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AbnerCYH's biology [94 articles]

Recent papers added to AbnerCYH's library classified by the tag biology. You can also see everyone's biology.
  • PPiClust: EFFICIENT CLUSTERING OF 3D PROTEIN–PROTEIN INTERACTION INTERFACES
    Journal of Bioinformatics and Computational Biology, Vol. 6, No. 3. (July 2008), pp. 415-433.
    by AUNG Zeyar, TAN Soon-Heng, NG See-Kiong, TAN Kian-Lee
    posted to biology algorithms by AbnerCYH on 2008-09-19 16:50:46 as **
  • Network Analysis of Intrinsic Functional Brain Connectivity in Alzheimer's Disease
    PLoS Comput Biol, Vol. 4, No. 6. (27 June 2008), e1000100.
    by Kaustubh Supekar, Vinod Menon, Daniel Rubin, Mark Musen, Michael D Greicius
    posted to kdd graph complex biology by AbnerCYH on 2008-09-09 12:05:43 as ** along with 2 people and 1 group pbellec Borelli resting-state_networks
  • Insights into Protein–DNA Interactions through Structure Network Analysis
    PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000170.
    by R Sathyapriya, MS Vijayabaskar, Saraswathi Vishveshwara
    posted to kdd graph complex biology algorithms by AbnerCYH on 2008-09-08 07:14:20 as ** along with 7 people and 1 group Zephyrus Ema emptyhb aalibes Totobox zwang hmk Roswell Cancer Crosstalk
  • An algorithm based on graph theory for the assembly of contigs in physical mapping of DNA.
    Computer applications in the biosciences : CABIOS, Vol. 10, No. 3. (June 1994), pp. 309-317.
    by P Zhang, EA Schon, SG Fischer, E Cayanis, J Weiss, S Kistler, PE Bourne
    posted to graph biology algorithms by AbnerCYH on 2008-09-08 06:18:26 as ** along with 1 person Neeperando
  • Robust and efficient identification of biomarkers by classifying features on graphs
    Bioinformatics, Vol. 24, No. 18. (15 September 2008), pp. 2023-2029.
    by Taehyun Hwang, Hugues Sicotte, Ze Tian, Baolin Wu, Jean-Pierre Kocher, Dennis A Wigle, Vipin Kumar, Rui Kuang
    posted to graph biology algorithms by AbnerCYH on 2008-09-08 06:16:32 as ** along with 4 people nuin GeeSharpMinor mitko sg45653
  • Immunology for physicists
    Reviews of Modern Physics, Vol. 69, No. 4. (1 October 1997), 1219.
    by Alan S Perelson, Gérard Weisbuch
    posted to biology complex by AbnerCYH on 2008-09-01 06:09:47 as ** along with 1 person awooga
  • Getting Started in Computational Immunology
    PLoS Comput Biol, Vol. 4, No. 8. (2008), e1000128.
    by Steven H Kleinstein
    posted to algorithms biology complex by AbnerCYH on 2008-08-30 20:06:43 as ** along with 8 people and 2 groups Zephyrus nuin barry reyez dakelley GeeSharpMinor rebeccamancy jjray Roswell Cancer Crosstalk Bioinformatics
  • Genome-Scale Computational Biology and Bioinformatics in Australia
    PLoS Comput Biol, Vol. 4, No. 8. (2008), e1000068.
    by Mark A Ragan, Tim Littlejohn, Bruce Ross
    posted to algorithms biology by AbnerCYH on 2008-08-30 20:02:36 as ** along with 4 people reyez dullhunk barry neils
  • Networking metabolites and diseases
    Proceedings of the National Academy of Sciences, Vol. 105, No. 29. (22 July 2008), pp. 9849-9850.
    by Pascal Braun, Edward Rietman, Marc Vidal
    posted to biology complex graph by AbnerCYH on 2008-08-29 11:56:18 as ** along with 4 people roys ptrobajo jyuh Borelli
  • Geometric Interpretation of Gene Coexpression Network Analysis
    PLoS Comput Biol, Vol. 4, No. 8. (2008), e1000117.
    by Steve Horvath, Jun Dong
    posted to algorithms biology complex graph kdd by AbnerCYH on 2008-08-20 14:30:21 as ** along with 12 people pengchy nolodie druvus aramesh2 kengg roys Ema tmmurali Borelli Totobox davidchavalarias caseybrown
  • From the Cover: Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
    PNAS, Vol. 102, No. 43. (25 October 2005), pp. 15545-15550.
    by Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander, Jill P Mesirov
    posted to biology complex kdd by AbnerCYH on 2008-08-20 09:39:42 as ** along with 23 people and 4 groups ihpark chrisamiller dragonrez jfr balajis maryee xwbcn hpiwowar aviad_work ealloza jdiggans jeremymiller frohike hawkeyehammer schuylrp natstreet heliopais shikin waghsk roys ellakat srp33 sgoetz Bioinformatics BioinfoCIPF GeschwindLab Indigene
  • An Experimental Study of the Coloring Problem on Human Subject Networks
    Science, Vol. 313, No. 5788. (11 August 2006), pp. 824-827.
    by Michael Kearns, Siddharth Suri, Nick Montfort
    posted to biology complex graph kdd by AbnerCYH on 2008-08-20 03:52:48 as ** along with 2 people maralena ssuri
  • On the origin of distribution patterns of motifs in biological networks.
    BMC Systems Biology, Vol. 2, No. 1. (2008)
    by Arun Konagurthu, Arthur Lesk
    posted to algorithms biology complex graph kdd by AbnerCYH on 2008-08-13 06:36:51 as ** along with 2 people lptolik barriot
  • Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis
    Science, Vol. 320, No. 5883. (20 June 2008), pp. 1632-1635.
    by Ari Loytynoja, Nick Goldman
    posted to algorithms biology by AbnerCYH on 2008-07-26 06:14:04 as ** along with 22 people and 3 groups marti bpcusack chad_davis hpaces dinnes gjuggler djkt ArtemPankin phoenixzxl jago marck imtechnology aprasad zwang bmaust bpb michaelbarton Schmidtc gulsacan emptyhb jlgreen nuin Khavkin's lab iSEEM Green Lab
  • Semantic integration to identify overlapping functional modules in protein interaction networks
    BMC Bioinformatics, Vol. 8 (24 July 2007), 265.
    by Young-Rae Cho, Woochang Hwang, Murali Ramanathan, Aidong Zhang
    posted to algorithms biology complex kdd by AbnerCYH on 2008-07-21 14:52:45 as ** along with 4 people and 2 groups jyuh tmmurali grahamc carlk ParkinsonLab_at_MaRS csb_journal_club_public
  • Molecular interaction maps of bioregulatory networks: a general rubric for systems biology.
    Mol Biol Cell, Vol. 17, No. 1. (January 2006), pp. 1-13.
    by KW Kohn, MI Aladjem, JN Weinstein, Y Pommier
    posted to algorithms biology complex graph by AbnerCYH on 2008-07-19 19:15:38 as ** along with 4 people and 1 group eckart_bindewald wnpx karthikram lenov Neoscientists
  • Decomposition of overlapping protein complexes: A graph theoretical method for analyzing static and dynamic protein associations
    Algorithms for Molecular Biology, Vol. 1, No. 1. (26 April 2006), 7.
    by Elena Zotenko, Katia S Guimarães, Raja Jothi, Teresa M Przytycka
    posted to algorithms biology complex graph kdd by AbnerCYH on 2008-07-19 19:15:26 as read along with 2 people and 1 group lfriedl chad_davis kdl
  • Charting protein complexes, signaling pathways, and networks in the immune system
    Immunological Reviews, Vol. 210, No. 1. (April 2006), pp. 187-207.
    by Bauch, Angela, Superti-Furga, Giulio
    posted to algorithms biology complex graph by AbnerCYH on 2008-07-19 19:15:14 as **
  • Evaluation of clustering algorithms for protein-protein interaction networks
    BMC Bioinformatics, Vol. 7 (06 November 2006), 488.
    by Sylvain Brohee, Jacques van Helden
    posted to algorithms biology complex graph kdd by AbnerCYH on 2008-07-19 19:14:55 as ** along with 15 people and 1 group pdelosri jfr chad_davis balajis nirfriedman dquest grahamc cjeans hpaces Pao-Yang oktie carlk Borelli cerca ethkim EPFL_SB_ITP_LBS
  • Iterative Cluster Analysis of Protein Interaction Data
    Bioinformatics, Vol. 21, No. 3. (01 February 2005), 364.
    by Vicente Arnau, Sergio Mars, Ignacio Marin
    posted to algorithms biology complex graph kdd by AbnerCYH on 2008-07-19 19:14:42 as ** along with 3 people jiny mdimmic tny
  • Discovery of biological networks from diverse functional genomic data.
    Genome Biol, Vol. 6, No. 13. (2005)
    by CL Myers, D Robson, A Wible, MA Hibbs, C Chiriac, CL Theesfeld, K Dolinski, OG Troyanskaya
    posted to algorithms biology complex graph by AbnerCYH on 2008-07-19 19:14:28 as ** along with 2 people grahamc carlk
  • On the complexity of deriving position specific score matrices from positive and negative sequences
    Discrete Applied Mathematics, Vol. 155, No. 6-7. (1 April 2007), pp. 676-685.
    by Tatsuya Akutsu, Hideo Bannai, Satoru Miyano, Sascha Ott
    posted to algorithms biology complexity by AbnerCYH on 2008-07-19 09:18:35 as **
  • Unraveling Protein Networks with Power Graph Analysis
    PLoS Comput Biol, Vol. 4, No. 7. (11 July 2008), e1000108.
    by Loïc Royer, Matthias Reimann, Bill Andreopoulos, Michael Schroeder
    posted to algorithms biology complex graph by AbnerCYH on 2008-07-18 18:28:57 as ** along with 20 people and 2 groups jfr jiny aramesh2 jmuhlich MatthiasReimann royerloic Ema lptolik kengg roys reyez tmmurali nuin Borelli askrajiv renatomilani chad_davis stajich sebk rsantana Berkeley Mycology OPIG
  • Modular decomposition of protein-protein interaction networks.
    Genome Biol, Vol. 5, No. 8. (2004)
    by J Gagneur, R Krause, T Bouwmeester, G Casari
    posted to algorithms biology graph by AbnerCYH on 2008-07-15 03:23:42 as read along with 2 people ezotenko tmmurali
  • Cluster analysis for gene expression data: a survey
    Knowledge and Data Engineering, IEEE Transactions on, Vol. 16, No. 11. (2004), pp. 1370-1386.
    by Daxin Jiang, Chun Tang, Aidong Zhang
    posted to algorithms biology kdd by AbnerCYH on 2008-07-06 07:29:57 as ** along with 5 people bozdagd bayesian archroad dps burtonwu
  • Transcription factor modularity in a gene-centered C. elegans core neuronal protein-DNA interaction network
    Genome Res., Vol. 17, No. 7. (1 July 2007), pp. 1061-1071.
    by Vanessa Vermeirssen, Inmaculada M Barrasa, Cesar A Hidalgo, Jenny A Babon, Reynaldo Sequerra, Lynn Doucette-Stamm, Albert-Laszlo Barabasi, Albertha J Walhout
    posted to biology complex graph kdd by AbnerCYH on 2008-07-03 20:20:30 as ** along with 1 person and 1 group tharris C. elegans / WormBase
  • Epidemic dynamics and endemic states in complex networks
    Physical Review E, Vol. 63, No. 6. (22 May 2001), 066117.
    by Romualdo Pastor-Satorras, Alessandro Vespignani
    posted to biology complex dynamics graph by AbnerCYH on 2008-07-03 19:28:36 as **
  • Epidemic Spreading in Scale-Free Networks
    Physical Review Letters, Vol. 86, No. 14. (2 April 2001), 3200.
    by Romualdo Pastor-Satorras, Alessandro Vespignani
    posted to biology complex dynamics graph by AbnerCYH on 2008-07-03 19:28:17 as ** along with 2 people pdelosri rcrane
  • An algorithm for modularity analysis of directed and weighted biological networks based on edge-betweenness centrality.
    Bioinformatics (Oxford, England), Vol. 22, No. 24. (15 December 2006), pp. 3106-3108.
    by J Yoon, A Blumer, K Lee
    posted to algorithms biology complex graph kdd by AbnerCYH on 2008-07-01 03:36:10 as *** along with 1 person hryk
  • A computational analysis of the protein-protein interaction networks in neurodegenerative diseases
    BMC Systems Biology, Vol. 2, No. 1. (2008)
    by Joaquin Goni, Francisco Esteban, Nieves V de Mendizabal, Jorge Sepulcre, Sergio A Treijano, Ion Agirrezabal, Pablo Villoslada
    posted to algorithms biology complex graph kdd by AbnerCYH on 2008-06-27 05:29:43 as ** along with 3 people renatomilani bootsy reyez
  • Modular cell biology: retroactivity and insulation
    Mol Syst Biol, Vol. 4 (12 February 2008)
    by Domitilla Del Vecchio, Alexander J Ninfa, Eduardo D Sontag
    posted to biology complex graph by AbnerCYH on 2008-06-26 03:48:59 as ** along with 5 people austin margaritis rsantana pmendes roys
  • Fast Network Component Analysis (FastNCA) for gene regulatory network reconstruction from microarray data.
    Bioinformatics (Oxford, England) (9 April 2008)
    by Chunqi Chang, Zhi Ding, Yeung Sam S Hung, Peter Chin Wan C Fung
    posted to algorithms biology complex graph by AbnerCYH on 2008-05-24 12:01:59 as ** along with 3 people jyuh jfr roys
  • Classes of complex networks defined by role-to-role connectivity profiles
    Nat Phys, Vol. 3, No. 1. (January 2007), pp. 63-69.
    by Roger Guimera, Marta Sales-Pardo, Luis A Amaral
    posted to biology complex graph by AbnerCYH on 2008-05-16 05:28:44 as ** along with 5 people and 1 group aalibes okarsligil jaspervoskuilen biehl Diego_Prada Bioinformatics
  • Evolvability and hierarchy in rewired bacterial gene networks
    Nature, Vol. 452, No. 7189. (17 April 2008), pp. 840-845.
    by Mark Isalan, Caroline Lemerle, Konstantinos Michalodimitrakis, Carsten Horn, Pedro Beltrao, Emanuele Raineri, Mireia Garriga-Canut, Luis Serrano
    posted to biology complex graph by AbnerCYH on 2008-05-16 05:28:30 as ** along with 18 people and 4 groups aalibes tmmurali dullhunk neils cmzmasek josedavid biehl caseybrown Garamonfok austin hryk dbikard cactus margaritis chad_davis michaelbarton aheilbut zwang GEB Centre de Recherches Interdisciplinaires SynBioSys BergmanLab
  • Complex networks: Lies, damned lies and statistics
    Nat Phys, Vol. 2, No. 2. (February 2006), pp. 75-76.
    by Nunes, Roger Guimera
    posted to biology complex graph kdd stochastic by AbnerCYH on 2008-05-14 06:50:56 as ** along with 2 people RobMills Evangelia
  • Complex networks: Role model for modules
    Nat Phys, Vol. 3, No. 1. (January 2007), pp. 18-19.
    by Sergei Maslov
    posted to biology complex graph by AbnerCYH on 2008-05-14 06:24:07 as read
  • Protein Structure from Contact Maps: A Case-Based Reasoning Approach
    Information Systems Frontiers, Vol. 8, No. 1. (February 2006), pp. 29-36.
    by Janice Glasgow, Tony Kuo, Jim Davies
    posted to algorithms biology complex kdd by AbnerCYH on 2008-05-09 13:15:47 as ** along with 1 person babakap
  • The use of receiver operating characteristic curves in biomedical informatics
    Journal of Biomedical Informatics, Vol. 38, No. 5. (October 2005), pp. 404-415.
    by Thomas A Lasko, Jui G Bhagwat, Kelly H Zou, Lucila Ohno-Machado
    posted to biology complex information kdd math stochastic by AbnerCYH on 2008-05-09 09:22:01 as ** along with 3 people and 1 group microserf yas vmoa T_lab
  • Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology
    Research in Computational Molecular Biology (2007), pp. 16-31.
    by Rohit Singh, Jinbo Xu, Bonnie Berger
    posted to algorithms biology graph by AbnerCYH on 2008-05-08 19:53:01 as ***** along with 1 person carlk
  • Protein side-chain packing problem: a maximum edge-weight clique algorithmic approach
    (2004), pp. 191-200.
    by Dukka KC Bahadur, Tatsuya Akutsu, Etsuji Tomita, Tomokazu Seki
    posted to algorithms biology graph by AbnerCYH on 2008-05-08 18:56:43 as **
  • Fast and accurate algorithms for protein side-chain packing
    J. ACM, Vol. 53, No. 4. (July 2006), pp. 533-557.
    by Jinbo Xu, Bonnie Berger
    posted to algorithms biology graph by AbnerCYH on 2008-05-08 18:56:38 as **
  • Recognizing the fold of a protein structure
    Bioinformatics, Vol. 19, No. 14. (22 September 2003), pp. 1748-1759.
    by Andrew Harrison, Frances Pearl, Ian Sillitoe, Tim Slidel, Richard Mott, Janet Thornton, Christine Orengo
    posted to algorithms biology complex graph by AbnerCYH on 2008-05-08 07:55:35 as **
  • Evolution of Eukaryotic Transcription Circuits
    Science, Vol. 319, No. 5871. (28 March 2008), pp. 1797-1799.
    by Brian B Tuch, Hao Li, Alexander D Johnson
    posted to biology complex graph by AbnerCYH on 2008-04-05 05:39:19 as ** along with 2 people djkt bpcusack
  • Gene Regulation in the Third Dimension
    Science, Vol. 319, No. 5871. (28 March 2008), pp. 1793-1794.
    by Job Dekker
    posted to biology geometries by AbnerCYH on 2008-04-05 05:07:34 as ** along with 10 people and 2 groups operon ealloza biomcgary sunhwan dlobo lambda Haze emptyhb inesdesantiago ArtemPankin GEB Khavkin's lab
  • The Eukaryotic Genome as an RNA Machine
    Science, Vol. 319, No. 5871. (28 March 2008), pp. 1787-1789.
    by Paulo P Amaral, Marcel E Dinger, Tim R Mercer, John S Mattick
    posted to biology by AbnerCYH on 2008-04-05 04:51:13 as ** along with 6 people and 1 group operon dullhunk biomcgary dlobo dquest siebert GEB
  • Closed-loop control of cellular functions using combinatory drugs guided by a stochastic search algorithm
    Proceedings of the National Academy of Sciences, Vol. 105, No. 13. (1 April 2008), pp. 5105-5110.
    by Pak K Wong, Fuqu Yu, Arash Shahangian, Genhong Cheng, Ren Sun, Chih-Ming Ho
    posted to algorithms biology complex stochastic by AbnerCYH on 2008-04-02 01:15:45 as **
  • From time series to complex networks: The visibility graph
    Proceedings of the National Academy of Sciences, Vol. 105, No. 13. (1 April 2008), pp. 4972-4975.
    by Lucas Lacasa, Bartolo Luque, Fernando Ballesteros, Jordi Luque, Juan C Nuno
    posted to biology complex graph by AbnerCYH on 2008-04-02 01:15:29 as ** along with 2 people biehl vrich
  • A Parameterized Algorithm for Protein Structure Alignment
    Journal of Computational Biology, Vol. 14, No. 5. (2007), pp. 564-577.
    by Jinbo Xu, Feng Jiao, Bonnie Berger
    posted to algorithms biology by AbnerCYH on 2008-03-27 16:06:25 as *****
  • QPath: a method for querying pathways in a protein-protein interaction network
    BMC Bioinformatics, Vol. 7 (2006), 199.
    by Tomer Shlomi, Daniel Segal, Eytan Ruppin, Roded Sharan
    posted to algorithms biology complex graph by AbnerCYH on 2008-03-24 14:07:13 as **
  • PathBLAST: a tool for alignment of protein interaction networks.
    Nucleic Acids Res, Vol. 32, No. Web Server issue. (1 July 2004)
    by BP Kelley, B Yuan, F Lewitter, R Sharan, BR Stockwell, T Ideker
    posted to algorithms biology complex graph by AbnerCYH on 2008-03-24 13:59:56 as ** along with 5 people sza dragonrez nuke2005 koller carlk
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