Publications

Please contact Dr. Koch for PDF copies of the articles below if you do not have electronic access otherwise.

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Please also see Dr. Koch's Google Scholar profile.

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Newest first.

* = co-first author; Koch lab graduate/undergraduate students.

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Preprints

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• A.O. Yusuf *, Z.K. Modi *, M.D. Koch (2026) "The construction and operation of type IV pili impose a variable energetic burden across phylogenetically distant bacteria". bioRxiv.

• F. Haque, Z.K. Modi, L. Mazumder, A.O. Yusuf, R. Raam, M.D. Koch (2026) "Pil-Chp orchestrates a multi-level regulatory system to control type IV pilus dynamics in Pseudomonas aeruginosa". bioRxiv.

• A.O. Yusuf, Z.K. Modi, M.D. Koch (2026) "Rapid activation of dormant type IV pili enables a dispersal–infection tradeoff in environments with fluctuating nutrients". bioRxiv

• A.M. Shuppara, M.D. Koch, J.E. Sanfilippo (2026) "Flow-driven delivery boosts antibiotic effectiveness by overwhelming bacterial defenses". bioRxiv.

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Independent lab

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2026

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• Z.K. Modi, J.L. Reed, A.O. Yusuf, F. Haque, T.M. Payne, N. Chalemela, S.D.J. Denison, M.D. Koch (2026) "Type IV pilus length determines virulence by regulating a putative subpopulation of non-contributing filaments in Pseudomonas aeruginosa". Communications Biology.

• G.C. Padron, S. Chen, A. Sharma, Z. Modi, M.D. Koch, J.E. Sanfilippo (2026) "Shear flow promotes bacterial growth and shapes spatial gradients by rapidly replenishing scarce nutrients". mBio.

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2025

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• V.L. Taylor, M. Shah, P.H. Patel, A. Yusuf, C.M. Burk, Z. Gitai, A.R. Davidson, M.D. Koch, K.L. Maxwell (2025) "Prophages block cell surface receptors to preserve their viral progeny". Nature.

• A.M. Shuppara, G.C. Padron, A. Sharma, Z. Modi, M.D. Koch, J.E. Sanfilippo (2025) "Shear flow patterns antimicrobial gradients across bacterial populations". Science Advances.

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2024

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• H. Hendrix, A. Itterbeek, H. Longin, L. Delanghe, E. Vriens, M. Vallino, E.M. Lammens, F. Haque, A. Yusuf, J.P. Noben, M. Boon, M.D. Koch, V. van Noort, R. Lavigne (2024) "PlzR regulates type IV pili assembly in Pseudomonas aeruginosa via PilZ binding". Nature Communications.

• J. Thongchol, Z. Yu, L. Harb, Y. Lin, M.D. Koch, M. Theodore, U. Narsaria, J.W. Shaevitz, Z. Gitai, Y. Wu, J. Zhang, L. Zeng (2024) "Removal of Pseudomonas Type IV Pili by a Small RNA Virus". Science.

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2023

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• K. Schroven, L. Putzeys, A. Kerremans, P.-J. Ceyssens, M. Vallino, J. Paeshuyse, F. Haque, A. Yusuf, M.D. Koch, R. Lavigne (2023) "The phage-encoded PIT4 protein affects multiple two-component systems of Pseudomonas aeruginosa". Microbiology Spectrum.

• J.S. Palalay, A.N. Simsek, J. Reed, M.D. Koch, B. Sabass, J.E. Sanfilippo (2023) "Shear force enhances adhesion of Pseudomonas aeruginosa by counteracting pilus-driven surface departure". PNAS.

• G.C. Padron, A.M. Shuppara, A. Sharma, M.D. Koch, J.S. Palalay, J.N. Radin, T.E. Kehl-Fie, J.A. Imlay, J.E. Sanfilippo (2023) "Shear rate sensitizes bacterial pathogens to H2O2 stress". PNAS.

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Postdoc

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• E. Han, C. Fei, R. Alert, K. Copenhagen, M.D. Koch, N.S. Wingreen, J.W. Shaevitz (2025) "Local polar order controls mechanical stress and triggers layer formation in developing Myxococcus xanthus colonies". Nature Communications.​​

• A.N. Simsek*, M.D. Koch*, J.E. Sanfilippo, Z. Gitai, G. Gompper, B. Sabass (2024) "Type-IV pili tune an adhesion-migration trade-off during surface colonization of Pseudomonas aeruginosa". PRX Life.​​

• B. Wang, A.E. Lin, J. Yuan, M.D. Koch, N.S. Wingreen, B. Adamson, Z. Gitai (2023) "Single-cell massively-parallel multiplexed microbial sequencing (M3-Seq) identifies rare bacterial populations and profiles phage infection". Nature Microbiology.​​

• M.D. Koch and J.W. Shaevitz (2022) "Art Ashkin and the origins of optical trapping and particle manipulation”. Methods in Molecular Biology Vol 2478: Optical Tweezers – Methods and Protocols, 2nd ed.

• M.D. Koch, M.E. Black, E. Han, J.W. Shaevitz, Z. Gitai (2022) "Pseudomonas aeruginosa distinguishes surfaces by stiffness using retraction of type IV pili" PNAS​​

• M.D. Koch, C. Fei, N.S. Wingreen, J.W. Shaevitz, and Z. Gitai (2021) "Competitive binding of independent extension and retraction motors explains the quantitative dynamics of type IV pili" PNAS

• R.J. Scheffler, Y. Sugimoto, B.P. Bratton, C.K. Ellison, M.D. Koch, M.S. Donia, Z. Gitai (2021) "Pseudomonas aeruginosa detachment from surfaces via a self-made small molecule". Journal of Biological Chemistry

• ​​A. Simsek, A. Braeutigam, M.D. Koch, J.W. Shaevitz, Y. Huang, G. Gompper, B. Sabass (2019) "Substrate-rigidity dependent migration of an idealized twitching bacterium". Soft Matter

• J.E. Sanfilippo*, A. Lorestani*, M.D. Koch, B.P. Bratton, A. Siryaporn, H.A. Stone, Z. Gitai (2019) "Microfluidic-based transcriptomics reveal force-independent bacterial rheosensing". Nature Microbiology​

• B. Sabass, M.D. Koch, G. Liu, H.A. Stone, and J.W. Shaevitz (2017) "Force generation by groups of migrating bacteria". PNAS

• M.D. Koch and J.W. Shaevitz (2017) "Introduction to Optical Tweezers". Methods in Molecular Biology Vol. 1486: Optical Tweezers – Methods and Protocols, 1st ed.

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PhD

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• J. Roth*, M.D. Koch*, and A. Rohrbach (2018) "Dynamics of a protein chain motor driving helical bacteria under stress". Biophysical Journal

• M.D. Koch and A. Rohrbach (2018) "Label-free imaging and bending analysis of microtubules by ROCS microscopy and optical trapping". Biophysical Journal

• M.D. Koch, N. Schneider, P. Nick, and A. Rohrbach (2017) "Single microtubules and small networks become significantly stiffer on short time-scales upon mechanical stimulation". Scientific Reports

• M.D. Koch and A. Rohrbach (2014) "How to calibrate an object-adapted optical trap for force sensing and interferometric shape tracking of asymmetric structures". Optics Express

• M.D. Koch, J. Roth, and A. Rohrbach (2014) "Bakterien gefangen im Licht". BIOspektrum (Invited news article)

• M.D. Koch and A. Rohrbach (2012) "Object-adapted optical trapping and shape-tracking of energy-switching helical bacteria". Nature Photonics