Preprints and manuscripts under review

Shemonti AS, Eisenberg JD, Heuckeroth RO, Howard MJ, Pothen A, Rajwa B. Generative modeling of the enteric nervous system employing point pattern analysis and graph construction. arXiv; 2022.
Shemonti AS, Plebani E, Biscola NP, Jaffey DM, Havton LA, Keast JR, Pothen A, Dundar MM, Rajwa B. A novel statistical methodology for quantifying the spatial arrangements of axons in peripheral nerves. arXiv; 2022.
Cheng Y, Rajwa B, Dundar M. Bayesian nonparametrics for non-exhaustive learning. arXiv:190809736 [cs, stat]. 2019;

Peer-reviewed papers

Scherl DS, Coffman L, Mansoor A, Rajwa B, Patsekin V, Robinson JP. A semi-automated method for measuring biofilm accumulation on the teeth using quantitative light-induced fluorescence in dogs and cats. J Vet Dent. 2022;39(2):122–32.
Doh I-J, Dowden B, Patsekin V, Rajwa B, Robinson JP, Bae E. Development of a smartphone-integrated reflective scatterometer for bacterial identification. Sensors. 2022;22(7):2646.
Plebani E, Biscola NP, Havton LA, Rajwa B, Shemonti AS, Jaffey D, Powley T, Keast JR, et al. High-throughput segmentation of unmyelinated axons by deep learning. Sci Rep. 2022;12(1):1198.
Nestor-Kalinoski A, Smith-Edwards KM, Meerschaert K, Margiotta JF, Rajwa B, Davis BM, Howard MJ. Unique neural circuit connectivity of mouse proximal, middle, and distal colon defines regional colonic motor patterns. Cellular and Molecular Gastroenterology and Hepatology. 2022;13(1):309-337.e3.
Franco J, Rajwa B, Gomes P, HogenEsch H. Local and systemic changes in lipid profile as potential biomarkers for canine atopic dermatitis. Metabolites. 2021;11(10):670.
Bieberich AA, Rajwa B, Irvine A, Fatig RO, Fekete A, Jin H, Kutlina E, Urban L. Acute cell stress screen with supervised machine learning predicts cytotoxicity of excipients. Journal of Pharmacological and Toxicological Methods. 2021;111:107088.
Doh I-J, Kim H, Sturgis J, Rajwa B, Robinson JP, Bae E. Optical multi-channel interrogation instrument for bacterial colony characterization. PLoS One. 2021;16(2):e0247721.
Cortés-Selva D, Gibbs L, Ready A, Ekiz HA, O’Connell R, Rajwa B, Fairfax KC. Maternal schistosomiasis impairs offspring Interleukin-4 production and B cell expansion. PLoS Pathogens. 2021;17(2):e1009260.
Kobos L, Ferreira CR, Sobreira TJP, Rajwa B, Shannahan J. A novel experimental workflow to determine the impact of storage parameters on the mass spectrometric profiling and assessment of representative phosphatidylethanolamine lipids in mouse tissues. Anal Bioanal Chem. 2021;413(7):1837–49.
Tan ZT, Ward M, Phillips RJ, Zhang X, Jaffey DM, Chesney L, Rajwa B, Baronowsky EA, et al. Stomach region stimulated determines effects on duodenal motility in rats. American Journal of Physiology-Regulatory, Integrative and Comparative Physiology. 2021;320(3):R331–41.
Franco J, Rajwa B, Ferreira CR, Sundberg JP, HogenEsch H. Lipidomic profiling of the epidermis in a mouse model of dermatitis reveals sexual dimorphism and changes in lipid composition before the onset of clinical disease. Metabolites. 2020;10(7):299.
Gondhalekar C, Biela E, Rajwa B, Bae E, Patsekin V, Sturgis J, Reynolds C, Doh I-J, et al. Detection of E. coli labeled with metal-conjugated antibodies using lateral-flow assay and laser-induced breakdown spectroscopy. Anal Bioanal Chem. 2020;412(6):1291–301.
Ward MP, Gupta A, Wo JM, Rajwa B, Furness JB, Powley TL, Nowak T. An emerging method to noninvasively measure and identify vagal response markers to enable bioelectronic control of gastroparesis symptoms with gastric electrical stimulation. J Neurosci Methods. 2020;336:108631.
Cossarizza A, Chang H-D, Radbruch A, Acs A, Adam D, Adam-Klages S, Agace WW, Aghaeepour N, ... Rajwa B, ... et al. Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition). Eur J Immunol. 2019;49(10):1457–973.
Allan MC, Grush EN, Rajwa BP, Butzke CE, Mauer LJ. Determination of the water activities of wines and spirits. Food Anal Meth. 2019;12(12):2753–63.
Doh I-J, Gondhalekar C, Patsekin V, Rajwa B, Hernandez K, Bae E, Robinson JP. A portable spark-induced breakdown spectroscopic (SIBS) instrument and its analytical performance. Appl Spectrosc. 2019;73(6):698–708.
Cortes‐Selva D, Ready A, Gibbs L, Rajwa B, Fairfax KC. IL-4 promotes stromal cell expansion and is critical for development of a type-2, but not a type 1 immune response. European Journal of Immunology. 2019;49(3):428–42.
Chen Y, Calvert RD, Azad A, Rajwa B, Fleet J, Ratliff T, Pothen A. Phenotyping Immune Cells in Tumor and Healthy Tissue Using Flow Cytometry Data. In: Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. New York, NY, USA: Association for Computing Machinery; 2018. p. 73–8. (BCB ’18).
Gondhalekar C, Rajwa B, Patsekin V, Ragheb K, Sturgis J, Robinson JP. Alternatives to current flow cytometry data analysis for clinical and research studies. Methods. 2018;134:113–29.
Calvert RD, Fleet JC, Chen Y, Pothen A, Rajwa B, Fournier PG, Juarez P, Guise TA, et al. Monocytic myeloid derived suppressor cells (M-MDSC) from spleen are multipotent while tumor M-MDSC have limited plasticity. Cancer Res. 2018;78(13).
Allan MC, Rajwa B, Mauer LJ. Effects of sugars and sugar alcohols on the gelatinization temperature of wheat starch. Food Hydrocolloids. 2018;84:593–607.
Cortes-Selva D, Elvington AF, Ready A, Rajwa B, Pearce EJ, Randolph GJ, Fairfax KC. Schistosoma mansoni infection-induced transcriptional changes in hepatic macrophage metabolism correlate with an athero-protective phenotype. Front Immunol. 2018;9:2580.
Zhang C, Huang K-C, Rajwa B, Li J, Yang S, Lin H, Liao C, Eakins G, et al. Stimulated Raman scattering flow cytometry for label-free single-particle analysis. Optica. 2017;4(1):103–9.
Cossarizza A, Chang H-D, Radbruch A, Akdis M, Andrae I, Annunziato F, Bacher P, Barnaba V, ... Rajwa B, ... et al. Guidelines for the use of flow cytometry and cell sorting in immunological studies. Eur J Immunol. 2017;47(10):1584–797.
Thomas FM, Goode KM, Rajwa B, Bieberich AA, Avramova LV, Hazbun TR, Davisson VJ. A chemogenomic screening platform used to identify chemotypes perturbing HSP90 pathways. SLAS DISCOVERY: Advancing Life Sciences R&D. 2017;22(6):706–19.
Rajwa B. Effect-size measures as descriptors of assay quality in high-content screening: a brief review of some available methodologies. ASSAY and Drug Development Technologies. 2017;15(1):15–29.
Kim H, Rajwa B, Bhunia AK, Robinson JP, Bae E. Development of a multispectral light-scatter sensor for bacterial colonies. J Biophotonics. 2017;10(5):634–44.
Rajwa B, Wallace PK, Griffiths EA, Dundar M. Automated assessment of disease progression in acute myeloid leukemia by probabilistic analysis of flow cytometry data. IEEE Trans Biomed Eng. 2017;64(5):1089–98.
Bae E, Kim H, Rajwa B, Thomas JG, Robinson JP. Current status and future prospects of using advanced computer-based methods to study bacterial colonial morphology. Expert Rev Anti-Infect Ther. 2016;14(2):207–18.
Azad A, Rajwa B, Pothen A. Immunophenotype discovery, hierarchical organization, and template-based classification of flow cytometry samples. Front Oncol. 2016;6:UNSP 188.
Azad A, Rajwa B, Pothen A. flowVS: channel-specific variance stabilization in flow cytometry. BMC Bioinformatics. 2016;17:291.
Mohammed SI, Ren W, Flowers L, Rajwa B, Chibwesha CJ, Parham GP, Irudayaraj JMK. Point-of-care test for cervical cancer in LMICs. Oncotarget. 2016;7(14):18787–97.
Dundar M, Kou Q, Zhang B, He Y, Rajwa B. Simplicity of kmeans versus deepness of deep learning: a case of unsupervised feature learning with limited data. In: 2015 IEEE 14th International Conference on Machine Learning and Applications (ICMLA). Amsterdam: Elsevier Science BV; 2015. p. 883–8.
Ito D, Childress M, Mason N, Winter A, O’Brien T, Henson M, Borgatti A, Lewellen M, et al. A double blinded, placebo-controlled pilot study to examine reduction of CD34+/CD117+/CD133+lymphoma progenitor cells and duration of remission induced by neoadjuvant valspodar in dogs with large B-cell lymphoma. F1000Res. 2015;4:42.
Mansoor A, Patsekin V, Scherl D, Robinson JP, Rajwa B. A statistical modeling approach to computer-aided quantification of dental biofilm. IEEE Journal of Biomedical and Health Informatics. 2015;19(1):358–66.
Yerebakan HZ, Rajwa B, Dundar M. The infinite mixture of infinite Gaussian mixtures. In: Ghahramani Z, Welling M, Cortes C, Lawrence ND, Weinberger KQ, editors. Advances in Neural Information Processing Systems 27 (NIPS 2014). La Jolla: Neural Information Processing Systems (NIPS); 2014.
Tang Y, Kim H, Singh AK, Aroonnual A, Bae E, Rajwa B, Fratamico PM, Bhunia AK. Light scattering sensor for direct identification of colonies of Escherichia coli serogroups O26, O45, O103, O111, O121, O145 and O157. PLoS One. 2014;9(8):e105272.
Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H, Xiao G, Li Y, et al. A community computational challenge to predict the activity of pairs of compounds. Nat Biotechnol. 2014;32(12):1213-+.
Dundar M, Akova F, Yerebakan HZ, Rajwa B. A non-parametric Bayesian model for joint cell clustering and cluster matching: identification of anomalous sample phenotypes with random effects. BMC Bioinformatics. 2014;15(1):314.
Benson AR, Lee JD, Rajwa B, Gleich DF. Scalable methods for nonnegative matrix factorizations of near-separable tall-and-skinny matrices. In: Ghahramani Z, Welling M, Cortes C, Lawrence ND, Weinberger KQ, editors. Advances in Neural Information Processing Systems 27 (NIPS 2014). La Jolla: Neural Information Processing Systems (NIPS); 2014.
Singh AK, Bettasso AM, Bae E, Rajwa B, Dundar MM, Forster MD, Liu L, Barrett B, et al. Laser optical sensor, a label-free on-plate salmonella enterica colony detection tool. mBio. 2014;5(1):e01019-13.
Dundar M, Li L, Rajwa B. Partially-observed models for classifying minerals on Mars. In: 2013 5th Workshop on Hyperspectral Image and Signal Processing: Evolution in Remote Sensing (WHISPERS). 2013. p. 1–4.
Novo D, Gregori G, Rajwa B. Generalized unmixing model for multispectral flow cytometry utilizing nonsquare compensation matrices. Cytom Part A. 2013;83A(5):508–20.
Ahmed WM, Bayraktar B, Bhunia AK, Hirleman ED, Robinson JP, Rajwa B. Classification of bacterial contamination using image processing and distributed computing. IEEE J Biomed Health Inform. 2013;17(1):232–9.
Robinson JP, Patsekin V, Holdman C, Ragheb K, Sturgis J, Fatig R, Avramova LV, Rajwa B, et al. High-throughput secondary screening at the single-cell level. JALA. 2013;18(1):85–98.
Huff K, Aroonnual A, Littlejohn AEF, Rajwa B, Bae E, Banada PP, Patsekin V, Hirleman ED, et al. Light-scattering sensor for real-time identification of Vibrio parahaemolyticus, Vibrio vulnificus and Vibrio cholerae colonies on solid agar plate. Microb Biotechnol. 2012;5(5):607–20.
Gregori G, Patsekin V, Rajwa B, Jones J, Ragheb K, Holdman C, Robinson JP. Hyperspectral cytometry at the single-cell level using a 32-channel photodetector. Cytom Part A. 2012;81A(1):35–44.
Akova F, Dundar M, Qi Y, Rajwa B. Self-adjusting models for semi-supervised learning in partially observed settings. In: Zaki MJ, Siebes A, Yu JX, Goethals B, Webb G, Wu X, editors. 12th IEEE International Conference on Data Mining (ICDM 2012). New York: Ieee; 2012. p. 21–30.
Bae E, Ying D, Kramer D, Patsekin V, Rajwa B, Holdman C, Sturgis J, Davisson VJ, et al. Portable bacterial identification system based on elastic light scatter patterns. J Biol Eng. 2012;6(1):12.
Tsiper MV, Sturgis J, Avramova LV, Parakh S, Fatig R, Juan-Garcia A, Li N, Rajwa B, et al. Differential mitochondrial toxicity screening and multi-parametric data analysis. PLoS One. 2012;7(10):e45226.
Robinson JP, Rajwa B, Patsekin V, Davisson VJ. Computational analysis of high-throughput flow cytometry data. Expert Opin Drug Discov. 2012;7(8):679–93.
Bae E, Patsekin V, Rajwa B, Bhunia AK, Holdman C, Davisson VJ, Hirleman ED, Robinson JP. Development of a microbial high-throughput screening instrument based on elastic light scatter patterns. Rev Sci Instrum. 2012;83(4):044304.
Bernas T, Starosolski R, Robinson JP, Rajwa B. Application of detector precision characteristics and histogram packing for compression of biological fluorescence micrographs. Comput Methods Programs Biomed. 2012;108(2):511–23. 10.1016/j.cmpb.2011.03.012
Rajwa B. Just compensation? Cytom Part A. 2011;79A(12):973–4.
Robinson JP, Patsekin V, Rajwa B, Davisson VJ, Li N, Narayanan P. High-Throughput Flow Cytometry. Genet Eng Biotechnol News. 2011;31(8):20-+.
Rajwa B, Dundar MM, Akova F, Bettasso A, Patsekin V, Hirleman ED, Bhunia AK, Robinson JP. Discovering the unknown: detection of emerging pathogens using a label-free light-scattering system. Cytom Part A. 2010;77A(12):1103–12.
Duerstock BS, Cirillo J, Rajwa B. Theta rotation and serial registration of light microscopical images using a novel camera rotating device. Microsc microanal. 2010;16(3):239–47.
Dundar MM, Hirleman ED, Bhunia AK, Robinson JP, Rajwa B. Learning with a non-exhaustive training dataset: a case study: detection of bacteria cultures using optical-scattering technology. In: Proceedings of the 15th ACM SIGKDD international conference on Knowledge discovery and data mining. Paris, France: Association for Computing Machinery; 2009. p. 279–88. (KDD ’09).
Akova F, Hirleman D, Bhunia AK, Rajwa B, Dundar MM. Non-exhaustive learning for bacteria detection. In: 2009 International Conference on Network-Based Information Systems. New York: IEEE; 2009. p. 206–11.
Banada PP, Huff K, Bae E, Rajwa B, Aroonnual A, Bayraktar B, Adil A, Robinson JP, et al. Label-free detection of multiple bacterial pathogens using light-scattering sensor. Biosens Bioelectron. 2009;24(6):1685–92.
Venkatapathi M, Rajwa B, Ragheb K, Banada PP, Lary T, Robinson JP, Hirleman ED. High speed classification of individual bacterial cells using a model-based light scatter system and multivariate statistics. Appl Optics. 2008;47(5):678–86.
Rajwa B, Venkatapathi M, Ragheb K, Banada PP, Hirleman ED, Lary T, Robinson JP. Automated classification of bacterial particles in flow by multiangle scatter measurement and support vector machine classifier. Cytom Part A. 2008;73A(4):369–79.
Li M, Ong SS, Rajwa B, Thieu VT, Geahlen RL, Harrison ML. The SH3 domain of Lck modulates T-Cell receptor-dependent activation of extracellular signal-regulated kinase through activation of Raf-1. Mol Cell Biol. 2008;28(2):630–41.
Bernas T, Asem EK, Robinson JP, Rajwa B. Application of wavelet denoising to improve compression efficiency while preserving integrity of digital micrographs. J Microsc. 2008;231(1):81–96.
Ahmed WM, Leavesley SJ, Rajwa B, Ayyaz MN, Ghafoor A, Robinson JP. State of the art in information extraction and quantitative analysis for multimodality biomolecular imaging. Proc IEEE. 2008;96(3):512–31.
Leavesley S, Jiang Y, Patsekin V, Rajwa B, Robinson JP. An excitation wavelength-scanning spectral imaging system for preclinical imaging. Rev Sci Instrum. 2008;79(2):023707.
Bernas T, Asem EK, Robinson JP, Rajwa B. Quadratic form: A robust metric for quantitative comparison of flow cytometric histograms. Cytometry Part A. 2008;73A(8):715–26.
Rajwa B, Bernas T, Acker H, Dobrucki J, Robinson JP. Single- and two-photon spectral imaging of intrinsic fluorescence of transformed human hepatocytes. Microscopy Research and Technique. 2007;70(10):869–79.
Bernas T, Barnes D, Asem EK, Robinson JP, Rajwa B. Precision of light intensity measurement in biological optical microscopy. J Microsc. 2007;226(2):163–74.
Ahmed WM, Ayyaz MN, Rajwa B, Khan F, Ghafoor A, Robinson JP. Semantic analysis of biological imaging data: challenges and opportunities. Int J Semant Comput. 2007;1(1):67–85.
Banada PP, Guo S, Bayraktar B, Bae E, Rajwa B, Robinson JP, Hirleman ED, Bhunia AK. Optical forward-scattering for detection of Listeria monocytogenes and other Listeria species. Biosens Bioelectron. 2007;22(8):1664–71.
Xi P, Rajwa B, Jones JT, Robinson JP. The design and construction of a cost-efficient confocal laser scanning microscope. Am J Phys. 2007;75(3):203–7.
Krzeszowiec W, Rajwa B, Dobrucki J, Gabrys H. Actin cytoskeleton in Arabidopsis thaliana under blue and red light. Biol Cell. 2007;99(5):251–60.
Rajwa B. Image cytometry goes multiphoton. Cytom Part A. 2007;71A(12):973–5.
Bayraktar B, Bernas T, Robinson JP, Bartek Rajwa. A numerical recipe for accurate image reconstruction from discrete orthogonal moments. Pattern Recognition. 2007;40(2):659–69.
Bernas T, Asem EK, Robinson JP, Rajwa B. Compression of fluorescence microscopy images based on the signal-to-noise estimation. Microsc Res Tech. 2006;69(1):1–9.
Bayraktar B, Banada PP, Hirleman ED, Bhunia AK, Robinson JP, Rajwa B. Feature extraction from light-scatter patterns of Listeria colonies for identification and classification. J Biomed Opt. 2006;11(3):034006.
McNally HA, Rajwa B, Sturgis J, Robinson JP. Comparative three-dimensional imaging of living neurons with confocal and atomic force microscopy. J Neurosci Methods. 2005;142(2):177–84.
Kolcz J, Drukala J, Bzowska M, Rajwa B, Korohoda W, Malec E. The expression of connexin 43 in children with tetralogy of Fallot. Cell Mol Biol Lett. 2005;10(2):287–303.
Bernas T, Robinson JP, Asem EK, Rajwa B. Loss of image quality in photobleaching during microscopic imaging of fluorescent probes bound to chromatin. J Biomed Opt. 2005;10(6):064015.
Wolnicka-Glubisz A, Rajwa B, Dobrucki J, Skrzeczynska-Monucznik J, van Henegouwen GB, Sarna T. Phototoxicity, distribution and kinetics of association of UVA-activated chlorpromazine, 8-methoxypsoralen, and 4.6,4 ’-trimethylangelicin in Jurkat cells. J Photochem Photobiol B-Biol. 2005;78(2):155–64.
Czyz J, Rajwa B, Bzowska M, Dobrucki J, Korohoda W. Spreading-independent growth of normal fibroblasts in three-dimensional cultures. Folia Biol-Krakow. 2004;52(1–2):19–24.
Sun YL, Rajwa B, Robinson JP. Adaptive image-processing technique and effective visualization of confocal microscopy images. Microsc Res Tech. 2004;64(2):156–63.
Rajwa B, McNally HA, Varadharajan P, Sturgis J, Robinson JP. AFM/CLSM data visualization and comparison using an open-source toolkit. Microsc Res Tech. 2004;64(2):176–84.
Wu J, Rajwa B, Filmer DL, Hoffmann CM, Yuan B, Chiang C-S, Sturgis J, Robinson JP. Analysis of orientations of collagen fibers by novel fiber-tracking software. Microscopy and Microanalysis. 2003;9(6):574–80.
Li NY, Ragheb K, Lawler G, Sturgist J, Rajwa B, Melendez JA, Robinson JP. Mitochondrial complex I inhibitor rotenone induces apoptosis through enhancing mitochondrial reactive oxygen species production. J Biol Chem. 2003;278(10):8516–25.
Wu J, Rajwa B, Filmer DL, Hoffmann CM, Yuan B, Chiang C, Sturgis J, Robinson JP. Automated quantification and reconstruction of collagen matrix from 3D confocal datasets. Journal of Microscopy. 2003;210(2):158–65.
Li N, Ragheb K, Lawler G, Sturgis J, Rajwa B, Melendez JA, Robinson JP. DPI induces mitochondrial superoxide-mediated apoptosis. Free Radical Biology and Medicine. 2003;34(4):465–77.
Drukala J, Rajwa B, Pietrzkowski Z, Korohoda W. Comparison of daunomycin effects on human keratinocytes and melanoma HTB 1410 cells. Image cytometry study. Anticancer Res. 2003;23(1A):419–26.
Kolcz J, Rajwa B, Drukala J, Dobrucki J, Korohoda W, Malec E. Three-dimensional visualization of connexin 43 on the human cardiomyocytes. Appl Immunohistochem. 2002;10(3):247–52.
Bugusu BA, Hamaker BR, Rajwa B. Interaction of maize zein with wheat gluten in composite dough and bread as determined by confocal laser scanning microscopy. Scanning. 2002;24(1):1–5.
Voytik-Harbin SL, Rajwa B, Robinson JP. Three-dimensional imaging of extracellular matrix and extracellular matrix-cell interactions. In: Methods in Cell Biology. Academic Press; 2001. p. 583–97. (Cytometry; vol. 63).
Drukala J, Rajwa B, Pietrzkowski Z. Effect of daunomycin on expression of CD44H protein in HTB140 melanoma cells in vitro. Anticancer Res. 2001;21(6A):3793–8.
Tworzydlo M, Laczka M, Rajwa B, Dobrucki J, Turyna B. Evaluation of biocompatibility of apatite-wollastonite ceramics in fibroblast cultures. Folia Histochem Cytobiol. 2000;38(3):133–41.
Brightman AO, Rajwa BP, Sturgis JE, McCallister ME, Robinson JP, Voytik‐Harbin SL. Time-lapse confocal reflection microscopy of collagen fibrillogenesis and extracellular matrix assembly in vitro. Biopolymers. 2000;54(3):222–34.<222::AID-BIP80>3.0.CO;2-K

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