Publications

Featured

Brisimi, T. S., Xu, T., Wang, T., Dai, W., & Paschalidis, I. C. (2019). Predicting diabetes-related hospitalizations based on electronic health records. Statistical Methods in Medical Research, 28(12), 3667–3682. https://doi.org/10.1177/0962280218810911

Ruidi Chen, Ioannis Ch. Paschalidis, Hiroto Hatabu, Vladimir I. Valtchinov, Jenifer Siegelman (2019). Detection of unwarranted CT radiation exposure from patient and imaging protocol meta-data using regularized regression. European Journal of Radiology Open. Volume 6, 2019. 206-211. ISSN 2352-0477. https://doi.org/10.1016/j.ejro.2019.04.007.2018

Thommes M, Wang T, Zhao Q, Paschalidis IC, Segrè D. 2019. Designing metabolic division of labor in microbial communities. mSystems 4:e00263-18. https://doi.org/10.1128/mSystems.00263-18.

Sevenler, D., Trueb J., MS Ünlü (2019). “Beating the reaction limits of biosensor sensitivity with dynamic tracking of single binding events.” Proc Natl Acad Sci U S A.

Featured

Varongchayakul, N., Song, J., Meller, A., Grinstaff, M. “Single-molecule protein sensing in a nanopore: a tutorial.” Chem Soc Rev. 2018 Nov 26; 47(23): 8512-8524.

Dubinett SM, Spira AE. Impact of Chronic Obstructive Pulmonary Disease on Immune-based Treatment for Lung Cancer. Moving toward Disease Interception. Am J Respir Crit Care Med. 2018 Feb 01; 197(3):278-280. PMID: 29072842.

Billatos E, Vick JL, Lenburg ME, Spira AE. The Airway Transcriptome as a Biomarker for Early Lung Cancer Detection. Clin Cancer Res. 2018 Feb 20. View Related Profiles. PMID: 29463557.

Brisimi, T. S., Chen, R., Mela, T., Olshevsky, A., Paschalidis, I. C., & Shi, W. (2018). Federated learning of predictive models from federated Electronic Health Records. International Journal of Medical Informatics. Vol. 112, 2018, April, pages 59-67, doi: dx.doi.org/10.1016/j.ijmedinf.2018.01.007.

Pratt GW, Fan A, Melakeberhan B, Klapperich CM. A competitive lateral flow assay for the detection of tenofovir. Anal Chim Acta. 2018 Aug 09; 1017:34-40. PMID: 29534793.

Devika Nadkarni, Hala Ghattas, Imad Elhajj, Zaher Dawy and Muhammad H. Zaman Examining the need & potential for biomedical engineering to strengthen health care delivery for displaced populations & victims of conflict. Conflict and Health. 201711:20.

Shain WJ, Vickers NA, Li J, Han X, Bifano T, Mertz J, “Axial localization with modulated-illumination extended-depth-of-field microscopy,” Biomedical Optics Express, [9], 1771-1782, 2018.

Ozkumur, AY., Kanik FE.,Trueb, JT., Yurdakul C., Ünlü (2018). “Interferometric Detection and Enumeration of Viral Particles using Si-Based Microfluidics.” IEEE Journal of Selected Topics in Quantum Electronics 25 (1), 1-7.

Sevenler D., Daaboul GG., Kanik FE., NL Ünlü, MS Ünlü. (2018). “Digital microarrays: Single-molecule readout with interferometric detection of plasmonic nanorod labels.” ACS nano 12 (6), 5880-5887.

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Other

Kantrowitz J, Sinjab A, Xu L, McDowell TL, Sivakumar S, Lang W, Nunomura-Nakamura S, Fukuoka J, Nemer G, Darwiche N, Chami H, Tfayli A, Wistuba II, Scheet P, Fujimoto J, Spira AE, Kadara H. Genome-Wide Gene Expression Changes in the Normal-Appearing Airway during the Evolution of Smoking-Associated Lung Adenocarcinoma. Cancer Prev Res (Phila). 2018 Apr; 11(4):237-248. PMID: 29382653.

Robert Seager, Andrew Acevedo, Fabian Spill and Muhammad H. Zaman Solid dissolution in a fluid solvent is characterized by the interplay of surface area-dependent diffusion and physical fragmentation (Scientific Reports, In Press, 2018).

Brisimi, T. S., Xu, T., Wang, T., Dai, W., Adams, W. G., & Paschalidis, I. C. (2018). Predicting Chronic Disease Hospitalizations from Electronic Health Records: An Interpretable Classification Approach. Proceedings of the IEEE, 106(4), 690-707. doi:10.1109/JPROC.2017.2789319.

Featured

Weinstein ZB, Zaman MH. Quantitative bioassay to identify antimicrobial drugs through drug interaction fingerprint analysis. Sci Rep. 2017 Feb 16; 7:42644. View Related Profiles. PMID: 28205640; DOI: 10.1038/srep42644.

Spira A, Yurgelun MB, Alexandrov L, Rao A, Bejar R, Polyak K, Giannakis M, Shilatifard A, Finn OJ, Dhodapkar M, Kay NE, Braggio E, Vilar E, Mazzilli SA, Rebbeck TR, Garber JE, Velculescu VE, Disis ML, Wallace DC, Lippman SM. Precancer Atlas to Drive Precision Prevention Trials. Cancer Res. 2017 Apr 01; 77(7):1510-1541. View Related Profiles. PMID: 28373404; DOI: 10.1158/0008-5472.CAN-16-2346.

Oh DJ, Lakin BA, Stewart RC, Wiewiorski M, Freedman JD, Grinstaff MW, Snyder BD. Contrast-enhanced CT imaging as a non-destructive tool for ex vivo examination of the biochemical content and structure of the human meniscus. J Orthop Res. 2017 May; 35(5):1018-1028. View Related Profiles. PMID: 27302693; DOI: 10.1002/jor.23337.

“How Machine Learning Is Helping Us Predict Heart Disease and Diabetes”, Harvard Business Review, May 30, 2017.

Manson AL, Abeel T, Galagan JE, Sundaramurthi JC, Salazar A, Gehrmann T, Shanmugam SK, Palaniyandi K, Narayanan S, Swaminathan S, Earl AM. Mycobacterium tuberculosis Whole Genome Sequences From Southern India Suggest Novel Resistance Mechanisms and the Need for Region-Specific Diagnostics. Clin Infect Dis. 2017 Jun 01; 64(11):1494-1501. PMID: 28498943.

Reynolds DS, Tevis KM, Blessing WA, Colson YL, Zaman MH, Grinstaff MW. Breast Cancer Spheroids Reveal a Differential Cancer Stem Cell Response to Chemotherapeutic Treatment. Sci Rep. 2017 Sep 04; 7(1):10382. View Related Profiles. PMID: 28871147.

Khalil AA, Sivakumar S, Lucas FAS, McDowell T, Lang W, Tabata K, Fujimoto J, Yatabe Y, Spira A, Scheet P, Nemer G, Kadara H. TBX2 subfamily suppression in lung cancer pathogenesis: a high-potential marker for early detection. Oncotarget. 2017 Sep 15; 8(40):68230-68241. PMID: 28978111.

Tessema M, Yingling CM, Picchi MA, Wu G, Ryba T, Lin Y, Bungum AO, Edell ES, Spira A, Belinsky SA. ANK1 Methylation regulates expression of MicroRNA-486-5p and discriminates lung tumors by histology and smoking status. Cancer Lett. 2017 Dec 01; 410:191-200. PMID: 28965852.

Kolluri N, Klapperich CM, Cabodi M. Towards lab-on-a-chip diagnostics for malaria elimination. Lab Chip. 2017 Dec 19; 18(1):75-94. PMID: 29125615.

Falde EJ, Wang J, Grinstaff MW. Surface Tension Sensor Meshes for Rapid Alcohol Quantification. RSC Adv. 2017; 7(78):49795-49798. PMID: 29276584.

El-Khatib, F. H., et al. (2017). “Home use of a bihormonal bionic pancreas versus insulin pump therapy in adults with type 1 diabetes: a multicentre randomised crossover trial.” Lancet 389(10067): 369-380.

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Other

Moses E, Wang T, Corbett S, Jackson GR, Drizik E, Perdomo C, Perdomo C, Kleerup E, Brooks D, O’Connor G, Dubinett S, Hayden P, Lenburg ME, Spira A. Molecular Impact of Electronic Cigarette Aerosol Exposure in Human Bronchial Epithelium. Toxicol Sci. 2017 Jan; 155(1):248-257. View Related Profiles. PMID: 27701119; DOI: 10.1093/toxsci/kfw198.

Manson AL, Cohen KA, Abeel T, Desjardins CA, Armstrong DT, Barry CE, Brand J, 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. Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance. Nat Genet. 2017 Mar; 49(3):395-402. View Related Profiles. PMID: 28092681; DOI: 10.1038/ng.3767.

Vachani A, Sequist LV, Spira A. AJRCCM: 100-Year Anniversary. The Shifting Landscape for Lung Cancer: Past, Present, and Future. Am J Respir Crit Care Med. 2017 May 01; 195(9):1150-1160. PMID: 28459327.

Obeidat M, Nie Y, Fishbane N, Li X, Bossé Y, Joubert P, Nickle DC, Hao K, Postma DS, Timens W, Sze MA, Shannon CP, Hollander Z, Ng RT, McManus B, Miller BE, Rennard S, Spira A, Hackett TL, Lam W, Lam S, Faner R, Agusti A, Hogg JC, Sin DD, Paré PD. Integrative Genomics of Emphysema-Associated Genes Reveals Potential Disease Biomarkers. Am J Respir Cell Mol Biol. 2017 Oct; 57(4):411-418. PMID: 28459279.

Jain A, Khalid M, Qureshi MM, Georgian-Smith D, Kaplan JA, Buch K, Grinstaff MW, Hirsch AE, Hines NL, Anderson SW, Gallagher KM, Bates DDB, Bloch BN. Stereotactic core needle breast biopsy marker migration: An analysis of factors contributing to immediate marker migration. Eur Radiol. 2017 Nov; 27(11):4797-4803. View Related Profiles. PMID: 28526892; DOI: 10.1007/s00330-017-4851-7.

Pavel AB, Campbell JD, Liu G, Elashoff D, Dubinett S, Smith K, Whitney D, Lenburg ME, Spira A. Alterations in Bronchial Airway miRNA Expression for Lung Cancer Detection. Cancer Prev Res (Phila). 2017 Nov; 10(11):651-659. View Related Profiles. PMID: 28877936.

Ekladious I, Liu R, Zhang H, Foil DH, Todd DA, Graf TN, Padera RF, Oberlies NH, Colson YL, Grinstaff MW. Synthesis of poly(1,2-glycerol carbonate)-paclitaxel conjugates and their utility as a single high-dose replacement for multi-dose treatment regimens in peritoneal cancer. Chem Sci. 2017 Dec 01; 8(12):8443-8450. PMID: 29619192.

Daniel S. Reynolds, Kristie M. Tevis, William A. Blessing, Yolonda L. Colson, Muhmmad H. Zaman* and Mark W. Grinstaff*. Breast Cancer Spheroids Reveal a Differential Cancer Stem Cell Response to Chemotherapeutic Treatment Scientific Reports 7, Article number: 10382 (2017).

Brisimi, T., Shi, W., Olshevsky, A., & Paschalidis, I. C. (2017). A Decentralized Primal Dual Method for Large-Scale Sparse Support Vector Machines. In SIAM Conference on Optimization. Vancouver, Canada.

Shain WJ, Vickers NA, Negash A, Bifano T, Sentenac A, Mertz J, “Dual fluorescence-absorption deconvolution applied to extended-depth-of-field microscopy,” Optics Letters, [42], 4183-4186, 2017.

Shain WJ, Vickers NA, Goldberg BB, Bifano T, Mertz J, “Extended depth-of-field microscopy with a high-speed deformable mirror,” Optics Letters, [42], 995-998, 2017.

Dennis, A. M.; Chern, M.; Nguyen, T. T.; Mahler, A. H. Shell thickness effects on quantum dot brightness and energy transfer. Nanoscale. 2017, 9, 16446-16458.

Featured

Kensler TW, Spira A, Garber JE, Szabo E, Lee JJ, Dong Z, Dannenberg AJ, Hait WN, Blackburn E, Davidson NE, Foti M, Lippman SM. Transforming Cancer Prevention through Precision Medicine and Immune-oncology. Cancer Prev Res (Phila). 2016 Jan; 9(1):2-10. PMID: 26744449; PMCID: PMC4955753; DOI: 10.1158/1940-6207.CAPR-15-0406.

Rodriguez NM, Wong WS, Liu L, Dewar R, Klapperich CM. A fully integrated paperfluidic molecular diagnostic chip for the extraction, amplification, and detection of nucleic acids from clinical samples. Lab Chip. 2016 Feb 21; 16(4):753-63. PMID: 26785636; PMCID: PMC4747825; DOI: 10.1039/c5lc01392e.

Kaplan JA, Grinstaff MW, Bloch BN. Polymer film-nanoparticle composites as new multimodality, non-migrating breast biopsy markers. Eur Radiol. 2016 Mar; 26(3):866-73. View Related Profiles. PMID: 26060064; DOI: 10.1007/s00330-015-3852-7.

Ferguson JS, Van Wert R, Choi Y, Rosenbluth MJ, Smith KP, Huang J, Spira A. Impact of a bronchial genomic classifier on clinical decision making in patients undergoing diagnostic evaluation for lung cancer. BMC Pulm Med. 2016 May 17; 16(1):66. PMID: 27184093; PMCID: PMC4869188; DOI: 10.1186/s12890-016-0217-1.

Boardman AK, Wong WS, Premasiri WR, Ziegler LD, Lee JC, Miljkovic M, Klapperich CM, Sharon A, Sauer-Budge AF. Rapid Detection of Bacteria from Blood with Surface-Enhanced Raman Spectroscopy. Anal Chem. 2016 Aug 16; 88(16):8026-35. View Related Profiles. PMID: 27429301; PMCID: PMC4988670; DOI: 10.1021/acs.analchem.6b01273.

Farhat MR, Sultana R, Iartchouk O, Bozeman S, Galagan J, Sisk P, Stolte C, Nebenzahl-Guimaraes H, Jacobson K, Sloutsky A, Kaur D, Posey J, Kreiswirth BN, Kurepina N, Rigouts L, Streicher EM, Victor TC, Warren RM, van Soolingen D, Murray M. Genetic Determinants of Drug Resistance in Mycobacterium tuberculosis and Their Diagnostic Value. Am J Respir Crit Care Med. 2016 Sep 01; 194(5):621-30. View Related Profiles. PMID: 26910495; PMCID: PMC5027209; DOI: 10.1164/rccm.201510-2091OC.

Spira A, Disis ML, Schiller JT, Vilar E, Rebbeck TR, Bejar R, Ideker T, Arts J, Yurgelun MB, Mesirov JP, Rao A, Garber J, Jaffee EM, Lippman SM. Leveraging premalignant biology for immune-based cancer prevention. Proc Natl Acad Sci U S A. 2016 09 27; 113(39):10750-8. PMID: 27638202; DOI: 10.1073/pnas.1608077113.

Liu R, Colby AH, Gilmore D, Schulz M, Zeng J, Padera RF, Shirihai O, Grinstaff MW, Colson YL. Nanoparticle tumor localization, disruption of autophagosomal trafficking, and prolonged drug delivery improve survival in peritoneal mesothelioma. Biomaterials. 2016 Sep; 102:175-86. View Related Profiles. PMID: 27343465; PMCID: PMC4948582; DOI: 10.1016/j.biomaterials.2016.06.031.

“A joint sparse clustering and classification approach with applications to hospitalization prediction”, (with Tingting Xu, Theodora Brisimi, Taiyao Wang, Wuyang Dai), Proceedings of the 55th IEEE Conference on Decision and Control, pages 4566-4571, December 12-14, 2016, Las Vegas, Nevada.

Kim CS, Vanture S, Cho M, Klapperich CM, Wang C, Huang FW. Awareness, Interest, and Preferences of Primary Care Providers in Using Point-of-Care Cancer Screening Technology. PLoS One. 2016; 11(1):e0145215. View Related Profiles. PMID: 26771309; PMCID: PMC4714834; DOI: 10.1371/journal.pone.0145215.

Krueger AS, Munck C, Dantas G, Church GM, Galagan J, Lehár J, Sommer MO. Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis. PLoS One. 2016; 11(1):e0147651. View Related Profiles. PMID: 26821252; PMCID: PMC4731467; DOI: 10.1371/journal.pone.0147651.

Grace Wu, Hatice Imran Gungordu, Navaporn Tagontong, Peter Hall and Muhammad H. Zaman. Development of a novel method of misoprostol detection on filter paper. Biomedical Engineering Letters, 6 (2), 94-99, 2016.

Dennis, A. M.; Delehanty, J.; Medintz, I. Emerging Physicochemical Phenomena along with New Opportunities at the Biomolecular–Nanoparticle Interface. Journal of Physical Chemistry Letters 2016, 7(11), 2139-2150.

Russell, S. J., et al. (2016). “Day and night glycaemic control with a bionic pancreas versus conventional insulin pump therapy in preadolescent children with type 1 diabetes: a randomised crossover trial.” Lancet Diabetes Endocrinol 4(3): 233-243.

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Other

Linnes JC, Rodriguez NM, Liu L, Klapperich CM. Polyethersulfone improves isothermal nucleic acid amplification compared to current paper-based diagnostics. Biomed Microdevices. 2016 Apr; 18(2):30. PMID: 26906904; PMCID: PMC4855516; DOI: 10.1007/s10544-016-0057-z.

Hofferberth SC, Grinstaff MW, Colson YL. Nanotechnology applications in thoracic surgery. Eur J Cardiothorac Surg. 2016 Jul; 50(1):6-16. PMID: 26843431; PMCID: PMC4913874; DOI: 10.1093/ejcts/ezw002.

Vachani A, Whitney DH, Parsons EC, Lenburg M, Ferguson JS, Silvestri GA, Spira A. Clinical Utility of a Bronchial Genomic Classifier in Patients With Suspected Lung Cancer. Chest. 2016 Jul; 150(1):210-8. View Related Profiles. PMID: 26896702; DOI: 10.1016/j.chest.2016.02.636.

Rahman SM, Ji X, Zimmerman LJ, Li M, Harris BK, Hoeksema MD, Trenary IA, Zou Y, Qian J, Slebos RJ, Beane J, Spira A, Shyr Y, Eisenberg R, Liebler DC, Young JD, Massion PP. The airway epithelium undergoes metabolic reprogramming in individuals at high risk for lung cancer. JCI Insight. 2016 Nov 17; 1(19):e88814. PMID: 27882349.

Sharp, J. D., A. K. Singh, S. T. Park, A. Lyubetskaya, M. W. Peterson, A. L. Gomes, L. P. Potluri, S. Raman, J. E. Galagan, and R. N. Husson. 2016. ‘Comprehensive Definition of the SigH Regulon of Mycobacterium tuberculosis Reveals Transcriptional Control of Diverse Stress Responses’, PLoS One, 11: e0152145.

Ranganathan, S., G. Bai, A. Lyubetskaya, G. S. Knapp, M. W. Peterson, M. Gazdik, C. Gomes AL, J. E. Galagan, and K. A. McDonough. 2016. ‘Characterization of a cAMP responsive transcription factor, Cmr (Rv1675c), in TB complex mycobacteria reveals overlap with the DosR (DevR) dormancy regulon’, Nucleic Acids Res, 44: 134-51.

Fabian Spill, Zohar Weinstein, Nga Ho, Atena Shemirani, Darash Desai and Muhammad H. Zaman. Controlling uncertainty in aptamer selection. Proceedings of the National Academy of Sciences, vol. 113 no. 43 12076-12081 2016.

Katie Clifford and Muhammad H. Zaman. Engineering, Global Health and Inclusive Innovation: Focus on partnership, system strengthening and local impact for SDGs. Global Health Action, 2016; 9: 10.3402/gha.v9.30175.

Qi Zhao, Arion Stettner, Ed Reznik, I. Ch. Paschalidis, and Daniel Segre, “Mapping the landscape of metabolic goals of a cell”, Genome Biology, 2016, 17:109, doi: 10.1186/s13059-016-0968-2.

Li J, Bifano TG, Mertz J, “Widefield fluorescence microscopy with sensor-based conjugate adaptive optics using oblique back illumination,” Journal of Biomedical Optics, [21], 121504-121504, 2016.

Imboden M, Chang J, Pollock C, Lowell E, Akbulut M, Morrison J, Stark T, Bifano TG, Bishop DJ, “High-Speed Control of Electromechanical Transduction: Advanced Drive Techniques for Optimized Step-and-Settle Response of MEMS Micromirrors,” IEEE Control Systems, [36], 48-76, 2016.

Featured

Wu G, Zaman MH. Amperometric measurements of ethanol on paper with a glucometer. Talanta. 2015 Mar; 134:194-9. PMID: 25618657; DOI: 10.1016/j.talanta.2014.10.061.

Derda R, Gitaka J, Klapperich CM, Mace CR, Kumar AA, Lieberman M, Linnes JC, Jores J, Nasimolo J, Ndung’u J, Taracha E, Weaver A, Weibel DB, Kariuki TM, Yager P. Enabling the Development and Deployment of Next Generation Point-of-Care Diagnostics. PLoS Negl Trop Dis. 2015 May; 9(5):e0003676. PMID: 25973602; PMCID: PMC4431858; DOI: 10.1371/journal.pntd.0003676.

Gesthalter YB, Vick J, Steiling K, Spira A. Translating the transcriptome into tools for the early detection and prevention of lung cancer. Thorax. 2015 May; 70(5):476-81. View Related Profiles. PMID: 25628310; DOI: 10.1136/thoraxjnl-2014-206605.

Ho NT, Desai D, Zaman MH. Rapid and specific drug quality testing assay for artemisinin and its derivatives using a luminescent reaction and novel microfluidic technology. Am J Trop Med Hyg. 2015 Jun; 92(6 Suppl):24-30. PMID: 25897061; PMCID: PMC4455072; DOI: 10.4269/ajtmh.14-0392.

Falde EJ, Yohe ST, Grinstaff MW. Sensors: Surface Tension Triggered Wetting and Point of Care Sensor Design (Adv. Healthcare Mater. 11/2015). Adv Healthc Mater. 2015 Aug; 4(11):1653. PMID: 26097150; DOI: 10.1002/adhm.201570066.

Darash Desai and Muhammad H. Zaman. Continuous Flow Microfluidic Solution for Quantitative Analysis of Active Pharmaceutical Ingredient Content and Kinetic Release. Analytical Methods, 2015. 7, 1914-1923.

Q. Zhao, T. Edrich, and I. Ch. Paschalidis, “Adaptive Control of Bivalirudin in the Cardiac Intensive Care Unit”, IEEE Transactions on Biomedical Engineering, Vol. 62 (2015), No 2, pages 638-647, doi: 10.1109/TBME.2014.2362761.

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Other

Zaman MH. Maternal health in developing countries: engineering approaches and future outlook. IEEE Pulse. 2015 Jan-Feb; 6(1):25-7. PMID: 25616265; DOI: 10.1109/MPUL.2014.2366894.

Silvestri GA, Vachani A, Whitney D, Elashoff M, Porta Smith K, Ferguson JS, Parsons E, Mitra N, Brody J, Lenburg ME, Spira A. A Bronchial Genomic Classifier for the Diagnostic Evaluation of Lung Cancer. N Engl J Med. 2015 Jul 16; 373(3):243-51. View Related Profiles. PMID: 25981554; DOI: 10.1056/NEJMoa1504601.

Rodriguez NM, Linnes JC, Fan A, Ellenson CK, Pollock NR, Klapperich CM. Paper-Based RNA Extraction, in Situ Isothermal Amplification, and Lateral Flow Detection for Low-Cost, Rapid Diagnosis of Influenza A (H1N1) from Clinical Specimens. Anal Chem. 2015 Aug 4; 87(15):7872-9. PMID: 26125635; PMCID: PMC4878390; DOI: 10.1021/acs.analchem.5b01594.

Wuyang Dai, Theodora Brisimi, Tingting Xu, Taiyao Wang, Venkatesh Saligrama, and I. Ch. Paschalidis, “A Joint Clustering and Classification Approach for Healthcare Predictive Analytics”, 2nd Workshop on Data Mining for Medical Informatics (DMMI 2015), November 14th, 2015, San Francisco, California.

Ranganathan, S., G. Bai, A. Lyubetskaya, G. S. Knapp, M. W. Peterson, M. Gazdik, A. L. Gomes, J. E. Galagan, and K. A. McDonough. 2015. ‘Characterization of a cAMP responsive transcription factor, Cmr (Rv1675c), in TB complex mycobacteria reveals overlap with the DosR (DevR) dormancy regulon‘, Nucleic Acids Res.

Knapp, G. S., A. Lyubetskaya, M. W. Peterson, A. L. Gomes, Z. Ma, J. E. Galagan, and K. A. McDonough. 2015. ‘Role of intragenic binding of cAMP responsive protein (CRP) in regulation of the succinate dehydrogenase genes Rv0249c-Rv0247c in TB complex mycobacteria’, Nucleic Acids Res, 43: 5377-93.

Garay, C. D., J. M. Dreyfuss, and J. E. Galagan. 2015. ‘Metabolic modeling predicts metabolite changes in Mycobacterium tuberculosis‘, BMC Syst Biol, 9: 57.

Whitney DH, Elashoff MR, Porta-Smith K, Gower AC, Vachani A, Ferguson JS, Silvestri GA, Brody JS, Lenburg ME, Spira A. Derivation of a bronchial genomic classifier for lung cancer in a prospective study of patients undergoing diagnostic bronchoscopy. BMC Med Genomics. 2015; 8:18. View Related Profiles. PMID: 25944280; PMCID: PMC4434538; DOI: 10.1186/s12920-015-0091-3.

Sinefeld D, Paudel HP, Ouzounov DG, Bifano TG, Xu C, “Adaptive optics in multiphoton microscopy: comparison of two, three and four photon fluorescence,” Optics Express, [23], 31472-31483, 2015.

Li J, Beaulieu DR, Paudel H, Barankov R, Bifano TG, Mertz J, “Conjugate adaptive optics in widefield microscopy with an extended-source wavefront sensor,” Optica, [2], 682-688, 2015.

Paudel HP, Taranto J, Mertz J, Bifano T, “Axial range of conjugate adaptive optics in two-photon microscopy,” Optics Express, [23], 20849-20857, 2015.

Mertz J, Paudel H, Bifano TG, “Field of view advantage of conjugate adaptive optics in microscopy applications,” Applied Optics, [54], 3498-3506, 2015.

Dennis, A.M.; Chou, K. F., Förster Resonance Energy Transfer between Quantum Dot Donors and Quantum Dot Acceptors. Sensors. 13(6), 13288-13325.

Featured

Linnes JC, Fan A, Rodriguez NM, Lemieux B, Kong H, Klapperich CM. Paper-based molecular diagnostic for Chlamydia trachomatis. RSC Adv. 2014 Jan 01; 4(80):42245-42251. PMID: 25309740.

Charoen KM, Fallica B, Colson YL, Zaman MH, Grinstaff MW. Embedded multicellular spheroids as a biomimetic 3D cancer model for evaluating drug and drug-device combinations. Biomaterials. 2014 Feb; 35(7):2264-71. View Related Profiles. PMID: 24360576; PMCID: PMC3923358; DOI: 10.1016/j.biomaterials.2013.11.038.

Q. Zhao, T. Edrich, and I. Ch. Paschalidis, “Predicting and Evaluating the Effect of Bivalirudin in Cardiac Surgical Patients”, IEEE Transactions on Biomedical Engineering, Vol. 61 (2014), No. 2 (February), pages 435-443, doi:10.1109/TBME.2013.2280636.

Grace Wu, Jaya Srivastava and Muhammad H. Zaman. Stability measurements of antibodies stored on paper. Analytical Biochemistry. 2014. doi: 10.1016/j.ab.2013.12.012.

W. Dai, T. Brisimi, V. Saligrama, W. Adams, T. Mela, and I. Ch. Paschalidis, “Prediction of hospitalization due to heart diseases by supervised learning methods”, International Journal of Medical Informatics, 2014, doi: 10.1016/j.ijmedinf.2014.10.002.

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Jaini, S, A. Lyubetskaya, A Gomes, M Peterson, S. T. Park, S Raman, G. Schoolnik, and J.E. Galagan. 2014. ‘Transcription Factor Binding Site Mapping Using ChIP-Seq.’ in G Hatfull and W. R. Jacobs, Jr. (eds.), Molecular Genetics of Mycobacteria, 2nd Edition (ASM Press).

Hurley, J. M., A. Dasgupta, J. M. Emerson, X. Zhou, C. S. Ringelberg, N. Knabe, A. M. Lipzen, E. A. Lindquist, C. G. Daum, K. W. Barry, I. V. Grigoriev, K. M. Smith, J. E. Galagan, D. Bell-Pedersen, M. Freitag, C. Cheng, J. J. Loros, and J. C. Dunlap. 2014. ‘Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential‘, Proc Natl Acad Sci U S A, 111: 16995-7002.

Gomes, A. L., T. Abeel, M. Peterson, E. Azizi, A. Lyubetskaya, L. Carvalho, and J. Galagan. 2014. ‘Decoding ChIP-Seq peaks with a double-binding signal refines binding peaks to single-nucleotide and predicts cooperative interaction‘, Genome Res.

Kathuria H, Gesthalter Y, Spira A, Brody JS, Steiling K. Updates and controversies in the rapidly evolving field of lung cancer screening, early detection, and chemoprevention. Cancers (Basel). 2014; 6(2):1157-79. View Related Profiles. PMID: 24840047; DOI: 10.3390/cancers6021157.

Vigil K, Lu Y, Yurt A, Cilingiroglu TB, Bifano TG, Ünlü MS, Goldberg BB, “Integrated Circuit Super-Resolution Failure Analysis with Solid Immersion Lenses,” Electronic Device Failure Analysis, [16], 26-32, 2014.

Russell, S. J., et al. (2014). “Outpatient glycemic control with a bionic pancreas in type 1 diabetes.” N Engl J Med 371(4): 313-325.

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J. Chau, and T.D.C. Little, “Challenges in Retaining Privacy in Smart Spaces,” Proc. 4th Intl. Conf. on Ambient Systems, Networks and Technologies, June 25-28, 2013, Halifax, Nova Scotia, Canada.

Huang S, Do J, Mahalanabis M, Fan A, Zhao L, Jepeal L, Singh SK, Klapperich CM. Low cost extraction and isothermal amplification of DNA for infectious diarrhea diagnosis. PLoS One. 2013; 8(3):e60059. View Related Profiles. PMID: 23555883; PMCID: PMC3610934; DOI: 10.1371/journal.pone.0060059.

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Byrnes S, Fan A, Trueb J, Jareczek F, Mazzochette M, Sharon A, Sauer-Budge AF, Klapperich CM. A Portable, Pressure Driven, Room Temperature Nucleic Acid Extraction and Storage System for Point of Care Molecular Diagnostics. Anal Methods. 2013 Jul 07; 5(13):3177-3184. PMID: 23914255.

J. Gancarz, H. Elgala, and T.D.C. Little, “Impact of Lighting Requirements on VLC Systems,” in IEEE Communications Magazine, Special Issue on Visible Light Communications — The Road to Standardization and Commercialization, December 2013.

Pepperell, C. S., A. M. Casto, A. Kitchen, J. M. Granka, O. E. Cornejo, E. C. Holmes, B. Birren, J. Galagan, and M. W. Feldman. 2013. ‘The role of selection in shaping diversity of natural M. tuberculosis populations‘, PLoS Pathog, 9: e1003543.

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Galagan, J., A. Lyubetskaya, and A. Gomes. 2013. ‘ChIP-Seq and the complexity of bacterial transcriptional regulation‘, Curr Top Microbiol Immunol, 363: 43-68.

Dreyfuss, J. M., J. D. Zucker, H. M. Hood, L. R. Ocasio, M. S. Sachs, and J. E. Galagan. 2013. ‘Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM‘, PLoS Comput Biol, 9: e1003126.

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Y. Zhang, K.G.M. Beenakker, P.M. Butala, C.-C. Lin, T.D.C. Little, A.B. Maier, M. Stijntjes, R. Vartanian, and R.C. Wagenaar, “Monitoring Walking and Cycling of Middle-Aged to Older Community Dwellers Using Wireless Wearable Accelerometers,” in Proc. 34th Annual Intl. Conf. IEEE Engineering in Medicine and Biology Society, San Diego, CA, August 2012.

Dennis, A. M.; Rhee, W. J.; Sotto, D.; Dublin, S. N.; Bao, G. Quantum Dot-Fluorescent Protein FRET Probes for Sensing Intracellular pH. ACS Nano 2012, 6, 2917-2924.

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Russell, S. J., et al. (2012). “Blood glucose control in type 1 diabetes with a bihormonal bionic endocrine pancreas.” Diabetes Care 35(11): 2148-2155.

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Y. Zhang, I. Sapir, S. Markovic, R.C. Wagenaar, and T.D.C. Little, “Continuous Functional Activity Monitoring Based on Wearable Tri-Axial Accelerometer and Gyroscope,” Proc. Workshop on Cognitive Sensor Networks for Pervasive Health (CoSN-PH 2011), 5th Intl. Conf. on Pervasive Computing Technologies for Healthcare (PervasiveHealth 2011), Dublin Ireland, May 2011.

R.C. Wagenaar, I. Sapir, Y. Zhang, S. Markovic, L.M. Vaina, and T.D.C. Little, “Continuous Monitoring of Functional Activities using Wearable, Wireless Gyroscope and Accelerometer Technology,” Proc. 33rd Annual Intl. Conf. of the IEEE Engineering in Medicine and Biology Society, Boston, MA, August 30, 2011.