TS
Timothy I. Shaw
Leukemia, Myeloid, AcuteproteomicsSoftwareGene Expression Profilingmass spectrometryBrain Neoplasmsdatabase searchgenomicsMelanomapediatric cancer
On Valency
published · living versionsW_26xzgw86·v1 · currentpublished
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
with Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov, Paul Baranay +86
1 version
Preprints & journals
84 papers in the corpus · 2010–2026The E3 ubiquitin ligase HECTD3 controls immune colonic inflammation by restricting MyD88 activation and signaling.42784256 · Islam, Shamima, Mannan, Shahnewaj, Zuniga, Ashley et al.2026 · 0 citationsJCI insight. 2026;11(20)
BCL11B targeting in tumor CD8 + T cells amplifies anti-tumor response by blocking exhaustion while promoting stemness and cytotoxicity.42601873 · Silvane, Leonardo, Zelenka, Tomas, Talada, Divya P et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2026
The Oncology Research Information Exchange Network (ORIEN) - Building a Real-World Collaborative, Patient-driven Infrastructure for Discovery Research and Precision Oncology.42281974 · Churchman, Michelle L, Lu, Xin, McKean, David M et al.2026 · 0 citationsResearch square. 2026
Taxane chemotherapy promotes response to TIM-3 checkpoint blockade via STING-mediated ER stress and HMGB1 secretion.42097146 · Onimus, Alexis, Celias, Daiana, Chang, Shiun et al.2026 · 1 citationCell reports. Medicine. 2026;7(5):102788
Medium-Chain Fatty Acid Receptor GPR84 Modulates Cytotoxic CD8 T-cell Antitumor Immunity through Metabolic Reprogramming.41557755 · Philbrook, Phaethon, Dean, Matthew J, Sanchez-Pino, Maria Dulfary et al.2026 · 2 citationsCancer immunology research. 2026;14(4):640-657
Spatial Transcriptomics Reveals Distinct Architectures but Shared Vulnerabilities in Primary and Metastatic Liver Tumors.41097737 · Adapa, Swamy R, Porshe, Sahanama, Talada, Divya Priyanka et al.2025 · 12 citationsCancers. 2025;17(19)
Lymphoma accelerates T cell and tissue aging.40845845 · Hesterberg, Rebecca S, Davis, Joshua T, Handoo, Komal J et al.2025 · 12 citationsCancer cell. 2025;43(10):1917-1936.e8
ShinyEvents: harmonizing longitudinal data for real world survival estimation.40799741 · Obermayer, Alyssa, Davis, Joshua, Talada, Divya Priyanka et al.2026 · 1 citationResearch square. 2025
SmartImpute is a targeted imputation framework for single-cell transcriptome data.40763742 · Yao, Sijie, Li, Tingyi, Davis, Joshua T et al.2025 · 2 citationsCell reports methods. 2025;5(8):101122
Integrative Immune Signature of Complementary Circulating and Tumoral Biomarkers Maximizes the Predictive Power of Adjuvant Immunotherapeutic Benefits in High-risk Melanoma.40392969 · Tarhini, Ahmad A, Obermayer, Alyssa, Lee, Sandra J et al.2025 · 4 citationsClinical cancer research : an official journal of the American Association for Cancer Research. 2025;31(15):3249-3258
Mitigating T-cell mitochondrial dysfunction in CLL to augment CAR T-cell therapy: evaluation in an immunocompetent model.39938006 · Gamal, Wael, Goedhart, Nienke B, Simon-Molas, Helga et al.2025 · 13 citationsBlood advances. 2025;9(10):2511-2529
CAR T cell-driven induction of iNOS in tumor-associated macrophages promotes CAR T cell resistance in B cell lymphoma.40235478 · Davila, Marco, Lee, Sae Bom, Kang, Yun Pyo et al.2026 · 3 citationsResearch square. 2025
Effector T cells under hypoxia have an altered transcriptome similar to tumor-stressed T cells found in non-responsive melanoma patients.40010774 · Nagy, Mate Z, Plaza-Rojas, Lourdes B, Boucher, Justin C et al.2025 · 13 citationsJournal for immunotherapy of cancer. 2025;13(2)
Interleukin-1α release during necrotic-like cell death generates myeloid-driven immunosuppression that restricts anti-tumor immunity.39577420 · Hänggi, Kay, Li, Jie, Gangadharan, Achintyan et al.2024 · 76 citationsCancer cell. 2024;42(12):2015-2031.e11
IL-18R supported CAR T cells targeting oncofetal tenascin C for the immunotherapy of pediatric sarcoma and brain tumors.39572158 · Wickman, Elizabeth, Lange, Shannon, Wagner, Jessica et al.2024 · 27 citationsJournal for immunotherapy of cancer. 2024;12(11)
BatchFLEX: feature-level equalization of X-batch.39360977 · Davis, Joshua T, Obermayer, Alyssa N, Soupir, Alex C et al.2024 · 3 citationsBioinformatics (Oxford, England). 2024;40(10)
Jagged2 targeting in lung cancer activates anti-tumor immunity via Notch-induced functional reprogramming of tumor-associated macrophages.38636522 · Mandula, Jay K, Sierra-Mondragon, Rosa A, Jimenez, Rachel V et al.2024 · 35 citationsImmunity. 2024;57(5):1124-1140.e9
Comprehensive genomic analysis reveals molecular heterogeneity in pediatric ALK-positive anaplastic large cell lymphoma.38585847 · Shaw, Timothy I, Pounds, Stanley, Cao, Xueyuan et al.2025 · 9 citationsResearch square. 2024
An Epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level.38335222 · Liu, Xiang, Gillis, Nancy, Jiang, Chang et al.2024 · 1 citationPLoS computational biology. 2024;20(2):e1011873
Discovery of immunotherapy targets for pediatric solid and brain tumors by exon-level expression.38260279 · Shaw, Timothy I, Wagner, Jessica, Tian, Liqing et al.2024 · 27 citationsResearch square. 2024
Genetic and epigenetic features of bilateral Wilms tumor predisposition in patients from the Children's Oncology Group AREN18B5-Q.38110397 · Murphy, Andrew J, Cheng, Changde, Williams, Justin et al.2023 · 34 citationsNature communications. 2023;14(1):8006
CBFA2T3-GLIS2-dependent pediatric acute megakaryoblastic leukemia is driven by GLIS2 and sensitive to navitoclax.37716355 · Neault, Mathieu, Lebert-Ghali, Charles-Étienne, Fournier, Marilaine et al.2023 · 15 citationsCell reports. 2023;42(9):113084
Comprehensive molecular and clinical characterization of NUP98 fusions in pediatric acute myeloid leukemia.36815378 · Bertrums, Eline J M, Smith, Jenny L, Harmon, Lauren et al.2023 · 83 citationsHaematologica. 2023;108(8):2044-2058
BERLIN: Basic Explorer for single-cell RNAseq analysis and cell Lineage Determination.10.1101/2023.07.13.548919v1 · Nobles, G., Obermayer, A., Yang, C.-Y. et al.2023 · 1 citationbioRxiv
An Assessment of the Penile Squamous Cell Carcinoma Surfaceome for Biomarker and Therapeutic Target Discovery.37509297 · Grass, George Daniel, Ercan, Dalia, Obermayer, Alyssa N et al.2023 · 2 citationsCancers. 2023;15(14)
PATH-SURVEYOR: pathway level survival enquiry for immuno-oncology and drug repurposing.37380943 · Obermayer, Alyssa N, Chang, Darwin, Nobles, Gabrielle et al.2023 · 8 citationsBMC bioinformatics. 2023;24(1):266
Bcl11b sustains multipotency and restricts effector programs of intestinal-resident memory CD8+ T cells.37115913 · Helm, Eric Y, Zelenka, Tomas, Cismasiu, Valeriu B et al.2023 · 21 citationsScience immunology. 2023;8(82):eabn0484
Etiology of oncogenic fusions in 5,190 childhood cancers and its clinical and therapeutic implication.37019972 · Liu, Yanling, Klein, Jonathon, Bajpai, Richa et al.2023 · 37 citationsNature communications. 2023;14(1):1739
Malignant Progression of an Ancestral Bone Marrow Clone Harboring a CIC-NUTM2A Fusion in Isolated Myeloid Sarcoma.36637394 · Kamens, Jennifer L, Dang, Jinjun, Shaw, Timothy I et al.2023 · 4 citationsMolecular cancer research : MCR. 2023;21(4):301-306
The Genetic and Epigenetic Features of Bilateral Wilms Tumor Predisposition: A Report from the Children's Oncology Group AREN18B5-Q Study.36993649 · Murphy, Andrew J, Cheng, Changde, Williams, Justin et al.2025 · 2 citationsResearch square. 2023
DRPPM-PATH-SURVEIOR: Plug-and-Play Survival Analysis of Pathway-level Signatures and Immune Components.36993526 · Obermayer, Alyssa, Chang, Darwin, Nobles, Gabrielle et al.2024 · 0 citationsResearch square. 2023
Long Noncoding RNA Expression Independently Predicts Outcome in Pediatric Acute Myeloid Leukemia.36795987 · Farrar, Jason E, Smith, Jenny L, Othus, Megan et al.2023 · 31 citationsJournal of clinical oncology : official journal of the American Society of Clinical Oncology. 2023;41(16):2949-2962
Multi-omics approach to identifying isoform variants as therapeutic targets in cancer patients.36505834 · Shaw, Timothy I, Zhao, Bi, Li, Yuxin et al.2022 · 17 citationsFrontiers in oncology. 2022;12:1051487
Alzheimer's disease-associated U1 snRNP splicing dysfunction causes neuronal hyperexcitability and cognitive impairment.36636325 · Chen, Ping-Chung, Han, Xian, Shaw, Timothy I et al.2023 · 61 citationsNature aging. 2022;2(10):923-940
Ablation of the endoplasmic reticulum stress kinase PERK induces paraptosis and type I interferon to promote anti-tumor T cell responses.36150390 · Mandula, Jessica K, Chang, Shiun, Mohamed, Eslam et al.2022 · 175 citationsCancer cell. 2022;40(10):1145-1160.e9
Integrated stem cell signature and cytomolecular risk determination in pediatric acute myeloid leukemia.36123353 · Huang, Benjamin J, Smith, Jenny L, Farrar, Jason E et al.2022 · 48 citationsNature communications. 2022;13(1):5487
Summarizing internal dynamics boosts differential analysis and functional interpretation of super enhancers.35234924 · Liu, Xiang, Zhao, Bo, Shaw, Timothy I et al.2022 · 6 citationsNucleic acids research. 2022;50(6):3115-3127
DRPPM-EASY: A Web-Based Framework for Integrative Analysis of Multi-Omics Cancer Datasets.35205126 · Obermayer, Alyssa, Dong, Li, Hu, Qianqian et al.2024 · 8 citationsBiology. 2022;11(2)
Chromatin architecture at susceptible gene loci in cerebellar Purkinje cells characterizes DNA damage-induced neurodegeneration.34910524 · Kwak, Young Don, Shaw, Timothy I, Downing, Susanna M et al.2024 · 30 citationsScience advances. 2021;7(51):eabg6363
CBFB-MYH11 fusion transcripts distinguish acute myeloid leukemias with distinct molecular landscapes and outcomes.34547772 · Huang, Benjamin J, Smith, Jenny L, Wang, Yi-Cheng et al.2022 · 12 citationsBlood advances. 2021;5(23):4963-4968
The landscape of coding RNA editing events in pediatric cancer.34789196 · Wen, Ji, Rusch, Michael, Brady, Samuel W et al.2022 · 19 citationsBMC cancer. 2021;21(1):1233
JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics.34747401 · Vanderwall, David, Suresh, Poudel, Fu, Yingxue et al.2022 · 13 citationsJournal of visualized experiments : JoVE. 2021(176)
Genome instability independent of type I interferon signaling drives neuropathology caused by impaired ribonucleotide excision repair.34655526 · Aditi, Downing, Susanna M, Schreiner, Patrick A et al.2022 · 40 citationsNeuron. 2021;109(24):3962-3979.e6
Metabolomic and transcriptomic analysis reveals endogenous substrates and metabolic adaptation in rats lacking Abcg2 and Abcb1a transporters.34255797 · Ganguly, Samit, Finkelstein, David, Shaw, Timothy I et al.2021 · 23 citationsPloS one. 2021;16(7):e0253852
Cell-surface antigen profiling of pediatric brain tumors: B7-H3 is consistently expressed and can be targeted via local or systemic CAR T-cell delivery.33320196 · Haydar, Dalia, Houke, Haley, Chiang, Jason et al.2021 · 147 citationsNeuro-oncology. 2021;23(6):999-1011
Integrative network analysis reveals USP7 haploinsufficiency inhibits E-protein activity in pediatric T-lineage acute lymphoblastic leukemia (T-ALL).33664368 · Shaw, Timothy I, Dong, Li, Tian, Liqing et al.2021 · 12 citationsScientific reports. 2021;11(1):5154
Antitumor Effects of CAR T Cells Redirected to the EDB Splice Variant of Fibronectin.33355188 · Wagner, Jessica, Wickman, Elizabeth, Shaw, Timothy I et al.2021 · 46 citationsCancer immunology research. 2021;9(3):279-290
Toxicoproteomic Profiling of hPXR Transgenic Mice Treated with Rifampicin and Isoniazid.32660103 · Brewer, Christopher Trent, Kodali, Kiran, Wu, Jing et al.2021 · 9 citationsCells. 2020;9(7)
Deep Multilayer Brain Proteomics Identifies Molecular Networks in Alzheimer's Disease Progression.32437656 · Bai, Bing, Wang, Xusheng, Li, Yuxin et al.2020 · 78 citationsNeuron. 2020;106(4):700
JUMPm: A Tool for Large-Scale Identification of Metabolites in Untargeted Metabolomics.32408578 · Wang, Xusheng, Cho, Ji-Hoon, Poudel, Suresh et al.2020 · 26 citationsMetabolites. 2020;10(5)
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