Comput Biol Chem - Determining common insertion sites based on retroviral insertion distribution across tumors.

Tópicos

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

Resumo

A CIS (common insertion site) indicates a genome region that is hit more frequently by retroviral insertions than expected by chance. Such a region is strongly related to cancer gene loci, which leads to the detection of cancer genes. An algorithm for detecting CISs should satisfy the following: (1) it does not require any prior knowledge of underlying insertion distribution; (2) it can resolve the insertion biases caused by hotspots; (3) it can detect CISs of any biological width; (4) it can identify noises resulting from statistic mistakes and non-CIS insertions; and (5) it can identify the widths of CISs as accurately as possible. We develop a method to resolve these difficulties. We verify a region's significance from two perspectives: distribution width and distribution depth. The former indicates how many insertions in a region while the latter evaluates the insertion distribution across the tumors in a region. We compare our method with kernel density estimation and sliding window on the simulated data, showing that our method not only identifies cancer-related insertions effectively, but also filters noises correctly. The experiments on the real data show that taking insertion distribution into account can highlight significant CISs. We detect 53 novel CISs, some of which have been proven correct by the biological literature.

Resumo Limpo

cis common insert site indic genom region hit frequent retrovir insert expect chanc region strong relat cancer gene loci lead detect cancer gene algorithm detect ciss satisfi follow requir prior knowledg under insert distribut can resolv insert bias caus hotspot can detect ciss biolog width can identifi nois result statist mistak nonci insert can identifi width ciss accur possibl develop method resolv difficulti verifi region signific two perspect distribut width distribut depth former indic mani insert region latter evalu insert distribut across tumor region compar method kernel densiti estim slide window simul data show method identifi cancerrel insert effect also filter nois correct experi real data show take insert distribut account can highlight signific ciss detect novel ciss proven correct biolog literatur

Resumos Similares

Int J Med Robot - Computer-guided rapid-prototyped templates for segmental mandibular osteotomies: a preliminary report. ( 0,625853915250361 )
Int J Comput Assist Radiol Surg - A Kohonen neural network description of scoliosis fused regions and their corresponding Lenke classification. ( 0,624070244621052 )
Int J Comput Assist Radiol Surg - Validation of minimally invasive, image-guided cochlear implantation using Advanced Bionics, Cochlear, and Medel electrodes in a cadaver model. ( 0,606097333236949 )
Int J Med Robot - Accuracy of a computer-assisted planning and placement system for anatomical femoral tunnel positioning in anterior cruciate ligament reconstruction. ( 0,601759344383747 )
Med Biol Eng Comput - Accuracy and efficacy of thoracic pedicle screws in scoliosis with patient-specific drill template. ( 0,595221432403877 )
Int J Comput Assist Radiol Surg - Calibrated segmentation of CBCT and CT images for digitization of dental prostheses. ( 0,59078231352628 )
Int J Comput Assist Radiol Surg - Percutaneous lung biopsy: comparison between an augmented reality CT navigation system and standard CT-guided technique. ( 0,587656897266872 )
Int J Med Robot - Surgeon radiation exposure in cone beam computed tomography-based, image-guided spinal surgery. ( 0,580255848240255 )
Int J Health Geogr - Developing the atlas of cancer in Queensland: methodological issues. ( 0,560931706692305 )
Spat Spatiotemporal Epidemiol - Error propagation models to examine the effects of geocoding quality on spatial analysis of individual-level datasets. ( 0,555934787520806 )
Int J Comput Assist Radiol Surg - The role of automatic computer-aided surgical trajectory planning in improving the expected safety of stereotactic neurosurgery. ( 0,555320592651152 )
Int J Health Geogr - Smart density: A more accurate method of measuring rural residential density for health-related research. ( 0,553402445476766 )
Comput. Biol. Med. - Factors affecting accuracy of implant placement with mucosa-supported stereolithographic surgical guides in edentulous mandibles. ( 0,545496289957377 )
Int J Med Robot - Assessing the feasibility of full robotic interaortocaval nodal dissection for locally advanced gastric cancer. ( 0,544806366876817 )
Int J Comput Assist Radiol Surg - A laboratory comparison of computer navigation and individualized guides for distal radius osteotomy. ( 0,542950557803117 )
Int J Comput Assist Radiol Surg - Estimation of optimal pivot point for remote center of motion alignment in surgery. ( 0,539452201803883 )
Methods Inf Med - Surgical workflow management schemata for cataract procedures. process model-based design and validation of workflow schemata. ( 0,536291654973063 )
Int J Med Robot - Initial laboratory experience with a novel ultrasound probe for standard and single-port robotic kidney surgery: increasing console surgeon autonomy and minimizing instrument clashing. ( 0,533755664253585 )
Int J Comput Assist Radiol Surg - Design considerations for a novel MRI compatible manipulator for prostate cryoablation. ( 0,531973683612767 )
Neural Comput - Optimal population codes for space: grid cells outperform place cells. ( 0,53135000249001 )
BMC Med Inform Decis Mak - A method for managing re-identification risk from small geographic areas in Canada. ( 0,531193856824419 )
Int J Health Geogr - Global spatiotemporal and genetic footprint of the H5N1 avian influenza virus. ( 0,530520014248447 )
Comput Methods Programs Biomed - A novel method of obtaining 3D images of detached retina. ( 0,529736258525997 )
Int J Comput Assist Radiol Surg - Multi-trajectories automatic planner for StereoElectroEncephaloGraphy (SEEG). ( 0,528662385229351 )
Comput Biol Chem - DNA clustering and genome complexity. ( 0,52723830002085 )
Spat Spatiotemporal Epidemiol - Adjusted significance cutoffs for hypothesis tests applied with generalized additive models with bivariate smoothers. ( 0,527010696540896 )
IEEE Trans Image Process - Robust pairwise matching of interest points with complex wavelets. ( 0,526949593953275 )
Int J Comput Assist Radiol Surg - Ventilatory impairment detection based on distribution of respiratory-induced changes in pixel values in dynamic chest radiography: a feasibility study. ( 0,526232118728528 )
Spat Spatiotemporal Epidemiol - Spatial patterns of human papillomavirus-associated cancers within the state of Minnesota, 1998-2007. ( 0,524991232009458 )
Comput. Aided Surg. - Comparison of analog 2D and digital 3D preoperative templating for predicting implant size in total knee arthroplasty. ( 0,523347457314967 )
Int J Med Robot - En bloc resection of epiglottic tumors with transoral robotic approach - preliminary results. ( 0,522822465673153 )
Comput. Aided Surg. - Computer assisted planning of autologous fat grafting in breast. ( 0,522149777087496 )
Spat Spatiotemporal Epidemiol - Violent crime in San Antonio, Texas: an application of spatial epidemiological methods. ( 0,521655792588055 )
Int J Comput Assist Radiol Surg - Electronic device for endosurgical skills training (EDEST): study of reliability. ( 0,521602965790584 )
Int J Comput Assist Radiol Surg - Observation of the temporal crest canal in the mandibular ramus by cone beam computed tomography and macroscopic study. ( 0,520704420497061 )
Int J Med Robot - Forces exerted during microneurosurgery: a cadaver study. ( 0,520544594569873 )
Comput. Aided Surg. - Efficacy and accuracy of a novel rapid prototyping drill template for cervical pedicle screw placement. ( 0,51987213581942 )
Int J Med Robot - Robotic transanal total mesorectal excision for rectal cancer: experience with a first case. ( 0,517088063869791 )
AMIA Annu Symp Proc - Improving prediction of surgery duration using operational and temporal factors. ( 0,516285867008017 )
Int J Med Robot - Reviewing the technological challenges associated with the development of a laparoscopic palpation device. ( 0,516152677691302 )
Int J Med Robot - Robot-assisted laparoscopic (RAL) surgery for gastric cancer. ( 0,516130961791163 )
Spat Spatiotemporal Epidemiol - Quantifying the magnitude of environmental exposure misclassification when using imprecise address proxies in public health research. ( 0,515813634106177 )
Int J Health Geogr - Density estimation and adaptive bandwidths: a primer for public health practitioners. ( 0,515747559984678 )
Int J Med Robot - CT-guided robotic needle biopsy of lung nodules with respiratory motion - experimental system and preliminary test. ( 0,514397213130366 )
Int J Med Robot - Robot-assisted laparoscopic abdominoperineal resection for low rectal cancer. ( 0,514083243966991 )
J Integr Bioinform - Inter-dinucleotide distances in the human genome: an analysis of the whole-genome and protein-coding distributions. ( 0,513959470102295 )
J Med Syst - A multiple stage approach for performance improvement of primary healthcare practice. ( 0,513373682857905 )
Int J Med Robot - An optimal design for patient-specific templates for pedicle spine screws placement. ( 0,510705262587505 )
Comput Methods Programs Biomed - Adaptive network based on fuzzy inference system for equilibrated urea concentration prediction. ( 0,51039623309022 )
Int J Health Geogr - Enhancing spatial detection accuracy for syndromic surveillance with street level incidence data. ( 0,510123506870689 )
Int J Health Geogr - Alcohol outlets and clusters of violence. ( 0,509644472607715 )
Int J Med Robot - Robotic retroperitoneal approach - a new technique for the upper urinary tract and adrenal gland. ( 0,509199039845096 )
Int J Med Robot - Robotic central pancreatectomy with stented pancreaticogastrostomy: operative details. ( 0,508034311987454 )
Int J Comput Assist Radiol Surg - A novel four-wire-driven robotic catheter for radio-frequency ablation treatment. ( 0,507641996942138 )
Int J Med Robot - Quantitative assessment of manual and robotic microcannulation for eye surgery using new eye model. ( 0,507343441395395 )
Int J Health Geogr - Data-driven inference for the spatial scan statistic. ( 0,505925504518686 )
Int J Health Geogr - Including the urban heat island in spatial heat health risk assessment strategies: a case study for Birmingham, UK. ( 0,5047559845065 )
Comput. Aided Surg. - Robotic assisted microsurgery in hypothenar hammer syndrome: a case report. ( 0,504082380513662 )
Int J Health Geogr - Nonparametric intensity bounds for the delineation of spatial clusters. ( 0,503826735216895 )
Int J Med Robot - Insertion force in manual and robotic corneal suturing. ( 0,503340459494643 )
Comput Methods Programs Biomed - 3D navigation and monitoring for spinal milling operation based on registration between multiplanar fluoroscopy and CT images. ( 0,500867985572134 )
Int J Med Robot - Robotic sacral hysteropexy for pelvic organ prolapse. ( 0,500742081016855 )
Comput. Aided Surg. - Integration of CAD/CAM planning into computer assisted orthopaedic surgery. ( 0,50057567837482 )
Int J Med Robot - The current and future use of imaging in urological robotic surgery: a survey of the European Association of Robotic Urological Surgeons. ( 0,500424870069956 )
Int J Comput Assist Radiol Surg - Neurosurgical craniotomy localization using a virtual reality planning system versus intraoperative image-guided navigation. ( 0,500031027818686 )
Int J Health Geogr - A high resolution spatial population database of Somalia for disease risk mapping. ( 0,499485502327052 )
Spat Spatiotemporal Epidemiol - Residential address errors in public health surveillance data: a description and analysis of the impact on geocoding. ( 0,499018906734083 )
Int J Med Robot - Development of a medical robot system for minimally invasive surgery. ( 0,498561823973623 )
Int J Med Robot - Robotic transaxillary thyroidectomy with gasless approach in a girl with goitre. ( 0,497923929618503 )
Int J Health Geogr - Feasibility and utility of mapping disease risk at the neighbourhood level within a Canadian public health unit: an ecological study. ( 0,497795278345569 )
Comput. Biol. Med. - Subdividing globally important zones based on data distribution across multiple genome fragments. ( 0,496559085183344 )
Int J Health Geogr - A spatially filtered multilevel model to account for spatial dependency: application to self-rated health status in South Korea. ( 0,49572031115614 )
Int J Med Robot - Force feedback in a piezoelectric linear actuator for neurosurgery. ( 0,495682438451804 )
Int J Med Robot - Development of a robotic FD-CT-guided navigation system for needle placement-preliminary accuracy tests. ( 0,495603112152716 )
Int J Comput Assist Radiol Surg - Navigated laparoscopic ultrasound in abdominal soft tissue surgery: technological overview and perspectives. ( 0,49559127680494 )
Comput Math Methods Med - Modeling the spatial distribution of chronic tumor hypoxia: implications for experimental and clinical studies. ( 0,495440034548433 )
Int J Med Robot - The learning curve of robot-assisted laparoscopic fundoplication in children: a prospective evaluation and CUSUM analysis. ( 0,494954680041263 )
Int J Comput Assist Radiol Surg - A fluorolaser navigation system to guide linear surgical tool insertion. ( 0,49485143274459 )
Comput Biol Chem - Conserved patterns in bacterial genomes: a conundrum physically tailored by evolutionary tinkering. ( 0,49450291544919 )
Int J Med Robot - 3D navigated implantation of the glenoid component in reversed shoulder arthroplasty. Feasibility and results in an anatomic study. ( 0,493878171364786 )
Int J Health Geogr - Does context matter for the relationship between deprivation and all-cause mortality? The West vs. the rest of Scotland. ( 0,493240886461326 )
Int J Comput Assist Radiol Surg - Suspension laryngoscopy using a curved-frame trans-oral robotic system. ( 0,492975281243101 )
Int J Med Robot - Generation of mineral density distribution maps from subject-specific models of mandibles - a preliminary study. ( 0,492753239863203 )
IEEE Trans Image Process - S3: a spectral and spatial measure of local perceived sharpness in natural images. ( 0,492560870837772 )
Int J Health Geogr - Spatial accessibility of primary health care utilising the two step floating catchment area method: an assessment of recent improvements. ( 0,491900028477234 )
Spat Spatiotemporal Epidemiol - Measuring the spatial accuracy of the spatial scan statistic. ( 0,491465072214921 )
Comput. Aided Surg. - Navigated percutaneous lumbosacral interbody fusion: a feasibility study. ( 0,490795723971747 )
Int J Health Geogr - An open source software for fast grid-based data-mining in spatial epidemiology (FGBASE). ( 0,489785836269012 )
Int J Health Geogr - A geographic analysis of population density thresholds in the influenza pandemic of 1918-19. ( 0,48963549433149 )
Int J Comput Assist Radiol Surg - The effects of real-time image navigation in operative liver surgery. ( 0,48852352007086 )
Int J Med Robot - Robotic arthroscopic surgery: a new challenge in arthroscopic surgery Part-I: Robotic shoulder arthroscopy; a cadaveric feasibility study. ( 0,487141012213632 )
Comput. Biol. Med. - Detection of masses in mammogram images using CNN, geostatistic functions and SVM. ( 0,486581038038531 )
Int J Health Geogr - Identifying landscape features associated with Rift Valley fever virus transmission, Ferlo region, Senegal, using very high spatial resolution satellite imagery. ( 0,486364806766436 )
Int J Health Geogr - Hand, foot and mouth disease: spatiotemporal transmission and climate. ( 0,486220360430833 )
Int J Health Geogr - Demarcation of local neighborhoods to study relations between contextual factors and health. ( 0,485551764944779 )
Int J Health Geogr - Geospatial association of endemicity of ataxic polyneuropathy and highly cyanogenic cassava cultivars. ( 0,485459257729296 )
Int J Med Robot - Overcoming extreme obesity with robotic surgery. ( 0,48499434707462 )
Int J Health Geogr - Potential corridors and barriers for plague spread in Central Asia. ( 0,484520859593662 )
Int J Med Robot - A case series on the technical use of three-dimensional image guidance in subaxial anterior cervical surgery. ( 0,484232368434061 )
Int J Med Robot - Laparoendoscopic single-site surgery using a multi-functional miniature in vivo robot. ( 0,484043871507067 )