| 2020 |
H. Lei, B. Lyu, E. M. Gertz, A. A. Schaeffer, X. Shi, K. Wu, G. Li, L. Xu, Y. Hu, M. Dean, R. Schwartz. “Tumor copy number deconvolution integrating bulk and single-cell sequencing data.” Journal of Computational Biology, 27(4):565-598, 2020. |
| 2020 |
Sauerwald, Natalie, Akshat Singhal, and Carl Kingsford. "Analysis of the structural variability of topologically associated domains as revealed by Hi-C." NAR genomics and bioinformatics 2.1 (2020): lqz008. |
| 2020 |
Vinod, N.; Hwang, D.; Azam, S. H.; Swearingen, A. E. D. V.; Wayne, EC.; Fussell, S. C.; Sokolsky-Papkov, M.; Pecot, C. V.; Kabanov, A. V. High-Capacity Poly(2-Oxazoline) Formulation of TLR 7/8 Agonist Extends Survival in a Chemo-Insensitive, Metastatic Model of Lung Adenocarcinoma. Sci. Adv. 2020, 6 (25). Citations: 1 |
| 2020 |
Wan, L., Neumann, C.*, LeDuc, P.R.* Tumor on a Chip for Integrating A 3D Tumor Microenvironment: Mechanical, Chemical, and Oxygen Factors. Lab on a Chip (in press). |
| 2020 |
Y Tao, S Ren, MQ Ding, R Schwartz, X Lu. “Predicting Drug Sensitivity of Cancer Cell Lines via Collaborative Filtering with Contextual Attention.” Machine Learning for Healthcare Conference, 660-684. |
| 2020 |
Y. Tao, H. Lei, X. Fu, A. Lee, J. Ma, R. Schwartz. “Robust and accurate deconvolution of tumor populations uncovers evolutionary mechanisms of breast cancer metastasis.” Bioinformatics (ISMB 2020 Proceedings Special Issue), 36:i407-i416, 2020. |
| 2020 |
Z. Cheng, X. Han, and S.-Y. Zheng, Magnetically driven nanotransporter assisted intracellular delivery and autonomous release of proteins. ACS Applied Materials & Interfaces, 12: 41096-41104, (2020). |
| 2019 |
A. Klimas, O. Bucur, B Njeri, Y. Zhao*, “Nanoscopic Imaging of Human Tissue Sections via Physical and Isotropic Expansion”, Journal of Visualized Experiments, 2019, (151), e60195, doi:10.3791/60195. |
| 2019 |
A. T Wassie (equal contribution), Y. Zhao (equal contribution), E. S Boyden*, ‘Expansion Microscopy: Principles and Uses in Biology and Medicine’, Nature Methods, 2019, 16, 33–41. |
| 2019 |
Ma, Cong, and Carl Kingsford. "Detecting, Categorizing, and Correcting Coverage Anomalies of RNA-Seq Quantification." Cell Systems 9.6 (2019): 589-599. |
| 2019 |
Qiu, Yutong, et al. "Detecting Transcriptomic Structural Variants in Heterogeneous Contexts via the Multiple Compatible Arrangements Problem." BioRxiv (2019): 697367. 19th International Workshop on Algorithms in Bioinformatics (WABI 2019) 18:1–18:19 (2019) |
| 2019 |
Sauerwald, Natalie, Yihang Shen, and Carl Kingsford. "Topological Data Analysis Reveals Principles of Chromosome Structure in Cellular Differentiation." 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Schloss Dagstuhl-Leibniz-Zentrum fuer Informatik, 2019. |
| 2019 |
Wayne EC; Long, C.; Haney, M. J.; Batrakova, E. V.; Leisner, T. M.; Parise, L. V.; Kabanov, A. V. Targeted Delivery of SiRNA Lipoplexes to Cancer Cells Using Macrophage Transient Horizontal Gene Transfer. Advanced Science 2019, 6 (21), 1900582. https://doi.org/10.1002/advs.201900582. 2019 Top 10% Most downloaded article from Advanced Science Citations: 3 |
| 2019 |
Y. Tao, H. Lei, A. Lee, J. Ma and R. Schwartz. “Phylogenies Derived from Matched Transcriptome Reveal the Evolution of Cell Populations and Temporal Order of Perturbed Pathways in Breast Cancer Brain Metastases,” Proc. International Symposium on Mathematical and Computational Oncology, 2019. |
| 2019 |
Y. Wan, M. Maurer, H.-Z. He, Y.-Q. Xia, W.-L. Zhang, S.-J. Hao, N. S. Yee, and S.-Y. Zheng, Enrichment of Extracellular Vesicles with Lipid Nanoprobe Functionalized Nanostructured Silica. Lab on a Chip, 19(14): 2346-2355, (2019). |
| 2018 |
D. Wangsa, M. Schieffer, R. Meyer, D. Bronder, H. M. Padilla-Nash, I. Torres, L. Warner, Y. Hu, E. M. Gertz, R. Schwartz, A. A. Schäffer, D. Hirsch, T. Gaiser, J. Camps, K. Heselmeyer-Haddad, and T. Ried. “The evolution of single cell-derived colorectal cancer cell lines is dominated by the continued selection of tumor specific genomic imbalances, despite random chromosomal instability.” Carcinogenesis, 1:13, 2018. |
| 2018 |
G. Cheng, W. Li, L. Ha, X. Han, S. Hao, Y. Wan, Z. Wang, F. Dong, X. Zou, Y. Mao, and S.-Y. Zheng, Self-assembly of extracellular vesicle-like metal-organic framework nanoparticles for protection and intracellular delivery of biofunctional proteins. Journal of the American Chemical Society, 140, 7282-7291, (2018). (Supplementary cover article) |
| 2018 |
J. Eaton, J. Wang, and R. Schwartz. “Deconvolution and phylogeny inference of structural variations in tumor genomic samples.” Bioinformatics (ISMB special proceedings issue), 34(13):i357-i365, 2018. |
| 2018 |
J. Kang, T. Rancati, S. Lee, J.-H. Oh, S. L. Kerns, J. G. Scott, R. S. Schwartz, S. Kim, J. Deasy, B. S. Rosenstein. “Machine learning and radiogenomics: lessons learned and future directions.” Frontiers in Oncology, 8:228, 2018. |
| 2018 |
J. Oltmann, K. Heselmeyer-Haddad, L.S. Hernandez, R. Meyer, I. Torres, Y. Hu, N. Doberstein, J.K. Killian, D. Petersen, Y.J. Zhu, D.C. Edelman, P.S. Meltzer, R. Schwartz, E.M. Gertz, A.A. Schäffer, G. Auer, J.K. Habermann, T. Ried. “Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patients.” Genes, Chromosomes & Cancer, 57(4):165-175, 2018. |
| 2018 |
Lee, Heewook, and Carl Kingsford. "Kourami: graph-guided assembly for novel human leukocyte antigen allele discovery." Genome biology 19.1 (2018): 16. |
| 2018 |
Ma, Cong, Mingfu Shao, and Carl Kingsford. "SQUID: transcriptomic structural variation detection from RNA-seq." Genome biology 19.1 (2018): 52. |
| 2018 |
S. Hao, L. Ha, G. Cheng, Y. Wan, Y. Xia, D. M. Sosnoski, A. M. Mastro, and S.-Y. Zheng, A spontaneous 3D bone-on-a-chip for bone metastasis study of breast cancer cells. Small, 14, 1702787, (2018). |
| 2018 |
S. Hao, Y. Wan, Y.-Q. Xia, X. Zou, and S.-Y. Zheng, Size-based separation methods of circulating tumor cells. Advanced Drug Delivery Reviews, 125, 3-20, (2018). |
| 2018 |
Sauerwald, Natalie, and Carl Kingsford. "Quantifying the similarity of topological domains across normal and cancer human cell types." Bioinformatics 34.13 (2018): i475-i483. |
| 2018 |
W. Li, L. Sun, Y. Xia, S.-J. Hao, G. Cheng, Z. Wang, Y. Wan, C. Zhu, H. He, and S.-Y. Zheng, Pre-occupation of empty carriers decreases endo/lysosome escape and reduces the protein delivery efficiency of mesoporous silica nanoparticles. ACS Applied Materials & Interfaces, 10, 5340-5347, (2018). |
| 2018 |
W. Li, Z. Wang, S. Hao, L. Sun, M. Nisic, G. Cheng, C. Zhu, Y. Wan, L. Ha, and S.-Y. Zheng, Mitochondria-based aircraft carrier enhances in vivo imaging of carbon quantum dots and delivery of anticancer drug. Nanoscale, 10, 3744-3752, (2018). |
| 2018 |
Y. Wan, B. Liu, H. Lei, B. Zhang, Y. Wang, H. Huang, S. Chen, Y. Feng, L. Zhu, Y. Gu, Q. Zhang, H. Ma, and S.-Y. Zheng, Nanoscale extracellular vesicle-derived DNA is superior to circulating cell free DNA for mutation detection in early-stage non-small cell lung cancer. Annals of Oncology, 29(12): 2379-2383, (2018). |
| 2018 |
Y. Wan, L. Wang, C. Zhu, Q. Zheng, G. Wang, J. Tong, Y. Fang, Y.-Q. Xia, G. Cheng, X. He, and S.-Y. Zheng, Aptamer conjugated extracellular nanovesicles for in vivo targeted drug delivery. Cancer Research, 78, 798-808, (2018). |
| 2018 |
Y. Xia, Y. Wan, S. Hao, M. Nisic, R. A. Harouaka, Y. Chen, X. Zou, and S.-Y. Zheng, Nucleus of circulating tumor cell determines its translocation through biomimetic microconstrictions and its physical enrichment by microfiltration. Small, 14(44): e1802899, (2018). |
| 2017 |
R. Schwartz and A. A. Schaffer. “The evolution of tumor phylogenetics: principles and practice.” Nature Reviews Genetics, 18(4):213-229, 2017. |
| 2017 |
Rajaraman A and Ma J. Towards recovering allele-specific cancer genome graphs. RECOMB, 2017. |
| 2017 |
T. Roman, L. Xie, and R. Schwartz. “Automated deconvolution of structured mixtures from heterogeneous tumor genomic data.” PLOS Computational Biology, 13(10), e1005815, 2017. |
| 2017 |
W. Li, Z. Wang, S.-J. Hao, H. He, Y. Wan, C. Zhu, L. Sun, G. Cheng, & S.-Y. Zheng, Mitochondria-targeting polydopamine nanoparticles to deliver doxorubicin for overcoming drug resistance. ACS Applied Materials & Interfaces, 9, 16793–16802, (2017). |
| 2017 |
Wan, L., Skoko, J., Yu, J., LeDuc, P.R.* Neumann, C,* Mimicking Embedded Vasculature Structure for 3D Cancer on a Chip Approaches through Micromilling. Scientific Reports (Nature Publishing Group) 7: 16724 (2017). |
| 2017 |
Y. Wan, G. Cheng, X. Liu, S.-J. Hao, M. Nisic, C.-D. Zhu, Y.-Q. Xia, W.-Q. Li, Z.-G. Wang, W.-L. Zhang, S. J. Rice, A. Sebastian, I. Albert, C. P. Belani & S.-Y. Zheng, Rapid magnetic isolation of extracellular vesicles via lipid-based nanoprobes. Nature Biomedical Engineering, 1 (4), 0058, 1-11, (2017). (Featured as the front cover article and highlighted with an editorial) |
| 2017 |
Y. Zhao (equal contribution), O. Bucur (equal contribution), H. Irshad, F. Chen, A. Weins, A. L. Stancu, E – Y. Oh, M. DiStasio, V. Torous, B. Glass, I. E. Stillman, S. J. Schnitt, A. H. Beck*, E. S. Boyden*, ‘Nanoscale imaging of clinical specimens using pathology-optimized expansion microscopy.’ Nature Biotechnology, 2017, 35 (8), 757–764. |
| 2017 |
Y.-T. Yeh, R. A. Harouaka, & S.-Y. Zheng, Evaluating a novel dimensional reduction approach for mechanical fractionation of cells using a tandem flexible micro spring array (tFMSA). Lab on a Chip, 17 (4), 691-701 (2017). |
| 2016 |
D. Catanzaro, S. Shackney, A. Schäffer, and R. Schwartz. "Classifying the progression of ductal carcinoma from single-cell sampled data via integer linear programming: a case study." IEEE/ACM Transactions on Computational Biology and Bioinformatics, 13(4):643-655, 2016. |
| 2016 |
D. Wangsa, S. A. Chowdhury, M. Ryott, E. M. Gertz, G. Elmberger, G. Auer, E. A. Lundqvist, S. Küffer, P. Ströbel, A. A. Schäffer, R. Schwartz, E. Munck-Wikland, T. Ried, K. Heselmeyer-Haddad. "Phylogenetic analysis of multiple FISH markers in oral tongue squamous cell carcinoma suggests that a diverse distribution of copy number changes in associated with poor prognosis." International Journal of Cancer, 138(1), 2016. |
| 2016 |
E.M. Gertz, S.A. Chowdhury, W.-J. Lee, D. Wangsa, K. Heselmeyer-Haddad, T. Ried, R. Schwartz, A.A. Schäffer. “FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe.” PLOS ONE, 11(6): e0158569, 2016. |
| 2016 |
Hou JP†, Emad A†, Puleo GJ, Ma J*, and Milenkovic O*. A new correlation clustering method for cancer mutation analysis. Bioinformatics, 32(24):3717-28, 2016. |
| 2016 |
Li Y, Zhou S, Schwartz DC, and Ma J. Allele-specific quantification of structural variations in cancer genomes. Cell Systems, 3(1):21-34, 2016. RECOMB, 2016. |
| 2016 |
T. Roman, L. Xie, and R. Schwartz. "Automated deconvolution of structured mixtures from bulk tumor genomic data." RECOMB Satellite Conference on Computational Cancer Biology (published as arXiv preprint arXiv:1604.02487), 2016. |
| 2016 |
T. Roman, L. Xie, and R. Schwartz. "Medoidshift clustering applied to genomic bulk tumor data." BMC Genomics, 17(S1):6, 2016. |
| 2016 |
Wayne, EC, Chandrasekaran, S, Mitchell, MJ, Chan MF, Lee, RE, Schaffer, CB, & King, MR (2016). TRAIL-coated leukocytes that prevent the bloodborne metastasis of prostate cancer. Journal of Controlled Release. Journal of Controlled Release, 223, 215–223. http://doi.org/10.1016/j.jconrel.2015.12.048 Featured on Journal Cover. Citations: 35 |
| 2015 |
J. Kang, R. Schwartz, J. Flickinger, and S. Beriwal. "Machine learning approaches to predicting radiotherapy outcomes: A clinician's perspective." International Journal of Radiation Oncology, Biology, Physics, 93(5), 2015. |
| 2015 |
SA Chowdhury, E Gertz, D Wangsa, K Heselmeyer-Haddad, T Ried, A Schaffer and R Schwartz. "Inferring models of multiscale copy number evolution for single-tumor phylogenetics." Bioinformatics, 31(12):i258-i267, 2015. |
| 2015 |
Subramanian and R. Schwartz. "Reference-free inference of tumor phylogenies from single-cell sequencing data." BMC Genomics, 16S11:S7, 2015. |
| 2015 |
T. Roman, B. Fasy, A. Nayyeri, and R. Schwartz. "A simplicial complex-based approach to unmixing tumor progression data." BMC Bioinformatics, 16:254, 2015. |
| 2014 |
E. Shackney, S. A. Chowdhury, R. Schwartz. “A novel subset of human tumors that simultaneously overexpress multiple E2F responsive genes found in breast, ovarian, and prostate cancer.” Cancer Informatics, 13(S5):89, 2014. |
| 2014 |
H. Ashktorab, M. Daremipouran, J. Devaney, S. Varma, H. Rahi, E., Lee, B. Shokrani, R. Schwartz, M. Nickerson, H. Brim. "Identification of novel mutations by exome sequencing in African American colorectal cancer patients", Cancer, 121(1):34-42, 2014. |
| 2014 |
Hou JP and Ma J. DawnRank: Discovering personalized driver genes in cancer. Genome Medicine, 6:56, 2014. |
| 2014 |
K. Heselmeyer-Haddad, L.Y. Berroa Garcia, A. Bradley, L. Hernandez, Y. Hu, J.K. Habermann, C. Dumke, C. Thorns, S. Perner, E. Pestova, C. Burke, S.A. Chowdhury, R. Schwartz, A.A. Schäffer, P. Paris, T. Ried. "Single-cell genetic analysis reveals insights into clonal development of prostate cancers and indicates loss of PTEN as a marker of poor prognosis", American Journal of Pathology, 184(10):2671-2686, 2014. |
| 2014 |
Liu Y, Gu Q, Hou JP, Han J, and Ma J. A network-assisted co-clustering algorithm to discover cancer subtypes based on gene expression. BMC Bioinformatics, 15:37, 2014. |
| 2014 |
M.-D. Zhou, S. Hao, A. J. Williams†, R. A. Harouaka, B. Schrand, S. Rawal, Z. Ao, R. Brennaman, E. Gilboa, B. Lu, S. Wang, J. Zhu, R. Datar, R. Cote, Y.-C. Tai*, and S.-Y. Zheng*, Separable bilayer microfiltration device for viable label-free enrichment of circulating tumour cells, Scientific Reports, 4: 7392, 1-10, (2014). |
| 2014 |
Mitchell MJ, Wayne EC, Rana K, Schaffer CB, King MR. (2014) TRAIL-Coated Leukocytes that Kill Cancer Cells in the Circulation. PNAS 111(3) 930–935, https://doi.org/10.1073/pnas.1316312111 Citations: 136 |
| 2014 |
R. A. Harouaka, M.-D. Zhou, Y.-T. Yeh, W. J. Khan, A. Das, X. Liu, C. C. Christ, D. T. Dicker, T. S. Baney, J. T. Kaifi, C. P. Belani, C. I. Truica, W. S. El-Deiry, J. P. Allerton, and S.-Y. Zheng, Flexible micro spring array device for high throughput enrichment of viable circulating tumor cells, Clinical Chemistry, vol. 60, pp. 323-333, (2014). |
| 2014 |
R. A. Harouaka, Z. Kang, S.-Y. Zheng, L. Cao, Circulating tumor cells: advances in isolation and analysis, and challenges for clinical applications, Pharmacology and Therapeutics, vol.141, pp. 209-221, (2014). |
| 2014 |
S.A. Chowdhury, S.E. Shackney, K. Heselmeyer-Haddad, T. Ried, A. Schaffer, R. Schwartz. “Algorithms to model single gene, single chromosome, and whole genome copy number changes jointly in tumor phylogenetics,” PLoS Computational Biology, 10(7):e1003740, 2014. |
| 2013 |
R. A. Harouaka, M. Nisic, S.-Y. Zheng, Circulating tumor cell enrichment based on physical properties, Journal of Laboratory Automation, vol. 18, pp. 455-468, (2013). |
| 2013 |
S. A. Chowdhury, S. E. Shackney, K. Heselmeyer-Haddad, T. Ried, A. A. Schäffer, R. Schwartz. “Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations.” Bioinformatics, 29(13):i189-i198, 2013. |
| 2012 |
K. Heselmeyer-Haddad, L. Y. Berroa Garcia, A. Bradley, C. Ortiz-Melendez, W.-J. Lee, R. Christensen, S. A. Prindiville, K. A. Calzone, P. W. Soballe, Y. Hu, S. A. Chowdhury, R. Schwartz, A. A. Schäffer, and T. Ried. “Single-cell genetic analysis of ductal carcinoma in situ and invasive breast cancer reveals enormous tumor heterogeneity, yet conserved genomic imbalances and gain of MYC during progression.” American Journal of Pathology, 181(11):1807-1822, 2012. |
| 2011 |
Li Y, Chien J, Smith DI, and Ma J. FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq. Bioinformatics, 27(12):1708-10, 2011. |
| 2011 |
S. Zheng, H. K. Lin, B. Lu, A. Williams, R. H. Datar, R. J. Cote RJ, Y.-C. Tai, 3D Microfilter Device for Viable Circulating Tumor Cell (CTC) Enrichment from Blood, Biomedical Microdevices, vol.13, pp. 203-213, (2011). |
| 2011 |
Subramanian, S. Shackney, and R. Schwartz. “Inference of tumor phylogenies from genomic assays on heterogeneous samples.” Journal of Biomedicine and Biotechnology, 2012:798812, 2012. C. E. Tsourakakis, R. Peng, M. A. Tsiarli, G. L. Miller, and R. Schwartz. “Approximation algorithms for speeding up dynamic programming and denoising aCGH data.” Journal of Experimental Algorithmics, 16:1.8, 2011. |
| 2010 |
D. Tolliver, C. Tsourakakis, A. Subramanian, S. Shackney, and R. Schwartz. “Robust unmixing of tumor states in array comparative genomic hybridization data.” Bioinformatics, 26(12):i106-i114, 2010. |
| 2010 |
H. K. Lin*, S. Zheng*, A. J. Williams, M. Balic, S. Groshen, H. I. Scher, M. Fleisher, W. Stadler, R. H. Datar, Y.-C. Tai, R. J. Cote, Portable filter-based microdevice for detection and characterization of circulating tumor cells, Clinical Cancer Research, vol 16, pp. 5011-5018, (2010). |
| 2010 |
R. Schwartz and S. Shackney. “Applying unmixing to gene expression data for tumor phylogeny inference.” BMC Bioinformatics, 11:42, 2010. |
| 2009 |
Y. Park, S. Shackney, and R. Schwartz. “Network-based inference of cancer progression from microarray data.” IEEE Transactions on Computational Biology and Bioinformatics, 6(2):200-212, 2009. |
| 2007 |
G. Pennington, C. E. Smith, S. Shackney, and R. Schwartz. “Reconstructing tumor phylogenies from single-cell data.” Journal of Bioinformatics and Computational Biology, 5(02A):407-427, 2007. |
| 2007 |
S. Zheng, H. Lin, J.-Q. Liu, M. Balic, R. Datar, R. J. Cote, and Y.-C. Tai, Membrane microfilter device for selective capture, electrolysis and genomic analysis of human circulating tumor cells, Journal of Chromatography A, vol. 1162, pp. 154-161, (2007). |
| 2006 |
D. R. Emlet, R. Schwartz, K. Brown, A. A. Pollice, C. A. Smith, and S. E. Schackney. “HER2 expression as a potential marker for response to therapy targeted to the EGFR.” British Journal of Cancer, 94(8):1144-1153, 2006. |
| 2006 |
G. Pennington, C. A. Smith, S. Shackney, and R. Schwartz. “Expectation-maximization method for the reconstruction of tumor phylogenies from single-cell data.” Proceedings of the Computational Systems Bioinformatics Conference (CSB06), pp. 371-380, 2006. |