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\n  \n 2024\n \n \n (6)\n \n \n
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\n \n\n \n \n \n \n \n Identification of a Notch transcriptomic signature for breast cancer.\n \n \n \n\n\n \n Braune, E.; Geist, F.; Tang, X.; Kalari, K.; Boughey, J.; Wang, L.; Leon-Ferre, R. A; D’Assoro, A. B; Ingle, J. N; Goetz, M. P; and others\n\n\n \n\n\n\n Breast Cancer Research, 26(1): 4. 2024.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{braune2024identification,\n  title={Identification of a Notch transcriptomic signature for breast cancer},\n  author={Braune, Eike-Benjamin and Geist, Felix and Tang, Xiaojia and Kalari, Krishna and Boughey, Judy and Wang, Liewei and Leon-Ferre, Roberto A and D’Assoro, Antonino B and Ingle, James N and Goetz, Matthew P and others},\n  journal={Breast Cancer Research},\n  volume={26},\n  number={1},\n  pages={4},\n  year={2024},\n  publisher={BioMed Central London}\n}\n\n
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\n \n\n \n \n \n \n \n Abstract B002: Exploiting JAK/STAT signaling to inhibit highly advanced and resistant forms of ovarian cancer.\n \n \n \n\n\n \n Rodman, E.; Emch, M.; Bajaj, A.; Tang, X.; Hou, X.; Kaufmann, S.; Kalari, K.; Weroha, J.; and Hawse, J.\n\n\n \n\n\n\n Cancer Research, 84(5_Supplement_2): B002–B002. 2024.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{rodman2024abstract,\n  title={Abstract B002: Exploiting JAK/STAT signaling to inhibit highly advanced and resistant forms of ovarian cancer},\n  author={Rodman, Esther and Emch, Michael and Bajaj, Archit and Tang, Xiaojia and Hou, Xiaonan and Kaufmann, Scott and Kalari, Krishna and Weroha, John and Hawse, John},\n  journal={Cancer Research},\n  volume={84},\n  number={5\\_Supplement\\_2},\n  pages={B002--B002},\n  year={2024},\n  publisher={The American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n OmicsFootPrint: a framework to integrate and interpret multi-omics data using circular images and deep neural networks.\n \n \n \n\n\n \n Tang, X.; Prodduturi, N.; Thompson, K. J; Weinshilboum, R.; O’Sullivan, C. C; Boughey, J. C; Tizhoosh, H. R; Klee, E. W; Wang, L.; Goetz, M. P; and others\n\n\n \n\n\n\n Nucleic Acids Research,gkae915. 2024.\n \n\n\n\n
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@article{tang2024omicsfootprint,\n  title={OmicsFootPrint: a framework to integrate and interpret multi-omics data using circular images and deep neural networks},\n  author={Tang, Xiaojia and Prodduturi, Naresh and Thompson, Kevin J and Weinshilboum, Richard and O’Sullivan, Ciara C and Boughey, Judy C and Tizhoosh, Hamid R and Klee, Eric W and Wang, Liewei and Goetz, Matthew P and others},\n  journal={Nucleic Acids Research},\n  pages={gkae915},\n  year={2024},\n  publisher={Oxford University Press}\n}\n\n
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\n \n\n \n \n \n \n \n Trends over time in liquid biopsy testing in patients with metastatic breast cancer (MBC) across the Mayo Clinic enterprise.\n \n \n \n\n\n \n Yadav, S. K.; Rajput, S.; Samineni, T.; Thompson, K.; Tang, X.; Leon-Ferre, R. A.; O'Sullivan, C. C.; Peethambaram, P. P; Advani, P. P.; Sideras, K.; and others\n\n\n \n\n\n\n 2024.\n \n\n\n\n
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@misc{yadav2024trends,\n  title={Trends over time in liquid biopsy testing in patients with metastatic breast cancer (MBC) across the Mayo Clinic enterprise.},\n  author={Yadav, Sumeet Kumar and Rajput, Sanjna and Samineni, Thoshik and Thompson, Kevin and Tang, Xiaojia and Leon-Ferre, Roberto Antonio and O'Sullivan, Ciara Catherine and Peethambaram, Prema P and Advani, Pooja Prem and Sideras, Kostandinos and others},\n  year={2024},\n  publisher={American Society of Clinical Oncology}\n}\n\n
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\n \n\n \n \n \n \n \n Molecular profiling of serial liquid biopsy specimens utilizing cell free DNA (cfDNA) and circulating tumor cells (CTCs) in TBCRC041: A phase II study of alisertib in endocrine resistant metastatic breast cancer (MBC).\n \n \n \n\n\n \n Giridhar, K.; Suman, V. J.; Tang, X.; Ye, H.; Campbell, J.; Mayer, E. L; Karuturi, M. S.; Morikawa, A.; Kimmick, G. G.; Isaacs, C.; and others\n\n\n \n\n\n\n 2024.\n \n\n\n\n
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@misc{giridhar2024molecular,\n  title={Molecular profiling of serial liquid biopsy specimens utilizing cell free DNA (cfDNA) and circulating tumor cells (CTCs) in TBCRC041: A phase II study of alisertib in endocrine resistant metastatic breast cancer (MBC).},\n  author={Giridhar, Karthik and Suman, Vera Jean and Tang, Xiaojia and Ye, Hong and Campbell, Jordan and Mayer, Erica L and Karuturi, Meghan Sri and Morikawa, Aki and Kimmick, Gretchen Genevieve and Isaacs, Claudine and others},\n  year={2024},\n  publisher={American Society of Clinical Oncology}\n}\n\n
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\n \n\n \n \n \n \n \n Molecular mechanisms underlying amyloid beta peptide mediated upregulation of vascular cell adhesion molecule-1 in Alzheimer's disease.\n \n \n \n\n\n \n Salian, V. S; Tang, X.; Thompson, K. J; Curran, G. L; Lowe, V. J; Li, L.; Kalari, K. R; and Kandimalla, K. K\n\n\n \n\n\n\n Journal of Pharmacology and Experimental Therapeutics. 2024.\n \n\n\n\n
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@article{salian2024molecular,\n  title={Molecular mechanisms underlying amyloid beta peptide mediated upregulation of vascular cell adhesion molecule-1 in Alzheimer's disease.},\n  author={Salian, Vrishali S and Tang, Xiaojia and Thompson, Kevin J and Curran, Geoffry L and Lowe, Val J and Li, Ling and Kalari, Krishna R and Kandimalla, Karunya K},\n  journal={Journal of Pharmacology and Experimental Therapeutics},\n  year={2024},\n  publisher={American Society for Pharmacology and Experimental Therapeutics}\n}\n
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\n  \n 2023\n \n \n (7)\n \n \n
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\n \n\n \n \n \n \n \n Integration of multiomics data shows down regulation of mismatch repair and tubulin pathways in triple-negative chemotherapy-resistant breast tumors.\n \n \n \n\n\n \n Tang, X.; Thompson, K. J; Kalari, K. R; Sinnwell, J. P; Suman, V. J; Vedell, P. T; McLaughlin, S. A; Northfelt, D. W; Aspitia, A. M.; Gray, R. J; and others\n\n\n \n\n\n\n Breast Cancer Research, 25(1): 57. 2023.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{tang2023integration,\n  title={Integration of multiomics data shows down regulation of mismatch repair and tubulin pathways in triple-negative chemotherapy-resistant breast tumors},\n  author={Tang, Xiaojia and Thompson, Kevin J and Kalari, Krishna R and Sinnwell, Jason P and Suman, Vera J and Vedell, Peter T and McLaughlin, Sarah A and Northfelt, Donald W and Aspitia, Alvaro Moreno and Gray, Richard J and others},\n  journal={Breast Cancer Research},\n  volume={25},\n  number={1},\n  pages={57},\n  year={2023},\n  publisher={BioMed Central London}\n}\n\n
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\n \n\n \n \n \n \n \n Abstract P3-11-04: Endoxifen Downregulates AKT Phosphorylation Through Protein Kinase C Beta 1 in ER+/HER2-Breast Cancer.\n \n \n \n\n\n \n Jayaraman, S.; Wu, X.; Kalari, K. R; Tang, X.; Kuffel, M.; Bruinsma, E. S; Renuse, S.; Ingle, J. N; Reid, J.; Schellenberg, M.; and others\n\n\n \n\n\n\n Cancer Research, 83(5_Supplement): P3–11. 2023.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{jayaraman2023abstract,\n  title={Abstract P3-11-04: Endoxifen Downregulates AKT Phosphorylation Through Protein Kinase C Beta 1 in ER+/HER2-Breast Cancer},\n  author={Jayaraman, Swaathi and Wu, Xinyan and Kalari, Krishna R and Tang, Xiaojia and Kuffel, Mary and Bruinsma, Elizabeth S and Renuse, Santosh and Ingle, James N and Reid, Joel and Schellenberg, Matthew and others},\n  journal={Cancer Research},\n  volume={83},\n  number={5\\_Supplement},\n  pages={P3--11},\n  year={2023},\n  publisher={The American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n The role of circular RNAs in triple negative breast cancer and chemotherapy resistance.\n \n \n \n\n\n \n Wang, X.; Emch, M. J; Tang, X.; Yu, J.; Kalari, K. R; Wang, L.; Goetz, M. P; and Hawse, J. R\n\n\n \n\n\n\n Cancer Research, 83(7_Supplement): 1689–1689. 2023.\n \n\n\n\n
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@article{wang2023role,\n  title={The role of circular RNAs in triple negative breast cancer and chemotherapy resistance},\n  author={Wang, Xiyin and Emch, Michael J and Tang, Xiaojia and Yu, Jia and Kalari, Krishna R and Wang, Liewei and Goetz, Matthew P and Hawse, John R},\n  journal={Cancer Research},\n  volume={83},\n  number={7\\_Supplement},\n  pages={1689--1689},\n  year={2023},\n  publisher={The American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n Estrogen-regulated miRs in bone enhance osteoblast differentiation and matrix mineralization.\n \n \n \n\n\n \n Emch, M. J; Wicik, Z.; Aspros, K. G.; Vukajlovic, T.; Pitel, K. S; Narum, A. K; Weivoda, M. M; Tang, X.; Kalari, K. R; Turner, R. T; and others\n\n\n \n\n\n\n Molecular Therapy-Nucleic Acids, 33: 28–41. 2023.\n \n\n\n\n
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@article{emch2023estrogen,\n  title={Estrogen-regulated miRs in bone enhance osteoblast differentiation and matrix mineralization.},\n  author={Emch, Michael J and Wicik, Zofia and Aspros, Kirsten GM and Vukajlovic, Tanja and Pitel, Kevin S and Narum, Anders K and Weivoda, Megan M and Tang, Xiaojia and Kalari, Krishna R and Turner, Russell T and others},\n  journal={Molecular Therapy-Nucleic Acids},\n  volume={33},\n  pages={28--41},\n  year={2023},\n  publisher={Elsevier}\n}\n\n
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\n \n\n \n \n \n \n \n Microbiome Prevents Sudden Death Through Occult Cardiac Sub-micrometastasis in Mice.\n \n \n \n\n\n \n Aalam, S. M. M.; Tang, X.; Hari, P.; Salem, S. M; Al Jarrad, A.; Noseworthy, P. A; Behfar, A.; Sadanandam, A.; Kalari, K.; Kashyap, P. C; and others\n\n\n \n\n\n\n bioRxiv,2023–07. 2023.\n \n\n\n\n
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@article{aalam2023microbiome,\n  title={Microbiome Prevents Sudden Death Through Occult Cardiac Sub-micrometastasis in Mice},\n  author={Aalam, Syed Mohammed Musheer and Tang, Xiaojia and Hari, PS and Salem, Salem M and Al Jarrad, Ahmad and Noseworthy, Peter A and Behfar, Atta and Sadanandam, Anguraj and Kalari, Krishna and Kashyap, Purna C and others},\n  journal={bioRxiv},\n  pages={2023--07},\n  year={2023},\n  publisher={Cold Spring Harbor Laboratory}\n}\n\n
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\n \n\n \n \n \n \n \n Abstract B013: Identification of a Notch transcriptomic signature for breast cancer.\n \n \n \n\n\n \n Braune, E.; Geist, F.; Tang, X.; Kalari, K.; Boughey, J.; Wang, L.; Leon-Ferre, R. A; D’Assoro, A. B; Ingle, J. N; Goetz, M. P; and others\n\n\n \n\n\n\n Molecular Cancer Therapeutics, 22(12_Supplement): B013–B013. 2023.\n \n\n\n\n
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@article{braune2023abstract,\n  title={Abstract B013: Identification of a Notch transcriptomic signature for breast cancer},\n  author={Braune, Eike-Benjamin and Geist, Felix and Tang, Xiaojia and Kalari, Krishna and Boughey, Judy and Wang, Liewei and Leon-Ferre, Roberto A and D’Assoro, Antonino B and Ingle, James N and Goetz, Matthew P and others},\n  journal={Molecular Cancer Therapeutics},\n  volume={22},\n  number={12\\_Supplement},\n  pages={B013--B013},\n  year={2023},\n  publisher={The American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n Endoxifen downregulates AKT phosphorylation through protein kinase C beta 1 inhibition in ER$α$+ breast cancer.\n \n \n \n\n\n \n Jayaraman, S.; Wu, X.; Kalari, K. R; Tang, X.; Kuffel, M. J; Bruinsma, E. S; Jalali, S.; Peterson, K. L; Correia, C.; Kudgus, R. A; and others\n\n\n \n\n\n\n NPJ Breast Cancer, 9(1): 101. 2023.\n \n\n\n\n
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@article{jayaraman2023endoxifen,\n  title={Endoxifen downregulates AKT phosphorylation through protein kinase C beta 1 inhibition in ER$\\alpha$+ breast cancer},\n  author={Jayaraman, Swaathi and Wu, Xinyan and Kalari, Krishna R and Tang, Xiaojia and Kuffel, Mary J and Bruinsma, Elizabeth S and Jalali, Shahrzad and Peterson, Kevin L and Correia, Cristina and Kudgus, Rachel A and others},\n  journal={NPJ Breast Cancer},\n  volume={9},\n  number={1},\n  pages={101},\n  year={2023},\n  publisher={Nature Publishing Group UK London}\n}\n\n
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\n \n\n \n \n \n \n \n Age-dependent changes in the plasma and brain pharmacokinetics of amyloid-$β$ peptides and insulin.\n \n \n \n\n\n \n Zhou, A. L; Sharda, N.; Sarma, V. V; Ahlschwede, K. M; Curran, G. L; Tang, X.; Poduslo, J. F; Kalari, K. R; Lowe, V. J; and Kandimalla, K. K\n\n\n \n\n\n\n Journal of Alzheimer's Disease, 85(3): 1031–1044. 2022.\n \n\n\n\n
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@article{zhou2022age,\n  title={Age-dependent changes in the plasma and brain pharmacokinetics of amyloid-$\\beta$ peptides and insulin},\n  author={Zhou, Andrew L and Sharda, Nidhi and Sarma, Vidur V and Ahlschwede, Kristen M and Curran, Geoffry L and Tang, Xiaojia and Poduslo, Joseph F and Kalari, Krishna R and Lowe, Val J and Kandimalla, Karunya K},\n  journal={Journal of Alzheimer's Disease},\n  volume={85},\n  number={3},\n  pages={1031--1044},\n  year={2022},\n  publisher={IOS Press}\n}\n\n
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\n \n\n \n \n \n \n \n Estrogen receptor beta repurposes EZH2 to suppress oncogenic NF$κ$B/p65 signaling in triple negative breast cancer.\n \n \n \n\n\n \n Aspros, K. G.; Carter, J. M; Hoskin, T. L; Suman, V. J; Subramaniam, M.; Emch, M. J; Ye, Z.; Sun, Z.; Sinnwell, J. P; Thompson, K. J; and others\n\n\n \n\n\n\n NPJ Breast Cancer, 8(1): 20. 2022.\n \n\n\n\n
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@article{aspros2022estrogen,\n  title={Estrogen receptor beta repurposes EZH2 to suppress oncogenic NF$\\kappa$B/p65 signaling in triple negative breast cancer},\n  author={Aspros, Kirsten GM and Carter, Jodi M and Hoskin, Tanya L and Suman, Vera J and Subramaniam, Malayannan and Emch, Michael J and Ye, Zhenqing and Sun, Zhifu and Sinnwell, Jason P and Thompson, Kevin J and others},\n  journal={NPJ Breast Cancer},\n  volume={8},\n  number={1},\n  pages={20},\n  year={2022},\n  publisher={Nature Publishing Group UK London}\n}\n\n
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\n \n\n \n \n \n \n \n Abstract P5-13-22: Serum thymidine kinase 1 activity (TKa) levels and progression-free survival (PFS) in patients (pts) with hormone receptor positive (HR+) HER2-negative metastatic breast cancer (MBC) on palbociclib (Pb) and endocrine therapy (ET).\n \n \n \n\n\n \n O'Sullivan, C. C; He, J.; Sinnwell, J.; Suman, V. J; Kalari, K. R; Vedell, P. T; Moyer, A. M; Tang, X.; Thompson, K. J; Casey, A. E.; and others\n\n\n \n\n\n\n Cancer Research, 82(4_Supplement): P5–13. 2022.\n \n\n\n\n
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@article{o2022abstract,\n  title={Abstract P5-13-22: Serum thymidine kinase 1 activity (TKa) levels and progression-free survival (PFS) in patients (pts) with hormone receptor positive (HR+) HER2-negative metastatic breast cancer (MBC) on palbociclib (Pb) and endocrine therapy (ET)},\n  author={O'Sullivan, Ciara C and He, Jun and Sinnwell, Jason and Suman, Vera J and Kalari, Krishna R and Vedell, Peter T and Moyer, Ann M and Tang, Xiaojia and Thompson, Kevin J and Casey, Abe Eyman and others},\n  journal={Cancer Research},\n  volume={82},\n  number={4\\_Supplement},\n  pages={P5--13},\n  year={2022},\n  publisher={The American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n Abstract P3-08-02: the frequency and somatic mutation landscape of Fibroblast growth factor receptor (FGFR) alterations in breast cancer.\n \n \n \n\n\n \n Giridhar, K. V; Sokol, E. S; Vedell, P. T; Sinnwell, J. P; Desai, A.; Haddad, T. C; O’Sullivan, C. C; Leon-Ferre, R. A; Yadav, S.; Sideras, K.; and others\n\n\n \n\n\n\n Cancer Research, 82(4_Supplement): P3–08. 2022.\n \n\n\n\n
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@article{giridhar2022abstract,\n  title={Abstract P3-08-02: the frequency and somatic mutation landscape of Fibroblast growth factor receptor (FGFR) alterations in breast cancer},\n  author={Giridhar, Karthik V and Sokol, Ethan S and Vedell, Peter T and Sinnwell, Jason P and Desai, Aakash and Haddad, Tufia C and O’Sullivan, Ciara C and Leon-Ferre, Roberto A and Yadav, Siddhartha and Sideras, Kostandinos and others},\n  journal={Cancer Research},\n  volume={82},\n  number={4\\_Supplement},\n  pages={P3--08},\n  year={2022},\n  publisher={The American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n Abstract P4-01-05: Multi-omics data shows downregulation of mismatch repair, purin and tublin pathways in AR-negative triple-negative chemotherapy-resistant tumors.\n \n \n \n\n\n \n Kalari, K. R; Suman, V. J; Tang, X.; Sinnwell, J. P; Thompson, K. J; Vedell, P. T; Carter, J. M; McLaughlin, S. A; Aspitia, A. M.; Northfelt, D. W; and others\n\n\n \n\n\n\n Cancer Research, 82(4_Supplement): P4–01. 2022.\n \n\n\n\n
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@article{kalari2022abstract,\n  title={Abstract P4-01-05: Multi-omics data shows downregulation of mismatch repair, purin and tublin pathways in AR-negative triple-negative chemotherapy-resistant tumors},\n  author={Kalari, Krishna R and Suman, Vera J and Tang, Xiaojia and Sinnwell, Jason P and Thompson, Kevin J and Vedell, Peter T and Carter, Jodi M and McLaughlin, Sarah A and Aspitia, Alvaro Moreno and Northfelt, Donald W and others},\n  journal={Cancer Research},\n  volume={82},\n  number={4\\_Supplement},\n  pages={P4--01},\n  year={2022},\n  publisher={The American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n Abstract P4-01-03: Multiomics data reveal novel biomarkers for CDK4/6 resistance.\n \n \n \n\n\n \n Kalari, K. R; Thompson, K. J; Sinnwell, J.; Tang, X.; Suman, V. J; He, J.; Byeon, S. K.; Pandey, A.; Casey, A. E.; Vedell, P. T; and others\n\n\n \n\n\n\n Cancer Research, 82(4_Supplement): P4–01. 2022.\n \n\n\n\n
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@article{kalari2022abstract,\n  title={Abstract P4-01-03: Multiomics data reveal novel biomarkers for CDK4/6 resistance},\n  author={Kalari, Krishna R and Thompson, Kevin J and Sinnwell, Jason and Tang, Xiaojia and Suman, Vera J and He, Jun and Byeon, Seul Kee and Pandey, Akhilesh and Casey, Abe Eyman and Vedell, Peter T and others},\n  journal={Cancer Research},\n  volume={82},\n  number={4\\_Supplement},\n  pages={P4--01},\n  year={2022},\n  publisher={The American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n Multi-omics data shows downregulation of mismatch repair, purin and tublin pathways in AR-negative triple-negative chemotherapy-resistant tumors.\n \n \n \n\n\n \n Kalari, K. R; Suman, V. J; Tang, X.; Sinnwell, J. P; Thompson, K. J; Vedell, P. T; Carter, J. M; McLaughlin, S. A; Aspitia, A. M.; Northfelt, D. W; and others\n\n\n \n\n\n\n In CANCER RESEARCH, volume 82, 2022. AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA …\n \n\n\n\n
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@inproceedings{kalari2022multi,\n  title={Multi-omics data shows downregulation of mismatch repair, purin and tublin pathways in AR-negative triple-negative chemotherapy-resistant tumors},\n  author={Kalari, Krishna R and Suman, Vera J and Tang, Xiaojia and Sinnwell, Jason P and Thompson, Kevin J and Vedell, Peter T and Carter, Jodi M and McLaughlin, Sarah A and Aspitia, Alvaro Moreno and Northfelt, Donald W and others},\n  booktitle={CANCER RESEARCH},\n  volume={82},\n  number={4},\n  year={2022},\n  organization={AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA~…}\n}\n\n
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\n \n\n \n \n \n \n \n Serum thymidine kinase 1 activity (TKa) levels and progression-free survival (PFS) in patients (pts) with hormone receptor positive (HR+) HER2-negative metastatic breast cancer (MBC) on palbociclib (Pb) and endocrine therapy (ET).\n \n \n \n\n\n \n O'Sullivan, C. C; He, J.; Sinnwell, J.; Suman, V. J; Kalari, K. R; Vedell, P. T; Moyer, A. M; Tang, X.; Thompson, K. J; Casey, A. E.; and others\n\n\n \n\n\n\n In CANCER RESEARCH, volume 82, 2022. AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA …\n \n\n\n\n
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@inproceedings{o2022serum,\n  title={Serum thymidine kinase 1 activity (TKa) levels and progression-free survival (PFS) in patients (pts) with hormone receptor positive (HR+) HER2-negative metastatic breast cancer (MBC) on palbociclib (Pb) and endocrine therapy (ET)},\n  author={O'Sullivan, Ciara C and He, Jun and Sinnwell, Jason and Suman, Vera J and Kalari, Krishna R and Vedell, Peter T and Moyer, Ann M and Tang, Xiaojia and Thompson, Kevin J and Casey, Abe Eyman and others},\n  booktitle={CANCER RESEARCH},\n  volume={82},\n  number={4},\n  year={2022},\n  organization={AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA~…}\n}\n\n
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\n \n\n \n \n \n \n \n Abstract LB564:($±$) 14, 15-epoxyeicosatrienoic acid induces hallmark ER and MYC gene expression and associated ER and c-Myc nuclear translocation in ER+/HER2-breast cancer cells.\n \n \n \n\n\n \n Lei, J.; Guo, Z.; Molina-Vega, J.; Cervantes, P.; Jayaraman, S.; Hawse, J. R; Perez, C.; Abrahante, J.; Tang, X.; Kalari, K.; and others\n\n\n \n\n\n\n Cancer Research, 82(12_Supplement): LB564–LB564. 2022.\n \n\n\n\n
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@article{lei2022abstract,\n  title={Abstract LB564:($\\pm$) 14, 15-epoxyeicosatrienoic acid induces hallmark ER and MYC gene expression and associated ER and c-Myc nuclear translocation in ER+/HER2-breast cancer cells},\n  author={Lei, Jianxun and Guo, Zhijun and Molina-Vega, Julissa and Cervantes, Paloma and Jayaraman, Swaathi and Hawse, John R and Perez, Carlos and Abrahante, Juan and Tang, Xiaojia and Kalari, Krishna and others},\n  journal={Cancer Research},\n  volume={82},\n  number={12\\_Supplement},\n  pages={LB564--LB564},\n  year={2022},\n  publisher={The American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n DNA barcoded competitive clone-initiating cell analysis reveals novel features of metastatic growth in a cancer xenograft model.\n \n \n \n\n\n \n Aalam, S. M. M.; Tang, X.; Song, J.; Ray, U.; Russell, S. J; Weroha, S J.; Bakkum-Gamez, J.; Shridhar, V.; Sherman, M. E; Eaves, C. J; and others\n\n\n \n\n\n\n NAR cancer, 4(3): zcac022. 2022.\n \n\n\n\n
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@article{aalam2022dna,\n  title={DNA barcoded competitive clone-initiating cell analysis reveals novel features of metastatic growth in a cancer xenograft model},\n  author={Aalam, Syed Mohammed Musheer and Tang, Xiaojia and Song, Jianning and Ray, Upasana and Russell, Stephen J and Weroha, S John and Bakkum-Gamez, Jamie and Shridhar, Viji and Sherman, Mark E and Eaves, Connie J and others},\n  journal={NAR cancer},\n  volume={4},\n  number={3},\n  pages={zcac022},\n  year={2022},\n  publisher={Oxford University Press}\n}\n\n
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\n \n\n \n \n \n \n \n Mapping the dynamics of insulin-responsive pathways in the blood–brain barrier endothelium using time-series transcriptomics data.\n \n \n \n\n\n \n Wang, Z.; Tang, X.; Swaminathan, S. K; Kandimalla, K. K; and Kalari, K. R\n\n\n \n\n\n\n NPJ Systems Biology and Applications, 8(1): 29. 2022.\n \n\n\n\n
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@article{wang2022mapping,\n  title={Mapping the dynamics of insulin-responsive pathways in the blood--brain barrier endothelium using time-series transcriptomics data},\n  author={Wang, Zengtao and Tang, Xiaojia and Swaminathan, Suresh K and Kandimalla, Karunya K and Kalari, Krishna R},\n  journal={NPJ Systems Biology and Applications},\n  volume={8},\n  number={1},\n  pages={29},\n  year={2022},\n  publisher={Nature Publishing Group UK London}\n}\n\n
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\n \n\n \n \n \n \n \n (+/-) 14, 15-epoxyeicosatrienoic acid induces hallmark ER and MYC gene expression and associated ER and c-Myc nuclear translocation in ER+/HER2-breast cancer cells.\n \n \n \n\n\n \n Lei, J.; Guo, Z.; Molina-Vega, J.; Cervantes, P.; Jayaraman, S.; Hawse, J. R; Perez, C.; Abrahante, J.; Tang, X.; Kalari, K.; and others\n\n\n \n\n\n\n In Cancer Research, volume 82, 2022. AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA …\n \n\n\n\n
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@inproceedings{lei2022+,\n  title={(+/-) 14, 15-epoxyeicosatrienoic acid induces hallmark ER and MYC gene expression and associated ER and c-Myc nuclear translocation in ER+/HER2-breast cancer cells},\n  author={Lei, Jianxun and Guo, Zhijun and Molina-Vega, Julissa and Cervantes, Paloma and Jayaraman, Swaathi and Hawse, John R and Perez, Carlos and Abrahante, Juan and Tang, Xiaojia and Kalari, Krishna and others},\n  booktitle={Cancer Research},\n  volume={82},\n  number={12},\n  year={2022},\n  organization={AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA~…}\n}\n\n
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\n  \n 2021\n \n \n (17)\n \n \n
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\n \n\n \n \n \n \n \n COVID-19 transmission, current treatment, and future therapeutic strategies.\n \n \n \n\n\n \n Salian, V. S; Wright, J. A; Vedell, P. T; Nair, S.; Li, C.; Kandimalla, M.; Tang, X.; Carmona Porquera, E. M; Kalari, K. R; and Kandimalla, K. K\n\n\n \n\n\n\n Molecular pharmaceutics, 18(3): 754–771. 2021.\n \n\n\n\n
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@article{salian2021covid,\n  title={COVID-19 transmission, current treatment, and future therapeutic strategies},\n  author={Salian, Vrishali S and Wright, Jessica A and Vedell, Peter T and Nair, Sanjana and Li, Chenxu and Kandimalla, Mahathi and Tang, Xiaojia and Carmona Porquera, Eva M and Kalari, Krishna R and Kandimalla, Karunya K},\n  journal={Molecular pharmaceutics},\n  volume={18},\n  number={3},\n  pages={754--771},\n  year={2021},\n  publisher={American Chemical Society}\n}\n\n
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\n \n\n \n \n \n \n \n Abstract PD8-04: Antitumor activity of Z-endoxifen (ENDX) is mediated via PKC$β$1-dependent ER$α$ loss and cell cycle arrest in ER$α$-positive breast cancer.\n \n \n \n\n\n \n Jayaraman, S.; Kuffel, M. J; Kalari, K. R; Thompson, K. J; Tang, X.; Suman, V. J; Bruinsma, E. S; O'Sullivan, C. C; Wang, L.; Weinshilboum, R.; and others\n\n\n \n\n\n\n Cancer Research, 81(4_Supplement): PD8–04. 2021.\n \n\n\n\n
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@article{jayaraman2021abstract,\n  title={Abstract PD8-04: Antitumor activity of Z-endoxifen (ENDX) is mediated via PKC$\\beta$1-dependent ER$\\alpha$ loss and cell cycle arrest in ER$\\alpha$-positive breast cancer},\n  author={Jayaraman, Swaathi and Kuffel, Mary J and Kalari, Krishna R and Thompson, Kevin J and Tang, Xiaojia and Suman, Vera J and Bruinsma, Elizabeth S and O'Sullivan, Ciara C and Wang, Liewei and Weinshilboum, Richard and others},\n  journal={Cancer Research},\n  volume={81},\n  number={4\\_Supplement},\n  pages={PD8--04},\n  year={2021},\n  publisher={The American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n Abstract PD7-04: Association between patient derived xenograft (PDX) take rate and breast cancer recurrence in the prospective breast cancer genome guided therapy study (BEAUTY).\n \n \n \n\n\n \n Boughey, J. C; Suman, V. J; Yu, J.; Santo, K.; Sinnwell, J. P; Carter, J. M; Kalari, K. R; Tang, X.; McLaughlin, S. A; Aspitia, A. M.; and others\n\n\n \n\n\n\n Cancer Research, 81(4_Supplement): PD7–04. 2021.\n \n\n\n\n
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@article{boughey2021abstract,\n  title={Abstract PD7-04: Association between patient derived xenograft (PDX) take rate and breast cancer recurrence in the prospective breast cancer genome guided therapy study (BEAUTY)},\n  author={Boughey, Judy C and Suman, Vera J and Yu, Jia and Santo, Katelyn and Sinnwell, Jason P and Carter, Jodi M and Kalari, Krishna R and Tang, Xiaojia and McLaughlin, Sarah A and Aspitia, Alvaro Moreno and others},\n  journal={Cancer Research},\n  volume={81},\n  number={4\\_Supplement},\n  pages={PD7--04},\n  year={2021},\n  publisher={The American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n Abstract PS5-24: Novel genomic variants and pathways associated with baseline serum thymidine kinase 1 levels in HR-positive HER2-negative MBC patients commencing palbociclib and letrozole.\n \n \n \n\n\n \n Sullivan, C. C.; Kalari, K. R; Suman, V. J; Vedell, P. T; Moyer, A.; Casey, A. D E.; Sinnwell, J.; Tang, X.; Thompson, K.; Moreno-Aspitia, A.; and others\n\n\n \n\n\n\n Cancer Research, 81(4_Supplement): PS5–24. 2021.\n \n\n\n\n
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@article{sullivan2021abstract,\n  title={Abstract PS5-24: Novel genomic variants and pathways associated with baseline serum thymidine kinase 1 levels in HR-positive HER2-negative MBC patients commencing palbociclib and letrozole},\n  author={Sullivan, Ciara CO and Kalari, Krishna R and Suman, Vera J and Vedell, Peter T and Moyer, Ann and Casey, Abraham D Eyman and Sinnwell, Jason and Tang, Xiaojia and Thompson, Kevin and Moreno-Aspitia, Alvaro and others},\n  journal={Cancer Research},\n  volume={81},\n  number={4\\_Supplement},\n  pages={PS5--24},\n  year={2021},\n  publisher={The American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n Clustering-based time series analysis on insulin response in the blood-brain barrier.\n \n \n \n\n\n \n Kalari, K. R; Wang, Z.; Tang, X.; Swaminathan, S. K; and Kandimalla, K. K\n\n\n \n\n\n\n bioRxiv,2021–03. 2021.\n \n\n\n\n
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@article{kalari2021clustering,\n  title={Clustering-based time series analysis on insulin response in the blood-brain barrier},\n  author={Kalari, Krishna R and Wang, Zengtao and Tang, Xiaojia and Swaminathan, Suresh K and Kandimalla, Karunya K},\n  journal={bioRxiv},\n  pages={2021--03},\n  year={2021},\n  publisher={Cold Spring Harbor Laboratory}\n}\n\n
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\n \n\n \n \n \n \n \n Association between patient derived xenograft (PDX) take rate and breast cancer recurrence in the prospective breast cancer genome guided therapy study (BEAUTY).\n \n \n \n\n\n \n Boughey, J. C; Suman, V. J; Yu, J.; Santo, K.; Sinnwell, J. P; Carter, J. M; Kalari, K. R; Tang, X.; McLaughlin, S. A; Aspitia, A. M.; and others\n\n\n \n\n\n\n In CANCER RESEARCH, volume 81, 2021. AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA …\n \n\n\n\n
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@inproceedings{boughey2021association,\n  title={Association between patient derived xenograft (PDX) take rate and breast cancer recurrence in the prospective breast cancer genome guided therapy study (BEAUTY)},\n  author={Boughey, Judy C and Suman, Vera J and Yu, Jia and Santo, Katelyn and Sinnwell, Jason P and Carter, Jodi M and Kalari, Krishna R and Tang, Xiaojia and McLaughlin, Sarah A and Aspitia, Alvaro Moreno and others},\n  booktitle={CANCER RESEARCH},\n  volume={81},\n  number={4},\n  year={2021},\n  organization={AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA~…}\n}\n\n
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\n \n\n \n \n \n \n \n Antitumor activity of Z-endoxifen (ENDX) is mediated via PKC beta 1-dependent ER alpha loss and cell cycle arrest in ER alpha-positive breast cancer.\n \n \n \n\n\n \n Jayaraman, S.; Kuffel, M. J; Kalari, K. R; Thompson, K. J; Tang, X.; Suman, V. J; Bruinsma, E. S; O'Sullivan, C. C; Wang, L.; Weinshilboum, R.; and others\n\n\n \n\n\n\n In CANCER RESEARCH, volume 81, 2021. AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA …\n \n\n\n\n
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@inproceedings{jayaraman2021antitumor,\n  title={Antitumor activity of Z-endoxifen (ENDX) is mediated via PKC beta 1-dependent ER alpha loss and cell cycle arrest in ER alpha-positive breast cancer},\n  author={Jayaraman, Swaathi and Kuffel, Mary J and Kalari, Krishna R and Thompson, Kevin J and Tang, Xiaojia and Suman, Vera J and Bruinsma, Elizabeth S and O'Sullivan, Ciara C and Wang, Liewei and Weinshilboum, Richard and others},\n  booktitle={CANCER RESEARCH},\n  volume={81},\n  number={4},\n  year={2021},\n  organization={AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA~…}\n}\n\n
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\n \n\n \n \n \n \n \n Correction to: establishing and characterizing patient-derived xenografts using pre-chemotherapy percutaneous biopsy and post-chemotherapy surgical samples from a prospective neoadjuvant breast cancer study.\n \n \n \n\n\n \n Yu, J.; Qin, B.; Moyer, A. M; Sinnwell, J. P; Thompson, K. J; Copland III, J. A; Marlow, L. A; Miller, J. L; Yin, P.; Gao, B.; and others\n\n\n \n\n\n\n Breast Cancer Research: BCR, 23. 2021.\n \n\n\n\n
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@article{yu2021correction,\n  title={Correction to: establishing and characterizing patient-derived xenografts using pre-chemotherapy percutaneous biopsy and post-chemotherapy surgical samples from a prospective neoadjuvant breast cancer study},\n  author={Yu, Jia and Qin, Bo and Moyer, Ann M and Sinnwell, Jason P and Thompson, Kevin J and Copland III, John A and Marlow, Laura A and Miller, James L and Yin, Ping and Gao, Bowen and others},\n  journal={Breast Cancer Research: BCR},\n  volume={23},\n  year={2021},\n  publisher={BMC}\n}\n\n
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\n \n\n \n \n \n \n \n Novel genomic variants and pathways associated with baseline serum thymidine kinase 1 levels in HR-positive HER2-negative MBC patients commencing palbociclib and letrozole.\n \n \n \n\n\n \n Sullivan, C. C.; Kalari, K. R; Suman, V. J; Vedell, P. T; Moyer, A.; Casey, A. D E.; Sinnwell, J.; Tang, X.; Thompson, K.; Moreno-Aspitia, A.; and others\n\n\n \n\n\n\n In CANCER RESEARCH, volume 81, 2021. AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA …\n \n\n\n\n
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@inproceedings{sullivan2021novel,\n  title={Novel genomic variants and pathways associated with baseline serum thymidine kinase 1 levels in HR-positive HER2-negative MBC patients commencing palbociclib and letrozole},\n  author={Sullivan, Ciara CO and Kalari, Krishna R and Suman, Vera J and Vedell, Peter T and Moyer, Ann and Casey, Abraham D Eyman and Sinnwell, Jason and Tang, Xiaojia and Thompson, Kevin and Moreno-Aspitia, Alvaro and others},\n  booktitle={CANCER RESEARCH},\n  volume={81},\n  number={4},\n  year={2021},\n  organization={AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA~…}\n}\n\n
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\n \n\n \n \n \n \n \n Barcoded Competitive Clone-Initiating Cell (BC-CIC) analysis reveals differences in ovarian cancer cell genotype and niche specific clonal fitness during growth and metastasis in vivo.\n \n \n \n\n\n \n Aalam, S. M. M.; Tang, X.; Song, J.; Bakkum-Gamez, J.; Sherman, M. E; Ray, U.; Shridhar, V.; Knapp, D. J.; Kalari, K. R; and Kannan, N.\n\n\n \n\n\n\n bioRxiv,2021–04. 2021.\n \n\n\n\n
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@article{aalam2021barcoded,\n  title={Barcoded Competitive Clone-Initiating Cell (BC-CIC) analysis reveals differences in ovarian cancer cell genotype and niche specific clonal fitness during growth and metastasis in vivo},\n  author={Aalam, Syed Mohammed Musheer and Tang, Xiaojia and Song, Jianning and Bakkum-Gamez, Jamie and Sherman, Mark E and Ray, Upasana and Shridhar, Viji and Knapp, David JHF and Kalari, Krishna R and Kannan, Nagarajan},\n  journal={bioRxiv},\n  pages={2021--04},\n  year={2021},\n  publisher={Cold Spring Harbor Laboratory}\n}\n\n
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\n \n\n \n \n \n \n \n Transcriptomic analysis to identify genes associated with selective hippocampal vulnerability in Alzheimer’s disease.\n \n \n \n\n\n \n Crist, A. M; Hinkle, K. M; Wang, X.; Moloney, C. M; Matchett, B. J; Labuzan, S. A; Frankenhauser, I.; Azu, N. O; Liesinger, A. M; Lesser, E. R; and others\n\n\n \n\n\n\n Nature communications, 12(1): 2311. 2021.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{crist2021transcriptomic,\n  title={Transcriptomic analysis to identify genes associated with selective hippocampal vulnerability in Alzheimer’s disease},\n  author={Crist, Angela M and Hinkle, Kelly M and Wang, Xue and Moloney, Christina M and Matchett, Billie J and Labuzan, Sydney A and Frankenhauser, Isabelle and Azu, Nkem O and Liesinger, Amanda M and Lesser, Elizabeth R and others},\n  journal={Nature communications},\n  volume={12},\n  number={1},\n  pages={2311},\n  year={2021},\n  publisher={Nature Publishing Group UK London}\n}\n\n
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\n \n\n \n \n \n \n \n Establishing and characterizing patient-derived xenografts using pre-chemotherapy percutaneous biopsy and post-chemotherapy surgical samples from a prospective neoadjuvant breast cancer study (vol 19, 130, 2017).\n \n \n \n\n\n \n Yu, J.; Qin, B.; Moyer, A. M; Sinnwell, J. P; Thompson, K. J; Copland III, J. A; Marlow, L. A; Miller, J. L; Yin, P.; Gao, B.; and others\n\n\n \n\n\n\n BREAST CANCER RESEARCH, 23(1). 2021.\n \n\n\n\n
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@article{yu2021establishing,\n  title={Establishing and characterizing patient-derived xenografts using pre-chemotherapy percutaneous biopsy and post-chemotherapy surgical samples from a prospective neoadjuvant breast cancer study (vol 19, 130, 2017)},\n  author={Yu, Jia and Qin, Bo and Moyer, Ann M and Sinnwell, Jason P and Thompson, Kevin J and Copland III, John A and Marlow, Laura A and Miller, James L and Yin, Ping and Gao, Bowen and others},\n  journal={BREAST CANCER RESEARCH},\n  volume={23},\n  number={1},\n  year={2021},\n  publisher={BMC CAMPUS, 4 CRINAN ST, LONDON N1 9XW, ENGLAND}\n}\n\n
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\n \n\n \n \n \n \n \n Patient-derived xenograft engraftment and breast cancer outcomes in a prospective neoadjuvant study (BEAUTY).\n \n \n \n\n\n \n Boughey, J. C; Suman, V. J; Yu, J.; Santo, K.; Sinnwell, J. P; Carter, J. M; Kalari, K. R; Tang, X.; McLaughlin, S. A; Moreno-Aspitia, A.; and others\n\n\n \n\n\n\n Clinical Cancer Research, 27(17): 4696–4699. 2021.\n \n\n\n\n
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@article{boughey2021patient,\n  title={Patient-derived xenograft engraftment and breast cancer outcomes in a prospective neoadjuvant study (BEAUTY)},\n  author={Boughey, Judy C and Suman, Vera J and Yu, Jia and Santo, Katelyn and Sinnwell, Jason P and Carter, Jodi M and Kalari, Krishna R and Tang, Xiaojia and McLaughlin, Sarah A and Moreno-Aspitia, Alvaro and others},\n  journal={Clinical Cancer Research},\n  volume={27},\n  number={17},\n  pages={4696--4699},\n  year={2021},\n  publisher={American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n FOXA1 overexpression suppresses interferon signaling and immune response in cancer.\n \n \n \n\n\n \n He, Y.; Wang, L.; Wei, T.; Xiao, Y.; Sheng, H.; Su, H.; Hollern, D. P; Zhang, X.; Ma, J.; Wen, S.; and others\n\n\n \n\n\n\n The Journal of clinical investigation, 131(14). 2021.\n \n\n\n\n
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@article{he2021foxa1,\n  title={FOXA1 overexpression suppresses interferon signaling and immune response in cancer},\n  author={He, Yundong and Wang, Liguo and Wei, Ting and Xiao, Yu-Tian and Sheng, Haoyue and Su, Hengchuan and Hollern, Daniel P and Zhang, Xiaoling and Ma, Jian and Wen, Simeng and others},\n  journal={The Journal of clinical investigation},\n  volume={131},\n  number={14},\n  year={2021},\n  publisher={American Society for Clinical Investigation}\n}\n\n
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\n \n\n \n \n \n \n \n Abstract LB226: Maternal microbiome protects host against clonal de novo transformation, early onset systemic metastasis, and sudden death.\n \n \n \n\n\n \n Kannan, N.; Aalam, S. M. M.; Tang, X.; Kalari, K.; Kashyap, P.; Chen, J.; Johnson, S.; Sadanandam, A.; and Sherman, M.\n\n\n \n\n\n\n Cancer Research, 81(13_Supplement): LB226–LB226. 2021.\n \n\n\n\n
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@article{kannan2021abstract,\n  title={Abstract LB226: Maternal microbiome protects host against clonal de novo transformation, early onset systemic metastasis, and sudden death},\n  author={Kannan, Nagarajan and Aalam, Syed Mohammed Musheer and Tang, Xiaojia and Kalari, Krishna and Kashyap, Purna and Chen, Jun and Johnson, Stephen and Sadanandam, Anguraj and Sherman, Mark},\n  journal={Cancer Research},\n  volume={81},\n  number={13\\_Supplement},\n  pages={LB226--LB226},\n  year={2021},\n  publisher={The American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n Maternal microbiome protects host against clonal de novo transformation, early onset systemic metastasis, and sudden death.\n \n \n \n\n\n \n Kannan, N.; Aalam, S. M. M.; Tang, X.; Kalari, K.; Kashyap, P.; Chen, J.; Johnson, S.; Sadanandam, A.; and Sherman, M.\n\n\n \n\n\n\n In CANCER RESEARCH, volume 81, 2021. AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA …\n \n\n\n\n
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@inproceedings{kannan2021maternal,\n  title={Maternal microbiome protects host against clonal de novo transformation, early onset systemic metastasis, and sudden death.},\n  author={Kannan, Nagarajan and Aalam, Syed Mohammed Musheer and Tang, Xiaojia and Kalari, Krishna and Kashyap, Purna and Chen, Jun and Johnson, Stephen and Sadanandam, Anguraj and Sherman, Mark},\n  booktitle={CANCER RESEARCH},\n  volume={81},\n  number={13},\n  year={2021},\n  organization={AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA~…}\n}\n\n
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\n \n\n \n \n \n \n \n CORRECTION Open Access.\n \n \n \n\n\n \n Yu, J.; Qin, B.; Moyer, A. M; Sinnwell, J. P; Thompson, K. J; III, J. A C.; Marlow, L. A; Miller, J. L; Yin, P.; Gao13, B.; and others\n\n\n \n\n\n\n . 2021.\n \n\n\n\n
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@article{yu2021correction,\n  title={CORRECTION Open Access},\n  author={Yu, Jia and Qin, Bo and Moyer, Ann M and Sinnwell, Jason P and Thompson, Kevin J and III, John A Copland and Marlow, Laura A and Miller, James L and Yin, Ping and Gao13, Bowen and others},\n  year={2021}\n}\n\n
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\n  \n 2020\n \n \n (9)\n \n \n
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\n \n\n \n \n \n \n \n Abstract P2-11-07: Comprehensive tumor sequencing to identify biomarkers of palbociclib response: First report of the PROMISE study.\n \n \n \n\n\n \n Sullivan, C. C.; Kalari, K. R; Suman, V. J; Vedell, P. T; Moyer, A.; Carlson, E.; Sinnwell, J.; Alaparthi, T.; Tang, X.; Thompson, K.; and others\n\n\n \n\n\n\n Cancer Research, 80(4_Supplement): P2–11. 2020.\n \n\n\n\n
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@article{sullivan2020abstract,\n  title={Abstract P2-11-07: Comprehensive tumor sequencing to identify biomarkers of palbociclib response: First report of the PROMISE study},\n  author={Sullivan, Ciara CO and Kalari, Krishna R and Suman, Vera J and Vedell, Peter T and Moyer, Ann and Carlson, Erin and Sinnwell, Jason and Alaparthi, Tejaswi and Tang, Xiaojia and Thompson, Kevin and others},\n  journal={Cancer Research},\n  volume={80},\n  number={4\\_Supplement},\n  pages={P2--11},\n  year={2020},\n  publisher={The American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n Abstract P6-04-06: Protein kinase C beta 1 (PKC$β$1), a novel drug target of Z-endoxifen, inhibits growth of estrogen receptor positive (ER+) breast cancer via activation of the NF-kB transcription factor RelA.\n \n \n \n\n\n \n Jayaraman, S.; Kuffel, M. J; Kalari, K. R; Thompson, K. J; Tang, X.; Bruinsma, E. S; Hawse, J. R; and Goetz, M. P\n\n\n \n\n\n\n Cancer Research, 80(4_Supplement): P6–04. 2020.\n \n\n\n\n
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@article{jayaraman2020abstract,\n  title={Abstract P6-04-06: Protein kinase C beta 1 (PKC$\\beta$1), a novel drug target of Z-endoxifen, inhibits growth of estrogen receptor positive (ER+) breast cancer via activation of the NF-kB transcription factor RelA},\n  author={Jayaraman, Swaathi and Kuffel, Mary J and Kalari, Krishna R and Thompson, Kevin J and Tang, Xiaojia and Bruinsma, Elizabeth S and Hawse, John R and Goetz, Matthew P},\n  journal={Cancer Research},\n  volume={80},\n  number={4\\_Supplement},\n  pages={P6--04},\n  year={2020},\n  publisher={The American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n Abstract P4-09-03: Phenotypes of breast tumor cells and normal lymphocytes are determined by the integration of minor changes in expression of multiple genes: A new dimension in quantitative inheritance.\n \n \n \n\n\n \n Pease, L. R; Felts, S. J; Scheid, A. D; Tang, X.; and Kalari, K. R\n\n\n \n\n\n\n Cancer Research, 80(4_Supplement): P4–09. 2020.\n \n\n\n\n
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@article{pease2020abstract,\n  title={Abstract P4-09-03: Phenotypes of breast tumor cells and normal lymphocytes are determined by the integration of minor changes in expression of multiple genes: A new dimension in quantitative inheritance},\n  author={Pease, Larry R and Felts, Sara J and Scheid, Adam D and Tang, Xiaojia and Kalari, Krishna R},\n  journal={Cancer Research},\n  volume={80},\n  number={4\\_Supplement},\n  pages={P4--09},\n  year={2020},\n  publisher={The American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n Longitudinal multi-omics reveals subset-specific mechanisms underlying irritable bowel syndrome.\n \n \n \n\n\n \n Mars, R. A.; Yang, Y.; Ward, T.; Houtti, M.; Priya, S.; Lekatz, H. R; Tang, X.; Sun, Z.; Kalari, K. R; Korem, T.; and others\n\n\n \n\n\n\n Cell, 182(6): 1460–1473. 2020.\n \n\n\n\n
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@article{mars2020longitudinal,\n  title={Longitudinal multi-omics reveals subset-specific mechanisms underlying irritable bowel syndrome},\n  author={Mars, Ruben AT and Yang, Yi and Ward, Tonya and Houtti, Mo and Priya, Sambhawa and Lekatz, Heather R and Tang, Xiaojia and Sun, Zhifu and Kalari, Krishna R and Korem, Tal and others},\n  journal={Cell},\n  volume={182},\n  number={6},\n  pages={1460--1473},\n  year={2020},\n  publisher={Elsevier}\n}\n\n
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\n \n\n \n \n \n \n \n Antitumor activity of Z-endoxifen in aromatase inhibitor-sensitive and aromatase inhibitor-resistant estrogen receptor-positive breast cancer.\n \n \n \n\n\n \n Jayaraman, S.; Hou, X.; Kuffel, M. J; Suman, V. J; Hoskin, T. L; Reinicke, K. E; Monroe, D. G; Kalari, K. R; Tang, X.; Zeldenrust, M. A; and others\n\n\n \n\n\n\n Breast Cancer Research, 22: 1–12. 2020.\n \n\n\n\n
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@article{jayaraman2020antitumor,\n  title={Antitumor activity of Z-endoxifen in aromatase inhibitor-sensitive and aromatase inhibitor-resistant estrogen receptor-positive breast cancer},\n  author={Jayaraman, Swaathi and Hou, Xiaonan and Kuffel, Mary J and Suman, Vera J and Hoskin, Tanya L and Reinicke, Kathryn E and Monroe, David G and Kalari, Krishna R and Tang, Xiaojia and Zeldenrust, Megan A and others},\n  journal={Breast Cancer Research},\n  volume={22},\n  pages={1--12},\n  year={2020},\n  publisher={BioMed Central}\n}\n\n
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\n \n\n \n \n \n \n \n Frequency of MicroRNA response elements identifies pathologically relevant signaling pathways in triple-negative breast cancer.\n \n \n \n\n\n \n Nair, A. A; Tang, X.; Thompson, K. J; Vedell, P. T; Kalari, K. R; and Subramanian, S.\n\n\n \n\n\n\n Iscience, 23(6). 2020.\n \n\n\n\n
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@article{nair2020frequency,\n  title={Frequency of MicroRNA response elements identifies pathologically relevant signaling pathways in triple-negative breast cancer},\n  author={Nair, Asha A and Tang, Xiaojia and Thompson, Kevin J and Vedell, Peter T and Kalari, Krishna R and Subramanian, Subbaya},\n  journal={Iscience},\n  volume={23},\n  number={6},\n  year={2020},\n  publisher={Elsevier}\n}\n\n
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\n \n\n \n \n \n \n \n Protein kinase C beta 1 (PKC beta 1), a novel drug target of Z-endoxifen, inhibits growth of estrogen receptor positive (ER plus) breast cancer via activation of the NF-kB transcription factor RelA.\n \n \n \n\n\n \n Jayaraman, S.; Kuffel, M. J; Kalari, K. R; Thompson, K. J; Tang, X.; Bruinsma, E. S; Hawse, J. R; and Goetz, M. P\n\n\n \n\n\n\n In CANCER RESEARCH, volume 80, 2020. AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA …\n \n\n\n\n
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@inproceedings{jayaraman2020protein,\n  title={Protein kinase C beta 1 (PKC beta 1), a novel drug target of Z-endoxifen, inhibits growth of estrogen receptor positive (ER plus) breast cancer via activation of the NF-kB transcription factor RelA},\n  author={Jayaraman, Swaathi and Kuffel, Mary J and Kalari, Krishna R and Thompson, Kevin J and Tang, Xiaojia and Bruinsma, Elizabeth S and Hawse, John R and Goetz, Matthew P},\n  booktitle={CANCER RESEARCH},\n  volume={80},\n  number={4},\n  year={2020},\n  organization={AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA~…}\n}\n\n
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\n \n\n \n \n \n \n \n Phenotypes of breast tumor cells and normal lymphocytes are determined by the integration of minor changes in expression of multiple genes: A new dimension in quantitative inheritance.\n \n \n \n\n\n \n Pease, L. R; Felts, S. J; Scheid, A. D; Tang, X.; and Kalari, K. R\n\n\n \n\n\n\n In CANCER RESEARCH, volume 80, 2020. AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA …\n \n\n\n\n
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@inproceedings{pease2020phenotypes,\n  title={Phenotypes of breast tumor cells and normal lymphocytes are determined by the integration of minor changes in expression of multiple genes: A new dimension in quantitative inheritance},\n  author={Pease, Larry R and Felts, Sara J and Scheid, Adam D and Tang, Xiaojia and Kalari, Krishna R},\n  booktitle={CANCER RESEARCH},\n  volume={80},\n  number={4},\n  year={2020},\n  organization={AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA~…}\n}\n\n
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\n \n\n \n \n \n \n \n Leveraging selective hippocampal vulnerability among Alzheimer’s disease subtypes reveals a novel tau binding partner SERPINA5.\n \n \n \n\n\n \n Crist, A. M; Hinkle, K. M; Wang, X.; Moloney, C. M; Matchett, B. J; Labuzan, S. A; Frankenhauser, I.; Azu, N. O; Liesinger, A. M; Lesser, E. R; and others\n\n\n \n\n\n\n bioRxiv,2020–12. 2020.\n \n\n\n\n
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@article{crist2020leveraging,\n  title={Leveraging selective hippocampal vulnerability among Alzheimer’s disease subtypes reveals a novel tau binding partner SERPINA5},\n  author={Crist, Angela M and Hinkle, Kelly M and Wang, Xue and Moloney, Christina M and Matchett, Billie J and Labuzan, Sydney A and Frankenhauser, Isabelle and Azu, Nkem O and Liesinger, Amanda M and Lesser, Elizabeth R and others},\n  journal={bioRxiv},\n  pages={2020--12},\n  year={2020},\n  publisher={Cold Spring Harbor Laboratory}\n}\n\n
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\n  \n 2019\n \n \n (11)\n \n \n
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\n \n\n \n \n \n \n \n Abstract P3-06-10: Multiscale modeling of omics data for precision breast cancer treatment.\n \n \n \n\n\n \n Kalari, K.; Sinnwell, J.; Thompson, K.; Tang, X; Carlson, E.; Alaparthi, T; Yu, J; Vedell, P.; Kalmbach, M.; Bockol, M.; and others\n\n\n \n\n\n\n Cancer Research, 79(4_Supplement): P3–06. 2019.\n \n\n\n\n
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@article{kalari2019abstract,\n  title={Abstract P3-06-10: Multiscale modeling of omics data for precision breast cancer treatment},\n  author={Kalari, KR and Sinnwell, JP and Thompson, KJ and Tang, X and Carlson, EE and Alaparthi, T and Yu, J and Vedell, PT and Kalmbach, MT and Bockol, MA and others},\n  journal={Cancer Research},\n  volume={79},\n  number={4\\_Supplement},\n  pages={P3--06},\n  year={2019},\n  publisher={The American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n Abstract P1-03-04: Molecular subtyping of androgen receptor-positive patients using gene expression profiles.\n \n \n \n\n\n \n Thompson, K.; Alaparthi, T; Sinnwell, J.; Carlson, E.; Tang, X; Bockol, M; Vedell, P.; Ingle, J.; Suman, V; Weinshilboum, R.; and others\n\n\n \n\n\n\n Cancer Research, 79(4_Supplement): P1–03. 2019.\n \n\n\n\n
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@article{thompson2019abstract,\n  title={Abstract P1-03-04: Molecular subtyping of androgen receptor-positive patients using gene expression profiles},\n  author={Thompson, KJ and Alaparthi, T and Sinnwell, JP and Carlson, EE and Tang, X and Bockol, M and Vedell, PT and Ingle, JN and Suman, V and Weinshilboum, RM and others},\n  journal={Cancer Research},\n  volume={79},\n  number={4\\_Supplement},\n  pages={P1--03},\n  year={2019},\n  publisher={The American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n Abstract P3-08-01: Characteristics, outcomes and prognostic factors of luminal androgen receptor (LAR) triple-negative breast cancer (TNBC).\n \n \n \n\n\n \n Leon-Ferre, R.; Polley, M.; Liu, H; Kalari, K.; Boughey, J.; Liu, M.; Cafourek, V; Negron, V; Ingle, J.; Thompson, K.; and others\n\n\n \n\n\n\n Cancer Research, 79(4_Supplement): P3–08. 2019.\n \n\n\n\n
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@article{leon2019abstract,\n  title={Abstract P3-08-01: Characteristics, outcomes and prognostic factors of luminal androgen receptor (LAR) triple-negative breast cancer (TNBC)},\n  author={Leon-Ferre, RA and Polley, MY and Liu, H and Kalari, KR and Boughey, JC and Liu, MC and Cafourek, V and Negron, V and Ingle, JN and Thompson, KJ and others},\n  journal={Cancer Research},\n  volume={79},\n  number={4\\_Supplement},\n  pages={P3--08},\n  year={2019},\n  publisher={The American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n Stochastic changes in gene expression promote chaotic dysregulation of homeostasis in clonal breast tumors.\n \n \n \n\n\n \n Felts, S. J; Tang, X.; Willett, B.; Van Keulen, V. P; Hansen, M. J; Kalari, K. R; and Pease, L. R\n\n\n \n\n\n\n Communications Biology, 2(1): 206. 2019.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{felts2019stochastic,\n  title={Stochastic changes in gene expression promote chaotic dysregulation of homeostasis in clonal breast tumors},\n  author={Felts, Sara J and Tang, Xiaojia and Willett, Benjamin and Van Keulen, Virginia P and Hansen, Michael J and Kalari, Krishna R and Pease, Larry R},\n  journal={Communications Biology},\n  volume={2},\n  number={1},\n  pages={206},\n  year={2019},\n  publisher={Nature Publishing Group UK London}\n}\n\n
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\n \n\n \n \n \n \n \n Deep sequencing across germline genome-wide association study signals relating to breast cancer events in women receiving aromatase inhibitors for adjuvant therapy of early breast cancer.\n \n \n \n\n\n \n Ingle, J. N; Kalari, K. R; Momozawa, Y.; Kubo, M.; Furukawa, Y.; Shepherd, L. E; Ellis, M. J; Goss, P. E; Barman, P.; Carlson, E. E; and others\n\n\n \n\n\n\n Pharmacogenetics and genomics, 29(8): 183–191. 2019.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{ingle2019deep,\n  title={Deep sequencing across germline genome-wide association study signals relating to breast cancer events in women receiving aromatase inhibitors for adjuvant therapy of early breast cancer},\n  author={Ingle, James N and Kalari, Krishna R and Momozawa, Yukihide and Kubo, Michiaki and Furukawa, Yoichi and Shepherd, Lois E and Ellis, Matthew J and Goss, Paul E and Barman, Poulami and Carlson, Erin E and others},\n  journal={Pharmacogenetics and genomics},\n  volume={29},\n  number={8},\n  pages={183--191},\n  year={2019},\n  publisher={LWW}\n}\n\n
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\n \n\n \n \n \n \n \n Stochastic variation in gene expression is selected during clonal evolution of spontaneous mouse mammary tumors.\n \n \n \n\n\n \n Felts, S. J; Tang, X.; Keulen, V. P V.; Kalari, K. R; and Pease, L. R\n\n\n \n\n\n\n Cancer Research, 79(13_Supplement): 2898–2898. 2019.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{felts2019stochastic,\n  title={Stochastic variation in gene expression is selected during clonal evolution of spontaneous mouse mammary tumors},\n  author={Felts, Sara J and Tang, Xiaojia and Keulen, Virginia P Van and Kalari, Krishna R and Pease, Larry R},\n  journal={Cancer Research},\n  volume={79},\n  number={13\\_Supplement},\n  pages={2898--2898},\n  year={2019},\n  publisher={The American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n CTG Repeat Expansion in TCF4 without Phenotypic Fuchs Dystrophy: a Genetic Analysis.\n \n \n \n\n\n \n Baratz, K. H; Fautsch, M. P; Aleff, R. A; Tang, X.; Kalari, K. R; Patel, S. V; Maguire, L. J; and Wieben, E.\n\n\n \n\n\n\n Investigative Ophthalmology & Visual Science, 60(9): 3876–3876. 2019.\n \n\n\n\n
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@article{baratz2019ctg,\n  title={CTG Repeat Expansion in TCF4 without Phenotypic Fuchs Dystrophy: a Genetic Analysis},\n  author={Baratz, Keith H and Fautsch, Michael P and Aleff, Ross A and Tang, Xiaojia and Kalari, Krishna R and Patel, Sanjay V and Maguire, Leo J and Wieben, Eric},\n  journal={Investigative Ophthalmology \\& Visual Science},\n  volume={60},\n  number={9},\n  pages={3876--3876},\n  year={2019},\n  publisher={The Association for Research in Vision and Ophthalmology}\n}\n\n
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\n \n\n \n \n \n \n \n Gene expression and missplicing in the corneal endothelium of patients with a TCF4 trinucleotide repeat expansion without fuchs' endothelial corneal dystrophy.\n \n \n \n\n\n \n Wieben, E. D; Baratz, K. H; Aleff, R. A; Kalari, K. R; Tang, X.; Maguire, L. J; Patel, S. V; and Fautsch, M. P\n\n\n \n\n\n\n Investigative ophthalmology & visual science, 60(10): 3636–3643. 2019.\n \n\n\n\n
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@article{wieben2019gene,\n  title={Gene expression and missplicing in the corneal endothelium of patients with a TCF4 trinucleotide repeat expansion without fuchs' endothelial corneal dystrophy},\n  author={Wieben, Eric D and Baratz, Keith H and Aleff, Ross A and Kalari, Krishna R and Tang, Xiaojia and Maguire, Leo J and Patel, Sanjay V and Fautsch, Michael P},\n  journal={Investigative ophthalmology \\& visual science},\n  volume={60},\n  number={10},\n  pages={3636--3643},\n  year={2019},\n  publisher={The Association for Research in Vision and Ophthalmology}\n}\n\n
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\n \n\n \n \n \n \n \n A tailored approach to fusion transcript identification increases diagnosis of rare inherited disease.\n \n \n \n\n\n \n Oliver, G. R; Tang, X.; Schultz-Rogers, L. E; Vidal-Folch, N.; Jenkinson, W G.; Schwab, T. L; Gaonkar, K.; Cousin, M. A; Nair, A.; Basu, S.; and others\n\n\n \n\n\n\n PLoS One, 14(10): e0223337. 2019.\n \n\n\n\n
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@article{oliver2019tailored,\n  title={A tailored approach to fusion transcript identification increases diagnosis of rare inherited disease},\n  author={Oliver, Gavin R and Tang, Xiaojia and Schultz-Rogers, Laura E and Vidal-Folch, Noemi and Jenkinson, W Garrett and Schwab, Tanya L and Gaonkar, Krutika and Cousin, Margot A and Nair, Asha and Basu, Shubham and others},\n  journal={PLoS One},\n  volume={14},\n  number={10},\n  pages={e0223337},\n  year={2019},\n  publisher={Public Library of Science San Francisco, CA USA}\n}\n\n
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\n \n\n \n \n \n \n \n Frequency of MicroRNA Response Elements Identifies Pathologically Relevant Signaling Pathways in Cancers.\n \n \n \n\n\n \n Nair, A. A; Tang, X.; Thompson, K. J; Kalari, K. R; and Subramanian, S.\n\n\n \n\n\n\n bioRxiv,817098. 2019.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{nair2019frequency,\n  title={Frequency of MicroRNA Response Elements Identifies Pathologically Relevant Signaling Pathways in Cancers},\n  author={Nair, Asha A and Tang, Xiaojia and Thompson, Kevin J and Kalari, Krishna R and Subramanian, Subbaya},\n  journal={bioRxiv},\n  pages={817098},\n  year={2019},\n  publisher={Cold Spring Harbor Laboratory}\n}\n\n
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\n \n\n \n \n \n \n \n Tu1790–Bacteria Derived Tryptamine Production Alters Host Gene Expression Associated with Intestinal Inflammation.\n \n \n \n\n\n \n Bhattarai, Y.; Williams, B. B; Krishna, K.; Tang, X.; Battaglioli, E.; Fischbach, M.; Grover, M.; Farrugia, G.; and Kashyap, P.\n\n\n \n\n\n\n Gastroenterology, 156(6): S–1124. 2019.\n \n\n\n\n
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@article{bhattarai2019tu1790,\n  title={Tu1790--Bacteria Derived Tryptamine Production Alters Host Gene Expression Associated with Intestinal Inflammation},\n  author={Bhattarai, Yogesh and Williams, Brianna B and Krishna, Kalari and Tang, Xiaojia and Battaglioli, Eric and Fischbach, Micheal and Grover, Madhusudan and Farrugia, Gianrico and Kashyap, Purna},\n  journal={Gastroenterology},\n  volume={156},\n  number={6},\n  pages={S--1124},\n  year={2019},\n  publisher={WB Saunders}\n}\n\n
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\n  \n 2018\n \n \n (5)\n \n \n
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\n \n\n \n \n \n \n \n PANOPLY: omics-guided drug prioritization method tailored to an individual patient.\n \n \n \n\n\n \n Kalari, K. R; Sinnwell, J. P; Thompson, K. J; Tang, X.; Carlson, E. E; Yu, J.; Vedell, P. T; Ingle, J. N; Weinshilboum, R. M; Boughey, J. C; and others\n\n\n \n\n\n\n JCO clinical cancer informatics, 2: 1–11. 2018.\n \n\n\n\n
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@article{kalari2018panoply,\n  title={PANOPLY: omics-guided drug prioritization method tailored to an individual patient},\n  author={Kalari, Krishna R and Sinnwell, Jason P and Thompson, Kevin J and Tang, Xiaojia and Carlson, Erin E and Yu, Jia and Vedell, Peter T and Ingle, James N and Weinshilboum, Richard M and Boughey, Judy C and others},\n  journal={JCO clinical cancer informatics},\n  volume={2},\n  pages={1--11},\n  year={2018},\n  publisher={American Society of Clinical Oncology}\n}\n\n
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\n \n\n \n \n \n \n \n Differential effects of Alzheimer’s disease A$β$40 and 42 on endocytosis and intraneuronal trafficking.\n \n \n \n\n\n \n Omtri, R. S; Thompson, K. J; Tang, X.; Gali, C. C; Panzenboeck, U.; Davidson, M. W; Kalari, K. R; and Kandimalla, K. K\n\n\n \n\n\n\n Neuroscience, 373: 159–168. 2018.\n \n\n\n\n
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@article{omtri2018differential,\n  title={Differential effects of Alzheimer’s disease A$\\beta$40 and 42 on endocytosis and intraneuronal trafficking},\n  author={Omtri, Rajesh S and Thompson, Kevin J and Tang, Xiaojia and Gali, Chaitanya C and Panzenboeck, Ute and Davidson, Michael W and Kalari, Krishna R and Kandimalla, Karunya K},\n  journal={Neuroscience},\n  volume={373},\n  pages={159--168},\n  year={2018},\n  publisher={Pergamon}\n}\n\n
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\n \n\n \n \n \n \n \n Gene expression in the corneal endothelium of Fuchs endothelial corneal dystrophy patients with and without expansion of a trinucleotide repeat in TCF4.\n \n \n \n\n\n \n Wieben, E. D; Aleff, R. A; Tang, X.; Kalari, K. R; Maguire, L. J; Patel, S. V; Baratz, K. H; and Fautsch, M. P\n\n\n \n\n\n\n PloS one, 13(7): e0200005. 2018.\n \n\n\n\n
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@article{wieben2018gene,\n  title={Gene expression in the corneal endothelium of Fuchs endothelial corneal dystrophy patients with and without expansion of a trinucleotide repeat in TCF4},\n  author={Wieben, Eric D and Aleff, Ross A and Tang, Xiaojia and Kalari, Krishna R and Maguire, Leo J and Patel, Sanjay V and Baratz, Keith H and Fautsch, Michael P},\n  journal={PloS one},\n  volume={13},\n  number={7},\n  pages={e0200005},\n  year={2018},\n  publisher={Public Library of Science San Francisco, CA USA}\n}\n\n
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\n \n\n \n \n \n \n \n HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data.\n \n \n \n\n\n \n Baheti, S.; Tang, X.; O’Brien, D. R; Chia, N.; Roberts, L. R; Nelson, H.; Boughey, J. C; Wang, L.; Goetz, M. P; Kocher, J. A; and others\n\n\n \n\n\n\n BMC bioinformatics, 19: 1–11. 2018.\n \n\n\n\n
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@article{baheti2018hgt,\n  title={HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data},\n  author={Baheti, Saurabh and Tang, Xiaojia and O’Brien, Daniel R and Chia, Nicholas and Roberts, Lewis R and Nelson, Heidi and Boughey, Judy C and Wang, Liewei and Goetz, Matthew P and Kocher, Jean-Pierre A and others},\n  journal={BMC bioinformatics},\n  volume={19},\n  pages={1--11},\n  year={2018},\n  publisher={BioMed Central}\n}\n\n
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\n \n\n \n \n \n \n \n RNA splicing and gene expression in corneal endothelium in Fuchs dystrophy from patients with and without TCF4 trinucleotide repeat expansion.\n \n \n \n\n\n \n Baratz, K. H; Aleff, R.; Tang, X.; Kalari, K. R; Maguire, L. J; Patel, S. V; Fautsch, M. P; and Wieben, E.\n\n\n \n\n\n\n Investigative Ophthalmology & Visual Science, 59(9): 4434–4434. 2018.\n \n\n\n\n
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@article{baratz2018rna,\n  title={RNA splicing and gene expression in corneal endothelium in Fuchs dystrophy from patients with and without TCF4 trinucleotide repeat expansion.},\n  author={Baratz, Keith H and Aleff, Ross and Tang, Xiaojia and Kalari, Krishna R and Maguire, Leo J and Patel, Sanjay V and Fautsch, Michael P and Wieben, Eric},\n  journal={Investigative Ophthalmology \\& Visual Science},\n  volume={59},\n  number={9},\n  pages={4434--4434},\n  year={2018},\n  publisher={The Association for Research in Vision and Ophthalmology}\n}\n\n
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\n  \n 2017\n \n \n (5)\n \n \n
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\n \n\n \n \n \n \n \n Trinucleotide repeat expansion in the transcription factor 4 (TCF4) gene leads to widespread mRNA splicing changes in Fuchs' endothelial corneal dystrophy.\n \n \n \n\n\n \n Wieben, E. D; Aleff, R. A; Tang, X.; Butz, M. L; Kalari, K. R; Highsmith, E. W; Jen, J.; Vasmatzis, G.; Patel, S. V; Maguire, L. J; and others\n\n\n \n\n\n\n Investigative Ophthalmology & Visual Science, 58(1): 343–352. 2017.\n \n\n\n\n
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@article{wieben2017trinucleotide,\n  title={Trinucleotide repeat expansion in the transcription factor 4 (TCF4) gene leads to widespread mRNA splicing changes in Fuchs' endothelial corneal dystrophy},\n  author={Wieben, Eric D and Aleff, Ross A and Tang, Xiaojia and Butz, Malinda L and Kalari, Krishna R and Highsmith, Edward W and Jen, Jin and Vasmatzis, George and Patel, Sanjay V and Maguire, Leo J and others},\n  journal={Investigative Ophthalmology \\& Visual Science},\n  volume={58},\n  number={1},\n  pages={343--352},\n  year={2017},\n  publisher={The Association for Research in Vision and Ophthalmology}\n}\n\n
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\n \n\n \n \n \n \n \n Tumor sequencing and patient-derived xenografts in the neoadjuvant treatment of breast cancer.\n \n \n \n\n\n \n Goetz, M. P; Kalari, K. R; Suman, V. J; Moyer, A. M; Yu, J.; Visscher, D. W; Dockter, T. J; Vedell, P. T; Sinnwell, J. P; Tang, X.; and others\n\n\n \n\n\n\n JNCI: Journal of the National Cancer Institute, 109(7): djw306. 2017.\n \n\n\n\n
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@article{goetz2017tumor,\n  title={Tumor sequencing and patient-derived xenografts in the neoadjuvant treatment of breast cancer},\n  author={Goetz, Matthew P and Kalari, Krishna R and Suman, Vera J and Moyer, Ann M and Yu, Jia and Visscher, Daniel W and Dockter, Travis J and Vedell, Peter T and Sinnwell, Jason P and Tang, Xiaojia and others},\n  journal={JNCI: Journal of the National Cancer Institute},\n  volume={109},\n  number={7},\n  pages={djw306},\n  year={2017},\n  publisher={Oxford University Press}\n}\n\n
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\n \n\n \n \n \n \n \n Characterization of gene mis-splicing events in Fuchs endothelial corneal dystrophy primary cell cultures.\n \n \n \n\n\n \n Rinkoski, T. A; Bahler, C. K; Tang, X.; Kalari, K. R; Baratz, K.; Patel, S. V; Fautsch, M. P; and Wieben, E.\n\n\n \n\n\n\n Investigative Ophthalmology & Visual Science, 58(8): 1433–1433. 2017.\n \n\n\n\n
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@article{rinkoski2017characterization,\n  title={Characterization of gene mis-splicing events in Fuchs endothelial corneal dystrophy primary cell cultures},\n  author={Rinkoski, Tommy A and Bahler, Cindy K and Tang, Xiaojia and Kalari, Krishna R and Baratz, Keith and Patel, Sanjay V and Fautsch, Michael P and Wieben, Eric},\n  journal={Investigative Ophthalmology \\& Visual Science},\n  volume={58},\n  number={8},\n  pages={1433--1433},\n  year={2017},\n  publisher={The Association for Research in Vision and Ophthalmology}\n}\n\n
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\n \n\n \n \n \n \n \n A comprehensive analysis of breast cancer microbiota and host gene expression.\n \n \n \n\n\n \n Thompson, K. J; Ingle, J. N; Tang, X.; Chia, N.; Jeraldo, P. R; Walther-Antonio, M. R; Kandimalla, K. K; Johnson, S.; Yao, J. Z; Harrington, S. C; and others\n\n\n \n\n\n\n PloS one, 12(11): e0188873. 2017.\n \n\n\n\n
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@article{thompson2017comprehensive,\n  title={A comprehensive analysis of breast cancer microbiota and host gene expression},\n  author={Thompson, Kevin J and Ingle, James N and Tang, Xiaojia and Chia, Nicholas and Jeraldo, Patricio R and Walther-Antonio, Marina R and Kandimalla, Karunya K and Johnson, Stephen and Yao, Janet Z and Harrington, Sean C and others},\n  journal={PloS one},\n  volume={12},\n  number={11},\n  pages={e0188873},\n  year={2017},\n  publisher={Public Library of Science San Francisco, CA USA}\n}\n\n
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\n \n\n \n \n \n \n \n Establishing and characterizing patient-derived xenografts using pre-chemotherapy percutaneous biopsy and post-chemotherapy surgical samples from a prospective neoadjuvant breast cancer study.\n \n \n \n\n\n \n Yu, J.; Qin, B.; Moyer, A. M; Sinnwell, J. P; Thompson, K. J; Copland, J. A; Marlow, L. A; Miller, J. L; Yin, P.; Gao, B.; and others\n\n\n \n\n\n\n Breast Cancer Research, 19: 1–13. 2017.\n \n\n\n\n
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@article{yu2017establishing,\n  title={Establishing and characterizing patient-derived xenografts using pre-chemotherapy percutaneous biopsy and post-chemotherapy surgical samples from a prospective neoadjuvant breast cancer study},\n  author={Yu, Jia and Qin, Bo and Moyer, Ann M and Sinnwell, Jason P and Thompson, Kevin J and Copland, John A and Marlow, Laura A and Miller, James L and Yin, Ping and Gao, Bowen and others},\n  journal={Breast Cancer Research},\n  volume={19},\n  pages={1--13},\n  year={2017},\n  publisher={BioMed Central}\n}\n\n
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\n  \n 2016\n \n \n (6)\n \n \n
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\n \n\n \n \n \n \n \n BBBomics-human blood brain barrier transcriptomics hub.\n \n \n \n\n\n \n Kalari, K. R; Thompson, K. J; Nair, A. A; Tang, X.; Bockol, M. A; Jhawar, N.; Swaminathan, S. K; Lowe, V. J; and Kandimalla, K. K\n\n\n \n\n\n\n Frontiers in Neuroscience, 10: 71. 2016.\n \n\n\n\n
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@article{kalari2016bbbomics,\n  title={BBBomics-human blood brain barrier transcriptomics hub},\n  author={Kalari, Krishna R and Thompson, Kevin J and Nair, Asha A and Tang, Xiaojia and Bockol, Matthew A and Jhawar, Navya and Swaminathan, Suresh K and Lowe, Val J and Kandimalla, Karunya K},\n  journal={Frontiers in Neuroscience},\n  volume={10},\n  pages={71},\n  year={2016},\n  publisher={Frontiers Media SA}\n}\n\n
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\n \n\n \n \n \n \n \n Role of germline BRCA status and tumor homologous recombination (HR) deficiency in response to neoadjuvant weekly paclitaxel followed by anthracycline-based chemotherapy.\n \n \n \n\n\n \n Boughey, J. C; Kalari, K. R; Suman, V. J; McLaughlin, S. A; Moreno-Aspitia, A.; Moyer, A. M; and others\n\n\n \n\n\n\n Cancer Res, 76(suppl 4): P3–07. 2016.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{boughey2016role,\n  title={Role of germline BRCA status and tumor homologous recombination (HR) deficiency in response to neoadjuvant weekly paclitaxel followed by anthracycline-based chemotherapy},\n  author={Boughey, Judy C and Kalari, Krishna R and Suman, Vera J and McLaughlin, Sarah A and Moreno-Aspitia, Alvaro and Moyer, Ann M and others},\n  journal={Cancer Res},\n  volume={76},\n  number={suppl 4},\n  pages={P3--07},\n  year={2016}\n}\n\n
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\n \n\n \n \n \n \n \n Luminal Androgen Receptor (LAR) Subtype Breast Cancers Are Not Histologically Defined by Apocrine Morphology.\n \n \n \n\n\n \n Moyer, A. M; Wu, X.; Visscher, D. W; Kalari, K. R; Thompson, K. J; Tang, X.; Suman, V. J; Dockter, T. J; McLaughlin, S. A; Moreno-Aspitia, A.; and others\n\n\n \n\n\n\n In LABORATORY INVESTIGATION, volume 96, pages 59A–59A, 2016. NATURE PUBLISHING GROUP 75 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USA\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@inproceedings{moyer2016luminal,\n  title={Luminal Androgen Receptor (LAR) Subtype Breast Cancers Are Not Histologically Defined by Apocrine Morphology},\n  author={Moyer, Ann M and Wu, Xuemei and Visscher, Daniel W and Kalari, Krishna R and Thompson, Kevin J and Tang, Xiaojia and Suman, Vera J and Dockter, Travis J and McLaughlin, Sarah A and Moreno-Aspitia, Alvaro and others},\n  booktitle={LABORATORY INVESTIGATION},\n  volume={96},\n  pages={59A--59A},\n  year={2016},\n  organization={NATURE PUBLISHING GROUP 75 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USA}\n}\n\n
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\n \n\n \n \n \n \n \n Distinct microbiome populations within breast cancer microenvironments.\n \n \n \n\n\n \n Thompson, K. J; Sinnwell, J.; Tang, X.; Ingle, J. N; Goetz, M. P; and Kalari, K. R\n\n\n \n\n\n\n Cancer Research, 76(14_Supplement): 3298–3298. 2016.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{thompson2016distinct,\n  title={Distinct microbiome populations within breast cancer microenvironments},\n  author={Thompson, Kevin J and Sinnwell, Jason and Tang, Xiaojia and Ingle, James N and Goetz, Matthew P and Kalari, Krishna R},\n  journal={Cancer Research},\n  volume={76},\n  number={14\\_Supplement},\n  pages={3298--3298},\n  year={2016},\n  publisher={The American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n Circular RNAs and their associations with breast cancer subtypes.\n \n \n \n\n\n \n Nair, A. A; Niu, N.; Tang, X.; Thompson, K. J; Wang, L.; Kocher, J.; Subramanian, S.; and Kalari, K. R\n\n\n \n\n\n\n Oncotarget, 7(49): 80967. 2016.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{nair2016circular,\n  title={Circular RNAs and their associations with breast cancer subtypes},\n  author={Nair, Asha A and Niu, Nifang and Tang, Xiaojia and Thompson, Kevin J and Wang, Liewei and Kocher, Jean-Pierre and Subramanian, Subbaya and Kalari, Krishna R},\n  journal={Oncotarget},\n  volume={7},\n  number={49},\n  pages={80967},\n  year={2016},\n  publisher={Impact Journals, LLC}\n}\n\n
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\n \n\n \n \n \n \n \n Abstract P3-07-29: Role of germline BRCA status and tumor homologous recombination (HR) deficiency in response to neoadjuvant weekly paclitaxel followed by anthracycline-based chemotherapy.\n \n \n \n\n\n \n Boughey, J.; Kalari, K.; Suman, V.; McLaughlin, S.; Moreno Aspitia, A; Moyer, A.; Northfelt, D.; Gray, R.; Vedell, P.; Tang, X; and others\n\n\n \n\n\n\n Cancer Research, 76(4_Supplement): P3–07. 2016.\n \n\n\n\n
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@article{boughey2016abstract,\n  title={Abstract P3-07-29: Role of germline BRCA status and tumor homologous recombination (HR) deficiency in response to neoadjuvant weekly paclitaxel followed by anthracycline-based chemotherapy},\n  author={Boughey, JC and Kalari, KR and Suman, VJ and McLaughlin, SA and Moreno Aspitia, A and Moyer, AM and Northfelt, DW and Gray, RJ and Vedell, PT and Tang, X and others},\n  journal={Cancer Research},\n  volume={76},\n  number={4\\_Supplement},\n  pages={P3--07},\n  year={2016},\n  publisher={The American Association for Cancer Research}\n}\n\n
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\n  \n 2015\n \n \n (3)\n \n \n
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\n \n\n \n \n \n \n \n RNA toxicity and missplicing in the common eye disease fuchs endothelial corneal dystrophy.\n \n \n \n\n\n \n Du, J.; Aleff, R. A; Soragni, E.; Kalari, K.; Nie, J.; Tang, X.; Davila, J.; Kocher, J.; Patel, S. V; Gottesfeld, J. M; and others\n\n\n \n\n\n\n Journal of Biological Chemistry, 290(10): 5979–5990. 2015.\n \n\n\n\n
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@article{du2015rna,\n  title={RNA toxicity and missplicing in the common eye disease fuchs endothelial corneal dystrophy},\n  author={Du, Jintang and Aleff, Ross A and Soragni, Elisabetta and Kalari, Krishna and Nie, Jinfu and Tang, Xiaojia and Davila, Jaime and Kocher, Jean-Pierre and Patel, Sanjay V and Gottesfeld, Joel M and others},\n  journal={Journal of Biological Chemistry},\n  volume={290},\n  number={10},\n  pages={5979--5990},\n  year={2015},\n  publisher={Elsevier}\n}\n\n
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\n \n\n \n \n \n \n \n Abstract PD3-3: Impact of neoadjuvant chemotherapy on the clonal composition of breast cancer.\n \n \n \n\n\n \n Goetz, M. P; Barrett, M. T; Kalari, K. R; Suman, V. J; McLaughlin, S. A; Moreno-Aspitia, A.; Moyer, A. M; Northfelt, D. W; Gray, R. J; Sinnwell, J.; and others\n\n\n \n\n\n\n Cancer Research, 75(9_Supplement): PD3–3. 2015.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{goetz2015abstract,\n  title={Abstract PD3-3: Impact of neoadjuvant chemotherapy on the clonal composition of breast cancer},\n  author={Goetz, Matthew P and Barrett, Michael T and Kalari, Krishna R and Suman, Vera J and McLaughlin, Sarah A and Moreno-Aspitia, Alvaro and Moyer, Ann M and Northfelt, Donald W and Gray, Richard J and Sinnwell, Jason and others},\n  journal={Cancer Research},\n  volume={75},\n  number={9\\_Supplement},\n  pages={PD3--3},\n  year={2015},\n  publisher={The American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n Exome sequencing reveals frequent deleterious germline variants in cancer susceptibility genes in women with invasive breast cancer undergoing neoadjuvant chemotherapy.\n \n \n \n\n\n \n Ellingson, M. S; Hart, S. N; Kalari, K. R; Suman, V.; Schahl, K. A; Dockter, T. J; Felten, S. J; Sinnwell, J. P; Thompson, K. J; Tang, X.; and others\n\n\n \n\n\n\n Breast cancer research and treatment, 153: 435–443. 2015.\n \n\n\n\n
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@article{ellingson2015exome,\n  title={Exome sequencing reveals frequent deleterious germline variants in cancer susceptibility genes in women with invasive breast cancer undergoing neoadjuvant chemotherapy},\n  author={Ellingson, Marissa S and Hart, Steven N and Kalari, Krishna R and Suman, Vera and Schahl, Kimberly A and Dockter, Travis J and Felten, Sara J and Sinnwell, Jason P and Thompson, Kevin J and Tang, Xiaojia and others},\n  journal={Breast cancer research and treatment},\n  volume={153},\n  pages={435--443},\n  year={2015},\n  publisher={Springer US}\n}\n\n
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\n  \n 2014\n \n \n (8)\n \n \n
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\n \n\n \n \n \n \n \n Transcriptome-wide analysis of UTRs in non-small cell lung cancer reveals cancer-related genes with SNV-induced changes on RNA secondary structure and miRNA target sites.\n \n \n \n\n\n \n Sabarinathan, R.; Wenzel, A.; Novotny, P.; Tang, X.; Kalari, K. R; and Gorodkin, J.\n\n\n \n\n\n\n PloS one, 9(1): e82699. 2014.\n \n\n\n\n
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@article{sabarinathan2014transcriptome,\n  title={Transcriptome-wide analysis of UTRs in non-small cell lung cancer reveals cancer-related genes with SNV-induced changes on RNA secondary structure and miRNA target sites},\n  author={Sabarinathan, Radhakrishnan and Wenzel, Anne and Novotny, Peter and Tang, Xiaojia and Kalari, Krishna R and Gorodkin, Jan},\n  journal={PloS one},\n  volume={9},\n  number={1},\n  pages={e82699},\n  year={2014},\n  publisher={Public Library of Science}\n}\n\n
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\n \n\n \n \n \n \n \n MAP-RSeq: Mayo analysis pipeline for RNA sequencing.\n \n \n \n\n\n \n Kalari, K. R; Nair, A. A; Bhavsar, J. D; O’Brien, D. R; Davila, J. I; Bockol, M. A; Nie, J.; Tang, X.; Baheti, S.; Doughty, J. B; and others\n\n\n \n\n\n\n BMC bioinformatics, 15: 1–11. 2014.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{kalari2014map,\n  title={MAP-RSeq: Mayo analysis pipeline for RNA sequencing},\n  author={Kalari, Krishna R and Nair, Asha A and Bhavsar, Jaysheel D and O’Brien, Daniel R and Davila, Jaime I and Bockol, Matthew A and Nie, Jinfu and Tang, Xiaojia and Baheti, Saurabh and Doughty, Jay B and others},\n  journal={BMC bioinformatics},\n  volume={15},\n  pages={1--11},\n  year={2014},\n  publisher={BioMed Central}\n}\n\n
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\n \n\n \n \n \n \n \n The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data.\n \n \n \n\n\n \n Tang, X.; Baheti, S.; Shameer, K.; Thompson, K. J; Wills, Q.; Niu, N.; Holcomb, I. N; Boutet, S. C; Ramakrishnan, R.; Kachergus, J. M; and others\n\n\n \n\n\n\n Nucleic acids research, 42(22): e172–e172. 2014.\n \n\n\n\n
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@article{tang2014esnv,\n  title={The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data},\n  author={Tang, Xiaojia and Baheti, Saurabh and Shameer, Khader and Thompson, Kevin J and Wills, Quin and Niu, Nifang and Holcomb, Ilona N and Boutet, Stephane C and Ramakrishnan, Ramesh and Kachergus, Jennifer M and others},\n  journal={Nucleic acids research},\n  volume={42},\n  number={22},\n  pages={e172--e172},\n  year={2014},\n  publisher={Oxford University Press}\n}\n\n
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\n \n\n \n \n \n \n \n Feasibility of using percutaneous tumor biopsies from a prospective neoadjuvant breast cancer study to develop patient derived xenografts and assess in vivo chemotherapy sensitivity.\n \n \n \n\n\n \n Yu, J.; Yin, P.; Gao, B.; Sinnwell, J. P; Moyer, A. M; Visscher, D. W; Conners, A. L; Dockter, T. J; Kalari, K. R; Tang, X.; and others\n\n\n \n\n\n\n Cancer Research, 74(19_Supplement): 1195–1195. 2014.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{yu2014feasibility,\n  title={Feasibility of using percutaneous tumor biopsies from a prospective neoadjuvant breast cancer study to develop patient derived xenografts and assess in vivo chemotherapy sensitivity},\n  author={Yu, Jia and Yin, Ping and Gao, Bowen and Sinnwell, Jason P and Moyer, Ann M and Visscher, Daniel W and Conners, Amy L and Dockter, Travis J and Kalari, Krishna R and Tang, Xiaojia and others},\n  journal={Cancer Research},\n  volume={74},\n  number={19\\_Supplement},\n  pages={1195--1195},\n  year={2014},\n  publisher={The American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n Transcriptome-Wide Association of MKI67 Expression: Pre-and Post-Neoadjuvant Paclitaxel.\n \n \n \n\n\n \n Moyer, A.; Kalari, K.; Thompson, K.; Visscher, D.; Suman, V.; Eckel-Passow, J; Sicotte, H; Hart, S.; Sinnwell, J.; Dockter, T.; and others\n\n\n \n\n\n\n In MODERN PATHOLOGY, volume 27, pages 69A–69A, 2014. NATURE PUBLISHING GROUP 75 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USA\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@inproceedings{moyer2014transcriptome,\n  title={Transcriptome-Wide Association of MKI67 Expression: Pre-and Post-Neoadjuvant Paclitaxel},\n  author={Moyer, AM and Kalari, KR and Thompson, KJ and Visscher, DW and Suman, VJ and Eckel-Passow, J and Sicotte, H and Hart, SN and Sinnwell, JP and Dockter, TJ and others},\n  booktitle={MODERN PATHOLOGY},\n  volume={27},\n  pages={69A--69A},\n  year={2014},\n  organization={NATURE PUBLISHING GROUP 75 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USA}\n}\n\n
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\n \n\n \n \n \n \n \n Molecular classification of triple negative breast cancer via RNA-sequencing data.\n \n \n \n\n\n \n Thompson, K. J; Tang, X.; Sun, Z.; Sinnwell, J. P; Sicotte, H.; Mahoney, D. W; Hart, S.; Vedell, P. T; Barman, P.; Passow, J. E E.; and others\n\n\n \n\n\n\n Cancer Research, 74(19_Supplement): 5592–5592. 2014.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{thompson2014molecular,\n  title={Molecular classification of triple negative breast cancer via RNA-sequencing data},\n  author={Thompson, Kevin J and Tang, Xiaojia and Sun, Zhifu and Sinnwell, Jason P and Sicotte, Hugues and Mahoney, Douglas W and Hart, Steven and Vedell, Peter T and Barman, Poulami and Passow, Jeanette E Eckel and others},\n  journal={Cancer Research},\n  volume={74},\n  number={19\\_Supplement},\n  pages={5592--5592},\n  year={2014},\n  publisher={The American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n Analysis of sequencing data to identify potential drug targets for an individual newly diagnosed with basal breast cancer who failed to respond to current standard neoadjuvant chemotherapy.\n \n \n \n\n\n \n Kalari, K. R; Tang, X.; Thompson, K. J; Mahoney, D. W; Barman, P.; Sinnwell, J. P; Sicotte, H.; Vedell, P.; Hart, S. N; Dockter, T. J; and others\n\n\n \n\n\n\n Cancer Research, 74(19_Supplement): 4185–4185. 2014.\n \n\n\n\n
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@article{kalari2014analysis,\n  title={Analysis of sequencing data to identify potential drug targets for an individual newly diagnosed with basal breast cancer who failed to respond to current standard neoadjuvant chemotherapy},\n  author={Kalari, Krishna R and Tang, Xiaojia and Thompson, Kevin J and Mahoney, Douglas W and Barman, Poulami and Sinnwell, Jason P and Sicotte, Hugues and Vedell, Peter and Hart, Steven N and Dockter, Travis J and others},\n  journal={Cancer Research},\n  volume={74},\n  number={19\\_Supplement},\n  pages={4185--4185},\n  year={2014},\n  publisher={The American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing.\n \n \n \n\n\n \n Kocher, J. A; Asmann, Y. W; Thompson, A. E; Sicotte, H.; Middha, S.; Doughty, J. B; Baheti, S.; Tang, X.; Nie, J.; Bockol, M. A; and others\n\n\n \n\n\n\n . 2014.\n \n\n\n\n
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@article{kocher2014map,\n  title={MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing},\n  author={Kocher, Jean-Pierre A and Asmann, Yan W and Thompson, Aubrey E and Sicotte, Hugues and Middha, Sumit and Doughty, Jay B and Baheti, Saurabh and Tang, Xiaojia and Nie, Jinfu and Bockol, Matthew A and others},\n  year={2014}\n}\n\n
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\n  \n 2013\n \n \n (4)\n \n \n
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\n \n\n \n \n \n \n \n An integrated model of the transcriptome of HER2-positive breast cancer.\n \n \n \n\n\n \n Kalari, K. R; Necela, B. M; Tang, X.; Thompson, K. J; Lau, M.; Eckel-Passow, J. E; Kachergus, J. M; Anderson, S K.; Sun, Z.; Baheti, S.; and others\n\n\n \n\n\n\n PloS one, 8(11): e79298. 2013.\n \n\n\n\n
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@article{kalari2013integrated,\n  title={An integrated model of the transcriptome of HER2-positive breast cancer},\n  author={Kalari, Krishna R and Necela, Brian M and Tang, Xiaojia and Thompson, Kevin J and Lau, Melissa and Eckel-Passow, Jeanette E and Kachergus, Jennifer M and Anderson, S Keith and Sun, Zhifu and Baheti, Saurabh and others},\n  journal={PloS one},\n  volume={8},\n  number={11},\n  pages={e79298},\n  year={2013},\n  publisher={Public Library of Science}\n}\n\n
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\n \n\n \n \n \n \n \n Abstract P1-08-10: Integration of next generation sequencing (NGS) and patient derived xenografts (PDX) to identify novel markers of paclitaxel (T) response in the breast cancer genome guided therapy study (BEAUTY).\n \n \n \n\n\n \n Goetz, M.; Boughey, J.; Kalari, K.; Eckel-Passow, J; Suman, V.; Sicotte, H; Hart, S.; Moyer, A.; Visscher, D.; Yu, J; and others\n\n\n \n\n\n\n Cancer Research, 73(24_Supplement): P1–08. 2013.\n \n\n\n\n
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@article{goetz2013abstract,\n  title={Abstract P1-08-10: Integration of next generation sequencing (NGS) and patient derived xenografts (PDX) to identify novel markers of paclitaxel (T) response in the breast cancer genome guided therapy study (BEAUTY)},\n  author={Goetz, MP and Boughey, JC and Kalari, KR and Eckel-Passow, J and Suman, VJ and Sicotte, H and Hart, SN and Moyer, AM and Visscher, DW and Yu, J and others},\n  journal={Cancer Research},\n  volume={73},\n  number={24\\_Supplement},\n  pages={P1--08},\n  year={2013},\n  publisher={The American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n The eSNV-Detect: a computational system to identify expressed single nucleotide variants from tumor transcriptomes.\n \n \n \n\n\n \n Tang, X.; Baheti, S.; Shameer, K.; Thompson, K. J; Kocher, J.; Perez, E. A; Thompson, A. E; and Kalari, K. R\n\n\n \n\n\n\n Cancer Research, 73(8_Supplement): 3185–3185. 2013.\n \n\n\n\n
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@article{tang2013esnv,\n  title={The eSNV-Detect: a computational system to identify expressed single nucleotide variants from tumor transcriptomes.},\n  author={Tang, Xiaojia and Baheti, Saurabh and Shameer, Khader and Thompson, Kevin J and Kocher, Jean-Pierre and Perez, Edith A and Thompson, Aubrey E and Kalari, Krishna R},\n  journal={Cancer Research},\n  volume={73},\n  number={8\\_Supplement},\n  pages={3185--3185},\n  year={2013},\n  publisher={American Association for Cancer Research}\n}\n\n
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\n \n\n \n \n \n \n \n Integration of next generation sequencing (NGS) and patient derived xenografts (PDX) to identify novel markers of paclitaxel (T) response in the breast cancer genome guided therapy study (BEAUTY).\n \n \n \n\n\n \n Goetz, M.; Boughey, J.; Katari, K.; Eckel-Passow, J; Suman, V.; Sicotte, H; Hart, S.; Moyer, A.; Visscher, D.; Yu, J; and others\n\n\n \n\n\n\n In CANCER RESEARCH, volume 73, 2013. AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA …\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@inproceedings{goetz2013integration,\n  title={Integration of next generation sequencing (NGS) and patient derived xenografts (PDX) to identify novel markers of paclitaxel (T) response in the breast cancer genome guided therapy study (BEAUTY)},\n  author={Goetz, MP and Boughey, JC and Katari, KR and Eckel-Passow, J and Suman, VJ and Sicotte, H and Hart, SN and Moyer, AM and Visscher, DW and Yu, J and others},\n  booktitle={CANCER RESEARCH},\n  volume={73},\n  year={2013},\n  organization={AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA~…}\n}\n\n
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\n  \n 2012\n \n \n (4)\n \n \n
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\n \n\n \n \n \n \n \n Deep sequence analysis of non-small cell lung cancer: integrated analysis of gene expression, alternative splicing, and single nucleotide variations in lung adenocarcinomas with and without oncogenic KRAS mutations.\n \n \n \n\n\n \n Kalari, K. R; Rossell, D.; Necela, B. M; Asmann, Y. W; Nair, A.; Baheti, S.; Kachergus, J. M; Younkin, C. S; Baker, T.; Carr, J. M; and others\n\n\n \n\n\n\n Frontiers in oncology, 2: 12. 2012.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{kalari2012deep,\n  title={Deep sequence analysis of non-small cell lung cancer: integrated analysis of gene expression, alternative splicing, and single nucleotide variations in lung adenocarcinomas with and without oncogenic KRAS mutations},\n  author={Kalari, Krishna R and Rossell, David and Necela, Brian M and Asmann, Yan W and Nair, Asha and Baheti, Saurabh and Kachergus, Jennifer M and Younkin, Curtis S and Baker, Tiffany and Carr, Jennifer M and others},\n  journal={Frontiers in oncology},\n  volume={2},\n  pages={12},\n  year={2012},\n  publisher={Frontiers Research Foundation}\n}\n\n
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\n \n\n \n \n \n \n \n Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis.\n \n \n \n\n\n \n Wang, S.; Yin, Y.; Ma, Q.; Tang, X.; Hao, D.; and Xu, Y.\n\n\n \n\n\n\n BMC plant biology, 12: 1–12. 2012.\n \n\n\n\n
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@article{wang2012genome,\n  title={Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis},\n  author={Wang, Shan and Yin, Yanbin and Ma, Qin and Tang, Xiaojia and Hao, Dongyun and Xu, Ying},\n  journal={BMC plant biology},\n  volume={12},\n  pages={1--12},\n  year={2012},\n  publisher={BioMed Central}\n}\n\n
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\n \n\n \n \n \n \n \n Transcriptome analysis of garlic-induced hepatoprotection against alcoholic fatty liver.\n \n \n \n\n\n \n Raghu, R.; Liu, C.; Tsai, M.; Tang, X.; Kalari, K. R; Subramanian, S.; and Sheen, L.\n\n\n \n\n\n\n Journal of agricultural and food chemistry, 60(44): 11104–11119. 2012.\n \n\n\n\n
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@article{raghu2012transcriptome,\n  title={Transcriptome analysis of garlic-induced hepatoprotection against alcoholic fatty liver},\n  author={Raghu, Rajasekaran and Liu, Chun-Ting and Tsai, Mong-Hsun and Tang, Xiaojia and Kalari, Krishna R and Subramanian, Subbaya and Sheen, Lee-Yan},\n  journal={Journal of agricultural and food chemistry},\n  volume={60},\n  number={44},\n  pages={11104--11119},\n  year={2012},\n  publisher={American Chemical Society}\n}\n\n
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\n \n\n \n \n \n \n \n Modeling the transcriptome landscape of HER2+ breast cancer.\n \n \n \n\n\n \n Kalari, K. R; Chai, H.; Asmann, Y. W; Tang, X.; Rossell, D.; Baheti, S.; Nair, A.; Baker, T. R; Necela, B. M; Carr, J. M; and others\n\n\n \n\n\n\n Cancer Research, 72(8_Supplement): 4926–4926. 2012.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{kalari2012modeling,\n  title={Modeling the transcriptome landscape of HER2+ breast cancer},\n  author={Kalari, Krishna R and Chai, High-Seng and Asmann, Yan W and Tang, Xiaojia and Rossell, David and Baheti, Saurabh and Nair, Asha and Baker, Tiffany R and Necela, Brian M and Carr, Jennifer M and others},\n  journal={Cancer Research},\n  volume={72},\n  number={8\\_Supplement},\n  pages={4926--4926},\n  year={2012},\n  publisher={American Association for Cancer Research}\n}\n\n
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\n  \n 2011\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n Systems biology of the qa gene cluster in Neurospora crassa.\n \n \n \n\n\n \n Tang, X.; Dong, W.; Griffith, J.; Nilsen, R.; Matthes, A.; Cheng, K. B; Reeves, J.; Schuttler, H.; Case, M. E; Arnold, J.; and others\n\n\n \n\n\n\n PloS one, 6(6): e20671. 2011.\n \n\n\n\n
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@article{tang2011systems,\n  title={Systems biology of the qa gene cluster in Neurospora crassa},\n  author={Tang, Xiaojia and Dong, Wubei and Griffith, James and Nilsen, Roger and Matthes, Allison and Cheng, Kevin B and Reeves, Jaxk and Schuttler, H-Bernd and Case, Mary E and Arnold, Jonathan and others},\n  journal={PloS one},\n  volume={6},\n  number={6},\n  pages={e20671},\n  year={2011},\n  publisher={Public Library of Science}\n}\n\n
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\n  \n 2010\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n Statistical identification of the quinic acid responsive genes in Neurospora crassa.\n \n \n \n\n\n \n Tang, X.\n\n\n \n\n\n\n Ph.D. Thesis, uga, 2010.\n \n\n\n\n
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@phdthesis{tang2010statistical,\n  title={Statistical identification of the quinic acid responsive genes in Neurospora crassa},\n  author={Tang, Xiaojia},\n  year={2010},\n  school={uga}\n}\n\n
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\n  \n 2009\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n Computational systems biology for the biological clock of Neurospora crassa.\n \n \n \n\n\n \n Tang, X.\n\n\n \n\n\n\n Ph.D. Thesis, University of Georgia, 2009.\n \n\n\n\n
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@phdthesis{tang2009computational,\n  title={Computational systems biology for the biological clock of Neurospora crassa},\n  author={Tang, Xiaojia},\n  year={2009},\n  school={University of Georgia}\n}\n\n
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\n  \n 2008\n \n \n (3)\n \n \n
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\n \n\n \n \n \n \n \n Systems biology of the clock in Neurospora crassa.\n \n \n \n\n\n \n Dong, W.; Tang, X.; Yu, Y.; Nilsen, R.; Kim, R.; Griffith, J.; Arnold, J.; and Schüttler, H.\n\n\n \n\n\n\n PloS one, 3(8): e3105. 2008.\n \n\n\n\n
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@article{dong2008systems,\n  title={Systems biology of the clock in Neurospora crassa},\n  author={Dong, Wubei and Tang, Xiaojia and Yu, Yihai and Nilsen, Roger and Kim, Rosemary and Griffith, James and Arnold, Jonathan and Sch{\\"u}ttler, H-Bernd},\n  journal={PloS one},\n  volume={3},\n  number={8},\n  pages={e3105},\n  year={2008},\n  publisher={Public Library of Science}\n}\n\n
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\n \n\n \n \n \n \n \n Temperature compensation model for the circadian clock of Neurospora crassa.\n \n \n \n\n\n \n Tang, X.; Schüttler, H.; and Arnold, J.\n\n\n \n\n\n\n In APS March Meeting Abstracts, pages D16–013, 2008. \n \n\n\n\n
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@inproceedings{tang2008temperature,\n  title={Temperature compensation model for the circadian clock of Neurospora crassa},\n  author={Tang, Xiaojia and Sch{\\"u}ttler, Heinz-Bernd and Arnold, Jonathan},\n  booktitle={APS March Meeting Abstracts},\n  pages={D16--013},\n  year={2008}\n}\n\n
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\n \n\n \n \n \n \n \n Temperature compensation model for the circadian clock of$\\$textit $\\{$Neurospora crassa$\\}$.\n \n \n \n\n\n \n Tang, X.; Arnold, J.; and others\n\n\n \n\n\n\n Bulletin of the American Physical Society, 53. 2008.\n \n\n\n\n
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@article{tang2008temperature,\n  title={Temperature compensation model for the circadian clock of$\\backslash$textit $\\{$Neurospora crassa$\\}$},\n  author={Tang, Xiaojia and Arnold, Jonathan and others},\n  journal={Bulletin of the American Physical Society},\n  volume={53},\n  year={2008},\n  publisher={American Physical Society}\n}\n\n
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\n  \n 2007\n \n \n (2)\n \n \n
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\n \n\n \n \n \n \n \n A genetic network for the clock of Neurospora crassa.\n \n \n \n\n\n \n Yu, Y.; Dong, W.; Altimus, C.; Tang, X.; Griffith, J.; Morello, M.; Dudek, L.; Arnold, J.; and Schüttler, H.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences, 104(8): 2809–2814. 2007.\n \n\n\n\n
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@article{yu2007genetic,\n  title={A genetic network for the clock of Neurospora crassa},\n  author={Yu, Yihai and Dong, Wubei and Altimus, Cara and Tang, Xiaojia and Griffith, James and Morello, Melissa and Dudek, Lisa and Arnold, Jonathan and Sch{\\"u}ttler, Heinz-Bernd},\n  journal={Proceedings of the National Academy of Sciences},\n  volume={104},\n  number={8},\n  pages={2809--2814},\n  year={2007},\n  publisher={National Academy of Sciences}\n}\n\n
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\n \n\n \n \n \n \n \n Systems biology of the Neurospora biological clock.\n \n \n \n\n\n \n Dong, W; Tang, X; Yu, Y; Griffith, J; Nilsen, R; Choi, D; Baldwin, J; Hilton, L; Kelps, K; Mcguire, J; and others\n\n\n \n\n\n\n IET systems biology, 1(5): 257–265. 2007.\n \n\n\n\n
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@article{dong2007systems,\n  title={Systems biology of the Neurospora biological clock},\n  author={Dong, W and Tang, X and Yu, Y and Griffith, J and Nilsen, R and Choi, D and Baldwin, J and Hilton, L and Kelps, K and Mcguire, J and others},\n  journal={IET systems biology},\n  volume={1},\n  number={5},\n  pages={257--265},\n  year={2007},\n  publisher={IET}\n}\n\n
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\n  \n 2006\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n A genetic network for the clock of neurospora crassa, or what makes a biological clock tick.\n \n \n \n\n\n \n Yu, Y.; Dong, W.; Altimus, C.; Tang, X.; Griffith, J.; Morello, M.; Dudek, L.; Arnold, J.; and Schüttler, H.\n\n\n \n\n\n\n PNAS,1–6. 2006.\n \n\n\n\n
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@article{yu2006genetic,\n  title={A genetic network for the clock of neurospora crassa, or what makes a biological clock tick},\n  author={Yu, Yihai and Dong, Wubei and Altimus, Cara and Tang, Xiaojia and Griffith, James and Morello, Melissa and Dudek, Lisa and Arnold, Jonathan and Sch{\\"u}ttler, Heinz-Bernd},\n  journal={PNAS},\n  pages={1--6},\n  year={2006}\n}\n\n
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\n \n\n \n \n \n \n \n Inferring clinical phenotypes of expressed single nucleotide variants in cancer.\n \n \n \n\n\n \n Tang, X.; and Thompson, K. J\n\n\n \n\n\n\n . .\n \n\n\n\n
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@article{tanginferring,\n  title={Inferring clinical phenotypes of expressed single nucleotide variants in cancer},\n  author={Tang, Xiaojia and Thompson, Kevin J}\n}\n\n
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