Ghaffari, S., Hanson, C., Schmidt, R. E., Bouchonville, K. J., Offer, S. M., & Sinha, S. (2021). An integrated multi-omics approach to identify regulatory mechanisms in cancer metastatic processes. Genome biology, 22(1), [19]. https://doi.org/10.1186/s13059-020-02213-x
Witt, K. E., Yarlagadda, K., Allen, J. M., Bader, A. C., Simon, M. L., Kuehn, S. R., Swanson, K. S., Cross, T. W. L., Hedman, K. M., Ambrose, S. H., & Malhi, R. S. (2021). Author Correction: Integrative analysis of DNA, macroscopic remains and stable isotopes of dog coprolites to reconstruct community diet (Scientific Reports, (2021), 11, 1, (3113), 10.1038/s41598-021-82362-6). Scientific reports, 11(1), [11445]. https://doi.org/10.1038/s41598-021-90889-x
Emad, A., & Sinha, S. (2021). Inference of phenotype-relevant transcriptional regulatory networks elucidates cancer type-specific regulatory mechanisms in a pan-cancer study. npj Systems Biology and Applications, 7(1), [9]. https://doi.org/10.1038/s41540-021-00169-7
Witt, K. E., Yarlagadda, K., Allen, J. M., Bader, A. C., Simon, M. L., Kuehn, S. R., Swanson, K. S., Cross, T. W. L., Hedman, K. M., Ambrose, S. H., & Malhi, R. S. (2021). Integrative analysis of DNA, macroscopic remains and stable isotopes of dog coprolites to reconstruct community diet. Scientific reports, 11(1), [3113]. https://doi.org/10.1038/s41598-021-82362-6
Sachs, R., Ouellette, L. L., Price II, W. N., & Sherkow, J. S. (2021). Innovation Law and COVID-19: Promoting Incentives and Access for New Healthcare Technologies. https://ssrn.com/abstract=3855608
Ksiazkiewicz, A., & Friesen, A. (2021). The Higher Power of Religiosity Over Personality on Political Ideology. Political Behavior, 43(2), 637-661. https://doi.org/10.1007/s11109-019-09566-5
AIRR Community, Trück, J., Eugster, A., Barennes, P., Tipton, C. M., Luning Prak, E. T., Bagnara, D., Soto, C., Sherkow, J. S., Payne, A. S., Lefranc, M. P., Farmer, A., Bostick, M., & Mariotti-Ferrandiz, E. (2021). Biological controls for standardization and interpretation of adaptive immune receptor repertoire profiling. eLife, 10. https://doi.org/10.7554/eLife.66274
Baek, A. E., Krawczynska, N., Das Gupta, A., Dvoretskiy, S. V., You, S., Park, J., Deng, Y-H., Sorrells, J. E., Smith, B. P., Ma, L., Nelson, A. T., McDowell, H. B., Sprenger, A., Henn, M. A., Madak-Erdogan, Z., Kong, H., Boppart, S. A., Boppart, M. D., & Nelson, E. R. (Accepted/In press). The cholesterol metabolite 27-hydroxycholesterol increases the secretion of extracellular vesicles which promote breast cancer progression. Endocrinology, [bqab095]. https://doi.org/10.1210/endocr/bqab095
You, S., Chaney, E. J., Tu, H., Sun, Y., Sinha, S., & Boppart, S. A. (2021). Label-free deep profiling of the tumor microenvironment. Cancer Research, 81(9), 2534-2544. https://doi.org/10.1158/0008-5472.CAN-20-3124
Arredondo Eve, A., Tunc, E., Liu, Y-J., Agrawal, S., Erbak Yilmaz, H., Emren, S. V., Akyıldız Akçay, F., Mainzer, L., Žurauskienė, J., & Madak Erdogan, Z. (2021). Identification of Circulating Diagnostic Biomarkers for Coronary Microvascular Disease in Postmenopausal Women Using Machine-Learning Techniques. Metabolites, 11(6). https://doi.org/10.3390/metabo11060339
Banerjee, S. S., Jha, S., Kalbarczyk, Z., & Iyer, R. K. (2021). BayesPerf: Minimizing performance monitoring errors using Bayesian statistics. In Proceedings of the 26th ACM International Conference on Architectural Support for Programming Languages and Operating Systems, ASPLOS 2021 (pp. 832-844). (International Conference on Architectural Support for Programming Languages and Operating Systems - ASPLOS). Association for Computing Machinery. https://doi.org/10.1145/3445814.3446739
Ouellette, L. L., Price II, W. N., Sachs, R., & Sherkow, J. S. (2021). Innovation Institutions and COVID-19. https://doi.org/10.2139/ssrn.3826687
Capodiferro, M. R., Aram, B., Raveane, A., Rambaldi Migliore, N., Colombo, G., Ongaro, L., Rivera, J., Mendizábal, T., Hernández-Mora, I., Tribaldos, M., Perego, U. A., Li, H., Scheib, C. L., Modi, A., Gòmez-Carballa, A., Grugni, V., Lombardo, G., Hellenthal, G., Pascale, J. M., ... Achilli, A. (2021). Archaeogenomic distinctiveness of the Isthmo-Colombian area. Cell, 184(7), 1706-1723.e24. https://doi.org/10.1016/j.cell.2021.02.040
Perri, A. R., Feuerborn, T. R., Frantz, L. A. F., Larson, G., Malhi, R. S., Meltzer, D. J., & Witt, K. E. (2021). Dog domestication and the dual dispersal of people and dogs into the Americas. Proceedings of the National Academy of Sciences of the United States of America, 118(6), [e2010083118]. https://doi.org/10.1073/pnas.2010083118
de Flamingh, A., Coutu, A., Sealy, J., Chirikure, S., Bastos, A. D. S., Libanda-Mubusisi, N. M., Malhi, R. S., & Roca, A. L. (2021). Sourcing Elephant Ivory from a Sixteenth-Century Portuguese Shipwreck. Current Biology, 31(3), 621-628.e4. https://doi.org/10.1016/j.cub.2020.10.086
Shinn, L. M., Li, Y., Mansharamani, A., Auvil, L. S., Welge, M. E., Bushell, C. B., Khan, N. A., Charron, C. S., Novotny, J. A., Baer, D. J., Zhu, R., & Holscher, H. D. (2021). Fecal Bacteria as Biomarkers for Predicting Food Intake in Healthy Adults. The Journal of nutrition, 151(2), 423-433. https://doi.org/10.1093/jn/nxaa285
Guo, B., Holscher, H. D., Auvil, L. S., Welge, M. E., Bushell, C. B., Novotny, J. A., Baer, D. J., Burd, N. A., Khan, N. A., & Zhu, R. (Accepted/In press). Estimating Heterogeneous Treatment Effect on Multivariate Responses Using Random Forests. Statistics in Biosciences. https://doi.org/10.1007/s12561-021-09310-w
Macintosh, K. L., Cohen, I. G., Sherkow, J. S., & Adashi, E. Y. (2021). Letter to the Editor. The Journal of law, medicine & ethics : a journal of the American Society of Law, Medicine & Ethics, 49(1), 156-157. https://doi.org/10.1017/jme.2021.21
Jones, B. M., Rao, V. D., Gernat, T., Jagla, T., Cash-ahmed, A. C., Rubin, B. E., Comi, T. J., Bhogale, S., Husain, S. S., Blatti, C., Middendorf, M., Sinha, S., Chandrasekaran, S., & Robinson, G. E. (2020). Individual differences in honey bee behavior enabled by plasticity in brain gene regulatory networks. eLife, 9. https://doi.org/10.7554/eLife.62850
Guerrini, C. J., Sherkow, J. S., Meyer, M. N., & Zettler, P. J. (2020). Transparency is key to ethical vaccine research-Response. Science (New York, N.Y.), 370(6523), 1423. https://doi.org/10.1126/science.abf4883
Buonasera, T., Eerkens, J., de Flamingh, A., Engbring, L., Yip, J., Li, H., Haas, R., DiGiuseppe, D., Grant, D., Salemi, M., Nijmeh, C., Arellano, M., Leventhal, A., Phinney, B., Byrd, B. F., Malhi, R. S., & Parker, G. (2020). A comparison of proteomic, genomic, and osteological methods of archaeological sex estimation. Scientific reports, 10(1), [11897]. https://doi.org/10.1038/s41598-020-68550-w
Huerta, E. A., Khan, A., Davis, E., Bushell, C., Gropp, W. D., Katz, D. S., Kindratenko, V., Koric, S., Kramer, W. T. C., McGinty, B., McHenry, K., & Saxton, A. (2020). Convergence of artificial intelligence and high performance computing on NSF-supported cyberinfrastructure. Journal of Big Data, 7(1), [88]. https://doi.org/10.1186/s40537-020-00361-2
Smith, B. P., Auvil, L. S., Welge, M., Bushell, C. B., Bhargava, R., Elango, N., Johnson, K., & Madak-Erdogan, Z. (2020). Identification of early liver toxicity gene biomarkers using comparative supervised machine learning. Scientific reports, 10(1), [19128]. https://doi.org/10.1038/s41598-020-76129-8
De Flamingh, A., Coutu, A., Sealy, J., Chirikure, S., Bastos, A. D. S., Libanda-Mubusisi, N. M., Malhi, R. S., & Roca, A. L. (Accepted/In press). Sourcing Elephant Ivory from a Sixteenth-Century Portuguese Shipwreck. Current Biology. https://doi.org/10.1016/j.cub.2020.10.086
Cazier, J-B., Mainzer, L. S., Ge, W., Žurauskienė, J., & Madak-Erdogan, Z. (2020). Health disparities research is enabled by data diversity but requires much tighter integration of collaborative efforts. Journal of Global Health, 10(2), 020351. https://doi.org/10.7189/jogh.10.020351
Ksiazkiewicz, A., & Friesen, A. (2020). Slimy worms or sticky kids How caregiving tasks and gender identity attenuate disgust response. Politics and the Life Sciences, 39(2), 167-186. https://doi.org/10.1017/pls.2020.21
Tabe-Bordbar, S., Song, Y. J., Lunt, B. J., Prasanth, K. V., & Sinha, S. (2020). Mechanistic analysis of enhancer sequences in the Estrogen Receptor transcriptional program. Unknown Journal. https://doi.org/10.1101/2020.11.08.373555
Qiu, H., Banerjee, S. S., Jha, S., Kalbarczyk, Z. T., & Iyer, R. K. (2020). FIRM: An Intelligent Fine-grained Resource Management Framework for SLO-Oriented Microservices. In 14th USENIX Symposium on Operating Systems Design and Implementation (OSDI 20) USENIX Association. https://www.usenix.org/conference/osdi20/presentation/qiu
Angrist, M., Barrangou, R., Baylis, F., Brokowski, C., Burgio, G., Caplan, A., Chapman, C. R., Church, G. M., Cook-Deegan, R., Cwik, B., Doudna, J. A., Evans, J. H., Greely, H. T., Hercher, L., Hurlbut, J. B., Hynes, R. O., Ishii, T., Kiani, S., Lee, L. H., ... Davies, K. (2020). Reactions to the National Academies/Royal Society Report on Heritable Human Genome Editing. CRISPR Journal, 3(5), 332-349. https://doi.org/10.1089/crispr.2020.29106.man
Li, G., Li, Y., Jha, S., Tsai, T., Sullivan, M., Hari, S. K. S., Kalbarczyk, Z., & Iyer, R. (2020). AV-FUZZER: Finding safety violations in autonomous driving systems. In M. Vieira, H. Madeira, N. Antunes, & Z. Zheng (Eds.), Proceedings - 2020 IEEE 31st International Symposium on Software Reliability Engineering, ISSRE 2020 (pp. 25-36). [09251068] (Proceedings - International Symposium on Software Reliability Engineering, ISSRE; Vol. 2020-October). IEEE Computer Society. https://doi.org/10.1109/ISSRE5003.2020.00012
Shinn, L. M., Li, Y., Mansharamani, A., Auvil, L. S., Welge, M. E., Bushell, C., Khan, N. A., Charron, C. S., Novotny, J. A., Baer, D. J., Zhu, R., & Holscher, H. D. (2020). Fecal Bacteria as Biomarkers for Predicting Food Intake in Healthy Adults. The Journal of nutrition. https://doi.org/10.1093/jn/nxaa285
Guerrini, C. J., Sherkow, J. S., Meyer, M. N., & Zettler, P. J. (2020). Self-experimentation, ethics, and regulation of vaccines. Science, 369(6511), 1570-1572. [eabe1963]. https://doi.org/10.1126/science.abe1963
Dibaeinia, P., & Sinha, S. (2020). SERGIO: A Single-Cell Expression Simulator Guided by Gene Regulatory Networks. Cell Systems, 11(3), 252-271.e11. https://doi.org/10.1016/j.cels.2020.08.003
Sinha, S., Jones, B. M., Traniello, I. M., Bukhari, S. A., Halfon, M. S., Hofmann, H. A., Huang, S., Katz, P. S., Keagy, J., Lynch, V. J., Sokolowski, M. B., Stubbs, L. J., Tabe-Bordbar, S., Wolfner, M. F., & Robinson, G. E. (2020). Behavior-related gene regulatory networks: A new level of organization in the brain. Proceedings of the National Academy of Sciences of the United States of America, 117(38), 23270-23279. https://doi.org/10.1073/pnas.1921625117
Jones, B. M., Rao, V. D., Gernat, T., Jagla, T., Cash-Ahmed, A., Rubin, B. E. R., Comi, T. J., Bhogale, S., Husain, S. S., Blatti, C., Middendorf, M., Sinha, S., Chandrasekaran, S., & Robinson, G. E. (2020). Individual differences in honey bee (Apis mellifera) behavior enabled by plasticity in brain gene regulatory networks. Unknown Journal. https://doi.org/10.1101/2020.09.09.289272
Cohen, I. G., Sherkow, J. S., & Adashi, E. Y. (2020). Gene Editing Sperm and Eggs (not Embryos): Does it Make a Legal or Ethical Difference? Journal of Law, Medicine and Ethics, 48(3), 619-621. https://doi.org/10.1177/1073110520958891
Yao, L., Witt, K., Li, H., Rice, J., Salinas, N. R., Martin, R. D., Huerta-Sánchez, E., & Malhi, R. S. (2020). Population genetics of wild Macaca fascicularis with low-coverage shotgun sequencing of museum specimens. American journal of physical anthropology, 173(1), 21-33. https://doi.org/10.1002/ajpa.24099
Sherkow, J. S., & Aboy, M. (2020). The FDA De Novo medical device pathway, patents and anticompetition. Nature Biotechnology, 38(9), 1028-1029. https://doi.org/10.1038/s41587-020-0653-6
Long, Y., Wang, L., Bu, D., Bindschaedler, V., Wang, X., Tang, H., Gunter, C. A., & Chen, K. (2020). A Pragmatic Approach to Membership Inferences on Machine Learning Models. In Proceedings - 5th IEEE European Symposium on Security and Privacy, Euro S and P 2020 (pp. 521-534). [9230385] (Proceedings - 5th IEEE European Symposium on Security and Privacy, Euro S and P 2020). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/EuroSP48549.2020.00040
Cotul, E. K., Zuo, Q., Santaliz-Casiano, A., Imir, O. B., Mogol, A. N., Tunc, E., Duong, K., Lee, J. K., Ramesh, R., Odukoya, E., Kesavadas, M. P., Ziogaite, M., Smith, B. P., Mao, C., Shapiro, D. J., Park, B. H., Katzenellenbogen, B. S., Daly, D., Aranda, E., ... Madak-Erdogan, Z. (2020). Combined Targeting of Estrogen Receptor Alpha and Exportin 1 in Metastatic Breast Cancers. Cancers, 12(9), 1-22. [2397]. https://doi.org/10.3390/cancers12092397
Chen, J., Banerjee, S. S., Kalbarczyk, Z. T., & Iyer, R. K. (2020). Machine learning for load balancing in the Linux kernel. In APSys 2020 - Proceedings of the 2020 ACM SIGOPS Asia-Pacific Workshop on Systems (pp. 67-74). (APSys 2020 - Proceedings of the 2020 ACM SIGOPS Asia-Pacific Workshop on Systems). Association for Computing Machinery. https://doi.org/10.1145/3409963.3410492
Eve, A. A., Liu, X., Wang, Y., Miller, M. J., Jeffery, E. H., & Madak-Erdogan, Z. (2020). Biomarkers of Broccoli Consumption: Implications for Glutathione Metabolism and Liver Health. Nutrients, 12(9), [2514]. https://doi.org/10.3390/nu12092514
Qiu, H., Banerjee, S. S., Jha, S., Kalbarczyk, Z. T., & Iyer, R. K. (2020). FIRM: An intelligent fine-grained resource management framework for SLO-oriented microservices. Unknown Journal.
Zuo, Q., & Madak Erdogan, Z. (2020). The Window of Vulnerability for Uterus. Endocrinology, 161(8). https://doi.org/10.1210/endocr/bqaa104
Graff, G. D., & Sherkow, J. S. (2020). Models of Technology Transfer for Genome-Editing Technologies. Annual Review of Genomics and Human Genetics, 21(1), 509-534. https://doi.org/10.1146/annurev-genom-121119-100145
Emad, A., Ray, T., Jensen, T. W., Parat, M., Natrajan, R., Sinha, S., & Ray, P. S. (2020). Superior breast cancer metastasis risk stratification using an epithelial-mesenchymal-amoeboid transition gene signature. Breast Cancer Research, 22(1), [1304]. https://doi.org/10.1186/s13058-020-01304-8
Huang, H. Y., Tuncay, G. S., Demetriou, S., Gunter, C. A., Banerjee, R., & Bashir, M. (2020). Smartphone Security Behavioral Scale: A New Psychometric Measurement for Smartphone Security. Unknown Journal.
Sherkow, J. S., & Minssen, T. (Accepted/In press). AIRR Data Under the E.U. Trade Secrets Directive: Aligning Scientific Practices with Commercial Realities. In J. Schovsbo, T. Minssen, & T. Riis (Eds.), The Harmonization and Protection of Trade Secrets in the EU: An Appraisal of the EU Directive Edward Elgar Publishing.
Hudson, M., Garrison, N. A., Sterling, R., Caron, N. R., Fox, K., Yracheta, J., Anderson, J., Wilcox, P., Arbour, L., Brown, A., Taualii, M., Kukutai, T., Haring, R., Te Aika, B., Baynam, G. S., Dearden, P. K., Chagné, D., Malhi, R. S., Garba, I., ... Carroll, S. R. (2020). Rights, interests and expectations: Indigenous perspectives on unrestricted access to genomic data. Nature Reviews Genetics, 21(6), 377-384. https://doi.org/10.1038/s41576-020-0228-x
Jha, S., Cui, S., Banerjee, S., Cyriac, J., Tsai, T., Kalbarczyk, Z., & Iyer, R. K. (2020). ML-Driven Malware that Targets AV Safety. In Proceedings - 50th Annual IEEE/IFIP International Conference on Dependable Systems and Networks, DSN 2020 (pp. 113-124). [9153375] (Proceedings - 50th Annual IEEE/IFIP International Conference on Dependable Systems and Networks, DSN 2020). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/DSN48063.2020.00030
Kumar, R., Jha, S., Mahgoub, A., Kalyanam, R., Harrell, S., Song, X. C., Kalbarczyk, Z., Kramer, W., Iyer, R., & Bagchi, S. (2020). The Mystery of the Failing Jobs: Insights from Operational Data from Two University-Wide Computing Systems. In Proceedings - 50th Annual IEEE/IFIP International Conference on Dependable Systems and Networks, DSN 2020 (pp. 158-171). [9153410] (Proceedings - 50th Annual IEEE/IFIP International Conference on Dependable Systems and Networks, DSN 2020). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/DSN48063.2020.00034
Loog, L., Thalmann, O., Sinding, M. H. S., Schuenemann, V. J., Perri, A., Germonpré, M., Bocherens, H., Witt, K. E., Samaniego Castruita, J. A., Velasco, M. S., Lundstrøm, I. K. C., Wales, N., Sonet, G., Frantz, L., Schroeder, H., Budd, J., Jimenez, E. L., Fedorov, S., Gasparyan, B., ... Manica, A. (2020). Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia. Molecular ecology, 29(9), 1596-1610. https://doi.org/10.1111/mec.15329
Jha, S., Cui, S., Banerjee, S. S., Cyriac, J., Tsai, T., Kalbarczyk, Z. T., & Iyer, R. K. (2020). ML-driven malware that targets AV safety. Unknown Journal.
IGPA COVID-19 Pandemic Task Force, Hewings, G. J. D., Finkin, M. W., Reif, J., Fullerton, D., Jones, F., DeBrock, L. M., Gaines, B. J., Leytham Powell, T., Wilson, R. F., Lawless, R. M., & Powers, E. T. (2020). What Policymakers Should Know About the Fiscal Impact of COVID-19 on Illinois. (Economic & Fiscal Impact Group Report; No. 1). Institute of Government and Public Affairs, University of Illinois.
Flamingh, A., Coutu, A., Roca, A. L., & Malhi, R. S. (2020). Accurate sex identification of ancient elephant and other animal remains using low-coverage DNA shotgun sequencing data. G3: Genes, Genomes, Genetics, 10(4), 1427-1432. https://doi.org/10.1534/g3.119.400833
Huerta, E. A., Khan, A., Davis, E., Bushell, C., Gropp, W. D., Katz, D. S., Kindratenko, V., Koric, S., Kramer, W. T. C., McGinty, B., McHenry, K., & Saxton, A. (2020). Convergence of artificial intelligence and high performance computing on NSF-supported cyberinfrastructure. Unknown Journal.
Long, Y., Xu, L., & Gunter, C. A. (2020). A Hypothesis Testing Approach to Sharing Logs with Confidence. In CODASPY 2020 - Proceedings of the 10th ACM Conference on Data and Application Security and Privacy (pp. 307-318). (CODASPY 2020 - Proceedings of the 10th ACM Conference on Data and Application Security and Privacy). Association for Computing Machinery, Inc. https://doi.org/10.1145/3374664.3375743
Lin, H., Alemzadeh, H., Kalbarczyk, Z., & Iyer, R. (2020). Challenges and Opportunities in the Detection of Safety-Critical Cyberphysical Attacks. Computer, 53(3), 26-37. https://doi.org/10.1109/MC.2019.2915045
Tunc, E., Eve, A. A., & Madak-Erdogan, Z. (2020). Coronary Microvascular Dysfunction and Estrogen Receptor Signaling. Trends in Endocrinology and Metabolism, 31(3), 228-238. https://doi.org/10.1016/j.tem.2019.11.001
Khajouei, F., Samper, N., Djabrayan, N. J., Lunt, B., Jiménez, G., & Sinha, S. (2020). Model-based analysis of polymorphisms in an enhancer reveals cis-regulatory mechanisms. Unknown Journal. https://doi.org/10.1101/2020.02.07.939264
Huang, S., Blatti, C., Sinha, S., & Parameswaran, A. G. (2020). GENVISAGE: Rapid identification of discriminative and explainable feature pairs for genomic analysis. Unknown Journal. https://doi.org/10.1101/2020.02.05.935411
Oktay, K., Santaliz-Casiano, A., Patel, M., Marino, N., Storniolo, A. M. V., Torun, H., Acar, B., & Madak Erdogan, Z. (2020). A Computational Statistics Approach to Evaluate Blood Biomarkers for Breast Cancer Risk Stratification. Hormones and Cancer, 11(1), 17-33. https://doi.org/10.1007/s12672-019-00372-3
Rahimi, N., Carmon, S., Averbukh, I., Khajouei, F., Sinha, S., Schejter, E. D., Barkai, N., & Shilo, B. Z. (2020). Global shape of Toll activation is determined by wntD enhancer properties. Proceedings of the National Academy of Sciences of the United States of America, 117(3), 1552-1558. https://doi.org/10.1073/pnas.1918268117
Miao, R., Badger, T. C., Groesch, K., Diaz-Sylvester, P. L., Wilson, T., Ghareeb, A., Martin, J. A., Cregger, M., Welge, M., Bushell, C., Auvil, L., Zhu, R., Brard, L., & Braundmeier-Fleming, A. (2020). Assessment of peritoneal microbial features and tumor marker levels as potential diagnostic tools for ovarian cancer. PloS one, 15(1), [e0227707]. https://doi.org/10.1371/journal.pone.0227707
Ksiazkiewicz, A. (2020). Conservative larks, liberal owls: The relationship between chronotype and political ideology. Journal of Politics, 82(1), 367-371. https://doi.org/10.1086/705927
Robison, H. M., Escalante, P., Valera, E., Erskine, C. L., Auvil, L., Sasieta, H. C., Bushell, C., Welge, M., & Bailey, R. C. (2020). Multiplexed cytokine detection for immunodiagnostics using silicon photonic microring resonator arrays. In 21st International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2017 (pp. 3-4). (21st International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2017). Chemical and Biological Microsystems Society.
Lin, Y. W., Ahsen, M. E., Shaw, M. J., & Seshadri, S. (2020). The impacts of patients' sentiment trajectory features on their willingness to share in online support groups. In 40th International Conference on Information Systems, ICIS 2019 (40th International Conference on Information Systems, ICIS 2019). Association for Information Systems.
May, M. J., Lux, K. D., & Gunter, C. A. (Accepted/In press). WSEmail: An architecture and system for secure Internet messaging based on web services. Service Oriented Computing and Applications. https://doi.org/10.1007/s11761-019-00283-9
Lou, X., Tran, C., Tan, R., Yau, D. K. Y., Kalbarczyk, Z. T., Banerjee, A. K., & Ganesh, P. (2020). Assessing and mitigating impact of time delay attack: Case studies for power grid controls. IEEE Journal on Selected Areas in Communications, 38(1), 141-155. [8892729]. https://doi.org/10.1109/JSAC.2019.2951982
Park, J., Chaney, E., You, S., Abdelrahman, A. M., Leiting, J. L., Yonkus, J. A., Groves, P. D., Harrington, J. J., Spillman, D. R., Lynch, I. T., Marjanovic, M., Tu, H., Bushell, C. B., Nelson, H., Truty, M. J., & Boppart, S. A. (2020). Characterizing treatment response of pancreatic tumor patient-derived xenografts in mice by Simultaneous Label-Free Autofluorescence Multi-Harmonic (SLAM) microscopy. In Clinical and Translational Biophotonics, Translational 2020 (Optics InfoBase Conference Papers; Vol. Part F178-Translational-2020). OSA - The Optical Society.
Qiu, H., Banerjee, S. S., Jha, S., Kalbarczyk, Z. T., & Iyer, R. K. (2020). Firm: An intelligent fine-grained resource management framework for SLO-Oriented microservices. In Proceedings of the 14th USENIX Symposium on Operating Systems Design and Implementation, OSDI 2020 (pp. 805-825). (Proceedings of the 14th USENIX Symposium on Operating Systems Design and Implementation, OSDI 2020). USENIX Association.
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Jha, S., Patke, A., Brandt, J., Gentile, A., Lim, B., Showerman, M., Bauer, G., Kaplan, L., Kalbarczyk, Z., Kramer, W., & Iyer, R. (2020). Measuring congestion in high-performance datacenter interconnects. In Proceedings of the 17th USENIX Symposium on Networked Systems Design and Implementation, NSDI 2020 (pp. 37-57). (Proceedings of the 17th USENIX Symposium on Networked Systems Design and Implementation, NSDI 2020). USENIX Association.
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HamediRad, M., Chao, R., Weisberg, S., Lian, J., Sinha, S., & Zhao, H. (2019). Towards a fully automated algorithm driven platform for biosystems design. Nature communications, 10(1), [5150]. https://doi.org/10.1038/s41467-019-13189-z
Wang, Q., Datta, P., Yang, W., Liu, S., Bates, A., & Gunter, C. A. (2019). Charting the atack surface of trigger-action IoT platforms. In CCS 2019 - Proceedings of the 2019 ACM SIGSAC Conference on Computer and Communications Security (pp. 1439-1453). (Proceedings of the ACM Conference on Computer and Communications Security). Association for Computing Machinery. https://doi.org/10.1145/3319535.3345662
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Lim, H. W., Temple, W. G., Tran, B. A. N., Chen, B., Kalbarczyk, Z., & Zhou, J. (2019). Data integrity threats and countermeasures in railway spot transmission systems. ACM Transactions on Cyber-Physical Systems, 4(1), [A7]. https://doi.org/10.1145/3300179
Xie, X., Hanson, C., & Sinha, S. (2019). Mechanistic interpretation of non-coding variants for discovering transcriptional regulators of drug response. BMC biology, 17(1), [62]. https://doi.org/10.1186/s12915-019-0679-8
Fogleman, A. J., Zahnd, W. E., Lipka, A. E., Malhi, R. S., Ganai, S., Delfino, K. R., & Jenkins, W. D. (2019). Knowledge, attitudes, and perceived barriers towards genetic testing across three rural Illinois communities. Journal of Community Genetics, 10(3), 417-423. https://doi.org/10.1007/s12687-019-00407-w
Zhou, Y., Sinha, S., Schwartz, J. L., & Adami, G. R. (2019). A subtype of oral, laryngeal, esophageal, and lung, squamous cell carcinoma with high levels of TrkB-T1 neurotrophin receptor mRNA. BMC Cancer, 19(1), [607]. https://doi.org/10.1186/s12885-019-5789-8
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Jha, S., Banerjee, S., Tsai, T., Hari, S. K. S., Sullivan, M. B., Kalbarczyk, Z. T., ... Iyer, R. K. (2019). ML-Based Fault Injection for Autonomous Vehicles: A Case for Bayesian Fault Injection. In Proceedings - 49th Annual IEEE/IFIP International Conference on Dependable Systems and Networks, DSN 2019 (pp. 112-124). [8809495] (Proceedings - 49th Annual IEEE/IFIP International Conference on Dependable Systems and Networks, DSN 2019). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/DSN.2019.00025
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Schablitsky, J. M., Witt, K. E., Madrigal, J. R., Ellegaard, M. R., Malhi, R. S., & Schroeder, H. (2019). Ancient DNA analysis of a nineteenth century tobacco pipe from a Maryland slave quarter. Journal of Archaeological Science, 105, 11-18. https://doi.org/10.1016/j.jas.2019.02.006
Bader, A. C., & Malhi, R. S. (2019). How Subjectivity Strengthens Research: Developing an Integrative Approach to Investigating Human Diet in the Pacific Northwest Coast. American Anthropologist, 121(2), 476-478. https://doi.org/10.1111/aman.13218
Malhi, R. S., Antón, S. C., & Fuentes, A. (2019). Increasing Diversity in Evolutionary Anthropological Sciences—the IDEAS Program. American Anthropologist, 121(2), 478-479. https://doi.org/10.1111/aman.13226
Lou, X., Tran, C., Tan, R., Yau, D. K. Y., & Kalbarczyk, Z. T. (2019). Assessing and mitigating impact of time delay attack: A case study for power grid frequency control. In G. S. Ramachandran, & J. Ortiz (Eds.), ICCPS 2019 - Proceedings of the 2019 ACM/IEEE International Conference on Cyber-Physical Systems (pp. 207-216). (ICCPS 2019 - Proceedings of the 2019 ACM/IEEE International Conference on Cyber-Physical Systems). Association for Computing Machinery, Inc. https://doi.org/10.1145/3302509.3311042
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Hojjati, A., Demetriou, S., Long, Y., & Gunter, C. (2019). Beeer: Distributed record and replay for medical devices in hospital operating rooms. In Proceedings of the 6th Annual Symposium on Hot Topics in the Science of Security, HotSoS 2019 [a1] (ACM International Conference Proceeding Series). Association for Computing Machinery. https://doi.org/10.1145/3314058.3314061
Chung, K., Cao, P., Wu, Y., Kalbarczyk, Z. T., Iyer, R. K., & Withers, A. (2019). Traction: An infrastructure for trusted alert sharing and collaborative mitigaTION. In Proceedings of the 6th Annual Symposium on Hot Topics in the Science of Security, HotSoS 2019 [a27] (ACM International Conference Proceeding Series). Association for Computing Machinery. https://doi.org/10.1145/3314058.3317292
Banerjee, S. S., El-Hadedy, M., Lim, J. B., Kalbarczyk, Z. T., Chen, D., Lumetta, S. S., & Iyer, R. K. (2019). ASAP: Accelerated Short-Read Alignment on Programmable Hardware. IEEE Transactions on Computers, 68(3), 331-346. [8490591]. https://doi.org/10.1109/TC.2018.2875733
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Lou, X., Tran, C., Tan, R., Yau, D. K. Y., Kalbarczyk, Z. T., Banerjee, A. K., & Ganesh, P. (Accepted/In press). Assessing and Mitigating Impact of Time Delay Attack: Case Studies for Power Grid Controls. IEEE Journal on Selected Areas in Communications. https://doi.org/10.1109/JSAC.2019.2951982
Tu, Y. J., Huang, Y. H., Strader, T. J., Subramanyam, R., & Shaw, M. J. (Accepted/In press). Candidate diversity and granularity in IT portfolio construction. Information Technology and Management. https://doi.org/10.1007/s10799-019-00312-1
Tunc, E., Eve, A. A., & Madak-Erdogan, Z. (Accepted/In press). Coronary Microvascular Dysfunction and Estrogen Receptor Signaling. Trends in Endocrinology and Metabolism. https://doi.org/10.1016/j.tem.2019.11.001
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Roy, J., Dibaeinia, P., Fan, T. M., Sinha, S., & Das, A. (2019). Global analysis of osteosarcoma lipidomes reveal altered lipid profiles in metastatic versus nonmetastatic cells. Journal of Lipid Research, 60(2), 375-387. https://doi.org/10.1194/jlr.M088559
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Kulkoyluoglu-Cotul, E., Arca, A., & Madak-Erdogan, Z. (2019). Crosstalk between Estrogen Signaling and Breast Cancer Metabolism. Trends in Endocrinology and Metabolism, 30(1), 25-38. https://doi.org/10.1016/j.tem.2018.10.006
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Chen, K. L. A., Liu, X., Zhao, Y. C., Hieronymi, K., Rossi, G., Auvil, L. S., ... Madak-Erdogan, Z. (2018). Long-Term Administration of Conjugated Estrogen and Bazedoxifene Decreased Murine Fecal β-Glucuronidase Activity Without Impacting Overall Microbiome Community. Scientific reports, 8(1), [8166]. https://doi.org/10.1038/s41598-018-26506-1
Chen, B., Nahrstedt, K., & Gunter, C. (2018). Response: Real-time, secure, and privacy-aware video redaction system. In Proceedings of the 15th EAI International Conference on Mobile and Ubiquitous Systems: Computing, Networking and Services, Mobiquitous 2018 (pp. 39-48). (ACM International Conference Proceeding Series). Association for Computing Machinery. https://doi.org/10.1145/3286978.3286990
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Jha, S., Brandt, J., Gentile, A., Kalbarczyk, Z. T., & Iyer, R. K. (2018). Characterizing Supercomputer Traffic Networks Through Link-Level Analysis. In Proceedings - 2018 IEEE International Conference on Cluster Computing, CLUSTER 2018 (pp. 562-570). [8514916] (Proceedings - IEEE International Conference on Cluster Computing, ICCC; Vol. 2018-September). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/CLUSTER.2018.00072
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Ganju, K., Wang, Q., Yang, W., Gunter, C. A., & Borisov, N. (2018). Property inference attacks on fully connected neural networks using permutation invariant representations. In CCS 2018 - Proceedings of the 2018 ACM SIGSAC Conference on Computer and Communications Security (pp. 619-633). (Proceedings of the ACM Conference on Computer and Communications Security). Association for Computing Machinery. https://doi.org/10.1145/3243734.3243834
Banerjee, S. S., Athreya, A. P., Kalbarczyk, Z. T., Lumetta, S. S., & Iyer, R. K. (2018). A ML-based runtime system for executing dataflow graphs on heterogeneous processors. In SoCC 2018 - Proceedings of the 2018 ACM Symposium on Cloud Computing (SoCC 2018 - Proceedings of the 2018 ACM Symposium on Cloud Computing). Association for Computing Machinery, Inc. https://doi.org/10.1145/3267809.3275474
Lin, H., Kalbarczyk, Z. T., & Iyer, R. K. (Accepted/In press). RAINCOAT: RAndomization of Network Communication in Power Grid Cyber INfrastructure to Mislead Attackers. IEEE Transactions on Smart Grid. https://doi.org/10.1109/TSG.2018.2870362
Khajouei, F., & Sinha, S. (2018). An information theoretic treatment of sequence-to-expression modeling. PLoS computational biology, 14(9), [e1006459]. https://doi.org/10.1371/journal.pcbi.1006459
Potter, B. A., Baichtal, J. F., Beaudoin, A. B., Fehren-Schmitz, L., Haynes, C. V., Holliday, V. T., ... Surovell, T. A. (2018). Current evidence allows multiple models for the peopling of the Americas. Science Advances, 4(8), [eaat5473]. https://doi.org/10.1126/sciadv.aat5473
Krishna, V. B., Gunter, C., & Sanders, W. H. (2018). Evaluating Detectors on Optimal Attack Vectors That Enable Electricity Theft and der Fraud. IEEE Journal on Selected Topics in Signal Processing, 12(4), 790-805. [8355252]. https://doi.org/10.1109/JSTSP.2018.2833749
Vitriol, J. A., Ksiazkiewicz, A. J., & Farhart, C. E. (2018). Implicit candidate traits in the 2016 U.S. Presidential Election: Replicating a dual-process model of candidate evaluations. Electoral Studies, 54, 261-268. https://doi.org/10.1016/j.electstud.2018.04.009
Hanson, C., Cairns, J., Wang, L., & Sinha, S. (2018). Principled multi-omic analysis reveals gene regulatory mechanisms of phenotype variation. Genome Research, 28(8), 1207-1216. https://doi.org/10.1101/gr.227066.117
Jha, S., Banerjee, S. S., Cyriac, J., Kalbarczyk, Z. T., & Iyer, R. K. (2018). AVFI: Fault Injection for Autonomous Vehicles. In Proceedings - 48th Annual IEEE/IFIP International Conference on Dependable Systems and Networks Workshops, DSN-W 2018 (pp. 55-56). [8416212] (Proceedings - 48th Annual IEEE/IFIP International Conference on Dependable Systems and Networks Workshops, DSN-W 2018). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/DSN-W.2018.00027
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Athreya, A. P., Gaglio, A. J., Cairns, J., Kalari, K. R., Weinshilboum, R. M., Wang, L., ... Iyer, R. K. (2018). Machine learning helps identify new drug mechanisms in triple-negative breast cancer. IEEE Transactions on Nanobioscience, 17(3), 251-259. [8401331]. https://doi.org/10.1109/TNB.2018.2851997
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Chung, K., Kalbarczyk, Z. T., & Iyer, R. K. (2018). Poster: Indirect cyber attacks by perturbation of environment control: A data driven attack model. In Proceedings of the 5th Annual Symposium and Bootcamp on Hot Topics in the Science of Security, HoTSoS 2018 [3191681] (ACM International Conference Proceeding Series). Association for Computing Machinery. https://doi.org/10.1145/3190619.3191681
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