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Group: SGU-CIPF - with tag bioinformatics [196 articles]

Recent papers posted by members of the SGU-CIPF group with tag bioinformatics
  • On the relationship between sequence and structure similarities in proteomics
    Bioinformatics, Vol. 23, No. 6. (15 March 2007), pp. 717-723.
    by K Evgeny
    posted to sequence-structure classification bioinformatics by marcius to the group SGU-CIPF on 2007-04-12 10:48:28 as ** along with 1 person and 1 group penka BioinfoCIPF
  • Deleterious SNP prediction: be mindful of your training data!
    Bioinformatics, Vol. 23, No. 6. (15 March 2007), pp. 664-672.
    by Care, A Matthew, Needham, J Chris, Bulpitt, J Andrew, Westhead, R David
    posted to snp bioinformatics by marcius to the group SGU-CIPF on 2007-04-12 10:45:50 as ** along with 3 people and 1 group happy_manatee penka Yumyai BioinfoCIPF
  • Modeling the Evolution of Protein Domain Architectures Using Maximum Parsimony
    Journal of Molecular Biology, Vol. 366, No. 1. (9 February 2007), pp. 307-315.
    by Jessica H Fong, Lewis Y Geer, Anna R Panchenko, Stephen H Bryant
    posted to protein_domains evolution bioinformatics algorithms by marcius to the group SGU-CIPF on 2007-01-25 08:31:09 as ** along with 5 people and 2 groups icases tny choonpeng redelings zwang BioinfoCIPF TNT
  • Sequence comparison by sequence harmony identifies subtype-specific functional sites
    Nucleic Acids Research, Vol. 34, No. 22. (December 2006), pp. 6540-6548.
    by W Pirovano, KA Feenstra, J Heringa
    posted to bioinformatics classification function protein sequence_alignment by marcius to the group SGU-CIPF on 2007-01-03 13:02:03 as ** along with 2 people and 1 group sriram_s marti BioinfoCIPF
  • Discovering disease-genes by topological features in human protein-protein interaction network
    Bioinformatics, Vol. 22, No. 22. (15 November 2006), pp. 2800-2805.
    by J Xu, Y Li
    posted to bioinformatics disease protein_interactions by marcius to the group SGU-CIPF on 2006-11-24 08:57:33 as ** along with 2 people and 1 group skhadar ealloza BioinfoCIPF
  • ProteinRNA interactions: exploring binding patterns with a three-dimensional superposition analysis of high resolution structures
    Bioinformatics, Vol. 22, No. 22. (15 November 2006), pp. 2746-2752.
    by N Morozova, J Allers, Y Shamoo
    posted to bioinformatics protein_interactions rna algorithms by marcius to the group SGU-CIPF on 2006-11-16 09:29:09 as ** along with 1 group BioinfoCIPF
  • 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 bioinformatics rna secondary_structure by marcius to the group SGU-CIPF on 2006-11-01 14:13:15 as ** along with 5 people and 2 groups tardigrade andersbj samal dquest plofje microRNA BioinfoCIPF
  • Three-dimensional comparative modeling of RNA.
    Nucleic Acids Symp Ser, No. 36. (1997), pp. 69-71.
    by C Zwieb, F Müller
    posted to algorithms bioinformatics comparative_modeling rna by marcius to the group SGU-CIPF on 2006-10-27 21:31:25 as ** along with 1 group BioinfoCIPF
  • From The Cover: Global mapping of the protein structure space and application in structure-based inference of protein function
    PNAS, Vol. 102, No. 10. (8 March 2005), pp. 3651-3656.
    by Jingtong Hou, Se-Ran Jun, Chao Zhang, Sung-Hou Kim
    posted to algorithms bioinformatics clustering protein_structure by marcius to the group SGU-CIPF on 2006-10-26 08:42:48 as ** along with 1 person and 1 group tny BioinfoCIPF
  • Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection
    Nucleic Acids Research, Vol. 34, No. 17. (October 2006), pp. e112-e112.
    by D Chivian, D Baker
    posted to algorithms bioinformatics comparative_modeling sequence_alignment by marcius to the group SGU-CIPF on 2006-10-25 21:43:08 as ** along with 1 person and 1 group j3xucite BioinfoCIPF
  • 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 bioinformatics comparative_docking protein_interactions by marcius to the group SGU-CIPF on 2006-10-22 12:11:09 as ** along with 5 people and 3 groups wilbur barry tjimenez bicko chad_davis structural_bioinformatics Bioinformatics BioinfoCIPF
  • Protemot: prediction of protein binding sites with automatically extracted geometrical templates.
    Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006)
    by DT Chang, YZ Weng, JH Lin, MJ Hwang, YJ Oyang
    posted to bioinformatics drug ligand protein by marcius to the group SGU-CIPF on 2006-10-21 14:24:50 as ** along with 1 group BioinfoCIPF
  • Structural bioinformatic approaches to the discovery of new antimycobacterial drugs.
    Curr Pharm Des, Vol. 10, No. 26. (2004), pp. 3195-3211.
    by K Kantardjieff, B Rupp
    posted to bioinformatics docking drug ligand protein review by marcius to the group SGU-CIPF on 2006-10-21 14:23:24 as ** along with 1 group BioinfoCIPF
  • Bayesian search of functionally divergent protein subgroups and their function specific residues
    Bioinformatics, Vol. 22, No. 20. (15 October 2006), pp. 2466-2474.
    by Marttinen, Pekka, Corander, Jukka, Toronen, Petri, Holm, Liisa
    posted to algorithms bioinformatics protein_function by marcius to the group SGU-CIPF on 2006-10-20 13:21:03 as ** along with 1 group BioinfoCIPF
  • Mining frequent stem patterns from unaligned RNA sequences
    Bioinformatics, Vol. 22, No. 20. (15 October 2006), pp. 2480-2487.
    by Hamada, Michiaki, Tsuda, Koji, Kudo, Taku, Kin, Taishin, Asai, Kiyoshi
    posted to algorithms alignment bioinformatics rna by marcius to the group SGU-CIPF on 2006-10-20 13:20:33 as ** along with 1 group BioinfoCIPF
  • Partial correlation coefficient between distance matrices as a new indicator of proteinprotein interactions
    Bioinformatics, Vol. 22, No. 20. (15 October 2006), pp. 2488-2492.
    by Sato, Tetsuya, Yamanishi, Yoshihiro, Horimoto, Katsuhisa, Kanehisa, Minoru, Toh, Hiroyuki
    posted to bioinformatics interaction protein_interactions by marcius to the group SGU-CIPF on 2006-10-20 13:20:00 as ** along with 1 group BioinfoCIPF
  • The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease.
    Science, Vol. 313, No. 5795. (29 September 2006), pp. 1929-1935.
    by J Lamb, ED Crawford, D Peck, JW Modell, IC Blat, MJ Wrobel, J Lerner, JP Brunet, A Subramanian, KN Ross, M Reich, H Hieronymus, G Wei, SA Armstrong, SJ Haggarty, PA Clemons, R Wei, SA Carr, ES Lander, TR Golub
    posted to bioinformatics disease drug genome by marcius to the group SGU-CIPF on 2006-10-04 13:02:14 as ** along with 21 people and 8 groups askrajiv BragilMassoud jyuh kuhn jfr yas balajis lhonigberg neveaire kengg ealloza koller mlovell jdiggans ezra jeremymiller frohike massivemayhem lp2 pablomendes jdiezperezj Biostatistics Computational-Genomics Bioinformatics Neuroscience T_lab BioinfoCIPF GeschwindLab Plantandetc
  • The Many Faces of Protein–Protein Interactions: A Compendium of Interface Geometry
    PLoS Computational Biology, Vol. 2, No. 9. (1 September 2006), e124.
    by Wan K Kim, Andreas Henschel, Christof Winter, Michael Schroeder
    posted to bioinformatics clustering protein_interactions by marcius to the group SGU-CIPF on 2006-09-29 08:58:11 as ** along with 1 group BioinfoCIPF
  • Evolution of alternative transcriptional circuits with identical logic
    Nature, Vol. 443, No. 7110. (2006), pp. 415-420.
    by Annie E Tsong, Brian B Tuch, Hao Li, Alexander D Johnson
    posted to bioengineering bioinformatics biophysics by marcius to the group SGU-CIPF on 2006-09-28 09:03:32 as ** along with 6 people and 3 groups emptyhb brant adepace aswin srfairclough cisevol EisenLab BioinfoCIPF cis-regulatory-evolution
  • Sequence and structural differences between enzyme and nonenzyme homologs.
    Structure (Camb), Vol. 10, No. 10. (October 2002), pp. 1435-1451.
    by AE Todd, CA Orengo, JM Thornton
    posted to bioinformatics classification function protein by marcius to the group SGU-CIPF on 2006-09-13 15:36:46 as ** along with 1 person and 1 group matzke BioinfoCIPF
  • Computational methods for RNA structure determination.
    Curr Opin Struct Biol, Vol. 11, No. 3. (June 2001), pp. 282-286.
    by F Major, R Griffey
    posted to algorithms bioinformatics review rna structure by marcius to the group SGU-CIPF on 2006-09-13 15:18:38 as ** along with 3 people and 1 group lillekatt P2324548 eckart_bindewald BioinfoCIPF
  • KemaDom: a web server for domain prediction using kernel machine with local context.
    Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006)
    by L Chen, W Wang, S Ling, C Jia, F Wang
    posted to ab-initio bioinformatics prediction protein_domains by marcius to the group SGU-CIPF on 2006-09-11 09:35:21 as ** along with 2 people and 1 group gulkur skhadar BioinfoCIPF
  • How do RNA folding algorithms work?
    Nature Biotechnology, Vol. 22, No. 11., 1457.
    by Sean R Eddy
    posted to algorithms bioinformatics biophysics folding review rna by marcius to the group SGU-CIPF on 2006-09-08 11:14:16 as ** along with 10 people and 1 group austin cambray evaf tardigrade mtagaya 3times3 cthachuk magnolia maralena guxiyou BioinfoCIPF
  • Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints.
    BMC Bioinformatics, Vol. 7 (04 September 2006), 400.
    by Robin D Dowell, Sean R Eddy
    posted to algorithms alignment bioinformatics prediction rna structure by marcius to the group SGU-CIPF on 2006-09-07 22:04:11 as ** along with 4 people and 1 group reyez eckart_bindewald dquest ilh BioinfoCIPF
  • Protein Molecular Function Prediction by Bayesian Phylogenomics.
    PLoS Comput Biol, Vol. 1, No. 5. (7 October 2005)
    by Barbara E E Engelhardt, Michael I I Jordan, Kathryn E E Muratore, Steven E E Brenner
    posted to bioinformatics prediction protein_function by marcius to the group SGU-CIPF on 2006-09-07 17:43:33 as ** along with 7 people and 3 groups kentsis ana eoghanharr Einat dlr sriram_s bootsy structural_bioinformatics Bioinformatics BioinfoCIPF
  • The RNA Ontology Consortium: an open invitation to the RNA community.
    RNA, Vol. 12, No. 4. (April 2006), pp. 533-541.
    by NB Leontis, RB Altman, HM Berman, SE Brenner, JW Brown, DR Engelke, SC Harvey, SR Holbrook, F Jossinet, SE Lewis, F Major, DH Mathews, JS Richardson, JR Williamson, E Westhof
    posted to bioinformatics classification clustering rna sequence structure by marcius to the group SGU-CIPF on 2006-09-07 17:37:08 as ** along with 2 people and 1 group reyez debatebob BioinfoCIPF
  • Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology.
    Proteins, Vol. 58, No. 4. (1 March 2005), pp. 855-865.
    by JV Ponomarenko, PE Bourne, IN Shindyalov
    posted to bioinformatics evolution protein_function protein_structure by marcius to the group SGU-CIPF on 2006-09-07 17:24:49 as ** along with 1 group BioinfoCIPF
  • Exploiting sequence and structure homologs to identify protein-protein binding sites.
    Proteins, Vol. 62, No. 3. (15 March 2006), pp. 630-640.
    by JL Chung, W Wang, PE Bourne
    posted to bioinformatics evolution protein_interactions by marcius to the group SGU-CIPF on 2006-09-07 17:22:13 as ** along with 2 people and 1 group bicko ameetsoni BioinfoCIPF
  • Partitioning Protein Structures into Domains: Why Is it so Difficult?
    Journal of Molecular Biology, Vol. 361, No. 3. (18 August 2006), pp. 562-590.
    by Timothy A Holland, Stella Veretnik, Ilya N Shindyalov, Philip E Bourne
    posted to bioinformatics protein_domains review by marcius to the group SGU-CIPF on 2006-09-07 17:18:43 as ** along with 2 people and 1 group chad_davis tny BioinfoCIPF
  • Probabilistic annotation of protein sequences based on functional classifications.
    BMC Bioinformatics, Vol. 6 (2005)
    by ED Levy, CA Ouzounis, WR Gilks, B Audit
    posted to algorithms bioinformatics protein_function statistics by marcius to the group SGU-CIPF on 2006-09-07 17:17:23 as ** along with 2 people and 1 group shung sgoetz BioinfoCIPF
  • Equivalent binding sites reveal convergently evolved interaction motifs
    Bioinformatics, Vol. 22, No. 5. (1 March 2006), pp. 550-555.
    by Andreas Henschel, Wan K Kim, Michael Schroeder
    posted to bioinformatics evolution protein_domains protein_interactions by marcius to the group SGU-CIPF on 2006-09-07 17:16:11 as ** along with 2 people and 1 group chad_davis nickolay BioinfoCIPF
  • Mathematics is biology's next microscope, only better; biology is mathematics' next physics, only better.
    PLoS Biol, Vol. 2, No. 12. (December 2004)
    by JE Cohen
    posted to bioinformatics biology views by marcius to the group SGU-CIPF on 2006-09-07 13:33:18 as ** along with 35 people and 12 groups joseph_x_zhou grahamc bpcusack jn221 quianominorleo rklancer BioGeek betainverse korakot cito pete hamish karbak A_Olympia beccaf22 rmj001 devin dsquared nozeresc DineshGaitonde macowell marimo bpb grzegorz cmmorel bayesian piscinero eckart_bindewald eweaver wnpx dullhunk caporaso mmt xinian jrbanga biophysics bioNetwork_sysBio Philosophy_of_Information Blog_and_Wiki_Research Fluid-Mechanics-and-Thermal-Science-Research MathBio EisenLab Computational_Systems_Biology XMLDataManagement biomedical-nlp BUiGEM BioinfoCIPF
  • Global topological features of cancer proteins in the human interactome
    Bioinformatics, Vol. 22, No. 18. (15 September 2006), pp. 2291-2297.
    by Pall F Jonsson, Paul A Bates
    posted to bioinformatics protein_interactions by marcius to the group SGU-CIPF on 2006-09-07 13:32:15 as ** along with 6 people and 1 group aalibes bicko ealloza IbnBio namtonthat dejori BioinfoCIPF
  • Computer modeling 16 S ribosomal RNA
    Journal of Molecular Biology, Vol. 221, No. 3. (5 October 1991), pp. 889-907.
    by John M Hubbard, John E Hearst
    posted to algorithms bioinformatics rna structure_prediction by marcius to the group SGU-CIPF on 2006-09-07 13:31:07 as ** along with 1 person and 1 group eckart_bindewald BioinfoCIPF
  • Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions.
    Nat Struct Mol Biol (20 August 2006)
    by Dominic Didiano, Oliver Hobert
    posted to bioinformatics microrna motif by marcius to the group SGU-CIPF on 2006-09-06 21:15:43 as ** along with 5 people and 2 groups heliopais tardigrade andersbj mtagaya lp2 microRNA BioinfoCIPF
  • Secondary Structure Prediction of Interacting RNA Molecules
    Journal of Molecular Biology, Vol. 345, No. 5., pp. 987-1001.
    by Mirela Andronescu, Zhi C Zhang, Anne Condon
    posted to algorithms bioinformatics rna secondary_structure software by marcius to the group SGU-CIPF on 2006-09-06 10:36:45 as ** along with 4 people and 1 group eckart_bindewald Hosna cthachuk physics BioinfoCIPF
  • A new algorithm for RNA secondary structure design.
    J Mol Biol, Vol. 336, No. 3. (20 February 2004), pp. 607-624.
    by M Andronescu, AP Fejes, F Hutter, HH Hoos, A Condon
    posted to algorithms bioinformatics rna secondary_structure software by marcius to the group SGU-CIPF on 2006-09-06 10:36:07 as ** along with 5 people and 3 groups eckart_bindewald gane5h cthachuk mgaldzic smallbadguy 18th-century_history_culture_and_society BioinfoCIPF CHIP
  • RNAsoft: A suite of RNA secondary structure prediction and design software tools.
    Nucleic Acids Res, Vol. 31, No. 13. (1 July 2003), pp. 3416-3422.
    by M Andronescu, R Aguirre-Hernández, A Condon, HH Hoos
    posted to bioinformatics rna secondary_structure software by marcius to the group SGU-CIPF on 2006-09-06 10:35:54 as ** along with 6 people and 3 groups eckart_bindewald stsaft Hosna cthachuk mgaldzic stajich BioinfoCIPF CHIP Berkeley Mycology
  • Searching RNA motifs and their intermolecular contacts with constraint networks.
    Bioinformatics (4 July 2006)
    by P Thébault, S de Givry, T Schiex, C Gaspin
    posted to algorithms bioinformatics motif rna by marcius to the group SGU-CIPF on 2006-08-23 13:32:31 as ** along with 3 people and 3 groups tardigrade dquest bsmagic Bioinformatics BioinfoCIPF bioinplant
  • CONTRAfold: RNA secondary structure prediction without physics-based models.
    Bioinformatics, Vol. 22, No. 14. (15 July 2006)
    by CB Do, DA Woods, S Batzoglou
    posted to algorithms bioinformatics rna secondary_structure statistics by marcius to the group SGU-CIPF on 2006-08-23 13:19:28 as ** along with 6 people and 2 groups austin balajis tardigrade penka condon acarbo beta BioinfoCIPF
  • A bayesian statistical algorithm for RNA secondary structure prediction.
    Comput Chem, Vol. 23, No. 3-4. (15 June 1999), pp. 387-400.
    by Y Ding, CE Lawrence
    posted to bioinformatics rna secondary_structure statistics by marcius to the group SGU-CIPF on 2006-08-23 13:17:05 as ** along with 3 people and 2 groups eckart_bindewald arcticrasta condon beta BioinfoCIPF
  • Next station in microarray data analysis: GEPAS.
    Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006)
    by D Montaner, J Tárraga, J Huerta-Cepas, J Burguet, JM Vaquerizas, L Conde, P Minguez, J Vera, S Mukherjee, J Valls, MA Pujana, E Alloza, J Herrero, F Al-Shahrour, J Dopazo
    posted to bioinformatics genome microarray servers by marcius to the group SGU-CIPF on 2006-08-23 13:15:19 as ** along with 5 people and 1 group tardigrade rdiaz ealloza schuylrp sgoetz BioinfoCIPF
  • BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.
    Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006)
    by F Al-Shahrour, P Minguez, J Tárraga, D Montaner, E Alloza, JM Vaquerizas, L Conde, C Blaschke, J Vera, J Dopazo
    posted to bioinformatics function genome servers by marcius to the group SGU-CIPF on 2006-08-23 13:14:46 as ** along with 2 people and 1 group ealloza Garamonfok BioinfoCIPF
  • Identification of similar regions of protein structures using integrated sequence and structure analysis tools
    BMC Structural Biology, Vol. 6 (09 March 2006), 4.
    by Brandon Peters, Charles Moad, Eunseog Youn, Kris Buffington, Randy Heiland, Sean Mooney
    posted to bioinformatics servers structure_alignment by marcius to the group SGU-CIPF on 2006-08-09 17:00:00 as ** along with 1 person and 1 group Ema BioinfoCIPF
  • Allosteric determinants in guanine nucleotide-binding proteins.
    Proc Natl Acad Sci U S A, Vol. 100, No. 24. (25 November 2003), pp. 14445-14450.
    by ME Hatley, SW Lockless, SK Gibson, AG Gilman, R Ranganathan
    posted to allosteric bioinformatics biophysics statistical_potentials by marcius to the group SGU-CIPF on 2006-08-09 16:38:51 as ** along with 4 people and 4 groups barry lna Einat caporaso structural_bioinformatics Bioinformatics biomedical-nlp BioinfoCIPF
  • Structural determinants of allosteric ligand activation in RXR heterodimers.
    Cell, Vol. 116, No. 3. (6 February 2004), pp. 417-429.
    by AI Shulman, C Larson, DJ Mangelsdorf, R Ranganathan
    posted to allosteric bioinformatics biophysics statistical_potentials by marcius to the group SGU-CIPF on 2006-08-09 16:38:37 as ** along with 3 people and 2 groups lna gbart caporaso biomedical-nlp BioinfoCIPF
  • Knowledge-based potentials in protein design
    Current Opinion in Structural Biology, Vol. 16, No. 4. (August 2006), pp. 508-513.
    by Alan M Poole, Rama Ranganathan
    posted to bioinformatics review statistical_potentials by marcius to the group SGU-CIPF on 2006-08-09 16:37:43 as ** along with 3 people and 1 group nigham rabio bethbromley BioinfoCIPF
  • Combinatorics of RNA secondary structures
    Discrete Appl. Math., Vol. 88, No. 1-3. (1998), pp. 207-237.
    by Ivo L Hofacker, Peter Schuster, Peter F Stadler
    posted to bioinformatics rna secondary_structure by marcius to the group SGU-CIPF on 2006-07-28 12:38:52 as ** along with 2 people and 1 group ilh mtw BioinfoCIPF
  • From sequences to shapes and back: a case study in RNA secondary structures.
    Proc R Soc Lond B Biol Sci, Vol. 255, No. 1344. (22 March 1994), pp. 279-284.
    by P Schuster, W Fontana, PF Stadler, IL Hofacker
    posted to bioinformatics biophysics rna secondary_structure by marcius to the group SGU-CIPF on 2006-07-28 12:38:26 as ** along with 3 people and 1 group evaf ilh mtw BioinfoCIPF
  • Ecological networks and their fragility
    Nature, Vol. 442, No. 7100., pp. 259-264.
    by Josã© M Montoya, Stuart L Pimm, Ricard V Solã©
    posted to bioinformatics evolution by marcius to the group SGU-CIPF on 2006-07-24 12:49:27 as ** along with 3 people and 4 groups cmm mattjb stefanoallesina FAB-lab ComplexAdaptiveSystems BioinfoCIPF DSTO-CAS
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