0092-8674(14)00342-0?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867414003420%3Fshowall%3Dtrue Nucleobase characterisation. Inventors: Mark Bradley and Juan J. Diaz-Mochon. United States Patent: US 8716457 B2, Publication Date: 6 May 2014; (Hyb4) https://www.google.com/patents/US8716457 Vergleichende Analyse genomischer Aberrationen in Primärtumoren und Hirnmetastasen von Karzinompatienten. Niclas Detels MD Theses, Der Medizinischen Fakultät der Universität Hamburg, 14 August 2014; 123 pp. (HS) http://ediss.sub.uni-hamburg.de/volltexte/2014/6957/pdf/Dissertation.pdf Damaged mitochondria in Fanconi anemia—an isolated event or a general phenomenon?. Giovanni Pagano, Pavithra Shyamsunder, Rama S. Verma, and Alex Lyakhovich. Oncoscience, 21 April 2014; 1(4): 287-295. (HS) https://www.researchgate.net/profile/Pavithra_Shyamsunder2/publication/261911535_Damaged_mitochondria_in_Fanconi_anemia__an_isolated_event_or_a_general_phenomenon/links/00463535e4bb93a2b3000000.pdf Biomolecule interaction using atomic force microscope Inventors: Joon Won Park, Yu Jin Jung, Bong Jin Hong, Saul Tendler, Stephanie Allen US Patent Application: 2014/0315319 A1, Publication Date: 23 October 2014; (HS) http://www.freepatentsonline.com/y2014/0315319.html Ascorbate Peroxidase, a Key Molecule Regulating Amphotericin B Resistance in Clinical Isolates of Leishmania donovani . Ashish Kumar, Sushmita Das, Bidyut Purkait, Abul Hasan Sardar, Ayan Kumar Ghosh, Manas Ranjan Dikhit, Kumar Abhishek, and Pradeep Das. Antimicrobial Agents and Chemotherapy, October 2014; 58(10): 6172-6184. (HS) http://aac.asm.org/content/58/10/6172.full An integrated "omics" approach to the characterization of maize (Zea mays L.) mutants deficient in the expression of two genes encoding cytosolic glutamine synthetase. Nardjis Amiour, Sandrine Imbaud, Gilles Clément, Nicolas Agier, Michel Zivy, Benoît Valot, Thierry Balliau, Isabelle Quilleré, Thérèse Tercé-Laforgue, Céline Dargel-Graffin, Bertrand Hirel BMC Genomics, 20 November 2014; 15:1005, 19 pp. (GeneTAC) http://www.biomedcentral.com/content/pdf/1471-2164-15-1005.pdf F1 hybrids of BALB/c and C57BL/6 mouse strains respond differently to low-dose ionizing radiation exposure. Sanjay Mukherjee, K. B. Sainis, and Deepti D. Deobagkar. Journal of Genetics, December 2014; 93(3): 667-682. (HS) http://www.ias.ac.in/jgenet/Vol93No3/667.pdf 2013. Vaccinia and influenza A viruses select rather than adjust tRNAs to optimize translation. Mariana Pavon-Eternod, Alexandre David, Kimberly Dittmar, Peter Berglund, Tao Pan, Jack R. Bennink, and Jonathan W. Yewdell. Nucleic Acids Research, February 2013; 41(3): 1914-1921. (Hyb4)

http://nar.oxfordjournals.org/content/41/3/1914.full.pdf+html Identification of TRPC6 as a possible candidate target gene within an amplicon at 11q21-q22. 2 for migratory capacity in head and neck squamous cell carcinomas. Sandra Bernaldo de Quirós, Anna Merlo, Pablo Secades, Iriana Zambrano, Ines Saenz de Santa María, Nerea Ugidos, Eloisa Jantus-Lewintre, Rafael Sirera, Carlos Suarez, María-Dolores Chiara. BMC Cancer, 14 March 2013; 13(1): 116, 11 pp. (HS) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3606258/ Isolierung und funktionelle Charakterisierung neuartiger Hydrogenasen sowie synthetischer [FeS] Cluster Proteine. Jana Riethausen Ph.D. Theses, 27 May 2013; Heinrich-Heine-Universität Düsseldorf, Germany, 217 pp. (Hyb4) http://docserv.uni-duesseldorf.de/servlets/DerivateServlet/Derivate-27890/Riethausen_Dissertation_final.pdf An ER-directed transcriptional response to unfolded protein stress in the absence of conserved sensor-transducer proteins in Giardia lamblia . Cornelia Spycher, Emily K. Herman, Laura Morf, Weihong Qi, Hubert Rehrauer, Catharine Aquino Fournier, Joel B. Dacks, and Adrian B. Hehl. Molecular Microbiology, May 2013; 88(4): 754-771. (HS) http://onlinelibrary.wiley.com/doi/10.1111/mmi.12218/full 3, 4-Dimethoxyphenyl Bis-benzimidazole Derivative, Mitigates Radiation-Induced DNA Damage. Atul Ranjan, Navrinder Kaur, Vinod Tiwari, Yogendra Singh, Madan Mohan Chaturvedi, and Vibha Tandon. Radiation Research, June 2013; 179(6): 647-662. (HS) Measurement device used for specifically detecting substance to be examined using photocurrent, sensor unit used for same, and method for specifically detecting substance to be examined using photocurrent. Inventors: Makoto Bekki, and Shuji Sonezaki. United States Patent: US 8501492 B2, Publication Date: 6 August 2013; (Hyb4) https://www.google.com/patents/US8501492 Comparative Gene Expression Analyses of Campylobacter jejuni Strains Isolated from Clinical, Environmental and Animal Sources Ghiwa Azzi MS Theses, 2013; University of Ottawa, Canada, 220 pp. (HS) http://www.ruor.uottawa.ca/bitstream/10393/24193/1/Azzi_Ghiwa_2013_thesis.pdf 2012. Method of detecting amplification or deletion in genomic DNA Fragment. Inventors: Makoto Amano, Naoyuki Yamamoto United States Patent: 8105770 B2, Publication Date: 31 January 2012; (HS) https://www.google.com/patents/US8105770 Gene expression profiling of HCV genotype 3a initial liver fibrosis and cirrhosis patients using microarray. Waqar Ahmad, Bushra Ijaz, and Sajida Hassan. Journal Translational Medicine, 7 March 2012; 10: 41, 17 pp. (HS) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3348056/

Differential gene expression segregates cattle confirmed positive for bovine tuberculosis from antemortem tuberculosis test-false positive cattle originating from herds free of bovine tuberculosis. Ailam Lim, Juan P. Steibel, Paul M. Coussens, Daniel L. Grooms, and Steven R. Bolin. Veterinary Medicine International, 2 April 2012; 2012: 192926, 12 pp. (HS) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3373196/ CDK-4 inhibitor P276 sensitizes pancreatic cancer cells to gemcitabine-induced apoptosis. Dharmalingam Subramaniam, Giridharan Periyasamy, Sivapriya Ponnurangam, Debarshi Chakrabarti, Aravind Sugumar, Muralidhara Padigaru, Scott J. Weir, Arun Balakrishnan, Somesh Sharma, and Shrikant Anant. Molecular Cancer Therapeutics, July 2012; 11(7): 1598-1608. (HS) http://mct.aacrjournals.org/content/11/7/1598.long Non structural protein of avian influenza A (H11N1) virus is a weaker suppressor of immune responses but capable of inducing apoptosis in host cells. Sanjay Mukherjee, Shamik Majumdar, Veena C. Vipat, Akhilesh C. Mishra, Alok K. Chakrabarti. Virology Journal, 6 August 2012; 9(1): 149, 11 pp. (HS) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3490754/ NF-κB dependent anti-inflammatory activity of chlorojanerin isolated from Saussurea heteromalla. Arvind Saklani, Bindu Hegde, Prabha Mishra, Ruchi Singh, Monica Mendon, Debarshi Chakrabarty, Divya V. Kamath, Aurelio Lobo, Prabhu Dutt Mishra, Nilesh M. Dagia, Muralidhara Padigaru, Asha A. Kulkarni-Almeida Phytomedicine, 15 August 2012; 19(11): 988-997. (HS) The use of metabolomics integrated with transcriptomic and proteomic studies for identifying key steps involved in the control of nitrogen metabolism in crops such as maize. Nardjis Amiour, Sandrine Imbaud, Gilles Clément, Nicolas Agier, Michel Zivy, Benoît Valot, Thierry Balliau et al. Patrick Armengaud, Isabelle Quilleré,Rafael Cañas, Thérèse Tercet-Laforgue and Bertrand Hirel Journal of Experimental Botany, September 2012; 63(14): 5017-5033. (HS) http://jxb.oxfordjournals.org/content/63/14/5017.long Spider glue proteins have distinct architectures compared with traditional spidroin family members. Keshav Vasanthavada, Xiaoyi Hu, Tiffany Tuton-Blasingame, Yang Hsia, Sujatha Sampath, Ryan Pacheco, Jordan Freeark et al. Arnold M. Falickhttp://www.jbc.org/content/287/43/35986.short - aff-1, Simon Tang, Justine Fong, Kristin Kohler, Coby La Mattina-Hawkins and Craig Vierra Journal of Biological Chemistry, 19 October 2012; 287(43): 35986-35999. (Hyb4) http://www.jbc.org/content/287/43/35986.full Misacylation of tRNA with methionine in Saccharomyces cerevisiae. Elizabeth Wiltrout, Jeffrey M. Goodenbour, Mathieu Fréchin, and Tao Pan. Nucleic Acids Research, 2 November 2012; 40(20):10494-10506, 13 pp. (Hyb4) http://nar.oxfordjournals.org/content/early/2012/08/30/nar.gks805.full.pdf+html Genome-wide identification and quantitative analysis of cleaved tRNA fragments induced by cellular stress. Mridusmita Saikia, Dawid Krokowski, Bo-Jhih Guan, Pavel Ivanov, Marc Parisien, Guo-fu Hu, Paul Anderson, Tao Pan, and Maria Hatzoglou.

Journal of Biological Chemistry, 14 December 2012; 287(51): 42708-42725. (Hyb4) http://www.jbc.org/content/287/51/42708.full.pdf+html 2011. Mesenteric lymph node transcriptome profiles in BALB/c mice sensitized to three common food allergens Mainul Husain, Herman J Boermans and Niel A Karrow BMC Genomics, 6 January 2011; 12: 12, 16 pp. (HS) http://www.biomedcentral.com/1471-2164/12/12 Nucleobase characterisation. Inventors: Mark Bradley, Juan J. Diaz-Mochon US Patent Application: US 2011/0028337 A1, Publication Date: 3 February 2011; (Hyb4) http://www.google.com/patents/US20110028337 Genomic profiling of sinonasal squamous cell carcinoma. Fernando López, José L. Llorente, Cristina García-Inclán, Marta Alonso-Guervós, Mari Paz Cuesta-Albalad, Manuel Florentino Fresno, César Álvarez-Marcos, Carlos Suárez and Mario A. Hermsen. Head & Neck, February 2011; 33(2): 145-153. (HS) http://www.sbccp.org.br/arquivos/HN_02-2011_genomic_profiling_of_sinonasal.pdf Microarray-based genotyping of Salmonella: Inter-laboratory evaluation of reproducibility and standardization potential. Hugo Grønlund, Leise Riber, Håkan Vigre, Charlotta Löfström, Liselotte Folling, Stephan Huehn, Burkhard Malorny, Peter Rådström, Knut Rudi and Jeffrey Hoorfar International Journal of Food Microbiology, 1 March 2011; 145(Suppl.1): S79-S85. (HS) C terminus of Clostridium perfringens enterotoxin downregulates CLDN4 and sensitizes ovarian cancer cells to Taxol and Carboplatin. Zhijian Gao, Xiaoyin Xu, Bruce McClane, Qing Zeng, Babak Litkouhi, William R. Welch, Ross S. Berkowitz , Samuel C. Mok, and Elizabeth I.O. Garner Clinical Cancer Research, 1 March 2011; 17(5): 1065-1074. (Hyb4) http://clincancerres.aacrjournals.org/content/17/5/1065.full.pdf+html Pandemic (H1N1) 2009 influenza virus induces weaker host immune responses in vitro: a possible mechanism of high transmissibility. Sanjay Mukherjee, Veena C Vipat, Akhilesh C Mishra, Shailesh D Pawar and Alok K Chakrabarti Virology Journal, 25 March 2011; 8:140, 10 pp. (HS) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3076257/ Misacylation of specific nonmethionyl tRNAs by a bacterial methionyl-tRNA synthetase. Thomas E. Jones, Rebecca W. Alexander, and Tao Pan Proceedings National Academy of Sciences USA, 26 April 2011; 108(17): 6933-6938. (Hyb4) http://www.pnas.org/content/108/17/6933.full Development and validation of a microarray for the confirmation and typing of norovirus RT-PCR products. Kirsten Mattison, Nathalie Corneau, Ingvild Berg, Albert Bosch, Erwin Duizer, Ion Gutiérrez-Aguirre, Yvan L’Homme, Yalda Lucero, Zhiyao Luo, Alexander Martyres, Mette Myrmel, Miguel O’Ryan, Franco Pagotto, Daisuke Sano, Sanela Svraka, Ulises Urzua and Sabah Bidawid

Journal of Virological Methods, May 2011; 173(2): 233-250. (HS) Regulation of Cell Division, Biofilm Formation, and Virulence by FlhC in Escherichia coli O157:H7 Grown on Meat. Preeti Sule, Shelley M. Horne, Catherine M. Logue, and Birgit M. Prüß Applied and Environmental Microbiology, June 2011; 77(11): 3653-3662. (Hyb4) http://aem.asm.org/content/77/11/3653.full.pdf+html The Hepatitis E Virus ORF3 Protein Regulates the Expression of Liver-Specific Genes by Modulating Localization of Hepatocyte Nuclear Factor 4. Vivek Chandra, Prasida Holla, Dhrubaa Ghosh, Debarshi Chakrabarti, Muralidhara Padigaru, Shahid Jameel PLoS One, 20 July 2011; 6(7):e22412, pp. (HS) http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0022412 Microarray generation of thousand-member oligonucleotide libraries. Nina Svensen, Juan José Díaz-Mochón, and Mark Bradley. PLoS One, 23 September 2011; 6(9): e24906, 8 pp. (Hyb4) http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0024906#pone-0024906-g004 Genome wide gene expression regulation by HIP1 Protein Interactor, HIPPI: Prediction and validation. Moumita Datta, Ananyo Choudhury, Ansuman Lahiri, and Nitai P. Bhattacharyya. BMC Genomics, 26 September 2011; 12: 463, 17 pp. (HS) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3228557/ Hepatic Gene Expression Profiling to Predict Future Lactation Performance in Dairy Cattle. John Doelman PhD Theses, The University of Guelph, October 2011, 145 pp. (HS) https://dspace.lib.uoguelph.ca/xmlui/bitstream/handle/10214/3062/Complete%20Thesis%206%20October%202011.pdf?sequence=1 Novel synergistic combination of gemcitabine with P276-00 or P1446A in treatment of cancer. Inventors: Periyasamy Giridharan, Debarshi Chakrabarti,Amit Khanna, Urvi Ved, Asha Almeida, Somesh Sharma, Muralidhara Padigaru, Arun Balakrishnan US Patent Application: 2011/0312528 A1, Publication Date: 22 December 2011; (HS) https://www.google.com/patents/US20110312528 Discovery Approaches to UPR in Athero-Susceptible Endothelium In Vivo . Mete Civelek, Elisabetta Manduchi, Gregory R. Grant, Christian J. Stoeckert Jr, Peter F. Davies. Methods in Enzymology: The Unfolded Protein Response and Cellular Stress, 2011; 489: 109-126. (HS) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3833809/ 2010. Recurrent copy number changes in mentally retarded children harbour genes involved in cellular localization and the glutamate receptor complex. Martin Poot, Marc J Eleveld, Ruben van 't Slot, Hans Kristian Ploos van Amstel and Ron Hochstenbach

European Journal of Human Genetics, January 2010; 18(1): 39–46. (HS) Immunomodulatory cytokines determine the outcome of Japanese encephalitis virus infection in mice. Biswas SM, Kar S, Singh R, Chakraborty D, Vipat V, Raut CG, Mishra AC, Gore MM, Ghosh D. J Med Virology, February 2010; 82(2): 304-310. (HS) Methods and means for regulating gene expression. Inventors: Den Hengst, Christiaan Daniël; Gajic, Olivera; Kuipers, Oscar Paul; Kok, Jan; Sikkema, Jan; Geurts, Johannes Marie Wilhelmus; Nauta, Arjen European Patent: EP1649024 B1, Publication Date: 24 March 2010; (HS) Gene expression profiling during the byssogenesis of zebra mussel (Dreissena polymorpha). Wei Xu and Mohamed Faisal Mol Genet Genomics, 2010 April; 283(4): 327-339. (HS) Factorial microarray analysis of zebra mussel (Dreissena polymorpha: Dreissenidae, Bivalvia) adhesion. Wei Xu and Mohamed Faisal BMC Genomics, 28 May 2010; 11: 341, pp. (HS) Hybridization system using the control of pump and valves in closed system. Inventors: Lee, Soo-suk; Jung, Sung-ouk; Yoo, Chang-eun; Lee, Hun-joo; Ko, Christopher Hansung; Huh, Nam United States Patent: 7732191 B2, Publication Date: 8 June 2010; (HS) Novel synergistic combination of gemcitabine with P276-00 or P1446A in treatment of cancer. Inventors: Periyasamy Giridharan, Debarshi Chakrabarti, Amit Khanna, Urvi Ved, Asha Almeida, Somesh Sharma, Muralidhara Padigaru, Arun Balakrishnan US Patent Application: 2010/0152129 A1, Publication Date: 17 June 2010; (HS) Genome-wide Analysis of Aminoacylation (Charging) Levels of tRNA Using Microarrays John Zaborske, Tao Pan J Visualized Experiments, 18 June 2010; 40: e2007, 3 pp. (Hyb4) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3153904/ Starvation alters the liver transcriptome of the innate immune response in Atlantic salmon (Salmo salar). Samuel AM Martin, Alex Douglas, Dominic F Houlihan and Christopher J Secombes BMC Genomics, 5 July 2010; 11: 418, pp. (HS) Intestinal Ischemic Preconditioning After Ischemia/Reperfusion Injury in Rat Intestine: Profiling Global Gene Expression Patterns. Stacey D. Moore-Olufemi, Shodimu-Emmanuel Olufemi, Steve Lott, Norio Sato, Rosemary A. Kozar, Frederick A. Moore, Ravi S. Radhakrishnan, Shinil Shah, Fernando Jimenez, Bruce C. Kone, Cox CS Jr. Digestive Diseases and Sciences, July 2010; 55(7): 1866-1877. (HS) Genome-wide analysis of N1-methyl-adenosine modification in human tRNAs Mridusmita Saikia, Ye Fu, Mariana Pavon-Eternod, Chuan He and Tao Pan RNA, July 2010; 16(7): 1317-1327. (Hyb4) http://rnajournal.cshlp.org/content/16/7/1317.full tRNAs as Biomarkers and Regulators for Breast Cancer. Tao Pan, and Marsha Rosner Final U.S. DTIC Grant Report, August 2010; Chicago University, IL, USA, 30 pp. (Hyb4) http://oai.dtic.mil/oai/oai?verb=getRecord&metadataPrefix=html&identifier=ADA540678

Array comparative genomic hybridization analysis revealed four genomic prognostic biomarkers for primary gastric cancers. Nobumoto Tomioka, Keiko Morita, Nozomi Kobayashi, Mitsuhiro Tada, Tomoo Itoh, Soichiro Saitoh, Masao Kondo, Norihiko Takahashi, Akihiko Kataoka, Kazuaki Nakanishi, Masato Takahashi, Toshiya Kamiyama, Michitaka Ozaki, Takashi Hirano and Satoru Todo Cancer Genetics and Cytogenetics, August 2010; 201(1): 6-14. (HS) Host gene expression profiling in influenza A virus-infected lung epithelial (A549) cells: a comparative analysis between highly pathogenic and modified H5N1 viruses. Alok K Chakrabarti, Veena C Vipat, Sanjay Mukherjee, Rashmi Singh, Shailesh D Pawar, Akhilesh C Mishra Virology Journal, 9 September 2010; 7: 219, pp. (HS) Gene expression profiling of PBMCs from Holstein and Jersey cows sub-clinically infected with Mycobacterium avium ssp. Paratuberculosis. Chris P. Verschoor, Sameer D. Pant, Qiumei You, David F. Kelton and Niel A. Karrow Veterinary Immunology and Immunopathology, 15 September 2010; 137(1-2): 1-11. (HS) Glucosylceramide synthesis inhibition affects cell cycle progression, membrane trafficking, and stage differentiation in Giardia lamblia. Saša Štefanić , Cornelia Spycher, Laura Morf, Gemma Fabriàs, Josefina Casas, Elisabeth Schraner, Peter Wild, Adrian B. Hehl and Sabrina Sonda The Journal of Lipid Research, September 2010; 51(9): 2527-2545. (HS) High-Resolution Analysis of Genomic Copy Number Changes. Mario Hermsen, Jordy Coffa, Bauke Ylstra, Gerrit Meijer, Hans Morreau, Ronald van Eijk, Jan Oosting and Tom van Wezel In: Genomics: Essential Methods (eds M. Starkey and R. Elaswarapu), John Wiley & Sons, Ltd, Chichester, UK, 22 November 2010; pp. 1-31. (HS) Detection and Isolation of Selected Genes of Interest from Metagenomic Libraries by a DNA Microarray Approach. Gopal P. Pathak and Wolfgang Gärtner Methods in Molecular Biology, 2010; 668 (Metagenomics): 299-312. (Hyb4) 2009. Gene expression profiling of bovine preovulatory follicles: gonadotropin surge and prostanoid-dependent up-regulation of genes potentially linked to the ovulatory process. Qinglei Li, Fermin Jimenez-Krassel, James J Ireland and George W Smith Reproduction, 1 February 2009; 137(2): 297-307. (HS) A Novel 6.14 Mb Duplication of Chromosome 8p21 in a Patient with Autism and Self Mutilation. Heval M. Ozgen, Wouter G. Staal, John C. Barber, Maretha V. de Jonge, Marc J. Eleveld, Frits A. Beemer, Ron Hochstenbach and Martin Poot Journal of Autism and Developmental Disorders, February 2009; 39(2): 322-329. (HS) Genome-wide analysis of genetic changes in intestinal-type sinonasal adenocarcinoma. Mario A. Hermsen, José Luis Llorente, Jhudit Pérez-Escuredo, Fernando López, Bauke Ylstra, César Álvarez-Marcos, Carlos Suárez

Head & Neck, March 2009; 31(3): 290–297. (HS) Multicompartment device comprising immobilized biopolymers for use in analyzing the results of hybridization reactions involving nucleic acids and proteins. Inventor: Joseph P. Fredrick United States Patent: US 7517498 B2, Publication Date: April 14, 2009; (Hyb4/Hyb12) https://www.google.com/patents/US7517498 Methylation markers for early detection and prognosis of colon cancers. Inventors: Straub, Jozef; Van Criekenge, Wim; De Carvalho, Beatriz Pinto Morais; Meijer, Gerritt EU Patent Application: EP 2050828 A2, Publication Date: 22 April 2009; (HS) Development of a cDNA microarray of zebra mussel (Dreissena polymorpha) foot and its use in understanding the early stage of underwater adhesion. Wei Xu and Mohamed Faisal Gene, 1 May 2009; 436(1-2): 71-80. (HS) HSP90B1, a thyroid hormone-responsive heat shock protein gene involved in photoperiodic signaling. Gemma Graham, Peter J. Sharp, Qiushi Li, Peter W. Wilson, Richard T. Talbot, Alison Downing and Timothy Boswell Brain Research Bulletin, 29 May 2009; 79(3-4): 201-207. (HS) Chromosomal changes in sporadic and familial head and neck paragangliomas. María A. Sevilla, Mario A. Hermsen, Marjan M. Weiss, Anneliese Grimbergen, Milagros Balbín, José Luis Llorente, Juan Pablo Rodrigo and Carlos Suárez Otolaryngology - Head and Neck Surgery, May 2009; 140(5): 724-729. (HS) Hybridization chamber agitation device using pump and valves. Inventors: Sung-ouk Jung, Nam Huh, Soo-suk Lee, Chang-eun Yoo, Hun-joo Lee United States Patent: 7544505 B2; Publication Date: 9 June 2009; (HS) High levels of tRNA abundance and alteration of tRNA charging by bortezomib in multiple myeloma. Ying Zhou, Jeffrey M. Goodenbour, Lucy A. Godley, Amittha Wickrema and Tao Pan Biochemical and Biophysical Research Communications, 24 July 2009; 385(2): 160-164. (Hyb4) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774282/ Chronic Endoplasmic Reticulum Stress Activates Unfolded Protein Response in Arterial Endothelium in Regions of Susceptibility to Atherosclerosis. Mete Civelek, Elisabetta Manduchi, Rebecca J. Riley, Christian J. Stoeckert Jr, Peter F. Davies Circ Research, 28 August 2009; 105(5): 453-461. (HS) Novel blue light-sensitive proteins from a metagenomic approach. G. P. Pathak, A. Ehrenreich, A. Losi, W. R. Streit, W. G rtner Environmental Microbiology, September 2009; 11(9): 2388–2399. (Hyb4) http://www.fis.unipr.it/home/aba.losi/metagenomics.pdf Microarray Analysis of GFP-Expressing Mouse Dopamine Neurons Isolated by Laser Capture Microdissection. Christina Vlachouli Ph.D. Theses, 7 October 2009; S.I.S.S.A. - I.S.A.S., Trieste, Italy, 184 pp. (Hyb4) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774282/

Innate immune and chemically triggered oxidative stress modifies translational fidelity. Nir Netzer, Jeffrey M. Goodenbour, Alexandre David, Kimberly A. Dittmar, Richard B. Jones, Jeffrey R. Schneider, David Boone, Eva M. Eves, Marsha R. Rosner, James S. Gibbs, Alan Embry, Brian Dolan, Suman Das, Heather D. Hickman, Peter Berglund, Jack R. Bennink, Jonathan W. Yewdell & Tao Pan Nature, 26 November 2009; 462(7272): 522-526. (Hyb4) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2785853/ tRNA over-expression in breast cancer and functional consequences. Mariana Pavon-Eternod, Suzanna Gomes, Renaud Geslain, Qing Dai, Marsha Rich Rosner, Tao Pan Nucleic Acids Research, November 2009; 37(21): 7268-7280. (Hyb4) http://nar.oxfordjournals.org/content/37/21/7268.long 2008. Development and validation of microarray-based assay for epidemiological study of MRSA. Junnosuke Otsuka, Yasumitsu Kondoh, Tomoyuki Amemiya, Akio Kitamura, Teruyo Ito, Satoshi Baba, Longzhu Cui, Keiichi Hiramatsu, Tomoko Tashiro and Hideo Tashiro Molecular and Cellular Probes, February 2008; 22(1): 1-13. (HS) Radiation-induced gene expression in human subcutaneous fibroblasts is predictive of radiation-induced fibrosis. Olaug Kristin Rødningen, Anne-Lise Børresen-Dale, Jan Alsner, Trevor Hastie and Jens Overgaard Radiotherapy and Oncology, March 2008; 86(3): 314-320. (HS) Therapeutic targets and biomarkers in lung cancer. Mariëlle I Gallegos Ruiz MD Theses, 22 April 2008; de Vrije Universiteit Amsterdam, 231 pp. (HS) Anchoring of unmodified oligonucleotides on a chitosan-based array: applications to genotyping and gene expression. Clarissa Consolandi, Marco Severgnini, Giada Caredda and Gianluca De Bellis Analytical Biochemistry, 1 May 2008; 376(1): 39-43. 22 April 2008; (HS) Genome Sequence of the Streptomycin-Producing Microorganism Streptomyces griseus IFO 13350. Yasuo Ohnishi, Jun Ishikawa, Hirofumi Hara, Hirokazu Suzuki, Miwa Ikenoya, Haruo Ikeda, Atsushi Yamashita, Masahira Hattori, and Sueharu Horinouchi Journal of Bacteriology, June 2008; 90(11): 4050-4060. (HS) A description of the origins, design and performance of the TRAITS–SGP Atlantic salmon Salmo salar L. cDNA microarray. J. B. Taggart, J. E. Bron, S. A. M. Martin, P. J. Seear,, B. Høyheim, R. Talbot, S. N. Carmichael, L. A. N. Villeneuve, G. E. Sweeney, D. F. Houlihan, C. J. Secombes, D. R. Tocher, A. J. Teale Journal of Fish Biology, June 2008; 72(9): 2071–2094. (HS) Variation in the ovine cortisol response to systemic bacterial endotoxin challenge is predominantly determined by signalling within the hypothalamic–pituitary–adrenal axis. Qiumei You, Niel A. Karrow, Honghe Cao, Alexander Rodriguez, Bonnie A. Mallard and Herman J. Boermans Toxicology and Applied Pharmacology, 1 July 2008; 230(1): 1-8. (HS)

Development of a DNA Microarray for the Simultaneous Detection and Genotyping of Noroviruses Pagotto, Franco; Corneau, Nathalie; Mattison, Kirsten; Bidawid, Sabah Journal of Food Protection, July 2008; 71(7): 1434-1441. (HS) Differential Gene Expression Between the Biotrophic-Like and Saprotrophic Mycelia of the Witches’ Broom Pathogen Moniliophthora perniciosa. Johana Rincones, Leandra M. Scarpari, Marcelo F. Carazzolle, Jorge M. C. Mondego, Eduardo F. Formighieri, Joan G. Barau, Gustavo G. L. Costa, Dirce M. Carraro, Helena P. Brentani, Laurival A. Vilas-Boas, Bruno V. de Oliveira, Maricene Sabha, Robson Dias, Júlio M. Cascardo, Ricardo A. Azevedo, Lyndel W. Meinhardt, and Gonçalo A. G. Pereira Mol Plant Microbe Interaction, 2008 July; 21(7): 891-908. (HS) MITOCHIP assessment of differential gene expression in the skeletal muscle of Ant1 knockout mice: Coordinate regulation of OXPHOS, antioxidant, and apoptotic genes. Vaidya Subramaniam, Pawel Golik, Deborah G. Murdock, Shawn Levy, Keith W. Kerstann, Pinar E. Coskun, Goarik A. Melkonian and Douglas C. Wallace Biochimica et Biophysica Acta (BBA) - Bioenergetics, July-August 2008; 1777(7-8): 666-675. (HS) Expression profile of interferon stimulated genes in central nervous system of mice infected with dengue virus Type-1. Juliano Bordignon, Christian M. Probst, Ana Luiza P. Mosimann, Daniela P. Pavoni, Vanessa Stella, Gregory A. Buck, Nusara Satproedprai, Paul Fawcett, Sílvio M. Zanata, Lucia de Noronha, Marco A. Krieger and Claudia N. Duarte dos Santos Virology, 1 August 2008; 377(2): 319-329. (HS) A Resource for Transcriptomic Analysis in the Mouse Brain. Charles Plessy, Michela Fagiolini, Akiko Wagatsuma, Norihiro Harasawa, Takenobu Kuji, Atsuko Asaka-Oba, Yukari Kanzaki, Sayaka Fujishima, Kazunori Waki, Hiroyuki Nakahara, Takao K. Hensch, Piero Carninci PLoS ONE, 20 August 2008; 3(8): e3012, pp. (HS) Evaluation of automated and conventional microarray hybridization: a question of data quality and best practice? Violet K. Peeva, Jessica L. Lynch, Christopher J. S. DeSilva, Nigel R. Swanson Biotechnology and Applied Biochemistry, August 2008; 50(4): 181–190. (HS) Use of genomic DNA as an indirect reference for identifying gender-associated transcripts in morphologically identical, but chromosomally distinct, Schistosoma mansoni cercariae. Fitzpatrick JM, Protasio AV, McArdle AJ, Williams GA, Johnston DA, Hoffmann KF. PLoS Negl Trop Diseases, 22 October 2008; 2(10): e323. (Hyb4) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2565838/ A network biology approach evaluating the anticancer effects of bortezomib identifi es SPARC as a therapeutic target in adult T-cell leukemia cells. Junko H Ohyashiki, Ryoko Hamamura, Chiaki Kobayashi, Yu Zhang, Kazuma Ohyashiki Advances and Applications in Bioinformatics and Chemistry, October 2008; 2008(1): 85–98. (HS) Integrated Genomic and Transcriptional Profiling Identifies Chromosomal Loci with Altered Gene Expression in Cervical Cancer. Saskia M. Wilting, Jillian de Wilde, Chris J. L. M. Meijer, Johannes Berkhof, Yajun Yi, Wessel N. van Wieringen, Boudewijn J. M. Braakhuis, Gerrit A. Meijer, Bauke Ylstra, Peter J. F. Snijders, and Renske D. M. Steenbergen Genes Chromosomes Cancer, October 2008; 47(10): 890–905. (HS)

2007. Genetic heterogeneity in patients with multiple neoplastic lung lesions: a report of three cases. Mariëlle I Gallegos Ruiz, Hester van Cruijsen, Egbert F Smit, Katrien Grünberg,; Gerrit A Meijer, José A Rodriguez, Bauke Ylstra and Giuseppe Giaccone J Thoracic Oncology, January 2007; 2(1): 12-21. (HS) Modulation of gene expression in a human cell line caused by poliovirus, vaccinia virus and interferon. Bjørn Grinde, Marc Gayorfar and Gunnar Hoddevik Virology Journal, 5 March 2007; 4: 24, pp. (HS) Nucleic acid probes and broad-range primers from regions in topoisomerase genes, and methods in which they are used. Inventors: Stina Roth, Jari Jalava, Simo Nikkari European Patent: EP1565573 B1, Publication Date: 21 March 2007; (HS) Chromosomal instability in human mesenchymal stem cells immortalized with human papilloma virus E6, E7, and hTERT genes. Masao Takeuchi & Kikuko Takeuchi & Arihiro Kohara & Motonobu Satoh & Setsuko Shioda & Yutaka Ozawa &Azusa Ohtani & Keiko Morita & Takashi Hirano & Masanori Terai & Akihiro Umezawa & Hiroshi Mizusawa In Vitro Cellular & Developmental Biology - Animal, March-April 2007; 43(3-4): 129-138. (HS) BAC Clones Related to Prognosis in Patients with Esophageal Squamous Carcinoma: An Array Comparative Genomic Hybridization Study. Shigeo Hirasaki Tsuyoshi Noguchi, Koshi Mimori, Junko Onuki, Keiko Morita, Hiroshi Inoue, Kenichi Sugihara, Masaki Mori and Takashi Hirano The Oncologist, April 2007; 12(4): 406-417. (HS) Dandy-Walker complex in a boy with a 5 Mb deletion of region 1q44 due to a paternal t(1;20)(q44;q13.33). Martin Poot, Hester Y. Kroes, Suzanne E. v. d. Wijst, Marc J. Eleveld, Liesbeth Rooms, Rutger A.J. Nievelstein, Daniel O. Weghuis, Rene C. Vreuls, Gerard Hageman, Frank Kooy, Ron Hochstenbach Am J Med Genetics, Part A, 15 May 2007; 143A(10): 1038–1044. (HS) Detection of Minimal Gastric Cancer Cells in Peritoneal Washings by Focused Microarray Analysis with Multiple Markers: Clinical Implications. Kazuhiko Mori, Tomohiro Suzuki, Hiroshi Uozaki, Hayao Nakanishi, Tetsuya Ueda, Yoshihiro Matsuno, Yasuhiro Kodera, Hiromi Sakamoto, Nobuko Yamamoto, Mitsuru Sasako, M. Kaminishi, H. Sasaki Annals of Surgical Oncology, May 2007; 14(5): 1694-1702. (HS) Histone Deacetylase 7 Functions as a Key Regulator of Genes Involved in both Positive and Negative Selection of Thymocytes. Herbert G. Kasler, and Eric Verdin Molecular and Cellular Biology, July 2007; 27(14): 5184-5200. (HS) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1951960/ Cytogenetic aberrations in neuropathy associated with IgM monoclonal gammopathy.

Marijke Eurelings, Henk M. Lokhorst, Nicolette C. Notermans, Pieter Jaap Krijtenburg, Berris van Kessel, Mark J. Eleveld, Andries Bloem, John H. Wokke, Martin Poot and Arjan Buijs Journal of the Neurological Sciences, 15 September 2007; 260(1-2): 124-131. (HS) Nucleic Acid Probes and Broad-Range Primers from Regions in DNA Directed RNA Polymerase Subunit B genes, and Methods in which they are Used. Inventors: Jaan Palgi, Jari Jalava, Simo Nikkari US Patent Application: 2007/0243530 A1, Publication Date: 18 October 2007; (HS) http://www.google.com/patents/US20070243530 Methods and Means for Regulating Gene Expression. Inventors: Christiaan Daniel Dan Hengst, Olivera Gajic, Oscar Paul Kuipers, Jan Kok, Jan Sikkema, Johannes Marie Wilhelmus Geurts, Arjen Nauta US Patent Application: 2007/0243303 A1, Publication Date: 28 October 2007; (HS) http://www.google.com/patents/US20070243303 Unmasking of a hemizygous WFS1 gene mutation by a chromosome 4p deletion of 8.3 Mb in a patient with Wolf–Hirschhorn syndrome. Klara Flipsen-ten Berg, Peter M van Hasselt, Marc J Eleveld, Suzanne E van der Wijst, Frans A Hol, Monique A M de Vroede, Frits A Beemer, P F Ron Hochstenbach and Martin Poot European Journal of Human Genetics, November 2007; 15(11): 1132–1138. (HS) http://www.nature.com/ejhg/journal/v15/n11/full/5201899a.html Proportional growth failure and oculocutaneous albinism in a girl with a 6.87 Mb deletion of region 15q26.2→qter. Martin Poot, Marc J. Eleveld, Ruben van ’t Slot, Maria M. van Genderen, Annemarie A. Verrijn Stuart, Ron Hochstenbach and Frits A. Beemer European Journal of Medical Genetics, November-December 2007; 50(6): 432-440. (HS) Interferon type I and type II responses in an Atlantic salmon (Salmo salar) SHK-1 cell line by the salmon TRAITS/SGP microarray. S. A. M. Martin, J. B. Taggart, P. Seear, J. E. Bron, R. Talbot, A. J. Teale, G. E. Sweeney, B. Høyheim, D. F. Houlihan, D. R. Tocher, J. Zou and C. J. Secombes Physiological Genomics, December 2007; 32(1): 33-44. (HS) Optimization Workflow for the Processing of High Quality Glass-Based Microarrays Applications in DNA, Peptide, Antibody, and Carbohydrate Microarraying. Jens Sobek, Catharine Aquino and Ralph Schlapbach Methods in Molecular Biology, 2007; 382(Microarrays): 33-51. (HS) Processing Protocols for High Quality Glass-Based Microarrays Applications in DNA, Peptide, Antibody, and Carbohydrate Microarraying Jens Sobek, Catharine Aquino and Ralph Schlapbach Methods in Molecular Biology, 2007; 382(Microarrays): 53-66. (HS) Oligonucleotide Array Comparative Genomic Hybridization. Paul van den IJssel and Bauke Ylstra Methods in Molecular Biology, 2007; 396(III, Comparative Genomics): 207-221. (HS) 2006.

Investigation of changes in global gene expression in the frontal cortex of early-weaned and socially isolated piglets using microarray and quantitative real-time RT-PCR R. Poletto, J.M. Siegford, J.P. Steibel, P.M. Coussens and A.J. Zanella Brain Research, 12 January 2006; 1068(1): 7-15. (HS) Regulatory roles of psrA and rpoS in phenazine-1-carboxamide synthesis by Pseudomonas chlororaphis PCL1391. Geneviève Girard, E. Tjeerd van Rij, Ben J. J. Lugtenberg and Guido V. Bloemberg Microbiology, January 2006; 152(1): 43-58. (HS) Composition of microbial communities in hexachlorocyclohexane (HCH) contaminated soils from Spain revealed with a habitat-specific microarray. Josh D. Neufeld , William W. Mohn, Victor De Lorenzo Environmental Microbiology, January 2006; 8(1): 126–140. (HS) Virilization of the external genitalia and severe mental retardation in a girl with an unbalanced translocation 1;18 J.M. de Pater, M. Poot, F.A. Beemer, J.B. Bijlsma, W.W.M. Hack, W.M. Van Dam, M.J. Eleveld, W.H. Loneus and J.J.M. Engelen European Journal of Medical Genetics, January-February 2006; 49(1): 19-27. (HS) Nucleic acid probes and broad-range primers from regions in topoisomerase genes, and methods in which they are used. Inventors: Roth, Stina; Jalava, Jari; Nikkari, Simo US Patent Application: 2006/0024675 A1, Publication Date: 02 February 2006; (HS) http://www.google.com/patents/US20060024675 Methods of manipulating nucleic acids. Inventors: Xiang, Charlie; Brownstein, Michael J. US Patent Application: 2006/0040283 A1, Publication Date: 23 February 2006; (HS) http://www.google.com/patents/US20060040283 Transcriptional profiling of Epstein–Barr virus (EBV) genes and host cellular genes in nasal NK/T-cell lymphoma and chronic active EBV infection. Y Zhang, J H Ohyashiki, T Takaku, N Shimizu and K Ohyashiki British Journal of Cancer, 27 February 2006; 94(4): 599-608. (HS) Hypoparathyroidism-retardation-dysmorphism syndrome in a girl: A new variant not caused by a TBCE mutation—clinical report and review. Winnie Courtens, Wim Wuyts, Martin Poot, Karoly Szuhai, Jan Wauters, Edwin Reyniers, Marc Eleveld, George Diaz, Markus M. Nöthen, Ruti Parvari American Journal of Medical Genetics. Part A, 15 March 2006; 140A(6): 611–617. (HS) Global gene regulation in Yersinia enterocolitica: effect of FliA on the expression levels of flagellar and plasmid-encoded virulence genes. Shelley M. Horne and Birgit M. Prüß Archives Microbiology, March 2006; 185(2): 115-126. (Hyb4) A Structured Chitosan-Based Platform for Biomolecule Attachment to Solid Surfaces: Application to DNA Microarray Preparation.

Clarissa Consolandi, Marco Severgnini, Bianca Castiglioni, Roberta Bordoni, Andrea Frosini, Cristina Battaglia, Luigi Rossi Bernardi, and Gianluca De Bellis Bioconjugate Chemistry, March-April 2006; 17 (2): 371–377. (HS) Genome-wide DNA copy number alterations in head and neck squamous cell carcinomas with or without oncogene-expressing human papillomavirus. Smeets SJ, Braakhuis BJ, Abbas S, Snijders PJ, Ylstra B, van de Wiel MA, Meijer GA, Leemans CR, Brakenhoff RH. Oncogene, 20 April 2006; 25(17):2558-2564. (HS) DNA Microarray Analysis Yasuko Sasaki 腸内フローラの構造解析―DNA マイクロアレイによる腸内細菌および細菌叢の解析―. 佐々木泰子. 腸内細菌学雑誌 (Journal of Intestinal Microbiology), 25 May 2006; 20(2): 193-199. (Hyb4) https://www.jstage.jst.go.jp/article/jim/20/2/20_2_193/_article/-char/ja/ The Arabidopsis thaliana Transcriptome in Response to Agrobacterium tumefaciens. Renata F. Ditt, Kathleen F. Kerr, Paul de Figueiredo, Jeff Delrow, Luca Comai,javascript:popRef('c1') Eugene W. Nester Molecular Plant-Microbe Interaction, June 2006; 19(6): 665-681. (HS) Hybridization system using the control of pump and valves in closed system. Inventors: Lee, Soo-suk; Jung, Sung-ouk; Yoo, Chang-eun; Lee, Hun-joo; Ko, Christopher Hansung; Huh, Nam US Patent Application: 2006/0154360 A1, Publication Date: 13 July 2006; (HS) Growth of Escherichia coli MG1655 on LB medium: monitoring utilization of sugars, alcohols, and organic acids with transcriptional microarrays Mark V. Baev, Dmitry Baev, Agnes Jancso Radek and John W. Campbell Applied Microbiology and Biotechnology, July 2006; 71(3): 310-316. (HS) Growth of Escherichia coli MG1655 on LB medium: monitoring utilization of amino acids, peptides, and nucleotides with transcriptional microarrays. Mark V. Baev, Dmitry Baev, Agnes Jansco Radek and John W. Campbell Applied Microbiology and Biotechnology, July 2006; 71(3): 317-322. (HS) Microarray analysis of blood microvessels from PDGF-B and PDGF-Rß mutant mice identifies novel markers for brain pericytes. Cecilia Bondjers, Liqun He, Minoru Takemoto, Jenny Norlin, Noomi Asker, Mats Hellström, Per Lindahl and Christer Betsholtz The FASEB Journal, 1 August 2006; 20(10): 1703-1705. (HS) A High-throughput Genomic Tool: Diversity Array Technology Complementary for Rice Genotyping. Yong Xie, Kenneth McNally, Cheng-Yun Li, Hei Leung, You-Yong Zhu Journal of Integrative Plant Biology, September 2006; 48(9): 1069–1076. (HS) Transcriptomic Assessment of Isozymes in the Biphenyl Pathway of Rhodococcus sp. Strain RHA1. Edmilson R. Gonçalves, Hirofumi Hara, Daisuke Miyazawa, Julian E. Davies, Lindsay D. Eltis, and William W. Mohn Applied and Environmental Microbiology, September 2006; 72(9): 6183-6193. (HS)

Identification of Tumor-Specific Molecular Signatures in Intracranial Ependymoma and Association With Clinical Characteristics. Piergiorgio Modena, Elena Lualdi, Federica Facchinetti, Joris Veltman, James F. Reid, Simone Minardi, Irene Janssen, Felice Giangaspero, Marco Forni, Gaetano Finocchiaro, Lorenzo Genitori, Flavio Giordano, Riccardo Riccardi, Eric F.P.M. Schoenmakers, Maura Massimino, Gabriella Sozzi J Clinical Oncology, 20 November 2006; 24(33): 5223-5233. (HS) Characterization of ovine hepatic gene expression profiles in response to Escherichia coli lipopolysaccharide using a bovine cDNA microarray Honghe Cao, Leah C Kabaroff, Qiumei You, Alexander Rodriguez, Herman J Boermans and Niel A Karrow BMC Veterinary Research 29 November 2006, 2: 34, pp. (HS) Lithium Treatment Prevents Neurocognitive Deficit Resulting from Cranial Irradiation. Eugenia M. Yazlovitskaya , Eric Edwards, Dinesh Thotala, Allie Fu, Kate L. Osusky, William O. Whetsell Jr., Braden Boone, Eric T. Shinohara, and Dennis E. Hallahan Cancer Research, 1 December 2006; 66(23): 11179-11186. (HS) Detekcja ekspresji genów drzew leśnych za pomocą mikromacierzy DNA. (Gene-expression in forest-tree species assessed with microarrays as a tool) Justyna A. Nowakowska Sylwan, 2006; 4(33): 43. (Hyb4) http://www.researchgate.net/profile/Justyna_Nowakowska/publication/259840860_Geneexpression_in_foresttree_species_assessed_with_microarrays_as_a_tool/links/00b7d52e1247e33ea4000000.pdf 2005. Supernumerary ring chromosome 7 mosaicism: case report, investigation of the gene content, and delineation of the phenotype. Lichtenbelt KD, Hochstenbach R, van Dam WM, Eleveld MJ, Poot M, Beemer FA. Am J Med Genetics. A, 1 January 2005; 132A(1): 93-100. (HS) Methods and means for regulating gene expression. Inventors: Den, Hengst Christiaan Daniel;Kuipers, Oscar Paul; Kok, Jan; Geurts, Johannes Marie Wilhelmu; Nauta, Arjen European Patent Application: EP1493816 A1, Publication Date: 05 January 2005; (HS) Genomic Technical Note. Microarrays—Solutions to the Protein Challenge. Jeremy Clarke BioTechniques, January 2005; 38(1): 149–151. (HS) Effective transcriptome amplification for expression profiling on sense-oriented oligonucleotide microarrays. Joerg Schlingemann, Olaf Thuerigen, Carina Ittrich, Grischa Toedt, Heidi Kramer, Meinhard Hahn and Peter Lichter Nucleic Acids Research, 17 February 2005; 33(3): e29, pp. (HS) Apparatus for substrate handling. Inventor: Joseph P. Fredrick EU Patent Application: EP 2004/0254856 A2; Publication Date: 23 February 2005; (HS/Hyb4)

Apparatus for substrate handling. Inventor: Joseph P. Fredrick US Patent Application: 2005/0042768 A1; Publication Date: 24 February 2005; (HS/Hyb4) Differential Gene Expression Profiling of CD34+ CD133+ Umbilical Cord Blood Hematopoietic Stem Progenitor Cells. Xianghui He, Veronica Gonzalez, Amy Tsang, Jennifer Thompson, Tom C. Tsang and Dr. David T. Harris. Stem Cells and Development, April 2005; 14(2): 188-198. (HS) Devices and methods for performing array based assays. Inventor: Tsai, George Paul US Patent Application: 2005/0098032 A1, Publication Date: 12 May 2005; (HS) Validation and application of a high fidelity mRNA linear amplification procedure for profiling gene expression. Osman V. Patel, Steve P. Suchyta, Sue S. Sipkovsky, Jianbo Yao, James J. Ireland, Paul M. Coussens and George W. Smith Veterinary Immunology and Immunopathology, 15 May 2005; 105(3-4): 331-342. (HS) DNA microarrays on nanoscale-controlled surface. Bong Jin Hong, Vijaya Sunkara and Joon Won Park Nucleic Acids Research, 7 July 2005; 33(12): e106, pp. (HS) UNIT 4.13: The BAC Resource: Tools for Array CGH and FISH. Norma J. Nowak, Antoine M. Snijders, Jeffrey M. Conroy, Donna G. Albertson In: Current Protocols in Human Genetics, 1 August 2005; Wiley Online Library, 46:4.13.1–4.13.36. (HS) Influence of fusaric acid on phenazine-1-carboxamide synthesis and gene expression of Pseudomonas chlororaphis strain PCL1391 E. Tjeerd van Rij, Geneviève Girard, Ben J. J. Lugtenberg and Guido V. Bloemberg Microbiology, August 2005; 151(8): 2805-2814. (HS) Gene expression profile of mechanically impacted bovine articular cartilage explants. Chan PS, Schlueter AE, Coussens PM, Rosa GJ, Haut RC, Orth MW. J Orthopaedic Research, September 2005; 23(5): 1146-1151. (HS) Chromosomal imbalances in a recurrent solitary fibrous tumor of the orbit. Gro Oddveig Ness, Helle Lybæk, Jarle Arnes and Eyvind Rødahl Cancer Genetics and Cytogenetics, 1 October 2005; 162(1): 38-44. (HS) Estimating immunoregulatory gene networks in human herpesvirus type 6-infected T cells. Tomoiku Takaku, Junko H. Ohyashiki, Yu Zhang and Kazuma Ohyashiki Biochemical and Biophysical Research Communications, 21 October 2005; 336(2): 469-477. (HS) Upregulation of ASCL1 and inhibition of Notch signaling pathway characterize progressive astrocytoma. Kumaravel Somasundaram, Sreekanth P Reddy, Katyayni Vinnakota, Ramona Britto, Madhavan Subbarayan, Sandeep Nambiar, Aparna Hebbar, Cini Samuel, Mitesh Shetty, Hari Kishore Sreepathi, Vani Santosh, Alangar Sathyaranjandas Hegde, Sridevi Hegde, Paturu Kondaiah and M R S Rao Oncogene, 27 October 2005; 24(47): 7073-7083. (HS) Human and mouse oligonucleotide-based array CGH.

Paul van den IJssel, Marianne Tijssen, Suet-Feung Chin, Paul Eijk, Beatriz Carvalho, Erik Hopmans, Henne Holstege, Dhinoth Kumar Bangarusamy, Jos Jonkers, Gerrit A. Meijer, Carlos Caldas and Bauke Ylstra Nucleic Acids Research, 16 December 2005; 33(22): e192, pp. (HS) Microarray analysis of the transcriptional responseto single or multiple doses of ionizing radiation in human subcutaneous fibroblasts. Olaug Kristin Rødningen, Jens Overgaard, Jan Alsner, Trevor Hastie and Anne-Lise Børresen-Dale Radiotherapy and Oncology, December 2005; 77(3): 231-240. (HS) Matrix metalloproteinase expression in the development of ovarian cancer. Jamie Marie Dibble MS Thesis, The University of Arizona, 2005; 80 pp. (HS) 2004. Intensity-based analysis of two-colour microarrays enables efficient and flexible hybridization designs. Peter A. C. ’t Hoen , Rolf Turk, Judith M. Boer, Ellen Sterrenburg, Renée X. de Menezes, Gert-Jan B. van Ommen and Johan T. den Dunnen Nucleic Acids Research, 24 February 2004; 32(4): e41, pp. (HS) Microarray technology for identification and distinction of hantaviruses. Henrik Nordström, Patrik Johansson, Quan-Gen Li, Åke Lundkvist, Peter Nilsson, Fredrik Elgh Journal of Medical Virology, April 2004; 72(4): 646–655. (HS) Analysis of Plant Gene Expression Responses to the Pathogen and Natural Genetic Engineer Agrobacterium tumefaciens. Renata Fava Ditt PhD Thesis, University of Washington, 30 June 2004; 110 pp. (HS) https://digital.lib.washington.edu/researchworks/handle/1773/5148 Gene array analysis of Yersinia enterocolitica FlhD and FlhC: regulation of enzymes affecting synthesis and degradation of carbamoylphosphate Vinayak Kapatral, John W. Campbell, Scott A. Minnich, Nicholas R. Thomson, Philip Matsumura and Birgit M. Prüß Microbiology, July 2004; 150(7): 2289-2300. (HS) http://mic.sgmjournals.org/content/150/7/2289.long Expression profiling of sodium butyrate (NaB)-treated cells: identification of regulation of genes related to cytokine signaling and cancer metastasis by NaB. Jeena Joseph, Giridhar Mudduluru, Sini Antony, Surabhi Vashistha, Parthasarathi Ajitkumar and Kumaravel Somasundaram Oncogene, 19 August 2004; 23(37): 6304-6315. (HS) http://www.nature.com/onc/journal/v23/n37/full/1207852a.html 2003.

FlhD/FlhC Is a Regulator of Anaerobic Respiration and the Entner-Doudoroff Pathway through Induction of the Methyl-Accepting Chemotaxis Protein Aer Birgit M. Prüß, John W. Campbell, Tina K. Van Dyk, Charles Zhu, Yakov Kogan, and Philip Matsumura Journal of Bacteriology, January 2003; 185(2): 534-543. (HS) http://jb.asm.org/content/185/2/534.full Resource and hardware options for microarray-based experimentation. Nabeel A. Affara Briefings in Functional Genomics and Proteomics, April 2003; 2 (1): 7-20. (HS) http://www.ncbi.nlm.nih.gov/pubmed/15239939 Identification of transcription coactivator OCA-B-dependent genes involved in antigen-dependent B cell differentiation by cDNA array analyses. Unkyu Kim, Rachael Siegel, Xiaodi Ren, Cary S. Gunther, Terry Gaasterland, and Robert G. Roeder PNAS, 22 July 2003; 100(15): 8868-8873. (HS) http://www.pnas.org/content/100/15/8868.full Development and testing of a high-density cDNA microarray resource for cattle. Steven P. Suchyta, Sue Sipkovsky, Rachael Kruska, Abra Jeffers, Amanda McNulty, Matthew J. Coussens, Robert J. Tempelman, Robert G. Halgren, Peter M. Saama, Dale E. Bauman, Yves R. Boisclair, Jeanne L. Burton, Robert J. Collier, Edward J. DePeters, Theodore A. Ferris, Matthew C. Lucy, Mark A. McGuire, Juan F. Medrano, Thomas R. Overton, Timothy P. Smith, George W. Smith, Tad S. Sonstegard, James N. Spain, Donald E. Spiers, Jianbo Yao and Paul M. Coussens Physiological Genomics, October 2003; 15(2): 158-164. (HS) http://physiolgenomics.physiology.org/content/15/2/158 Enhanced Expression of Interleukin-1 and Tumor Necrosis Factor Receptor-Associated Protein 1 in Ileal Tissues of Cattle Infected with Mycobacterium avium subsp. Paratuberculosis. Abraham D. Aho, Amanda M. McNulty, and Paul M. Coussens Infection and Immunity, November 2003; 71(11): 6479-6486. (HS) http://iai.asm.org/content/71/11/6479.full Bovine mammary gene expression profiling using a cDNA microarray enhanced for mammary-specific transcripts. Steven P. Suchyta, Sue Sipkovsky, Robert G. Halgren, Rachael Kruska, Michael Elftman, Miriam Weber-Nielsen, Michael J. Vandehaar, Lan Xiao, Robert J. Tempelman and Paul M. Coussens Physiological Genomics, December 2003; 16(1): 8-18. (HS) http://physiolgenomics.physiology.org/content/16/1/8.short Development of a porcine brain cDNA library, EST database, and microarray resource. William Nobis, Xiaoning Ren, Steven P. Suchyta, Thomas R. Suchyta, Adroaldo J. Zanella and Paul M. Coussens Physiological Genomics, December 2003; 16(1): 153-159. (HS) http://physiolgenomics.physiology.org/content/16/1/153.short Sequence Mapping of Combinatorial Libraries on Macro- or Microarrays Experimental Design of DNA Arrays. Valérie Abécassis, Gilles Truan, Loïc Jaffrelo and Denis Pompon Methods in Molecular Biology, 2003; 231(II, Directed Evolution Library Creation): 189-198 (Hyb4) Development of O. minuta specific clones using representational difference analysis (RDA). C. Vitte, J. D. Talag, O. Panaud, M. A. Bernardo, and D. S. Brar.

Rice Genetics Newsletter, 2003; 20: 121-123. (HS) http://www.shigen.nig.ac.jp/rice/rgn/vol20/b51.html 2002. Hybridization array technology coupled with chemostat culture: Tools to interrogate gene expression in Saccharomyces cerevisiae. Andrew Hayes, Nianshu Zhang, Jian Wu, Philip R. Butler, Nicole C. Hauser, Joerg D. Hoheisel, Fei Ling Lim, Andrew D. Sharrocks and Stephen G. Oliver Methods, March 2002; 26(3): 281-290. (HS) New products. (Editor’s page). Molecular Biotechnology, June 2002; 1(2): 205-207. (HS) Transcriptome analysis and related databases of Lactococcus lactis. Oscar P. Kuipers, Anne de Jong, Richard J. S. Baerends, Sacha A. F. T. van Hijum, Aldert L. Zomer, Harma A. Karsens, Chris D. den Hengst, Naomi E. Kramer, Girbe Buist and Jan Kok Antonie Van Leeuwenhoek, August 2002; 82(1-4): 113-122. (HS) Thermal and fluid cycling device for nucleic acid hybridization. Inventors: Aaron Custance, Jonathan I. Parker US Patent Application: 2002/0192806 A1, Publication Date: 19 December 2002; (HS) http://www.google.com/patents/US20020192806 2001. Thermal and fluid cycling device for nucleic acid hybridization. Inventors: Aaron Custance, Jonathan I. Parker United States Patent: US 6238910 B1, Publication Date: 29 May 2001; (HS)