J. Comput. Biol. - Combinatorics of -structures.

Tópicos

{ sequenc(1873) structur(1644) protein(1328) }
{ error(1145) method(1030) estim(1020) }
{ import(1318) role(1303) understand(862) }
{ structur(1116) can(940) graph(676) }
{ can(774) often(719) complex(702) }
{ imag(1947) propos(1133) code(1026) }
{ framework(1458) process(801) describ(734) }
{ control(1307) perform(991) simul(935) }
{ method(984) reconstruct(947) comput(926) }
{ model(2656) set(1616) predict(1553) }
{ data(1737) use(1416) pattern(1282) }
{ method(1219) similar(1157) match(930) }
{ network(2748) neural(1063) input(814) }
{ take(945) account(800) differ(722) }
{ studi(2440) review(1878) systemat(933) }
{ learn(2355) train(1041) set(1003) }
{ howev(809) still(633) remain(590) }
{ signal(2180) analysi(812) frequenc(800) }
{ can(981) present(881) function(850) }
{ high(1669) rate(1365) level(1280) }
{ use(1733) differ(960) four(931) }
{ implement(1333) system(1263) develop(1122) }
{ activ(1452) weight(1219) physic(1104) }
{ detect(2391) sensit(1101) algorithm(908) }
{ model(3404) distribut(989) bayesian(671) }
{ inform(2794) health(2639) internet(1427) }
{ system(1976) rule(880) can(841) }
{ measur(2081) correl(1212) valu(896) }
{ imag(1057) registr(996) error(939) }
{ bind(1733) structur(1185) ligand(1036) }
{ featur(3375) classif(2383) classifi(1994) }
{ imag(2830) propos(1344) filter(1198) }
{ imag(2675) segment(2577) method(1081) }
{ patient(2315) diseas(1263) diabet(1191) }
{ motion(1329) object(1292) video(1091) }
{ assess(1506) score(1403) qualiti(1306) }
{ treatment(1704) effect(941) patient(846) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ problem(2511) optim(1539) algorithm(950) }
{ chang(1828) time(1643) increas(1301) }
{ concept(1167) ontolog(924) domain(897) }
{ clinic(1479) use(1117) guidelin(835) }
{ algorithm(1844) comput(1787) effici(935) }
{ extract(1171) text(1153) clinic(932) }
{ method(1557) propos(1049) approach(1037) }
{ data(1714) softwar(1251) tool(1186) }
{ design(1359) user(1324) use(1319) }
{ model(2220) cell(1177) simul(1124) }
{ care(1570) inform(1187) nurs(1089) }
{ general(901) number(790) one(736) }
{ search(2224) databas(1162) retriev(909) }
{ featur(1941) imag(1645) propos(1176) }
{ case(1353) use(1143) diagnosi(1136) }
{ data(3963) clinic(1234) research(1004) }
{ studi(1410) differ(1259) use(1210) }
{ risk(3053) factor(974) diseas(938) }
{ perform(999) metric(946) measur(919) }
{ research(1085) discuss(1038) issu(1018) }
{ system(1050) medic(1026) inform(1018) }
{ model(2341) predict(2261) use(1141) }
{ visual(1396) interact(850) tool(830) }
{ compound(1573) activ(1297) structur(1058) }
{ perform(1367) use(1326) method(1137) }
{ studi(1119) effect(1106) posit(819) }
{ blood(1257) pressur(1144) flow(957) }
{ spatial(1525) area(1432) region(1030) }
{ record(1888) medic(1808) patient(1693) }
{ health(3367) inform(1360) care(1135) }
{ model(3480) simul(1196) paramet(876) }
{ monitor(1329) mobil(1314) devic(1160) }
{ ehr(2073) health(1662) electron(1139) }
{ state(1844) use(1261) util(961) }
{ research(1218) medic(880) student(794) }
{ patient(2837) hospit(1953) medic(668) }
{ data(2317) use(1299) case(1017) }
{ age(1611) year(1155) adult(843) }
{ medic(1828) order(1363) alert(1069) }
{ cost(1906) reduc(1198) effect(832) }
{ group(2977) signific(1463) compar(1072) }
{ sampl(1606) size(1419) use(1276) }
{ gene(2352) biolog(1181) express(1162) }
{ data(3008) multipl(1320) sourc(1022) }
{ first(2504) two(1366) second(1323) }
{ intervent(3218) particip(2042) group(1664) }
{ activ(1138) subject(705) human(624) }
{ time(1939) patient(1703) rate(768) }
{ patient(1821) servic(1111) care(1106) }
{ use(2086) technolog(871) perceiv(783) }
{ analysi(2126) use(1163) compon(1037) }
{ health(1844) social(1437) communiti(874) }
{ cancer(2502) breast(956) screen(824) }
{ use(976) code(926) identifi(902) }
{ drug(1928) target(777) effect(648) }
{ result(1111) use(1088) new(759) }
{ survey(1388) particip(1329) question(1065) }
{ estim(2440) model(1874) function(577) }
{ decis(3086) make(1611) patient(1517) }
{ process(1125) use(805) approach(778) }
{ method(1969) cluster(1462) data(1082) }
{ method(2212) result(1239) propos(1039) }

Resumo

In this article we study canonical -structures, a class of RNA pseudoknot structures that plays a key role in the context of polynomial time folding of RNA pseudoknot structures. A -structure is composed of specific building blocks that have topological genus less than or equal to , where composition means concatenation and nesting of such blocks. Our main result is the derivation of the generating function of -structures via symbolic enumeration using so called irreducible shadows. We furthermore recursively compute the generating polynomials of irreducible shadows of genus = . The -structures are constructed via -matchings. For 1 = = 10, we compute Puiseux expansions at the unique, dominant singularities, allowing us to derive simple asymptotic formulas for the number of -structures.

Resumo Limpo

articl studi canon structur class rna pseudoknot structur play key role context polynomi time fold rna pseudoknot structur structur compos specif build block topolog genus less equal composit mean concaten nest block main result deriv generat function structur via symbol enumer use call irreduc shadow furthermor recurs comput generat polynomi irreduc shadow genus structur construct via match comput puiseux expans uniqu domin singular allow us deriv simpl asymptot formula number structur

Resumos Similares

Comput Biol Chem - Protein fold recognition based on functional domain composition. ( 0,857413417476046 )
J Chem Inf Model - Modules identification in protein structures: the topological and geometrical solutions. ( 0,848469641130028 )
J Chem Inf Model - Comparative analysis of threshold and tessellation methods for determining protein contacts. ( 0,837701719262878 )
Comput Biol Chem - Analysis of sequence repeats of proteins in the PDB. ( 0,8345763029525 )
Comput. Biol. Med. - An insight into the molecular basis for convergent evolution in fish antifreeze Proteins. ( 0,833088672662572 )
J Chem Inf Model - Protein secondary structure classification revisited: processing DSSP information with PSSC. ( 0,829185213915631 )
Comput Biol Chem - ProSTRIP: A method to find similar structural repeats in three-dimensional protein structures. ( 0,825865147767374 )
Comput Biol Chem - Bacterial protein structures reveal phylum dependent divergence. ( 0,824827416202347 )
Comput Biol Chem - Statistical analysis and exposure status classification of transmembrane beta barrel residues. ( 0,821937266372657 )
Comput Biol Chem - Identification of putative and potential cross-reactive chickpea (Cicer arietinum) allergens through an in silico approach. ( 0,81525842453213 )
J. Comput. Biol. - Statistical significance of optical map alignments. ( 0,812285145824683 )
Med Biol Eng Comput - The influence of alignment-free sequence representations on the semi-supervised classification of class C G protein-coupled receptors: semi-supervised classification of class C GPCRs. ( 0,811884745419435 )
Comput Biol Chem - Characterizing regions in the human genome unmappable by next-generation-sequencing at the read length of 1000 bases. ( 0,80938186828881 )
J. Comput. Biol. - Simultaneous alignment and folding of protein sequences. ( 0,807802887576594 )
Comput Biol Chem - The frequency of poly(G) tracts in the human genome and their use as a sensor of DNA damage. ( 0,806431064514702 )
Brief. Bioinformatics - De novo assembly of short sequence reads. ( 0,806025701813453 )
Comput Biol Chem - ProCoCoA: A quantitative approach for analyzing protein core composition. ( 0,803226477235329 )
J Chem Inf Model - ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures. ( 0,798248157187794 )
Comput Biol Chem - Human-chimpanzee alignment: ortholog exponentials and paralog power laws. ( 0,798132073691625 )
Comput Math Methods Med - DV-curve representation of protein sequences and its application. ( 0,798083829583749 )
Comput Math Methods Med - Quad-PRE: a hybrid method to predict protein quaternary structure attributes. ( 0,796673233222068 )
Comput. Biol. Med. - Improving protein secondary structure prediction using a multi-modal BP method. ( 0,794420945763659 )
J. Comput. Biol. - Evaluating, comparing, and interpreting protein domain hierarchies. ( 0,794181498991821 )
Brief. Bioinformatics - Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. ( 0,792801453883983 )
J Chem Inf Model - Tertiary structure prediction of RNA-RNA complexes using a secondary structure and fragment-based method. ( 0,789850682088894 )
Brief. Bioinformatics - Systematic identification of Class I HDAC substrates. ( 0,789421750277358 )
Brief. Bioinformatics - New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. ( 0,78906686989167 )
Curr Protoc Bioinformatics - Comparative Protein Structure Modeling Using MODELLER. ( 0,788037131125541 )
J Biomed Inform - A similarity network approach for the analysis and comparison of protein sequence/structure sets. ( 0,785909256844762 )
Comput Biol Chem - Subgrouping Automata: automatic sequence subgrouping using phylogenetic tree-based optimum subgrouping algorithm. ( 0,785554531485341 )
J Chem Inf Model - Protein secondary structure prediction with SPARROW. ( 0,78426645273321 )
BMC Med Inform Decis Mak - Efficient protein structure search using indexing methods. ( 0,784247809726107 )
Comput Methods Programs Biomed - Protein secondary structure prediction using modular reciprocal bidirectional recurrent neural networks. ( 0,782609842200917 )
Curr Protoc Bioinformatics - Using the RNAstructure Software Package to Predict Conserved RNA Structures. ( 0,780978126041347 )
J Chem Inf Model - Improved helix and kink characterization in membrane proteins allows evaluation of kink sequence predictors. ( 0,780365352646587 )
Comput Biol Chem - Identification and characterization of lysine-methylated sites on histones and non-histone proteins. ( 0,779411341556691 )
J. Comput. Biol. - ComB: SNP calling and mapping analysis for color and nucleotide space platforms. ( 0,777209801127856 )
Comput Biol Chem - Computational insight into nitration of human myoglobin. ( 0,772707810355476 )
Comput. Biol. Med. - Application of 2D graphic representation of protein sequence based on Huffman tree method. ( 0,772630351472326 )
J. Comput. Biol. - IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information. ( 0,771983123106002 )
Brief. Bioinformatics - Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. ( 0,771071967536985 )
Comput Biol Chem - Computational determination of the orientation of a heat repeat-like domain of DNA-PKcs. ( 0,763048810697353 )
J. Comput. Biol. - Reconstructing the history of large-scale genomic changes: biological questions and computational challenges. ( 0,761797981638969 )
J Chem Inf Model - Parallel and antiparallel ?-strands differ in amino acid composition and availability of short constituent sequences. ( 0,761330970412258 )
Comput. Biol. Med. - miRClassify: an advanced web server for miRNA family classification and annotation. ( 0,758565977862605 )
Comput Biol Chem - A novel feature representation method based on Chou's pseudo amino acid composition for protein structural class prediction. ( 0,756813811406456 )
Comput. Biol. Med. - Improving protein complex classification accuracy using amino acid composition profile. ( 0,75681215257065 )
J Integr Bioinform - Complementarity of network and sequence information in homologous proteins. ( 0,748257251827764 )
Comput Biol Chem - A local average connectivity-based method for identifying essential proteins from the network level. ( 0,747013509013446 )
J. Comput. Biol. - Statistical significance of threading scores. ( 0,746315332147772 )
Comput. Biol. Med. - A content and structural assessment of oxidative motifs across a diverse set of life forms. ( 0,746071991177625 )
J Chem Inf Model - Protein structural statistics with PSS. ( 0,744189354228329 )
J. Comput. Biol. - Nonparametric combinatorial sequence models. ( 0,743419329655057 )
J Integr Bioinform - Predicting protein distance maps according to physicochemical properties. ( 0,741452540086316 )
J Integr Bioinform - Exceptional single strand DNA word symmetry: analysis of evolutionary potentialities. ( 0,741372765628009 )
J Chem Inf Model - Building a knowledge-based statistical potential by capturing high-order inter-residue interactions and its applications in protein secondary structure assessment. ( 0,741308579206124 )
Brief. Bioinformatics - BamView: visualizing and interpretation of next-generation sequencing read alignments. ( 0,74024020369056 )
J Integr Bioinform - A hierarchical approach to protein fold prediction. ( 0,739386148313831 )
J. Comput. Biol. - Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis. ( 0,739135445032056 )
Sci Data - Comprehensive analysis of the venom gland transcriptome of the spider Dolomedes fimbriatus. ( 0,735922744262965 )
Comput Biol Chem - The challenge of annotating protein sequences: The tale of eight domains of unknown function in Pfam. ( 0,732549261226551 )
J. Comput. Biol. - Efficient traversal of beta-sheet protein folding pathways using ensemble models. ( 0,730655335853037 )
Med Biol Eng Comput - Enhanced spatio-temporal alignment of plantar pressure image sequences using B-splines. ( 0,729296457533457 )
Brief. Bioinformatics - Alpha shape and Delaunay triangulation in studies of protein-related interactions. ( 0,728795458856179 )
Comput Biol Chem - Tracing the evolution of the mitochondrial protein import machinery. ( 0,727722911610033 )
J. Comput. Biol. - Accurate mass spectrometry based protein quantification via shared peptides. ( 0,727717974263499 )
Comput Biol Chem - Identical sequence patterns in the ends of exons and introns of human protein-coding genes. ( 0,72692053283576 )
Comput Biol Chem - Support vector machine with a Pearson VII function kernel for discriminating halophilic and non-halophilic proteins. ( 0,725672510427442 )
J. Comput. Biol. - Sequence alignment of viral channel proteins with cellular ion channels. ( 0,724571965782174 )
J. Comput. Biol. - A novel technique for detecting putative horizontal gene transfer in the sequence space. ( 0,724256539387128 )
Comput Biol Chem - A novel empirical mutual information approach to identify co-evolving amino acid positions of influenza A viruses. ( 0,724024005720368 )
Comput Biol Chem - Multi-nucleation and vectorial folding pathways of large helix protein. ( 0,722948035085527 )
Brief. Bioinformatics - Ultrafast clustering algorithms for metagenomic sequence analysis. ( 0,721413009394189 )
Comput. Biol. Med. - New layers in understanding and predicting a-linolenic acid content in plants using amino acid characteristics of omega-3 fatty acid desaturase. ( 0,719874033065356 )
Sci Data - Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus. ( 0,719081232207617 )
Comput. Biol. Med. - Intron identification approaches based on weighted features and fuzzy decision trees. ( 0,717764404519119 )
Brief. Bioinformatics - A practical guide for the computational selection of residues to be experimentally characterized in protein families. ( 0,716694102285665 )
Comput Math Methods Med - Uses of phage display in agriculture: sequence analysis and comparative modeling of late embryogenesis abundant client proteins suggest protein-nucleic acid binding functionality. ( 0,716510257426404 )
J. Comput. Biol. - AREM: aligning short reads from ChIP-sequencing by expectation maximization. ( 0,716384069775674 )
J. Comput. Biol. - Computational techniques for human genome resequencing using mated gapped reads. ( 0,714548444124351 )
J Chem Inf Model - PocketAlign a novel algorithm for aligning binding sites in protein structures. ( 0,714237077054857 )
Brief. Bioinformatics - Ortholog identification in the presence of domain architecture rearrangement. ( 0,714029115685219 )
Comput Methods Programs Biomed - Sequence-based prediction of protein-binding sites in DNA: comparative study of two SVM models. ( 0,712546446525423 )
J. Comput. Biol. - Optimization of profile-to-profile alignment parameters for one-dimensional threading. ( 0,710911225904038 )
Comput Math Methods Med - Analyzing effects of naturally occurring missense mutations. ( 0,707624657217647 )
IEEE Trans Image Process - Pattern masking estimation in image with structural uncertainty. ( 0,705524807468983 )
J. Comput. Biol. - Parallel continuous flow: a parallel suffix tree construction tool for whole genomes. ( 0,705060667572256 )
Comput. Biol. Med. - A protein mapping method based on physicochemical properties and dimension reduction. ( 0,703320031206629 )
J Chem Inf Model - Critical residue that promotes protein dimerization: a story of partially exposed Phe25 in 14-3-3s. ( 0,70296996471268 )
Comput Biol Chem - Semantically predicting protein functions based on protein functional connectivity. ( 0,701886735393517 )
Comput Math Methods Med - ADLD: a novel graphical representation of protein sequences and its application. ( 0,701271597616757 )
Comput. Biol. Med. - A context evaluation approach for structural comparison of proteins using cross entropy over n-gram modelling. ( 0,697303277321381 )
Comput. Biol. Med. - Structural alphabet motif discovery and a structural motif database. ( 0,695439690869283 )
Brief. Bioinformatics - Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes). ( 0,694215126592763 )
Comput Biol Chem - Large replication skew domains delimit GC-poor gene deserts in human. ( 0,692850069610147 )
J. Comput. Biol. - Tracing the most parsimonious indel history. ( 0,692656361434725 )
J. Comput. Biol. - Accurate estimations of evolutionary times in the context of strong CpG hypermutability. ( 0,692074638045059 )
J Chem Inf Model - Dihedral-based segment identification and classification of biopolymers II: polynucleotides. ( 0,690684852695791 )
J. Comput. Biol. - Emergent protein folding modeled with evolved neural cellular automata using the 3D HP model. ( 0,688748209374314 )
J. Comput. Biol. - Detection of structural variants involving repetitive regions in the reference genome. ( 0,686188117860002 )