Selected Publications

• Improving deep neural network generalization and robustness to background bias via layer-wise relevance propagation optimization

  Bassi PR, Dertkigil SS, Cavalli A, 2024. Nature Communications, 15(1), p.291.

• Treatment outcomes and risk factors for an unsuccessful outcome among patients with highly drug-resistant tuberculosis in Ukraine

  Pedersen OS, Butova T, Kapustnyk V, Miasoiedov V, Kuzhko M, Hryshchuk L, Kornaha S, Borovok N, Raznatovska O, Fedorec A, Bogomolov A., Butov D. Clinical Microbiology and Infection. 2023.

• Assessing an AI-based smart imagery framing and truthing (SIFT) system to assist radiologists annotating lung abnormalities on chest x-ray images for development of deep learning models

  Guo L, Hong K, Zhang Z, Zheng B, Jaeger S, Fuhrman J, Li H, Giger M, Gabrielian A, Rosenthal A, Hurt DE, Yaniv Z, Lure YF. Medical Imaging 2023: Computer-Aided Diagnosis (Vol. 12465, pp. 147-155). SPIE. 2023.

• Patterns of genomic interrelatedness of publicly available samples in the TB portals database

  Wollenberg KR, Jeffrey BM, Harris MA, Gabrielian A, Hurt DE, Rosenthal A. Tuberculosis (Edinb). 2022.

• Benchmarking the empirical accuracy of short-read sequencing across the M. tuberculosis genome

  Marin M, Vargas R, Harris M, Jeffrey B, Epperson LE, Durbin D, Strong M, Salfinger M, Iqbal Z, Akhundova I, Vashakidze S, Crudu V, Rosenthal A, Farhat MR. Bioinformatics. 2022.

• Advancing TB research using digitized programmatic data

  Taaffe J, Croda J, Moultrie H, Silva DS, Rosenthal A, Farhat M. Int J Tuberc Lung Dis. 2021.

• Radiologist observations of computed tomography (CT) images predict treatment outcome in TB Portals, a real-world database of tuberculosis (TB) cases

  Rosenfeld G, Gabrielian A, Wang Q, Gu J, Hurt DE, Long A, Rosenthal A. PLoS One. 2021.

• TB DEPOT (Data Exploration Portal): A multi-domain tuberculosis data analysis resource

  Gabrielian A, Engle E, Harris M, Wollenberg K, Juarez-Espinosa O, Glogowski A, Long A, Patti L, Hurt DE, Rosenthal A, Tartakovsky M. PLoS One. 2019.

• Radiological signs associated with pulmonary multi-drug resistant tuberculosis: an analysis of published evidences

  Wáng YXJ, Chung MJ2, Skrahin A, Rosenthal A, Gabrielian A, Tartakovsky M. Quant Imaging Med Surg. 2018.

• The TB Portals: An open-access, web-based platform for global drug-resistant tuberculosis data sharing and analysis

  Rosenthal A, Gabrielian A, Engle E, Hurt DE, Alexandru S, Crudu V, Sergueev E, Kirichenko V, Lapitskii V, Snezhko E, Kovalev V, Astrovko A, Skrahina A, Taaffe J, Harris M, Long A, Wollenberg K, Akhundova I, Ismayilova S, Skrahin A, Mammadbayov E, Gadirova H, Abuzarov R, Seyfaddinova M, Avaliani Z, Strambu I, Zaharia D, Muntean A, Ghita E, Bogdan M, Mindru R, Spinu V, Sora A, Ene C, Vashakidze S, Shubladze N, Nanava U, Tuzikov A, Tartakovsky M. J Clin Microbiol. 2017 Sep 13.

• Whole-Genome Sequencing of Mycobacterium tuberculosis Provides Insight into the Evolution and Genetic Composition of Drug-Resistant Tuberculosis in Belarus

  Wollenberg KR, Desjardins CA, Zalutskaya A, Slodovnikova V, Oler AJ, Quinones M, Abeel T, Chapman SB, Tartakovsky M, Gabrielian A, Hoffner S, Skrahin A, Birren BW, Rosenthal A, Skrahina A, Earl AM. J Clin Microbiol. 2017.

• Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance

  Manson AL, Cohen KA, Abeel T, Desjardins CA, Armstrong DT, Barry CE, 3rd, Brand J, Consortium TBGG, Chapman SB, Cho SN, Gabrielian A, Gomez J, Jodals AM, Joloba M, Jureen P, Lee JS, Malinga L, Maiga M, Nordenberg D, Noroc E, Romancenco E, Salazar A, Ssengooba W, Velayati AA, Winglee K, Zalutskaya A, Via LE, Cassell GH, Dorman SE, Ellner J, Farnia P, Galagan JE, Rosenthal A, Crudu V, Homorodean D, Hsueh PR, Narayanan S, Pym AS, Skrahina A, Swaminathan S, Van der Walt M, Alland D, Bishai WR, Cohen T, Hoffner S, Birren BW, Earl AM. Nat Genet 49:395-402. 2017.

Additional Publications

• Genomic analyses of Mycobacterium tuberculosis from human lung resections reveal a high frequency of polyclonal infections

  Moreno-Molina M, Shubladze N, Khurtsilava I, Avaliani Z, Bablishvili N, Torres-Puente M, Villamayor L, Gabrielian A, Rosenthal A, Vilaplana C, Gagneux S, Kempker RR, Vashakidze S, Comas I. Nat Commun. 2021.

• Metabolic Fate of Human Immunoactive Sterols in Mycobacterium tuberculosis

  Varaksa T, Bukhdruker S, Grabovec I, Marin E, Kavaleuski A, Gusach A, Kovalev K, Maslov I, Luginina A, Zabelskii D, Astashkin R, Shevtsov M, Smolskaya S, Kavaleuskaya A, Shabunya P, Baranovsky A, Dolgopalets V, Charnou Y, Savachka A, Litvinovskaya R, Hurski A, Shevchenko E, Rogachev A, Mishin A, Gordeliy V, Gabrielian A, Hurt DE, Nikonenko B, Majorov K, Apt A, Rosenthal A, Gilep A, Borshchevskiy V, Strushkevich N. J Mol Biol. 2021.

• The technology behind TB DEPOT: a novel public analytics platform integrating tuberculosis clinical, genomic, and radiological data for visual and statistical exploration

  Long A, Glogowski A, Meppiel M, De Vito L, Engle E, Harris M, Ha G, Schneider, D Gabrielian A, Hurt DE, Rosenthal A. AMIA 2020.

• Performance of Qure.ai automatic classifiers against a large annotated database of patients with diverse forms of tuberculosis.

  Engle E, Gabrielian A, Long A, Hurt DE, Rosenthal A. PLoS One. 2020.

• A retrospective genomic analysis of drug-resistant strains of M. tuberculosis in a high-burden setting, with an emphasis on comparative diagnostics and reactivation and reinfection status.

  Wollenberg K, Harris M, Gabrielian A, Ciobanu N, Chesov D, Long A, Taaffe J, Hurt D, Rosenthal A, Tartakovsky M, Crudu V. BMC Infect Dis. 2020.

• Comparative analysis of genomic variability for drug-resistant strains of Mycobacterium tuberculosis: The special case of Belarus

  Gabrielian A, Engle E, Harris M, Wollenberg K, Glogowski A, Long A, Hurt DE, Rosenthal A. Infect Genet Evol. 2019.

• Prediction of multiple drug resistant pulmonary tuberculosis against drug sensitive pulmonary tuberculosis by CT nodular consolidation sign

  Huang XL, Skrahin A, Lu PX, Alexandru S, Crudu V, Astrovko A, Skrahina A, Taaffe J, Harris M, Long A, Wollenberg K, Engle E, Hurt E, Akhundova I, Ismayilov S, Mammadbayov E, Gadirova H, Abuzarov R, Seyfaddinova M, Avaliani Z, Vashakidze S, Shubladze N, Nanava U, Strambu I, Zaharia D, Muntean A, Ghita A, Bogdan M, Mindru R, Spinu V, Sora A, Ene C, Sergueev E, Kirichenko V, Lapitski V, Snezhko E, Kovalev V, Tuzikov A, Gabrielian A, Rosenthal A, Tartakovsky M, Wang Y bioRxiv 833954. 2019.

• ImageCLEF 2019: Projection-based CT Image Analysis for TB Severity Scoring and CT Report Generation

  Liauchuk, V. CLEF2019 Working Notes, 2380, 9-12. 2019.

• Overview of Image CLEF tuberculosis 2019 - Automatic CT-based Report Generation and Tuberculosis Severity Assessment

  Dicente Cid Y, Liauchuk V, Klimuk D, Tarasau A, Kovalev V, Müller H. CLEF 2019 Working Notes. 2019

• Genome-Wide Analysis of MDR and XDR Tuberculosis from Belarus: Machine-Learning Approach

  Sergeev R , Kavaliou I, Sataneuski U, Gabrielian A , A Rosenthal, Tartakovsky M , Tuzikov A. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2019.

• Updates on 18F-FDG-PET/CT as a clinical tool for tuberculosis evaluation and therapeutic monitoring

  Yu, WY, Lu, PX, Assadi, M, Huang, XL, Skrahin, A, Rosenthal, A, Gabrielian, A, Tartakovsky M, Wáng, YXJ. Quantitative imaging in medicine and surgery, 9(6), 1132. 2019.

• Examining the utility of clinical, laboratory and radiological data for scoring severity of pulmonary tuberculosis

  Kovalev, V., Liauchuk, V., Skrahina, A., Astrauko, A., Rosenthal, A., & Gabrielian, A. In Computer Assisted Radiology and Surgury-32nd International Congress and Exhibition (CARS-2018) (Vol. 13, pp. 143-144). 2018.

• ImageCLEF 2018: Lesion-based tb descriptor for CT image analysis.

  Liauchuk V, Tarasau A, Snezhko E, Kovalev V. CLEF 2018 Working Notes. 2018.

• Detecting drug-resistant tuberculosis in chest radiographs.

  Jaeger S, Juarez-Espinosa OH, Candemir S, Poostchi M, Yang F, Kim L, Ding M, Folio LR, Antani S, Gabrielian A, Hurt D, Rosenthal A, Thoma G. Int J Comput Assist Radiol Surg. 2018.

• Examining the ability of convolutional neural networks to detect lesions in lung CT images

  Liauchuk V, Kovalev V, Kalinovsky A, Tarasau A, Gabrielian A, Rosenthal A. Proceedings of International Congress on Computer Assisted Radiology and Surgery. 2017.

• Methods for Genome-Wide Analysis of MDR and XDR Tuberculosis from Belarus

  Sergeev R, Kavaliou I, Gabrielian A, Rosenthal A, Tuzikov A. Bioinformatics Research and Applications, Isbra 2016 9683:258-268. 2016.

• Utilizing radiological images for predicting drug resistance of lung tuberculosis

  Kovalev V, Liauchuk V, Kalinovsky A, Rosenthal A, Gabrielian A, Skrahina A, Astrauko A, Tarasau A. International Journal of Computer Assisted Radiology and Surgery 10:1-312. 2015.

• PET/CT imaging correlates with treatment outcome in patients with multidrug-resistant tuberculosis

  Chen, R. Y., Dodd, L. E., Lee, M., Paripati, P., Hammoud, D. A., Mountz, J. M., Jeon, D., Zia, N., Zahiri, H., Coleman, M. T., Carroll, M. W., Lee, J. D., Jeong, Y. J., Herscovitch, P., Lahouar, S., Tartakovsky, M., Rosenthal, A., Somaiyya, S., Lee, S., Goldfeder, L. C., Cai, Y., Via, L. E., Park, S. K., Cho, S. N. and Barry, C. E, III. Sci Transl Med.;6(265):265ra166. 2014

• Automatic Tuberculosis Screening Using Chest Radiographs

  Jaeger S, Karargyris A, Candemir S, Folio L, Siegelman J, Callaghan F, Xue Z, Palaniappan K, Singh RK, Antani S, Thoma G, Wang Y-X, Lu P-X, McDonald CJ. IEEE Transactions on Medical Imaging 33:233-245. 2014.