RESEARCH PUBLICATIONS

S.NO.	TAUBER BIOINFORMATICS RESEARCH CENTER PUBLICATIONS IN COLLABORATION WITH PINE BIOTECH
01	Xiao, Y., Lidsky, P. V., Shirogane, Y., Aviner, R., Wu, C. T., Li, W., Zheng, W., Talbot, D., Catching, A., Doitsh, G., Su, W., Gekko, C. E., Nayak, A., Ernst, J. D., Brodsky, L., Brodsky, E., Rousseau, E., Capponi, S., Bianco, S., . . . Andino, R. (2021). A defective viral genome strategy elicits broad protective immunity against respiratory viruses. Cell, 184(25), 6037-6051.e14. https://doi.org/10.1016/j.cell.2021.11.023
02	Kapun, M., Nunez, J. C. B., Bogaerts-Márquez, M., Murga-Moreno, J., Paris, M., Outten, J., Coronado-Zamora, M., Tern, C., Rota-Stabelli, O., Guerreiro, M. P. G., Casillas, S., Orengo, D. J., Puerma, E., Kankare, M., Ometto, L., Loeschcke, V., Onder, B. S., Abbott, J. K., Schaeffer, S. W., . . . Bergland, A. O. (2021) Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource. Molecular Biology and Evolution, 38(12), 5782–5805. https://doi.org/10.1093/molbev/msab259
03	Pegoraro, M., Fishman, B., Zonato, V., Zouganelis, G., Francis, A., Kyriacou, C. P., & Tauber, E. (2022). Photoperiod-Dependent Expression of MicroRNA in Drosophila. International Journal of Molecular Sciences, 23(9), 4935. https://doi.org/10.3390/ijms23094935
04	Fleyshman, D. I., Wakshlag, J. J., Huson, H. J., Loftus, J. P., Olby, N. J., Brodsky, L., Gudkov, A. V., & Andrianova, E. L. (2021). Development of infrastructure for a systemic multidisciplinary approach to study aging in retired sled dogs. Aging, 13(18), 21814–21837. https://doi.org/10.18632/aging.203600
05	Rezelj, V. V., Carrau, L., Merwaiss, F., Levi, L. I., Erazo, D., Tran, Q. D., Henrion-Lacritick, A., Gausson, V., Suzuki, Y., Shengjuler, D., Meyer, B., Vallet, T., Weger-Lucarelli, J., Bernhauerová, V., Titievsky, A., Sharov, V., Pietropaoli, S., Diaz-Salinas, M. A., Legros, V., . . . Vignuzzi, M. (2021). Defective viral genomes as therapeutic interfering particles against flavivirus infection in mammalian and mosquito hosts. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-22341-7
06	Wichert, B., Milde-Langosch, K., Galatenko, V., Schmalfeldt, B., & Oliveira-Ferrer, L. (2018). Prognostic role of the sialyltransferase ST6GAL1 in ovarian cancer. Glycobiology, 28(11), 898–903. https://doi.org/10.1093/glycob/cwy065
07	Galatenko, V. V., Maltseva, D. V., Galatenko, A. V., Rodin, S., & Tonevitsky, A. G. (2018). Cumulative prognostic power of laminin genes in colorectal cancer. BMC Medical Genomics, 11(S1). https://doi.org/10.1186/s12920-018-0332-3
08	Sharov, V., Rezelj, V. V., Galatenko, V. V., Titievsky, A., Panov, J., Chumakov, K., Andino, R., Vignuzzi, M., & Brodsky, L. (2021). Intra- and Inter-cellular Modeling of Dynamic Interaction between Zika Virus and Its Naturally Occurring Defective Viral Genomes. Journal of Virology, 95(22). https://doi.org/10.1128/jvi.00977-21
09	Mechtler, P., Johnson, S., Slabodkin, H., Cohanim, A. B., Brodsky, L., & Kandel, E. S. (2017b). The evidence for a microRNA product of human DROSHA gene. RNA Biology, 14(11), 1508–1513. https://doi.org/10.1080/15476286.2017.1342934
10	Li, K., Zhang, S., Song, X., Weyrich, A., Wang, Y., Liu, X., Wan, N., Liu, J., Lövy, M., Cui, H., Frenkel, V., Titievsky, A., Panov, J., Brodsky, L., & Nevo, E. (2020). Genome evolution of blind subterranean mole rats: Adaptive peripatric versus sympatric speciation. Proceedings of the National Academy of Sciences, 117(51), 32499–32508. https://doi.org/10.1073/pnas.2018123117
11	Rai, P., Chuong, C., LeRoith, T., Smyth, J. W., Panov, J., Levi, M., Kehn-Hall, K., Duggal, N. K., & Lucarelli, J. W. (2021). Adenovirus transduction to express human ACE2 causes obesity-specific morbidity in mice, impeding studies on the effect of host nutritional status on SARS-CoV-2 pathogenesis. Virology, 563, 98–106. https://doi.org/10.1016/j.virol.2021.08.014
12	Hyams, Y., Panov, J., Rosner, A., Brodsky, L., Rinkevich, Y., & Rinkevich, B. (2022). Transcriptome landscapes that signify Botrylloides leachi (Ascidiacea) torpor states. Developmental Biology, 490, 22–36. https://doi.org/10.1016/j.ydbio.2022.06.005
13	Butenko, S., Satyanarayanan, S. K., Assi, S., Schif-Zuck, S., Barkan, D., Sher, N., & Ariel, A. (2020). Corrigendum: Transcriptomic Analysis of Monocyte-Derived Non-Phagocytic Macrophages Favors a Role in Limiting Tissue Repair and Fibrosis. Frontiers in Immunology, 11. https://doi.org/10.3389/fimmu.2020.01003
14	Safina, A., Cheney, P., Pal, M., Brodsky, L., Ivanov, A., Kirsanov, K., Lesovaya, E., Naberezhnov, D., Nesher, E., Koman, I., Wang, D., Wang, J., Yakubovskaya, M., Winkler, D., & Gurova, K. (2017). FACT is a sensor of DNA torsional stress in eukaryotic cells. Nucleic Acids Research, gkw1366. https://doi.org/10.1093/nar/gkw1366
15	Xiao, Y., Dolan, P. T., Goldstein, E. F., Li, M., Farkov, M., Brodsky, L., & Andino, R. (2017). Poliovirus intrahost evolution is required to overcome tissue-specific innate immune responses. Nature Communications, 8(1). https://doi.org/10.1038/s41467-017-00354-5
16	Xiao, Y., Rouzine, I., Bianco, S., Acevedo, A., Goldstein, E., Farkov, M., Brodsky, L., & Andino, R. (2016). RNA Recombination Enhances Adaptability and Is Required for Virus Spread and Virulence. Cell Host &Amp; Microbe, 19(4), 493–503. https://doi.org/10.1016/j.chom.2016.03.009
17	Fang, X., Nevo, E., Han, L., Levanon, E. Y., Zhao, J., Avivi, A., Larkin, D., Jiang, X., Feranchuk, S., Zhu, Y., Fishman, A., Feng, Y., Sher, N., Xiong, Z., Hankeln, T., Huang, Z., Gorbunova, V., Zhang, L., Zhao, W., . . . Wang, J. (2014). Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax. Nature Communications, 5(1). https://doi.org/10.1038/ncomms4966
18	Acevedo, A., Brodsky, L., & Andino, R. (2013). Mutational and fitness landscapes of an RNA virus revealed through population sequencing. Nature, 505(7485), 686–690. https://doi.org/10.1038/nature12861
19	Pfaller, C. K., Donohue, R. C., Nersisyan, S., Brodsky, L., & Cattaneo, R. (2018). Extensive editing of cellular and viral double-stranded RNA structures accounts for innate immunity suppression and the proviral activity of ADAR1p150. PLOS Biology, 16(11), e2006577. https://doi.org/10.1371/journal.pbio.2006577

OmicsLogic is a program that embeds data-driven concepts into biological projects, spanning the student learning journey from observer to participant in research. This journey begins with identifying an interesting biological research problem or question that can be answered with data, continues with the collection and organization of data, and concludes with students interpreting and drawing conclusions about the data and the possibility of research publications. It is a training program developed by Pine Biotech in collaboration with the Tauber Bioinformatics Research Center from the University of Haifa, Israel. It is currently available at campuses around the world and online. Learn More

S.NO.	PINE BIOTECH - OMICS LOGIC RESEARCH FELLOWS PUBLICATION
01	Parekh, U., Mazumder, M., Kaur, H., & Brodsky, E. (2021). In Silico Analysis and Characterization of Differentially Expressed Genes to Distinguish Glioma Stem Cells from Normal Neural Stem Cells. BioRxiv. https://doi.org/10.1101/2021.04.05.438487
02	Diken, D. (2021, January 1). Radiation Threats to Humans in Space and an alternative approach with Probiotics. bioRxiv. https://www.biorxiv.org/content/10.1101/2021.03.12.435153v3
03	Dolaner, S. (2021, May 24). Identification of LncRNAs as Therapeutic Targets in Chronic Lymphocytic Leukemia \| Columbia Undergraduate Science Journal. https://journals.library.columbia.edu/index.php/cusj/article/view/7787
04	Dey, S., Kaur, H., Mazumder, M., & Brodsky, E. (2022). Analysis of gene expression profiles to study malaria vaccine dose efficacy and immune response modulation. Genomics &Amp; Informatics, 20(3), e32. https://doi.org/10.5808/gi.22049
05	Vaja, R., Kaur, H., Mazumder, M., & Brodsky, E. (2021). In silico Analysis of Transcriptomic Profiling and Affected Biological pathways in Multiple Sclerosis. Immunogenetics: Open Access. https://doi.org/10.1101/2021.08.15.456398
06	Sen, P., & Kaur, H. (2023). In silico transcriptional analysis of asymptomatic and severe COVID-19 patients reveals the susceptibility of severe patients to other comorbidities and non-viral pathological conditions. Human Gene, 35, 201135. https://doi.org/10.1016/j.humgen.2022.201135
07	Boateng, R. A., Myers-Hansen, J. L., Dolling, N. N. O., Mensah, B. A., Brodsky, E., Mazumder, M., & Ghansah, A. (2022). Global Analysis of Plasmodium falciparum Dihydropteroate Synthase Variants Associated with Sulfadoxine Resistance Reveals Variant Distribution and Mechanisms of Resistance:A Computational-Based Study. Molecules, 28(1), 145. https://doi.org/10.3390/molecules28010145

Check out our more student projects on different specialization areas (Oncology, Precision Medicine, Space Omics, etc.) on the OmicsLogic Portal OmicsLogic – Research Projects

The T-BioInfo Bioinformatics Platform was developed by the experts from the Tauber Bioinformatics Research Center at the University of Haifa, Israel. The center is under the guidance of its founders, Dr. Alfred Tauber and Dr. Leonid Brodsky. This research center recognized the importance of user-friendly bioinformatics tools and hands-on learning as the exponential growth of data is transforming basic research and clinical applications. Together with research and industry collaborators, the team built an interactive ‘omics platform that contained built-in learning tips, an A.I. engine to guide decision making, and a rich visual analytics interface to simplify the interpretation of the data. Learn more