Search Results - "Breese, Marcus R"

Genome-Informed Targeted Therapy for Osteosarcoma by Sayles, Leanne C, Breese, Marcus R, Koehne, Amanda L, Leung, Stanley G, Lee, Alex G, Liu, Heng-Yi, Spillinger, Aviv, Shah, Avanthi T, Tanasa, Bogdan, Straessler, Krystal, Hazard, Florette K, Spunt, Sheri L, Marina, Neyssa, Kim, Grace E, Cho, Soo-Jin, Avedian, Raffi S, Mohler, David G, Kim, Mi-Ok, DuBois, Steven G, Hawkins, Douglas S, Sweet-Cordero, E Alejandro

“…Osteosarcoma is a highly aggressive cancer for which treatment has remained essentially unchanged for more than 30 years. Osteosarcoma is characterized by…”
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NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets by Breese, Marcus R, Liu, Yunlong

“…NGSUtils is a suite of software tools for manipulating data common to next-generation sequencing experiments, such as FASTQ, BED and BAM format files. These…”
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Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures by Pfeil, Jacob, Sanders, Lauren M, Anastopoulos, Ioannis, Lyle, A Geoffrey, Weinstein, Alana S, Xue, Yuanqing, Blair, Andrew, Beale, Holly C, Lee, Alex, Leung, Stanley G, Dinh, Phuong T, Shah, Avanthi Tayi, Breese, Marcus R, Devine, W Patrick, Bjork, Isabel, Salama, Sofie R, Sweet-Cordero, E Alejandro, Haussler, David, Vaske, Olena Morozova

“…Precision oncology has primarily relied on coding mutations as biomarkers of response to therapies. While transcriptome analysis can provide valuable…”
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Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data by Zhou, Ao, Breese, Marcus R, Hao, Yangyang, Edenberg, Howard J, Li, Lang, Skaar, Todd C, Liu, Yunlong

“…Alternative splicing increases proteome diversity by expressing multiple gene isoforms that often differ in function. Identifying alternative splicing events…”
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Long noncoding RNA EWSAT1-mediated gene repression facilitates Ewing sarcoma oncogenesis by Marques Howarth, Michelle, Simpson, David, Ngok, Siu P, Nieves, Bethsaida, Chen, Ron, Siprashvili, Zurab, Vaka, Dedeepya, Breese, Marcus R, Crompton, Brian D, Alexe, Gabriela, Hawkins, Doug S, Jacobson, Damon, Brunner, Alayne L, West, Robert, Mora, Jaume, Stegmaier, Kimberly, Khavari, Paul, Sweet-Cordero, E Alejandro

“…Chromosomal translocation that results in fusion of the genes encoding RNA-binding protein EWS and transcription factor FLI1 (EWS-FLI1) is pathognomonic for…”
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Osteosarcoma PDX-Derived Cell Line Models for Preclinical Drug Evaluation Demonstrate Metastasis Inhibition by Dinaciclib through a Genome-Targeted Approach by Schott, Courtney R, Koehne, Amanda L, Sayles, Leanne C, Young, Elizabeth P, Luck, Cuyler, Yu, Katherine, Lee, Alex G, Breese, Marcus R, Leung, Stanley G, Xu, Hang, Shah, Avanthi Tayi, Liu, Heng-Yi, Spillinger, Aviv, Behroozfard, Inge H, Marini, Kieren D, Dinh, Phuong T, Pons Ventura, María V, Vanderboon, Emma N, Hazard, Florette K, Cho, Soo-Jin, Avedian, Raffi S, Mohler, David G, Zimel, Melissa, Wustrack, Rosanna, Curtis, Christina, Sirota, Marina, Sweet-Cordero, E Alejandro

“…Models to study metastatic disease in rare cancers are needed to advance preclinical therapeutics and to gain insight into disease biology. Osteosarcoma is a…”
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A Comprehensive Circulating Tumor DNA Assay for Detection of Translocation and Copy-Number Changes in Pediatric Sarcomas by Shah, Avanthi Tayi, Azad, Tej D, Breese, Marcus R, Chabon, Jacob J, Hamilton, Emily G, Straessler, Krystal, Kurtz, David M, Leung, Stanley G, Spillinger, Aviv, Liu, Heng-Yi, Behroozfard, Inge H, Wittber, Frederick M, Hazard, Florette K, Cho, Soo-Jin, Daldrup-Link, Heike E, Vo, Kieuhoa T, Rangaswami, Arun, Pribnow, Allison, Spunt, Sheri L, Lacayo, Norman J, Diehn, Maximilian, Alizadeh, Ash A, Sweet-Cordero, E Alejandro

“…Most circulating tumor DNA (ctDNA) assays are designed to detect recurrent mutations. Pediatric sarcomas share few recurrent mutations but rather are…”
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NUP98-NSD1 Driven MDS/MPN in Childhood Masquerading as JMML by Behnert, Astrid, Lee, Alex G., Young, Elizabeth P., Breese, Marcus R., Leung, Stanley G., Behroozfard, Inge, Maruffi, Maria, Sweet-Cordero, E. Alejandro, Dvorak, Christopher C., Chu, Julia, Stieglitz, Elliot

“…Overlapping myelodysplastic/myeloproliferative neoplasms (MDS/MPN) are clonal hematopoietic disorders with features of myelodysplasia and myeloproliferation…”
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Comparative RNA-seq analysis aids in diagnosis of a rare pediatric tumor by Sanders, Lauren M, Rangaswami, Arun, Bjork, Isabel, Lam, Du Linh, Beale, Holly C, Kephart, Ellen Towle, Durbin, Ann, Learned, Katrina, Currie, Rob, Lyle, A Geoffrey, Pfeil, Jacob, Shah, Avanthi Tayi, Lee, Alex G, Leung, Stanley G, Behroozfard, Inge H, Breese, Marcus R, Peralez, Jennifer, Hazard, Florette K, Lacayo, Norman, Spunt, Sheri L, Haussler, David, Salama, Sofie R, Sweet-Cordero, E Alejandro, Vaske, Olena M

“…Gliomatosis peritonei is a rare pathologic finding that is associated with ovarian teratomas and malignant mixed germ cell tumors. The occurrence of…”
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Abstract B03: Methods for integrated analysis of RNA and DNA sequencing in pediatric cancers by Breese, Marcus R., Lee, Alex G., Shah, Avanthi T., Martell, Henry J., Sweet-Cordero, Alejandro

“…Abstract Pediatric cancers have a very different genomic profile from adult cancers. For example, single-nucleotide variants (SNVs) are common drivers in many…”
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Abstract A45: Targeted drug therapies for osteosarcoma by Sayles, Leanne C., Breese, Marcus R., Martell, Henry, Lee, Alex G., Leung, Stanley, Shah, Avanthi T., Sweet-Cordero, E. Alejandro

“…Abstract Osteosarcoma (OS) is a highly aggressive cancer that has had no new treatments options in over 30 years. OS is a heterogeneous disease that is…”
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Abstract 07: Using copy number alterations to identify targeted therapies in a preclinical model of osteosarcoma by Breese, Marcus R., Sayles, Leanne C., Sweet-Cordero, Alejandro

“…Abstract Osteosarcoma (OS) is an aggressive bone malignancy affecting approximately 400 pediatric patients in the United States annually. Compared with other…”
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Abstract 2880: Targeted drug therapies for osteosarcoma by Sayles, Leanne C., Koehne, Amanda, Marini, Kieren, Lee, Alex G., Leung, Stanley G., Shah, Avanthi T., Breese, Marcus R., Sweet-Cordero, E. Alejandro

“…Abstract Osteosarcoma (OS) is a highly aggressive cancer that has had no new treatments options in over 30 years. OS is a heterogeneous disease which is…”
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Abstract B25: Integrative analysis of whole-genome and RNA sequencing in high-risk pediatric malignancies by Breese, Marcus R., Shah, Avanthi T., Tanasa, Bogdan, Lee, Alex G., Leung, Stanley G., Spillinger, Aviv, Liu, Heng-Yi, Hazard, Florette K., Sweet-Cordero, Alejandro

“…Abstract Clinical use of gene-panel based tumor sequencing has expanded exponentially over the past few years. While in some cases this molecular testing…”
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A comprehensive circulating tumor DNA assay for detection of translocations and copy number changes in pediatric sarcomas by Shah, Avanthi Tayi, Azad, Tej D., Breese, Marcus R., Chabon, Jacob J., Hamilton, Emily G., Straessler, Krystal, Kurtz, David M., Leung, Stanley G., Spillinger, Aviv, Liu, Heng-Yi, Behroozfard, Inge, Wittber, Frederick M., Hazard, Florette K., Cho, Soo-Jin, Daldrup-Link, Heike, Vo, Kieuhoa T., Rangaswami, Arun, Pribnow, Allison, Spunt, Sheri L., Lacayo, Norman J., Diehn, Maximilian, Alizadeh, Ash A., Sweet-Cordero, E. Alejandro

“…Most circulating tumor DNA (ctDNA) assays are designed to detect recurrent mutations.Pediatric sarcomas share few recurrent mutations but rather are…”
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Abstract A35: Characterization of the genomic landscape of osteosarcoma metastasis by Koehne, Amanda L., Sayles, Leanne C., Breese, Marcus R., Vaka, Dedeepya, Sweet-Cordero, Alejandro

“…Abstract Early metastasis to the lungs is a cardinal feature of osteosarcoma (OS), and complications from metastatic disease remain the most common cause of…”
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Abstract B20: Integrative analysis of whole-genome and RNA sequencing in high-risk pediatric malignancies by Shah, Avanthi T., Breese, Marcus R., Lee, Alex G., Martell, Henry J., Tanasa, Bogdan, Leung, Stanley G., Spillingeer, Aviv, Liu, Heng-Yi, Behroozfard, Inge, Dinh, Phuong, Hazard, Florette K., Cho, Soo-Jin, Rangaswami, Arun, Lacayo, Norman J., Spunt, Sheri L., Cooney, Tabitha, Michlitsch, Jennifer G., Agarwaal, Anurag K., Sweet-Cordero, Alejandro

“…Abstract Targeted gene panel sequencing has become increasingly common in the management of pediatric cancer patients. For some patients, these cancer gene…”
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Abstract 214: Patient-specific mapping of oncogenic structural changes in pediatric osteosarcoma by Clugston, Andrew S., Ostrowski, Megan, Wu, Coco, Sayles, Leanne, Leung, Stanley G., Ramani, Vijay, Sweet-Cordero, E. Alejandro, Breese, Marcus R.

“…Abstract We have leveraged long-read and spatial sequencing modalities to identify patient-specific oncogenic alterations for treatment of pediatric…”
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Small molecule inhibition of cAMP response element binding protein in human acute myeloid leukemia cells by Mitton, B, Chae, H -D, Hsu, K, Dutta, R, Aldana-Masangkay, G, Ferrari, R, Davis, K, Tiu, B C, Kaul, A, Lacayo, N, Dahl, G, Xie, F, Li, B X, Breese, M R, Landaw, E M, Nolan, G, Pellegrini, M, Romanov, S, Xiao, X, Sakamoto, K M

“…The transcription factor CREB (cAMP Response-Element Binding Protein) is overexpressed in the majority of acute myeloid leukemia (AML) patients, and this is…”
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Abstract 3665: Integrative analysis of whole-genome and RNA sequencing in high-risk pediatric malignancies by Breese, Marcus R., Shah, Avanthi T., Lee, Alex G., Tanasa, Bogdan, Leung, Stanley G., Spillinger, Aviv, Liu, Heng-Yi, Behroozfard, Inge, Dinh, Phuong, Hazard, Florette K., Rangaswami, Arun, Spunt, Sheri L., Lacayo, Norman J., Cooney, Tabitha, Michlitsch, Jennifer G., Agrawal, Anurag K., Sweet-Cordero, E. Alejandro

“…Abstract Clinical use of gene-panel based sequencing has become increasingly common in the management of pediatric cancer patients. For many patients,…”
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