Explanipedia

sCCIgen: a high-fidelity spatially resolved transcriptomics data simulator for cell–cell interaction studies Open

Xiaoyu Song, Joselyn Cristina Chávez-Fuentes, Weiping Ma, Weijia Fu, Sujung Crystal Shin , et al. · 2025

sCCIgen: A high-fidelity spatially resolved transcriptomics data simulator for cell-cell interaction studies Open

Xiaoyu Song, Joselyn Cristina Chávez-Fuentes, Weiping Ma, Weijia Fu, Pei Wang , et al. · 2025

Spatially resolved transcriptomics (SRT) provides an invaluable avenue for examining cell-cell interactions within native tissue environments. The development and evaluation of analytical tools for SRT data necessitate tools for generating…

The Open Pediatric Cancer Project Open

Zhuangzhuang Geng, Eric Wafula, Ryan J. Corbett, Yuanchao Zhang, Run Jin , et al. · 2025

Background In 2019, the Open Pediatric Brain Tumor Atlas (OpenPBTA) was created as a global, collaborative open-science initiative to genomically characterize 1,074 pediatric brain tumors and 22 patient-derived cell lines. Here, we present…

Protocol for using Multiomics2Targets to identify targets and driver kinases for cancer cohorts profiled with multi-omics assays Open

Giacomo B. Marino, Eden Z. Deng, Daniel Clarke, Ido Diamant, Adam Resnick , et al. · 2024

Prediction of hepatocellular carcinoma response to radiation segmentectomy using an MRI-based machine learning approach Open

Daniel Stocker, Stefanie J. Hectors, Brett Marinelli, Guillermo Carbonell, Octavia Bane , et al. · 2024

Multiomics2Targets identifies targets from cancer cohorts profiled with transcriptomics, proteomics, and phosphoproteomics Open

Eden Z. Deng, Giacomo B. Marino, Daniel Clarke, Ido Diamant, Adam Resnick , et al. · 2024

The availability of multi-omics data applied to profile cancer cohorts is rapidly increasing. Multiomics2Targets is a computational pipeline that can identify driver cell signaling pathways, protein kinases, and cell-surface targets for im…

The Open Pediatric Cancer Project Open

Zhuangzhuang Geng, Eric Wafula, Ryan J. Corbett, Yuanchao Zhang, Run Jin , et al. · 2024

Background In 2019, the Open Pediatric Brain Tumor Atlas (OpenPBTA) was created as a global, collaborative open-science initiative to genomically characterize 1,074 pediatric brain tumors and 22 patient-derived cell lines. Here, we present…

Multi-scale signaling and tumor evolution in high-grade gliomas Open

Jingxian Liu, Song Cao, Kathleen J. Imbach, Marina Gritsenko, T. Mamie Lih , et al. · 2024

Multiomic foundations of human prefrontal cortex tissue function Open

Brian H. Kopell, Deepak Kaji, Lora E. Liharska, Eric Vornholt, Alissa A. Valentine , et al. · 2024

The prefrontal cortex (PFC) is a region of the brain that in humans is involved in the production of higher-order functions such as cognition, emotion, perception, and behavior. Neurotransmission in the PFC produces higher-order functions …

Comprehensive proteogenomic characterization of rare kidney tumors Open

Ginny Xiaohe Li, Lijun Chen, Yi Hsiao, Rahul Mannan, Yuping Zhang , et al. · 2024

Non-clear cell renal cell carcinomas (non-ccRCCs) encompass diverse malignant and benign tumors. Refinement of differential diagnosis biomarkers, markers for early prognosis of aggressive disease, and therapeutic targets to complement immu…

Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer Open

Shrabanti Chowdhury, Jacob J. Kennedy, Richard G. Ivey, Oscar Murillo, Noshad Hosseini , et al. · 2024

Pan-cancer proteogenomics characterization of tumor immunity Open

Francesca Petralia, Weiping Ma, Tomer M. Yaron, Francesca Pia Caruso, Nicole Tignor , et al. · 2024

RECCIPE: A new framework assessing localized cell-cell interaction on gene expression in multicellular ST data Open

Weiping Ma, Xiaoyu Song, Guo‐Cheng Yuan, Pei Wang · 2024

Cell-cell interaction (CCI) plays a pivotal role in cellular communication within the tissue microenvironment. The recent development of spatial transcriptomics (ST) technology and associated data analysis methods has empowered researchers…

EPCO-53. MULTI-SCALE REGULATION OF SIGNALING CASCADES AND TUMOR EVOLUTION IN HIGH GRADE ASTROCYTOMAS Open

Milan G. Chheda, Jingxian Liu, Song Cao, Kathleen J. Imbach, Marina Gritsenko , et al. · 2023

The National Cancer Institute Clinical Proteomic Atlas Consortium (CPTAC) herein reports our deep characterization of 228 grade IV IDH1 WT and mutant astrocytomas (including 28 matched primary and recurrent GBMs) using 15 proteogenomic and…

Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin Open

Wen-Wei Liang, Rita Jui-Hsien Lu, Reyka G. Jayasinghe, Steven M. Foltz, Eduard Porta‐Pardo , et al. · 2023

Deep learning integrates histopathology and proteogenomics at a pan-cancer level Open

Joshua M. Wang, Runyu Hong, Elizabeth G. Demicco, Jimin Tan, Rossana Lazcano , et al. · 2023

Proteogenomic data and resources for pan-cancer analysis Open

Yize Li, Yongchao Dou, Felipe da Veiga Leprevost, Yifat Geffen, Anna Calinawan , et al. · 2023

Pan-cancer proteogenomics connects oncogenic drivers to functional states Open

Yize Li, Eduard Porta‐Pardo, Collin Tokheim, Matthew H. Bailey, Tomer M. Yaron , et al. · 2023

Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer Open

Shrabanti Chowdhury, Jacob J. Kennedy, Richard G. Ivey, Oscar Murillo, Noshad Hosseini , et al. · 2023

To improve the understanding of chemo-refractory high-grade serous ovarian cancers (HGSOCs), we characterized the proteogenomic landscape of 242 (refractory and sensitive) HGSOCs, representing one discovery and two validation cohorts acros…

Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation Open

Yifat Geffen, Shankara Anand, Yo Akiyama, Tomer M. Yaron, Yizhe Song , et al. · 2023

Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness Open

Yize Li, T. Mamie Lih, Saravana M. Dhanasekaran, Rahul Mannan, Lijun Chen , et al. · 2022

CPTAC Pancancer Phosphoproteomics Kinase Enrichment Analysis with ProKAP Provides Insights into Immunogenic Signaling Pathways Open

Anna Calinawan, Weiping Ma, John Erol Evangelista, Boris Reva, Francesca Petralia , et al. · 2021

The National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) initiative has generated extensive phosphoproteomics and proteomics data for tumor and tumor-adjacent normal tissue across multiple cancer types. This…

Importance of applying Mixed Generalized Additive Model (MGAM) as a method for assessing the environmental health impacts: Ambient temperature and Acute Myocardial Infarction (AMI), among elderly in Shanghai, China Open

Xiaoqian Huang, Weiping Ma, Chi-kin Law, Jianfeng Luo, Naiqing Zhao · 2021

Association between acute myocardial infarction (AMI) morbidity and ambient temperature has been examined with generalized linear model (GLM) or generalized additive model (GAM). However, the effect size by these two methods might be biase…

A community effort to identify and correct mislabeled samples in proteogenomic studies Open

Seungyeul Yoo, Zhiao Shi, Bo Wen, Soon Jye Kho, Renke Pan , et al. · 2021

Proteogenomic and metabolomic characterization of human glioblastoma Open

Liang-Bo Wang, Alla Karpova, Marina Gritsenko, Jennifer Kyle, Song Cao , et al. · 2021

TBIO-19. INTEGRATED GENOMIC, PROTEOMIC AND PHOSPHOPROTEOMIC ANALYSIS OF SEVEN TYPES OF PEDIATRIC BRAIN CANCER Open

Francesca Petralia, Nicole Tignor, Dmitri Rykunov, Boris Revas, Shrabanti Chowdhury , et al. · 2020

We performed a comprehensive proteogenomic analysis across seven childhood brain tumors for a deeper understanding of their functional biology. Whole genome sequencing, RNAseq, quantitative proteomic profiling and phosphoproteomics were pe…

Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer Open

Francesca Petralia, Nicole Tignor, Boris Reva, Mateusz Koptyra, Shrabanti Chowdhury , et al. · 2020

Multiscale causal networks identify VGF as a key regulator of Alzheimer’s disease Open

Noam D. Beckmann, Wei‐Jye Lin, Minghui Wang, Ariella Cohain, Alexander W. Charney , et al. · 2020

Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics Open

Mi Yang, Francesca Petralia, Zhi Li, Hongyang Li, Weiping Ma , et al. · 2020

Cancer is driven by genomic alterations, but the processes causing this disease are largely performed by proteins. However, proteins are harder and more expensive to measure than genes and transcripts. To catalyze developments of methods t…

DreamAI: algorithm for the imputation of proteomics data Open

Weiping Ma, Sunkyu Kim, Shrabanti Chowdhury, Zhi Li, Mi Yang , et al. · 2020

Deep proteomics profiling using labeled LC-MS/MS experiments has been proven to be powerful to study complex diseases. However, due to the dynamic nature of the discovery mass spectrometry, the generated data contain a substantial fraction…

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