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jfr annotation [42 articles]

Recent papers added to jfr library classified by the tag annotation. You can also see everyone's annotation.
  • Integrating biological data - the Distributed Annotation System
    BMC Bioinformatics, Vol. 9, No. Suppl 8. (2008)
    by Andrew Jenkinson, Mario Albrecht, Ewan Birney, Hagen Blankenburg, Thomas Down, Robert Finn, Henning Hermjakob, Tim Hubbard, Rafael Jimenez, Philip Jones, Andreas Kahari, Eugene Kulesha, Jose Macias, Gabrielle Reeves, Andreas Prlic
    posted to software integration annotation by jfr on 2008-10-08 15:11:26 as ** along with 4 people jyuh chad_davis aconesa djkt
  • Use and misuse of the gene ontology annotations.
    Nature reviews. Genetics (13 May 2008)
    by Seung Yon Rhee, Valerie Wood, Kara Dolinski, Sorin Draghici
    posted to gene_ontology annotation by jfr on 2008-09-24 14:08:40 as ** along with 21 people and 2 groups djkt jyuh aheilbut mariakmejia cmzmasek A_Olympia realzhang carlk roys gjuggler fpattyn RamuAnandakrishnan ptrobajo giovenko cabbagesofdoom tmmurali renatomilani capitall marck rvosa bpcusack logics of knowledge FAB-lab
  • The "street light syndrome", or how protein taxonomy can bias experimental manipulations.
    BioEssays : news and reviews in molecular, cellular and developmental biology, Vol. 30, No. 4. (April 2008), pp. 349-357.
    by G Markov, G Lecointre, B Demeneix, V Laudet
    posted to genomics annotation by jfr on 2008-09-15 10:24:33 as **
  • Calling on a million minds for community annotation in WikiProteins
    Genome Biology, Vol. 9, No. 5. (2008)
    by Barend Mons, Michael Ashburner, Christine Chichester, Erik van Mulligen, Marc Weeber, Johan den Dunnen, Gert J van Ommen, Mark Musen, Matthew Cockerill, Henning Hermjakob, Albert Mons, Abel Packer, Roberto Pacheco, Suzanna Lewis, Alfred Berkeley, William Melton, Nickolas Barris, Jimmy Wales, Gerard Meijssen, Erik Moeller, Peter Roes, Katy Borner, Amos Bairoch
    posted to software proteomics annotation by jfr on 2008-09-05 13:35:59 as ** along with 17 people and 1 group yas AlexanderPico thomaskelder dullhunk tharris renatomilani neils chad_davis fpattyn sjc Katje jamselem ChrisEvelo carlk jyuh xingxu rholz microbiology_nijmegen
  • Lightweight Genome Viewer: portable software for browsing genomics data in its chromosomal context
    BMC Bioinformatics, Vol. 8 (18 September 2007), 344.
    by Jeremiah J Faith, Andrew J Olson, Timothy S Gardner, Ravi Sachidanandam
    posted to annotation bioinformatics genome_browser software by jfr on 2008-05-16 10:09:05 as * along with 1 person jyuh
  • Human Proteinpedia enables sharing of human protein data
    Nature Biotechnology, Vol. 26, No. 2., pp. 164-167.
    by Suresh Mathivanan, Mukhtar Ahmed, Natalie G Ahn, Hainard Alexandre, Ramars Amanchy, Philip C Andrews, Joel S Bader, Brian M Balgley, Marcus Bantscheff, Keiryn L Bennett, Erik Björling, Blagoy Blagoev, Ron Bose, Samir K Brahmachari, Alma S Burlingame, Xosé R Bustelo, Gerard Cagney, Greg T Cantin, Helene L Cardasis, Julio E Celis, Raghothama Chaerkady, Feixia Chu, Philip A Cole, Catherine E Costello, Robert J Cotter, David Crockett, James P Delany, Angelo M De Marzo, Leroi V Desouza, Eric W Deutsch, Eric Dransfield, Gerard Drewes, Arnaud Droit, Michael J Dunn, Kojo Elenitoba-Johnson, Rob M Ewing, Jennifer Van Eyk, Vitor Faca, Jayson Falkner, Xiangming Fang, Catherine Fenselau, Daniel Figeys, Pierre Gagné, Cecilia Gelfi, Kris Gevaert, Jeffrey M Gimble, Florian Gnad, Renu Goel, Pavel Gromov, Samir M Hanash, William S Hancock, HC Harsha, Gerald Hart, Faith Hays, Fuchu He, Prashantha Hebbar, Kenny Helsens, Heiko Hermeking, Winston Hide, Karin Hjernø, Denis F Hochstrasser, Oliver Hofmann, David M Horn, Ralph H Hruban, Nieves Ibarrola, Peter James, Ole N Jensen, Pia H Jensen, Peter Jung, Kumaran Kandasamy, Indu Kheterpal, Reiko F Kikuno, Ulrike Korf, Roman Körner, Bernhard Kuster, Min-Seok Kwon, Hyoung-Joo Lee, Young-Jin Lee, Michael Lefevre, Minna Lehvaslaiho, Pierre Lescuyer, Fredrik Levander, Megan S Lim, Christian Löbke, Joseph A Loo, Matthias Mann, Lennart Martens, Juan Martinez-Heredia, Mark Mccomb, James Mcredmond, Alexander Mehrle, Rajasree Menon, Christine A Miller, Harald Mischak, Sujatha S Mohan, Riaz Mohmood, Henrik Molina, Michael F Moran, James D Morgan, Robert Moritz, Martine Morzel, David C Muddiman, Anuradha Nalli, Daniel J Navarro, Thomas A Neubert, Osamu Ohara, Rafael Oliva, Gilbert S Omenn, Masaaki Oyama, Young-Ki Paik, Kyla Pennington, Rainer Pepperkok, Balamurugan Periaswamy, Emanuel F Petricoin, Guy G Poirier, Keshava TS Prasad, Samuel O Purvine, Abdul B Rahiman, Prasanna Ramachandran, YL Ramachandra, Robert H Rice, Jens Rick, Ragna H Ronnholm, Johanna Salonen, Jean-Charles Sanchez, Thierry Sayd, Beerelli Seshi, Kripa Shankari, Shi J Sheng, Vivekananda Shetty, K Shivakumar, Richard J Simpson, Ravi Sirdeshmukh, Michael KW Siu, Jeffrey C Smith, Richard D Smith, David J States, Sumio Sugano, Matthew Sullivan, Giulio Superti-Furga, Maarit Takatalo, Visith Thongboonkerd, Jonathan C Trinidad, Mathias Uhlen, Joël Vandekerckhove, Julian Vasilescu, Timothy D Veenstra, José-Manuel Vidal-Taboada, Mauno Vihinen, Robin Wait, Xiaoyue Wang, Stefan Wiemann, Billy Wu, Tao Xu, John R Yates, Jun Zhong, Ming Zhou, Yunping Zhu, Petra Zurbig, Akhilesh Pandey
    posted to annotation database protein_interaction proteomics resource by jfr on 2008-04-30 16:55:49 as read along with 5 people jyuh tmmurali dullhunk jdiezperezj drbal
  • Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases
    BMC Bioinformatics, Vol. 8 (04 October 2007), 372.
    by Seth I Berger, Jeremy M Posner, Avi Ma'ayan
    posted to annotation network software by jfr on 2008-04-09 15:29:32 as ** along with 2 people and 1 group jyuh shikin GeneGo
  • Novel definition files for human GeneChips based on GeneAnnot
    BMC Bioinformatics, Vol. 8 (15 November 2007), 446.
    by Francesco Ferrari, Stefania Bortoluzzi, Alessandro Coppe, Alexandra Sirota, Marilyn Safran, Michael Shmoish, Sergio Ferrari, Doron Lancet, Gian A Danieli, Silvio Bicciato
    posted to affy annotation software by jfr on 2008-03-17 15:20:14 as ** along with 2 people giovenko ghattem
  • A detailed transcript-level probe annotation reveals alternative splicing based microarray platform differences
    BMC Genomics, Vol. 8 (20 August 2007), 284.
    by Joseph C Lee, David Stiles, Jun Lu, Margaret C Cam
    posted to affy alternative_splicing annotation by jfr on 2008-02-19 16:28:14 as *** along with 1 person heliopais
  • AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets.
    Bioinformatics (27 July 2007)
    by Hongfang Liu, Barry R R Zeeberg, Qu Gang, A Gunes G Koru, Alessandro Ferrucci, Ari Kahn, Michael C C Ryan, Antej Nuhanovic, Peter J J Munson, William C C Reinhold, David W W Kane, John N N Weinstein
    posted to affy annotation by jfr on 2008-02-04 11:58:07 as read along with 7 people giovenko jyuh ghattem ryanraaum heliopais Montrachet bertelsen
  • DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis
    BMC Bioinformatics, Vol. 8 (02 November 2007), 426.
    by Brad T Sherman, Da W Huang, Qina Tan, Yongjian Guo, Stephan Bour, David Liu, Robert Stephens, Michael W Baseler, Clifford H Lane, Richard A Lempicki
    posted to annotation database functional_analysis by jfr on 2008-02-04 10:52:19 as read along with 4 people and 1 group jyuh ealloza barriot hpaces BioinfoCIPF
  • 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 affy annotation low_level by jfr on 2008-01-24 17:16:35 as ** along with 4 people ghattem niallhaslam bertelsen ptrobajo
  • AILUN: reannotating gene expression data automatically
    Nat Meth, Vol. 4, No. 11. (November 2007), pp. 879-879.
    by Rong Chen, Li Li, Atul J Butte
    posted to annotation database by jfr on 2007-12-18 13:04:22 as read along with 3 people and 1 group tmmurali incovoma jyuh csb_journal_club_public
  • DAVID Gene Functional Classification Tool: A novel biological module-centric algorithm to functionally analyze large gene list
    Genome Biology, Vol. 8 (04 September 2007), R183.
    by Da W Huang, Brad T Sherman, Qina Tan, Jack R Collins, Gregory W Alvord, Jean Roayaei, Robert Stephens, Michael W Baseler, Clifford H Lane, Richard A Lempicki
    posted to annotation database functional_classification by jfr on 2007-12-07 14:44:02 as read along with 7 people ndiaz jyuh aalibes dragonrez rdiaz mellabee heliopais
  • A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array
    Nucleic Acids Research, Vol. 33, No. 3. (2005), pp. e31-e31.
    by Jeremy Harbig, Robert Sprinkle, Steven A Enkemann
    posted to affy annotation by jfr on 2007-12-03 11:04:09 as read along with 3 people incovoma heliopais bertelsen
  • Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data
    BMC Bioinformatics, Vol. 8 (11 June 2007), 194.
    by Hui Yu, Feng Wang, Kang Tu, Lu Xie, Yuan-Yuan Li, Yi-Xue Li
    posted to affy annotation by jfr on 2007-11-28 13:13:39 as * along with 3 people jyuh heliopais bertelsen
  • nuID: A universal naming schema of oligonucleotides for Illumina, Affymetrix, and other microarrays
    Biology Direct, Vol. 2 (31 May 2007), 16.
    by Pan Du, Warren A Kibbe, Simon M Lin
    posted to annotation software by jfr on 2007-11-28 12:04:04 as ** along with 2 people heliopais jyuh
  • GOSim - An R-package for computation of information theoretic GO similarities between terms and gene products
    BMC Bioinformatics, Vol. 8 (22 May 2007), 166.
    by Holger Froehlich, Nora Speer, Annemarie Poustka, Tim Beissbarth
    posted to annotation go software by jfr on 2007-11-27 13:30:43 as ** along with 4 people jyuh macavity1g sgoetz RamuAnandakrishnan
  • 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 affy annotation by jfr on 2007-09-12 17:54:41 as **** along with 5 people and 1 group heliopais jyuh frohike ghattem bertelsen Bioinformatics
  • DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists.
    Nucleic Acids Res, Vol. 35, No. Web Server issue. (1 July 2007)
    by da W Huang, BT Sherman, Q Tan, J Kir, D Liu, D Bryant, Y Guo, R Stephens, MW Baseler, HC Lane, RA Lempicki
    posted to annotation bioinformatics by jfr on 2007-08-02 14:11:35 as read along with 1 person jyuh
  • From genes to functional classes in the study of biological systems
    BMC Bioinformatics, Vol. 8 (03 April 2007), 114.
    by Fatima Al-Shahrour, Leonardo Arbiza, Hernan Dopazo, Jaime Huerta-Cepas, Pablo Minguez, David Montaner, Joaquin Dopazo
    posted to annotation by jfr on 2007-07-23 19:09:59 as ** along with 6 people and 1 group Sharpshoot ealloza ajw Garamonfok djkt sgoetz BioinfoCIPF
  • Probe selection for high-density oligonucleotide arrays.
    Proc Natl Acad Sci U S A, Vol. 100, No. 20. (30 September 2003), pp. 11237-11242.
    by R Mei, E Hubbell, S Bekiranov, M Mittmann, FC Christians, MM Shen, G Lu, J Fang, WM Liu, T Ryder, P Kaplan, D Kulp, TA Webster
    posted to affy annotation probe_design by jfr on 2007-07-20 17:17:06 as **
  • A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat
    BMC Bioinformatics, Vol. 8 (20 April 2007), 132.
    by Rudi Alberts, Peter Terpstra, Menno Hardonk, Leonid V Bystrykh, Gerald de Haan, Rainer Breitling, Jan-Peter Nap, Ritsert C Jansen
    posted to affy annotation by jfr on 2007-07-19 14:37:31 as ** along with 2 people jyuh ghattem
  • FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.
    Nucleic Acids Res (3 May 2007)
    by Fátima Al-Shahrour, Pablo Minguez, Joaquín Tárraga, Ignacio Medina, Eva Alloza, David Montaner, Joaquín Dopazo
    posted to annotation functional_analysis by jfr on 2007-07-11 15:51:31 as ** along with 3 people and 1 group jyuh ealloza heliopais BioinfoCIPF
  • GENECODIS: A web-based tool for finding significant concurrent annotations in gene lists
    Genome Biology, Vol. 8 (04 January 2007), R3.
    by Pedro Carmona-Saez, Monica Chagoyen, Francisco Tirado, Jose M Carazo, Alberto Pascual-Montano
    posted to annotation bioinformatics by jfr on 2007-07-10 17:30:09 as ** along with 3 people and 1 group aalibes ealloza yas BioinfoCIPF
  • A comprehensive transcript index of the human genome generated using microarrays and computational approaches.
    Genome Biol, Vol. 5, No. 10. (2004)
    by EE Schadt, SW Edwards, D GuhaThakurta, D Holder, L Ying, V Svetnik, A Leonardson, KW Hart, A Russell, G Li, G Cavet, J Castle, P McDonagh, Z Kan, R Chen, A Kasarskis, M Margarint, RM Caceres, JM Johnson, CD Armour, PW Garrett-Engele, NF Tsinoremas, DD Shoemaker
    posted to annotation genomics by jfr on 2007-07-02 17:07:14 as * along with 1 person and 1 group kaspermunch Bioinformatics
  • Functional interpretation of microarray experiments.
    OMICS, Vol. 10, No. 3. (2006), pp. 398-410.
    by J Dopazo
    posted to annotation review by jfr on 2007-06-12 18:42:35 as ** along with 1 person and 1 group ealloza BioinfoCIPF
  • BayGO: Bayesian analysis of ontology term enrichment in microarray data.
    BMC Bioinformatics, Vol. 7 (2006)
    by RZ Vêncio, T Koide, SL Gomes, CA Pereira
    posted to annotation bioinformatics by jfr on 2007-06-08 17:09:48 as ** along with 1 person cmzmasek
  • Improved precision and accuracy for microarrays using updated probe set definitions
    BMC Bioinformatics, Vol. 8 (08 February 2007), 48.
    by Rickard Sandberg, Ola Larsson
    posted to affy annotation by jfr on 2007-06-08 16:06:37 as ** along with 5 people gpalidwor shigepong ghattem heliopais bertelsen
  • Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips
    BMC Bioinformatics, Vol. 8 (15 January 2007), 13.
    by Maria A Stalteri, Andrew P Harrison
    posted to affy annotation by jfr on 2007-05-11 14:51:16 as * along with 7 people jyuh gpalidwor hpiwowar frohike ghattem bertelsen heliopais
  • IDconverter and IDClight: Conversion and annotation of gene and protein IDs
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Andreu Alibes, Patricio Yankilevich, Andres Canada, Ramon D Uriarte
    posted to annotation software by jfr on 2007-05-10 17:30:45 as read along with 6 people and 1 group jyuh aalibes grahamc cerami srp33 mdstobbe ParkinsonLab_at_MaRS
  • CROPPER: A metagene creator resource for cross-platform and cross-species compendium studies
    BMC Bioinformatics, Vol. 7 (22 September 2006), 418.
    by Jussi Paananen, Markus Storvik, Garry Wong
    posted to software annotation by jfr on 2007-01-10 15:42:34 as * along with 1 person jyuh
  • Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data.
    Nucleic Acids Res, Vol. 33, No. 20. (2005)
    by M Dai, P Wang, AD Boyd, G Kostov, B Athey, EG Jones, WE Bunney, RM Myers, TP Speed, H Akil, SJ Watson, F Meng
    posted to annotation affy by jfr on 2007-01-10 10:44:38 as read along with 2 people pcahan1 tuck
  • The effect of GeneChip gene definitions on the microarray study of cancers.
    Bioessays, Vol. 28, No. 7. (July 2006), pp. 739-746.
    by X Lu, X Zhang
    posted to annotation affy by jfr on 2007-01-10 10:37:42 as * along with 1 person bertelsen
  • A Third Approach to Gene Prediction Suggests Thousands of Additional Human Transcribed Regions.
    PLoS Comput Biol, Vol. 2, No. 3. (17 March 2006)
    by Gustavo Glusman, Shizhen Qin, M Raafat R El-Gewely, Andrew F F Siegel, Jared C C Roach, Leroy Hood, Arian F A F Smit
    posted to annotation genomics by jfr on 2006-11-08 11:02:28 as ** along with 1 person and 1 group penka Nie
  • GATHER: a systems approach to interpreting genomic signatures.
    Bioinformatics (25 September 2006)
    by Jeffrey T T Chang, Joseph R R Nevins
    posted to annotation bioinformatics by jfr on 2006-11-08 10:35:33 as ** along with 1 person minostro
  • EGASP: the human ENCODE Genome Annotation Assessment Project.
    Genome Biol, Vol. 7 Suppl 1 (2006)
    by R Guigó, P Flicek, JF Abril, A Reymond, J Lagarde, F Denoeud, S Antonarakis, M Ashburner, VB Bajic, E Birney, R Castelo, E Eyras, C Ucla, TR Gingeras, J Harrow, T Hubbard, SE Lewis, MG Reese
    posted to annotation genomics by jfr on 2006-11-08 10:04:57 as ** along with 3 people and 2 groups indigoviolet wenhan timhubbard Bioinformatics EisenLab
  • Sequence biases in large scale gene expression profiling data.
    Nucleic Acids Res, Vol. 34, No. 12. (2006)
    by AS Siddiqui, AD Delaney, A Schnerch, OL Griffith, SJ Jones, MA Marra
    posted to annotation by jfr on 2006-11-06 16:05:28 as **
  • A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies
    Nature Biotechnology, Vol. 24, No. 7. (02 July 2006), pp. 832-840.
    by Winston P Kuo, Fang Liu, Jeff Trimarchi, Claudio Punzo, Michael Lombardi, Jasjit Sarang, Mark E Whipple, Malini Maysuria, Kyle Serikawa, Sun Y Lee, Donald Mccrann, Jason Kang, Jeffrey R Shearstone, Jocelyn Burke, Daniel J Park, Xiaowei Wang, Trent L Rector, Paola Ricciardi-Castagnoli, Steven Perrin, Sangdun Choi, Roger Bumgarner, Ju H Kim, Glenn F Short, Mason W Freeman, Brian Seed, Roderick Jensen, George M Church, Eivind Hovig, Connie L Cepko, Peter Park, Lucila Ohno-Machado, Tor-Kristian Jenssen
    posted to annotation by jfr on 2006-11-06 16:02:21 as ** along with 2 people and 2 groups dchughes stsaft G4ID Genetics-of-Gambling
  • Towards multidimensional genome annotation
    Nature Reviews Genetics, Vol. 7, No. 2., pp. 130-141.
    by Jennifer L Reed, Iman Famili, Ines Thiele, Bernhard O Palsson
    posted to annotation genomics by jfr on 2006-11-06 15:47:09 as ** along with 11 people and 4 groups druvus jyuh balajis eweaver dchughes cmm raiyar massivemayhem wenhan zwang lylu FAB-lab G4ID steinmetzlab Genetics-of-Gambling
  • SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data
    Nucl. Acids Res., Vol. 31, No. 1. (1 January 2003), pp. 219-223.
    by Maximilian Diehn, Gavin Sherlock, Gail Binkley, Heng Jin, John C Matese, Tina Hernandez-Boussard, Christian A Rees, Michael J Cherry, David Botstein, Patrick O Brown, Ash A Alizadeh
    posted to annotation bioinformatics by jfr on 2006-02-14 07:51:12 as read along with 2 people aalibes eweaver
  • A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array.
    Nucleic Acids Res, Vol. 33, No. 3. (2005)
    by J Harbig, R Sprinkle, SA Enkemann
    posted to annotation bioinformatics by jfr on 2005-08-14 17:28:05 as **
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