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Tag ppi [750 articles]

Recent papers classified by the tag ppi.
  • Evidence for dynamically organized modularity in the yeast protein-protein interaction network
    Nature, Vol. 430, No. 6995. (01 July 2004), pp. 88-93.
    by Jing-Dong J Han, Nicolas Bertin, Tong Hao, Debra S Goldberg, Gabriel F Berriz, Lan V Zhang, Denis Dupuy, Albertha JM Walhout, Michael E Cusick, Frederick P Roth, Marc Vidal
    posted to hubs ppi by winterschlaefer on 2008-03-03 10:39:28 as ** along with 24 people and 2 groups davidecellai dragonrez lfriedl balajis yoh j3xucite kintoki koller mikaelhuss ruvido gcalda grahamc iris_2001 lpfernandes Evangelia cdeane shung phoenixzxl stefanoallesina ellakat frohike shikin ksiek carlk kdl GeneGo
  • Network-based classification of breast cancer metastasis
    Mol Syst Biol, Vol. 3 (16 October 2007)
    by Han-Yu Chuang, Eunjung Lee, Yu-Tsueng Liu, Doheon Lee, Trey Ideker
    posted to ppi microarray cancer by winterschlaefer on 2008-10-08 09:59:50 as ** along with 18 people and 2 groups isimpson ihpark bertelsen jfr kengg frohike mikaelhuss cjeans zwang cerami abhattac shikin oelemento roys ptrobajo dap5087 saman_vp verdicchio Bioinformatics GeneGo
  • Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e178.
    by Ramon Aragues, Andrej Sali, Jaume Bonet, Marc A Marti-Renom, Baldo Oliva
    posted to hubs motif ppi by winterschlaefer on 2008-05-11 12:17:02 as ** along with 2 people zwang Ema
  • Confirmation of Organized Modularity in the Yeast Interactome
    PLoS Biology, Vol. 5, No. 6. (1 June 2007), e153.
    by Nicolas Bertin, Nicolas Simonis, Denis Dupuy, Michael E Cusick, Jing-Dong J Han, Hunter B Fraser, Frederick P Roth, Marc Vidal
    posted to hubs ppi by winterschlaefer on 2008-03-03 10:41:41 as ** along with 1 person kintoki
  • Unequal evolutionary conservation of human protein interactions in interologous networks
    Genome Biology, Vol. 8 (29 May 2007), R95.
    by Kevin R Brown, Igor Jurisica
    posted to evolution interologs ppi by winterschlaefer on 2007-08-24 11:21:34 as ** along with 2 people and 1 group grahamc zwang ParkinsonLab_at_MaRS
  • Principles of Protein-Protein Interactions: What are the Preferred Ways For Proteins To Interact?
    Chem. Rev. (21 March 2008)
    by O Keskin, A Gursoy, B Ma, R Nussinov
    posted to ppi by winterschlaefer on 2008-05-09 12:32:53 as ** along with 5 people and 1 group jmrivort higueruelo allmensch GermanErlenkamp kintoki Supramolecular
  • Coverage and error models of protein-protein interaction data by directed graph analysis
    Genome Biology, Vol. 8 (10 September 2007), R186.
    by Tony Chiang, Denise Scholtens, Deepayan Sarkar, Robert Gentleman, Wolfgang Huber
    posted to error ppi by winterschlaefer on 2007-09-18 10:33:02 as ** along with 5 people Yanno jfr chad_davis grahamc Pao-Yang
  • Still Stratus Not Altocumulus: Further Evidence against the Date/Party Hub Distinction
    PLoS Biology, Vol. 5, No. 6. (1 June 2007), e154.
    by Nizar N Batada, Teresa Reguly, Ashton Breitkreutz, Lorrie Boucher, Bobby-Joe Breitkreutz, Laurence D Hurst, Mike Tyers
    posted to hubs ppi by winterschlaefer on 2008-03-03 10:42:40 as ** along with 3 people carlk antonkratz cdeane
  • Specificity in protein interactions and its relationship with sequence diversity and coevolution.
    Proc Natl Acad Sci U S A (27 April 2007)
    by Luke Hakes, Simon C C Lovell, Stephen G G Oliver, David L L Robertson
    posted to evolution ismb08 ppi by winterschlaefer on 2008-02-17 16:48:12 as ** along with 9 people and 2 groups stevanspringer bjorns cjeans zwang Garamonfok cursonivel1 tale phoenixzxl chrys FAB-lab cursonivel1
  • Structure-Templated Predictions of Novel Protein Interactions from Sequence Information
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e182.
    by Doron Betel, Kevin E Breitkreuz, Ruth Isserlin, Danielle Dewar-Darch, Mike Tyers, Christopher W Hogue
    posted to ppi prediction structure by winterschlaefer on 2008-04-24 13:46:44 as ** along with 3 people agustinarce cjeans zwang
  • Predicting protein-protein interactions based only on sequences information
    PNAS, Vol. 104, No. 11. (13 March 2007), pp. 4337-4341.
    by Juwen Shen, Jian Zhang, Xiaomin Luo, Weiliang Zhu, Kunqian Yu, Kaixian Chen, Yixue Li, Hualiang Jiang
    posted to sequence prediction ppi by winterschlaefer on 2008-10-08 13:33:16 as ** along with 6 people and 1 group samjlord Dualsystems ruvido cjeans huyun110 phoenixzxl moernerlab
  • An assessment of the uses of homologous interactions
    Bioinformatics (27 November 2007), btm576.
    by Ramazan Saeed, Charlotte Deane
    posted to ppi orthology by winterschlaefer on 2008-10-06 11:49:35 as ** along with 8 people chad_davis grahamc cjeans laughcry mingzhi cdeane Pao-Yang samesense
  • A network of protein-protein interactions in yeast.
    Nat Biotechnol, Vol. 18, No. 12. (December 2000), pp. 1257-1261.
    by B Schwikowski, P Uetz, S Fields
    posted to high-throughput ppi yeast by winterschlaefer on 2007-08-27 10:51:26 as ** along with 4 people dragonrez ichbins81 jiny carlk
  • Stratus Not Altocumulus: A New View of the Yeast Protein Interaction Network.
    PLoS Biol, Vol. 4, No. 10. (19 September 2006)
    by Nizar N N Batada, Teresa Reguly, Ashton Breitkreutz, Lorrie Boucher, Bobby-Joe J Breitkreutz, Laurence D D Hurst, Mike Tyers
    posted to hubs ppi by winterschlaefer on 2008-03-03 10:40:57 as ** along with 6 people aswin jpoyatos iris_2001 Evangelia carlk cdeane
  • Predicting disease genes using protein-protein interactions.
    J Med Genet, Vol. 43, No. 8. (August 2006), pp. 691-698.
    by M Oti, B Snel, MA Huynen, HG Brunner
    posted to ppi disease by winterschlaefer on 2008-09-12 16:03:28 as ** along with 5 people bicko jiny svdate xingxu balicea
  • Predicting protein--protein interactions from primary structure.
    Bioinformatics, Vol. 17, No. 5. (May 2001), pp. 455-460.
    by JR Bock, DA Gough
    posted to ppi structure by wilbur on 2008-04-28 08:29:54 as ** along with 5 people maryee leelarcombe cjeans Evangelia iris_2001
  • ProteomicsProtein complexes take the bait
    Nature, Vol. 415, No. 6868. (10 January 2002), pp. 123-124.
    by Anuj Kumar, Michael Snyder
    posted to ppi by wilbur on 2008-04-21 14:50:59 as read along with 2 people and 1 group lfriedl marcio kdl
  • Localization of protein-binding sites within families of proteins.
    Protein Sci, Vol. 14, No. 9. (September 2005), pp. 2350-2360.
    by D Korkin, FP Davis, A Sali
    posted to ppi scop by wilbur on 2008-05-16 10:19:45 as ** along with 5 people and 4 groups barry tjimenez bicko chad_davis marcius structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • Development of unified statistical potentials describing protein-protein interactions.
    Biophys J, Vol. 84, No. 3. (March 2003), pp. 1895-1901.
    by H Lu, L Lu, J Skolnick
    posted to ppi usp by wilbur on 2008-04-28 08:28:32 as ** along with 7 people bicko mdimmic chad_davis cjeans selrac iris_2001 kgutwin
  • Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets
    Nature Genetics, Vol. 38, No. 3. (24 February 2006), pp. 285-293.
    by TKB Gandhi, Jun Zhong, Suresh Mathivanan, L Karthick, KN Chandrika, Sujatha S Mohan, Salil Sharma, Stefan Pinkert, Shilpa Nagaraju, Balamurugan Periaswamy, Goparani Mishra, Kannabiran Nandakumar, Beiyi Shen, Nandan Deshpande, Rashmi Nayak, Malabika Sarker, Jef D Boeke, Giovanni Parmigiani, Jörg Schultz, Joel S Bader, Akhilesh Pandey
    posted to comparative domain_interaction human ppi by tny on 2006-02-28 07:39:35 as ** along with 12 people and 2 groups aprildh31 balajis indigoviolet spavey TheresaNiederberger cjeans alwinpremanand dejori Pao-Yang pmendes carlk cerca EisenLab FAB-lab
  • Discovering functional interaction patterns in protein-protein interaction networks
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Mehmet Turanalp, Tolga Can
    posted to bioinfpdl frequent graph mining network ppi by Tingting on 2008-06-12 06:38:45 as **** along with 4 people and 1 group jyuh maralena renatomilani aprildh31 Proteasome
  • Functional centrality: detecting lethality of proteins in protein interaction networks.
    Genome informatics. International Conference on Genome Informatics, Vol. 19 (2007), pp. 166-177.
    by KL Tew, XL Li, SH Tan
    posted to ppi by Takayuki on 2008-06-15 10:15:58 as ***
  • Protein co-evolution, co-adaptation and interactions
    The EMBO Journal, Vol. aop, No. current. (25 September 2008)
    by Florencio Pazos, Alfonso Valencia
    posted to ppi co-evolution by sjcockell on 2008-09-29 19:52:14 as ** along with 1 person and 3 groups barry structural_bioinformatics McCammon Bioinformatics
  • How complete are current yeast and human protein-interaction networks?
    Genome Biology, Vol. 7 (01 December 2006), 120.
    by Traver G Hart, Arun K Ramani, Edward M Marcotte
    posted to network ppi systems_biology by shikin on 2008-04-17 14:25:58 as ** along with 4 people and 1 group eukfn Pao-Yang carlk phoenixzxl GeneGo
  • A comprehensive two-hybrid analysis to explore the yeast protein interactome.
    Proc Natl Acad Sci U S A, Vol. 98, No. 8. (10 April 2001), pp. 4569-4574.
    by T Ito, T Chiba, R Ozawa, M Yoshida, M Hattori, Y Sakaki
    posted to ppi systems_biology by shikin on 2008-04-17 18:35:59 as ** along with 14 people and 2 groups adiel dragonrez okarsligil lfriedl chad_davis balajis nuke2005 kengg ruvido gcalda lpfernandes hplatero csanford carlk kdl Bioinformatics
  • Protein interactions: two methods for assessment of the reliability of high throughput observations.
    Mol Cell Proteomics, Vol. 1, No. 5. (May 2002), pp. 349-356.
    by CM Deane, Ł Salwiński, I Xenarios, D Eisenberg
    posted to network ppi systems_biology by shikin on 2008-04-17 14:59:39 as ** along with 10 people and 1 group tmmurali lfriedl bluto henschel ruvido iris_2001 cdeane Pao-Yang ras chasmand kdl
  • Comparative assessment of large-scale data sets of protein-protein interactions.
    Nature, Vol. 417, No. 6887. (23 May 2002), pp. 399-403.
    by C von Mering, R Krause, B Snel, M Cornell, SG Oliver, S Fields, P Bork
    posted to ppi systems_biology by shikin on 2008-04-17 12:38:49 as ** along with 21 people and 6 groups camster barry dragonrez bicko lfriedl chad_davis alexg j3xucite bundschu yeastyboy ruvido raiyar grahamc iris_2001 cmor shu Evangelia Pao-Yang carlk cerca ethkim dbk-lab structural_bioinformatics kdl Bioinformatics generif_paper GeneGo
  • Profile of the Polish poultry industry
    World's Poultry Science Journal, Vol. 61, No. 4. (December 2005), pp. 694-694.
    by J Sobczak, A Nowak
    posted to ppi by sauerkraut on 2008-07-26 10:41:01 as **
  • Extracting human protein interactions from MEDLINE using a full-sentence parser.
    Bioinformatics, Vol. 20, No. 5. (22 March 2004), pp. 604-611.
    by N Daraselia, A Yuryev, S Egorov, S Novichkova, A Nikitin, I Mazo
    posted to bionlp parsing ppi textmining by satre on 2008-07-22 18:59:46 as *** along with 6 people and 1 group bqchinh irenas Enro miguel natsu zlu dbk-lab
  • ALIBABA: PubMed as a graph
    Bioinformatics, Vol. 22, No. 19. (1 October 2006), pp. 2444-2445.
    by Conrad Plake, Torsten Schiemann, Marcus Pankalla, Jorg Hakenberg, Ulf Leser
    posted to bionlp ppi textmining by satre on 2008-07-22 22:43:17 as ** along with 5 people and 2 groups jyuh ianturton avivagabriel dagmar A_Hoogendam dIEMoSIRIS compneur
  • Assisted curation: does text mining really help?
    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2008), pp. 556-567.
    by B Alex, C Grover, B Haddow, M Kabadjov, E Klein, M Matthews, S Roebuck, R Tobin, X Wang
    posted to bionlp ner ppi by satre on 2008-07-20 11:40:07 as *** along with 1 person and 1 group henk-cul dbmi-nlp
  • Biomedical Language Processing: What's Beyond PubMed?
    Mol Cell, Vol. 21, No. 5. (3 March 2006), pp. 589-594.
    by L Hunter, KB Cohen
    posted to annotation bionlp corpus informationextraction ppi review textmining by satre on 2008-07-24 14:20:59 as ** along with 7 people and 3 groups irenas andytseng yas hpiwowar caporaso jacky957 TheresaNiederberger dbk-lab T_lab biomedical-nlp
  • Finding the evidence for protein-protein interactions from PubMed abstracts.
    Bioinformatics, Vol. 22, No. 14. (15 July 2006)
    by H Jang, J Lim, JH Lim, SJ Park, KC Lee, SH Park
    posted to bionlp ner ppi by satre on 2008-07-22 22:30:50 as ** along with 1 person jyuh
  • Detecting gene relations from Medline abstracts.
    Pac Symp Biocomput (2001), pp. 483-495.
    by M Stephens, M Palakal, S Mukhopadhyay, R Raje, J Mostafa
    posted to bionlp ner ppi textmining by satre on 2008-07-22 21:53:55 as ** along with 1 person and 1 group yas T_lab
  • Discovering patterns to extract protein-protein interactions from the literature: Part II.
    Bioinformatics, Vol. 21, No. 15. (1 August 2005), pp. 3294-3300.
    by Y Hao, X Zhu, M Huang, M Li
    posted to biocreative bionlp corpus parsing ppi textmining by satre on 2008-07-22 22:21:54 as *** along with 2 people davidandrzej natsu
  • Extracting Protein-Protein Interactions from the Literature Using the Hidden Vector State Model
    Computational Science – ICCS 2006 (2006), pp. 718-725.
    by Deyu Zhou, Yulan He, Chee Kwoh
    posted to bionlp ppi svm textmining by satre on 2008-07-22 03:07:27 as ***
  • Identifying the Interaction between Genes and Gene Products Based on Frequently Seen Verbs in Medline Abstracts.
    Genome informatics. Workshop on Genome Informatics, Vol. 9 (1998), pp. 62-71.
    by T Sekimizu, HS Park, J Tsujii
    posted to bionlp parsing ppi rulebased textmining by satre on 2008-07-22 08:25:43 as **
  • Task-oriented Evaluation of Syntactic Parsers and Their Representations
    (June 2008), pp. 46-54.
    by Yusuke Miyao, Rune Sætre, Kenji Sagae, Takuya Matsuzaki, Jun'ichi Tsujii
    posted to bionlp parsing ppi by satre on 2008-07-29 13:55:10 as read along with 1 person JeremyKahn
  • Mining MEDLINE: abstracts, sentences, or phrases?
    Pac Symp Biocomput (2002), pp. 326-337.
    by J Ding, D Berleant, D Nettleton, E Wurtele
    posted to annotation bionlp informationextraction ppi textmining by satre on 2008-07-24 14:39:52 as ** along with 4 people and 2 groups yas zlu bundschu ianturton T_lab generif_paper
  • BIND--The Biomolecular Interaction Network Database.
    Nucleic Acids Res, Vol. 29, No. 1. (1 January 2001), pp. 242-245.
    by GD Bader, I Donaldson, C Wolting, BF Ouellette, T Pawson, CW Hogue
    posted to database ner pathway ppi by satre on 2008-07-26 13:52:22 as *** along with 4 people wnpx blackbart ruvido carlk
  • Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information.
    BMC Bioinformatics, Vol. 6, No. 1. (7 June 2005)
    by James W Cooper, Aaron Kershenbaum
    posted to bionlp ibm ppi rulebased svm textmining by satre on 2008-07-22 12:46:44 as *** along with 3 people snuppepuppan pggm chad_davis
  • IntAct: an open source molecular interaction database.
    Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004)
    by H Hermjakob, L Montecchi-Palazzi, C Lewington, S Mudali, S Kerrien, S Orchard, M Vingron, B Roechert, P Roepstorff, A Valencia, H Margalit, J Armstrong, A Bairoch, G Cesareni, D Sherman, R Apweiler
    posted to annotation ppi by satre on 2008-07-24 14:25:19 as *** along with 7 people and 1 group irenas fisherp frohike grahamc lpfernandes wilbur jeremymiller dbk-lab
  • PIE: an online prediction system for protein-protein interactions from text
    Nucl. Acids Res. (28 May 2008), gkn281.
    by Sun Kim, Soo-Yong Shin, In-Hee Lee, Soo-Jin Kim, Ram Sriram, Byoung-Tak Zhang
    posted to bionlp ppi textmining by satre on 2008-07-22 14:40:56 as ** along with 3 people neils tharris jyuh
  • Extracting Protein-Protein Interaction Information from Biomedical Text with SVM
    IEICE - Trans. Inf. Syst., Vol. E89-D, No. 8. (2006), pp. 2464-2466.
    by Tomohiro Mitsumori, Masaki Murata, Yasushi Fukuda, Kouichi Doi, Hirohumi Doi
    posted to bionlp ppi svm textmining by satre on 2008-07-22 03:03:44 as ** along with 1 person farzanehs
  • PreBIND and Textomy--mining the biomedical literature for protein-protein interactions using a support vector machine.
    BMC Bioinformatics, Vol. 4 (27 March 2003)
    by I Donaldson, J Martin, B de Bruijn, C Wolting, V Lay, B Tuekam, S Zhang, B Baskin, GD Bader, K Michalickova, T Pawson, CW Hogue
    posted to bionlp ppi svm ui-system by satre on 2008-07-18 17:52:28 as *** along with 3 people chad_davis blackbart bouncingbudha
  • RelExRelation extraction using dependency parse trees
    Bioinformatics, Vol. 23, No. 3. (1 February 2007), pp. 365-371.
    by Fundel, Katrin, Kuffner, Robert, Zimmer, Ralf
    posted to bionlp parsing ppi textmining by satre on 2008-07-19 07:12:54 as ** along with 6 people farzanehs chad_davis bhaddow vlachmore TheresaNiederberger gilesc
  • Manual curation is not sufficient for annotation of genomic databases
    Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. i41-48.
    by William A Baumgartner, Bretonnel K Cohen, Lynne M Fox, George Acquaah-Mensah, Lawrence Hunter
    posted to annotation database ppi by satre on 2008-07-24 14:31:21 as ** along with 1 person sgoetz
  • A text-mining perspective on the requirements for electronically annotated abstracts.
    FEBS letters, Vol. 582, No. 8. (9 April 2008), pp. 1178-1181.
    by F Leitner, A Valencia
    posted to annotation biocreative bionlp ppi textmining by satre on 2008-07-22 16:27:49 as *** along with 2 people ianturton jyuh
  • Developing a Robust Part-of-Speech Tagger for Biomedical Text
    Advances in Informatics (2005), pp. 382-392.
    by Yoshimasa Tsuruoka, Yuka Tateishi, Jin-Dong Kim, Tomoko Ohta, John Mcnaught, Sophia Ananiadou, Jun’ichi Tsujii
    posted to bionlp maximum-entropy-modeling ner parsing ppi textmining by satre on 2008-07-26 14:21:22 as **
  • Extracting Protein-Protein Interactions from MEDLINE using the Hidden Vector State model.
    International journal of bioinformatics research and applications, Vol. 4, No. 1. (2008), pp. 64-80.
    by D Zhou, Y He, CK Kwoh
    posted to bionlp ppi svm textmining by satre on 2008-07-22 07:58:17 as **
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