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Detecting copy number variation in next generation sequencing data from diagnostic gene panels

Ashish Kumar Singh, Maren Fridtjofsen Olsen, Liss Anne Solberg Lavik, Trine Vold, Finn Drabløs, Wenche Sjursen
2021 BMC Medical Genomics  
We have detected whole gene level deletion/duplication, single/multi exonic level deletion/duplication, partial exonic deletion and mosaic deletion.  ...  This is computed by comparing the mean coverage of the sample with the mean coverage of the same region in other samples, defined as a pool.  ...  normal samples with similar coverage depth as the query sample.  ... 
doi:10.1186/s12920-021-01059-x pmid:34465341 fatcat:cmwfsdhee5gedcqludgxinwbum

Semantic clustering of images using patterns of relevance feedback

Donn Morrison, Stephane Marchand-Maillet, Eric Bruno
2008 2008 International Workshop on Content-Based Multimedia Indexing  
Interestingly, the system shows reasonable performance with just 30% relevance feedback coverage (70% simulated element deletion).  ...  For example, noise generated at a coverage percentage of 80% would randomly delete 80% of the elements in the image-session matrix, simulating the sparsity seen in the realworld data.  ... 
doi:10.1109/cbmi.2008.4564964 dblp:conf/cbmi/MorrisonMB08 fatcat:cn5l7qyh5vaojeeyskzhqrjpu4

Leveraging multiple genomic data to prioritize disease-causing indels from exome sequencing data

Mengmeng Wu, Ting Chen, Rui Jiang
2017 Scientific Reports  
SNV (single nucleotide variants), indel (micro-insertion or micro-deletion), SV (structural variants), etc.  ...  in deed helped to improve the overall coverage.  ...  is ∑ β = − = − ( ) ( ) K m p p 1 ( 11 ) m i m K m i m K m ( ) ( ) Then the integrated p-value is approximated as β = = ..  p K min RRA i K m 1, , , where K is used as Bonferroni correction.  ... 
doi:10.1038/s41598-017-01834-w pmid:28496131 pmcid:PMC5431795 fatcat:ffv4a5cynjhizeywqiil6aw4eq

A Novel Study for Spatio-Temporal Query Processing using Privacy Preservation

Dileep Kumar
2021 Zenodo  
Finally we will quantify the benefits of our approach using sampled results through experiments that the proposed cloaking algorithm is scalable, efficient and robust to support anonymity irrespective  ...  of scale of user queries in real time scenario.  ...  and robust cloaking algorithm.  ... 
doi:10.5281/zenodo.4661499 fatcat:wmintauf2rfytdkbdxwxevckca

Genetic interaction networks mediate individual statin drug response in Saccharomyces cerevisiae

Bede P. Busby, Eliatan Niktab, Christina A. Roberts, Jeffrey P. Sheridan, Namal V. Coorey, Dinindu S. Senanayake, Lisa M. Connor, Andrew B. Munkacsi, Paul H. Atkinson
2019 npj Systems Biology and Applications  
Here we created deletion libraries in three additional genetic backgrounds. Statin response was probed with five queries against four genetic backgrounds.  ...  Eukaryotic genetic interaction networks (GINs) are extensively described in the Saccharomyces cerevisiae S288C model using deletion libraries, yet being limited to this one genetic background, not informative  ...  i k j 2m !  ... 
doi:10.1038/s41540-019-0112-5 pmid:32242013 fatcat:kilza4xplzdlreysdvmunv6s54

A robust/fast spoken term detection method based on a syllable n-gram index with a distance metric

Seiichi Nakagawa, Keisuke Iwami, Yasuhisa Fujii, Kazumasa Yamamoto
2013 Speech Communication  
The retrieval results show that we can detect OOV words in a database containing 44 h of audio in less than 10 m sec per query with an F-measure of 0:54.  ...  :- When using the kth candidate in a lattice, the distance is defined as follows: Ins=Del ¼ 1 if a dða; bÞ min k fdða; b k Þ þ k Á cg ð 10Þ where b k and k Á c denote the kth syllable candidate and the  ...  Finally, to address deletion errors, we search for edited queries from which one syllable has been deleted.  ... 
doi:10.1016/j.specom.2012.12.001 fatcat:7affzhgpafaxbku4ga3dijdjde

Three Approximation Algorithms for Energy-Efficient Query Dissemination in Sensor Database System [chapter]

Zhao Zhang, Xiaofeng Gao, Xuefei Zhang, Weili Wu, Hui Xiong
2009 Lecture Notes in Computer Science  
An update to R can be an insert, a delete, or modifications of record in R.  ...  will form a k-connected subgraph.  ...  They proposed a new kind of probabilistic queries called Probabilistic Threshold Query.  ... 
doi:10.1007/978-3-642-03573-9_68 fatcat:cnidlx3c4rc5hbpqtufa7e2e6e

Spatial R-Tree Index Based on Grid Division for Query Processing

Esraa Rslan, Hala Abdel Hameed, Ehab Ezzat
2017 International Journal of Database Management Systems  
The most wellknown kinds of queries strategies in moving objects databases are Rang, Point and K-Nearest Neighbour and inquiries.  ...  This study uses R-tree method to get detailed range query results efficiently. But using R-tree only will generate much overlapping and coverage between MBR.  ...  Query Processing Two main types of queries are discussed: Range Query and K-nearest neighbour query.  ... 
doi:10.5121/ijdms.2017.9602 fatcat:662lp5ylyngpnpubs3jiszda7y

Linking functionally related genes by sensitive and quantitative characterization of genetic interaction profiles

L. Decourty, C. Saveanu, K. Zemam, F. Hantraye, E. Frachon, J.-C. Rousselle, M. Fromont-Racine, A. Jacquier
2008 Proceedings of the National Academy of Sciences of the United States of America  
In a pilot experiment (41 genome-wide screens), we quantified the fitness of 140,000 double deletion strains relative to the corresponding single mutants and identified many genetic interactions.  ...  These weak effects, rarely meaningful when considered individually, were crucial to defining specific signatures for many gene deletions and had a major contribution in defining clusters of functionally  ...  For a robust estimation of the values, two reference deletions were used in independent hybridizations for most experiments.  ... 
doi:10.1073/pnas.0710533105 pmid:18408161 pmcid:PMC2311358 fatcat:gu5g6wb6drdphmoutubzxgv6ba

Fully Dynamic Algorithm for Constrained Submodular Optimization [article]

Silvio Lattanzi, Slobodan Mitrović, Ashkan Norouzi-Fard, Jakub Tarnawski, Morteza Zadimoghaddam
2020 arXiv   pre-print
task of maximizing a monotone submodular function under a cardinality constraint is at the core of many machine learning and data mining applications, including data summarization, sparse regression and coverage  ...  the values of f for blocks of queries (insertions and deletions) for a fixed k (as the plots in Fig. 9 ).  ...  Consider a set of k elements sampled uniformly at random from the ground set. 2 . This set of elements is very robust against deletions.  ... 
arXiv:2006.04704v1 fatcat:enk7gqxxafg57jguhapc2svnxu

Querying peer-to-peer networks using P-trees

Adina Crainiceanu, Prakash Linga, Johannes Gehrke, Jayavel Shanmugasundaram
2004 Proceedings of the 7th International Workshop on the Web and Databases colocated with ACM SIGMOD/PODS 2004 - WebDB '04  
Peer-to-peer (P2P) systems provide a robust, scalable and decentralized way to share and publish data.  ...  Ptrees efficiently evaluate range queries in addition to equality queries.  ...  such that p.node[l][k].value ∈ (p.value, lb] 16: send Search(lb,ub, originator) message to p.node[l][k].peer 17: end if sage to p = p.node[l][j − 1].peer, and asking for p .node[l − 1][d].value.  ... 
doi:10.1145/1017074.1017082 dblp:conf/webdb/CrainiceanuLGS04 fatcat:w76lgrqimjewxlo7djpzarazcm

Web-scale information extraction with vertex

Pankaj Gulhane, Amit Madaan, Rupesh Mehta, Jeyashankher Ramamirtham, Rajeev Rastogi, Sandeep Satpal, Srinivasan H Sengamedu, Ashwin Tengli, Charu Tiwari
2011 2011 IEEE 27th International Conference on Data Engineering  
a host of novel algorithms for (1) Grouping similar structured pages in a Web site, (2) Picking the appropriate sample pages for wrapper inference, (3) Learning XPath-based extraction rules that are robust  ...  1 do if best XP ath = NULL and ((dist(X) > min dist) or (dist(X) = min dist and sup(X) ≤ max sup)) then delete X from L k+1 ; end if end for C k+1 = {k+1-sets F : all k-subsets of F are in L k+1 }; k =  ...  queries.  ... 
doi:10.1109/icde.2011.5767842 dblp:conf/icde/GulhaneMMRRSSTT11 fatcat:7vznvx5atzaxhh6su6bzuvlm5i


Raju Balakrishnan, Subbarao Kambhampati
2010 Proceedings of the 19th international conference on World wide web - WWW '10  
One immediate challenge in searching the deep web databases is source selection-i.e. selecting the most relevant web databases for answering a given query.  ...  The existing database selection methods (both text and relational) assess the source quality based on the query-similarity-based relevance assessment.  ...  As key word queries for sampling, we use partial titles of the books/movies. We generate partial title queries by randomly deleting words from titles of length more than one word.  ... 
doi:10.1145/1772690.1772801 dblp:conf/www/BalakrishnanK10 fatcat:lbw3ynupmncs7mbhwebcdhmeju

A New R*Q-tree Spatial Index based on the Delaying Selection and Clustering Splitting

Quanyou Song, Wan-gao Li
2011 International Journal of Wireless and Microwave Technologies  
The original R*Q-tree is an important class of query index in the spatial database, but when carry on frequent insertion and deletion, the efficiency is very low, because its construction cost is much  ...  more than that of the other query methods.  ...  Oversized coverage can result in large dead space and reduce the query efficiency [2] [3] .  ... 
doi:10.5815/ijwmt.2011.04.06 fatcat:qk4vmdelkvhnfe4s4uy64fvshi

Assessing relevance and trust of the deep web sources and results based on inter-source agreement

Raju Balakrishnan, Subbarao Kambhampati, Manishkumar Jha
2013 ACM Transactions on the Web  
Further extending SourceRank to multi-domain search, we propose a source ranking sensitive to the query domains.  ...  Though there are existing methods for both the steps, they assess the relevance of the sources and the results using the query-result similarity.  ...  The same set of sampling methods and list of queries are used. But instead of generating partial queries by deleting words randomly, we use full titles as queries.  ... 
doi:10.1145/2460383.2460390 fatcat:zpjfoaf4cnaxneviljvhqqio34
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