Publications

• Exploiting fluctuations in gene expression to detect causal interactions between genes  [Link]
  Joly-Smith E, Talpur M, Allard P, Papazotos F, Potvin-Trottier L, Hilfinger, A.
  eLife Reviewed Preprint - under revision 

• Characterizing the non-monotonic behavior of mutual information along biochemical reaction cascades  [Link PDF]
  Fan R &  Hilfinger A, Phys. Rev. E 110, 034309 (2024)

• Measuring prion propagation in single bacteria elucidates a mechanism of loss  [Link PDF]
  Jager K, Orozco-Hildago MT, Springstein BL, Joly-Smith E, Papazotos F, McDonough E, Fleming E, McCallum G, Hilfinger A, Hochschild A, and Potvin-Trottier L,  Proc. Natl. Acad. Sci. USA. 120 (39) e2221539120 (2023)

• Noise properties of adaptation-conferring biochemical control modules  [Link PDF]
  Kell B, Ripsman R, Hilfinger A, Proc. Natl. Acad. Sci. USA. 120(38), e2302016120 (2023)

As summarized on Kudos.

• Quantifying metal-binding specificity of CcNikZ-II from Clostridium carboxidivorans in the presence of competing metal ions  [Link PDF]
  Diep P, Kell B, Yakunin A, Hilfinger A, Mahadevan R, Analytical Biochemistry. 676, 115182 (2023)

• The effect of microRNA on protein variability and gene expression fidelity  [Link PDF]
  Fan R &  Hilfinger A, Biophysical Journal. 122, 1–19, (2023)

• Quantifying biochemical reaction rates from static population variability within incompletely observed complex networks [Link PDF]
  Wittenstein T, Leibovich N, Hilfinger A, PLoS Computational Biology. 18(6), e1010183 (2022)

• Visual barcodes for clonal-multiplexing of live microscopy-based assays  [Link PDF]
  Kaufman T, Nitzan E, Firestein N, Ginzberg MB, Iyengar S, Patel N, Ben-Hamo R, Porat Z, Hunter J, Hilfinger A, Rotter V, Kafri R, Straussman R Nature Communications. 13, 2725 (2022)

• Inferring gene regulation dynamics from static snapshots of gene expression variability [Link PDF]
  Joly-Smith E,  Wang ZJ,  Hilfinger A, Phys. Rev. E. 104:044406 (2021)

As summarized in our Blog Post.

• Cell size homeostasis is maintained by CDK4-dependent activation of p38 MAPK [Link PDF]
  Tan C, Ginzberg MB, Webster R, Iyengar S, Liu S, Papadopoli D, Concannon J, Wang Y, Auld DS, Jenkins JL, Rost H, Topisirovic I, Hilfinger A, Derry WB, Patel N, Kafri R, Developmental Cell. 56, 12, 1756-1769.e7 (2021)

As highlighted in CDK4: Linking cell size to cell cycle control

• Kinetic Uncertainty Relations for the Control of Stochastic Reaction Networks [Link PDF]
  Yan J, Hilfinger A, Vinnicombe G,  Paulsson J, Phys. Rev. Lett. 123:108101 (2019)

• Exploiting natural fluctuations to identify kinetic mechanisms in sparsely characterized systems [Link PDF]
  Hilfinger A, Norman TM, Paulsson J,  Cell Systems. 2 (4):251-259 (2016)

As highlighted in Staying Clear of the Dragons

• Constraints on fluctuations in sparsely characterized biological systems [Link PDF]
  Hilfinger A, Norman TM, Vinnicombe G, Paulsson J, Phys. Rev. Lett. 116:058101 (2016)

As highlighted in APS Viewpoint: Putting Bounds on Biochemical Noise

• Systems biology: Defiant daughters and coordinated cousins [Link]
  Hilfinger A & Paulsson J, Invited Commentary: Nature News & Views. 519:422-3 (2015)

• Using temporal correlations and full distributions to separate intrinsic and extrinsic fluctuations in biological systems [Link PDF]
  Hilfinger A, Chen M, Paulsson J, Phys. Rev. Lett. 109 :248104 (2012)

• Separating intrinsic from extrinsic fluctuations in dynamic biological systems [Link PDF]
  Hilfinger A & Paulsson J, Proc. Natl. Acad. Sci. USA. 108:12167-72 (2011)

• Nonlinear dynamics of cilia and flagella [Link PDF]
  Hilfinger A, Chattopadhyay AK, Jülicher F, Phys. Rev. E. 79:051918 (2009)

• The chirality of ciliary beats [Link PDF]
  Hilfinger A, Jülicher F, Physical Biology. 5:016003 (2008)

• How molecular motors shape the flagellar beat [Link PDF]
  Riedel-Kruse IH, Hilfinger A, Howard J, Jülicher F, Human Frontiers of Science Journal. 1 (3): 192-208 (2007)

As highlighted in Nature News & Views: How cilia beat