Publication list on hydroshear use (to 11 January 2017) 2017
Accessing the Transcriptome: How to Normalize mRNA Pools
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Accessing the Transcriptome: How to Normalize mRNA Pools.Heiko Vogel, Christopher W. WheatMethods in Molecular Biology, 2011; 772 (Molecular Methods for Evolutionary Genetics): 105-128 Production of Fosmid Genomic Libraries Optimized for Liquid Culture Recombineering and Cross-Species Transgenesis. Radoslaw Kamil Ejsmont, Maria Bogdanzaliewa, Kamil Andrzej Lipinski, and Pavel Tomancak. Methods in Molecular Biology, 2011; 772 (Molecular Methods for Evolutionary Genetics): 423-443. NxSeq™ DNA Sample Prep Kits.Lucigen Inc., 2011; http://lucigen.com/store/docs/manuals/MA134-NxSeq-DNA-Prep-Kit.pdf2010. High divergence across the whole mitochondrial genome in the “pan-Antarctic” springtail Friesea grisea: Evidence for cryptic species? Giulia Torricelli, Antonio Carapelli, Peter Convey, Francesco Nardi, Jeffrey Boore, Francesco Frati Gene, 1 January 2010, 449(1-2): 30-40. https://www.researchgate.net/profile/Antonio_Carapelli/publication/26839579_Torricelli_G_Carapelli_A_Convey_P_Nardi_F_Boore_JL_Frati_F._High_divergence_across_the_whole_mitochondrial_genome_in_the_pan-Antarctic_springtail_Friesea_grisea_evidence_for_cryptic_species_Gene/links/552e2b1a0cf2d4950717b73f.pdf Sequence analysis of pKF3-70 in Klebsiella pneumoniae: probable origin from R100-like plasmid of Escherichia coli. Huiguang Yi, Yali Xi, Jing Liu, Junrong Wang, Jinyu Wu, Teng Xu, Wei Chen, Biaobang Chen, Meili Lin, Huan Wang, Mingming Zhou, Jinsong Li, Zuyuan Xu, Shouguang Jin, Qiyu Bao. PLoS One, 6 January 2010; 5(1): e8601, 9 pp. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008601 Comparative metagenomics and population dynamics of the gut microbiota in mother and infant. Parag A. Vaishampayan, Jennifer V. Kuehl, Jeffrey L. Froula, Jenna L. Morgan, Howard Ochman, and M. Pilar Francino. Genome Biology and Evolution, 6 January 2010; 2: 53-66. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2839348/ In vivo induced genes of mycobacterium tuberculosis. Inventor: Jeffrey D. Hillman US Patent Application: 2010/0008922 Al, Publication Date: 14 January 2010 Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species. John H. Werren, Stephen Richards, Christopher A. Desjardins, Oliver Niehuis, Jürgen Gadau, John K. Colbourne,The Nasonia Genome Working Group (Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Beukeboom LW, Desplan C, Elsik CG, Grimmelikhuijzen CJ, Kitts P, Lynch JA, Murphy T, Oliveira DC, Smith CD, van de Zande L, Worley KC, Zdobnov EM, Aerts M, Albert S, Anaya VH, Anzola JM, Barchuk AR, Behura SK, Bera AN, Berenbaum MR, Bertossa RC, Bitondi MM, Bordenstein SR, Bork P, Bornberg-Bauer E, Brunain M, Cazzamali G, Chaboub L, Chacko J, Chavez D, Childers CP, Choi JH, Clark ME, Claudianos C, Clinton RA, Cree AG, Cristino AS, Dang PM, Darby AC, de Graaf DC, Devreese B, Dinh HH, Edwards R, Elango N, Elhaik E, Ermolaeva O, Evans JD, Foret S, Fowler GR, Gerlach D, Gibson JD, Gilbert DG, Graur D, Gründer S, Hagen DE, Han Y, Hauser F, Hultmark D, Hunter HC 4th, Hurst GD, Jhangian SN, Jiang H, Johnson RM, Jones AK, Junier T, Kadowaki T, Kamping A, Kapustin Y, Kechavarzi B, Kim J, Kim J, Kiryutin B, Koevoets T, Kovar CL, Kriventseva EV, Kucharski R, Lee H, Lee SL, Lees K, Lewis LR, Loehlin DW, Logsdon JM Jr, Lopez JA, Lozado RJ, Maglott D, Maleszka R, Mayampurath A, Mazur DJ, McClure MA, Moore AD, Morgan MB, Muller J, Munoz-Torres MC, Muzny DM, Nazareth LV, Neupert S, Nguyen NB, Nunes FM, Oakeshott JG, Okwuonu GO, Pannebakker BA, Pejaver VR, Peng Z, Pratt SC, Predel R, Pu LL, Ranson H, Raychoudhury R, Rechtsteiner A, Reese JT, Reid JG, Riddle M, Robertson HM, Romero-Severson J, Rosenberg M, Sackton TB, Sattelle DB, Schlüns H, Schmitt T, Schneider M, Schüler A, Schurko AM, Shuker DM, Simões ZL, Sinha S, Smith Z, Solovyev V, Souvorov A, Springauf A, Stafflinger E, Stage DE, Stanke M, Tanaka Y, Telschow A, Trent C, Vattathil S, Verhulst EC, Viljakainen L, Wanner KW, Waterhouse RM, Whitfield JB, Wilkes TE, Williamson M, Willis JH, Wolschin F, Wyder S, Yamada T, Yi SV, Zecher CN, Zhang L, Gibbs RA.) Science, 15 January 2010; 327(5963), 343-348 U87MG Decoded: The Genomic Sequence of a Cytogenetically Aberrant Human Cancer Cell Line. Michael James Clark, Nils Homer, Brian D. O'Connor, Zugen Chen, Ascia Eskin, Hane Lee, Barry Merriman, and Stanley F. Nelson PLoS Genetics, 29 January 2010; 6(1): e1000832, 16 pp. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2813426/ Functional viral metagenomics and the next generation of molecular tools. Thomas Schoenfeld, Mark Liles, K. Eric Wommack, Shawn W Polson, Ronald Godiska, David Mead Trends in Microbiology, January 2010; 18(1): 20-29. Complete genome sequence of Anaplasma marginale subsp. centrale. David R. Herndon, Guy H. Palmer, Varda Shkap, Donald P. Knowles, and Kelly A. Brayton. Journal of Bacteriology, January 2010; 192(1): 379-380. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2798241/pdf/1330-09.pdf Complete nucleotide sequence and organization of the mitogenome of endangered Eumenis autonoe (Lepidoptera: Nymphalidae). Min Jee Kim, Xinlong Wan, Ki-Gyoung Kim, Jae Sam Hwang and Iksoo Kim African Journal of Biotechnology, 1 February 2010; 9(5): 735-754. http://www.ajol.info/index.php/ajb/article/view/78110/68497 Systematic overrepresentation of DNA termini and underrepresentation of subterminal regions among sequencing templates prepared from hydrodynamically sheared linear DNA molecules. Sherri L Schwartz, Mark L Farman BMC Genomics, 2 February 2010; 11: 87, 12 pp. http://www.biomedcentral.com/1471-2164/11/87 DNA amplification and sequencing using DNA molecules generated by random fragmentation. Inventors: Vladimir L. Makarov; Sleptsova, Irina; Kamberov, Emmanuel; Bruening, Eric United States Patent: US 7655791 B2, Publication Date: 2 February 2010 https://www.google.com/patents/US7655791 Analysis of High-Throughput Sequencing and Annotation Strategies for Phage Genomes. Matthew R. Henn, Matthew B. Sullivan, Nicole Stange-Thomann, Marcia S. Osburne, Aaron M. Berlin, Libusha Kelly, Chandri Yandava, Chinnappa Kodira, Qiandong Zeng, Michael Weiand, Todd Sparrow, Sakina Saif, Georgia Giannoukos, Sarah K. Young, Chad Nusbaum, Bruce W. Birren, and Sallie W. Chisholm PLoS One, 5 February 2010; 5(2): e9083, 12 pp. http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009083 β-Agarase isolated from Thalassomonas agarivorans, preparation process and uses thereof. Inventors: Shu-shan Liang; Chen, Yi-hong; Liaw, Li-ling United States Patent: US 7662606 B1, Publication Date: 16 February 2010 https://www.google.com/patents/US7662606 Tumor Transcriptome Sequencing Reveals Allelic Expression Imbalances Associated with Copy Number Alterations. Brian B. Tuch, Rebecca R. Laborde, Xing Xu, Jian Gu, Christina B. Chung, Cinna K. Monighetti, Sarah J. Stanley, Kerry D. Olsen, Jan L. Kasperbauer, Eric J. Moore, Adam J. Broomer, Ruoying Tan, Pius M. Brzoska, Matthew W. Muller, Asim S. Siddiqui, Yan W. Asmann, Yongming Sun, Scott Kuersten, Melissa A. Barker, Francisco M. De La Vega, and David I. Smith PLoS One, 19 February 2010; 5(2): e9317, 17 pp. http://www.readcube.com/articles/10.1371/journal.pone.0009317?locale=en Methods to stimulate biogenic methane production from hydrocarbon-bearing formations. Inventors: Gerardo Vicente Toledo; Richardson, Toby Howard; Stingl, Ulrich; Mathur, Eric J.; Venter, Craig J. US Patent Application: 2010/0047793 A1, Publication Date: 25 February 2010 Chloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes. Melvin J Oliver, Andrew G Murdock, Brent D Mishler, Jennifer V Kuehl, Jeffrey L Boore, Dina F Mandoli, Karin DE Everett, Paul G Wolf, Aaron M Duffy, Kenneth G Karol BMC Genomics, 27 February 2010, 11: 143, 8 pp. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2841679/ High-resolution mapping of the Brassica napus Rfp restorer locus using Arabidopsis-derived molecular markers. Nataša Formanová, Rachel Stollar, Rachel Geddy, Laetitia Mahé, Martin Laforest, Benoit S. Landry and Gregory G. Brown TAG Theoretical and Applied Genetics, February 2010; 120(4): 843-851. Implications of the Plastid Genome Sequence of Typha (Typhaceae, Poales) for Understanding Genome Evolution in Poaceae. Mary M. Guisinger, Timothy W. Chumley, Jennifer V. Kuehl, Jeffrey L. Boore, Robert K. Jansen Journal of Molecular Evolution, February 2010; 70(2): 149-166 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2825539/ Screening method for genes of brewing yeast. Inventors: Yoshihiro Nakao, Norihisa Nakamura, Yukiko Kodama, Tomoko Fujimura, Toshihiko Ashikari United States Patent: US 7670828 B2, Publication Date: 2 March 2010 http://www.google.com/patents/US7670828 Metagenomic Analysis of Microbial Symbionts in a Gutless Worm. Tanja Woyke, Hanno Teeling, Natalia N. Ivanova, Marcel Huntemann, Michael Richter, Frank Oliver Gloeckner, Dario Boffelli, Iain J. Anderson, Kerrie W. Barry, Harris J. Shapiro, Ernest Szeto, Nikos C. Kyrpides, Marc Mussmann, Rudolf Amann, Claudia Bergin, Caroline Ruehland, Edward M. Rubin & Nicole Dubilier
Liu Guo-Wen, Zhang Zhi-Gang, Yang Wen-Yan, Yang Lian-Yu, and Wang Zhe Bull Veterinary Institute in Pulawy, March 2010; 54(1): 15-17 http://www.piwet.pulawy.pl/bulletin/images/stories/pdf/20101/20101015018.pdf Strategy for Identification of Novel Fungal and Bacterial Glycosyl Hydrolase Hybrid Mixtures that can Efficiently Saccharify Pretreated Lignocellulosic Biomass. Dahai Gao, Shishir P. S. Chundawat, Tongjun Liu, Spencer Hermanson, Krishne Gowda, Phillip Brumm, Bruce E. Dale and Venkatesh Balan BioEnergy Research, March 2010; 3(1): 67-81 https://www.researchgate.net/profile/Tongjun_Liu/publication/225758456_Strategy_for_Identification_of_Novel_Fungal_and_Bacterial_Glycosyl_Hydrolase_Hybrid_Mixtures_that_can_Efficiently_Saccharify_Pretreated_Lignocellulosic_Biomass/links/0c960529cb52e74693000000.pdf National laboratory for scientific computation - LNCC, Laboratory for Bioinformatics Ana Tereza Vasconcelos. EMBNet.news, March 2010; 15(4): 25-28 http://www.no.embnet.org/embnet_news_15_4-high.pdf Methods for Detection of Methyl-CpG Dinucleotides. Inventor: John J. Dunn US Patent Application: 2010/0081174 A1, Publication Date: 1 April 2010 Sequencing and Genetic Variation of Multidrug Resistance Plasmids in Klebsiella pneumoniae. Fangqing Zhao, Jie Bai, Jinyu Wu, Jing Liu, Mingming Zhou, Shilin Xia, Shanjin Wang, Xiaoding Yao, Huiguang Yi, Meili Lin, Shengjie Gao, Tieli Zhou, Zuyuan Xu, Yuxin Niu, and Qiyu Bao PLoS One, 12 April 2010; 5(4): e10141, 9 pp. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2853573/ Helicase-assisted sequencing with molecular beacons. Inventor: Adrian Fehr U.S. Patent Application: 2010/0092960 A1, Publication Date: 15 April 2010; https://www.google.com/patents/US20100092960 Metagenomic Sequencing of an In Vitro-Simulated Microbial Community. Jenna L. Morgan, Aaron E. Darling, Jonathan A. Eisen PLoS One, 16 April 2010; 5(4): e10209, 10 pp. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2855710/ Using comparative genomic hybridization to survey genomic sequence divergence across species: a proof-of-concept from Drosophila. Suzy CP Renn, Heather E Machado, Albyn Jones, Kosha Soneji, Rob J Kulathinal, Hans A Hofmann BMC Genomics, 29 April 2010; 11: 271, 12 pp. http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-11-271 Linear plasmid vector for cloning of repetitive or unstable sequences in Escherichia coli. Ronald Godiska, David Mead, Vinay Dhodda, Chengcang Wu, Rebecca Hochstein, Attila Karsi, Karen Usdin, Ali Entezam and Nikolai Ravin Nucleic Acids Research, April 2010; 38(6): e88, 9 pp. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847241/ Brazilian EMBnet Node: progress Report Ana Tereza Vasconcelos, Wim M. Degrave, Goran Neshich EMBnet.news, April 2010; 15(4): 25-31 http://journal.embnet.org/index.php/embnetnews/article/view/76/178 Comprehensive High-Throughput Arrays for Relative Methylation (CHARM) Christine Ladd-Acosta, Martin J. Aryee, Jared M. Ordway, Andrew P. Feinberg Current Protocols Human Genetics, April 2010; John Wiley & Sons, Inc., 65:20.0.1-20.0.19. (HS+) Applied Biosystems SOLiD™ 4 System. Library Preparation Guide ABI Manual. April 2010.
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