Publications

. Radiomic analysis of patient and interorgan heterogeneity in response to immunotherapies and BRAF-targeted therapy in metastatic melanoma. J Immunother Cancer. 2025-02-12;13(2): doi: 10.1136/jitc-2024-009568. PubMed PMID: 39939139; PMCID: PMC11822426.

. Long-term outcomes by lobular versus ductal histology in four NSABP adjuvant breast cancer trials. J Natl Cancer Inst. 2025-01-01; doi: 10.1093/jnci/djae188. PubMed PMID: 39128018; PMCID: PMC11717417.

. Ten challenges and opportunities in computational immuno-oncology. J Immunother Cancer. 2024-10-26;12(10): doi: 10.1136/jitc-2024-009721. PubMed PMID: 39461879; PMCID: PMC11529678.

. Spatial molecular profiling of mixed invasive ductal and lobular breast cancers reveals heterogeneity in intrinsic molecular subtypes, oncogenic signatures, and mutations. Proc Natl Acad Sci U S A. 2024-07-30;121(31):e2322068121. doi: 10.1073/pnas.2322068121. PubMed PMID: 39042692; PMCID: PMC11295029.

. International survey on invasive lobular breast cancer identifies priority research questions. NPJ Breast Cancer. 2024-07-20;10(1):61. doi: 10.1038/s41523-024-00661-3. PubMed PMID: 39033157; PMCID: PMC11271268.

. Facts and hopes in using omics to advance combined immunotherapy strategies. Clin Cancer Res. 2024-05-01; doi: 10.1158/1078-0432.CCR-22-2241. PubMed PMID: 38236069; PMCID: PMC11062841.

. Machine Learning Predicts Oxaliplatin Benefit in Early Colon Cancer. J Clin Oncol. 2024-05-01;JCO2301080. doi: 10.1200/JCO.23.01080. PubMed PMID: 38315963; PMCID: PMC11095904.

. Intragenic Rearrangement Burden Associates with Immune Cell Infiltration and Response to Immune Checkpoint Blockade in Cancer. Cancer Immunol Res. 2024-03-04;OF1-OF9. doi: 10.1158/2326-6066.CIR-22-0637. PubMed PMID: 38345376; PMCID: PMC11107381.

. Effects of socioeconomic status and race on survival and treatment in metastatic breast cancer. NPJ Breast Cancer. 2023-11-01;9(1):90. doi: 10.1038/s41523-023-00595-2. PubMed PMID: 37914742; PMCID: PMC10620133.

. Clinical Trial Strategies Fueled by Informatics Innovation Catalyze Translational Research. JAMA Netw Open. 2023-10-02;6(10):e2336480. doi: 10.1001/jamanetworkopen.2023.36480. PubMed PMID: 37796508.

. Identification of tumor-intrinsic drivers of immune exclusion in acral melanoma. J Immunother Cancer. 2023-10-01;11(10): doi: 10.1136/jitc-2023-007567. PubMed PMID: 37857525; PMCID: PMC10603348.

. The EstroGene Database Reveals Diverse Temporal, Context-Dependent, and Bidirectional Estrogen Receptor Regulomes in Breast Cancer. Cancer Res. 2023-08-15;83(16):2656-2674. doi: 10.1158/0008-5472.CAN-23-0539. PubMed PMID: 37272757; PMCID: PMC10527051.

. Discovering selective antiferroptotic inhibitors of the 15LOX/PEBP1 complex noninterfering with biosynthesis of lipid mediators. Proc Natl Acad Sci U S A. 2023-06-20;120(25):e2218896120. doi: 10.1073/pnas.2218896120. PubMed PMID: 37327313; PMCID: PMC10288584.

. The Great Immune Escape: Understanding the Divergent Immune Response in Breast Cancer Subtypes. Cancer Discov. 2023-01-09;13(1):23-40. doi: 10.1158/2159-8290.CD-22-0475. PubMed PMID: 36620880; PMCID: PMC9833841.

. The Great Immune Escape: Understanding the Divergent Immune Response in Breast Cancer Subtypes. Cancer Discov. 2022-12-06;OF1-OF18. doi: 10.1158/2159-8290.CD-22-0475. PubMed PMID: 36473061.

. Interpretable deep learning for chromatin-informed inference of transcriptional programs driven by somatic alterations across cancers. Nucleic Acids Res. 2022-10-28;50(19):10869-10881. doi: 10.1093/nar/gkac881. PubMed PMID: 36243974; PMCID: PMC9638905.

. An integral genomic signature approach for tailored cancer therapy using genome-wide sequencing data. Nat Commun. 2022-05-26;13(1):2936. doi: 10.1038/s41467-022-30449-7. PubMed PMID: 35618721; PMCID: PMC9135729.

. ESR1 mutant breast cancers show elevated basal cytokeratins and immune activation. Nat Commun. 2022-04-19;13(1):2011. doi: 10.1038/s41467-022-29498-9. PubMed PMID: 35440136; PMCID: PMC9019037.

. Hotspot ESR1 Mutations Are Multimodal and Contextual Modulators of Breast Cancer Metastasis. Cancer Res. 2022-04-01;82(7):1321-1339. doi: 10.1158/0008-5472.CAN-21-2576. PubMed PMID: 35078818; PMCID: PMC8983597.

. Coupling high-throughput mapping with proteomics analysis delineates cis-regulatory elements at high resolution. Nucleic Acids Res. 2022-01-11;50(1):e5. doi: 10.1093/nar/gkab890. PubMed PMID: 34634809; PMCID: PMC8754656.

. SPaRTAN, a computational framework for linking cell-surface receptors to transcriptional regulators. Nucleic Acids Res. 2021-09-27;49(17):9633-9647. doi: 10.1093/nar/gkab745. PubMed PMID: 34500467; PMCID: PMC8464045.

. Immunogenomic determinants of tumor microenvironment correlate with superior survival in high-risk neuroblastoma. J Immunother Cancer. 2021-07-01;9(7): doi: 10.1136/jitc-2021-002417. PubMed PMID: 34272305; PMCID: PMC8287618.

. Syngeneic tobacco carcinogen-induced mouse lung adenocarcinoma model exhibits PD-L1 expression and high tumor mutational burden. JCI Insight. 2021-02-08;6(3): doi: 10.1172/jci.insight.145307. PubMed PMID: 33351788; PMCID: PMC7934870.

. Fecal microbiome and metabolome differ in healthy and food-allergic twins. J Clin Invest. 2021-01-19;131(2): doi: 10.1172/JCI141935. PubMed PMID: 33463536; PMCID: PMC7810484.

. Single-Cell Transcriptomic Heterogeneity in Invasive Ductal and Lobular Breast Cancer Cells. Cancer Res. 2021-01-15;81(2):268-281. doi: 10.1158/0008-5472.CAN-20-0696. PubMed PMID: 33148662; PMCID: PMC7856056.

. Proteomic approach to discover human cancer viruses from formalin-fixed tissues. JCI Insight. 2020-11-19;5(22): doi: 10.1172/jci.insight.143003. PubMed PMID: 33055416; PMCID: PMC7710300.

. Multisystem Inflammatory Syndrome in Children in the United States. N Engl J Med. 2020-10-29;383(18):1794. doi: 10.1056/NEJMc2026136. PubMed PMID: 33085853.

. Molecular correlates and therapeutic targets in T cell-inflamed versus non-T cell-inflamed tumors across cancer types. Genome Med. 2020-10-27;12(1):90. doi: 10.1186/s13073-020-00787-6. PubMed PMID: 33106165; PMCID: PMC7590690.

. Live-cell imaging and analysis reveal cell phenotypic transition dynamics inherently missing in snapshot data. Sci Adv. 2020-09-01;6(36): doi: 10.1126/sciadv.aba9319. PubMed PMID: 32917609; PMCID: PMC7473671.

. Spatial domain analysis predicts risk of colorectal cancer recurrence and infers associated tumor microenvironment networks. Nat Commun. 2020-07-14;11(1):3515. doi: 10.1038/s41467-020-17083-x. PubMed PMID: 32665557; PMCID: PMC7360741.

. A sequential methodology for the rapid identification and characterization of breast cancer-associated functional SNPs. Nat Commun. 2020-07-03;11(1):3340. doi: 10.1038/s41467-020-17159-8. PubMed PMID: 32620845; PMCID: PMC7334201.

. Differences in the intrinsic spatial dynamics of the chromatin contribute to cell differentiation. Nucleic Acids Res. 2020-02-20;48(3):1131-1145. doi: 10.1093/nar/gkz1102. PubMed PMID: 31828312; PMCID: PMC7026660.

. Metastatic breast cancers have reduced immune cell recruitment but harbor increased macrophages relative to their matched primary tumors. J Immunother Cancer. 2019-10-18;7(1):265. doi: 10.1186/s40425-019-0755-1. PubMed PMID: 31627744; PMCID: PMC6798422.

. Chromatin-informed inference of transcriptional programs in gynecologic and basal breast cancers. Nat Commun. 2019-09-25;10(1):4369. doi: 10.1038/s41467-019-12291-6. PubMed PMID: 31554806; PMCID: PMC6761109.

. Shared Signature Dynamics Tempered by Local Fluctuations Enables Fold Adaptability and Specificity. Mol Biol Evol. 2019-09-01;36(9):2053-2068. doi: 10.1093/molbev/msz102. PubMed PMID: 31028708; PMCID: PMC6736388.

. Monoamine transporters: structure, intrinsic dynamics and allosteric regulation. Nat Struct Mol Biol. 2019-07-01;26(7):545-556. doi: 10.1038/s41594-019-0253-7. PubMed PMID: 31270469; PMCID: PMC6712983.

. Comprehensive Phenotypic Characterization of Human Invasive Lobular Carcinoma Cell Lines in 2D and 3D Cultures. Cancer Res. 2018-11-01;78(21):6209-6222. doi: 10.1158/0008-5472.CAN-18-1416. PubMed PMID: 30228172; PMCID: PMC6507416.

. Loss of E-cadherin Enhances IGF1-IGF1R Pathway Activation and Sensitizes Breast Cancers to Anti-IGF1R/InsR Inhibitors. Clin Cancer Res. 2018-10-15;24(20):5165-5177. doi: 10.1158/1078-0432.CCR-18-0279. PubMed PMID: 29941485; PMCID: PMC6821389.

. High-throughput identification of noncoding functional SNPs via type IIS enzyme restriction. Nat Genet. 2018-08-01;50(8):1180-1188. doi: 10.1038/s41588-018-0159-z. PubMed PMID: 30013183; PMCID: PMC6072570.

. Developmental Loci Harbor Clusters of Accelerated Regions That Evolved Independently in Ape Lineages. Mol Biol Evol. 2018-08-01;35(8):2034-2045. doi: 10.1093/molbev/msy109. PubMed PMID: 29897475; PMCID: PMC6063267.

. Active Estrogen Receptor-alpha Signaling in Ovarian Cancer Models and Clinical Specimens. Clin Cancer Res. 2017-07-15;23(14):3802-3812. doi: 10.1158/1078-0432.CCR-16-1501. PubMed PMID: 28073843; PMCID: PMC5503796.

. Intrinsic Subtype Switching and Acquired ERBB2/HER2 Amplifications and Mutations in Breast Cancer Brain Metastases. JAMA Oncol. 2017-05-01;3(5):666-671. doi: 10.1001/jamaoncol.2016.5630. PubMed PMID: 27926948; PMCID: PMC5508875.

. Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings. Nucleic Acids Res. 2017-04-20;45(7):3663-3673. doi: 10.1093/nar/gkx172. PubMed PMID: 28334818; PMCID: PMC5397156.

. Non-coding single nucleotide variants affecting estrogen receptor binding and activity. Genome Med. 2016-12-13;8(1):128. doi: 10.1186/s13073-016-0382-0. PubMed PMID: 27964748; PMCID: PMC5154163.

. Signal-Oriented Pathway Analyses Reveal a Signaling Complex as a Synthetic Lethal Target for p53 Mutations. Cancer Res. 2016-12-01;76(23):6785-6794. doi: 10.1158/0008-5472.CAN-16-1740. PubMed PMID: 27758891; PMCID: PMC5165695.

. Intratumor Heterogeneity Affects Gene Expression Profile Test Prognostic Risk Stratification in Early Breast Cancer. Clin Cancer Res. 2016-11-01;22(21):5362-5369. doi: 10.1158/1078-0432.CCR-15-2889. PubMed PMID: 27185370; PMCID: PMC5093028.

. Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data. Nucleic Acids Res. 2016-03-18;44(5):e47. doi: 10.1093/nar/gkv1234. PubMed PMID: 26582927; PMCID: PMC4797269.

. Sensitive Detection of Mono- and Polyclonal ESR1 Mutations in Primary Tumors, Metastatic Lesions, and Cell-Free DNA of Breast Cancer Patients. Clin Cancer Res. 2016-03-01;22(5):1130-7. doi: 10.1158/1078-0432.CCR-15-1534. PubMed PMID: 26500237; PMCID: PMC4775406.

. iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics. Nucleic Acids Res. 2016-01-04;44(D1):D415-22. doi: 10.1093/nar/gkv1236. PubMed PMID: 26582920; PMCID: PMC4702874.