Publications

Data Science

Zhang H, Lee S, Muthakana RR, Lu B, Boone DN, Lee D, Wang XS. Intragenic Rearrangement Burden Associates with Immune Cell Infiltration and Response to Immune Checkpoint Blockade in Cancer. Cancer Immunol Res. 2024-02-09;OF1-OF9. doi: 10.1158/2326-6066.CIR-22-0637. PubMed PMID: 38345376.
Chen L, Wang Y, Cai C, Ding Y, Kim RS, Lipchik C, Gavin PG, Yothers G, Allegra CJ, Petrelli NJ, Suga JM, Hopkins JO, Saito NG, Evans T, Jujjavarapu S, Wolmark N, Lucas PC, Paik S, Sun M, Pogue-Geile KL, Lu X. Machine Learning Predicts Oxaliplatin Benefit in Early Colon Cancer. J Clin Oncol. 2024-02-05;JCO2301080. doi: 10.1200/JCO.23.01080. PubMed PMID: 38315963.
Augustin RC, Cai WL, Luke JJ, Bao R. Facts and hopes in using omics to advance combined immunotherapy strategies. Clin Cancer Res. 2024-01-18; doi: 10.1158/1078-0432.CCR-22-2241. PubMed PMID: 38236069.
Puthanmadhom Narayanan S, Ren D, Oesterreich S, Lee AV, Rosenzweig MQ, Brufsky AM. 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.
Becich MJ. 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.
Augustin RC, Newman S, Li A, Joy M, Lyons M, Pham MP, Lucas P, Smith K, Sander C, Isett B, Davar D, Najjar YG, Zarour HM, Kirkwood JM, Luke JJ, Bao R. 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.
Rashid R, Copelli S, Silverstein JC, Becich MJ. REDCap and the National Mesothelioma Virtual Bank-a scalable and sustainable model for rare disease biorepositories. J Am Med Inform Assoc. 2023-09-25; doi: 10.1093/jamia/ocad132. PubMed PMID: 37487555; PMCID: PMC10531116.
Li Z, Li T, Yates ME, Wu Y, Ferber A, Chen L, Brown DD, Carroll JS, Sikora MJ, Tseng GC, Oesterreich S, Lee AV. 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.
Ramjattun K, Ma X, Gao SJ, Singh H, Osmanbeyoglu HU. COVID-19db linkage maps of cell surface proteins and transcription factors in immune cells. J Med Virol. 2023-06-01;95(6):e28887. doi: 10.1002/jmv.28887. PubMed PMID: 37341527; PMCID: PMC10478683.
Vilardaga JP, Clark LJ, White AD, Sutkeviciute I, Lee JY, Bahar I. Molecular Mechanisms of PTH/PTHrP Class B GPCR Signaling and Pharmacological Implications. Endocr Rev. 2023-05-08;44(3):474-491. doi: 10.1210/endrev/bnac032. PubMed PMID: 36503956; PMCID: PMC10461325.
Oesterreich S, Lee AV, Carleton N. Response to Maltoni, Puccetti, Poli, et al. J Natl Cancer Inst. 2023-04-11;115(4):479-481. doi: 10.1093/jnci/djad022. PubMed PMID: 36762844; PMCID: PMC10086617.
Oesterreich S, Aird KM. Senescence and Immunotherapy: Redundant Immunomodulatory Pathways Promote Resistance. Cancer Immunol Res. 2023-04-03;11(4):401-404. doi: 10.1158/2326-6066.CIR-23-0051. PubMed PMID: 36826438.
Zong W, Rahman T, Zhu L, Zeng X, Zhang Y, Zou J, Liu S, Ren Z, Li JJ, Sibille E, Lee AV, Oesterreich S, Ma T, Tseng GC. Transcriptomic congruence analysis for evaluating model organisms. Proc Natl Acad Sci U S A. 2023-02-07;120(6):e2202584120. doi: 10.1073/pnas.2202584120. PubMed PMID: 36730203; PMCID: PMC9963430.
Wu T, Wu Y, Jiang D, Sun W, Zou M, Vasamsetti SB, Dutta P, Leers SA, Di W, Li G. SATB2, coordinated with CUX1, regulates IL-1β-induced senescence-like phenotype in endothelial cells by fine-tuning the atherosclerosis-associated p16(INK4a) expression. Aging Cell. 2023-02-01;22(2):e13765. doi: 10.1111/acel.13765. PubMed PMID: 36633253; PMCID: PMC9924951.
Onkar SS, Carleton NM, Lucas PC, Bruno TC, Lee AV, Vignali DAA, Oesterreich S. 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.
Onkar SS, Carleton NM, Lucas PC, Bruno TC, Lee AV, Vignali DAA, Oesterreich S. 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.
Oesterreich S, Nasrazadani A, Zou J, Carleton N, Onger T, Wright MD, Li Y, Demanelis K, Ramaswamy B, Tseng G, Lee AV, Williams N, Kruse M. Clinicopathological Features and Outcomes Comparing Patients With Invasive Ductal and Lobular Breast Cancer. J Natl Cancer Inst. 2022-11-14;114(11):1511-1522. doi: 10.1093/jnci/djac157. PubMed PMID: 36239760; PMCID: PMC9664185.
Tao Y, Ma X, Palmer D, Schwartz R, Lu X, Osmanbeyoglu HU. 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.
Wang XS, Lee S, Zhang H, Tang G, Wang Y. 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.
Li Z, McGinn O, Wu Y, Bahreini A, Priedigkeit NM, Ding K, Onkar S, Lampenfeld C, Sartorius CA, Miller L, Rosenzweig M, Cohen O, Wagle N, Richer JK, Muller WJ, Buluwela L, Ali S, Bruno TC, Vignali DAA, Fang Y, Zhu L, Tseng GC, Gertz J, Atkinson JM, Lee AV, Oesterreich S. 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.
Li Z, Wu Y, Yates ME, Tasdemir N, Bahreini A, Chen J, Levine KM, Priedigkeit NM, Nasrazadani A, Ali S, Buluwela L, Arnesen S, Gertz J, Richer JK, Troness B, El-Ashry D, Zhang Q, Gerratana L, Zhang Y, Cristofanilli M, Montanez MA, Sundd P, Wallace CT, Watkins SC, Fumagalli C, Guerini-Rocco E, Zhu L, Tseng GC, Wagle N, Carroll JS, Jank P, Denkert C, Karsten MM, Blohmer JU, Park BH, Lucas PC, Atkinson JM, Lee AV, Oesterreich S. 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.
Wu T, Jiang D, Zou M, Sun W, Wu D, Cui J, Huntress I, Peng X, Li G. 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.
Ma X, Somasundaram A, Qi Z, Hartman DJ, Singh H, Osmanbeyoglu HU. 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.
Chen F, Shi Q, Pei F, Vogt A, Porritt RA, Garcia G Jr, Gomez AC, Cheng MH, Schurdak ME, Liu B, Chan SY, Arumugaswami V, Stern AM, Taylor DL, Arditi M, Bahar I. A systems-level study reveals host-targeted repurposable drugs against SARS-CoV-2 infection. Mol Syst Biol. 2021-08-01;17(8):e10239. doi: 10.15252/msb.202110239. PubMed PMID: 34339582; PMCID: PMC8328275.
Bao R, Spranger S, Hernandez K, Zha Y, Pytel P, Luke JJ, Gajewski TF, Volchenboum SL, Cohn SL, Desai AV. 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.
Meirovitch H, Bahar I. Harold A. Scheraga (10/18/1921-8/1/2020): A pioneering scientist who laid the foundations of protein science in the 20th century. Proc Natl Acad Sci U S A. 2021-02-23;118(8): doi: 10.1073/pnas.2026796118. PubMed PMID: 33547253; PMCID: PMC7923550.
Bao R, Hesser LA, He Z, Zhou X, Nadeau KC, Nagler CR. 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.
Chen F, Ding K, Priedigkeit N, Elangovan A, Levine KM, Carleton N, Savariau L, Atkinson JM, Oesterreich S, Lee AV. 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.
Arditi M, Bahar I. 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.
Bao R, Stapor D, Luke JJ. 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.
Cheng MH, Zhang S, Porritt RA, Noval Rivas M, Paschold L, Willscher E, Binder M, Arditi M, Bahar I. Superantigenic character of an insert unique to SARS-CoV-2 spike supported by skewed TCR repertoire in patients with hyperinflammation. Proc Natl Acad Sci U S A. 2020-10-13;117(41):25254-25262. doi: 10.1073/pnas.2010722117. PubMed PMID: 32989130; PMCID: PMC7568239.
Levine KM, Ding K, Chen L, Oesterreich S. FGFR4: A promising therapeutic target for breast cancer and other solid tumors. Pharmacol Ther. 2020-10-01;214107590. doi: 10.1016/j.pharmthera.2020.107590. PubMed PMID: 32492514; PMCID: PMC7494643.
Wang W, Douglas D, Zhang J, Kumari S, Enuameh MS, Dai Y, Wallace CT, Watkins SC, Shu W, Xing J. 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.
Uttam S, Stern AM, Sevinsky CJ, Furman S, Pullara F, Spagnolo D, Nguyen L, Gough A, Ginty F, Lansing Taylor D, Chakra Chennubhotla S. 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.
Zhao Y, Wu D, Jiang D, Zhang X, Wu T, Cui J, Qian M, Zhao J, Oesterreich S, Sun W, Finkel T, Li G. 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.
Zhang S, Chen F, Bahar I. 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.
Zhu L, Narloch JL, Onkar S, Joy M, Broadwater G, Luedke C, Hall A, Kim R, Pogue-Geile K, Sammons S, Nayyar N, Chukwueke U, Brastianos PK, Anders CK, Soloff AC, Vignali DAA, Tseng GC, Emens LA, Lucas PC, Blackwell KL, Oesterreich S, Lee AV. 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.
Osmanbeyoglu HU, Shimizu F, Rynne-Vidal A, Alonso-Curbelo D, Chen HA, Wen HY, Yeung TL, Jelinic P, Razavi P, Lowe SW, Mok SC, Chiosis G, Levine DA, Leslie CS. 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.
Yeh CY, Ye Z, Moutal A, Gaur S, Henton AM, Kouvaros S, Saloman JL, Hartnett-Scott KA, Tzounopoulos T, Khanna R, Aizenman E, Camacho CJ. Defining the Kv2.1-syntaxin molecular interaction identifies a first-in-class small molecule neuroprotectant. Proc Natl Acad Sci U S A. 2019-07-30;116(31):15696-15705. doi: 10.1073/pnas.1903401116. PubMed PMID: 31308225; PMCID: PMC6681760.
Cheng MH, Bahar I. 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.
Tasdemir N, Bossart EA, Li Z, Zhu L, Sikora MJ, Levine KM, Jacobsen BM, Tseng GC, Davidson NE, Oesterreich S. 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.
Nagle AM, Levine KM, Tasdemir N, Scott JA, Burlbaugh K, Kehm J, Katz TA, Boone DN, Jacobsen BM, Atkinson JM, Oesterreich S, Lee AV. 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.
Kurland BF, Oesterreich S. Heterogeneity in Metastatic Breast Cancer (18)F-Fluoroestradiol Uptake: Clinically Actionable, Biologically Illuminating? J Nucl Med. 2018-08-01;59(8):1210-1211. doi: 10.2967/jnumed.118.214304. PubMed PMID: 29903931; PMCID: PMC6071507.
Li G, Martínez-Bonet M, Wu D, Yang Y, Cui J, Nguyen HN, Cunin P, Levescot A, Bai M, Westra HJ, Okada Y, Brenner MB, Raychaudhuri S, Hendrickson EA, Maas RL, Nigrovic PA. 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.
Oesterreich S, Lucas PC, McAuliffe PF, Bruno TC, Vignali DAA. Opening the Door for Immune Oncology Studies in Invasive Lobular Breast Cancer. J Natl Cancer Inst. 2018-07-01;110(7):696-698. doi: 10.1093/jnci/djy014. PubMed PMID: 29471462.
Ponzoni L, Bahar I. Structural dynamics is a determinant of the functional significance of missense variants. Proc Natl Acad Sci U S A. 2018-04-17;115(16):4164-4169. doi: 10.1073/pnas.1715896115. PubMed PMID: 29610305; PMCID: PMC5910821.
Andersen CL, Sikora MJ, Boisen MM, Ma T, Christie A, Tseng G, Park Y, Luthra S, Chandran U, Haluska P, Mantia-Smaldone GM, Odunsi K, McLean K, Lee AV, Elishaev E, Edwards RP, Oesterreich S. 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.
Priedigkeit N, Hartmaier RJ, Chen Y, Vareslija D, Basudan A, Watters RJ, Thomas R, Leone JP, Lucas PC, Bhargava R, Hamilton RL, Chmielecki J, Puhalla SL, Davidson NE, Oesterreich S, Brufsky AM, Young L, Lee AV. 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.
Sauerwald N, Zhang S, Kingsford C, Bahar I. 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.
Bahreini A, Levine K, Santana-Santos L, Benos PV, Wang P, Andersen C, Oesterreich S, Lee AV. 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.
Lu S, Cai C, Yan G, Zhou Z, Wan Y, Chen V, Chen L, Cooper GF, Obeid LM, Hannun YA, Lee AV, Lu X. 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.
Gyanchandani R, Lin Y, Lin HM, Cooper K, Normolle DP, Brufsky A, Fastuca M, Crosson W, Oesterreich S, Davidson NE, Bhargava R, Dabbs DJ, Lee AV. 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.
Tian XJ, Zhang H, Sannerud J, Xing J. Achieving diverse and monoallelic olfactory receptor selection through dual-objective optimization design. Proc Natl Acad Sci U S A. 2016-05-24;113(21):E2889-98. doi: 10.1073/pnas.1601722113. PubMed PMID: 27162367; PMCID: PMC4889386.
Liu S, Tsai WH, Ding Y, Chen R, Fang Z, Huo Z, Kim S, Ma T, Chang TY, Priedigkeit NM, Lee AV, Luo J, Wang HW, Chung IF, Tseng GC. 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.
Wang P, Bahreini A, Gyanchandani R, Lucas PC, Hartmaier RJ, Watters RJ, Jonnalagadda AR, Trejo Bittar HE, Berg A, Hamilton RL, Kurland BF, Weiss KR, Mathew A, Leone JP, Davidson NE, Nikiforova MN, Brufsky AM, Ambros TF, Stern AM, Puhalla SL, Lee AV, Oesterreich S. 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.
Li H, Chang YY, Yang LW, Bahar I. 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.
Lee AV, Oesterreich S, Davidson NE. MCF-7 cells--changing the course of breast cancer research and care for 45 years. J Natl Cancer Inst. 2015-07-01;107(7): doi: 10.1093/jnci/djv073. PubMed PMID: 25828948.
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