J. Comput. Biol. - Pathset graphs: a novel approach for comprehensive utilization of paired reads in genome assembly.

Tópicos

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

Resumo

One of the key advances in genome assembly that has led to a significant improvement in contig lengths has been improved algorithms for utilization of paired reads (mate-pairs). While in most assemblers, mate-pair information is used in a post-processing step, the recently proposed Paired de Bruijn Graph (PDBG) approach incorporates the mate-pair information directly in the assembly graph structure. However, the PDBG approach faces difficulties when the variation in the insert sizes is high. To address this problem, we first transform mate-pairs into edge-pair histograms that allow one to better estimate the distance between edges in the assembly graph that represent regions linked by multiple mate-pairs. Further, we combine the ideas of mate-pair transformation and PDBGs to construct new data structures for genome assembly: pathsets and pathset graphs.

Resumo Limpo

one key advanc genom assembl led signific improv contig length improv algorithm util pair read matepair assembl matepair inform use postprocess step recent propos pair de bruijn graph pdbg approach incorpor matepair inform direct assembl graph structur howev pdbg approach face difficulti variat insert size high address problem first transform matepair edgepair histogram allow one better estim distanc edg assembl graph repres region link multipl matepair combin idea matepair transform pdbgs construct new data structur genom assembl pathset pathset graph

Resumos Similares

IEEE Trans Vis Comput Graph - Output-Sensitive Construction of Reeb Graphs. ( 0,845467391058896 )
J. Comput. Biol. - Random matrix approach to the distribution of genomic distance. ( 0,745403497192208 )
J. Comput. Biol. - Paired de bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers. ( 0,744214313927746 )
J. Comput. Biol. - The approximability of shortest path-based graph orientations of protein-protein interaction networks. ( 0,74239051967478 )
Comput Biol Chem - On topological indices for small RNA graphs. ( 0,734314503060398 )
IEEE Trans Image Process - Constrained and dimensionality-independent path openings. ( 0,72620403998622 )
IEEE Trans Image Process - 3-D curvilinear structure detection filter via structure-ball analysis. ( 0,716049138089841 )
IEEE Trans Image Process - Hyperspectral image representation and processing with binary partition trees. ( 0,715660053495591 )
J. Comput. Biol. - Parallel continuous flow: a parallel suffix tree construction tool for whole genomes. ( 0,712347500198436 )
IEEE Trans Pattern Anal Mach Intell - A Robust O(n) Solution to the Perspective-n-Point Problem. ( 0,709759006659044 )
IEEE Trans Pattern Anal Mach Intell - The Sum-over-Forests Density Index: Identifying Dense Regions in a Graph. ( 0,700764888226735 )
J Chem Inf Model - Beyond terrestrial biology: charting the chemical universe of a-amino acid structures. ( 0,693607172029607 )
IEEE Trans Vis Comput Graph - The Design Space of Implicit Hierarchy Visualization: A Survey. ( 0,69093595323125 )
IEEE Trans Vis Comput Graph - Visual Analysis of Large Graphs Using (X,Y)-clustering and Hybrid Visualizations. ( 0,690653377377301 )
Comput Biol Chem - Exploring the limits of fold discrimination by structural alignment: a large scale benchmark using decoys of known fold. ( 0,681887320088774 )
AMIA Annu Symp Proc - Synergism between the mapping projects from SNOMED CT to ICD-10 and ICD-10-CM. ( 0,681667189373277 )
IEEE Trans Image Process - Complex object correspondence construction in two-dimensional animation. ( 0,677936370878678 )
IEEE Trans Vis Comput Graph - Image-Based Modeling of Unwrappable Fa?ades. ( 0,672977377572707 )
IEEE Trans Image Process - A co-saliency model of image pairs. ( 0,670350236124048 )
IEEE Trans Image Process - Toward a unified color space for perception-based image processing. ( 0,663625658619621 )
Comput Biol Chem - Subgrouping Automata: automatic sequence subgrouping using phylogenetic tree-based optimum subgrouping algorithm. ( 0,661726919166368 )
IEEE Trans Vis Comput Graph - Graph Drawing Aesthetics — Created by Users not Algorithms. ( 0,657658183036055 )
IEEE Trans Vis Comput Graph - Dynamic Network Visualization with Extended Massive Sequence Views. ( 0,65732118133445 )
Neural Comput - Intrinsic graph structure estimation using graph Laplacian. ( 0,654559254641482 )
Comput. Biol. Med. - Automating fault tolerance in high-performance computational biological jobs using multi-agent approaches. ( 0,653978954952106 )
Comput Methods Programs Biomed - TreeVis: a MATLAB-based tool for tree visualization. ( 0,653333333333333 )
Brief. Bioinformatics - Computational methods for Gene Orthology inference. ( 0,652711386709958 )
J. Comput. Biol. - Shapes of RNA pseudoknot structures. ( 0,651273262728556 )
Comput. Biol. Med. - Hyperbolic Dirac Nets for medical decision support. Theory, methods, and comparison with Bayes Nets. ( 0,650622704916878 )
IEEE Trans Image Process - Connected filtering based on multivalued component-trees. ( 0,650506570515058 )
IEEE Trans Image Process - Coding order decision of B frames for rate-distortion performance improvement in single-view video and multiview video coding. ( 0,650359989499684 )
IEEE Trans Image Process - Stereo matching and view interpolation based on image domain triangulation. ( 0,646418265293594 )
J. Comput. Biol. - Simultaneous folding of alternative RNA structures with mutual constraints: an application to next-generation sequencing-based RNA structure probing. ( 0,644846755539249 )
J. Comput. Biol. - An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure. ( 0,641283905087192 )
Comput Biol Chem - A novel feature representation method based on Chou's pseudo amino acid composition for protein structural class prediction. ( 0,638748776906853 )
J. Comput. Biol. - A theoretical model for whole genome alignment. ( 0,638678463423277 )
IEEE Trans Image Process - Anisotropic morphological filters with spatially-variant structuring elements based on image-dependent gradient fields. ( 0,630243601383265 )
IEEE Trans Vis Comput Graph - Flow Visualization with Quantified Spatial and Temporal Errors Using Edge Maps. ( 0,62994997458129 )
Comput. Biol. Med. - A protein mapping method based on physicochemical properties and dimension reduction. ( 0,628866640098524 )
J Biomed Inform - Tree kernel-based protein-protein interaction extraction from biomedical literature. ( 0,627472325276057 )
IEEE Trans Pattern Anal Mach Intell - Learning AND-OR Templates for Object Recognition and Detection. ( 0,624631590193452 )
Int J Med Inform - Use of order sets in inpatient computerized provider order entry systems: a comparative analysis of usage patterns at seven sites. ( 0,624440844403378 )
IEEE Trans Image Process - W-tree indexing for fast visual word generation. ( 0,62375054966023 )
IEEE Trans Vis Comput Graph - Link Conditions for Simplifying Meshes with Embedded Structures. ( 0,621984846167209 )
IEEE Trans Pattern Anal Mach Intell - Trinary-Projection Trees for Approximate Nearest Neighbor Search. ( 0,621640395734701 )
J Chem Inf Model - Characterization of heterocyclic rings through quantum chemical topology. ( 0,614344654765311 )
J Med Syst - Energy-aware Gateway Selection for increasing the lifetime of Wireless Body Area Sensor Networks. ( 0,614125865886285 )
IEEE Trans Pattern Anal Mach Intell - Graph Regularized Nonnegative Matrix Factorization for Data Representation. ( 0,613196971874282 )
J. Comput. Biol. - Detection of structural variants involving repetitive regions in the reference genome. ( 0,610118807220832 )
J Chem Inf Model - Time-averaged distributions of solute and solvent motions: exploring proton wires of GFP and PfM2DH. ( 0,610002462529329 )
J Biomed Inform - Decision support from local data: creating adaptive order menus from past clinician behavior. ( 0,609069414494351 )
IEEE Trans Pattern Anal Mach Intell - An Extended Path Following Algorithm for Graph-Matching Problem. ( 0,600124986981879 )
Comput Biol Chem - A degree-distribution based hierarchical agglomerative clustering algorithm for protein complexes identification. ( 0,598937738913102 )
J. Comput. Biol. - A Bayesian sampler for optimization of protein domain hierarchies. ( 0,598321953375939 )
Neural Comput - A network of spiking neurons for computing sparse representations in an energy-efficient way. ( 0,596045361522679 )
IEEE Trans Vis Comput Graph - Grouper: A Compact, Streamable Triangle Mesh Data Structure. ( 0,595986577030054 )
IEEE Trans Image Process - The Roadmaker's algorithm for the discrete pulse transform. ( 0,59562710947648 )
Neural Comput - Temporal order detection and coding in nervous systems. ( 0,59467712582367 )
IEEE Trans Pattern Anal Mach Intell - C^4: Exploring Multiple Solutions in Graphical Models by Cluster Sampling. ( 0,592812986829814 )
Brief. Bioinformatics - Structural mapping: how to study the genetic architecture of a phenotypic trait through its formation mechanism. ( 0,591710458728191 )
IEEE Trans Image Process - On the construction of topology-preserving deformation fields. ( 0,584091285466395 )
IEEE Trans Image Process - Topology preserving warping of 3-D binary images according to continuous one-to-one mappings. ( 0,582206755270285 )
Comput. Biol. Med. - Effect of bunching of cilia and their interplay on muco-ciliary transport. ( 0,579811881718388 )
Int J Comput Assist Radiol Surg - Complete fully automatic model-based segmentation of normal and pathological lymph nodes in CT data. ( 0,57074443465917 )
J. Comput. Biol. - Statistical significance of optical map alignments. ( 0,568354955659842 )
Comput. Biol. Med. - Forest classification trees and forest support vector machines algorithms: Demonstration using microarray data. ( 0,568289729252842 )
Int J Comput Assist Radiol Surg - Visualization support for the planning of hepatic needle placement. ( 0,567623651876392 )
IEEE Trans Vis Comput Graph - Simplification of Node Position Data ;for Interactive Visualization of Dynamic Data Sets. ( 0,567581800498456 )
Neural Comput - Refined rademacher chaos complexity bounds with applications to the multikernel learning problem. ( 0,567525423556495 )
IEEE Trans Image Process - A Geometric Framework for Rectangular Shape Detection. ( 0,56752155684942 )
Brief. Bioinformatics - A bioinformatician's guide to the forefront of suffix array construction algorithms. ( 0,565730750491152 )
J Med Syst - Manual refinement system for graph-based segmentation results in the medical domain. ( 0,565418082179463 )
IEEE Trans Vis Comput Graph - Computing Reeb Graphs as a Union of Contour Trees. ( 0,565315618968227 )
J Chem Inf Model - Generative topographic mapping-based classification models and their applicability domain: application to the biopharmaceutics Drug Disposition Classification System (BDDCS). ( 0,563742236961639 )
J. Comput. Biol. - Counting RNA pseudoknotted structures. ( 0,563731410734115 )
Comput Biol Chem - Metabolic network motifs can provide novel insights into evolution: The evolutionary origin of Eukaryotic organelles as a case study. ( 0,562616625865481 )
J Chem Inf Model - Protein secondary structure classification revisited: processing DSSP information with PSSC. ( 0,559892275112287 )
Comput. Biol. Med. - Finding splitting lines for touching cell nuclei with a shortest path algorithm. ( 0,557602782730998 )
J Biomed Inform - A similarity network approach for the analysis and comparison of protein sequence/structure sets. ( 0,554388866162889 )
J Med Syst - Associating clinical archetypes through UMLS Metathesaurus term clusters. ( 0,554381755142413 )
IEEE Trans Pattern Anal Mach Intell - Building Development Monitoring in Multitemporal Remotely Sensed Image Pairs with Stochastic Birth-Death Dynamics. ( 0,554061816157756 )
Int J Comput Assist Radiol Surg - Evolutionistic or revolutionary paths? A PACS maturity model for strategic situational planning. ( 0,547868083830577 )
IEEE Trans Vis Comput Graph - A Structure-Based Distance Metric for High-Dimensional Space Exploration with Multi-Dimensional Scaling. ( 0,547343411512902 )
IEEE Trans Image Process - Histogram contextualization. ( 0,546106853225549 )
J. Comput. Biol. - Finding maximum colorful subtrees in practice. ( 0,545548912780662 )
J Chem Inf Model - Stereochemically consistent reaction mapping and identification of multiple reaction mechanisms through integer linear optimization. ( 0,543546891669177 )
IEEE Trans Pattern Anal Mach Intell - Shape Analysis of Elastic Curves in Euclidean Spaces. ( 0,54253387720544 )
J. Comput. Biol. - Modeling alternative splicing variants from RNA-Seq data with isoform graphs. ( 0,540852788779382 )
IEEE Trans Image Process - LULU operators and discrete pulse transform for multi-dimensional arrays. ( 0,540422370029377 )
J Chem Inf Model - sc-PDB-Frag: a database of protein-ligand interaction patterns for Bioisosteric replacements. ( 0,539754330081849 )
Comput Math Methods Med - Coarse-grained simulation of myosin-V movement. ( 0,538085967050348 )
J Biomed Inform - SYFSA: a framework for systematic yet flexible systems analysis. ( 0,535425111652606 )
J Chem Inf Model - Addressing challenges of identifying geometrically diverse sets of crystalline porous materials. ( 0,534574343128416 )
J. Comput. Biol. - Combinatorics of -structures. ( 0,533723939896965 )
J. Comput. Biol. - Gene prediction based on DNA spectral analysis: a literature review. ( 0,533666562565053 )
Comput Biol Chem - Quick path finding--quick algorithmic solution for unambiguous labeling of phylogenetic tree nodes. ( 0,53350874308428 )
IEEE Trans Image Process - Directional lapped orthogonal transform: theory and design. ( 0,532412999026665 )
J Chem Inf Model - Idealized models of protofilaments of human islet amyloid polypeptide. ( 0,532264652571781 )
J Med Syst - A lightweight security scheme for wireless body area networks: design, energy evaluation and proposed microprocessor design. ( 0,530103099546436 )
IEEE Trans Vis Comput Graph - A Graph-Based Interface for Visual Analytics of 3D Streamlines and Pathlines. ( 0,528732824780153 )