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Tag oligonucleotide [56 articles]

Recent papers classified by the tag oligonucleotide.
  • Quantifying DNA-protein binding specificities by using oligonucleotide mass tags and mass spectroscopy
    PNAS, Vol. 104, No. 9. (27 February 2007), pp. 3061-3066.
    by Lingang Zhang, Simon Kasif, And C Cantor
    posted to protein oligonucleotide massspectrometry dna by zwang on 2007-04-23 04:03:20 as ** along with 2 people and 1 group guhjy cwbrown EisenLab
  • Investigations of Oligonucleotide Usage Variance Within and Between Prokaryotes
    PLoS Comput Biol, Vol. 4, No. 4. (18 April 2008), e1000057.
    by Jon Bohlin, Eystein Skjerve, David W Ussery
    posted to prokaryote oligonucleotide gc compoosition by treangen on 2008-11-26 13:16:27 as ** along with 2 people and 2 groups djkt jlgreen iSEEM Green Lab
  • Specific and non specific hybridization of oligonucleotide probes on microarrays
    Biophys. J. (15 April 2005), biophysj.104.055343.
    by Hans Binder, Stephan Preibisch
    posted to microarray oligonucleotide signal-intensity by niallhaslam on 2007-10-03 15:31:54 as ***** along with 1 person ptrobajo
  • Primer design for multiplexed genotyping.
    Methods Mol Biol, Vol. 402 (2007), pp. 269-286.
    by L Kaderali
    posted to microarray oligonucleotide primer-design resequencing sequencing design by niallhaslam on 2007-10-25 09:17:10 as ****
  • OligoCalc: an online oligonucleotide properties calculator.
    Nucleic Acids Res, Vol. 35, No. Web Server issue. (1 July 2007)
    by WA Kibbe
    posted to melting microarray oligonucleotide temperature by niallhaslam on 2007-08-21 13:01:50 as ** along with 2 people guhjy austin
  • Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Agnes Baross, Allen Delaney, Irene H Li, Tarun Nayar, Stephane Flibotte, Hong Qian, Susanna Chan, Jennifer Asano, Adrian Ally, Manqiu Cao, Patricia Birch, Mabel B John, Nicole Fernandes, Anne Go, Giulia Kennedy, Sylvie Langlois, Patrice Eydoux, J Friedman, Marco Marra
    posted to microarray oligonucleotide by niallhaslam on 2007-10-03 14:46:54 as *** along with 1 person jfr
  • Filtering genes to improve sensitivity in oligonucleotide microarray data analysis.
    Nucleic Acids Res (15 August 2007)
    by Stefano Calza, Wolfgang Raffelsberger, Alexander Ploner, Jose Sahel, Thierry Leveillard, Yudi Pawitan
    posted to microarray oligonucleotide by niallhaslam on 2007-08-21 13:00:28 as ** along with 7 people heliopais frohike guhjy jfr rdiaz waszak laral
  • A semi-rational design strategy of directed evolution combined with chemical synthesis of DNA sequences.
    Biol Chem, Vol. 388, No. 12. (December 2007), pp. 1291-1300.
    by AS Xiong, RH Peng, J Zhuang, JG Liu, F Gao, F Xu, B Cai, QH Yao
    posted to design microarray oligonucleotide resequencing resistance sequencing by niallhaslam on 2008-02-14 10:45:34 as **
  • Extending microarray quality control and analysis algorithms to illumina chip platform.
    Conf Proc IEEE Eng Med Biol Soc, Vol. 1 (2007), pp. 4637-4640.
    by TH Stokes, X Han, RA Moffitt, MD Wang
    posted to affymetrix hybridisation illumina microarray oligonucleotide primer-design signal-intensity temperature thermodynamics by niallhaslam on 2007-11-29 10:31:45 as *** along with 1 person flexer
  • A general framework for designing and validating oligomer-based DNA microarrays and its application to Clostridium acetobutylicum.
    Appl Environ Microbiol, Vol. 73, No. 14. (July 2007), pp. 4631-4638.
    by CJ Paredes, RS Senger, IS Spath, JR Borden, R Sillers, ET Papoutsakis
    posted to hybridisation microarray oligonucleotide by niallhaslam on 2007-10-02 10:16:41 as ***
  • Oligonucleotide microarrays: widely applied poorly understood
    Brief Funct Genomic Proteomic, Vol. 6, No. 2. (1 June 2007), pp. 141-148.
    by Alex E Pozhitkov, Diethard Tautz, Peter A Noble
    posted to microarray oligonucleotide signal-intensity by niallhaslam on 2007-10-03 13:34:08 as ***** along with 1 person jfr
  • Primique: automatic design of specific PCR primers for each sequence in a family
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Jakob Fredslund, Mette Lange
    posted to microarray oligonucleotide primer-design by niallhaslam on 2007-10-03 14:47:45 as *** along with 1 person guhjy
  • Improving comparability between microarray probe signals by thermodynamic intensity correction.
    Nucleic Acids Res (2 March 2007)
    by Georg M M Bruun, Rasmus Wernersson, Agnieszka S S Juncker, Hanni Willenbrock, Henrik Bjørn B Nielsen
    posted to microarray oligonucleotide signal-intensity by niallhaslam on 2007-10-03 13:48:54 as ***** along with 5 people guhjy ghattem GeeSharpMinor talponer waszak
  • An algorithm and program for finding sequence specific oligonucleotide probes for species identification.
    BMC Bioinformatics, Vol. 3 (2002)
    by AE Pozhitkov, D Tautz
    posted to microarray oligonucleotide by niallhaslam on 2007-10-03 13:35:16 as ***
  • Probe selection for DNA microarrays using OligoWiz.
    Nat Protoc, Vol. 2, No. 11. (2007), pp. 2677-2691.
    by R Wernersson, AS Juncker, HB Nielsen
    posted to microarray oligonucleotide probe-design probe-selection signal-intensity by niallhaslam on 2007-11-29 10:33:36 as ***
  • Thermodynamic Behavior of Short Oligonucleotides in Microarray Hybridizations Can Be Described Using Gibbs Free Energy in a Nearest-Neighbor Model.
    J Phys Chem B (10 November 2007)
    by Stefan Weckx, Enrico Carlon, Luc D Vuyst, Paul V Hummelen
    posted to affymetrix design melting oligonucleotide sequencing short-read signal-intensity temperature thermodynamics by niallhaslam on 2007-11-29 10:28:54 as ***
  • Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification.
    Nucleic Acids Res (7 August 2007)
    by Thomas E E Royce, Joel S S Rozowsky, Mark B B Gerstein
    posted to design microarray oligonucleotide universal by niallhaslam on 2007-09-03 13:20:38 as ***** along with 4 people bertelsen GeeSharpMinor jfr sebastien_vigneau
  • Microarray-based DNA resequencing using 3' blocked primers.
    Anal Biochem (4 November 2007)
    by Jakub Sram, Steve S S Sommer, Qiang Liu
    posted to design microarray oligonucleotide resequencing by niallhaslam on 2007-12-03 10:17:56 as **** along with 1 person guhjy
  • Short oligonucleotide probes containing G-stacks display abnormal binding affinity on Affymetrix microarrays
    Bioinformatics, Vol. 23, No. 19. (1 October 2007), pp. 2566-2572.
    by Chunlei Wu, Haitao Zhao, Keith Baggerly, Roberto Carta, Li Zhang
    posted to interactions microarray oligonucleotide short-read signal-intensity by niallhaslam on 2007-11-12 09:59:53 as **** along with 1 person jfr
  • Characterization of Mismatch and High-signal Intensity Probes Associated with Affymetrix Genechips.
    Bioinformatics (6 June 2007)
    by Yonghong Wang, Ze-Hong H Miao, Yves Pommier, Ernest S S Kawasaki, Audrey Player
    posted to hybridisation melting microarray oligonucleotide resequencing sequencing signal-intensity by niallhaslam on 2007-09-11 11:17:16 as ***** along with 2 people ghattem bertelsen
  • Analysis of probe level patterns in Affymetrix microarray data
    BMC Bioinformatics, Vol. 8 (04 May 2007), 146.
    by Alexander C Cambon, Abdelnaby Khalyfa, Nigel GF Cooper, Caryn M Thompson
    posted to microarray oligonucleotide signal-intensity by niallhaslam on 2007-10-03 13:48:36 as ***** along with 4 people jfr ghattem bertelsen ptrobajo
  • Novel method for immobilization of enzymes to magnetic nanoparticles
    Journal of Nanoparticle Research, Vol. 10, No. 6. (2008), pp. 1009-1025.
    by Andrew Johnson, Anna Zawadzka, Lee Deobald, Ronald Crawford, Andrzej Paszczynski
    posted to enzyme iron-oxide-affinity-peptide oligonucleotide scanning-electron-microscopy silica-affinity-peptide silica-coat superparamagnetic-iron-oxide-nanoparticle by ml115 on 2008-08-08 21:05:28 as **
  • Molecular biomarkers of oxidative stress associated with bromate carcinogenicity.
    Toxicology, Vol. 221, No. 2-3. (17 April 2006), pp. 158-165.
    by D Delker, G Hatch, J Allen, B Crissman, M George, D Geter, S Kilburn, T Moore, G Nelson, B Roop, R Slade, A Swank, W Ward, A DeAngelo
    posted to analysis array bromates carcinogens oligonucleotide potassiumbromate sequence by medref2 on 2008-04-07 16:10:24 as read
  • In silico microarray probe design for diagnosis of multiple pathogens
    BMC Genomics, Vol. 9 (21 October 2008), 496.
    by Ravi V Satya, Nela Zavaljevski, Kamal Kumar, Elizabeth Bode, Susana Padilla, Leonard Wasieloski, Jeanne Geyer, Jaques Reifman
    posted to oligonucleotide microarray kumar kamal fingerprint dna diagnostic bioinformatics bioanalysis bhsai assay by kamalkumar on 2008-11-14 15:30:58 as read
  • SELEX--a (r)evolutionary method to generate high-affinity nucleic acid ligands.
    Biomol Eng, Vol. 24, No. 4. (October 2007), pp. 381-403.
    by R Stoltenburg, C Reinemann, B Strehlitz
    posted to affinity aptamer dna evolution ligands molecular oligonucleotide polymerase protein proteomics research rna science selection selex by jonathanjacobs on 2008-05-14 18:48:28 as read along with 2 people erdos guhjy
  • Diversity of Oligonucleotide Functions
    Annual Review of Biochemistry, Vol. 64, No. 1. (1995), pp. 763-797.
    by L Gold, B Polisky, O Uhlenbeck, M Yarus
    posted to dna ligands oligonucleotide protein rna selex structure by jonathanjacobs on 2008-06-23 16:20:18 as **
  • BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis.
    Bioinformatics, Vol. 21, No. 16. (15 August 2005), pp. 3439-3440.
    by S Durinck, Y Moreau, A Kasprzyk, S Davis, B De Moor, A Brazma, W Huber
    posted to algorithms analysis and array database databases expression gene information integration management oligonucleotide profiling protein retrieval sequence software storage systems by incovoma on 2007-07-13 12:56:37 as ** along with 3 people kshameer dullhunk fisherp
  • Reliable gene signatures for microarray classification: assessment of stability and performance.
    Bioinformatics (31 July 2006)
    by Chad A A Davis, Fabian Gerick, Volker Hintermair, Caroline C C Friedel, Katrin Fundel, Robert Küffner, Ralf Zimmer
    posted to algorithms analysis and array biological cartilage computer expression gene humans markers models neoplasms of oligonucleotide osteoarthritis profiling proteins reproducibility results sensitivity sequence simulation specificity statistical by incovoma on 2007-07-13 11:42:45 as ** along with 5 people jfr chad_davis rdiaz efge ptrobajo
  • High density synthetic oligonucleotide arrays.
    Nat Genet, Vol. 21, No. 1 Suppl. (January 1999), pp. 20-24.
    by RJ Lipshutz, SP Fodor, TR Gingeras, DJ Lockhart
    posted to affymetrix chips gene oligonucleotide by incovoma on 2007-08-31 11:06:36 as ** along with 2 people and 1 group jeremymiller shikin GeschwindLab
  • Linking microarray data to the literature.
    Nat Genet, Vol. 28, No. 1. (May 2001), pp. 9-10.
    by DR Masys
    posted to analysis array bibliographic collection controlled data databases expression gene genes medline mining oligonucleotide profiling sequence software text vocabulary by incovoma on 2007-07-31 10:35:10 as **
  • Monitoring gene expression changes in bovine oviduct epithelial cells during the oestrous cycle.
    J Mol Endocrinol, Vol. 32, No. 2. (April 2004), pp. 449-466.
    by S Bauersachs, S Rehfeld, SE Ulbrich, S Mallok, K Prelle, H Wenigerkind, R Einspanier, H Blum, E Wolf
    posted to analysis animals array cattle cells chain cycle epithelial estrous expression fallopian female gene oligonucleotide polymerase profiling reaction regulation reverse sequence transcriptase tubes by incovoma on 2007-07-13 10:48:37 as **
  • Significance analysis of microarrays applied to the ionizing radiation response.
    Proc Natl Acad Sci U S A, Vol. 98, No. 9. (24 April 2001), pp. 5116-5121.
    by VG Tusher, R Tibshirani, G Chu
    posted to analysis apoptosis array cell cells cultured cycle damage dna down-regulation expression gene humans ionizing messenger of oligonucleotide profiling radiation regulation repair reproducibility results rna sam sequence statistics tumor up-regulation by incovoma on 2007-07-13 11:14:31 as ** along with 13 people ihpark bassene frohike paszkows miguel jen_drake gpalidwor olympos ccr ugengma shikin askrajiv renatomilani
  • Gene expression profiling of bovine endometrium during the oestrous cycle: detection of molecular pathways involved in functional changes
    J Mol Endocrinol, Vol. 34, No. 3. (1 June 2005), pp. 889-908.
    by S Bauersachs, SE Ulbrich, K Gross, SEM Schmidt, HHD Meyer, R Einspanier, H Wenigerkind, M Vermehren, H Blum, F Sinowatz, E Wolf
    posted to analysis animals array base cattle chain dna endometrium estrus expression female gene hybridization in oligonucleotide polymerase primers profiling reaction reverse sequence situ transcriptase by incovoma on 2007-07-13 10:42:06 as ** along with 1 person brmun
  • Embryo-induced transcriptome changes in bovine endometrium reveal species-specific and common molecular markers of uterine receptivity.
    Reproduction, Vol. 132, No. 2. (August 2006), pp. 319-331.
    by S Bauersachs, SE Ulbrich, K Gross, SE Schmidt, HH Meyer, H Wenigerkind, M Vermehren, F Sinowatz, H Blum, E Wolf
    posted to analysis animals array cattle chain embryo endometrium expression factor female gene genetic humans hybridization implantation in messenger mice oligonucleotide polymerase pregnancy primates profiling reaction regulation reverse rna sequence sheep situ stat1 transcriptase transcription by incovoma on 2007-07-13 10:45:08 as ** along with 1 person endo_anaphy
  • Statistical significance for genomewide studies.
    Proc Natl Acad Sci U S A, Vol. 100, No. 16. (5 August 2003), pp. 9440-9445.
    by JD Storey, R Tibshirani
    posted to algorithms alternative analysis animals array binding exons expression gene genetic genetics genome humans linkage oligonucleotide regulation sam sequence sites splicing statistics techniques transcription by incovoma on 2007-07-13 11:10:40 as ** along with 26 people and 2 groups daforerog treangen druvus vertikalist maximilianh diging_data egreenfest guhjy textoris RMGraze jen_drake hggr frohike schuylrp grahamc kynn sancho 7ofAnn nicholso shikin wirawan BrianTomasik roys sconlan zhouyu bpcusack BTS-PT-AS-CS Bioinformatics
  • Use of keyword hierarchies to interpret gene expression patterns.
    Bioinformatics, Vol. 17, No. 4. (April 2001), pp. 319-326.
    by DR Masys, JB Welsh, J Lynn Fink, M Gribskov, I Klacansky, J Corbeil
    posted to abstracting analysis and array databases expression factual gene indexing information medline mining oligonucleotide profiling retrieval sequence storage text by incovoma on 2007-07-31 10:38:38 as ** along with 2 people and 2 groups irenas yas dbk-lab T_lab
  • Mining microarray expression data by literature profiling.
    Genome Biol, Vol. 3, No. 10. (13 September 2002)
    by D Chaussabel, A Sher
    posted to analysis array biology cluster computational databases expression factual family gene genes genetic humans information internet multigene oligonucleotide profiling science sequence by incovoma on 2007-07-31 10:49:56 as **
  • Considerations when using the significance analysis of microarrays (SAM) algorithm.
    BMC Bioinformatics, Vol. 6 (2005)
    by O Larsson, C Wahlestedt, JA Timmons
    posted to adult aged algorithms analysis array automated biology computational data design expression gene genetic humans interpretation microarray middle models muscle oligonucleotide pattern phenotype profiling recognition research sequence skeletal software statistics by incovoma on 2007-07-13 11:05:36 as ** along with 2 people GeeSharpMinor renatomilani
  • Expression profiling using cDNA microarrays.
    Nat Genet, Vol. 21, No. 1 Suppl. (January 1999), pp. 10-14.
    by DJ Duggan, M Bittner, Y Chen, P Meltzer, JM Trent
    posted to analysis animals array complementary computer-assisted databases dna expressed expression factual gene humans image molecular oligonucleotide probe processing sequence tags techniques by incovoma on 2007-07-13 10:54:05 as ** along with 1 person leelarcombe
  • Oligonucleotide probes for the identification of three algal groups by dot blot and fluorescent whole-cell hybridization.
    J Eukaryot Microbiol, Vol. 47, No. 1. (b 2000), pp. 76-84.
    by N Simon, L Campbell, E Ornolfsdottir, R Groben, L Guillou, M Lange, LK Medlin
    posted to fish haptophyta oligonucleotide probe by Fabnot on 2007-02-15 20:40:31 as read
  • Selection of antisense oligonucleotides based on multiple predicted target mRNA structures.
    BMC Bioinformatics, Vol. 7, No. 1. (9 March 2006)
    by Xiaochen Bo, Shaoke Lou, Daochun Sun, Wenjie Shu, Jing Yang, Shengqi Wang
    posted to antisense design oligonucleotide by eckart_bindewald on 2006-03-13 19:01:16 as **
  • A general approach for the use of oligonucleotide effectors to regulate the catalysis of RNA-cleaving ribozymes and DNAzymes
    Nucl. Acids Res., Vol. 30, No. 8. (15 April 2002), pp. 1735-1742.
    by Dennis Y Wang, Beatrice H Lai, Anat R Feldman, Dipankar Sen
    posted to aptamer catalysis dna dnazyme effector oligonucleotide ribozyme rna by eckart_bindewald on 2007-11-06 16:20:55 as ***
  • Experimental analysis of oligonucleotide microarray design criteria to detect deletions by comparative genomic hybridization
    BMC Genomics, Vol. 9 (21 October 2008), 497.
    by Stephane Flibotte, Donald G Moerman
    posted to oligonucleotide microarray design deletions cgh analysis by dswan on 2008-11-17 10:36:25 as ** along with 2 people druvus natstreet
  • Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection
    PNAS, Vol. 98, No. 1. (2 January 2001), pp. 31-36.
    by Cheng Li, Wing H Wong
    posted to expression index microarray model oligonucleotide by bertelsen on 2008-04-28 22:28:27 as **** along with 1 person RMGraze
  • Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays
    BMC Bioinformatics, Vol. 8 (29 March 2007), 108.
    by Jun Lu, Joseph C Lee, Marc L Salit, Margaret C Cam
    posted to annotation high-resolution microarray oligonucleotide probe transcript by bertelsen on 2008-04-28 22:15:44 as read along with 5 people and 1 group heliopais guhjy jfr frohike ghattem Bioinformatics
  • Free energy of DNA duplex formation on short oligonucleotide microarrays
    Nucleic Acids Research, Vol. 35, No. 3. (February 2007), pp. e18-e18.
    by Zhang, Li, Wu, Chunlei, Carta, Roberto, Zhao, Haitao
    posted to hybridization microarray oligonucleotide by bertelsen on 2008-04-29 08:09:33 as **** along with 1 person stsaft
  • A model of molecular interactions on short oligonucleotide microarrays.
    Nat Biotechnol, Vol. 21, No. 7. (July 2003), pp. 818-821.
    by L Zhang, MF Miles, KD Aldape
    posted to interactions microarray model molecular oligonucleotide by bertelsen on 2008-04-29 10:13:20 as **** along with 3 people caseybrown nicholso talponer
  • Sequence dependence of cross-hybridization on short oligo microarrays
    Nucleic Acids Research, Vol. 33, No. 9. (2005), pp. e84-e84.
    by Chunlei Wu, Roberto Carta, Li Zhang
    posted to cross-hybridization dependence microarray oligonucleotide sequence by bertelsen on 2008-04-28 23:34:36 as ****
  • Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application
    Genome Biology, Vol. 2, No. 8. (2001), pp. research0032.1-research0032.11.
    by Cheng Li, Wing H Wong
    posted to array design mbei microarray model oligonucleotide by bertelsen on 2008-03-14 15:58:50 as **** along with 3 people and 1 group RMGraze fisherp jeremymiller GeschwindLab
  • A Model-Based Background Adjustment for Oligonucleotide Expression Arrays
    Journal of the American Statistical Association, Vol. 99, No. 468., 909.
    by Zhijin Wu, Rafael A Irizarry, Robert Gentleman, Francisco Martinez-Murillo, Forrest Spencer
    posted to adjustment array background expression microarray model oligonucleotide by bertelsen on 2008-04-28 22:44:55 as *** along with 5 people GeeSharpMinor RMGraze thomlo nicholso jo_davies
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