Mark A. Haidekker - List of Publications


For more detailed information about the books, click here.

Linear Feedback Controls -- The Essentials, Second Edition. M.A. Haidekker. Elsevier 2020. ISBN 978-0-124-05875-0
Link to publisher's web site

Linear Feedback Controls -- The Essentials. M.A. Haidekker. Elsevier Insights Series, Elsevier 2013. ISBN 978-0-1281-8778-4
Link to publisher's web site

Medical Imaging Technology. M.A. Haidekker. SpringerBriefs series in Physics, Springer 2013. ISBN 978-1-4614-7072-4
Link to publisher's web site

Advanced Biomedical Image Analysis. M.A. Haidekker. John Wiley & Sons, 2011. ISBN 978-0-470-62458-6.
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Book Chapters

Computer-Aided Diagnosis with MR Images of the Brain.
Haidekker MA, Dougherty G. In: Magnetic Resonance Imaging Handbook. Vol. 2 (Imaging of the Pelvis, Musculoskeletal System, and Special Applications to CAD) Saba L (Editor). CRC Press 2016, 2016, pp. 507--539.
ISBN 9781482216288.
Link to publisher's web site

Finite Element Analysis Based on Medical Images: Principles, Challenges, and Solutions.
Madison AM, Haidekker MA. In: Computational Bioengineering. Zhang G (Editor). CRC Press 2015, pp. 425--464.
Link to publisher's web site

Optical Projection and Transillumination Tomography for Multidimensional Mesoscopic Imaging.
Swoger J, Sharpe J, Haidekker MA. In: Optical Techniques in Regenerative Medicine. Morgan SP, Rose F (Editors). CRC Press 2013, pp. 239--266; ISBN 978-1-4398-5495-2.
Link to publisher's web site

Medical Imaging in the Diagnosis of Osteoporosis and Estimation of the Individual Bone Fracture Risk.
Haidekker MA, Dougherty G. In: Medical Image Processing: Techniques and Applications. Dougherty G (Editor). Springer-Verlag 2011, ISBN 978-1-4419-9769-2.
Link to publisher's web site

Dyes with segmental mobility: molecular rotors.
Haidekker MA, Nipper ME, Mustafic A, Lichlyter D, Dakanali M, Theodorakis EA. In: Advanced Fluorescence Reporters in Chemistry and Biology I. Fundamentals and Molecular Design. Demchenko AP (Editor). Springer Series on Fluorescence, Vol. 8. Wolfbeis O (series editor). Springer-Verlag, 2010, pp. 267-308. ISBN 978-3642047008.
Link to publisher's web site

Journal Articles

Most of the links to the online reprints (pdf format) are available by invitation only due to copyright restrictions. Please drop me an email if you want to access a reprint. Green reprint buttons indicate open or free access.

Brain-on-a-Chip Device for Modeling Multiregional Networks
Ndyabawe K, Cipriano M, Zhao W, Haidekker M, Yao K, Mao L, Kisaalita WS.
ACS Biomaterials Science & Engineering 2021; 7: 350-359.

Spheroid Trapping and Calcium Spike Estimation Techniques toward Automation of 3D Culture.
Ndyabawe K, Haidekker M, Asthana A, Kisaalita WS.
SLAS TECHNOLOGY 2020; Online First publication, not yet assigned to a volume. DOI: 10.1177/24726303

Calcium Oscillation Frequency Is a Potential Functional Complex Physiological Relevance Indicator for a Neuroblastoma-Based 3D Culture Model
Asthana A, Ndyabawe K, Mendez D, Douglass M, Haidekker MA, Kisaalita, WS.
ACS Biomaterials 2020; 6: 4314--4323.

Ratiometric Nanoviscometers: Applications for Measuring Cellular Physical Properties in 3D Cultures
White CM, Haidekker MA, Kisaalita, WS.
SLAS Technology 2020; 25: 243--246.

Far-red light enhances photochemical efficiency in a wavelength-dependent manner
Zhen S, Haidekker MA, van Iersel M.
Physiol.Plant. 2019; 167: 21--33.

Methods for Hyperspectral Microscope Calibration and Spectra Normalization from Images of Bacteria Cells
Eady M, Park B, Yoon SC, Haidekker MA, Lawrence KC.
Trans. ASABE 2018; 61: 437--448.

Onion Postharvest Quality Assessment with X-ray Computed Tomography -- A Pilot Study (invited article)
Speir R, Haidekker MA.
IEEE Instrumentation & Measurement Magazine 2017; 20: 15--19

Enhanced Dynamic Range X-ray Imaging
Haidekker MA, Morrison LD, Sharma A, Burke E.
Computers in Biology and Medicine 2017; 82: 40--48.

Ratiometric mechanosensitive fluorescent dyes: design and applications (invited review)
Haidekker MA, Theodorakis EA.
Journal of Materials Chemistry C 2016; 4: 2707--2718.

Using chlorophyll fluorescence to control lighting in controlled environment agriculture
van Iersel M, Mattos E, Weaver G, Ferrarezi RS, Haidekker MA.
Acta Hortic. 2016; 1134: 427--433 (published as Proc. VIII Int. Symp. on Light in Horticulture)

ASHS Outstanding Cross-Commodity Publication Award winner for papers published in 2016.

A Chlorophyll-Based Biofeedback System to Control Photosynthetic Lighting in Controlled-Environment Agriculture
van Iersel M, Weaver G, Martin MT, Ferrarezi RS, Mattos E, Haidekker MA.
Journal of the American Society for Horticultural Science (JASHS) 2016; 141: 169--176.

Astrocytes regulate alpha-secretase-cleaved soluble amyloid precursor protein secretion in neuronal cells: Involvement of group IIA secretory phospholipase A2
Yang X, Sheng W, Ridgley DM, Haidekker MA, Sun GY, Lee JCM.
Neuroscience 2015; 300: 508--517.

Apparent Shear Sensitivity of Molecular Rotors in Various Solvents
Mustafic A, Elbel KM, Theodorakis EA, Haidekker MA.
Journal of Fluorescence 2015; 25: 729-738.

Cyclopenta[b]naphthalene cyanoacrylate dyes: Synthesis and evaluation as fluorescent molecular rotors
Kocsis LS, Elbel KM, Hardigree BA, Brummond K, Haidekker MA, Theodorakis EA.
Organic & Biomolecular Chemistry 2015; 13: 2965--2973.

Noninvasive Intracranial Pressure Assessment in Canines via Biomechanical Response Behavior, Medical Imaging, and Finite Element Analysis: A Pilot Study
Madison AM, Sharma A, Haidekker MA.
American Journal of Veterinary Research 2015; 76(8): 667--678

Blue and UV LED-Induced Fluorescence in Cotton Foreign Matter
Mustafic A, Li C, Haidekker MA.
Journal of Biological Engineering 2014; 8: 1, 29.

Building a 3D Computed Tomography Scanner From Surplus Parts
Haidekker MA.
Biomedical Instrumentation & Technology 2014; 48(2): 142-151.

An Automated Approach to Peanut Drying with Real-Time Microwave Monitoring of In-Shell Kernel Moisture Content
Lewis MA, Trabelsi S, Nelson SO, Tollner EW, Haidekker MA.
Applied Engineering in Agriculture 2013; 29(4): 583-593.

LED-Induced Fluorescence and Image Analysis to Detect Stink Bug Damage in Cotton Bolls
Mustafic A, Roberts E, Toews MD, Haidekker MA.
Journal of Biological Engineering 2013; 7: 5.

Self-calibrating viscosity probes -- Design and subcellular localization
Dakanali M, Do, TH, Horn A, Chongchivivat A, Jarusreni T, Lichlyter D, Guizzunti G, Haidekker MA, Theodorakis EA.
Bioorganic and Medicinal Chemistry 2012; 20:4443-50

A Completely Open-Source Finite Element Modeling Chain for Tubular Tissue-Engineered Constructs
Madison A, Haidekker MA.
International Journal of Computer Science and Application (IJCSA) 2012; 1(2): 44-55.

Intrinsic and Extrinsic Temperature-Dependency of Viscosity-Sensitive Fluorescent Molecular Rotors
Howell S, Dakanali M, Theodorakis EA, Haidekker MA.
J Fluorescence 2012; 22: 457-465.

Stink Bug Feeding Induces Fluorescence in Developing Cotton Boll
Xia J, Mustafic A, Toews MD, Haidekker MA.
Journal of Biological Engineering 2011, 5:11.

Synthesis and evaluation of self-calibrating ratiometric viscosity sensors
Yoon H-J, Dakanali M, Lichlyter D, Chang WM, Nguyen K, Nipper ME, Haidekker MA, Theodorakis EA.
Org. Biomol. Chem 2011; 9: 3530 - 3540

This article has been named Hot Article in the Organic & Biomolecular Chemistry Blog.

Detection of Liposome Membrane Viscosity Perturbations with Ratiometric Molecular Rotors
Nipper ME, Dakanali M, Theodorakis EA, Haidekker MA.
Biochimie 2011; 93:988-994.

Analytical model of microfluidic transport of non-magnetic particles in ferrofluids under the influence of a permanent magnet
Zhu T, Lichlyter D, Haidekker MA, Mao L.
Microfluidics and Nanofluidics 2011; 10; 1233-1245.

Environment-Sensitive Behavior of Fluorescent Molecular Rotors (invited review)
Haidekker MA, Theodorakis EA.
Journal of Biological Engineering 2010; 4: 11. (doi:10.1186/1754-1611-4-11)

Imaging of Flow Patterns with Fluorescent Molecular Rotors
Mustafic A, Huang H-M, Theodorakis EA, Haidekker MA.
J Fluorescence 2010; 20(5): 1087-1098.

Molecular rotors: synthesis and evaluation as viscosity sensors
Sutharsan J, Lichlyter D, Wright NE, Dakanali M, Haidekker MA, Theodorakis EA.
Tetrahedron 2010; 66: 2582-2588.

Rational Design of Amyloid Binding Agents Based on the Molecular Rotor Motif
Sutharsan J, Dakanali M, Capule CC, Haidekker MA, Yang J, Theodorakis EA.
Chem Med Chem 2010; 5: 56-60.

Quantifying light scattering with single-mode fiber-optic confocal microscopy
LaCroix JT, Haidekker MA.
BMC Medical Imaging 2009; 9: 19.

Secretory phospholipase A2 Type III enhances α-secretase-dependent amyloid precursor protein processing through alterations in membrane fluidity
Yang X, Sheng W, Haidekker MA, Sun GY, Lee C-M.
Journal of Lipid Research 2010; 51: 957-966.

Immobilization Techniques for Molecular Rotors -- Towards a Solid-State viscosity sensor platform
Lichlyter D, Haidekker MA.
Sensors and Actuators B (Chemical) 2009; 139: 648-656.

NADPH oxidase-mediated reactive oxygen species alter astrocyte membrane molecular order via phospholipase A2
Zhu D, Hu C, Sheng W, Tan KS, Haidekker MA, Sun AY, Sun GY, Lee C-M.
Biochem J 2009; 421 : 201-210.

A Fully Automated Approach to Quantitatively Determine Thickness of Tissue-Engineered Cell Sheets
LaCroix JT, Xia J, Haidekker MA.
Annals of Biomedical Engineering 2009; 37: 1348-1357.

Fast Optical Transillumination Tomography with Large-Size Projection Acquisition
Huang H-M, Xia J, Haidekker MA.
Annals of Biomedical Engineering 2008; 36: 1699-1707.

Characterization of changes in the viscosity of lipid membranes with the molecular rotor FCVJ.
Nipper ME, Majd S, Mayer, M, Lee JCM, Theodorakis EA, Haidekker MA.
Biochim Biophys Acta (Biomembranes) 2008; 1778: 1148-1153.

Application of molecular rotors to the determination of the molecular weight dependence of viscosity in polymer melts
Zhu D, Haidekker MA, Lee JS, Won YY, Lee J-CM.
Macromolecules 2007; 40: 7730-7732.

Using ultrasonic methods to determine cooking degree of doneness in beef steaks
Blake ES, Haidekker MA, Viator JA, Hdeib MM, Lorenzen CL.
Journal of Muscle Foods 2008; 19: 111-124.

Molecular rotors--fluorescent biosensors for viscosity and flow
Haidekker MA, Theodorakis EA.
OBC 2007; 5: 1669-1678.

Synthesis and use of an in-solution ratiometric fluorescent viscosity sensor
Fischer D, Theodorakis EA, Haidekker MA.
Nature Protocols 2007; 2: 227-236.

Probing Polymerization Dynamics with Fluorescent Molecular Rotors and Magnetoelastic Sensors
Haidekker MA, Lichlyter D, Ben Johny M, Grimes CA.
Sensor Letters 2006; 4: 257-261.

Optical Fiber-Based Fluorescent Viscosity Sensor
Haidekker MA, Akers WJ, Fischer D, Theodorakis EA.
Optics Letters 2006; 31(17): 2529-2531.

Influence of gold nanoparticles on collagen fibril morphology quantified using transmission electron microscopy and image analysis
Haidekker MA, Boettcher LW, Suter JD, Rone R, Grant SA
BMC Medical Imaging 2006; 6: 4.

A Ratiometric Fluorescent Viscosity Sensor
Haidekker MA, Brady TP, Lichlyter D, Theodorakis EA
JACS 2006; 128: 398-399.

Texturpaprameter zur Bestimmung osteoporotisch bedingter Strukturveränderungen im CT-Bild der Wirbelkörperspongiosa - eine Vergleichsstudie
[Texture parameters to quantify osteoporosis-related structural changes in CT images of the vertebral spongiosa - a comparative study]
Haidekker MA, Bidesi A, Radmer S, Andresen R.
Osteologie 2006; 15: 120-130 (article in German).

Mercury free operation of the coulter counter multisizer II sampling stand
Benson JD, Haidekker MA, Benson CM, Critser JK.
Cryobiology 2005; 51: 344-347.

Temporal gradients in shear, but not spatial gradients, stimulate ERK1/2 activation in human endothelial cells
White CR, Stevens H, Haidekker MA, Frangos, JA.
Am J Physiol Heart Circ Physiol 2005;289:H2350-5.

Interaction of fluorescent molecular rotors with blood plasma proteins.
Akers WJ, Cupps JM, Haidekker MA.
Biorheology 2005;42(5):335-44.

Effects of solvent polarity and solvent viscosity on the fluorescent properties of molecular rotors and related probes
Haidekker MA, Brady TP, Lichlyter D, Theodorakis, EA.
Bioorganic Chemistry 2005; 33; 415-425.

A ratiometric fluorophotometer for fluorescence-based viscosity measurement with molecular rotors
Milich K, Akers WA, Haidekker MA
Sensor Letters 2005; 3: 237-243.

Optical Transillumination Tomography with tolerance against refraction mismatch
Haidekker MA
Computer Programs and Methods in Biomedicine 2005; 80: 225-235.

Transillumination optical tomography of tissue-engineered blood vessels: A Monte Carlo simulation
Yao G, Haidekker MA
Applied Optics 2005; 44: 4265-4271.

Precision Assessment of Biofluid Viscosity Measurements Using Molecular Rotors
Akers W, Haidekker MA
Journal of Biomechanical Engineering 2005; 127: 450-454.

Sensing of Flow and Shear Stress Using Fluorescent Molecular Rotors
Haidekker MA, Akers W, Lichlyter D, Brady TP, Theodorakis EA.
Sensor Letters 2005; 3: 42-48.

Optical Transillumination Tomography for Imaging of Tissue-Engineered Blood Vessels
Gladish JC, Yao G, L'Heureux N, Haidekker MA
Annals of Biomedical Engineering 2005; 33(3): 323-327

A Hands-on Model-computed Tomography Scanner for Teaching Biomedical Imaging Principles
Haidekker MA
Int J Engng Ed 2005; 21(2): 327-334

A Molecular Rotor as Viscosity Sensor in Aqueous Colloid Solutions.
Akers W, Haidekker MA
Journal of Biomechanical Engineering 2004; 126: 340-345.

Cell Membrane Fluidity Changes and Membrane Undulations Observed Using a Laser Scattering Technique
Haidekker MA, Stevens HY, Frangos JA.
Annals of Biomedical Engineering 2004; 32(4):531-536

Hydrophilic Molecular Rotor Derivatives - Synthesis and Characterization.
Haidekker MA, Brady T, Chalian SH, Akers W, Lichlyter D, Theodorakis EA.
Bioorganic Chemistry 2004; 32: 274-289.

Extracellular signal-regulated kinase activation and endothelin-1 production in human endothelial cells exposed to vibration
Haidekker MA1, White CR1, Stevens HY, Frangos JA.
J Physiol 2004; 555.2: 565-572.
1 Shared credit for primary authorship

Venous ligation-mediated bone adaptation is NOS 3 dependent.
Haidekker MA1, Bergula A1, Huang W, Stevens HY, Frangos JA.
Bone 2004; 34(3): 562-569.
1 Shared credit for primary authorship

Computerized Methods for X-ray based Small Bone Densitometry.
Haidekker MA, Stevens HY, Frangos JA.
Computer Methods and Programs in Biomedicine 2004; 73(1): 35-42.

Phospholipid-Bound Molecular Rotors: Synthesis and Characterization.
Haidekker MA, Brady T, Wen K, Okada C, Stevens HY, Snell JM, Frangos JA and Theodorakis EA.
Bioorganic and Medicinal Chemistry 2002; 10: 3627-3636.

Evidence for shear-induced increase in membrane fluidity in the dinoflagellate Lingulodinium polyedrum.
Haidekker MA1, Mallipattu SK1, Von Dassow P, Latz MI, Frangos JA.
J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2002 Jun;188(5):409-16.
1 Shared credit for primary authorship

A novel approach to blood plasma viscosity measurement using fluorescent molecular rotors.
Haidekker MA, Tsai AG, Brady T, Stevens HY, Frangos JA, Theodorakis E, Intaglietta M.
Am J Physiol Heart Circ Physiol 2002;282(5):H1609-14.

Analysis of temporal shear stress gradients during the onset phase of flow over a backward-facing step.
Haidekker MA, White CR, Frangos JA.
J Biomech Eng 2001 Oct;123(5):455-63.

Temporal gradients in shear, but not spatial gradients, stimulate endothelial cell proliferation.
Haidekker MA1, White CR1, Bao X, Frangos JA.
Circulation 2001 May 22;103(20):2508-13.
1 Shared credit for primary authorship

New fluorescent probes for the measurement of cell membrane viscosity.
Haidekker MA, Ling T, Anglo M, Stevens HY, Frangos JA, Theodorakis EA.
Chem Biol 2001 Feb;8(2):123-31.

A fluorescent molecular rotor for the study of membrane fluidity in endothelial cells under fluid shear stress
Haidekker MA, Frangos JA.
In: Diagnostics of Living Cells III (Farkas DL, Leif RC, Editors) Proc SPIE 2000; 3921: 101-112.

Fluid shear stress increases membrane fluidity in endothelial cells: a study with DCVJ fluorescence.
Haidekker MA, L'Heureux N, Frangos JA.
Am J Physiol Heart Circ Physiol 2000 Apr;278(4):H1401-6.

Issues of threshold selection when determining the fractal dimension in HRCT slices of lumbar vertebrae.
Haidekker MA, Andresen R, Evertsz CJ, Banzer D, Peitgen HO.
Br J Radiol 2000 Jan;73(865):69-72.

CT determination of bone mineral density and structural investigations on the axial skeleton for estimating the osteoporosis-related fracture risk by means of a risk score.
Andresen R, Haidekker MA, Radmer S, Banzer D.
Br J Radiol 1999 Jun;72(858):569-78.

Relationship between structural parameters, bone mineral density and fracture load in lumbar vertebrae, based on high- resolution computed tomography, quantitative computed tomography and compression tests.
Haidekker MA, Andresen R, Werner HJ.
Osteoporos Int 1999;9(5):433-40.

Computerized analysis of gray-value profiles in spongy and cortical bone. Clinical experience.
Andresen R, Haidekker MA, Radmer S, Banzer D.
Invest Radiol 1999 Sep;34(9):572-8.

Source analysis of acoustic emissions in aue granite cores under symmetric and asymmetric compressive loads.
Zang A, Wagner C, Stanchits S, Dresen G, Andresen R, Haidekker MA.
Geophys. J. Int. 135: 1113-1130, 1998

Projecting the sulcal pattern of human brains onto a 2D plane-- a new approach using potential theory and MRI.
Haidekker MA, Evertsz CJ, Fitzek C, Boor S, Andresen R, Falkai P, Stoeter P, Peitgen HO.
Psychiatry Res 1998 Aug 26;83(2):75-84.

Evaluation of the cortical structure in high resolution CT images of lumbar vertebrae by analysing low bone mineral density clusters and cortical profiles.
Haidekker MA, Andresen R, Evertsz CJ, Banzer D, Peitgen HO.
Br J Radiol 1997 Dec;70(840):1222-8.

Assessing the degree of osteoporosis in the axial skeleton using the dependence of the fractal dimension on the grey level threshold.
Haidekker MA, Andresen R, Evertsz CJ, Banzer D, Peitgen HO.
Br J Radiol 1997 Jun;70(834):586-93.


USPTO 9,933,364   Phase synchronizing pulse amplitude modulation fluorometer.     Issued 04/03/2018
USPTO 9,816,948   Computerized tomography detection of microbial damage of plant tissues.     Issued 11/14/2017
USPTO 9,606,059   Phase synchronizing pulse amplitude modulation fluorometer.     Issued 03/28/2017
USPTO 8,384,046 Noninvasive methods and apparatus for detecting insect-induced damage in a plant.   Issued 02/26/2013
USPTO 7,760,844 Supported molecular biofluid viscosity sensors for in vitro and in vivo use Issued 03/02/2010
USPTO 7,517,695 Local flow and shear stress sensor based on molecular rotors    Issued 04/14/2009