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BiofilmQ: a software tool for quantitative image analysis of microbial biofilm communities
R. Hartmann*, H. Jeckel*, E. Jelli*, P.K. Singh, S. Vaidya, M. Bayer, L. Vidakovic, F. Díaz-Pascual, J.C.N. Fong, A. Dragoš, O. Besharova, C.D. Nadell, V. Sourjik, A.T. Kovács, F.H. Yildiz, K. Drescher
submitted (2019). (* equal contribution) [bioRxiv] [journal link]
       -- download/use the BiofilmQ software tool, view video tutorials.

Flow-induced symmetry breaking in growing bacterial biofilms
P. Pearce, B. Song, D.J. Skinner, R. Mok, R. Hartmann, P.K. Singh, H. Jeckel, J.S. Oishi, K. Drescher, J. Dunkel
under review (2019). [bioRxiv] [journal link]

BacStalk: a comprehensive and interactive image analysis software tool for bacterial cell biology
R. Hartmann*, M.C.F. van Teeseling*, M. Thanbichler, K. Drescher
submitted (2019). (* equal contribution) [bioRxiv] [journal link]
       -- download/use the BacStalk software tool, view video tutorials.

Chemotactic behavior of Escherichia coli at high cell density
R. Colin, K. Drescher, V. Sourjik
under review (2019). [journal link]

Evolutionary dynamics of phage resistance in bacterial biofilms
M. Simmons, M.C. Bond, K. Drescher, V. Bucci, C.D. Nadell
under review (2019). [bioRxiv] [journal link]

Privatization of biofilm matrix in structurally heterogeneous biofilms
S.B. Otto, M. Martin, D. Schäfer, R. Hartmann, K. Drescher, S. Brix, A. Dragoš, A.T. Kovács
under review (2019). [bioRxiv] [journal link]

Journal articles

Breakdown of Vibrio cholerae biofilm architecture induced by antibiotics disrupts community barrier function
F. Diaz-Pascual, R. Hartmann, M. Lempp, L. Vidakovic, B. Song, H. Jeckel, K.M. Thormann, F.H. Yildiz, J. Dunkel, H. Link, C.D. Nadell, K. Drescher
Nature Microbiology, in press (2019). [journal link]

Common concepts for bacterial collectives
H. Jeckel, N. Matthey, K. Drescher
eLife 8, e42697 (2019). [journal link]

Bacterial multicellularity in biofilms
K. Drescher
BIOspektrum 25, 258-260 (2019). [journal link]

Learning the space-time phase diagram of bacterial swarm expansion
H. Jeckel, E. Jelli, R. Hartmann, P.K. Singh, R. Mok, J.F. Totz, L. Vidakovic, B. Eckhardt, J. Dunkel, K. Drescher
PNAS 116, 1489-1494 (2019). [Open Access] [dataset explorer]
       -- Youtube video summary.

Emergence of three-dimensional order and structure in growing biofilms
R. Hartmann, P.K. Singh*, P. Pearce*, R. Mok*, B. Song, F. Diaz-Pascual, J. Dunkel, K. Drescher
Nature Physics 15, 251-256 (2019). (* equal contribution) [journal link] [Europe PMC] [data repository]
       -- see Jordi Garcia-Ojalvo's Perspective in Nature Physics.
       -- see Phil Pearce's "Behind the paper" story.

Selective enrichment of slow-growing bacteria in a metabolism-wide CRISPRi library with a TIMER protein
D. Beuter, J. Gomes-Filho, L. Randau, F. Díaz-Pascual, K. Drescher, H. Link
ACS Synthetic Biology 7, 2775-2782 (2018). [journal link]

Kin discrimination in social yeast is mediated by cell surface receptors of the Flo11 adhesin family
S. Brückner, R. Schubert, T. Kraushaar, R. Hartmann, D. Hoffmann, K. Drescher, D. Müller, L.-O. Essen, H.-U. Mösch
in revision (2018). [journal link]

Division of labor during biofilm matrix production
A. Dragos, H.T. Kiesewalter, M. Martin, C.-Y. Hsu, R. Hartmann, T. Wechsler, K. Drescher, N. Stanley-Wall, R. Kümmerli, A.T. Kovacs
Current Biology 28, 1-11 (2018). [journal link]
       -- see highlight in Nature Rev. Microbiol. by A. York [link]
       -- see highlight in Current Biology by B. Momeni [link]
       -- see "Behind the Paper" story [link]

Cell adhesion and fluid flow jointly initiate biofilm genetic structure
R. Martinez-Garcia, C.D. Nadell, R. Hartmann, K. Drescher, J.A. Bonachela
PLoS Computational Biology 14, e1006094 (2018). [Open Access]

Dynamic biofilm architecture confers individual and collective mechanisms of viral protection
L. Vidakovic, P.K. Singh, R. Hartmann, C.D. Nadell, K. Drescher
Nature Microbiology 3, 26-31 (2018). [Open Access] [journal link] [Europe PMC]
       -- see perspective by J. Price & M.R. Chapman in Nature Microbiol. [link]

Phage mobility is a core determinant of phage-bacteria coexistence in biofilms
M. Simmons, K. Drescher, C.D. Nadell, V. Bucci
ISME Journal 12, 531-543 (2018). [Open Access]

Vibrio cholerae combines individual and collective sensing to trigger biofilm dispersal
P.K. Singh, S. Bartalomej, R. Hartmann, H. Jeckel, L. Vidakovic, C.D. Nadell, K. Drescher
Current Biology 27, 1-8 (2017). [Open Access]
       -- see F1000 recommendation by Chris Waters

Structural dynamics of RbmA governs plasticity of Vibrio cholerae biofilms
J.C. Fong, A. Rogers, A.K. Michael, N.C. Parsley, W.C. Cornell, Y.C. Lin, P.K. Singh, R. Hartmann, K. Drescher, E. Vinogradov, L.E. Dietrich, C.L. Partch, F.H. Yildiz
eLife 6, e26163 (2017). [Open Access]
       -- see highlight in eLife by Pierrat & Persat [link]
       -- see highlight in Nature Rev. Microbiol. by A. York [link]

Flow environment and matrix structure interact to determine spatial competition in Pseudomonas aeruginosa biofilms
C.D. Nadell, D. Ricaurte, J. Yan, K. Drescher, B.L. Bassler
eLife 6, e21855 (2017). [Open Access]
       -- see highlight in Trends in Microbiology by Chew & Yang [link]
       -- see article in Quanta Magazine by Carrie Arnold [link]

An emerging grip on the growth of grounded bacteria
C.D. Nadell, R. Hartmann, K. Drescher
ACS Nano 10, 9109-9110 (2016). [journal link]

Diversification of Gene Expression during Formation of Static Submerged Biofilms by Escherichia coli
O. Besharova, V.M. Suchanek, R. Hartmann, K. Drescher, V. Sourjik
Frontiers in Microbiology 7, 1568 (2016). [Open Access]

Spatial structure, cooperation, and competition in biofilms
C.D. Nadell, K. Drescher, K.R. Foster
Nature Reviews Microbiology 14, 589-600 (2016). [journal link]

Architectural transitions in Vibrio cholerae biofilms at single-cell resolution
K. Drescher, J. Dunkel, C.D. Nadell, S. van Teeffelen, I. Grnja, N.S. Wingreen, H.A. Stone, B.L. Bassler
PNAS 113, E2066–E2072 (2016). [journal link]
   -- see excellent perspective by Gerard C.L. Wong in PNAS [link, pdf]
       -- see highlight in PNAS [link]

The mechanical world of bacteria
A. Persat, C.D. Nadell, K.M. Kim, F. Ingremeau, A. Siryaporn, K. Drescher, N.S. Wingreen, B.L. Bassler, Z. Gitai, H.A. Stone
Cell 161, 988-997 (2015). [journal link]

Extracellular matrix structure governs invasion resistance in bacterial biofilms
C.D. Nadell, K. Drescher, N.S. Wingreen, B.L. Bassler
ISME Journal 9, 1700-1709 (2015). [journal link]

Solutions to the public goods dilemma in bacterial biofilms
K. Drescher, C.D. Nadell, H.A. Stone, N.S. Wingreen, B.L. Bassler
Current Biology 24, 50-55 (2014). [journal link]
   -- see perspective by M.S. Datta & J. Gore in Curr. Biol. [link]
  -- see highlight in Nature [link]
  -- see feature at National Institutes of Health (NIH/NIGMS) [link]
  -- see news story at Princeton [link]

Filaments in curved streamlines: Rapid formation of Staphylococcus aureus biofilm streamers
M.K. Kim, K. Drescher, O.S. Pak, B.L. Bassler, H.A. Stone
New Journal of Physics 16, 065024 (2014). [journal link]
   -- selected by NJP as one of the "Highlights of 2014"
       -- part of special issue on "Physics of Biofilms" [link]
  -- see NPR news story by K. Manke [link]

A quorum-sensing inhibitor blocks Pseudomonas aeruginosa virulence and biofilm formation
C.T. O'Loughlin, L.C. Miller, A. Siryaporn, K. Drescher, M.F. Semmelhack, B.L. Bassler
PNAS 110, 17981-17986 (2013). [journal link]
   -- see highlight in Nature Rev. Microbiol. by C. Tobin Kahrstrom [link]

Biofilm streamers cause catastrophic disruption of flow with consequences for environmental and medical systems
K. Drescher, Y. Shen, B.L. Bassler, H.A. Stone
PNAS 110, 4345-4350 (2013). [journal link]
  -- see highlight in PNAS [link
  -- see highlight by the NIH [link] and National Institute of General Medical Sciences [link]
  -- see highlight by the NSF [link]

Fluid dynamics of bacterial turbulence
J. Dunkel, S. Heidenreich, K. Drescher, H.H. Wensink, M. Bär, R.E. Goldstein
Physical Review Letters 110, 228102 (2013). [journal link]
  -- see viewpoint by I. Aranson in Physics [link]

Cutting through the complexity of cell collectives
C.D. Nadell*, V. Bucci*, K. Drescher*, S.A. Levin, B.L. Bassler, J.B. Xavier
Proceedings of the Royal Society B 280, 20122770 (2013). (* equal contribution) [journal link]

Swimming like algae: biomimetic soft artificial cilia
S. Sareh, J. Rossiter, A. Conn, K. Drescher, R.E. Goldstein
Journal of the Royal Society Interface 10, 20120666 (2013). [journal link]

Meso-scale turbulence in living fluids
H.H. Wensink*, J. Dunkel*, S. Heidenreich*, K. Drescher*, R.E. Goldstein, H. Löwen, J.M. Yeomans 
PNAS 109, 14308-14313 (2012). (* equal contribution) [journal link]
  -- see highlight by E. Frey in Physik Journal [pdf]

Fluid dynamics and noise in bacterial cell-cell and cell-surface interactions
K. Drescher, J. Dunkel, L.H. Cisneros, S. Ganguly, R.E. Goldstein 
PNAS 108, 10940-10945 (2011). [journal link] [pdf] [video]

The flagellar photoresponse in Volvox species
C.A. Solari, K. Drescher, R.E. Goldstein 
Journal of Phycology 47, 580-583 (2011). [journal pdf] [link]

Direct measurement of the flow field around swimming microorganisms
K. Drescher, R.E. Goldstein, N. Michel, M. Polin, I. Tuval 
Physical Review Letters 105, 168101 (2010). [pdf] [arxiv][videos: ChlamyVolvox]
  -- see viewpoint by D. Saintillan in Physics [pdf
  -- see commentaries in Physics World [link], Physics Today [link

Flagellar phenotypic plasticity in volvocalean algae correlates with Péclet number
C.A. Solari, K. Drescher, S. Ganguly, J.O. Kessler, R.E. Michod, R.E. Goldstein 
Journal of the Royal Society Interface 8, 1409-1417 (2011). [pdf]

Fidelity of adaptive phototaxis
K. Drescher, R.E. Goldstein, I. Tuval 
PNAS 107, 11171-11176 (2010). [pdf] [journal link
  -- see highlight in PNAS [pdf
  -- see summary on HFSP website[link]

Chlamydomonas swims with two 'gears' in a eukaryotic version of run-and-tumble locomotion
M. Polin, I. Tuval, K. Drescher, J.P. Gollub, R.E. Goldstein  
Science 325, 487-490 (2009). [pdf] [supporting material: pdf] [video summary]
  -- see viewpoint in Science by R. Stocker and W. Durham [pdf]
  -- see summary on HFSP website[link]

Dancing Volvox: Hydrodynamic bound states of swimming algae
K. Drescher, K.C. Leptos, I. Tuval, T. Ishikawa, T.J. Pedley, R.E. Goldstein
Physical Review Letters 102, 168101 (2009). [pdf] [arxiv] [videos: 12] [PRL coverwaltzing]
  -- see viewpoint by H. Stark in Physik Journal [pdf
  -- see highlights in Nature [pdf], New Scientist [link]
  -- and highlights in Science Now [link], Science News [link], Physics World [link
  -- see news by Wissenschaft [link], Smithsonian [link], BBSRC [link], Times of India [link], etc.

How to track protists in three dimensions
K. Drescher, K.C. Leptos, R.E. Goldstein
Review of Scientific Instruments 80, 014301 (2009). [pdf] [arxiv]

Comparison of hypercapnia-based calibration techniques for measurement of cerebral oxygen metabolism with MRI
D.P. Bulte, K. Drescher, P. Jezzard
Magnetic Resonance in Medicine 61, 391-398 (2009). [pdf]

  • Video describing how we used machine learning to discover the phase diagram of bacterial swarming (directed by M. Abt)

  • Video describing our work on bacterial biofilms in environments that mimic natural habitats: (directed by Z. Donnell)

  • Video of flow generated by a single swimming bacterium (E. coli). The flow field is so small that its effects are mostly drowned by diffusion.

  • How do multicellular organisms without a central nervous system of communication between the individual cells coordinate organism-level behaviors? This video, based on a mathematical model, shows that the spherical alga Volvox carteri can turn towards the light by endowing each cell on its surface with a common, fine-tuned response to light. The response magnitude is color-coded.

  • Video of dancing microorganisms: These bound states are due to hydrodynamic interactions between swimming Volvox carteri.