David Samuels’ peer-reviewed publications on genomic methods

Links to full text are in the journal names

 

Genome measures used for quality control are dependent on gene function and ancestry

Jing Wang, Leon Raskin, David C. Samuels Yu Shyr, Yan Guo (2015) to appear in Bioinformatics

 

Alternative applications for distinct RNA sequencing strategies

Leng Han, Kasey C. Vickers, David C. Samuels, Yan Guo (2015) to appear in Briefings in Bioinformatics

 

Illumina human exome genotyping array clustering and quality control

Yan Guo, Jing He, Shilin Zhao, Hui Wu, Xue Zhong, Quanhu Sheng, David C. Samuels, Yu Shyr, Jirong Long (2014), Nature Protocols, 9(11) 2643-2662.

 

High-throughput sequencing in mitochondrial DNA research

Fei Ye, David C. Samuels, Travis Clark, Yan Guo (2014) Mitochondrion 17, 157-163

 

Multi-perspective quality control of Illumina exome sequencing data using QC3

Yan Guo, Shilin Zhao, Quanhu Sheng, Fei Ye, Jiang Li, Brian Lehmann, Jennifer Pientenpol, David C. Samuels, Yu Shyr (2014) Genomics 103(5-6) 323-328.

 

Comparative Study of Exome Copy Number Variation Estimation Tools Using Array Comparative Genomic Hybridization as Control

Yan Guo, Quagho Sheng, David C. Samuels, Brian Lehmann, Joshua Bauer, J.A. Pietenpol, Yu Shyr (2013), BioMed Research International.

 

Three stage quality control strategies for DNA re-sequencing data

Yan Guo, Sheng Quanghu, Fei Ye, Travis Clark, David C. Samuels (2013), Briefings in Bioinformatics. 15(6) 879-889

 

Finding the Lost Treasures in Exome Sequencing Data

David C. Samuels, Leng Han, Jiang Li, Sheng Quanhu, Travis A. Clark, Yu Shyr, Yan Gou (2013), Trends in Genetics. 29(10) 593-599

 

Large scale comparisons of gene expression levels by microarrays and RNAseq using TCGA data

Yan Guo, Quanhu Sheng, Jiang Li, Fei Ye, David C. Samuels, Yu Shyr (2013) PLoS One. 8(8) e71462

 

MitoSeek: Extracting mitochondria information and performing high-throughput mitochondria sequencing analysis

Yan Guo, Jiang Li, Chung-I Li, Yu Shyr, David C Samuels (2013) Bioinformatics, 29 (9) 1210-1211.

 

Evaluation of Allele Freqency Estimation Using Pooled Sequencing Data Simulation

Yan Guo, David C. Samuels, Jiang Li, Travis Clark, Chung-I Li, Yu Shyr (2013), The Scientific World Journal article ID 895496 (9 pages). PMC3582166

 

The effect of strand bias in Illumina short-read sequencing data

Yan Guo, Jiang Li, Chung-I Li, Jirong Long, David C. Samuels, Yu Shyr (2012), BMC Genomics 13:666. PMC3532123