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XORRO: Rapid Paired-End Read Overlapper
XORRO: Rapid Paired-End Read Overlapper Russell J. Dickson, Gregory B. Gloor (Submitted on 16 Apr 2013) Background: Computational analysis of next-generation sequencing data is outpaced by data...
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Meta-Analysis of Gene Level Association Tests
Meta-Analysis of Gene Level Association Tests Dajiang J. Liu, Gina M. Peloso, Xiaowei Zhan, Oddgeir Holmen, Matthew Zawistowski, Shuang Feng, Majid Nikpay, Paul L. Auer, Anuj Goel, He Zhang, Ulrike...
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Bayesian test for co-localisation between pairs of genetic association...
Bayesian test for co-localisation between pairs of genetic association studies using summary statistics Claudia Giambartolomei (1), Damjan Vukcevic (2), Eric E. Schadt (3), Aroon D. Hingorani (1),...
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Wavelet-based genetic association analysis of functional phenotypes arising...
Wavelet-based genetic association analysis of functional phenotypes arising from high-throughput sequencing assays Heejung Shim, Matthew Stephens (Submitted on 27 Jul 2013) Understanding how genetic...
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Bayesian genome assembly and assessment by Markov Chain Monte Carlo sampling
Bayesian genome assembly and assessment by Markov Chain Monte Carlo sampling Mark Howison, Felipe Zapata, Erika J. Edwards, Casey W. Dunn (Submitted on 6 Aug 2013) Most genome assemblers provide a...
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Predicting genome-wide DNA methylation using methylation marks, genomic...
Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements Weiwei Zhang, Tim D Spector, Panos Deloukas, Jordana T Bell, Barbara E Engelhardt...
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Cell-cycle regulated transcription associates with DNA replication timing in...
Cell-cycle regulated transcription associates with DNA replication timing in yeast and human Hunter B. Fraser (Submitted on 8 Aug 2013) Eukaryotic DNA replication follows a specific temporal program,...
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Realistic simulations reveal extensive sample-specificity of RNA-seq biases
Realistic simulations reveal extensive sample-specificity of RNA-seq biases Botond Sipos, Greg Slodkowicz, Tim Massingham, Nick Goldman (Submitted on 14 Aug 2013) In line with the importance of...
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Bayesian Model Selection in Complex Linear Systems, as Illustrated in Genetic...
Bayesian Model Selection in Complex Linear Systems, as Illustrated in Genetic Association Studies Xiaoquan Wen (Submitted on 3 Sep 2013) Motivated by examples from genetic association studies, this...
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Waste Not, Want Not: Why Rarefying Microbiome Data is Inadmissible
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High-speed and accurate color-space short-read alignment with CUSHAW2
High-speed and accurate color-space short-read alignment with CUSHAW2 Yongchao Liu, Bernt Popp, Bertil Schmidt (Submitted on 17 Apr 2013) Summary: We present an extension of CUSHAW2 for fast and...
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XORRO: Rapid Paired-End Read Overlapper
XORRO: Rapid Paired-End Read Overlapper Russell J. Dickson, Gregory B. Gloor (Submitted on 16 Apr 2013) Background: Computational analysis of next-generation sequencing data is outpaced by data...
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High-speed and accurate color-space short-read alignment with CUSHAW2
High-speed and accurate color-space short-read alignment with CUSHAW2 Yongchao Liu, Bernt Popp, Bertil Schmidt (Submitted on 17 Apr 2013) Summary: We present an extension of CUSHAW2 for fast and...
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XORRO: Rapid Paired-End Read Overlapper
XORRO: Rapid Paired-End Read Overlapper Russell J. Dickson, Gregory B. Gloor (Submitted on 16 Apr 2013) Background: Computational analysis of next-generation sequencing data is outpaced by data...
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Principal component gene set enrichment (PCGSE)
Principal component gene set enrichment (PCGSE) H. Robert Frost, Zhigang Li, Jason H. Moore Motivation: Although principal component analysis (PCA) is widely used for the dimensional reduction of...
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Bayesian Model Comparison in Genetic Association Analysis: Linear Mixed...
Bayesian Model Comparison in Genetic Association Analysis: Linear Mixed Modeling and SNP Set Testing Xiaoquan Wen (Submitted on 29 Apr 2014) We consider the problems of hypothesis testing and model...
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A Simple Data-Adaptive Probabilistic Variant Calling Model
A Simple Data-Adaptive Probabilistic Variant Calling Model Steve Hoffmann, Peter F. Stadler, Korbinian Strimmer (Submitted on 20 May 2014) Background: Several sources of noise obfuscate the...
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Improved genome inference in the MHC using a population reference graph
Improved genome inference in the MHC using a population reference graph Alexander Dilthey, Charles J Cox, Zamin Iqbal, Matthew R Nelson, Gil McVean In humans and many other species, while much is known...
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Bayesian Structured Sparsity from Gaussian Fields
Bayesian Structured Sparsity from Gaussian Fields Barbara E. Engelhardt, Ryan P. Adams (Submitted on 8 Jul 2014) Substantial research on structured sparsity has contributed to analysis of many...
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Whole-genome sequencing is more powerful than whole-exome sequencing for...
Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants Aziz Belkadi, Alexandre Bolze, Yuval Itan, Quentin B Vincent, Alexander Antipenko, Bertrand Boisson,...
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