Matthew Ferguson, Ph.D.

Courses

• PHYS 325 Scientific Computing (Fa24)

Methods and practices of computing and computer modeling, with an emphasis on problems in science and engineering. Topics include model building, simulation of complex systems, numerical solutions of systems of differential equations, and scientific visualization.

• PHYS 301 Analog & Digital Electronics (Sp16, Sp17, Sp18, Sp19, Sp20, Sp22, Sp23, Sp24)

This course is an introduction to electronic test instrumentation, discrete semiconductor devices, and their use in integrated circuits.

• PHYS 504 – Molecular and Cellular Biophysics (Fa23)

An advanced introduction to biophysical methods and concepts focused on developing an in-depth understanding of the functionality of biological systems at the molecular and cellular level.

• PHYS 211L – Physics I with Calculus Lab (Fa21, Fa22)

Lab to be taken with PHYS 211. Basic experiments in kinematics, mechanics, and wave motion.

• BMOL 603 Biophysical Instrumentation and Techniques (Fa14, Fa15, Fa16, Fa17, Fa18, Fa19)

The goals of this course are to develop sufficient knowledge and intuition to critically understand the principles and applications of key biophysical methods and instruments used for the characterization of the structural, functional, and dynamical properties of biological molecules and their interactions.

• BMOL 605 Current Scientific Literature (Fa15,Fa16, Fa17, Fa18)

This course consists of a series of seminars presented by students enrolled in the class. This course is designed to acquaint students with this important means of communication.

• PHYS 436/536 Soft Matter (Sp14, Sp15)

This course is an introduction to the physical principles underlying the properties and behaviors of soft matter, including polymers, gels, colloids, and liquid crystals. Examples of soft matter include glues, paints, soaps, rubber, foams, gelatin, milk, and most materials of biological origin.

Articles

Google Scholar

PubMed

orcid:0000-0003-0760-757X

Selected Articles

1. Goelzer M, Goelzer J, Ferguson ML, Neu CP, Uzer G. Nuclear envelope mechanobiology: linking the nuclear structure and function. Nucleus. 2021.
2. Stavreva DA, Garcia DA, Fettweis G, Gudla PR, Zaki G, Soni V, McGowanA, Williams G, Huynh A, Palangat M, Schiltz RL, Johnson TA, Ferguson ML, Pegoraro G, Upadhyaya A, Hager GL, Transcriptional bursting and co-bursting regulation by steroid hormone release pattern and transcription factor mobility. Molecular Cell. 2019.
3. Donovan BT, Huynh A, Ball DB, Patel H, Poirier MG, Larson DR, Ferguson ML@, Lenstra TL@, Live‐cell imaging reveals the interplay between transcription factors, nucleosomes, and bursting. EMBO Journal. 2019. (preprint) (@ corresponding authors)
4. Dagher GG, Machado AP, Davis EC, Green T, Martin J, Ferguson ML. Data storage in cellular DNA: contextualizing diverse encoding schemes Evol. Intel. 2019.
5. Obert J., Ferguson ML. Deep Time Series Neural Networks and Fluorescence Data Stream Noise Detection. Intelligent Computing. SAI 2018.
6. Panchapakesan SSS, Ferguson ML, Hayden EJ, Chen X, Hoskins AA, Unrau PJ. Ribonucleoprotein Purification and Characterization using RNA Mango. RNA. 2017
7. Coulon* A, Ferguson* ML, de Turris V, Palangat M, Chow CC, Larson DR. Kinetic competition during the transcription cycle results in stochastic RNA processing. eLife. 2014 (*authors contributed equally)
8. Moutin E, Compan V, Raynaud F, Clerte C, Bouquier N, Labesse G, Ferguson ML, Fagni L, Royer CA, Perroy J. The stoichiometry of scaffold complexes in living neurons-DLC2 functions as a dimerization engine for GKAP. Journal of Cell Science. 2014
9. Ferguson ML, Larson DR. Measuring Transcription Dynamics in Living Cells using Fluctuation Analysis. Methods in Molecular Biology. 2013.

Before 2013

1. Ferguson ML, Le Coq D, Jules M, Aymerich S, Radulescu O, Declerck N, Royer CA.  Reconciling molecular regulatory mechanisms with noise patterns of bacterial metabolic promoters in induced and repressed states. Proc Natl Acad Sci U S A. 2012.
2. Ferguson ML, Le Coq D, Jules M, Aymerich S, Declerck N, Royer CA. Absolute quantification of gene expression in individual bacterial cells using two-photon fluctuation microscopy. Anal Biochem. 2011.
3. Savatier J, Jalaguier S, Ferguson ML, Cavailles V, Royer CA. Estrogen receptor interactions and dynamics monitored in live cells by fluorescence cross-correlation spectroscopy. Biochemistry. 2010.
4. Chaix D, Ferguson ML, Atmanene C, Van Dorsselaer A, Sanglier-Cianferani S, Royer CA, et al. Physical basis of the inducer-dependent cooperativity of the Central glycolytic genes Repressor/DNA complex. >Nucleic Acids Res. 2010
5. Ferguson ML, Prasad K, Boukari H, Sackett DL, Krueger S, Lafer EM, Nossal R. Clathrin triskelia show evidence of molecular flexibility. Biophys J. 2008.
6. Ferguson ML, Prasad K, Sackett DL, Boukari H, Lafer EM, Nossal R. Conformation of a clathrin triskelion in solution. Biochemistry. 2006.
7. Pomerance A, Matthews J, Ferguson M, Urbach JS, Losert W. Actin polymerization in a thermal gradient. Macromol Symp. 2005
8. Ferguson ML, Miller BN, Thompson MA. Dynamics of a gravitational billiard with a hyperbolic lower boundary. Chaos. 1999.
9. Sieminska L, Ferguson M, Zerda TW, Couch E. Diffusion of steroids in porous sol-gel glass: Application in slow drug delivery. J Sol-Gel Sci Techn. 1997.

Biography

Following two post-doctoral fellowships studying experimental biophysics at the Centre de Biochimie Structurale, in Montpellier, France, and at the National Institutes of Health, in Bethesda, MD, Dr. Matthew Ferguson joined the faculty of the Department of Physics at Boise State University in late 2013. He earned his doctorate in physics from the University of Maryland and his bachelors of science in physics & mathematics from Texas Christian University in Fort Worth. He is a tribal member of the Choctaw Nation of Oklahoma and a descendent of Tushpa “John Culberson”.

Dr. Ferguson’s current research focus is on understanding the physical basis of transcriptional regulation and splicing of RNA in eukaryotes by single molecule live cell fluorescence microscopy.  He is an experimental biophysicist. An underlying theme in his research has been the interface between dynamical systems and thermodynamics in both physical and biological systems. Through the combination of physics, computer simulation and multidimensional data analysis, he interprets the results of experiments in a straightforward way, turning information into knowledge about a physical or biological system.

Degrees

• Ph.D. Physics, University of Maryland College Park, 2007
  • Dissertation: A Biophysical Study of Clathrin Utilizing Light Scattering, Neutron Scattering and Structure Based Computer Modeling
• M.S. Physics, University of Maryland College Park, 2002
• B.S. Physics and Mathematics, Texas Christian University, 1997

Doctoral and Postdoctoral training

• 2011-2013 National Cancer Institute Postdoctoral Fellow, Systems Biology of Gene Expression, Bethesda, MD (w/ Daniel R. Larson)
• 2007-2011 NSF/EMBO/Marie Currie Postdoctoral Fellow, Centre de Biochimie Structurale, Montpellier, FR (w/ Catherine A. Royer)
• 2003-2007 Graduate Partnership Program, National Institutes of Child Health and Human Development, Bethesda, MD (w/ Ralph J. Nossal)

Courses and Workshops

• 2024 7th Institute of Computational Molecular Science Education Summer School: Molecular Dynamics, Boise State University, ID
• 2017 12th LFD Workshop: Laboratory for Fluorescence Dynamics, Irvine, CA
• 2012 GENEX: Course on Eukaryotic Gene Expression, Cold Spring Harbor Laboratory, NY
• 2007 BIOSAS: Course on Biomacromolecules in Solution Studied by Small-Angle Scattering, Copenhagen DK
• 2001 NSF Summer School on Nonequilibrium Statistical Physics, Boulder CO

Previous Employment in Private Industry

• 1997-1999 Operations Research Analyst, Lockheed Martin Tactical Aircraft Systems, Fort Worth, TX

Press

• Arrows in the quiver’: interdisciplinary team contributes to statewide COVID-19 modeling task force (5/20)
• Physics faculty and colleagues discover window into the human genome (12/19)
• Advanced imaging technology reveals pulsed hormone release regulates gene transcription (9/19)
• Boise State Biophysicist Awarded NIH Grant to Study How the Genome Works (8/17)
• Ph.D. in Biomolecular Sciences (10/16)
• Boise State Physicist Extracts Lessons from Sea Squirts (7/16)
• When Timing Matters (10/15)
• Microscope reveals a little splice of life(2/15)
• Faculty Update(2/15)
• Finding Order in Randomness: Single-Molecule Studies Reveal Stochastic RNA Processing(11/14)

Gallery and Animations

Pictures from Ferguson Lab

Fluorescence Cross Correlation Spectroscopy Simulation
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Brownian Dynamics Simulation
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