Publications
Below, you’ll find a selection of our recent publications that highlight our contributions to pediatric oncology research and precision medicine. These papers showcase our commitment to advancing knowledge, developing innovative tools, and collaborating with the broader scientific community. Dive in to explore the insights we’ve gained and the impact we’re making!
Publications by Year
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2025
Germline analysis of an international cohort of pediatric diffuse midline glioma patients.
Marion K Mateos, Pamela Ajuyah, Noemi Fuentes-Bolanos, Sam El-Kamand, Paulette Barahona, …, Sebastien Perreault, Chris Jones, Marie Wong-Erasmus, Mark J Cowley, David S Ziegler
Neuro-oncology
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12 Mar 2025
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pubmed:40072012
Germline pathogenic DROSHA variants are linked to pineoblastoma and Wilms tumor predisposition.
Peter N Fiorica, Lisa Golmard, Jung Kim, Riyue Bao, Frank Y Lin, …, Douglas R Stewart, D Williams Parsons, Sharon E Plon, Kris Ann P Schultz, Kenan Onel
Clinical cancer research : an official journal of the American Association for Cancer Research
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24 Feb 2025
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pubmed:39992227
Imaging Clusters of Pediatric Low-Grade Glioma are Associated with Distinct Molecular Characteristics.
Anahita Fathi Kazerooni, Adam Kraya, Komal S Rathi, Meen Chul Kim, Varun Kesherwani, …, Sabine Mueller, Jo Lynne Rokita, Michael J Fisher, Adam C Resnick, Ali Nabavizadeh
AJNR. American journal of neuroradiology
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14 Feb 2025
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pubmed:39952665
Germline pathogenic variation impacts somatic alterations and patient outcomes in pediatric CNS tumors.
Ryan J Corbett, Rebecca S Kaufman, Shelly W McQuaid, Zalman Vaksman, Saksham Phul, …, Angela J Waanders, Miriam Bornhorst, Suzanne P MacFarland, Jo Lynne Rokita, Sharon J Diskin
medRxiv : the preprint server for health sciences
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06 Feb 2025
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pubmed:39974082
Kinome reprogramming of G2/M kinases and repression of MYCN contribute to superior efficacy of lorlatinib in ALK-driven neuroblastoma.
Smita Matkar, Michael P East, Timothy J Stuhlmiller, Gabriela Witek, Alvin Farrel, …, Jo Lynne Rokita, Mark Gerelus, John M Maris, Gary L Johnson, Yael P Mossé
Molecular cancer therapeutics
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05 Feb 2025
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pubmed:39907037
Genetic ancestry superpopulations show distinct prevalence and outcomes across pediatric central nervous system tumors from the PBTA and PNOC.
Ryan J Corbett, Cricket C Gullickson, Zhuangzhuang Geng, Miguel A Brown, Bo Zhang, …, Angela J Waanders, Sebastian M Waszak, Sabine Mueller, Jo Lynne Rokita, Cassie Kline
Neuro-oncology
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23 Jan 2025
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pubmed:39847453
Neuronal cell adhesion molecule (NRCAM) variant defined by microexon skipping is an essential, antigenically distinct, and targetable proteoform in high-grade glioma.
Priyanka Sehgal, Ammar S Naqvi, Makenna Higgins, Jiageng Liu, Kyra Harvey, …, Adam C Resnick, Hagen U Tilgner, Thomas DeRaedt, Daniel J Powell, Andrei Thomas-Tikhonenko
bioRxiv : the preprint server for biology
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19 Jan 2025
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pubmed:39868324
2024
A proteogenomic surfaceome study identifies DLK1 as an immunotherapeutic target in neuroblastoma.
Amber K Hamilton, Alexander B Radaoui, Matthew Tsang, Daniel Martinez, Karina L Conkrite, …, Patrick H van Berkel, Malcolm A Smith, Benjamin A Garcia, John M Maris, Sharon J Diskin
Cancer cell
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24 Oct 2024
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pubmed:39454577
The Open Pediatric Cancer Project.
Zhuangzhuang Geng, Eric Wafula, Ryan J Corbett, Yuanchao Zhang, Run Jin, …, Ammar S Naqvi, Noel Coleman, Weiping Ma, Deanne Taylor, Jo Lynne Rokita
bioRxiv : the preprint server for biology
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11 Jul 2024
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pubmed:39026781
The Open Pediatric Cancer Project
AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification.
Jung Kim, Ammar S Naqvi, Ryan J Corbett, Rebecca S Kaufman, Zalman Vaksman, …, Phillip B Storm, Adam C Resnick, Douglas R Stewart, Jo Lynne Rokita, Sharon J Diskin
Bioinformatics (Oxford, England)
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29 Feb 2024
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pubmed:38426335
AutoGVP
BARD1 germline variants induce haploinsufficiency and DNA repair defects in neuroblastoma.
Michael P Randall, Laura E Egolf, Zalman Vaksman, Minu Samanta, Matthew Tsang, …, Mehdi Layeghifard, Adam Shlien, John M Maris, Sharon J Diskin, Kristopher R Bosse
Journal of the National Cancer Institute
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10 Jan 2024
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pubmed:37688570
A proteogenomic surfaceome study identifies DLK1 as an immunotherapeutic target in neuroblastoma.
Amber K Weiner, Alexander B Radaoui, Matthew Tsang, Daniel Martinez, Simone Sidoli, …, Patrick H van Berkel, Malcolm A Smith, Benjamin A Garcia, John M Maris, Sharon J Diskin
bioRxiv : the preprint server for biology
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07 Jan 2024
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pubmed:38106022
2023
A proteogenomic surfaceome study identifies DLK1 as an immunotherapeutic target in neuroblastoma
Amber K. Weiner, Alexander B. Radaoui, Matthew Tsang, Daniel Martinez, Simone Sidoli, …, Patrick H. van Berkel, Malcolm A. Smith, Benjamin A. Garcia, John M. Maris, Sharon J. Diskin
Cold Spring Harbor Laboratory
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08 Dec 2023
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doi:10.1101/2023.12.06.570390
AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification.
Jung Kim, Ammar S Naqvi, Ryan J Corbett, Rebecca S Kaufman, Zalman Vaksman, …, Phillip B Storm, Adam C Resnick, Douglas R Stewart, Jo Lynne Rokita, Sharon J Diskin
bioRxiv : the preprint server for biology
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01 Dec 2023
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pubmed:38076939
Everolimus for Children With Recurrent or Progressive Low-Grade Glioma: Results From the Phase II PNOC001 Trial.
Daphne A Haas-Kogan, Mariam S Aboian, Jane E Minturn, Sarah E S Leary, Mohamed S Abdelbaki, …, Joanna J Phillips, Michael Prados, Annette M Molinaro, Sebastian M Waszak, Sabine Mueller
Journal of clinical oncology : official journal of the American Society of Clinical Oncology
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17 Nov 2023
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pubmed:37978951
Alternative lengthening of telomeres (ALT) in pediatric high-grade gliomas can occur without ATRX mutation and is enriched in patients with pathogenic germline mismatch repair (MMR) variants.
Jennifer L Stundon, Heba Ijaz, Krutika S Gaonkar, Rebecca S Kaufman, Run Jin, …, Suzanne P MacFarland, Douglas R Stewart, Sharon J Diskin, Jo Lynne Rokita, Kristina A Cole
Neuro-oncology
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06 Jul 2023
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pubmed:36541551
OpenPBTA: The Open Pediatric Brain Tumor Atlas.
Joshua A Shapiro, Krutika S Gaonkar, Stephanie J Spielman, Candace L Savonen, Chante J Bethell, …, Miguel A Brown, Adam C Resnick, Casey S Greene, Jo Lynne Rokita, Jaclyn N Taroni
Cell genomics
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31 May 2023
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pubmed:37492101
Macrophages in SHH subgroup medulloblastoma display dynamic heterogeneity that varies with treatment modality.
Mai T Dang, Michael V Gonzalez, Krutika S Gaonkar, Komal S Rathi, Patricia Young, …, Candace Savonen, Fernanda Mafra, Hakon Hakonarson, Tom Curran, Malay Haldar
Cell reports
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25 May 2023
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pubmed:37235472
Supplementary Table S2 from Telomere Maintenance Mechanisms Define Clinical Outcome in High-Risk Neuroblastoma
Balakrishna Koneru, Gonzalo Lopez, Ahsan Farooqi, Karina L. Conkrite, Thinh H. Nguyen, …, Shengping Yang, David A. Wheeler, John M. Maris, Sharon J. Diskin, C. Patrick Reynolds
American Association for Cancer Research (AACR)
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31 Mar 2023
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doi:10.1158/0008-5472.22424626
Supplementary Table S2 from Telomere Maintenance Mechanisms Define Clinical Outcome in High-Risk Neuroblastoma
Balakrishna Koneru, Gonzalo Lopez, Ahsan Farooqi, Karina L. Conkrite, Thinh H. Nguyen, …, Shengping Yang, David A. Wheeler, John M. Maris, Sharon J. Diskin, C. Patrick Reynolds
American Association for Cancer Research (AACR)
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31 Mar 2023
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doi:10.1158/0008-5472.22424626.v1
Supplementary Table S1 from Telomere Maintenance Mechanisms Define Clinical Outcome in High-Risk Neuroblastoma
Balakrishna Koneru, Gonzalo Lopez, Ahsan Farooqi, Karina L. Conkrite, Thinh H. Nguyen, …, Shengping Yang, David A. Wheeler, John M. Maris, Sharon J. Diskin, C. Patrick Reynolds
American Association for Cancer Research (AACR)
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31 Mar 2023
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doi:10.1158/0008-5472.22424629
Supplementary Table S1 from Telomere Maintenance Mechanisms Define Clinical Outcome in High-Risk Neuroblastoma
Balakrishna Koneru, Gonzalo Lopez, Ahsan Farooqi, Karina L. Conkrite, Thinh H. Nguyen, …, Shengping Yang, David A. Wheeler, John M. Maris, Sharon J. Diskin, C. Patrick Reynolds
American Association for Cancer Research (AACR)
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31 Mar 2023
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doi:10.1158/0008-5472.22424629.v1
Supplementary Figure S6 from YAP1 Mediates Resistance to MEK1/2 Inhibition in Neuroblastomas with Hyperactivated RAS Signaling
Grace E. Coggins, Alvin Farrel, Komal S. Rathi, Colin M. Hayes, Laura Scolaro, Jo Lynne Rokita, John M. Maris
American Association for Cancer Research (AACR)
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31 Mar 2023
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doi:10.1158/0008-5472.22422428.v1
Supplementary Figure S6 from YAP1 Mediates Resistance to MEK1/2 Inhibition in Neuroblastomas with Hyperactivated RAS Signaling
Grace E. Coggins, Alvin Farrel, Komal S. Rathi, Colin M. Hayes, Laura Scolaro, Jo Lynne Rokita, John M. Maris
American Association for Cancer Research (AACR)
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31 Mar 2023
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doi:10.1158/0008-5472.22422428
Supplementary Figure S5 from YAP1 Mediates Resistance to MEK1/2 Inhibition in Neuroblastomas with Hyperactivated RAS Signaling
Grace E. Coggins, Alvin Farrel, Komal S. Rathi, Colin M. Hayes, Laura Scolaro, Jo Lynne Rokita, John M. Maris
American Association for Cancer Research (AACR)
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31 Mar 2023
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doi:10.1158/0008-5472.22422431
Supplementary Figure S5 from YAP1 Mediates Resistance to MEK1/2 Inhibition in Neuroblastomas with Hyperactivated RAS Signaling
Grace E. Coggins, Alvin Farrel, Komal S. Rathi, Colin M. Hayes, Laura Scolaro, Jo Lynne Rokita, John M. Maris
American Association for Cancer Research (AACR)
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31 Mar 2023
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doi:10.1158/0008-5472.22422431.v1
Supplementary Figure S4 from YAP1 Mediates Resistance to MEK1/2 Inhibition in Neuroblastomas with Hyperactivated RAS Signaling
Grace E. Coggins, Alvin Farrel, Komal S. Rathi, Colin M. Hayes, Laura Scolaro, Jo Lynne Rokita, John M. Maris
American Association for Cancer Research (AACR)
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31 Mar 2023
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doi:10.1158/0008-5472.22422434
Supplementary Figure S4 from YAP1 Mediates Resistance to MEK1/2 Inhibition in Neuroblastomas with Hyperactivated RAS Signaling
Grace E. Coggins, Alvin Farrel, Komal S. Rathi, Colin M. Hayes, Laura Scolaro, Jo Lynne Rokita, John M. Maris
American Association for Cancer Research (AACR)
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31 Mar 2023
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doi:10.1158/0008-5472.22422434.v1
Supplementary Figure S3 from YAP1 Mediates Resistance to MEK1/2 Inhibition in Neuroblastomas with Hyperactivated RAS Signaling
Grace E. Coggins, Alvin Farrel, Komal S. Rathi, Colin M. Hayes, Laura Scolaro, Jo Lynne Rokita, John M. Maris
American Association for Cancer Research (AACR)
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31 Mar 2023
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doi:10.1158/0008-5472.22422440
Supplementary Figure S3 from YAP1 Mediates Resistance to MEK1/2 Inhibition in Neuroblastomas with Hyperactivated RAS Signaling
Grace E. Coggins, Alvin Farrel, Komal S. Rathi, Colin M. Hayes, Laura Scolaro, Jo Lynne Rokita, John M. Maris
American Association for Cancer Research (AACR)
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31 Mar 2023
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doi:10.1158/0008-5472.22422440.v1
Supplementary Figure S2 from YAP1 Mediates Resistance to MEK1/2 Inhibition in Neuroblastomas with Hyperactivated RAS Signaling
Grace E. Coggins, Alvin Farrel, Komal S. Rathi, Colin M. Hayes, Laura Scolaro, Jo Lynne Rokita, John M. Maris
American Association for Cancer Research (AACR)
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31 Mar 2023
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doi:10.1158/0008-5472.22422443
Supplementary Figure S2 from YAP1 Mediates Resistance to MEK1/2 Inhibition in Neuroblastomas with Hyperactivated RAS Signaling
Grace E. Coggins, Alvin Farrel, Komal S. Rathi, Colin M. Hayes, Laura Scolaro, Jo Lynne Rokita, John M. Maris
American Association for Cancer Research (AACR)
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31 Mar 2023
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doi:10.1158/0008-5472.22422443.v1
Supplementary Figure S1 from YAP1 Mediates Resistance to MEK1/2 Inhibition in Neuroblastomas with Hyperactivated RAS Signaling
Grace E. Coggins, Alvin Farrel, Komal S. Rathi, Colin M. Hayes, Laura Scolaro, Jo Lynne Rokita, John M. Maris
American Association for Cancer Research (AACR)
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31 Mar 2023
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doi:10.1158/0008-5472.22422446.v1
Supplementary Figure S1 from YAP1 Mediates Resistance to MEK1/2 Inhibition in Neuroblastomas with Hyperactivated RAS Signaling
Grace E. Coggins, Alvin Farrel, Komal S. Rathi, Colin M. Hayes, Laura Scolaro, Jo Lynne Rokita, John M. Maris
American Association for Cancer Research (AACR)
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31 Mar 2023
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doi:10.1158/0008-5472.22422446
Supplementary Figure Legends from YAP1 Mediates Resistance to MEK1/2 Inhibition in Neuroblastomas with Hyperactivated RAS Signaling
Grace E. Coggins, Alvin Farrel, Komal S. Rathi, Colin M. Hayes, Laura Scolaro, Jo Lynne Rokita, John M. Maris
American Association for Cancer Research (AACR)
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31 Mar 2023
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doi:10.1158/0008-5472.22422449
Supplementary Figure Legends from YAP1 Mediates Resistance to MEK1/2 Inhibition in Neuroblastomas with Hyperactivated RAS Signaling
Grace E. Coggins, Alvin Farrel, Komal S. Rathi, Colin M. Hayes, Laura Scolaro, Jo Lynne Rokita, John M. Maris
American Association for Cancer Research (AACR)
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31 Mar 2023
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doi:10.1158/0008-5472.22422449.v1
Supplementary Data from Telomere Maintenance Mechanisms Define Clinical Outcome in High-Risk Neuroblastoma
Balakrishna Koneru, Gonzalo Lopez, Ahsan Farooqi, Karina L. Conkrite, Thinh H. Nguyen, …, Shengping Yang, David A. Wheeler, John M. Maris, Sharon J. Diskin, C. Patrick Reynolds
American Association for Cancer Research (AACR)
·
31 Mar 2023
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doi:10.1158/0008-5472.22424632
Supplementary Data from Telomere Maintenance Mechanisms Define Clinical Outcome in High-Risk Neuroblastoma
Balakrishna Koneru, Gonzalo Lopez, Ahsan Farooqi, Karina L. Conkrite, Thinh H. Nguyen, …, Shengping Yang, David A. Wheeler, John M. Maris, Sharon J. Diskin, C. Patrick Reynolds
American Association for Cancer Research (AACR)
·
31 Mar 2023
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doi:10.1158/0008-5472.22424632.v1
Supplementary Data from GAS7 Deficiency Promotes Metastasis in MYCN-Driven Neuroblastoma
Zhiwei Dong, Kok Siong Yeo, Gonzalo Lopez, Cheng Zhang, Erin N. Dankert Eggum, …, Jan M. van Deursen, Hu Li, Jennifer J. Westendorf, John M. Maris, Shizhen Zhu
American Association for Cancer Research (AACR)
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31 Mar 2023
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doi:10.1158/0008-5472.22429665.v1
Supplementary Data from GAS7 Deficiency Promotes Metastasis in MYCN-Driven Neuroblastoma
Zhiwei Dong, Kok Siong Yeo, Gonzalo Lopez, Cheng Zhang, Erin N. Dankert Eggum, …, Jan M. van Deursen, Hu Li, Jennifer J. Westendorf, John M. Maris, Shizhen Zhu
American Association for Cancer Research (AACR)
·
31 Mar 2023
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doi:10.1158/0008-5472.22429665
Supplemental Tables S1-5 from YAP1 Mediates Resistance to MEK1/2 Inhibition in Neuroblastomas with Hyperactivated RAS Signaling
Grace E. Coggins, Alvin Farrel, Komal S. Rathi, Colin M. Hayes, Laura Scolaro, Jo Lynne Rokita, John M. Maris
American Association for Cancer Research (AACR)
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31 Mar 2023
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doi:10.1158/0008-5472.22422452.v1
Supplemental Tables S1-5 from YAP1 Mediates Resistance to MEK1/2 Inhibition in Neuroblastomas with Hyperactivated RAS Signaling
Grace E. Coggins, Alvin Farrel, Komal S. Rathi, Colin M. Hayes, Laura Scolaro, Jo Lynne Rokita, John M. Maris
American Association for Cancer Research (AACR)
·
31 Mar 2023
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doi:10.1158/0008-5472.22422452
Data from YAP1 Mediates Resistance to MEK1/2 Inhibition in Neuroblastomas with Hyperactivated RAS Signaling
Grace E. Coggins, Alvin Farrel, Komal S. Rathi, Colin M. Hayes, Laura Scolaro, Jo Lynne Rokita, John M. Maris
American Association for Cancer Research (AACR)
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31 Mar 2023
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doi:10.1158/0008-5472.c.6511223
Data from YAP1 Mediates Resistance to MEK1/2 Inhibition in Neuroblastomas with Hyperactivated RAS Signaling
Grace E. Coggins, Alvin Farrel, Komal S. Rathi, Colin M. Hayes, Laura Scolaro, Jo Lynne Rokita, John M. Maris
American Association for Cancer Research (AACR)
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31 Mar 2023
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doi:10.1158/0008-5472.c.6511223.v1
Data from Telomere Maintenance Mechanisms Define Clinical Outcome in High-Risk Neuroblastoma
Balakrishna Koneru, Gonzalo Lopez, Ahsan Farooqi, Karina L. Conkrite, Thinh H. Nguyen, …, Shengping Yang, David A. Wheeler, John M. Maris, Sharon J. Diskin, C. Patrick Reynolds
American Association for Cancer Research (AACR)
·
31 Mar 2023
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doi:10.1158/0008-5472.c.6511828
Data from Telomere Maintenance Mechanisms Define Clinical Outcome in High-Risk Neuroblastoma
Balakrishna Koneru, Gonzalo Lopez, Ahsan Farooqi, Karina L. Conkrite, Thinh H. Nguyen, …, Shengping Yang, David A. Wheeler, John M. Maris, Sharon J. Diskin, C. Patrick Reynolds
American Association for Cancer Research (AACR)
·
31 Mar 2023
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doi:10.1158/0008-5472.c.6511828.v1
Data from GAS7 Deficiency Promotes Metastasis in MYCN-Driven Neuroblastoma
Zhiwei Dong, Kok Siong Yeo, Gonzalo Lopez, Cheng Zhang, Erin N. Dankert Eggum, …, Jan M. van Deursen, Hu Li, Jennifer J. Westendorf, John M. Maris, Shizhen Zhu
American Association for Cancer Research (AACR)
·
31 Mar 2023
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doi:10.1158/0008-5472.c.6513432
Data from GAS7 Deficiency Promotes Metastasis in MYCN-Driven Neuroblastoma
Zhiwei Dong, Kok Siong Yeo, Gonzalo Lopez, Cheng Zhang, Erin N. Dankert Eggum, …, Jan M. van Deursen, Hu Li, Jennifer J. Westendorf, John M. Maris, Shizhen Zhu
American Association for Cancer Research (AACR)
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31 Mar 2023
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doi:10.1158/0008-5472.c.6513432.v1
Identification of candidate genes for nicotine withdrawal in C57BL /6J × DBA /2J recombinant inbred mice
Maren L. Smith, Kristin M. Mignogna, Jo L. Rokita, Lorna MacLeod, M. Imad Damaj, Michael F. Miles
Genes, Brain and Behavior
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13 Feb 2023
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doi:10.1111/gbb.12844
Identification of candidate genes for nicotine withdrawal in C57BL/6J × DBA/2J recombinant inbred mice.
Maren L Smith, Kristin M Mignogna, Jo L Rokita, Lorna MacLeod, M Imad Damaj, Michael F Miles
Genes, brain, and behavior
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13 Feb 2023
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pubmed:36781202
BARD1 germline variants induce haploinsufficiency and DNA repair defects in neuroblastoma
Michael P Randall, Laura E Egolf, Zalman Vaksman, Minu Samanta, Matthew Tsang, …, Mehdi Layeghifard, Adam Shlien, John M Maris, Sharon J Diskin, Kristopher R Bosse
bioRxiv : the preprint server for biology
·
03 Feb 2023
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pubmed:36778420
Enhancing childhood cancer targetability.
Ammar S Naqvi, Jo Lynne Rokita
Nature cancer
·
01 Feb 2023
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pubmed:36585448
The children's brain tumor network (CBTN) - Accelerating research in pediatric central nervous system tumors through collaboration and open science
Jena V. Lilly, Jo Lynne Rokita, Jennifer L. Mason, Tatiana Patton, Stephanie Stefankiewiz, …, Phillip B. Storm, Rishi R. Lulla, Michael Prados, Adam C. Resnick, Angela J. Waanders
Neoplasia
·
01 Jan 2023
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doi:10.1016/j.neo.2022.100846
2022
Enhancing childhood cancer targetability
Ammar S. Naqvi, Jo Lynne Rokita
Nature Cancer
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30 Dec 2022
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doi:10.1038/s43018-022-00472-0
Alternative lengthening of telomeres (ALT) in pediatric high-grade gliomas can occur without ATRX mutation and is enriched in patients with pathogenic germline mismatch repair (MMR) variants
Jennifer L Stundon, Heba Ijaz, Krutika S Gaonkar, Rebecca S Kaufman, Run Jin, …, Suzanne P MacFarland, Douglas R Stewart, Sharon J Diskin, Jo Lynne Rokita, Kristina A Cole
Neuro-Oncology
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20 Dec 2022
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doi:10.1093/neuonc/noac278
The children's brain tumor network (CBTN) - Accelerating research in pediatric central nervous system tumors through collaboration and open science.
Jena V Lilly, Jo Lynne Rokita, Jennifer L Mason, Tatiana Patton, Stephanie Stefankiewiz, …, Phillip B Storm, Rishi R Lulla, Michael Prados, Adam C Resnick, Angela J Waanders
Neoplasia (New York, N.Y.)
·
03 Nov 2022
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pubmed:36335802
The Children’s Brain Tumor Network (CBTN) - Accelerating Research in Pediatric Central Nervous System Tumors through Collaboration and Open Science
Jena V. Lilly, Jo Lynne Rokita, Jennifer L. Mason, Tatiana Patton, Stephanie Stefankiewiz, …, Phillip B. Storm, Rishi R. Lulla, Michael Prados, Adam C. Resnick, Angela J. Waanders
Cold Spring Harbor Laboratory
·
18 Oct 2022
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doi:10.1101/2022.10.14.511975
OpenPBTA: An Open Pediatric Brain Tumor Atlas
Joshua A. Shapiro, Krutika S. Gaonkar, Candace L. Savonen, Stephanie J. Spielman, Chante J. Bethell, …, Sabine Mueller, Adam C. Resnick, Casey S. Greene, Jo Lynne Rokita, Jaclyn N. Taroni
Cold Spring Harbor Laboratory
·
16 Sep 2022
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doi:10.1101/2022.09.13.507832
Upfront Biology-Guided Therapy in Diffuse Intrinsic Pontine Glioma: Therapeutic, Molecular, and Biomarker Outcomes from PNOC003.
Cassie Kline, Payal Jain, Lindsay Kilburn, Erin R Bonner, Nalin Gupta, …, Michael Prados, Adam Resnick, Sebastian M Waszak, Javad Nazarian, Sabine Mueller
Clinical cancer research : an official journal of the American Association for Cancer Research
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15 Sep 2022
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pubmed:35852795
Development of GPC2-directed chimeric antigen receptors using mRNA for pediatric brain tumors
Jessica B Foster, Crystal Griffin, Jo Lynne Rokita, Allison Stern, Cameron Brimley, …, Phillip B Storm, David M Barrett, Adam C Resnick, John M Maris, Kristopher R Bosse
Journal for ImmunoTherapy of Cancer
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01 Sep 2022
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doi:10.1136/jitc-2021-004450
Development of GPC2-directed chimeric antigen receptors using mRNA for pediatric brain tumors.
Jessica B Foster, Crystal Griffin, Jo Lynne Rokita, Allison Stern, Cameron Brimley, …, Phillip B Storm, David M Barrett, Adam C Resnick, John M Maris, Kristopher R Bosse
Journal for immunotherapy of cancer
·
01 Sep 2022
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pubmed:36167467
Characterization of aberrant splicing in pediatric central nervous system tumors reveals
Ammar S Naqvi, Ryan J Corbett, Priyanka Seghal, Karina L Conkrite, Komal S Rathi, …, Peter J Madsen, Sharon J Diskin, Andrei Thomas-Tikhonenko, Adam C Resnick, Jo Lynne Rokita
bioRxiv : the preprint server for biology
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22 Aug 2022
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pubmed:39149264
Characterization of aberrant splicing in pediatric central nervous system tumors reveals CLK1 as a candidate oncogenic dependency
ALT in Pediatric High-Grade Gliomas Can Occur withoutATRXMutation and is Enriched in Patients with Pathogenic Germline MMR Variants
Jennifer L. Stundon, Heba Ijaz, Krutika S. Gaonkar, Rebecca S. Kaufman, Run Jin, …, Suzanne P. MacFarland, Douglas R. Stewart, Sharon J. Diskin, Jo Lynne Rokita, Kristina A. Cole
Cold Spring Harbor Laboratory
·
06 Aug 2022
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doi:10.1101/2022.08.05.502870
2021
Macrophages in SHH subgroup medulloblastoma display dynamic heterogeneity that varies with treatment modality.
Mai T Dang, Michael V Gonzalez, Krutika S Gaonkar, Komal S Rathi, Patricia Young, …, Candace Savonen, Fernanda Mafra, Hakon Hakonarson, Tom Curran, Malay Haldar
Cell reports
·
30 Mar 2021
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pubmed:33789113
GAS7 Deficiency Promotes Metastasis in MYCN-Driven Neuroblastoma
Zhiwei Dong, Kok Siong Yeo, Gonzalo Lopez, Cheng Zhang, Erin N. Dankert Eggum, …, Jan M. van Deursen, Hu Li, Jennifer J. Westendorf, John M. Maris, Shizhen Zhu
Cancer Research
·
18 Feb 2021
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doi:10.1158/0008-5472.CAN-20-1890
GAS7 Deficiency Promotes Metastasis in MYCN-Driven Neuroblastoma.
Zhiwei Dong, Kok Siong Yeo, Gonzalo Lopez, Cheng Zhang, Erin N Dankert Eggum, …, Jan M van Deursen, Hu Li, Jennifer J Westendorf, John M Maris, Shizhen Zhu
Cancer research
·
18 Feb 2021
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pubmed:33602789
2020
annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions.
Krutika S Gaonkar, Federico Marini, Komal S Rathi, Payal Jain, Yuankun Zhu, …, Pichai Raman, Adam C Resnick, Konstantin Strauch, Jaclyn N Taroni, Jo Lynne Rokita
BMC bioinformatics
·
14 Dec 2020
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pubmed:33317447
Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer.
Francesca Petralia, Nicole Tignor, Boris Reva, Mateusz Koptyra, Shrabanti Chowdhury, …, Amanda G Paulovich, Adam C Resnick, Phillip B Storm, Brian R Rood, Pei Wang
Cell
·
25 Nov 2020
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pubmed:33242424
A transcriptome-based classifier to determine molecular subtypes in medulloblastoma
Komal S. Rathi, Sherjeel Arif, Mateusz Koptyra, Ammar S. Naqvi, Deanne M. Taylor, Phillip B. Storm, Adam C. Resnick, Jo Lynne Rokita, Pichai Raman
PLOS Computational Biology
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29 Oct 2020
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doi:10.1371/journal.pcbi.1008263
A transcriptome-based classifier to determine molecular subtypes in medulloblastoma.
Komal S Rathi, Sherjeel Arif, Mateusz Koptyra, Ammar S Naqvi, Deanne M Taylor, Phillip B Storm, Adam C Resnick, Jo Lynne Rokita, Pichai Raman
PLoS computational biology
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29 Oct 2020
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pubmed:33119584
Telomere Maintenance Mechanisms Define Clinical Outcome in High-Risk Neuroblastoma
Balakrishna Koneru, Gonzalo Lopez, Ahsan Farooqi, Karina L. Conkrite, Thinh H. Nguyen, …, Shengping Yang, David A. Wheeler, John M. Maris, Sharon J. Diskin, C. Patrick Reynolds
Cancer Research
·
15 Jun 2020
·
doi:10.1158/0008-5472.CAN-19-3068
LIN28B promotes neuroblastoma metastasis and regulates PDZ binding kinase.
Dongdong Chen, Julie Cox, Jayabhargav Annam, Melanie Weingart, Grace Essien, …, Daisy Li, Cara Shields, Oskar Laur, John M Maris, Robert W Schnepp
Neoplasia (New York, N.Y.)
·
24 Apr 2020
·
pubmed:32339949
Limited antitumor activity of combined BET and MEK inhibition in neuroblastoma
Jason R. Healy, Lori S. Hart, Alexander L. Shazad, Maria E. Gagliardi, Matthew Tsang, …, Olena Barbash, Vandana Batra, Minu Samanta, John M. Maris, Robert W. Schnepp
Pediatric Blood & Cancer
·
19 Apr 2020
·
doi:10.1002/pbc.28267
Limited antitumor activity of combined BET and MEK inhibition in neuroblastoma.
Jason R Healy, Lori S Hart, Alexander L Shazad, Maria E Gagliardi, Matthew Tsang, …, Olena Barbash, Vandana Batra, Minu Samanta, John M Maris, Robert W Schnepp
Pediatric blood & cancer
·
19 Apr 2020
·
pubmed:32307821
Epigenomic profiling of neuroblastoma cell lines.
Kristen Upton, Apexa Modi, Khushbu Patel, Nathan M Kendsersky, Karina L Conkrite, …, Gregory I Sacks, Paolo Fortina, Sharon J Diskin, John M Maris, Jo Lynne Rokita
Scientific data
·
14 Apr 2020
·
pubmed:32286315
Telomere Maintenance Mechanisms Define Clinical Outcome in High-Risk Neuroblastoma.
Balakrishna Koneru, Gonzalo Lopez, Ahsan Farooqi, Karina L Conkrite, Thinh H Nguyen, …, Shengping Yang, David A Wheeler, John M Maris, Sharon J Diskin, C Patrick Reynolds
Cancer research
·
14 Apr 2020
·
pubmed:32291317
CAMKV Is a Candidate Immunotherapeutic Target in
Robyn T Sussman, Jo Lynne Rokita, Kevin Huang, Pichai Raman, Komal S Rathi, …, Maria Lane, Lori S Hart, Tricia Bhatti, Bruce Pawel, John M Maris
Frontiers in oncology
·
06 Mar 2020
·
pubmed:32211329
Pediatric high-grade glioma resources from the Children's Brain Tumor Tissue Consortium.
Heba Ijaz, Mateusz Koptyra, Krutika S Gaonkar, Jo Lynne Rokita, Valerie P Baubet, …, Maria Rita Santi, Phillip B Storm, Adam Resnick, Angela J Waanders, Kristina A Cole
Neuro-oncology
·
11 Jan 2020
·
pubmed:31613963
2019
YAP1 Mediates Resistance to MEK1/2 Inhibition in Neuroblastomas with Hyperactivated RAS Signaling
Grace E. Coggins, Alvin Farrel, Komal S. Rathi, Colin M. Hayes, Laura Scolaro, Jo Lynne Rokita, John M. Maris
Cancer Research
·
13 Dec 2019
·
doi:10.1158/0008-5472.CAN-19-1415
ASCL1 is a MYCN- and LMO1-dependent member of the adrenergic neuroblastoma core regulatory circuitry.
Lu Wang, Tze King Tan, Adam D Durbin, Mark W Zimmerman, Brian J Abraham, …, Jo Lynne Rokita, John M Maris, Richard A Young, A Thomas Look, Takaomi Sanda
Nature communications
·
09 Dec 2019
·
pubmed:31819055
Combined innate and adaptive immunotherapy overcomes resistance of immunologically cold syngeneic murine neuroblastoma to checkpoint inhibition.
Julie Voeller, Amy K Erbe, Jacob Slowinski, Kayla Rasmussen, Peter M Carlson, …, John Maris, Jacquelyn A Hank, Zachary S Morris, Alexander L Rakhmilevich, Paul M Sondel
Journal for immunotherapy of cancer
·
06 Dec 2019
·
pubmed:31810498
Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design.
Jo Lynne Rokita, Komal S Rathi, Maria F Cardenas, Kristen A Upton, Joy Jayaseelan, …, Malcolm A Smith, Richard B Lock, Pichai Raman, David A Wheeler, John M Maris
Cell reports
·
05 Nov 2019
·
pubmed:31693904
YAP1 Mediates Resistance to MEK1/2 Inhibition in Neuroblastomas with Hyperactivated RAS Signaling.
Grace E Coggins, Alvin Farrel, Komal S Rathi, Colin M Hayes, Laura Scolaro, Jo Lynne Rokita, John M Maris
Cancer research
·
31 Oct 2019
·
pubmed:31672841
Germline 16p11.2 Microdeletion Predisposes to Neuroblastoma.
Laura E Egolf, Zalman Vaksman, Gonzalo Lopez, Jo Lynne Rokita, Apexa Modi, Patricia V Basta, Hakon Hakonarson, Andrew F Olshan, Sharon J Diskin
American journal of human genetics
·
29 Aug 2019
·
pubmed:31474320
Pediatric High Grade Glioma Resources From the Children’s Brain Tumor Tissue Consortium (CBTTC) and Pediatric Brain Tumor Atlas (PBTA)
Heba Ijaz, Mateusz Koptyra, Krutika S. Gaonkar, Jo Lynne Rokita, Valerie P. Baubet, …, Maria Rita Santi, Phillip B. Storm, Adam Resnick, Angela J. Waanders, Kristina A. Cole
Cold Spring Harbor Laboratory
·
31 May 2019
·
doi:10.1101/656587
The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution.
Deanne M Taylor, Bruce J Aronow, Kai Tan, Kathrin Bernt, Nathan Salomonis, …, Yi Xing, Sek Won Kong, Carsten G Bönnemann, Kenneth D Mandl, Peter S White
Developmental cell
·
28 Mar 2019
·
pmid:30930166
The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution.
Deanne M Taylor, Bruce J Aronow, Kai Tan, Kathrin Bernt, Nathan Salomonis, …, Yi Xing, Sek Won Kong, Carsten G Bönnemann, Kenneth D Mandl, Peter S White
Developmental cell
·
28 Mar 2019
·
pubmed:30930166
Genomic profiling of childhood tumor patient-derived xenograft models to enable rational clinical trial design
Jo Lynne Rokita, Komal S. Rathi, Maria F. Cardenas, Kristen A. Upton, Joy Jayaseelan, …, Malcolm A. Smith, Richard B. Lock, Pichai Raman, David A. Wheeler, John M. Maris
Cold Spring Harbor Laboratory
·
06 Mar 2019
·
doi:10.1101/566455
2018
Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma
Presha Rajbhandari, Gonzalo Lopez, Claudia Capdevila, Beatrice Salvatori, Jiyang Yu, …, Antonio Iavarone, Anna Lasorella, Jose M. Silva, John M. Maris, Andrea Califano
Cancer Discovery
·
30 Apr 2018
·
doi:10.1158/2159-8290.cd-16-0861
Cross-Cohort Analysis Identifies a TEAD4-MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma.
Presha Rajbhandari, Gonzalo Lopez, Claudia Capdevila, Beatrice Salvatori, Jiyang Yu, …, Antonio Iavarone, Anna Lasorella, Jose M Silva, John M Maris, Andrea Califano
Cancer discovery
·
06 Mar 2018
·
pubmed:29510988
2017
Correction: Corrigendum: Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines
Jo Lynne Harenza, Maura A. Diamond, Rebecca N. Adams, Michael M. Song, Heather L. Davidson, Lori S. Hart, Maiah H. Dent, Paolo Fortina, C. Patrick Reynolds, John M. Maris
Scientific Data
·
05 Dec 2017
·
doi:10.1038/sdata.2017.183
Corrigendum: Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines.
Jo Lynne Harenza, Maura A Diamond, Rebecca N Adams, Michael M Song, Heather L Davidson, Lori S Hart, Maiah H Dent, Paolo Fortina, C Patrick Reynolds, John M Maris
Scientific data
·
05 Dec 2017
·
pubmed:29206221
Identification of GPC2 as an Oncoprotein and Candidate Immunotherapeutic Target in High-Risk Neuroblastoma.
Kristopher R Bosse, Pichai Raman, Zhongyu Zhu, Maria Lane, Daniel Martinez, …, Marco A Marra, Michael D Taylor, Dimiter S Dimitrov, Crystal L Mackall, John M Maris
Cancer cell
·
11 Sep 2017
·
pubmed:28898695
Identification of GPC2 as an Oncoprotein and Candidate Immunotherapeutic Target in High-Risk Neuroblastoma
Kristopher R. Bosse, Pichai Raman, Zhongyu Zhu, Maria Lane, Daniel Martinez, …, Marco A. Marra, Michael D. Taylor, Dimiter S. Dimitrov, Crystal L. Mackall, John M. Maris
Cancer Cell
·
01 Sep 2017
·
doi:10.1016/j.ccell.2017.08.003
Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines
Jo Lynne Harenza, Maura A. Diamond, Rebecca N. Adams, Michael M. Song, Heather L. Davidson, Lori S. Hart, Maiah H. Dent, Paolo Fortina, C. Patrick Reynolds, John M. Maris
Scientific Data
·
28 Mar 2017
·
doi:10.1038/sdata.2017.33
Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines.
Jo Lynne Harenza, Maura A Diamond, Rebecca N Adams, Michael M Song, Heather L Davidson, Lori S Hart, Maiah H Dent, Paolo Fortina, C Patrick Reynolds, John M Maris
Scientific data
·
28 Mar 2017
·
pubmed:28350380
2016
International Comparison of Enumeration-Based Quantification of DNA Copy-Concentration Using Flow Cytometric Counting and Digital Polymerase Chain Reaction
Hee-Bong Yoo, Sang-Ryoul Park, Lianhua Dong, Jing Wang, Zhiwei Sui, …, Jim F. Huggett, Helen Parkes, Margaret C. Kline, Jo Lynne Harenza, Peter M. Vallone
Analytical Chemistry
·
30 Nov 2016
·
doi:10.1021/acs.analchem.6b03076
International Comparison of Enumeration-Based Quantification of DNA Copy-Concentration Using Flow Cytometric Counting and Digital Polymerase Chain Reaction.
Hee-Bong Yoo, Sang-Ryoul Park, Lianhua Dong, Jing Wang, Zhiwei Sui, …, Jim F Huggett, Helen Parkes, Margaret C Kline, Jo Lynne Harenza, Peter M Vallone
Analytical chemistry
·
30 Nov 2016
·
pubmed:28193036
Identification of quantitative trait loci and candidate genes for an anxiolytic‐like response to ethanol in BXD recombinant inbred strains
A. H. Putman, A. R. Wolen, J. L. Harenza, R. K. Yordanova, B. T. Webb, E. J. Chesler, M. F. Miles
Genes, Brain and Behavior
·
01 Apr 2016
·
doi:10.1111/gbb.12289
2015
Abstract 1077: Use of the SVClassify algorithm to classify pediatric solid tumor translocation variant calls as likely true or false positives
Jo Lynne Harenza, Hemang M. Parikh, Jun S. Wei, Xinyu Wen, Sivasish Sindiri, Rajesh Patidar, Marc Salit, Paul S. Meltzer, Javed Khan, Justin Zook
Cancer Research
·
01 Aug 2015
·
doi:10.1158/1538-7445.am2015-1077
Inhibition of monoacylglycerol lipase reduces nicotine withdrawal
P P Muldoon, J Chen, J L Harenza, R A Abdullah, L J Sim‐Selley, B F Cravatt, M F Miles, X Chen, A H Lichtman, M I Damaj
British Journal of Pharmacology
·
08 Jan 2015
·
doi:10.1111/bph.12948
2014
The α3β4* nicotinic ACh receptor subtype mediates physical dependence to morphine: mouse and human studies
P P Muldoon, K J Jackson, E Perez, J L Harenza, S Molas, …, M Dierssen, M F Miles, X Chen, M De Biasi, M I Damaj
British Journal of Pharmacology
·
25 Jul 2014
·
doi:10.1111/bph.12741
2013
Genetic variation within the Chrna7 gene modulates nicotine reward‐like phenotypes in mice
J. L. Harenza, P. P. Muldoon, M. De Biasi, M. I. Damaj, M. F. Miles
Genes, Brain and Behavior
·
26 Dec 2013
·
doi:10.1111/gbb.12113
2012
Erratum: The Neuropeptide Galanin and Variants in the GalR1 Gene are Associated with Nicotine Dependence
Kia J Jackson, Xiangning Chen, Michael F Miles, JoLynne Harenza, M Imad Damaj
Neuropsychopharmacology
·
16 Aug 2012
·
doi:10.1038/npp.2012.95
2011
The Neuropeptide Galanin and Variants in the GalR1 Gene are Associated with Nicotine Dependence
Kia J Jackson, Xiangning Chen, Michael F Miles, JoLynne Harenza, M Imad Damaj
Neuropsychopharmacology
·
27 Jul 2011
·
doi:10.1038/npp.2011.123
Correction: Genetic Analysis of the Neurosteroid Deoxycorticosterone and Its Relation to Alcohol Phenotypes: Identification of QTLs and Downstream Gene Regulation
Patrizia Porcu, Todd K. O’Buckley, Soomin C. Song, Jo Lynne Harenza, Lu Lu, Xusheng Wang, Robert W. Williams, Michael F. Miles, A. Leslie Morrow
PLoS ONE
·
30 Jun 2011
·
doi:10.1371/annotation/ce7007ca-506f-4b54-b7ff-1e0a93d689f7
Genetic Analysis of the Neurosteroid Deoxycorticosterone and Its Relation to Alcohol Phenotypes: Identification of QTLs and Downstream Gene Regulation
Patrizia Porcu, Todd K. O’Buckley, Soomin C. Song, Jo Lynne Harenza, Lu Lu, Xusheng Wang, Robert W. Williams, Michael F. Miles, A. Leslie Morrow
PLoS ONE
·
08 Apr 2011
·
doi:10.1371/journal.pone.0018405
Genetic analysis of the neurosteroid deoxycorticosterone and its relation to alcohol phenotypes: identification of QTLs and downstream gene regulation.
Patrizia Porcu, Todd K O’Buckley, Soomin C Song, Jo Lynne Harenza, Lu Lu, Xusheng Wang, Robert W Williams, Michael F Miles, A Leslie Morrow
PloS one
·
08 Apr 2011
·
pubmed:21494628