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kaarsinogen's library [159 articles]

Recent papers added to kaarsinogen's library.
  • PISCES: a protein sequence culling server.
    Bioinformatics, Vol. 19, No. 12. (12 August 2003), pp. 1589-1591.
    by G Wang, RL Dunbrack
    posted to protein_structure by kaarsinogen on 2008-04-20 18:45:27 as ** along with 8 people and 2 groups barry aalibes j3xucite dgront blackbart mloewer ezralanglois chgjb structural_bioinformatics Bioinformatics
  • DNA methylation patterns and epigenetic memory
    Genes Dev., Vol. 16, No. 1. (1 January 2002), pp. 6-21.
    by Adrian Bird
    posted to cpg_islands by kaarsinogen on 2008-04-16 20:31:30 as **
  • Methylation, mutation and cancer.
    BioEssays : news and reviews in molecular, cellular and developmental biology, Vol. 14, No. 1. (January 1992), pp. 33-36.
    by PA Jones, WM Rideout, JC Shen, CH Spruck, YC Tsai
    posted to cpg_islands by kaarsinogen on 2008-04-16 05:42:18 as **
  • DNA methylation and the frequency of CpG in animal DNA
    Nucl. Acids Res., Vol. 8, No. 7. (11 April 1980), pp. 1499-1504.
    by Adrian P Bird
    posted to cpg_islands by kaarsinogen on 2008-04-16 05:37:31 as **
  • Tandem B1 elements located in a mouse methylation center provide a target for de novo DNA methylation.
    The Journal of biological chemistry, Vol. 274, No. 51. (17 December 1999), pp. 36357-36361.
    by PA Yates, RW Burman, P Mummaneni, S Krussel, MS Turker
    posted to cpg_islands by kaarsinogen on 2008-04-14 23:35:40 as **
  • Ubiquitous and tenacious methylation of the CpG site in codon 248 of the p53 gene may explain its frequent appearance as a mutational hot spot in human cancer.
    Molecular and cellular biology, Vol. 14, No. 6. (June 1994), pp. 4225-4232.
    by AN Magewu, PA Jones
    posted to cpg_islands by kaarsinogen on 2008-04-14 23:32:19 as **
  • Aberrant CpG island methylation in cancer cell lines arises in the primary cancers from which they were derived.
    Oncogene, Vol. 21, No. 13. (27 March 2002), pp. 2114-2117.
    by T Ueki, KM Walter, H Skinner, E Jaffee, RH Hruban, M Goggins
    posted to cpg_islands by kaarsinogen on 2008-04-14 22:13:03 as **
  • Comprehensive analysis of CpG islands in human chromosomes 21 and 22.
    Proc Natl Acad Sci U S A, Vol. 99, No. 6. (19 March 2002), pp. 3740-3745.
    by D Takai, PA Jones
    posted to cpg_islands by kaarsinogen on 2008-04-14 21:39:42 as ** along with 1 person aprasad
  • CpG islands in vertebrate genomes.
    Journal of molecular biology, Vol. 196, No. 2. (20 July 1987), pp. 261-282.
    by M Gardiner-Garden, M Frommer
    posted to cpg_islands by kaarsinogen on 2008-04-14 21:35:49 as **
  • Control of gene expression by CpG island methylation in normal cells.
    Biochemical Society transactions, Vol. 32, No. Pt 6. (December 2004), pp. 913-915.
    by G Strathdee, A Sim, R Brown
    posted to cpg_islands by kaarsinogen on 2008-04-10 23:22:46 as **
  • High-throughput methylation profiling by MCA coupled to CpG island microarray.
    Genome Res (4 September 2007)
    by Marcos R H R Estécio, Pearlly S S Yan, Ashraf E K E Ibrahim, Carmen S S Tellez, Lanlan Shen, Tim H-M H Huang, Jean-Pierre J P Issa
    posted to cpg_islands by kaarsinogen on 2008-04-10 23:18:53 as ** along with 2 people jfr epigenetics
  • Cell type-specific methylation of an intronic CpG island controls expression of the MCJ gene
    Carcinogenesis, Vol. 25, No. 5. (1 May 2004), pp. 693-701.
    by G Strathdee, BR Davies, JK Vass, N Siddiqui, R Brown
    posted to cpg_islands by kaarsinogen on 2008-04-10 23:16:33 as **
  • Association of tissue-specific differentially methylated regions (TDMs) with differential gene expression
    Proceedings of the National Academy of Sciences, Vol. 102, No. 9. (1 March 2005), pp. 3336-3341.
    by Fei Song, Joseph F Smith, Makoto T Kimura, Arlene D Morrow, Tomoki Matsuyama, Hiroki Nagase, William A Held
    posted to cpg_islands by kaarsinogen on 2008-04-10 23:13:52 as **
  • A novel CpG island set identifies tissue-specific methylation at developmental gene loci.
    PLoS Biol, Vol. 6, No. 1. (January 2008)
    by R Illingworth, A Kerr, D Desousa, H Jørgensen, P Ellis, J Stalker, D Jackson, C Clee, R Plumb, J Rogers, S Humphray, T Cox, C Langford, A Bird
    posted to cpg_islands by kaarsinogen on 2008-04-10 23:10:51 as ** along with 1 person rschulz
  • Drug sensitivity prediction by CpG island methylation profile in the NCI-60 cancer cell line panel.
    Cancer research, Vol. 67, No. 23. (1 December 2007), pp. 11335-11343.
    by L Shen, Y Kondo, S Ahmed, Y Boumber, K Konishi, Y Guo, X Chen, JN Vilaythong, JP Issa
    posted to cpg_islands by kaarsinogen on 2008-04-10 23:04:49 as **
  • DNA motifs associated with aberrant CpG island methylation
    Genomics, Vol. 87, No. 5. (May 2006), pp. 572-579.
    by Alex F Feltus, Eva K Lee, Joseph F Costello, Christoph Plass, Paula M Vertino
    posted to cpg_islands by kaarsinogen on 2008-04-10 23:02:30 as **
  • CpG Island Mapping by Epigenome Prediction.
    PLoS Comput Biol, Vol. 3, No. 6. (8 June 2007)
    by Christoph Bock, Jörn Walter, Martina Paulsen, Thomas Lengauer
    posted to cpg_islands by kaarsinogen on 2008-04-10 22:53:35 as ** along with 6 people sebastien_vigneau zwang oelemento fpattyn rschulz inesdesantiago
  • A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 11q: comparison with chromosome 21q.
    DNA sequence : the journal of DNA sequencing and mapping, Vol. 17, No. 4. (August 2006), pp. 300-306.
    by Y Yamada, T Shirakawa, TD Taylor, K Okamura, H Soejima, M Uchiyama, T Iwasaka, T Mukai, K Muramoto, Y Sakaki, T Ito
    posted to cpg_islands by kaarsinogen on 2008-04-10 22:46:16 as **
  • The CpG island in intron 22 of the factor VIII gene is predominantly methylated on the X chromosome of human males
    Journal of Human Genetics, Vol. 47, No. 5. (20 May 2002), pp. 239-242.
    by CD De Brasi, DJ Bowen, PW Collins, IB Larripa
    posted to cpg_islands by kaarsinogen on 2008-04-10 22:34:50 as **
  • Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis.
    Cell (30 August 2006)
    by Xiaoyu Zhang, Junshi Yazaki, Ambika Sundaresan, Shawn Cokus, Simon W-L W Chan, Huaming Chen, Ian R R Henderson, Paul Shinn, Matteo Pellegrini, Steve E E Jacobsen, Joseph R R Ecker
    posted to cpg_islands by kaarsinogen on 2008-04-10 22:30:51 as ** along with 2 people and 1 group kengg tinahu Plantandetc
  • DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project.
    PLoS Biol, Vol. 2, No. 12. (December 2004)
    by VK Rakyan, T Hildmann, KL Novik, J Lewin, J Tost, AV Cox, TD Andrews, KL Howe, T Otto, A Olek, J Fischer, IG Gut, K Berlin, S Beck
    posted to cpg_islands by kaarsinogen on 2008-04-10 22:25:30 as ** along with 3 people mc_hamming tuck balicea
  • A Comprehensive Analysis of Allelic Methylation Status of CpG Islands on Human Chromosome 21q
    Genome Res., Vol. 14, No. 2. (1 February 2004), pp. 247-266.
    by Yoichi Yamada, Hidemi Watanabe, Fumihito Miura, Hidenobu Soejima, Michiko Uchiyama, Tsuyoshi Iwasaka, Tsunehiro Mukai, Yoshiyuki Sakaki, Takashi Ito
    posted to cpg_islands by kaarsinogen on 2008-04-10 22:19:39 as **
  • Prediction of methylated CpGs in DNA sequences using a support vector machine.
    FEBS letters, Vol. 579, No. 20. (15 August 2005), pp. 4302-4308.
    by M Bhasin, H Zhang, EL Reinherz, PA Reche
    posted to cpg_islands by kaarsinogen on 2008-04-10 22:04:06 as **
  • Predicting methylation status of CpG islands in the human brain
    Bioinformatics, Vol. 22, No. 18. (15 September 2006), pp. 2204-2209.
    by Fang, Fang, Fan, Shicai, Zhang, Xuegong, Zhang, Q Michael
    posted to cpg_islands by kaarsinogen on 2008-04-10 21:56:23 as ** along with 1 person inesdesantiago
  • Predicting aberrant CpG island methylation
    Proceedings of the National Academy of Sciences, Vol. 100, No. 21. (14 October 2003), pp. 12253-12258.
    by FA Feltus, EK Lee, JF Costello, C Plass, PM Vertino
    posted to cpg_islands by kaarsinogen on 2008-04-10 21:51:15 as ** along with 1 person inesdesantiago
  • The DNA methylation paradox.
    Trends in genetics : TIG, Vol. 15, No. 1. (January 1999), pp. 34-37.
    by PA Jones
    posted to cpg_islands by kaarsinogen on 2008-04-10 21:44:37 as **
  • Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation.
    J Mol Biol, Vol. 285, No. 4. (29 January 1999), pp. 1735-1747.
    by JM Word, SC Lovell, JS Richardson, DC Richardson
    posted to protein_structure by kaarsinogen on 2008-04-02 17:34:43 as ** along with 4 people and 2 groups jwm Alan j3xucite blackbart Radiation_Damage Stressosome
  • Amino acid substitution matrices from protein blocks.
    Proc Natl Acad Sci U S A, Vol. 89, No. 22. (15 November 1992), pp. 10915-10919.
    by S Henikoff, JG Henikoff
    posted to no-tag by kaarsinogen on 2008-03-24 19:35:21 as ** along with 5 people ashwinma dgront gurkanbebek Iden-J_GluR cjeans
  • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
    Nucleic Acids Res, Vol. 25, No. 17. (1 September 1997), pp. 3389-3402.
    by SF Altschul, TL Madden, AA Schäffer, J Zhang, Z Zhang, W Miller, DJ Lipman
    posted to no-tag by kaarsinogen on 2008-03-24 19:26:49 as ** along with 41 people and 4 groups newton1234 david_parsons edvin bandrewfox mariakmejia knaseanka setar iakes miguel bjorns bicko jmeppley chad_davis balajis nuke2005 eweaver indigoviolet dullhunk robert dgront happy_manatee caporaso treangen kengg manzanita leelarcombe CitoJam jdelcampo aengisch rabio massivemayhem mirzazadeh azazello sujaikumar beatrizfernandez GustavoLacerda siebertm adijr viktor21614 mijam grottenolm EisenLab biomedical-nlp Microbial-Ecology Plantandetc
  • The Quickhull Algorithm for Convex Hulls
    ACM Transactions on Mathematical Software, Vol. 22, No. 4. (1996), pp. 469-483.
    by Bradford C Barber, David P Dobkin, Hannu Huhdanpaa
    posted to protein_structure by kaarsinogen on 2008-03-24 19:19:35 as ** along with 2 people yushkevich tigarmo
  • Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool.
    J Mol Biol, Vol. 267, No. 5. (18 April 1997), pp. 1268-1282.
    by MJ Bower, FE Cohen, RL Dunbrack
    posted to protein_structure by kaarsinogen on 2008-03-24 19:04:07 as ** along with 5 people and 1 group carlk jwm nknii blackbart mijam TCR_Signaling
  • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.
    Biopolymers, Vol. 22, No. 12. (December 1983), pp. 2577-2637.
    by W Kabsch, C Sander
    posted to protein_structure by kaarsinogen on 2008-03-24 18:26:31 as ** along with 14 people mschofie lna chad_davis wouterboomsma penka ffranca dgront choonpeng leelarcombe rabio gisle medic0747 martainn chgjb
  • Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential.
    Nucleic Acids Res, Vol. 33, No. 2. (2005), pp. 546-558.
    by Z Liu, F Mao, JT Guo, B Yan, P Wang, Y Qu, Y Xu
    posted to protein-dna_interaction by kaarsinogen on 2008-03-20 17:50:53 as ** along with 1 person and 1 group oannes Regulomics_UCHSC
  • Protein-RNA interactions: exploring binding patterns with a three-dimensional superposition analysis of high resolution structures.
    Bioinformatics (11 September 2006)
    by N Morozova, J Allers, J Myers, Y Shamoo
    posted to protein-dna_interaction by kaarsinogen on 2008-03-20 17:11:10 as ** along with 3 people and 2 groups marcius eckart_bindewald medic0747 BioinfoCIPF SGU-CIPF
  • An analysis of information content present in protein-DNA interactions.
    Pacific Symposium on Biocomputing, Vol. 13 (20 September 2008), pp. 477-488.
    by Kauffman
    posted to protein-dna_interaction by kaarsinogen on 2008-03-20 16:59:40 as **
  • A neural network method for identification of RNA-interacting residues in protein.
    Genome Inform., Vol. 15, No. 1. (2004), pp. 105-116.
    by Jeong
    posted to neural_network protein-rna by kaarsinogen on 2008-03-17 22:51:20 as **
  • Random Forests
    Machine Learning, Vol. V45, No. 1. (1 October 2001), pp. 5-32.
    by Leo Breiman
    posted to decision_tree by kaarsinogen on 2008-03-17 22:09:13 as ** along with 8 people carlk AbnerCYH sdvillal amirsaffari maheshj lp2 poluxmoon jdu
  • PISCES: recent improvements to a PDB sequence culling server.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005)
    by G Wang, RL Dunbrack
    posted to protein_structure by kaarsinogen on 2008-03-17 18:10:49 as ** along with 4 people chad_davis bicko blackbart chgjb
  • Predicting rRNA-, RNA-, and DNA-binding proteins from primary structure with support vector machines
    Journal of Theoretical Biology, Vol. 240, No. 2. (21 May 2006), pp. 175-184.
    by Xiaojing Yu, Jianping Cao, Yudong Cai, Tieliu Shi, Yixue Li
    posted to protein-dna_interaction protein-rna svm by kaarsinogen on 2008-03-17 15:51:01 as **
  • Prediction of RNA-binding proteins from primary sequence by a support vector machine approach
    RNA, Vol. 10, No. 3. (1 March 2004), pp. 355-368.
    by Lian YI Han, Cong ZHONG Cai, Siew LIN Lo, Maxey C Chung, Yu ZONG Chen
    posted to protein-rna svm by kaarsinogen on 2008-03-17 15:47:12 as **
  • Support vector machines for predicting rRNA-, RNA-, and DNA-binding proteins from amino acid sequence
    Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics, Vol. 1648, No. 1-2. (30 May 2003), pp. 127-133.
    by Yu-Dong Cai, Shuo L Lin
    posted to protein-rna svm by kaarsinogen on 2008-03-17 15:43:26 as **
  • LIBSVM: a Library for Support Vector Machines (Version 2.31)
    by Chih-Chung Chang, Chih-Jen Lin
    posted to machine_learning svm by kaarsinogen on 2008-03-13 14:09:26 as ** along with 8 people and 1 group gyuli grzegorz chad_davis craigtalbert zoop bundschu doubleshow vlachmore generif_paper
  • Support-Vector Networks
    Machine Learning, Vol. 20, No. 3. (1995), pp. 273-297.
    by Corinna Cortes, Vladimir Vapnik
    posted to machine_learning svm by kaarsinogen on 2008-03-13 14:08:19 as ** along with 4 people sesejun KaraNagai atbrew eddymier
  • Cost--Sensitive Learning by Cost-- Proportionate Example Weighting
    (2003)
    by B Zadrozny, J Langford, A Naoki
    posted to decision_tree machine_learning by kaarsinogen on 2008-03-12 23:18:16 as **
  • Bagging Predictors
    Machine Learning, Vol. 24, No. 2. (1996), pp. 123-140.
    by Leo Breiman
    posted to decision_tree machine_learning by kaarsinogen on 2008-03-12 22:48:53 as ** along with 17 people and 2 groups askom eegilbert gyuli kevynct neteler ChaTo lfriedl mukundn mthomure sdvillal KaraNagai lbatista Repton robincha girschick thangvu wlyu2001 kdl LIVIA
  • Experiments with a New Boosting Algorithm
    (1996), pp. 148-156.
    by Yoav Freund, Robert E Schapire
    posted to decision_tree machine_learning by kaarsinogen on 2008-03-12 22:26:17 as ** along with 13 people mdifranc gyuli ChaTo mukundn ebrochu dreamneo Aska amirsaffari awaljee jborn dimatura girschick assad79
  • Improved Boosting Using Confidence-rated Predictions
    Machine Learning, Vol. 37, No. 3. (1999), pp. 297-336.
    by Robert E Schapire, Yoram Singer
    posted to decision_tree machine_learning by kaarsinogen on 2008-03-12 22:22:23 as ** along with 6 people and 3 groups egibaja bpacker shilad Repton zk00006 matumio Boosting GroupLens vision-ng
  • The alternating decision tree learning algorithm,
    (1999), pp. 124-133.
    by Yoav Freund, Llew Mason
    posted to decision_tree machine_learning by kaarsinogen on 2008-03-12 16:28:44 as ** along with 1 person carlk
  • Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry
    Nucl. Acids Res. (14 February 2008), gkn008.
    by Yao C Chen, Carmay Lim
    posted to protein-rna by kaarsinogen on 2008-03-07 20:45:23 as ** along with 3 people and 1 group marck sobolevnrm sunhwan baker-group
  • Prediction of RNA binding sites in a protein using SVM and PSSM profile
    Proteins: Structure, Function, and Bioinformatics, Vol. 71, No. 1. (2008), pp. 189-194.
    by Manish Kumar, Michael M Gromiha, GPS Raghava
    posted to protein-rna svm by kaarsinogen on 2008-03-07 20:43:00 as **
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