Tag substitution [73 articles] Export

Recent papers classified by the tag substitution.

	Nonlinear Dynamics of Nonsynonymous (dN) and Synonymous (dS) Substitution Rates Affects Inference of Selection [My Copy] Genome Biol Evol, Vol. 2009, No. 0. (4 September 2009), pp. 308-319. by Jochen B. W. Wolf, Axel Kunstner, Kiwoong Nam, Mattias Jakobsson, Hans Ellegren posted to substitution dynamics ds dn by gwallau on 2009-08-31 15:20:50 as along with 5 people and 3 groups avilella operon stajich sharpton gjuggler Ensembl Compara citations Mycology iSEEM
	Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. [My Copy] BMC evolutionary biology, Vol. 6, No. 1. (2006) by T. M. Keane, C. J. Creevey, M. M. Pentony, T. J. Naughton, J. O. Mclnerney posted to amino-acid matrix substitution by niallhaslam on 2009-07-30 10:25:57 as along with 2 people clearbluespring JamesMcInerney
	Structural and functional restraints in the evolution of protein families and superfamilies. [My Copy] Biochemical Society transactions, Vol. 37, No. Pt 4. (August 2009), pp. 727-733. by S. Gong, C. L. Worth, G. R. Bickerton, S. Lee, D. Tanramluk, T. L. Blundell posted to environment-specific function protein sequence structure substitution by sebk to the group OPIG on 2009-07-21 13:16:00 as along with 1 person subramani
	First Principles Investigation of Mineral Component of Bone: CO3 Substitutions in Hydroxyapatite [My Copy] Chemistry of Materials, Vol. 17, No. 16. (1 August 2005), pp. 4125-4133. by R. Astala, M. J. Stott posted to apatite bone calcium carbonate defect phosphate substitution by paddydu on 2009-07-01 17:18:56 as
	Mutations in influenza virus replication and transcription: detection of amino acid substitutions in hemagglutinin of an avian influenza virus (H1N1) [My Copy] FASEB J. (24 June 2009), fj.09-134072. by Ning Liu, Genyan Wang, Kim C. Lee, Yi Guan, Honglin Chen, Zongwei Cai posted to evolution influenza substitution by zwang on 2009-06-29 08:32:14 as
	Strong Evidence for Lineage and Sequence Specificity of Substitution Rates and Patterns in Drosophila [My Copy] Mol Biol Evol, Vol. 26, No. 7. (1 July 2009), pp. 1591-1605. by Nadia D. Singh, Peter F. Arndt, Andrew G. Clark, Charles F. Aquadro posted to clock drosophila lineage molecular mutation rates substitution variation by katholt on 2009-06-26 13:05:04 as along with 5 people operon michaelbarton djkt bmajoros benjaminsb
	Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. [My Copy] Mol Biol Evol, Vol. 17, No. 1. (January 2000), pp. 32-43. by Z. Yang, R. Nielsen posted to nielsen rates substitution yang by katholt on 2009-06-18 18:16:32 as along with 9 people and 1 group bjorns fernan hdopazo BioNica timflutre Garamonfok ankur_iitg RamuAnandakrishnan Ema BioinfoCIPF
	Investigating the Relationship Between Genome Structure, Composition, and Ecology in Prokaryotes [My Copy] Mol Biol Evol, Vol. 19, No. 6. (1 June 2002), pp. 789-800. by Pietro Lio posted to indel homopeptide bias codon complexity composition dna evolution gene length low repeats sequence substitution by robfsouza on 2009-06-17 18:14:17 as along with 1 person marenzelleria
	Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution [My Copy] Cell, Vol. 134, No. 2. (25 July 2008), pp. 341-352. by Allan D. Drummond, Claus O. Wilke posted to accuracy bias codon evolution evolutionary expression gene level mutation protein rate selection substitution transcription translation by robfsouza on 2009-06-17 18:02:44 as along with 6 people nilsbecker scherrer jjray cambray bpcusack zwang
	Ulla: a program for calculating environment-specific amino acid substitution tables [My Copy] Bioinformatics (5 May 2009), btp300. by Semin Lee, Tom L. Blundell posted to acid amino mutation protein substitution by medic0747 on 2009-06-01 11:42:12 as along with 1 person operon
	Keynote address - data abstraction and hierarchy [My Copy] In OOPSLA '87: Addendum to the proceedings on Object-oriented programming systems, languages and applications (Addendum) (1987), pp. 17-34. by Barbara Liskov posted to liskov principle substitution by martinrytter on 2009-05-09 17:07:07 as along with 1 person michalpise
	Solvent effects on kinetics of an aromatic nucleophilic substitution reaction in mixtures of an ionic liquid with molecular solvents and prediction using artificial neural networks [My Copy] International Journal of Chemical Kinetics, Vol. 41, No. 3. (2009), pp. 153-159. by Aziz Habibi-Yangjeh, Yahya Jafari-Tarzanag, Ali R. Banaei posted to emimethylsulfate kinetics rtil solventeffect substitution by majdula on 2009-04-15 09:46:33 as
	Multiple amino acid substitutions are involved in the adaptation of H9N2 avian influenza virus to mice [My Copy] Veterinary Microbiology (13 March 2009) by Rui Wu, Hongbo Zhang, Keli Yang, et al.Wangwang Liang, Zhongliang Xiong, Zewen Liu, Xuehai Yang, Huabin Shao, Xinmin Zheng, Mingxin Chen posted to influenza substitution by zwang on 2009-04-08 02:09:53 as along with 1 person friendpine
	Asset Pricing in Economies with Frictions [My Copy] Econometrica, Vol. 64, No. 6. (1996), pp. 1439-1467. by Erzo G. J. Luttmer posted to asset equilibrium frictions general marginal pricing puzzle substitution by rivadeneyra on 2009-03-27 17:41:04 as
	What Level of Fixed Costs Can Reconcile Consumption and Stock Returns? [My Copy] Journal of Political Economy, Vol. 107, No. 5. (1 October 1999), pp. 969-997. by Erzo g Luttmer posted to asset costs equity frictions marginal premium pricing puzzle rate substitution transaction by rivadeneyra on 2009-03-27 17:39:10 as
	Discarding Functional Residues from the Substitution Table Improves Predictions of Active Sites within Three-Dimensional Structures [My Copy] PLoS Comput Biol, Vol. 4, No. 10. (3 October 2008), e1000179. by Sungsam Gong, Tom L. Blundell posted to environment-specific function protein sequence structure substitution by sebk on 2009-03-25 12:11:04 as along with 7 people ssgong gjuggler joseph_x_zhou zwang bicko massivemayhem reyez
	Understanding technological substitution: Generic types, substitution dynamics, and influence strategies [My Copy] Journal of Engineering and Technology Management, Vol. 9, No. 3-4. (December 1992), pp. 279-302. by C. Smith posted to dynamics generic influence strategies substitution technological types understanding by derchao on 2009-03-02 02:19:54 as
	Technological and Organizational Designs for Realizing Economies of Substitution [My Copy] Strategic Management Journal, Vol. 16 (1995), pp. 93-109. by Raghu Garud, Arun Kumaraswamy posted to designs economies organizational realizing substitution technological by derchao on 2009-02-27 08:58:23 as
	A unified hydrophobicity scale for multispan membrane proteins [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA. by Julia Koehler, Nils Woetzel, René Staritzbichler, Charles R. Sanders, Jens Meiler posted to alignment membrane protein sequence substitution by sebk on 2009-02-13 14:55:57 as along with 2 people RamuAnandakrishnan paulschlesinger
	Detecting remote homologues using scoring matrices calculated from the estimation of amino acid substitution rates of beta-barrel membrane proteins. [My Copy] Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference, Vol. 1 (2008), pp. 1347-1350. by D. Jimenez-Morales, L. Adamian, J. Liang posted to alignment membrane protein sequence substitution by sebk on 2009-02-13 14:51:22 as
	Methadone vs. buprenorphine/naloxone during early opioid substitution treatment: a naturalistic comparison of cognitive performance relative to healthy controls [My Copy] BMC Clinical Pharmacology, Vol. 7 (12 June 2007), 5. by Pekka Rapeli, Carola Fabritius, Hannu Alho, Mikko Salaspuro, Kristian Wahlbeck, Hely Kalska posted to buprenorphine finland naloxone opiate_addiction substance_abuse substitution by wahlbeck on 2009-01-05 21:14:40 as along with 1 person Terkko
	Suggestions for "safe" residue substitutions in site-directed mutagenesis. [My Copy] Journal of molecular biology, Vol. 217, No. 4. (20 February 1991), pp. 721-729. by D. Bordo, P. Argos posted to acid amino bordo91pdf mutagenesis substitution by paulschlesinger on 2009-01-02 01:13:22 as
	Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. [My Copy] Mol Biol Evol, Vol. 21, No. 3. (March 2004), pp. 468-488. by A. Siepel, D. Haussler posted to evolution likelihood maximum phylogenomics rates substitution by sriesenfeld on 2008-12-13 01:26:26 as along with 6 people mgledi mdimmic penka djkt tale uwe
	Comparison of methods for estimating the nucleotide substitution matrix [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008) by Maribeth Oscamou, Daniel Mcdonald, Von B. Yap, Gavin Huttley, Manuel Lladser, Rob Knight posted to matrix nucleotide substitution by nklee on 2008-12-10 08:16:15 as along with 4 people sconlan nuin treangen druvus
	Protein database searches using compositionally adjusted substitution matrices. [My Copy] FEBS J, Vol. 272, No. 20. (October 2005), pp. 5101-5109. by S. F. Altschul, J. C. Wootton, E. M. Gertz, et al.R. Agarwala, A. Morgulis, A. A. Schäffer, Y. K. Yu posted to amino-acid composition matrix review significance statistical substitution by treangen on 2008-11-22 20:50:22 as along with 1 person kgutwin
	Sequence alignment with an appropriate substitution matrix. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 15, No. 2. (March 2008), pp. 129-138. by X. Huang posted to alignment gap-penalty local matrix parameters substitution by treangen on 2008-11-22 20:49:18 as
	Amino acid substitution matrices from protein blocks. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 89, No. 22. (15 November 1992), pp. 10915-10919. by S. Henikoff, J. G. Henikoff posted to alignment protein sequence substitution by sebk on 2008-11-18 19:55:11 as along with 13 people rpetrenko BioNica maria_hauser cmura alefox j3xucite cen4ik kaarsinogen dgront gurkanbebek Iden-J_GluR cjeans ashwinma
	Adaptive Data Hiding in Edge Areas of Images With Spatial LSB Domain Systems [My Copy] IEEE Transactions on Information Forensics and Security In Information Forensics and Security, IEEE Transactions on, Vol. 3, No. 3. (September 2008), pp. 488-497. by Cheng-Hsing Yang, Chi-Yao Weng, Shiuh-Jeng Wang, Hung-Min Sun posted to adaptive capacity cryptography data differencing domain embedding encapsulation hiding higher image imperceptible k-bit larger least-significant-bit lsb method pixel-value pvd quality resolution spatial steganographic steganography stegoimages substitution systems by fujiyoshi-masaaki on 2008-11-18 08:41:10 as
	Hydrogen Bonding Lowers Intrinsic Nucleophilicity of Solvated Nucleophiles [My Copy] J. Am. Chem. Soc. (18 October 2008) by Xin Chen, John I. Brauman posted to nucleophilicity substitution by kmeisenh on 2008-10-30 21:09:55 as
	Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. [My Copy] J Mol Evol, Vol. 22, No. 2. (1985), pp. 160-174. by M. Hasegawa, H. Kishino, T. Yano posted to phylogenetics substitution by alexeid on 2008-10-20 17:42:52 as along with 4 people aprasad AaronDarling Natasha lusk
	Optimizing relevance and revenue in ad search: a query substitution approach [My Copy] In SIGIR '08: Proceedings of the 31st annual international ACM SIGIR conference on Research and development in information retrieval (2008), pp. 403-410. by Filip Radlinski, Andrei Broder, Peter Ciccolo, Evgeniy Gabrilovich, Vanja Josifovski, Lance Riedel posted to commercials engines query revenues search substitution by agulli on 2008-10-06 08:40:05 as along with 1 person bemike
	Human-specific gain of function in a developmental enhancer. [My Copy] Science (New York, N.Y.), Vol. 321, No. 5894. (5 September 2008), pp. 1346-1350. by Shyam Prabhakar, Axel Visel, Jennifer A. Akiyama, et al.Malak Shoukry, Keith D. Lewis, Amy Holt, Ingrid Plajzer-Frick, Harris Morrison, David R. Fitzpatrick, Veena Afzal, Len A. Pennacchio, Edward M. Rubin, James P. Noonan posted to chimpanzee conserved-non-coding-sequence enhancer evolution gain-of-function hacns1 human limb module substitution by sebastien_vigneau on 2008-09-07 21:20:07 as along with 14 people and 1 group paulrigor Annab jfr Stew shoshin bpcusack emptyhb Zephyrus djkt natstreet isimpson maximilianh caseybrown eskay Roswell Cancer Crosstalk
	A New Approach to Formal Language Theory by Kolmogorov Complexity [My Copy] (18 Oct 2001) by Ming Li, Paul Vitanyi posted to chomsky complex formal language substitution system by marcio on 2008-08-10 02:23:04 as along with 2 people Scis0000002 ansobol
	An improved general amino acid replacement matrix. [My Copy] Molecular biology and evolution, Vol. 25, No. 7. (1 July 2008), pp. 1307-1320. by Si Quang Q. Le, Olivier Gascuel posted to aa matric substitution by friendpine on 2008-07-10 01:54:21 as along with 5 people and 1 group BioNica lizbiogen druvus stajich dmp Mycology
	Inverted pattern approach to improve image quality of information hiding by LSB substitution [My Copy] Pattern Recognition, Vol. 41, No. 8. (August 2008), pp. 2674-2683. by Cheng-Hsing Yang posted to hiding image-processing information lsb security substitution by fujiyoshi-masaaki on 2008-06-18 05:05:03 as
	Maximum-Likelihood Analysis of Molecular Adaptation in Abalone Sperm Lysin Reveals Variable Selective Pressures Among Lineages and Sites [My Copy] Mol Biol Evol, Vol. 17, No. 10. (1 October 2000), pp. 1446-1455. by Ziheng Yang, Willie J. Swanson, Victor D. Vacquier posted to abalone codon likelihood maximum molevoltestis paml positive selection sperm substitution by skumagai on 2008-06-06 16:21:33 as along with 2 people and 1 group gjuggler stevanspringer FAB-lab
	An analysis of determinants of amino acids substitution rates in bacterial proteins. [My Copy] Mol Biol Evol, Vol. 21, No. 1. (January 2004), pp. 108-116. by E. P. Rocha, A. Danchin posted to acid amino bacillus coli escherichia expression molevoltestis substitution subtilis by skumagai on 2008-06-06 16:02:41 as along with 5 people and 1 group michaelbarton bjorns tny penka jpoyatos Nie
	The rapid generation of mutation data matrices from protein sequences. [My Copy] Computer applications in the biosciences : CABIOS, Vol. 8, No. 3. (June 1992), pp. 275-282. by D. T. Jones, W. R. Taylor, J. M. Thornton posted to acid amino jtt matrix molevoltestis substitution by skumagai on 2008-06-06 14:09:12 as along with 2 people BioNica ssgong
	Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. [My Copy] Mol Biol Evol, Vol. 17, No. 1. (January 2000), pp. 68-74. by L. Duret, D. Mouchiroud posted to expression intensity mammal molevoltestis mtation pattern rate selection substitution by skumagai on 2008-06-06 01:59:46 as along with 2 people gbloeb bjorns
	The Rate of Adaptive Evolution in Enteric Bacteria [My Copy] Molecular Biology and Evolution, Vol. 23, No. 7. (July 2006), pp. 1348-1356. by Charlesworth, Jane, Eyre-Walker, Adam posted to adaptive coli enterica escherichia evolution molevoltestis positive rate salmonella selection substitution by skumagai on 2008-06-06 01:47:48 as along with 1 person operon
	The genomic rate of adaptive amino acid substitution in Drosophila. [My Copy] Mol Biol Evol, Vol. 21, No. 7. (1 July 2004), pp. 1350-1360. by N. Bierne, A. Eyre-Walker posted to acid adaptive amino drosophila molevoltestis positive selection substitution by skumagai on 2008-06-06 01:44:36 as along with 1 person emptyhb
	Why buprenorphine is so successful in treating opiate addiction in France [My Copy] Current Psychiatry Reports, Vol. 9, No. 5. (October 2007), pp. 358-364. by M. Fatseas, M. Auriacombe posted to buprenorphine opiate substitution treatment by SHUaddicto on 2008-06-02 21:13:54 as
	Establishing homologies in protein sequences. [My Copy] Methods Enzymol, Vol. 91 (1983), pp. 524-545. by M. O. Dayhoff, W. C. Barker, L. T. Hunt posted to matrix pam substitution by ca3295 on 2008-05-27 14:15:15 as along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
	Simulating DNA coding sequence evolution with EvolveAGene 3 [My Copy] Mol Biol Evol (12 January 2008), msn008. by Barry G. Hall posted to evolution program simulation substitution by adacier on 2008-05-02 03:22:30 as along with 5 people gjuggler operon aprasad zwang friendpine
	Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites [My Copy] Genetics, Vol. 155, No. 1. (1 May 2000), pp. 431-449. by Ziheng Yang, Rasmus Nielsen, Nick Goldman, Anne-Mette K. Pedersen posted to evolution non-synonymous selection substitution synonymous by fernan on 2008-04-14 20:37:19 as along with 8 people druvus BioNica Natasha dylan77 Garamonfok tale gjuggler emptyhb
	Flexible substitution patterns in models of mode and time of day choice: new evidence from the UK and the Netherlands [My Copy] Transportation, Vol. 34, No. 2. (March 2007), pp. 213-238. by Hess, Stephane, Polak, et al. John, Daly, Andrew, Hyman, Geoffrey posted to mode mode-choice netherlands substitution time-of-day transport travel uk by suze on 2008-03-23 22:30:40 as
	Transcription Factor Substitution during the Evolution of Fungal Ribosome Regulation [My Copy] Molecular Cell, Vol. 29, No. 5. (14 March 2008), pp. 552-562. by Herve Hogues, Hugo Lavoie, Adnane Sellam, et al.Maria Mangos, Terry Roemer, Enrico Purisima, Andre Nantel, Malcolm Whiteway posted to evolution regulation substitution transcription by zwang on 2008-03-20 13:26:22 as along with 1 person and 1 group stajich Mycology
	Correlated substitution analysis and the prediction of amino acid structural contacts [My Copy] Brief Bioinform (13 November 2007), bbm052. by David S. Horner, Walter Pirovano, Graziano Pesole posted to co-evolution contact prediction structure substitution by zwang on 2008-03-20 13:25:08 as along with 6 people and 3 groups mgomes qluo RebeccaHamer barry sobolevnrm Lombardo_7 structural_bioinformatics Bioinformatics baker-group
	Selective Constraints, Amino Acid Composition, and the Rate of Protein Evolution [My Copy] Mol Biol Evol, Vol. 17, No. 4. (1 April 2000), pp. 656-664. by Nicolas J. Tourasse, Wen-Hsiung Li posted to membrane protein sequence substitution by sebk on 2008-03-13 17:51:48 as along with 3 people and 1 group penka RamuAnandakrishnan cdeane Nie
	Eigenvalue analysis of amino acid substitution matrices reveals a sharp transition of the mode of sequence conservation in proteins. [My Copy] Bioinformatics, Vol. 20, No. 16. (1 November 2004), pp. 2504-2508. by A. R. Kinjo, K. Nishikawa posted to protein sequence substitution by sebk to the group OPIG on 2008-03-13 17:45:35 as

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evolution	19
protein	16
sequence	11
structure	10
matrix	9
environment-specific	7
selection	7
acid	6
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pvd	1
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rtil	1
sid	1
sirna	1
spatial	1
steganographic	1
substance_abuse	1
systems	1
treatment	1
understanding	1
unification	1

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