Publications

2020

Lee J, Wang N, Turk S, Mohammed S, Lobo R, Kim J, Liao E, Camelo-Piragua S, Kim M, Junck L, Bapuraj J, Srinivasan A, Rao A, Discriminating Pseudoprogression and True Progression in Diffuse Infiltrating Glioma using Multi-parametric MRI data through Deep Learning. Scientific Reports, 2020;10(1):20331, PMID: 33230285
Steele, N.G, et al. Inhibition of Hedgehog signaling alters fibroblast composition in pancreatic cancer. Clinical Cancer Research (2020). (in press)
Mohammed S, Li T, Chen X et al. Density-based classification in diabetic retinopathy through thickness of retinal layers from optical coherence tomography. Sci Rep. 2020;10(1). doi:10.1038/s41598-020-72813-x
Warner E, Wang N, Lee J, Rao A. Meaningful incorporation of artificial intelligence for personalized patient management during cancer: Quantitative imaging, risk assessment, and therapeutic outcomes. Artif Intell Med. 2021:339-359. doi:10.1016/b978-0-12-821259-2.00017-x
Elhalawani H, Volpe S, Cardenas C et al. Investigation of Longitudinal Dose-weighted FDG-Positron Emission Tomography Metabolic Imaging Biomarkers (PET MIBs) of Radiation-associated Dysphagia in OPC Cohort. International Journal of Radiation Oncology*Biology*Physics. 2020;108(3):e312-e313. doi:10.1016/j.ijrobp.2020.07.746
Caissie A, Mierzwa M, Fuller C et al. Radiotherapy (RT) Patterns Of Practice Variability Identified As A Challenge To Real-World Big Data: Recommendations From The Learning From Analysis Of Multicenter Big Data Aggregation (LAMBDA) Consortium. International Journal of Radiation Oncology*Biology*Physics. 2020;108(3):e773-e774. doi:10.1016/j.ijrobp.2020.07.224
Steele N, Carpenter E, Kemp S et al. Multimodal mapping of the tumor and peripheral blood immune landscape in human pancreatic cancer. Nat Cancer. 2020;1(11):1097-1112. doi:10.1038/s43018-020-00121-4
Carpenter E, Steele N, Kemp S et al. S0002 Developing a Multimodal Platform for Precision Medicine Using Endoscopic Fine Needle Biopsies in Pancreatic Cancer. American Journal of Gastroenterology. 2020;115(1):S1-S1. doi:10.14309/01.ajg.0000697892.97250.42
Avanzo M, Wei L, Stancanello J et al. Machine and deep learning methods for radiomics. Med Phys. 2020;47(5). doi:10.1002/mp.13678
Saldarriaga O, Freiberg B, Krishnan S et al. Multispectral Imaging Enables Characterization of Intrahepatic Macrophages in Patients With Chronic Liver Disease. Hepatol Commun. 2020;4(5):708-723. doi:10.1002/hep4.1494
Espinosa Fernandez J, Eckhardt B, Lee J et al. Identification of triple-negative breast cancer cell lines classified under the same molecular subtype using different molecular characterization techniques: Implications for translational research. PLoS One. 2020;15(4):e0231953. doi:10.1371/journal.pone.0231953
Le H, Gupta R, Hou L et al. Utilizing Automated Breast Cancer Detection to Identify Spatial Distributions of Tumor-Infiltrating Lymphocytes in Invasive Breast Cancer. Am J Pathol. 2020;190(7):1491-1504. doi:10.1016/j.ajpath.2020.03.012
Lee S, Latha K, Manyam G, Yang Y, Rao A, Rao G. Role of CX3CR1 signaling in malignant transformation of gliomas. Neuro Oncol. 2020;22(10):1463-1473. doi:10.1093/neuonc/noaa075
Li T, Tripathi A, Yu F, Sherman D, Rao A. DDAP: docking domain affinity and biosynthetic pathway prediction tool for type I polyketide synthases. Bioinformatics. 2019. doi:10.1093/bioinformatics/btz677
Mayo C, Mierzwa M, Moran J et al. Combination of a Big Data Analytics Resource System With an Artificial Intelligence Algorithm to Identify Clinically Actionable Radiation Dose Thresholds for Dysphagia in Head and Neck Patients. Adv Radiat Oncol. 2020;5(6):1296-1304. doi:10.1016/j.adro.2019.12.007
Yang H, Baladandayuthapani V, Rao A, Morris J. Quantile Function on Scalar Regression Analysis for Distributional Data. J Am Stat Assoc. 2019;115(529):90-106. doi:10.1080/01621459.2019.1609969
Steen K, Vornhagen J, Weinberg Z et al. A Structured Professional Development Curriculum for Postdoctoral Fellows Leads to Recognized Knowledge Growth. 2020. doi:10.1101/2020.10.15.340059
Barua S, Elhalawani H, Volpe S et al. Discovering early imaging biomarkers of osteoradionecrosis in oropharyngeal cancer by characterization of temporal changes in computed tomography mandibular radiomic features. 2020. doi:10.1101/2020.10.09.20208827
Chekouo T, Mohammed S, Rao A. A Bayesian 2D functional linear model for gray-level co-occurrence matrices in texture analysis of lower grade gliomas. NeuroImage: Clinical. 2020;28:102437. doi:10.1016/j.nicl.2020.102437
Elhalawani H, Cardenas C, Volpe S et al. 18FDG Positron Emission Tomography Mining for Metabolic Imaging Biomarkers of Radiation-induced Xerostomia in Patients with Oropharyngeal Cancer. 2020. doi:10.1101/2020.05.17.20104737
Wang X, Mak P, Mu H et al. Combinatorial Inhibition of Focal Adhesion Kinase and BCL-2 Enhances Antileukemia Activity of Venetoclax in Acute Myeloid Leukemia. Mol Cancer Ther. 2020;19(8):1636-1648. doi:10.1158/1535-7163.mct-19-0841

2019

Kuthuru S, Szafran AT, Stossi F, Mancini MA, Rao A. Leveraging Image-Derived Phenotypic Measurements for Drug-Target Interaction Predictions. Cancer Inform. 2019 Jun 12;18:1176935119856595. doi: 10.1177/1176935119856595.
Kim D, Wang N, Ravikumar V, Raghuram DR, Li J, Patel A, Wendt RE 3rd, Rao G, Rao A. Prediction of 1p/19q Codeletion in Diffuse Glioma Patients Using Pre-operative Multiparametric Magnetic Resonance Imaging. Front Comput Neurosci. 2019 Jul 30;13:52. doi: 10.3389/fncom.2019.00052.
Ward Rashidi MR, Mehta P, Bregenzer M, Raghavan S, Fleck EM, Horst EN, Harissa Z, Ravikumar V, Brady S, Bild A, Rao A, Buckanovich RJ, Mehta G. Engineered 3D Model of Cancer Stem Cell Enrichment and Chemoresistance. Neoplasia. 2019 Aug;21(8):822-836. doi: 10.1016/j.neo.2019.06.005. Epub 2019 Jul 9.
Lazarus J, Oneka MD, Barua S, Maj T, Lanfranca MP, Delrosario L, Sun L, Smith JJ, D'Angelica MI, Shia J, Fang JM, Shi J, Di Magliano MP, Zou W, Rao A, Frankel TL. Mathematical Modeling of the Metastatic Colorectal Cancer Microenvironment Defines the Importance of Cytotoxic Lymphocyte Infiltration and Presence of PD-L1 on Antigen Presenting Cells. Ann Surg Oncol. 2019 Sep;26(9):2821-2830. doi: 10.1245/s10434-019-07508-3.
Li T, Tripathi A, Yu F, Sherman DH, Rao A. DDAP: docking domain affinity and biosynthetic pathway prediction tool for type I polyketide synthases. Bioinformatics. 2019 Sep 3. pii: btz677. doi: 10.1093/bioinformatics/btz677.
Hsieh CE, Venkatesulu BP, Lee CH, Hung SP, Wong PF, Aithala SP, Kim BK, Rao A, Tung-Chieh Chang J, Tsang NM, Wang CC, Lee CC, Lin CC, Tseng JH, Chou WC, Wang YC, Krishnan S, Hong JH. Predictors of Radiation-Induced Liver Disease in Eastern and Western Patients With Hepatocellular Carcinoma Undergoing Proton Beam Therapy. Int J Radiat Oncol Biol Phys. 2019 Sep 1;105(1):73-86. doi: 10.1016/j.ijrobp.2019.02.032.
Milgrom SA, Varghese B, Gladish GW, Choi AD, Dong W, Patel ZS, Chung CC, Rao A, Pinnix CC, Gunther JR, Dabaja BS, Lin SH, Hoffman KE, Huff JL, Slagowski J, Abe JI, Iliescu CA, Banchs J, Yusuf SW, Lopez-Mattei JC. Coronary Artery Dose-Volume Parameters Predict Risk of Calcification After Radiation Therapy. J Cardiovasc Imaging. 2019 Oct;27(4):268-279. doi:0.4250/jcvi.2019.27.e38.
Lara OD, Krishnan S, Wang Z, Corvigno S, Zhong Y, Lyons Y, Dood R, Hu W, Qi L, Liu J, Coleman RL, Westin SN, Fleming ND, Cristini V, Rao A, Burks J, Sood AK. Tumor core biopsies adequately represent immune microenvironment of high-grade serous carcinoma. Sci Rep. 2019 Nov 26;9(1):17589. doi:10.1038/s41598-019-53872-1.
Li X, Monga V, Rao UA. Analysis-Synthesis Learning with Shared Features:Algorithms for Histology Image Classification. IEEE Trans Biomed Eng. 2019 Jul 16. doi: 10.1109/TBME.2019.2928997.
Beesley LJ, Salvatore M, Fritsche LG, Pandit A, Rao A, Brummett C, Willer CJ, Lisabeth LD, Mukherjee B. The emerging landscape of health research based on biobanks linked to electronic health records: Existing resources, statistical challenges, and potential opportunities. Stat Med. 2019 Dec 20. doi: 10.1002/sim.8445.

2018

Lehrer M, Bhadra A, Aithala S, Ravikumar V, Zheng Y, Dogan B, Bonaccio E, Burnside ES, Morris E, Sutton E, Whitman GJ, Net J, Brandt K, Ganott M, Zuley M, Rao A; TCGA Breast Phenotype Research Group. High-dimensional regression analysis links magnetic resonance imaging features and protein expression and signaling pathway alterations in breast invasive carcinoma. Oncoscience. 2018 Feb 26;5(1-2):39-48. doi: 10.18632/oncoscience.397.
Barua S, Fang P, Sharma A, Fujimoto J, Wistuba I, Rao AUK, Lin SH. Spatial interaction of tumor cells and regulatory T cells correlates with survival in non-small cell lung cancer. Lung Cancer. 2018 Mar;117:73-79. doi: 10.1016/j.lungcan.2018.01.022.
Bhadra A, Rao A, Baladandayuthapani V. Inferring network structure in non-normal and mixed discrete-continuous genomic data. Biometrics. 2018 Mar;74(1):185-195. doi: 10.1111/biom.12711.
Cooper LA, Demicco EG, Saltz JH, Powell RT, Rao A, Lazar AJ. PanCancer insights from The Cancer Genome Atlas: the pathologist's perspective. J Pathol. 2018 Apr;244(5):512-524. doi: 10.1002/path.5028.
Saltz J, Gupta R, Hou L, Kurc T, Singh P, Nguyen V, Samaras D, Shroyer KR,
Zhao T, Batiste R, Van Arnam J; Cancer Genome Atlas Research Network, Shmulevich I, Rao AUK, Lazar AJ, Sharma A, Thorsson V. Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images. Cell Rep. 2018 Apr 3;23(1):181-193.e7. doi: 10.1016/j.celrep.2018.03.086.
Bambhroliya A, Van Wyhe RD, Kumar S, Debeb BG, Reddy JP, Van Laere S, El-Zein R, Rao A, Woodward WA. Gene set analysis of post-lactational mammary gland involution gene signatures in inflammatory and triple-negative breast cancer. PLoS One. 2018 Apr 4;13(4):e0192689. doi: 10.1371/journal.pone.0192689.
Berger AC, Korkut A, Kanchi RS, Hegde AM, Lenoir W, Liu W, Liu Y, Fan H, Shen H, Ravikumar V, Rao A, Schultz A, Li X, Sumazin P, Williams C, Mestdagh P, Gunaratne PH, Yau C, Bowlby R, Robertson AG, Tiezzi DG, Wang C, Cherniack AD, Godwin AK, Kuderer NM, Rader JS, Zuna RE, Sood AK, Lazar AJ, Ojesina AI, Adebamowo C, Adebamowo SN, Baggerly KA, Chen TW, Chiu HS, Lefever S, Liu L, MacKenzie K, Orsulic S, Roszik J, Shelley CS, Song Q, Vellano CP, Wentzensen N; Cancer Genome Atlas Research Network, Weinstein JN, Mills GB, Levine DA, Akbani R. A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. Cancer Cell. 2018 Apr 9;33(4):690-705.e9. doi: 10.1016/j.ccell.2018.03.014.
Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CE; Cancer Genome Atlas Research Network, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich L. The Immune Landscape of Cancer. Immunity. 2018 Apr 17;48(4):812-830.e14. doi: 10.1016/j.immuni.2018.03.023.
Ishizawa J, Nakamaru K, Seki T, Tazaki K, Kojima K, Chachad D, Zhao R, Heese L, Ma W, Ma MCJ, DiNardo C, Pierce S, Patel KP, Tse A, Davis RE, Rao A, Andreeff M. Predictive Gene Signatures Determine Tumor Sensitivity to MDM2 Inhibition. Cancer Res. 2018 May 15;78(10):2721-2731. doi: 10.1158/0008-5472.CAN-17-0949.
Eckhardt BL, Gagliardi M, Iles L, Evans K, Ivan C, Liu X, Liu CG, Souza G, Rao A, Meric-Bernstam F, Ueno NT, Bartholomeusz GA. Clinically relevant inflammatory breast cancer patient-derived xenograft-derived ex vivo model for evaluation of tumor-specific therapies. PLoS One. 2018 May 16;13(5):e0195932. doi: 10.1371/journal.pone.0195932.
Cardenas CE, McCarroll RE, Court LE, Elgohari BA, Elhalawani H, Fuller CD, Kamal MJ, Meheissen MAM, Mohamed ASR, Rao A, Williams B, Wong A, Yang J, Aristophanous M. Deep Learning Algorithm for Auto-Delineation of High-Risk Oropharyngeal Clinical Target Volumes With Built-In Dice Similarity Coefficient Parameter Optimization Function. Int J Radiat Oncol Biol Phys. 2018 Jun 1;101(2):468-478. doi: 10.1016/j.ijrobp.2018.01.114.
Kai K, Iwamoto T, Zhang D, Shen L, Takahashi Y, Rao A, Thompson A, Sen S, Ueno NT. CSF-1/CSF-1R axis is associated with epithelial/mesenchymal hybrid phenotype in epithelial-like inflammatory breast cancer. Sci Rep. 2018 Jun 21; 8(1):9427. doi: 10.1038/s41598-018-27409-x.
Latha K, Yan J, Yang Y, Gressot LV, Kong LY, Manyam G, Ezhilarasan R, Wang Q, Sulman EP, Eric Davis R, Huang S, Fuller GN, Rao A, Heimberger AB, Li S, Rao G. The Role of Fibrinogen-Like Protein 2 on Immunosuppression and Malignant Progression in Glioma. J Natl Cancer Inst. 2018 Jun 26. doi: 10.1093/jnci/djy107.
Barua S, Solis L, Parra ER, Uraoka N, Jiang M, Wang H, Rodriguez-Canales J, Wistuba I, Maitra A, Sen S, Rao A. A Functional Spatial Analysis Platform for Discovery of Immunological Interactions Predictive of Low-Grade to High-Grade Transition of Pancreatic Intraductal Papillary Mucinous Neoplasms. Cancer Inform. 2018 Jun 28;17:1176935118782880. doi: 10.1177/1176935118782880.
Krafft SP, Rao A, Stingo F, Briere TM, Court LE, Liao Z, Martel MK. The utility of quantitative CT radiomics features for improved prediction of radiation pneumonitis. Med Phys. 2018 Aug 22. doi: 10.1002/mp.13150.
Net JM, Whitman GJ, Morris E, Brandt KR, Burnside ES, Giger ML, Ganott M, Sutton EJ, Zuley ML, Rao A. Relationships Between Human-Extracted MRI Tumor Phenotypes of Breast Cancer and Clinical Prognostic Indicators Including Receptor Status and Molecular Subtype. Curr Probl Diagn Radiol. 2018 Aug 23. pii: S0363-0188(18)30157-9. doi: 10.1067/j.cpradiol.2018.08.003.
Farnum JA, Vikram R, Rao A, Bedi D, Dinney CP, Matin SF. Accuracy of High-Frequency Endoluminal Ultrasonography for Clinical Staging of Upper Tract Urothelial Carcinoma. J Endourol. 2018 Sep 12;32(9):806-811. doi: 10.1089/end.2018.0442.
El Naqa I, Ruan D, Valdes G, Dekker A, McNutt T, Ge Y, Wu QJ, Oh JH, Thor M, Smith W, Rao A, Fuller C, Xiao Y, Manion F, Schipper M, Mayo C, Moran JM, Ten Haken R. Machine learning and modeling: Data, validation, communication challenges. Med Phys. 2018 Oct;45(10):e834-e840. doi: 10.1002/mp.12811.
Matuszak MM, Fuller CD, Yock TI, Hess CB, McNutt T, Jolly S, Gabriel P, Mayo CS, Thor M, Caissie A, Rao A, Owen D, Smith W, Palta J, Kapoor R, Hayman J, Waddle M, Rosenstein B, Miller R, Choi S, Moreno A, Herman J, Feng M. Performance/outcomes data and physician process challenges for practical big data efforts in radiation oncology. Med Phys. 2018 Oct;45(10):e811-e819. doi: 10.1002/mp.13136.
Kuthuru S, Deaderick W, Bai H, Su C, Vu T, Monga V, Rao A. A Visually Interpretable, Dictionary-Based Approach to Imaging-Genomic Modeling, With Low-Grade Glioma as a Case Study. Cancer Inform. 2018 Oct 5;17:1176935118802796. doi: 10.1177/1176935118802796.
Korkut A, Zaidi S, Kanchi RS, Rao S, Gough NR, Schultz A, Li X, Lorenzi PL, Berger AC, Robertson G, Kwong LN, Datto M, Roszik J, Ling S, Ravikumar V, Manyam G, Rao A, Shelley S, Liu Y, Ju Z, Hansel D, de Velasco G, Pennathur A, Andersen JB, O'Rourke CJ, Ohshiro K, Jogunoori W, Nguyen BN, Li S, Osmanbeyoglu HU, Ajani JA, Mani SA, Houseman A, Wiznerowicz M, Chen J, Gu S, Ma W, Zhang J, Tong P,Cherniack AD, Deng C, Resar L; Cancer Genome Atlas Research Network, Weinstein JN, Mishra L, Akbani R. A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β Superfamily. Cell Syst. 2018 Oct 24;7(4):422-437.e7. doi: 10.1016/j.cels.2018.08.010.
Harano K, Wang Y, Lim B, Seitz RS, Morris SW, Bailey DB, Hout DR, Skelton RL, Ring BZ, Masuda H, Rao AUK, Laere SV, Bertucci F, Woodward WA, Reuben JM, Krishnamurthy S, Ueno NT. Rates of immune cell infiltration in patients with triple-negative breast cancer by molecular subtype. PLoS One. 2018 Oct 12;13(10):e0204513. doi: 10.1371/journal.pone.0204513.
K Bharath, S Kurtek, A Rao and V Baladandayuthapani, Radiologic image-based statistical shape analysis of brain tumours, Journal of the Royal Statistical Society, Series C, 67:5, 2018.
E. C. Chi, L. Hu, A. K. Saibaba, and A. U. K. Rao, Going off the Grid: Iterative Model Selection for Biclustered Matrix Completion, Journal of Computational and Graphical Statistics, DOI:10.1080/10618600.2018.1482763.
Lazarus J, Maj T, Smith JJ, Perusina Lanfranca M, Rao A, D'Angelica MI, Delrosario L, Girgis A, Schukow C, Shia J, Kryczek I, Shi J, Wasserman I, Crawford H, Nathan H, Pasca Di Magliano M, Zou W, Frankel TL. Spatial and phenotypic immune profiling of metastatic colon cancer. JCI Insight. 2018 Nov 15;3(22). pii: 121932. doi: 10.1172/jci.insight.121932.
Aung PP, Parra ER, Barua S, Sui D, Ning J, Mino B, Ledesma DA, Curry JL, Nagarajan P, Torres-Cabala CA, Efstathiou E, Hoang AG, Wong MK, Wargo JA, Lazar AJ, Rao A, Prieto VG, Wistuba I, Tetzlaff MT. B7-H3 Expression in Merkel Cell Carcinoma-Associated Endothelial Cells Correlates with Locally Aggressive Primary Tumor Features and Increased Vascular Density. Clin Cancer Res. 2019 Feb 26. doi: 10.1158/1078-0432.CCR-18-2355.
Kairemo K, Rohren EM, Anderson PM, Ravizzini G, Rao A, Macapinlac HA, Subbiah V. Development of sodium fluoride PET response criteria for solid tumours (NAFCIST) in a clinical trial of radium-223 in osteosarcoma: from RECIST to PERCIST to NAFCIST. ESMO Open. 2019 Feb 28;4(1):e000439. doi: 10.1136/esmoopen-2018-000439.
SM, Reuben A, Barua S, Jiang H, Zhang S, Wang L, Gopalakrishnan V,
Hudgens CW, Tetzlaff MT, Reuben JM, Tsujikawa T, Coussens LM, Wani K, He Y, Villareal L, Wood A, Rao A, Woodward WA, Ueno NT, Krishnamurthy S, Wargo JA, Mittendorf EA. Poor Response to Neoadjuvant Chemotherapy Correlates with Mast Cell Infiltration in Inflammatory Breast Cancer. Cancer Immunol Res. 2019 May 1. doi: 10.1158/2326-6066.CIR-18-0619.
Moriguchi T, Hoshino T, Rao A, Yu L, Takai J, Uemura S, Ise K, Nakamura Y, Lim KC, Shimizu R, Yamamoto M, Engel JD. A Gata3 3' Distal Otic Vesicle Enhancer Directs Inner Ear-Specific Gata3 Expression. Mol Cell Biol. 2018 Oct 15;38(21). pii: e00302-18. doi: 10.1128/MCB.00302-18.
Rosenstein BS, Rao A, Moran JM, Spratt DE, Mendonca MS, Al-Lazikani B, Mayo CS, Speers C. Genomics, bio specimens, and other biological data: Current status and future directions. Med Phys. 2018 Oct;45(10):e829-e833. doi: 10.1002/mp.12912.

2017

Powell RT, Olar A, Narang S, Rao G, Sulman E, Fuller GN, Rao A. Identification of Histological Correlates of Overall Survival in Lower Grade Gliomas Using a Bag-of-words Paradigm: A Preliminary Analysis Based on Hematoxylin & Eosin Stained Slides from the Lower Grade Glioma Cohort of The Cancer Genome Atlas. J Pathol Inform. 2017 Mar 10;8:9. doi: 10.4103/jpi.jpi_43_16.
Carstens JL, Correa de Sampaio P, Yang D, Barua S, Wang H, Rao A, Allison JP, LeBleu VS, Kalluri R. Spatial computation of intratumoral T cells correlates with survival of patients with pancreatic cancer. Nat Commun. 2017 Apr 27;8:15095. doi: 10.1038/ncomms15095.
Ingram WS, Yang J, Beadle BM, Wendt R 3rd, Rao A, Wang XA, Court LE. The feasibility of endoscopy-CT image registration in the head and neck without prospective endoscope tracking. PLoS One. 2017 May 18;12(5):e0177886. doi: 10.1371/journal.pone.0177886.
Lehrer M, Bhadra A, Ravikumar V, Chen JY, Wintermark M, Hwang SN, Holder CA, Huang EP, Fevrier-Sullivan B, Freymann JB, Rao A; TCGA Glioma Phenotype Research Group. Multiple-response regression analysis links magnetic resonance imaging features to de-regulated protein expression and pathway activity in lower grade glioma. Oncoscience. 2017 Jun 23;4(5-6):57-66. doi: 10.18632/oncoscience.353.
Ingram WS, Yang J, Wendt R 3rd, Beadle BM, Rao A, Wang XA, Court LE. The influence of non-rigid anatomy and patient positioning on endoscopy-CT image registration in the head and neck. Med Phys. 2017 Aug;44(8):4159-4168. doi: 10.1002/mp.12352.
Narang S, Kim D, Aithala S, Heimberger AB, Ahmed S, Rao D, Rao G, Rao A. Tumor image-derived texture features are associated with CD3 T-cell infiltration status in glioblastoma. Oncotarget. 2017 Sep 5;8(60):101244-101254. doi: 10.18632/oncotarget.20643.
Nolo R, Herbrich S, Rao A, Zweidler-McKay P, Kannan S, Gopalakrishnan V. Targeting P-selectin blocks neuroblastoma growth. Oncotarget. 2017 Sep 28;8(49):86657-86670.
Kesler SR, Rao V, Ray WJ, Rao A; Alzheimer's Disease Neuroimaging Initiative. Probability of Alzheimer's disease in breast cancer survivors based on gray-matter structural network efficiency. Alzheimers Dement (Amst). 2017 Nov 1;9:67-75. doi: 10.1016/j.dadm.2017.10.002.
Kesler SR, Rao A, Blayney DW, Oakley-Girvan IA, Karuturi M, Palesh O. Predicting Long-Term Cognitive Outcome Following Breast Cancer with Pre-Treatment Resting State fMRI and Random Forest Machine Learning. Front Hum Neurosci. 2017 Nov 15;11:555. doi: 10.3389/fnhum.2017.00555.
Sutton EJ, Huang EP, Drukker K, Burnside ES, Li H, Net JM, Rao A, Whitman GJ, Zuley M, Ganott M, Bonaccio E, Giger ML, Morris EA; TCGA group. Breast MRI radiomics: comparison of computer- and human-extracted imaging phenotypes. Eur Radiol Exp. 2017;1(1):22. doi: 10.1186/s41747-017-0025-2.
Dextraze K, Saha A, Kim D, Narang S, Lehrer M, Rao A, Narang S, Rao D, Ahmed S, Madhugiri V, Fuller CD, Kim MM, Krishnan S, Rao G, Rao A. Spatial habitats from multiparametric MR imaging are associated with signaling pathway activities and survival in glioblastoma. Oncotarget. 2017 Dec 5;8(68):112992-113001. doi: 10.18632/oncotarget.22947.

Peer-Reviewed Conference Papers

Krishnan S. Oneka M. et. al. A Quantitative Framework to Characterize Tumor-Immune Cell Spatial Interactions in Head and Neck Squamous Cell Carcinoma. Poster presented at Keystone eSymposia for Advances in Cancer Immunology; August 17, 2020; Virtual Conference
Rozek, L. Krishnan S. et. al. Synthesizing tumour-infiltrating Lymphocyte Patterns with Genomic Measurements for Head and Neck Cancer Survival. Poster presented at University of Michigan Precision Health Virtual Symposium; Septeber 23, 2020; Virtual Conference
X. Li, V. Monga, and A. U. K. Rao, "Analysis-Synthesis Model Learning With Shared Features: A New Framework For Histopathological Image Classification", in Proc. IEEE International Symposium on Biomedical Imaging (ISBI), Washington DC, USA, April 2018.
Tiep H. Vu, H. S. Mousavi, V. Monga, UK A. Rao, G Rao, "DFDL: Discriminative Feature-Oriented Dictionary Learning for Histopathological Image Classification". IEEE International Symposium on Biomedical Imaging (ISBI), 2015.
Rao A, “Exploring relationships between multivariate phenotype and genetic features: A case-study in Glioblastoma using the Cancer Genome Atlas”, IEEE GlobalSIP Conference, Austin, TX, 2013.
Olivares R, Rao A, Rao G, Morris J, Baladandayuthapani V., “Integrative Analysis of Multi-modal Correlated Imaging- Genomics Data in Glioblastoma”, IEEE Genomic Signal Processng Conference (GENSIPS), Houston TX, 2013.
Raja P, Jacob J, Bartholomeusz G, Yoon BJ, Rao A, “Automated Image Analysis and Inference of Gene Function From High- Content Screens”, 21st European Signal Processing Conference (EUSIPCO) 2013.
Rao A, Murphy RF. Determination of protein location diversity via analysis of immunohistochemical images from the Human Protein Atlas. IEEE International Symposium on Biological Imaging (ISBI), 3/2011.
TE Buck, A Rao, LP Coelho, MH Fuhrman, PB Berget, JW Jarvik, RF Murphy, “Protein Localization Dependence on Cell Cycle Inferred from Static, Asynchronous Images”, IEEE Engineering in Medicine and Biology Conference, Minneapolis, September, Sep 2009.
A Rao, AO Hero, DJ States, JD Engel, “Understanding Transcriptional Regulation using a combination of Sequence, Expression and Interactome Data”, Computational Systems Bioinformatics (CSB), Stanford, Aug 2009.
Newberg JY, Li J, Rao A, Pontén F, Uhlén M, Lundberg E, Murphy RF. Automated Analysis of Human Protein Atlas Immunofluorescence Images. Proc IEEE Int Symp Biomed Imaging 5193229:1023-1026, 2009. PMCID: PMC2901900.
P Harrington, A Rao and AO Hero, “Classification of Multiple Time-Series via Boosting”, IEEE DSP 2009, Florida, pp:410-415, Jan 2009.
A Rao, AO Hero, DJ States, JD Engel, “Using Directed Information for Structure Discovery in Interconnected Dynamical Systems”, 2008 SPIE Conference, San Diego, Aug 2008 (invited).
P Harrington, A Rao, M Kliger, P Woolf, AO Hero, “Socio-Molecular Predictors of Disease”, 2008 Information Theory and Applications (ITA), San Diego, Jan 2008 (invited).
Rao A, Hero AO, States DJ, Engel JD. Using directed information to build biologically relevant influence networks. Comput Syst Bioinformatics Conf 6:145-56, 2007. PMID: 17951820.
A Rao, AO Hero, DJ States, JD Engel, “Using Directed Information to Build Biologically Relevant Influence Networks”, 2007 Computational Systems Bioinformatics (CSB), San Diego, Aug 2007.
A Rao, AO Hero, DJ States, JD Engel, “Directed Information Based Feature Selection for Tissue-Specific Sequences”, 2007 IEEE Workshop on Statistical Signal Processing (SSP), Madison, pp:210-214, Aug 2007.
A Rao, AO Hero, DJ States, JD Engel, “Probabilistic integration and visualization for understanding transcriptional regulation”, 2006 European Conf. on Signal Processing (EUSIPCO), Florence, Sept. 2006 (invited).
A Rao, AO Hero, DJ States, JD Engel, “Inference of biologically relevant gene influence networks using the directed information criterion”, 2006 IEEE Intl. Conf. on Acoustics, Speech, and Signal Processing (ICASSP), Toulouse, France, II-1028-1031, May 2006.
A Rao, AO Hero, DJ States, JD Engel, “Manifold embedding of diverse data for understanding mechanisms of transcriptional regulation”, 2006 IEEE Workshop on Genomics, Signal Processing and Statistics (GENSIPS), College Station TX, May 2006.
A Rao, AO Hero, DJ States, JD Engel, “Inferring Time-varying Network Topologies from Gene Expression Data”, 2005 IEEE Workshop on Genomic Signal Processing and Statistics (GENSIPS) , Newport, May 2005.
A Rao, “A Clustering Algorithm for Gene Expression Data”, 2002 IEEE Asilomar Conference in Signals, Systems and Computers, Monterey, CA, USA.:I-316-319, Nov 2002.