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A Bayesian Analysis for Identifying DNA Copy Number Variations Using a Compound Poisson Process

Jie Chen, Ayten Yiğiter, Yu-Ping Wang, Hong-Wen Deng
2010 EURASIP Journal on Bioinformatics and Systems Biology  
on the chromosome using a compound Poisson process.  ...  To study chromosomal aberrations that may lead to cancer formation or genetic diseases, the array-based Comparative Genomic Hybridization (aCGH) technique is often used for detecting DNA copy number variants  ...  Acknowledgments Part of the paper was done while A. Yigiter was on leave from Hacettepe University and was a visiting scholar at the Univer-  ... 
doi:10.1155/2010/268513 pmid:20976296 pmcid:PMC3171362 fatcat:trkquxsfvjdu5auivepwomhami

Pattern discovery and cancer gene identification in integrated cancer genomic data

Qianxing Mo, Sijian Wang, Venkatraman E. Seshan, Adam B. Olshen, Nikolaus Schultz, Chris Sander, R. Scott Powers, Marc Ladanyi, Ronglai Shen
2013 Proceedings of the National Academy of Sciences of the United States of America  
To identify genomic features that contribute most to the biological variation and thus have direct relevance for characterizing the molecular subgroups, we apply a penalized  ...  Thus, there is a corresponding need for a forward-engineering process that synthesizes and integrates the information to extract biological principles from the massive amount of data to provide useful  ...  Atlas project, and by a Starr Cancer Consortium grant.  ... 
doi:10.1073/pnas.1208949110 pmid:23431203 pmcid:PMC3600490 fatcat:vx73girquzardhalcomylnxxka

Molecular dating when rates vary

J WELCH, L BROMHAM
2005 Trends in Ecology & Evolution  
Substitution model Single fixed- point calibration Compound Poisson process incorporating the Gamma Multiplier model Fixed Bayesian (rates not estimated) [30] Heuristic rate smoothing  ...  rate variation, and then exclude these from the analysis.  ...  Forthcoming Conferences Are you organizing a conference, workshop or meeting that would be of interest to TREE readers?  ... 
doi:10.1016/j.tree.2005.02.007 pmid:16701388 fatcat:7o2cz2vrmbgbpp67fiqinmlhie

Comparative Analysis of Apopellia endiviifolia Plastomes Reveals a Strikingly High Level of Differentiation between Its Terrestrial and Water Form

Jakub Sawicki, Katarzyna Krawczyk, Monika Ślipiko, Kamil Szandar, Monika Szczecińska
2021 Diversity  
Comparative analysis of typical, terrestrial and water forms revealed 4971 molecular diagnostic characters (MDCs), which exceeds numbers found in many well recognized liverworts taxa.  ...  The plastomes of A. endiviifolia are 120,537–120,947 bp long with a structure typical for most plants, including a pair of IR regions (each of 9092–9207 bp) separated by LSC (82,506–82,609 bp) and SSC  ...  The Poisson Tree Processes (PTP) method was applied to delimitate species boundaries [41] .  ... 
doi:10.3390/d13120674 fatcat:km7fs4icrvftpaw7xh65hijkqa

Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets

David C. Wedge, Gunes Gundem, Thomas Mitchell, Dan J. Woodcock, Inigo Martincorena, Mohammed Ghori, Jorge Zamora, Adam Butler, Hayley Whitaker, Zsofia Kote-Jarai, Ludmil B. Alexandrov, Peter Van Loo (+74 others)
2018 Nature Genetics  
Computational chemogenomic (canSAR) analysis of prostate cancer mutations identified 11 targets of approved drugs, 7 targets of investigational drugs, and 62 targets of compounds that may be active and  ...  From joint analysis of these cancers with those from previous studies (930 cancers in total), we found evidence for 22 previously unidentified putative driver genes harboring coding mutations, as well  ...  as a Poisson process.  ... 
doi:10.1038/s41588-018-0086-z pmid:29662167 pmcid:PMC6372064 fatcat:zshzdb75dndc3chtf5ujvwm3m4

A Survey on Bayesian Nonparametric Learning

Junyu Xuan, Jie Lu, Guangquan Zhang
2019 ACM Computing Surveys  
For example, developing a new stochastic process for a specific data structure or designing a more efficient inference algorithm.  ...  Second, Bayesian learning can smoothly encode the prior knowledge about a problem under study in parallel with the knowledge learned from observed data -an asset that is also useful for overcoming the  ...  Among a number of methodologies for music analysis, Bayesian techniques have been found to be very effective, which has paved the way for further advancements using BNL.  ... 
doi:10.1145/3291044 fatcat:aytdnsnrfvfnti5i64ne4icenu

A Bayesian Nonparametric Model for Inferring Subclonal Populations from Structured DNA Sequencing Data [article]

Shai He, Aaron Schein, Vishal Sarsani, Patrick Flaherty
2020 bioRxiv   pre-print
We develop a representation of the hierarchical Dirichlet process prior as a Gamma-Poisson hierarchy and we use this representation to derive a fast Gibbs sampling inference algorithm using the augment-and-marginalize  ...  Yet, within a single tumor there is often extensive genetic heterogeneity as evidenced by single-cell and bulk DNA sequencing data.  ...  The paper shows that copy-number variation data is essential for accurate subclonal reconstruction.  ... 
doi:10.1101/2020.11.10.330183 fatcat:moij5ayzkfbbjc47hd3csnxp2a

Efficacy of ivermectin against gastrointestinal nematodes of cattle in Denmark evaluated by different methods for analysis of faecal egg count reduction

Miguel Peña-Espinoza, Stig M. Thamsborg, Matthew J. Denwood, Markus Drag, Tina V. Hansen, Vibeke F. Jensen, Heidi L. Enemark
2016 International Journal for Parasitology: Drugs and Drug Resistance  
The authors gratefully acknowledge all the cattle farmers involved in the study and the veterinarians for their help in contacting the producers.  ...  We gratefully thank to Louise Schmidt, Matthias Enemark, Peter Janns, Anne Maria Dam, Aleksandra Tofteby and Leif Eiersted for their valuable help and technical support.  ...  Due to this defined BWs and the likely variation in the actual amount of active compound used for different animals following each prescription, the calculated number of treatments is only a proxy of the  ... 
doi:10.1016/j.ijpddr.2016.10.004 pmid:27835769 pmcid:PMC5107639 fatcat:w6tkotpbw5g7fdnpfpo2mmp6qa

Phylogenomics and barcoding of Panax: toward the identification of ginseng species

V. Manzanilla, A. Kool, L. Nguyen Nhat, H. Nong Van, H. Le Thi Thu, H. J. de Boer
2018 BMC Evolutionary Biology  
In this study, we use a full plastome phylogenomic framework to resolve relationships in Panax and to identify molecular markers for species discrimination.  ...  Conclusions: MBD2 depletion reduces the cost of plastome sequencing, which makes it a cost-effective alternative to Sanger sequencing based DNA barcoding for molecular identification.  ...  Acknowledgments The authors wish to thank the following people and organizations, Jarl Andreas Anmarkrud for his assistance for the enrichment, members of de Boer group for their helpful discussions and  ... 
doi:10.1186/s12862-018-1160-y pmid:29614961 pmcid:PMC5883351 fatcat:zoa36y4xnjdundcwdbyk5k43jm

Tracking the origins and drivers of subclonal metastatic expansion in prostate cancer

Matthew K.H. Hong, Geoff Macintyre, David C. Wedge, Peter Van Loo, Keval Patel, Sebastian Lunke, Ludmil B. Alexandrov, Clare Sloggett, Marek Cmero, Francesco Marass, Dana Tsui, Stefano Mangiola (+17 others)
2015 Nature Communications  
Tumour heterogeneity in primary prostate cancer is a well-established phenomenon.  ...  Here we reveal the precise direction of metastatic spread across four lethal prostate cancer patients using whole-genome and ultra-deep targeted sequencing of longitudinally collected primary and metastatic  ...  For copy-number variations, we used the Mann-Whitney U-test to test for significantly different gene copy-numbers between primary and metastatic samples across our cohort.  ... 
doi:10.1038/ncomms7605 pmid:25827447 pmcid:PMC4396364 fatcat:dzg274r5nzc67fvb7phhxoyvpu

Babesia microti from humans and ticks hold a genomic signature of strong population structure in the United States

Giovanna Carpi, Katharine S. Walter, Choukri Ben Mamoun, Peter J. Krause, Andrew Kitchen, Timothy J. Lepore, Ankit Dwivedi, Emmanuel Cornillot, Adalgisa Caccone, Maria A. Diuk-Wasser
2016 BMC Genomics  
Bayesian analyses of the apicoplast genomes suggest that the origin of the current diversity of B. microti in northeastern USA dates back 46 thousand years with a signature of recent population expansion  ...  Despite low genomic variation compared with other Apicomplexa, B. microti was strongly structured into three highly differentiated genetic clusters in the northeastern USA.  ...  Acknowledgements The authors thank Janna Brancato for technical assistance with DNA extraction of human samples.  ... 
doi:10.1186/s12864-016-3225-x pmid:27821055 pmcid:PMC5100190 fatcat:5bdtiz53bvgvdpzbcv47oaqmze

EMu: probabilistic inference of mutational processes and their localization in the cancer genome

Andrej Fischer, Christopher JR Illingworth, Peter J Campbell, Ville Mustonen
2013 Genome Biology  
We present a novel probabilistic method, EMu, to infer the mutational signatures of these processes from a collection of sequenced tumors.  ...  The spectrum of mutations discovered in cancer genomes can be explained by the activity of a few elementary mutational processes.  ...  We would like to acknowledge the Wellcome Trust for support under grant reference 098051. AF is supported by the German Research Foundation (DFG) under grant reference number FI 1882/1-1.  ... 
doi:10.1186/gb-2013-14-4-r39 pmid:23628380 pmcid:PMC3663107 fatcat:dzb2tkkterh7rk3u67uh2cjjia

Prospects for Admixture Mapping of Complex Traits

Paul M. McKeigue
2005 American Journal of Human Genetics  
Statistical-analysis programs for admixture mapping are now available, and a genomewide panel of markers for admixture mapping in populations formed by West African-European admixture has been assembled  ...  For detecting genes that contribute to ethnic variation in disease risk, admixture mapping has greater statistical power than family-linkage studies.  ...  Electronic-Database Information The URL for data presented herein is as follows: Bioethics Resources on the Web, http://www.nih.gov/sigs/ bioethics/named_populations.html  ... 
doi:10.1086/426949 pmid:15540159 pmcid:PMC1196412 fatcat:vjanbkykbvezlh7vrwc33mpsgm

A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data

Christopher Yau, Dmitri Mouradov, Robert N Jorissen, Stefano Colella, Ghazala Mirza, Graham Steers, Adrian Harris, Jiannis Ragoussis, Oliver Sieber, Christopher C Holmes
2010 Genome Biology  
Our approach allows us to model the joint effect of polyploidy, normal DNA contamination and intra-tumour heterogeneity within a single unified Bayesian framework.  ...  We describe a statistical method for the characterization of genomic aberrations in single nucleotide polymorphism microarray data acquired from cancer genomes.  ...  Acknowledgements The authors would like to thank Jean-Baptiste Cazier for general discussions and careful reading of this manuscript, Rachel Natrajan and Jorge Reis-Filho for discussion and advice on earlier  ... 
doi:10.1186/gb-2010-11-9-r92 pmid:20858232 pmcid:PMC2965384 fatcat:f4shxh5lofgkjdtsw24fm4wioi

Sparse discriminative latent characteristics for predicting cancer drug sensitivity from genomic features

David A. Knowles, Gina Bouchard, Sylvia Plevritis, Florian Markowetz
2019 PLoS Computational Biology  
We use ideas from Bayesian nonparametrics to automatically infer the appropriate number of these latent characteristics.  ...  Alongside these sensitivity measurements high dimensional molecular characterizations of the cell lines are typically available, including gene expression, copy number variation and genomic mutations.  ...  Per gene DNA copy number as determined using Affymetrix SNP6.0 arrays were obtained (analysis date 2013-12-03).  ... 
doi:10.1371/journal.pcbi.1006743 pmid:31136571 pmcid:PMC6555538 fatcat:kaxgf2wufzgkdpvzxmvktsf4na
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