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Journal Articles

Abstract 2444: A deep learning framework for the reconstruction of gene expression profiles derived from formalin-fixed paraffin-embedded samples

Lingli He, Kai Song, Ying Li, Celia Yujuan Dong, Cherry Y. Wong, Lin Qi, Xianrui Zhang, Yufeng Chen, Louis Vermeulen, Shentao Zhou, Simon Siu Ng, Xin Wang
Journal: Cancer Research
Cancer Res (2025) 85 (8_Supplement_1): 2444.
https://doi.org/10.1158/1538-7445.AM2025-2444
Published: 21 April 2025
View articletitled, Abstract 2444: A deep learning framework for the reconstruction of gene expression profiles derived from formalin-fixed paraffin-embedded samples
Journal Articles

Abstract 5106: Pharmacological targeting of LSD1 prolongs animal survival times in patient derived orthotopic xenograft models of posterior fossa ependymoma in combination with fractionated radiation

Milagros M. Suarez Palacios, Sibo Zhao, Huiyuan Zhang, Lin Qi, Holly Lindsay, Mari Kogiso, Frank Braun, Adekunle M. Adesina, Yuchen Du, Yongcheng Song, Xiao-Nan Li
Journal: Cancer Research
Cancer Res (2024) 84 (6_Supplement): 5106.
https://doi.org/10.1158/1538-7445.AM2024-5106
Published: 22 March 2024
View articletitled, Abstract 5106: Pharmacological targeting of LSD1 prolongs animal survival times in patient derived orthotopic xenograft models of posterior fossa ependymoma in combination with fractionated radiation
Journal Articles

Stimulated Raman Scattering Microscopy Enables Gleason Scoring of Prostate Core Needle Biopsy by a Convolutional Neural Network

Jianpeng Ao, Xiaoguang Shao, Zhijie Liu, Qiang Liu, Jun Xia, Yongheng Shi, Lin Qi, Jiahua Pan, Minbiao Ji
Journal: Cancer Research
Cancer Res (2023) 83 (4): 641–651.
https://doi.org/10.1158/0008-5472.CAN-22-2146
Published: 15 February 2023
View articletitled, Stimulated Raman Scattering Microscopy Enables Gleason Scoring of Prostate Core Needle Biopsy by a Convolutional Neural Network
Open the PDF for Stimulated Raman Scattering Microscopy Enables Gleason Scoring of Prostate Core Needle Biopsy by a Convolutional Neural Network in another window
Includes: Supplementary data
Journal Articles

Functional Precision Medicine Identifies New Therapeutic Candidates for Medulloblastoma

Jessica M. Rusert, Edwin F. Juarez, Sebastian Brabetz, James Jensen, Alexandra Garancher, Lianne Q. Chau, Silvia K. Tacheva-Grigorova, Sameerah Wahab, Yoko T. Udaka, Darren Finlay, Huriye Seker-Cin, Brendan Reardon, Susanne Gröbner, Jonathan Serrano, Jonas Ecker, Lin Qi, Mari Kogiso, Yuchen Du, Patricia A. Baxter, Jacob J. Henderson, Michael E. Berens, Kristiina Vuori, Till Milde, Yoon-Jae Cho, Xiao-Nan Li, James M. Olson, Iris Reyes, Matija Snuderl, Terence C. Wong, David P. Dimmock, Shareef A. Nahas, Denise Malicki, John R. Crawford, Michael L. Levy, Eliezer M. Van Allen, Stefan M. Pfister, Pablo Tamayo, Marcel Kool, Jill P. Mesirov, Robert J. Wechsler-Reya
Journal: Cancer Research
Cancer Res (2020) 80 (23): 5393–5407.
https://doi.org/10.1158/0008-5472.CAN-20-1655
Published: 02 December 2020
View articletitled, Functional Precision Medicine Identifies New Therapeutic Candidates for Medulloblastoma
Open the PDF for Functional Precision Medicine Identifies New Therapeutic Candidates for Medulloblastoma in another window
Includes: Supplementary data
Journal Articles

Abstract LB-320: PPTC testing of an OLIG2 inhibitor CT-179 in patient-derived orthotopic xenograft mouse models of pediatric GBM

Holly Lindsay, Yuchen Du, Lin Qi, Huiyuan Zhang, Sibo Zhao, Frank Braun, Mari Kogiso, Sarah Injac, Mary Sobieski, Clifford Stephan, Gordon Alton, Gregory Stein, Graham Beaton, Stephen Erickson, Beverly Teicher, Malcolm A. Smith, Xiao-Nan Li
Journal: Cancer Research
Cancer Res (2019) 79 (13_Supplement): LB-320.
https://doi.org/10.1158/1538-7445.AM2019-LB-320
Published: 01 July 2019
View articletitled, Abstract LB-320: PPTC testing of an OLIG2 inhibitor CT-179 in patient-derived orthotopic xenograft mouse models of pediatric GBM
Journal Articles

Abstract LB-041: Establishment and characterization of patient derived orthotopic xenograft mouse models representing a serial of primary and recurrent pediatric brain tumors

Yuchen Du, Mari Kogiso, Frank Braun, Lin Qi, Huiyuan Zhang, Holly Lindsay, Sibo Zhao, Sarah Injac, Marcel Cool, Clifford Stephan, Xiaonan Li
Journal: Cancer Research
Cancer Res (2018) 78 (13_Supplement): LB-041.
https://doi.org/10.1158/1538-7445.AM2018-LB-041
Published: 01 July 2018
View articletitled, Abstract LB-041: Establishment and characterization of patient derived orthotopic xenograft mouse models representing a serial of primary and recurrent pediatric brain tumors
Journal Articles

Abstract LB-069: Identification of personalized active agents in pediatric medulloblastoma through high-throughput drug screening in matching pairs of patient derived orthotopic xenograft neurosphere and monolayer cells

Lin Qi, Yuchen Du, Goeun Bae, Mari Mari, Frank Braun, Holly Lindsay, Huiyuan Zhang, Sibo Zhao, Sarah Injac, Patricia Baxter, Jack Su, Michael Mancini, Oliver Hampton, William Parsons, Mural Chintagumpala, Clifford Stephan, Peter Davies, Xiaonan Li
Journal: Cancer Research
Cancer Res (2018) 78 (13_Supplement): LB-069.
https://doi.org/10.1158/1538-7445.AM2018-LB-069
Published: 01 July 2018
View articletitled, Abstract LB-069: Identification of personalized active agents in pediatric medulloblastoma through high-throughput drug screening in matching pairs of patient derived orthotopic xenograft neurosphere and monolayer cells
Journal Articles

Abstract LB-167: Novel LSD-1 inhibitor validation in new established clinically PFA patient-derived orthotopic xenograft (PDOX) models of ependymoma

Huiyuan Zhang, Sibo Zhao, Yuchen Du, Lin Qi, Frank K. Braun, Mari Kogiso, Holly B. Lindsay, Sarah G. Injac, Laszlo Perlaky, Patricia Baxter, Jack M. Su, Xiao-Nan Li
Journal: Cancer Research
Cancer Res (2018) 78 (13_Supplement): LB-167.
https://doi.org/10.1158/1538-7445.AM2018-LB-167
Published: 01 July 2018
View articletitled, Abstract LB-167: Novel LSD-1 inhibitor validation in new established clinically PFA patient-derived orthotopic xenograft (PDOX) models of ependymoma
Journal Articles

Abstract 3841: A hybrid mapping approach improves genomic and transcriptomic analysis of patient derived orthotropic xenograft (PDOX) models of pediatric CNS tumors

Oliver A. Hampton, Michael C. Gundry, Mari Kogiso, Lin Qi, Yuchen Du, Yulun Huang, Frank K. Braun, Huiyuan Zhang, Sibo Zhao, Holly Lindsay, Sarah G. Injac, David A. Wheeler, Xiao-Nan Li, D. William Parsons
Journal: Cancer Research
Cancer Res (2017) 77 (13_Supplement): 3841.
https://doi.org/10.1158/1538-7445.AM2017-3841
Published: 01 July 2017
View articletitled, Abstract 3841: A hybrid mapping approach improves genomic and transcriptomic analysis of patient derived orthotropic xenograft (PDOX) models of pediatric CNS tumors
Journal Articles

Abstract 4214: Identification of personalized active agents in pediatric gliomas through high-throughput drug screening in matching pairs of patient derived orthotopic xenograft (PDOX) neurosphere and monolayer cells

Lin Qi, Yuchen Du, Mari Kogiso, Goeun Bae, Frank Braun, Holly Lindsay, Huiyuan Zhang, Sibo Zhao, Sarah Injac, Patricia Baxter, Jack Su, Michael Mancini, Oliver Hampton, William Parsons, Murali Chintagumpala, Clifford Stephan, Peter Davies, Xiao-Nan Li, Xiao-Nan Li
Journal: Cancer Research
Cancer Res (2017) 77 (13_Supplement): 4214.
https://doi.org/10.1158/1538-7445.AM2017-4214
Published: 01 July 2017
View articletitled, Abstract 4214: Identification of personalized active agents in pediatric gliomas through high-throughput drug screening in matching pairs of patient derived orthotopic xenograft (PDOX) neurosphere and monolayer cells
Journal Articles

Abstract 5058: Lysine specific demethylase-1 (LSD-1) Inhibitor SYC-836 in combination with radiation prolongs animal survival in patient-derived posterior fossa ependymoma xenograft mouse models

Sibo Zhao, Huiyuan Zhang, Lin Qi, Holly Lindsay, Yuchen Du, Mari Kogiso, Frank Braun, Sarah Injac, Laszlo Perlaky, Donald W. Parsons, Murali Chintagumpala, Adekunle Adesina, Yongcheng Song, Xiao-Nan Li
Journal: Cancer Research
Cancer Res (2017) 77 (13_Supplement): 5058.
https://doi.org/10.1158/1538-7445.AM2017-5058
Published: 01 July 2017
View articletitled, Abstract 5058: Lysine specific demethylase-1 (LSD-1) Inhibitor SYC-836 in combination with radiation prolongs animal survival in patient-derived posterior fossa ependymoma xenograft mouse models
Journal Articles

Abstract 4031: Mutant isocitrate dehydrogenase 1 (IDH1) inhibitor synergistically prolongs animal survival with standard therapies in patient-derived IDH1 mutant glioma xenograft mouse models

Mari Kogiso, Lin Qi, Huiyuan Zhang, Frank K. Braun, Yuchen Du, Yulun Huang, Holly Lindsay, Sibo Zhao, Sarah G. G. Injac, Zhen Liu, Patricia A. Baxter, Jack M. Su, Laszlo Perlaky, D. Williams Parsons, Murali Chintagumpala, Adekunle Adesina, Jialiang Wang, Yongcheng Song, Xiao-Nan Li
Journal: Cancer Research
Cancer Res (2017) 77 (13_Supplement): 4031.
https://doi.org/10.1158/1538-7445.AM2017-4031
Published: 01 July 2017
View articletitled, Abstract 4031: Mutant isocitrate dehydrogenase 1 (IDH1) inhibitor synergistically prolongs animal survival with standard therapies in patient-derived IDH1 mutant glioma xenograft mouse models
Journal Articles

Abstract 4812: A novel set of patient-derived orthotopic xenograft (PDOX) models of primary and recurrent intracranial meningioma

Huiyuan Zhang, Lin Qi, Yuchen Du, Frank K. Braun, Mari Kogiso, Sibo Zhao, Holly B. Lindsay, Sarah G. Injac, Patricia A. Baxter, Jack M. Su, Akash J. Patel, Xiao-nan Li, Baylor College of Medicine
Journal: Cancer Research
Cancer Res (2017) 77 (13_Supplement): 4812.
https://doi.org/10.1158/1538-7445.AM2017-4812
Published: 01 July 2017
View articletitled, Abstract 4812: A novel set of patient-derived orthotopic xenograft (PDOX) models of primary and recurrent intracranial meningioma
Journal Articles

Abstract 4874: Application of quantitative analysis of mouse cell contamination and purification of human tumor cells in patient derived orthotopic xenograft mouse models of pediatric brain tumors

Frank K. Braun, Mari Kogiso, Lin Qi, Huiyuan Zhang, Yuchen Du, Holly B. Lindsay, Sibo Zhao, Sarah G. Injac, Xiao-Nan Li
Journal: Cancer Research
Cancer Res (2017) 77 (13_Supplement): 4874.
https://doi.org/10.1158/1538-7445.AM2017-4874
Published: 01 July 2017
View articletitled, Abstract 4874: Application of quantitative analysis of mouse cell contamination and purification of human tumor cells in patient derived orthotopic xenograft mouse models of pediatric brain tumors
Journal Articles

Abstract 2821: Impact of SCID mouse gender on tumorigenicity, xenograft growth and drug-responses in patient derived orthotopic xenograft models (PDOX) of malignant brain tumors

Lin Qi, Mari Kogiso, Yuchen Du, Huiyuan Zhang, Frank Braun, Holly Lindsay, Sibo Zhao, Sarah Injac, Patricia Baxter, Zhigang Liu, Yujing Zhang, Jack Su, Adekunle Adesina, Andrew Walter, Jeffery Murray, Javad Nazarian, Will Parsons, Murali Chintagumpala, Xiao-nan Li
Journal: Cancer Research
Cancer Res (2017) 77 (13_Supplement): 2821.
https://doi.org/10.1158/1538-7445.AM2017-2821
Published: 01 July 2017
View articletitled, Abstract 2821: Impact of SCID mouse gender on tumorigenicity, xenograft growth and drug-responses in patient derived orthotopic xenograft models (PDOX) of malignant brain tumors
Journal Articles

Abstract 4390: SVV-001 prolongs animal survival in PDOX adult GBM models

Huiyuan Zhang, Lin Qi, Yuchen Du, Mari Kogiso, Frank K. Braun, Sibo Zhao, Holly Lindsay, Nabil Ahmed, Akash J. Patel, Patricia A. Baxter, Jack M. Su, Xiao-nan Li
Journal: Cancer Research
Cancer Res (2016) 76 (14_Supplement): 4390.
https://doi.org/10.1158/1538-7445.AM2016-4390
Published: 15 July 2016
View articletitled, Abstract 4390: SVV-001 prolongs animal survival in PDOX adult GBM models
Journal Articles

Abstract 2455: Development of patient-derived orthotopic xenograft mouse models of pediatric low grade gliomas

Mari Kogiso, Lin Qi, Frank K. Braun, Xiumei Zhao, Zhigang Liu, Holly B. Lindsay, Yuchen Du, Huiyuan Zhang, Sibo Zhao, Ching-Hua Liu, Vidya P. Mehta, Xiaoyun Shen, Jeffrey Murray, Laszlo Perlaky, Jack Su, Patricia Baxter, Adekunle Adesina, Donald W. Parsons, Xinyan Lu, Murali Chintagumpala, Xiao-Nan Li
Journal: Cancer Research
Cancer Res (2016) 76 (14_Supplement): 2455.
https://doi.org/10.1158/1538-7445.AM2016-2455
Published: 15 July 2016
View articletitled, Abstract 2455: Development of patient-derived orthotopic xenograft mouse models of pediatric low grade gliomas
Journal Articles

Abstract 1950: Whole genome microRNA profiling in functionally validated invasive GBM cells identifies a novel set of microRNAs driving GBM invasion

Lin Qi, Yu-lun Huang, Hua Mao, Mari Kogiso, Xiumei Zhao, Yuchen Du, Holly Lindsay, Xiaojun Yuan, Patricia Baxter, Jack Su, Chris Man, Laszlo Perlaky, Zhong Wang, You-Xing Zhou, Xiao-Nan Li
Journal: Cancer Research
Cancer Res (2016) 76 (14_Supplement): 1950.
https://doi.org/10.1158/1538-7445.AM2016-1950
Published: 15 July 2016
View articletitled, Abstract 1950: Whole genome microRNA profiling in functionally validated invasive GBM cells identifies a novel set of microRNAs driving GBM invasion
Journal Articles

Abstract 1450: Autopsy derived orthotopic xenograft (ADOX) mouse models for terminal pediatric brain tumors

Lin Qi, Baxter A. Patricia, Kogiso Mari, Du Yuchen, Lindsay Holly, Liu Zhigang, Xiumei Zhao, Yujing Zhang, Jack MF Su, Adekunle Adesina, Andrew W. Walter, Jeffery Murray, Rene McNall-Knapp, Javad Nazarian, Will Parsons, Murali Chintagumpala, Susan Blaney, Xiao-Nan Li
Journal: Cancer Research
Cancer Res (2015) 75 (15_Supplement): 1450.
https://doi.org/10.1158/1538-7445.AM2015-1450
Published: 01 August 2015
View articletitled, Abstract 1450: Autopsy derived orthotopic xenograft (ADOX) mouse models for terminal pediatric brain tumors
Journal Articles

Abstract 3292: Therapeutic targeting of INI1 deficiency in pediatric ATRT: a preclinical study utilizing patient-derived orthotopic xenograft (PDOX) models

Holly B. Lindsay, Mari Kogiso, Lin Qi, Jeffrey C. Murray, Laszlo Perlaky, Jack MF Su, Patricia Baxter, Adekunle Adesina, Donald W. Parsons, Murali Chintagumpala, Xiao-Nan Li
Journal: Cancer Research
Cancer Res (2015) 75 (15_Supplement): 3292.
https://doi.org/10.1158/1538-7445.AM2015-3292
Published: 01 August 2015
View articletitled, Abstract 3292: Therapeutic targeting of INI1 deficiency in pediatric ATRT: a preclinical study utilizing patient-derived orthotopic xenograft (PDOX) models