@article{jiang_li_motsinger-reif_2021, title={Knockoff boosted tree for model-free variable selection}, volume={37}, ISSN={["1460-2059"]}, DOI={10.1093/bioinformatics/btaa770}, abstractNote={The recently proposed knockoff filter is a general framework for controlling the false discovery rate (FDR) when performing variable selection. This powerful new approach generates a 'knockoff' of each variable tested for exact FDR control. Imitation variables that mimic the correlation structure found within the original variables serve as negative controls for statistical inference. Current applications of knockoff methods use linear regression models and conduct variable selection only for variables existing in model functions. Here, we extend the use of knockoffs for machine learning with boosted trees, which are successful and widely used in problems where no prior knowledge of model function is required. However, currently available importance scores in tree models are insufficient for variable selection with FDR control.We propose a novel strategy for conducting variable selection without prior model topology knowledge using the knockoff method with boosted tree models. We extend the current knockoff method to model-free variable selection through the use of tree-based models. Additionally, we propose and evaluate two new sampling methods for generating knockoffs, namely the sparse covariance and principal component knockoff methods. We test and compare these methods with the original knockoff method regarding their ability to control type I errors and power. In simulation tests, we compare the properties and performance of importance test statistics of tree models. The results include different combinations of knockoffs and importance test statistics. We consider scenarios that include main-effect, interaction, exponential and second-order models while assuming the true model structures are unknown. We apply our algorithm for tumor purity estimation and tumor classification using Cancer Genome Atlas (TCGA) gene expression data. Our results show improved discrimination between difficult-to-discriminate cancer types.The proposed algorithm is included in the KOBT package, which is available at https://cran.r-project.org/web/packages/KOBT/index.html.Supplementary data are available at Bioinformatics online.}, number={7}, journal={BIOINFORMATICS}, author={Jiang, Tao and Li, Yuanyuan and Motsinger-Reif, Alison A.}, year={2021}, month={Apr}, pages={976–983} }
 @article{jiang_wang_ruan_zhu_2019, title={Equi-biaxial compressive strain in graphene: Gruneisen parameter and buckling ridges}, volume={6}, ISSN={["2053-1583"]}, DOI={10.1088/2053-1583/aaf20a}, abstractNote={Strain and defects in graphene have critical impact on morphology and properties of graphene. Here we report equi-biaxial compressive strain in monolayer graphene on SiO2 and Si3N4 substrates induced by thermal cycling in vacuum. The equi-biaxial strain is attributed to the mismatch in coefficient of thermal expansion between graphene and the substrate and sliding of graphene on the substrate. The sliding occurs during heating at the temperatures of 390 and 360 K for graphene on SiO2 and Si3N4 substrates, respectively. The biaxial Grüneisen parameter is determined to be 1.95 and 3.15 for G and 2D Raman bands of graphene, respectively. As the heating temperature exceeds a threshold temperature (1040 K for graphene/SiO2 and 640 K for graphene/Si3N4), buckling ridges are observed in graphene after the thermal cycle, from which the biaxial buckling strain of graphene on SiO2 and Si3N4 substrates are obtained as 0.21% and 0.22%, respectively. Importantly, the induced buckling ridges in graphene exhibit a pattern representing the symmetry of graphene crystal structure, which indicates that graphene relieves the compressive stress mainly along its lattice symmetry directions. These thermally induced graphene ridges are also found reminiscent of those in the synthesized graphene, suggesting the same origin of formation of the buckling ridges under biaxial compression.}, number={1}, journal={2D MATERIALS}, author={Jiang, Tao and Wang, Zuyuan and Ruan, Xiulin and Zhu, Yong}, year={2019}, month={Jan} }
 @article{kennedy_thomas_durrant_jiang_motsinger-reif_breen_2019, title={Genome-wide DNA copy number analysis and targeted transcriptional analysis of canine histiocytic malignancies identifies diagnostic signatures and highlights disruption of spindle assembly complex}, volume={27}, ISSN={["1573-6849"]}, DOI={10.1007/s10577-019-09606-0}, abstractNote={Canine histiocytic malignancies (HM) are rare across the general dog population, but overrepresented in certain breeds, such as Bernese mountain dog and flat-coated retriever. Accurate diagnosis relies on immunohistochemical staining to rule out histologically similar cancers with different prognoses and treatment strategies (e.g., lymphoma and hemangiosarcoma). HM are generally treatment refractory with overall survival of less than 6 months. A lack of understanding regarding the mechanisms of disease development and progression hinders development of novel therapeutics. While the study of human tumors can benefit veterinary medicine, the rarity of the suggested orthologous disease (dendritic cell sarcoma) precludes this. This study aims to improve the understanding of underlying disease mechanisms using genome-wide DNA copy number and gene expression analysis of spontaneous HM across several dog breeds. Extensive DNA copy number disruption was evident, with losses of segments of chromosomes 16 and 31 detected in 93% and 72% of tumors, respectively. Droplet digital PCR (ddPCR) evaluation of these regions in numerous cancer specimens effectively discriminated HM from other common round cell tumors, including lymphoma and hemangiosarcoma, resulting in a novel, rapid diagnostic aid for veterinary medicine. Transcriptional analysis demonstrated disruption of the spindle assembly complex, which is linked to genomic instability and reduced therapeutic impact in humans. A key signature detected was up-regulation of Matrix Metalloproteinase 9 (MMP9), supported by an immunohistochemistry-based assessment of MMP9 protein levels. Since MMP9 has been linked with rapid metastasis and tumor aggression in humans, the data in this study offer a possible mechanism of aggression in HM.}, number={3}, journal={CHROMOSOME RESEARCH}, author={Kennedy, Katherine and Thomas, Rachael and Durrant, Jessica and Jiang, Tao and Motsinger-Reif, Alison and Breen, Matthew}, year={2019}, month={Sep}, pages={179–202} }
 @article{jiang_zhu_2015, title={Measuring graphene adhesion using atomic force microscopy with a microsphere tip}, volume={7}, ISSN={["2040-3372"]}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000356058600023&KeyUID=WOS:000356058600023}, DOI={10.1039/c5nr02480c}, abstractNote={This work reports a general method to measure adhesion energies between graphene and different materials using atomic force microscopy with microsphere tips.}, number={24}, journal={NANOSCALE}, author={Jiang, Tao and Zhu, Yong}, year={2015}, pages={10760–10766} }
 @article{jiang_2014, title={The electric field screening and crossing point shift effects in coated carbon nanotubes}, volume={116}, number={2}, journal={Applied physics. A, Materials science & processing}, author={Jiang, T.}, year={2014}, pages={629–633} }