Research Output

2019

CAPTAR: Causal-polytree-based anomaly reasoning for SCADA networks

Ren, W., Yu, T., Yardley, T. & Nahrstedt, K., Oct 2019, 2019 IEEE International Conference on Communications, Control, and Computing Technologies for Smart Grids, SmartGridComm 2019. Institute of Electrical and Electronics Engineers Inc., 8909766. (2019 IEEE International Conference on Communications, Control, and Computing Technologies for Smart Grids, SmartGridComm 2019).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Caudit: Continuous auditing of SSH servers to mitigate brute-force attacks

Cao, P. M., Wu, Y., Banerjee, S. S., Azoff, J., Withers, A., Kalbarczyk, Z. T. & Iyer, R. K., Jan 1 2019, Proceedings of the 16th USENIX Symposium on Networked Systems Design and Implementation, NSDI 2019. USENIX Association, p. 667-682 16 p. (Proceedings of the 16th USENIX Symposium on Networked Systems Design and Implementation, NSDI 2019).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Characterization of Cas proteins for CRISPR-Cas editing in streptomycetes

Yeo, W. L., Heng, E., Tan, L. L., Lim, Y. W., Lim, Y. H., Hoon, S., Zhao, H., Zhang, M. M. & Wong, F. T., Jan 1 2019, In : Biotechnology and bioengineering. 116, 9, p. 2330-2338 9 p.

Research output: Contribution to journalArticle

Characterization of glutamyl-tRNA–dependent dehydratases using nonreactive substrate mimics

Bothwell, I. R., Cogan, D. P., Kim, T., Reinhardt, C. J., van der Donk, W. A. & Nair, S. K., Aug 27 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 35, p. 17245-17250 6 p.

Research output: Contribution to journalArticle

Open Access

Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation

Muller, M. P., Jiang, T., Sun, C., Lihan, M., Pant, S., Mahinthichaichan, P., Trifan, A. & Tajkhorshid, E., May 8 2019, In : Chemical reviews. 119, 9, p. 6086-6161 76 p.

Research output: Contribution to journalReview article

Characterization of the flavin monooxygenase involved in biosynthesis of the antimalarial FR-900098

Nguyen, K., DeSieno, M. A., Bae, B., Johannes, T. W., Cobb, R. E., Zhao, H. & Nair, S. K., Jan 1 2019, In : Organic and Biomolecular Chemistry. 17, 6, p. 1506-1518 13 p.

Research output: Contribution to journalArticle

Characterizing Fatty Liver in vivo in Rabbits, Using Quantitative Ultrasound

Nguyen, T. N., Podkowa, A. S., Tam, A. Y., Arnold, E. C., Miller, R. J., Park, T. H., Do, M. N. & Oelze, M. L., Aug 2019, In : Ultrasound in Medicine and Biology. 45, 8, p. 2049-2062 14 p.

Research output: Contribution to journalArticle

Charge Transport and Quantum Interference Effects in Oxazole-Terminated Conjugated Oligomers

Li, S., Yu, H., Schwieter, K., Chen, K., Li, B., Liu, Y., Moore, J. S. & Schroeder, C. M., Oct 9 2019, In : Journal of the American Chemical Society. 141, 40, p. 16079-16084 6 p.

Research output: Contribution to journalArticle

Chemoselective methylene oxidation in aromatic molecules

Zhao, J., Nanjo, T., de Lucca, E. C. & White, M. C., Mar 1 2019, In : Nature Chemistry. 11, 3, p. 213-221 9 p.

Research output: Contribution to journalArticle

Chronic Exposure of Mice to Bisphenol-A Alters Uterine Fibroblast Growth Factor Signaling and Leads to Aberrant Epithelial Proliferation

Neff, A. M., Blanco, S. C., Flaws, J. A., Bagchi, I. C. & Bagchi, M. K., Jan 1 2019, In : Endocrinology. 160, 5, p. 1234-1246 13 p.

Research output: Contribution to journalArticle

Open Access

Cilostamide affects in a concentration and exposure time-dependent manner the viability and the kinetics of in vitro maturation of caprine and bovine oocytes

Correia, H. H. V., Vieira, L. A., Mielgo, C. M., Paes, V. M., Alves, B. G., Silva, J. R. V., Wheeler, M. B., Rodrigues, A. P. R. & Figueiredo, J. R., Feb 2019, In : Research in Veterinary Science. 122, p. 22-28 7 p.

Research output: Contribution to journalArticle

Circadian rhythm of redox state regulates membrane excitability in hippocampal CA1 neurons

Naseri Kouzehgarani, G., Bothwell, M. Y. & Gillette, M. U., Jan 1 2019, (Accepted/In press) In : European Journal of Neuroscience.

Research output: Contribution to journalArticle

Cognitive and neural architecture of decision making competence

Román, F. J., Colom, R., Hillman, C. H., Kramer, A. F., Cohen, N. J. & Barbey, A. K., Oct 1 2019, In : NeuroImage. 199, p. 172-183 12 p.

Research output: Contribution to journalArticle

Colonization of germ-free piglets with commensal lactobacillus amylovorus, lactobacillus mucosae, and probiotic e. Coli nissle 1917 and their interference with salmonella typhimurium

Splichal, I., Donovan, S. M., Splichalova, Z., Bunesova, V. N., Vlkova, E., Jenistova, V., Killer, J., Svejstil, R., Skrivanova, E. & Splichalova, A., Aug 2019, In : Microorganisms. 7, 8, 273.

Research output: Contribution to journalArticle

Open Access

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

AstraZeneca-Sanger Drug Combination DREAM Consortium, Dec 1 2019, In : Nature communications. 10, 1, 2674.

Research output: Contribution to journalArticle

Open Access

Comparative analysis of brain and fat body gene splicing patterns in the honey bee, Apis mellifera

Kannan, K., Shook, M., Li, Y., Robinson, G. E. & Ma, J., Jan 1 2019, In : G3: Genes, Genomes, Genetics. 9, 4, p. 1055-1063 9 p.

Research output: Contribution to journalArticle

Open Access

Comparison between optical coherence tomographic and histopathologic appearances of artifacts caused by common surgical conditions and instrumentation

Cocca, C. J., Selmic, L. E., Samuelson, J., Huang, P. C., Wang, J. & Boppart, S. A., Nov 1 2019, In : Veterinary Surgery. 48, 8, p. 1361-1371 11 p.

Research output: Contribution to journalArticle

Open Access

Competition of individual domain folding with inter-domain interaction in WW domain engineered repeat proteins

Dave, K., Gasic, A. G., Cheung, M. S. & Gruebele, M., Jan 1 2019, In : Physical Chemistry Chemical Physics. 21, 44, p. 24393-24405 13 p.

Research output: Contribution to journalArticle

Computational Dissection of Membrane Transport at a Microscopic Level

Jiang, T., Wen, P. C., Trebesch, N., Zhao, Z., Pant, S., Kapoor, K., Shekhar, M. & Tajkhorshid, E., Jan 1 2019, (Accepted/In press) In : Trends in Biochemical Sciences.

Research output: Contribution to journalReview article

Confined and interface optical phonon emission in GaN/InGaN double barrier quantum well heterostructures

Mohamed, A., Park, K., Bayram, C., Dutta, M. & Stroscio, M., Apr 2019, In : PloS one. 14, 4, e0214971.

Research output: Contribution to journalArticle

Open Access

Congress of neurological surgeons systematic review and evidence-based guidelines on the evaluation and treatment of patients with thoracolumbar spine trauma: Timing of surgical intervention

Eichholz, K. M., Rabb, C. H., Anderson, P. A., Arnold, P. M., Chi, J. H., Dailey, A. T., Dhall, S. S., Harrop, J. S., Hoh, D. J., Qureshi, S., Raksin, P. B., Kaiser, M. G. & O'Toole, J. E., Jan 1 2019, In : Clinical Neurosurgery. 84, 1, p. E53-E55

Research output: Contribution to journalReview article

Open Access

Congress of neurological surgeons systematic review and evidence-based guidelines on the evaluation and treatment of patients with thoracolumbar spine trauma: Prophylaxis and treatment of thromboembolic events

Raksin, P. B., Harrop, J. S., Anderson, P. A., Arnold, P. M., Chi, J. H., Dailey, A. T., Dhall, S. S., Eichholz, K. M., Hoh, D. J., Qureshi, S., Rabb, C. H., Kaiser, M. G. & O'Toole, J. E., Jan 1 2019, In : Clinical Neurosurgery. 84, 1, p. E39-E42

Research output: Contribution to journalReview article

Open Access

Congress of neurological surgeons systematic review and evidence-based guidelines on the evaluation and treatment of patients with thoracolumbar spine trauma: Neurological assessment

Harrop, J. S., Chi, J. H., Anderson, P. A., Arnold, P. M., Dailey, A. T., Dhall, S. S., Eichholz, K. M., Hoh, D. J., Qureshi, S., Rabb, C. H., Raksin, P. B., Kaiser, M. G. & O'Toole, J. E., Jan 1 2019, In : Clinical Neurosurgery. 84, 1, p. E32-E35

Research output: Contribution to journalReview article

Open Access

Congress of neurological surgeons systematic review and evidence-based guidelines on the evaluation and treatment of patients with thoracolumbar spine trauma: Nonoperative care

Hoh, D. J., Qureshi, S., Anderson, P. A., Arnold, P. M., John, H. C., Dailey, A. T., Dhall, S. S., Eichholz, K. M., Harrop, J. S., Rabb, C. H., Raksin, P. B., Kaiser, M. G. & O'Toole, J. E., Jan 1 2019, In : Clinical Neurosurgery. 84, 1, p. E46-E49

Research output: Contribution to journalReview article

Open Access

Conjugated Barcoded Particles for Multiplexed Biomarker Quantification with a Microfluidic Biochip

Prakash, S., Nagarajan, M., Doyle, P., Bashir, R. & Hassan, U., Nov 2019, 2019 IEEE Healthcare Innovations and Point of Care Technologies, HI-POCT 2019. Institute of Electrical and Electronics Engineers Inc., p. 139-142 4 p. 8962846. (2019 IEEE Healthcare Innovations and Point of Care Technologies, HI-POCT 2019).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Construction and Screening of an Antigen-Derived Peptide Library Displayed on Yeast Cell Surface for CD4+ T Cell Epitope Identification

Wen, F., Smith, M. R. & Zhao, H., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 213-234 22 p. (Methods in Molecular Biology; vol. 2024).

Research output: Chapter in Book/Report/Conference proceedingChapter

Contextualizing numeric clinical test results for gist comprehension: Implications for EHR patient portals

Morrow, D., Azevedo, R. F. L., Garcia-Retamero, R., Hasegawa-Johnson, M., Huang, T., Schuh, W., Gu, K. & Zhang, Y., Mar 2019, In : Journal of Experimental Psychology: Applied. 25, 1, p. 41-61 21 p.

Research output: Contribution to journalArticle

Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny

Amato, K. R., Mallott, E. K., McDonald, D., Dominy, N. J., Goldberg, T., Lambert, J. E., Swedell, L., Metcalf, J. L., Gomez, A., Britton, G. A. O., Stumpf, R. M., Leigh, S. R. & Knight, R., Oct 8 2019, In : Genome biology. 20, 1, 201.

Research output: Contribution to journalArticle

Open Access

Correction to: Allosteric interactions in human cytochrome P450 CYP3A4: The role of phenylalanine 213 (Biochemistry (2019) 58: 10 (1411-1422) DOI: 10.1021/acs.biochem.8b01268)

Denisov, I. G., Grinkova, Y. V., Nandigrami, P., Shekhar, M., Tajkhorshid, E. & Sligar, S. G., Jun 18 2019, In : Biochemistry. 58, 24, 1 p.

Research output: Contribution to journalComment/debate

Correction to: Superplastic Formation of Metal Nanostructure Arrays with Ultrafine Gaps (Advanced Materials, (2016), 28, 41, (9152-9162), 10.1002/adma.201602497)

Hu, Y., Xuan, Y., Wang, X., Deng, B., Saei, M., Jin, S., Irudayaraj, J. & Cheng, G. J., Apr 5 2019, In : Advanced Materials. 31, 14, 1900190.

Research output: Contribution to journalComment/debate

Open Access

Correction to: Recommendations for performance optimizations when using GATK3.8 and GATK4 (BMC Bioinformatics (2019) 20 (557) DOI: 10.1186/s12859-019-3169-7)

Heldenbrand, J. R., Baheti, S., Bockol, M. A., Drucker, T. M., Hart, S. N., Hudson, M. E., Iyer, R. K., Kalmbach, M. T., Kendig, K. I., Klee, E. W., Mattson, N. R., Wieben, E. D., Wiepert, M., Wildman, D. E. & Mainzer, L. S., Dec 17 2019, In : BMC bioinformatics. 20, 1, 722.

Research output: Contribution to journalComment/debate

Open Access

Coseismic deformation of the 6 February 2018 M w 6.2 Hualien earthquake based on strong-motion recordings

Tian, S., Gardoni, P. & Yuan, W., Feb 1 2019, In : Seismological Research Letters. 90, 1, p. 108-117 10 p.

Research output: Contribution to journalArticle

Counting growth factors in single cells with infrared quantum dots to measure discrete stimulation distributions

Le, P., Lim, S. J., Baculis, B. C., Chung, H. J., Kilian, K. A. & Smith, A. M., Dec 1 2019, In : Nature communications. 10, 1, 909.

Research output: Contribution to journalArticle

Open Access

Counting process-based dimension reduction methods for censored outcomes

Sun, Q., Zhu, R., Wang, T. & Zeng, D., Mar 1 2019, In : Biometrika. 106, 1, p. 181-186 6 p.

Research output: Contribution to journalArticle

Critical Phenomena in the Temperature-Pressure-Crowding Phase Diagram of a Protein

Gasic, A. G., Boob, M. M., Prigozhin, M. B., Homouz, D., Daugherty, C. M., Gruebele, M. & Cheung, M. S., Nov 18 2019, In : Physical Review X. 9, 4, 041035.

Research output: Contribution to journalArticle

Open Access

Cross-species systems analysis of evolutionary toolkits of neurogenomic response to social challenge

Saul, M. C., Blatti, C., Yang, W., Bukhari, S. A., Shpigler, H. Y., Troy, J. M., Seward, C. H., Sloofman, L., Chandrasekaran, S., Bell, A. M., Stubbs, L., Robinson, G. E., Zhao, S. D. & Sinha, S., Jan 2019, In : Genes, Brain and Behavior. 18, 1, p. e12502 e12502.

Research output: Contribution to journalArticle

CylA is a sequence-specific protease involved in toxin biosynthesis

Tang, W., Bobeica, S. C., Wang, L. & van der Donk, W. A., Mar 29 2019, In : Journal of Industrial Microbiology and Biotechnology. 46, 3-4, p. 537-549 13 p.

Research output: Contribution to journalArticle

Cytometric fingerprinting and machine learning (CFML): A novel label-free, objective method for routine mastitis screening

Dhoble, A. S., Ryan, K. T., Lahiri, P., Chen, M., Pang, X., Cardoso, F. & Bhalerao, K., Jul 2019, In : Computers and Electronics in Agriculture. 162, p. 505-513 9 p.

Research output: Contribution to journalArticle

Darwinian bee-keeping: lessons from the wild

Robinson, G., Jul 1 2019, In : Nature. 571, 7763, p. 34-35

Research output: Contribution to journalReview article

Data-driven elasticity imaging using cartesian neural network constitutive models and the autoprogressive method

Hoerig, C., Ghaboussi, J. & Insana, M. F., May 2019, In : IEEE transactions on medical imaging. 38, 5, p. 1150-1160 11 p., 8522049.

Research output: Contribution to journalArticle

Data-driven pricing for sensing effort elicitation in mobile crowd sensing systems

Jin, H., He, B., Su, L., Nahrstedt, K. & Wang, X., Dec 2019, In : IEEE/ACM Transactions on Networking. 27, 6, p. 2208-2221 14 p., 8894398.

Research output: Contribution to journalArticle

Data-theoretic methodology and computational platform to quantify organizational factors in socio-technical risk analysis

Pence, J., Sakurahara, T., Zhu, X., Mohaghegh, Z., Ertem, M., Ostroff, C. & Kee, E., May 2019, In : Reliability Engineering and System Safety. 185, p. 240-260 21 p.

Research output: Contribution to journalArticle

Debiasing-based noise suppression for ultrafast ultrasound microvessel imaging

Huang, C., Song, P., Gong, P., Trzasko, J. D., Manduca, A. & Chen, S., Aug 2019, In : IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control. 66, 8, p. 1281-1291 11 p., 8720262.

Research output: Contribution to journalArticle

Decision making based on the value of information of different inspection methods

Iannacone, L., Gardoni, P., Giordano, P. F. & Limongelli, M. P., Jan 1 2019, Structural Health Monitoring 2019: Enabling Intelligent Life-Cycle Health Management for Industry Internet of Things (IIOT) - Proceedings of the 12th International Workshop on Structural Health Monitoring. Chang, F-K., Guemes, A. & Kopsaftopoulos, F. (eds.). DEStech Publications Inc., p. 1479-1486 8 p. (Structural Health Monitoring 2019: Enabling Intelligent Life-Cycle Health Management for Industry Internet of Things (IIOT) - Proceedings of the 12th International Workshop on Structural Health Monitoring; vol. 1).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Defects in Self-Assembled Monolayers on Nanoparticles Prompt Phospholipid Extraction and Bilayer-Curvature-Dependent Deformations

Chong, G., Foreman-Ortiz, I. U., Wu, M., Bautista, A., Murphy, C. J., Pedersen, J. A. & Hernandez, R., Jan 1 2019, In : Journal of Physical Chemistry C.

Research output: Contribution to journalArticle

Delta integration CRISPR-Cas (Di-CRISPR) in saccharomyces cerevisiae

Shi, S., Liang, Y., Ang, E. L. & Zhao, H., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 73-91 19 p. (Methods in Molecular Biology; vol. 1927).

Research output: Chapter in Book/Report/Conference proceedingChapter

Dermoid sinus type VI associated with spina bifida and tethered cord syndrome in a French Bulldog

Kopke, M. A., Jack, M. W., Baltzer, W. I., Wightman, P. F. & Gal, A., Mar 1 2019, In : Journal of Veterinary Diagnostic Investigation. 31, 2, p. 294-297 4 p.

Research output: Contribution to journalArticle