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samal's library [37 articles]

Recent papers added to samal's library.
  • The statistical significance of nucleotide position-weight matrix matches
    Comput. Appl. Biosci., Vol. 12, No. 5. (1 October 1996), pp. 431-439.
    by Jean-Michel Claverie, Stephane Audic
    posted to algorithm bioinformatics matrix statistics by samal on 2006-09-10 03:27:32 as ** along with 2 people and 2 groups neils bsmagic Bioinformatics bioinplant
  • On counting position weight matrix matches in a sequence, with application to discriminative motif finding.
    Bioinformatics, Vol. 22, No. 14. (15 July 2006)
    by S Sinha
    posted to motif pattern prediction sequence by samal on 2006-08-31 16:09:20 as ** along with 2 people xili03 eckart_bindewald
  • Semi-supervised clustering by seeding
    (2002)
    by S Basu, A Banerjee, R Mooney
    posted to clustering em semisupervised by samal on 2006-08-22 15:05:33 as ** along with 4 people sona anon_pl jread82 nklee
  • Feature Weighting in <i>k</i>-Means Clustering
    Mach. Learn., Vol. 52, No. 3. (September 2003), pp. 217-237.
    by Dharmendra S Modha, Scott W Spangler
    posted to clustering feature selection unsupervised by samal on 2006-08-22 07:50:44 as ** along with 1 person alexhofmann
  • Simultaneous Feature Selection and Clustering Using Mixture Models
    by Martin HC Law, Mario AT Figueiredo, Anil K Jain
    posted to clustering feature filter selection unsupervised by samal on 2006-08-22 07:32:02 as ** along with 2 people luispedro alexhofmann
  • A New Conceptual Clustering Framework
    Machine Learning, Vol. 56, No. 1 - 3. (July 2004), pp. 115-151.
    by Nina Mishra, Dana Ron, Ram Swaminathan
    posted to clustering by samal on 2006-08-22 07:31:33 as ** along with 1 person kazuyah
  • A unified framework for model-based clustering
    (2002)
    by S Zhong, J Ghosh
    posted to clustering deterministic_annealing by samal on 2006-08-22 07:30:13 as *** along with 2 people anon_pl lfdoherty
  • Mining frequent stem patterns from unaligned RNA sequences.
    Bioinformatics (14 August 2006)
    by Michiaki Hamada, Koji Tsuda, Taku Kudo, Taishin Kin, Kiyoshi Asai
    posted to clustering motif ncrna structure by samal on 2006-08-22 07:28:40 as ** along with 5 people and 3 groups marcius tardigrade andersbj dquest plofje microRNA BioinfoCIPF SGU-CIPF
  • Defining the sequence-recognition profile of DNA-binding molecules
    PNAS, Vol. 103, No. 4. (24 January 2006), pp. 867-872.
    by Christopher L Warren, Natasha C Kratochvil, Karl E Hauschild, Shane Foister, Mary L Brezinski, Peter B Dervan, George N Phillips, Aseem Z Ansari
    posted to array binding factor selex transcription by samal on 2006-08-22 07:09:36 as ** along with 4 people and 1 group indigoviolet emilyhare stsaft blobbybirdman EisenLab
  • Integrated Assessment and Prediction of Transcription Factor Binding
    PLoS Computational Biology, Vol. 2, No. 6. (1 June 2006), e70.
    by Andreas Beyer, Christopher Workman, Jens Hollunder, Dörte Radke, Ulrich Möller, Thomas Wilhelm, Trey Ideker
    posted to prediction target tf transcription by samal on 2006-08-22 07:03:55 as ** along with 6 people and 1 group jfr balajis wnpx emilyhare reidy Ao_Li2007 EisenLab
  • Linking DNA-binding proteins to their recognition sequences by using protein microarrays.
    Proc Natl Acad Sci U S A (19 June 2006)
    by Su-Wen W Ho, Ghil Jona, Christina T L T Chen, Mark Johnston, Michael Snyder
    posted to array protein transcription by samal on 2006-08-22 07:00:23 as ** along with 4 people and 3 groups emilyhare nickluscombe kengg koller EisenLab EBI-regulation Plantandetc
  • The design of transcription-factor binding sites is affected by combinatorial regulation.
    Genome Biol, Vol. 6, No. 12. (2005)
    by Y Bilu, N Barkai
    posted to binding cooperativity factor factors grammar regulation site sites transcription yeast by samal on 2006-08-22 06:39:12 as ** along with 7 people and 1 group chrn dpollard tabu adepace lewbin nklee xili03 EisenLab
  • Statistical Methods in Bioinformatics : An Introduction (Statistics for Biology and Health)
    (05 March 2006)
    by Warren J Ewens, Gregory Grant
    posted to lab_library methods population_genetics by samal on 2006-08-22 05:27:41 as ** along with 4 people and 1 group dpollard wnpx hpiwowar echinotrix EisenLab
  • PLoS Biology: Plasticity of the cis-Regulatory Input Function of a Gene
    posted to bacteria evolution expression gene mutation placticity promoter regulation transcription_factor by samal on 2006-08-22 05:25:15 as ** along with 2 people and 1 group dpollard brixtonmc EisenLab
  • Periodicity of SNP distribution around transcription start sites.
    BMC Genomics, Vol. 7, No. 1. (3 April 2006)
    by Koichiro Higasa, Kenshi Hayashi
    posted to chimp human nucleosome promoter snps transcription by samal on 2006-08-22 05:24:28 as ** along with 1 person and 1 group dpollard EisenLab
  • A survey of motif discovery methods in an integrated framework
    Biology Direct, Vol. 1, No. 1. (06 April 2006), 11.
    by Geir K Sandve, Finn Drabløs
    posted to discovery motif review by samal on 2006-08-22 05:19:48 as ** along with 5 people and 1 group idonaldson aprasad dpollard yevishere csdhwang EisenLab
  • Close sequence comparisons are sufficient to identify human cis-regulatory elements.
    Genome Res (12 June 2006)
    by Shyam Prabhakar, Francis Poulin, Malak Shoukry, Veena Afzal, Edward M M Rubin, Olivier Couronne, Len A A Pennacchio
    posted to alignment annotation conserved constraint evolution footprinting human mammal mammals no-tag prediction rate selection tfbs transcription turnover by samal on 2006-08-22 05:18:32 as ** along with 7 people and 2 groups bpcusack mariakmejia indigoviolet dpollard nickluscombe olympos emptyhb EisenLab EBI-regulation
  • Enhancing the prediction of transcription factor binding sites by incorporating structural properties and nucleotide covariations.
    J Comput Biol, Vol. 13, No. 4. (May 2006), pp. 929-945.
    by S Gunewardena, P Jeavons, Z Zhang
    posted to binding motif prediction structure transcription by samal on 2006-08-20 12:01:00 as ** along with 2 people and 1 group dpollard nklee EisenLab
  • Unsupervised pattern recognition: An introduction to the whys and wherefores of clustering microarray data.
    Brief Bioinform, Vol. 6, No. 4. (December 2005), pp. 331-343.
    by PC Boutros, AB Okey
    posted to clustering microarray by samal on 2006-08-16 18:31:06 as ** along with 7 people bertelsen jfr metamerist tabu srfairclough akastrin xili03
  • Network structures and algorithms in Bioconductor
    Bioinformatics, Vol. 21, No. 1., 135.
    by Vincent J Carey, Jeff Gentry, Elizabeth Whalen, Robert Gentleman
    posted to network oconductor by samal on 2006-08-16 18:30:10 as ** along with 1 person tabu
  • Functional genomic hypothesis generation and experimentation by a robot scientist.
    Nature, Vol. 427, No. 6971. (15 January 2004), pp. 247-252.
    by RD King, KE Whelan, FM Jones, PG Reiser, CH Bryant, SH Muggleton, DB Kell, SG Oliver
    posted to automation biological design experimental for literature-based-discovery robot scientist systems by samal on 2006-08-16 18:28:18 as ** along with 7 people and 5 groups dbk tmmurali yas jtbates tabu dullhunk JeremyZucker streptomyces dbk-lab T_lab triplehelix MetabolicModeling
  • Genome-wide analysis of mammalian promoter architecture and evolution
    Nature Genetics, Vol. 38, No. 6. (28 April 2006), pp. 626-635.
    by Piero Carninci, Albin Sandelin, Boris Lenhard, Shintaro Katayama, Kazuro Shimokawa, Jasmina Ponjavic, Colin AM Semple, Martin S Taylor, Pär G Engström, Martin C Frith, Alistair RR Forrest, Wynand B Alkema, Sin L Tan, Charles Plessy, Rimantas Kodzius, Timothy Ravasi, Takeya Kasukawa, Shiro Fukuda, Mutsumi Kanamori-Katayama, Yayoi Kitazume, Hideya Kawaji, Chikatoshi Kai, Mari Nakamura, Hideaki Konno, Kenji Nakano, Salim Mottagui-Tabar, Peter Arner, Alessandra Chesi, Stefano Gustincich, Francesca Persichetti, Harukazu Suzuki, Sean M Grimmond, Christine A Wells, Valerio Orlando, Claes Wahlestedt, Edison T Liu, Matthias Harbers, Jun Kawai, Vladimir B Bajic, David A Hume, Yoshihide Hayashizaki
    posted to cage comparative-analysis genome human mammals motif promoter transcription by samal on 2006-08-11 16:01:51 as ** along with 10 people and 4 groups jasonflannick jfr xwbcn dchughes tabu nickluscombe xiaobeizhao cisevol eviledv gjuggler G4ID EBI-regulation Genetics-of-Gambling cis-regulatory-evolution
  • Generalized Nonparametric Mixed-Effect Models: Computation and Smoothing Parameter Selection
    Journal of Computational & Graphical Statistics, Vol. 14, No. 2. (June 2005), pp. 485-504.
    by Chong Gu, Ping Ma
    posted to mixed-effect models nonparametric by samal on 2006-08-11 10:02:38 as ** along with 1 person jclau
  • Transcriptional regulatory networks in Saccharomyces cerevisiae.
    Science, Vol. 298, No. 5594. (25 October 2002), pp. 799-804.
    by TI Lee, NJ Rinaldi, F Robert, DT Odom, Z Bar-Joseph, GK Gerber, NM Hannett, CT Harbison, CM Thompson, I Simon, J Zeitlinger, EG Jennings, HL Murray, DB Gordon, B Ren, JJ Wyrick, JB Tagne, TL Volkert, E Fraenkel, DK Gifford, RA Young
    posted to bivoc chip genomics network networks no-tag thesis transcriptional_regulation yeast by samal on 2006-08-11 09:59:21 as ** along with 24 people and 2 groups Takayuki Borelli kristallreiner brant camster snuppepuppan icases forluvoft ggrot alokm opheliav sameetmehta cconboy koller jguinney franklin timflutre jpoyatos lusk nklee karfunkel mimulus_99 roys njcitulike dbk-lab TNT
  • Degeneracy and complexity in biological systems.
    Proc Natl Acad Sci U S A, Vol. 98, No. 24. (20 November 2001), pp. 13763-13768.
    by GM Edelman, JA Gally
    posted to coding complexity genevariation networks by samal on 2006-08-11 09:58:20 as ** along with 2 people snuppepuppan bayesian
  • Locally Efficient Semiparametric Estimators for Generalized Skew-Elliptical Distributions
    Journal of the American Statistical Association, Vol. 100, No. 471. (September 2005), pp. 980-989.
    by Yanyuan Ma, Marc G Genton, Anastasios A Tsiatis
    posted to skew-elliptical by samal on 2006-08-11 09:54:08 as **
  • Studying complex biological systems using multifactorial perturbation.
    Nat Rev Genet, Vol. 4, No. 2. (February 2003), pp. 145-151.
    by RC Jansen
    posted to biological complex multifactorial perturbation studying systems using by samal on 2006-08-11 09:51:23 as ** along with 4 people snuppepuppan tmmurali jfr qfwills
  • Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease
    Nature Genetics, Vol. 37, No. 3. (13 February 2005), pp. 243-253.
    by Norbert Hubner, Caroline A Wallace, Heike Zimdahl, Enrico Petretto, Herbert Schulz, Fiona Maciver, Michael Mueller, Oliver Hummel, Jan Monti, Vaclav Zidek, Alena Musilova, Vladimir Kren, Helen Causton, Laurence Game, Gabriele Born, Sabine Schmidt, Anita Müller, Stuart A Cook, Theodore W Kurtz, John Whittaker, Michal Pravenec, Timothy J Aitman
    posted to medicine mesophysics pags sease by samal on 2006-08-11 09:50:19 as ** along with 6 people thomaskelder jo_davies snuppepuppan kentsis neveaire caseybrown
  • Robustness as a measure of plausibility in models of biochemical networks.
    J Theor Biol, Vol. 216, No. 1. (7 May 2002), pp. 19-30.
    by M Morohashi, AE Winn, MT Borisuk, H Bolouri, J Doyle, H Kitano
    posted to networks robustness by samal on 2006-08-11 09:49:43 as ** along with 3 people and 1 group camster snuppepuppan monod dbk-lab
  • Noise Propagation in Gene Networks
    Science, Vol. 307, No. 5717. (25 March 2005), pp. 1965-1969.
    by Juan M Pedraza, Alexander van Oudenaarden
    posted to avano_lab expression gene genecircuits geneticnetworks genevariation networks noise stochastic syntheticbiology by samal on 2006-08-11 09:49:05 as ** along with 12 people dylanwalker brianb jiny suizan rklancer snuppepuppan JKelly555 madhadron jiyu mhucka timflutre margaritis
  • An architecture for biological information extraction and representation.
    Bioinformatics, Vol. 21, No. 4. (15 February 2005), pp. 430-438.
    by A Vailaya, P Bluvas, R Kincaid, A Kuchinsky, M Creech, A Adler
    posted to abstracts bib bio ie information-extraction nlp textmining by samal on 2006-08-11 09:43:53 as ** along with 3 people and 2 groups snuppepuppan irenas yas dbk-lab T_lab
  • A probabilistic view of gene function.
    Nat Genet, Vol. 36, No. 6. (June 2004), pp. 559-564.
    by AG Fraser, EM Marcotte
    posted to bio bioinformatics gene gene-function networks no-tag probabilistic textmining by samal on 2006-08-11 09:27:44 as *** along with 9 people and 1 group snuppepuppan ziquje lfriedl opheliav wnpx grahamc massivemayhem bootsy vietanh0 kdl
  • A bottom-up approach to gene regulation
    Nature, Vol. 439, No. 7078. (16 February 2006), pp. 856-860.
    by Nicholas J Guido, Xiao Wang, David Adalsteinsson, David Mcmillen, Jeff Hasty, Charles R Cantor, Timothy C Elston, JJ Collins
    posted to collins collins_lab development evolution expression gene gene-expression gene_expression molecular-signaling morphogenesis networks noise regulation regulatory-cascades transcription transcriptional_regulation by samal on 2006-08-11 09:14:59 as ** along with 14 people and 2 groups tmmurali rklancer snuppepuppan jyuh okarsligil bayesian balicea madhadron balabu johncumbers mmt proulx dbikard nklee Bioinformatics SynBioSys
  • Integration of text- and data-mining using ontologies successfully selects disease gene candidates
    Nucleic Acids Research, Vol. 33, No. 5. (2005), pp. 1544-1552.
    by Nicki Tiffin, Janet F Kelso, Alan R Powell, Hong Pan, Vladimir B Bajic, Winston A Hide
    posted to disease findingtargets no-tag by samal on 2006-08-11 09:08:28 as *** along with 2 people snuppepuppan craigtalbert
  • Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes.
    Am J Hum Genet, Vol. 78, No. 6. (June 2006), pp. 1011-1025.
    by L Franke, H Bakel, L Fokkens, ED de Jong, M Egmont-Petersen, C Wijmenga
    posted to bio findingtargets human nettwork networks pathway by samal on 2006-08-11 09:07:06 as *** along with 6 people and 1 group snuppepuppan jyuh lfriedl tabu mmt raiyar kdl
  • Unknown
    by Skew
    posted to skew-elliptical by samal on 2006-01-17 08:50:49 as **
  • Generalized Skew-Elliptical Distributions
    by And T Quadratic
    posted to no-tag by samal on 2006-01-17 08:40:29 as ***
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