Papers
Top Papers Overall
Citations |
as of 10/10/2022 |
2351 |
|
790 |
|
739 |
|
736 |
|
589 |
2022
- Xiao C, Chen Z, Chen W, Padilla C, Colgan M, Wu W, Fang LT, Liu T, Yang Y, Schneider V, Wang C. Personalized genome assembly for accurate cancer somatic mutation discovery using tumor-normal paired reference samples. Genome Biology. 2022 Dec;23(1):1-34
- Talsania K, Shen TW, Chen X, Jaeger E, Li Z, Chen Z, Chen W, Tran B, Kusko R, Wang L, Pang AW. Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies. Genome Biology. 2022 Dec;23(1):1-33.
- Zhang et al, “Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples“, Genome Biology. 2022 June 12 (141)
- Gong et. al, “Ultra-deep sequencing data from a liquid biopsy proficiency study demonstrating analytic validity“, Scientific Data. 2022 Apr; 9(170)
- Sahraeian et. al, “Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample“, Genome Biology. 2022 Jan; 23(12)
- Pan et. al, “Assessing reproducibility of inherited variants detected with short-read whole genome sequencing“, Genome Biology. 2022 Jan; 23(2)
2021
- Khayat MM, Sahraeian SM, Zarate S, Carroll A, Hong H, Pan B, Shi L, Gibbs RA, Mohiyuddin M, Zheng Y, Sedlazeck FJ. Hidden biases in germline structural variant detection. Genome biology. 2021 Dec;22(1):1-5.
- Foox, J., et al. The SEQC2 epigenomics quality control (EpiQC) study, Genome Biology. 2021 Dec; 22(323)
- Li, D., et al. FDA-led consortium studies advance quality control of targeted next generation sequencing assays for precision oncology, Precision Cancer Medicine. 2021 Dec; (4)
- Mirzayi et al. Reporting guidelines for human microbiome research: the STORMS checklist, Nature Medicine. 2021 Nov (97)
- Willey, J. et al. Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA, Cell Reports Methods. 2021.
- Mercer, T. et al. The Sequencing Quality Control 2 study: establishing community standards for sequencing in precision medicine. Genome Biology. 2021; 22(306).
- Mammoliti, A.. et al. Orchestrating and sharing large multimodal data for transparent and reproducible research, Nature Communications. 2021 Oct;(12)
- Zhao, Y. et al. Whole genome and exome sequencing reference datasets from a multi-center and cross-platform benchmark study, Scientific Data. 2021 Oct;8(296)
Nature Biotechnology Sequencing Quality Control 2 Collection (Sept 9 2021)
- Xiao, W. et al. Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing, Nature Biotechnology. 2021 Sep;8(39)
- Fang, L.T. et al. Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing, Nature Biotechnology. 2021 Sep;8(39)
- Chen, W. et al. A multicenter study benchmarking single-cell RNA sequencing technologies using reference samples. Nature Biotechnology. 2021;8(39)
- Foox, J., et al., Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study. Nature Biotechnology. 2021:8(39)
- Chen, W. et al. A multi-center cross-platform single-cell RNA sequencing reference dataset, Scientific Data. 2021 Feb;8(39). (first published online in 2020)
- Deveson IW, Gong B, Lai K, LoCoco JS, Richmond TA, Schageman J, Zhang Z, Novoradovskaya N, Willey JC, Jones W, Kusko R, et. al., Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology. Nature biotechnology. 2021 Apr 12:1-4.
- Gong B, Li D, Kusko R, Novoradovskaya N, Zhang Y, Wang S, Pabón-Peña C, Zhang Z, Lai K, Cai W, LoCoco JS., et al., Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions. Genome Biology. 2021 Dec;22(1):1-23.
- Jones, W., Gong, B., Novoradovskaya, N., Li, D., Kusko, R., Richmond, T.A., Johann, D.J., Bisgin, H., Sahraeian, S.M.E., Bushel, P.R., Pirooznia, M., et al., 2021. A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency. Genome Biology, 22(1), pp.1-38.
- Zhang L, Shi J, Ouyang J, Zhang R, Tao Y, Yuan D, Lv C, Wang R, Ning B, Roberts R, Tong W. X-CNV: genome-wide prediction of the pathogenicity of copy number variations. Genome Medicine. 2021 Dec;13(1):1-5.
2020
Haibe-Kains B, Adam GA, Hosny A, Khodakarami F, Waldron L, Wang B, McIntosh C, Goldenberg A, Kundaje A, Greene CS, Broderick T. Transparency and reproducibility in artificial intelligence. Nature. 2020 Oct;586(7829):E14-6.
Chen, W. et al. A multicenter study benchmarking single-cell RNA sequencing technologies using reference samples. Nature Biotechnology. 2020. (also included in Nature Biotechnology 2021 collection)
2014
2009
2008
Shi, L., Jones, W.D., Jensen, R.V., Harris, S.C., Perkins, R.G., Goodsaid, F.M., Guo, L., Croner, L.J., Boysen, C., Fang, H. et al. The balance of reproducibility, sensitivity, and specificity of lists of differenctially expressed genes in microarray studies. BMC Bioinformatics, 9 Suppl 9:S10, 2008.
Shi, L., Perkins, R.G., Fang, H., Tong, W. Reproducible and reliable microarray results through quality control: good laboratory proficiency and appropriate data analysis practices are essential. Current Opinions on Biotechnology, 19(1):10-18, 2008.