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Items: 1 to 50 of 56

1.

Receptor crosstalk improves concentration sensing of multiple ligands.

Carballo-Pacheco M, Desponds J, Gavrilchenko T, Mayer A, Prizak R, Reddy G, Nemenman I, Mora T.

Phys Rev E. 2019 Feb;99(2-1):022423. doi: 10.1103/PhysRevE.99.022423.

PMID:
30934315
2.

Automated, predictive, and interpretable inference of Caenorhabditis elegans escape dynamics.

Daniels BC, Ryu WS, Nemenman I.

Proc Natl Acad Sci U S A. 2019 Apr 9;116(15):7226-7231. doi: 10.1073/pnas.1816531116. Epub 2019 Mar 22.

PMID:
30902894
3.

Millisecond Spike Timing Codes for Motor Control.

Sober SJ, Sponberg S, Nemenman I, Ting LH.

Trends Neurosci. 2018 Oct;41(10):644-648. doi: 10.1016/j.tins.2018.08.010. Epub 2018 Sep 25.

4.

Chance, long tails, and inference in a non-Gaussian, Bayesian theory of vocal learning in songbirds.

Zhou B, Hofmann D, Pinkoviezky I, Sober SJ, Nemenman I.

Proc Natl Acad Sci U S A. 2018 Sep 4;115(36):E8538-E8546. doi: 10.1073/pnas.1713020115. Epub 2018 Aug 20.

5.

Luria-Delbrück, revisited: the classic experiment does not rule out Lamarckian evolution.

Holmes CM, Ghafari M, Abbas A, Saravanan V, Nemenman I.

Phys Biol. 2017 Aug 21;14(5):055004. doi: 10.1088/1478-3975/aa8230.

PMID:
28825411
6.

Growth of bacteria in 3-d colonies.

Shao X, Mugler A, Kim J, Jeong HJ, Levin BR, Nemenman I.

PLoS Comput Biol. 2017 Jul 27;13(7):e1005679. doi: 10.1371/journal.pcbi.1005679. eCollection 2017 Jul.

7.

Single variant bottleneck in the early dynamics of H. influenzae bacteremia in neonatal rats questions the theory of independent action.

Shao X, Levin B, Nemenman I.

Phys Biol. 2017 Jun 15;14(4):045004. doi: 10.1088/1478-3975/aa731b.

PMID:
28617678
8.

Simple biochemical networks allow accurate sensing of multiple ligands with a single receptor.

Singh V, Nemenman I.

PLoS Comput Biol. 2017 Apr 14;13(4):e1005490. doi: 10.1371/journal.pcbi.1005490. eCollection 2017 Apr.

9.

Motor control by precisely timed spike patterns.

Srivastava KH, Holmes CM, Vellema M, Pack AR, Elemans CP, Nemenman I, Sober SJ.

Proc Natl Acad Sci U S A. 2017 Jan 31;114(5):1171-1176. doi: 10.1073/pnas.1611734114. Epub 2017 Jan 18.

10.

Stereotypical Escape Behavior in Caenorhabditis elegans Allows Quantification of Effective Heat Stimulus Level.

Leung K, Mohammadi A, Ryu WS, Nemenman I.

PLoS Comput Biol. 2016 Dec 27;12(12):e1005262. doi: 10.1371/journal.pcbi.1005262. eCollection 2016 Dec.

11.

Effects of receptor correlations on molecular information transmission.

Singh V, Tchernookov M, Nemenman I.

Phys Rev E. 2016 Aug;94(2-1):022425. doi: 10.1103/PhysRevE.94.022425. Epub 2016 Aug 31.

PMID:
27627350
12.

Role of spatial averaging in multicellular gradient sensing.

Smith T, Fancher S, Levchenko A, Nemenman I, Mugler A.

Phys Biol. 2016 May 20;13(3):035004. doi: 10.1088/1478-3975/13/3/035004.

PMID:
27203129
13.

Cell-cell communication enhances the capacity of cell ensembles to sense shallow gradients during morphogenesis.

Ellison D, Mugler A, Brennan MD, Lee SH, Huebner RJ, Shamir ER, Woo LA, Kim J, Amar P, Nemenman I, Ewald AJ, Levchenko A.

Proc Natl Acad Sci U S A. 2016 Feb 9;113(6):E679-88. doi: 10.1073/pnas.1516503113. Epub 2016 Jan 20.

14.

Limits to the precision of gradient sensing with spatial communication and temporal integration.

Mugler A, Levchenko A, Nemenman I.

Proc Natl Acad Sci U S A. 2016 Feb 9;113(6):E689-95. doi: 10.1073/pnas.1509597112. Epub 2016 Jan 20.

15.

The eighth q-bio conference: meeting report and special issue preface.

Hlavacek WS, Gnanakaran S, Munsky B, Wall ME, Faeder JR, Jiang Y, Nemenman I, Resnekov O.

Phys Biol. 2015 Dec 30;12(6):060401. doi: 10.1088/1478-3975/12/6/060401. No abstract available.

PMID:
26716953
16.

Automated adaptive inference of phenomenological dynamical models.

Daniels BC, Nemenman I.

Nat Commun. 2015 Aug 21;6:8133. doi: 10.1038/ncomms9133.

17.

Efficient inference of parsimonious phenomenological models of cellular dynamics using S-systems and alternating regression.

Daniels BC, Nemenman I.

PLoS One. 2015 Mar 25;10(3):e0119821. doi: 10.1371/journal.pone.0119821. eCollection 2015.

18.

Millisecond-scale motor encoding in a cortical vocal area.

Tang C, Chehayeb D, Srivastava K, Nemenman I, Sober SJ.

PLoS Biol. 2014 Dec 9;12(12):e1002018. doi: 10.1371/journal.pbio.1002018. eCollection 2014 Dec.

19.

Director field model of the primary visual cortex for contour detection.

Singh V, Tchernookov M, Butterfield R, Nemenman I.

PLoS One. 2014 Oct 17;9(10):e108991. doi: 10.1371/journal.pone.0108991. eCollection 2014.

20.

Zipf's law and criticality in multivariate data without fine-tuning.

Schwab DJ, Nemenman I, Mehta P.

Phys Rev Lett. 2014 Aug 8;113(6):068102. Epub 2014 Aug 7.

21.

The Seventh q-bio Conference: meeting report and preface.

Nemenman I, Faeder JR, Gnanakaran S, Hlavacek WS, Munsky B, Wall ME, Jiang Y.

Phys Biol. 2014 Aug;11(4):040301. doi: 10.1088/1478-3975/11/4/040301. Epub 2014 Jul 30. No abstract available.

22.

Cellular noise and information transmission.

Levchenko A, Nemenman I.

Curr Opin Biotechnol. 2014 Aug;28:156-64. doi: 10.1016/j.copbio.2014.05.002. Epub 2014 Jun 9. Review.

23.

Population-expression models of immune response.

Stromberg SP, Antia R, Nemenman I.

Phys Biol. 2013 Jun;10(3):035010. doi: 10.1088/1478-3975/10/3/035010. Epub 2013 Jun 4.

PMID:
23735782
24.

A large number of receptors may reduce cellular response time variation.

Cheng X, Merchan L, Tchernookov M, Nemenman I.

Phys Biol. 2013 Jun;10(3):035008. doi: 10.1088/1478-3975/10/3/035008. Epub 2013 Jun 4.

PMID:
23735700
25.

Special section dedicated to The Sixth q-bio Conference: meeting report and preface.

Nemenman I, Gnanakaran S, Munsky B, Wall ME, Jiang Y, Hlavacek WS, Faeder JR.

Phys Biol. 2013 Jun;10(3):030301. doi: 10.1088/1478-3975/10/3/030301. Epub 2013 Jun 4. No abstract available.

PMID:
23735417
26.

Genotype to phenotype mapping and the fitness landscape of the E. coli lac promoter.

Otwinowski J, Nemenman I.

PLoS One. 2013 May 1;8(5):e61570. doi: 10.1371/journal.pone.0061570. Print 2013.

27.

Speeding up Evolutionary Search by Small Fitness Fluctuations.

Otwinowski J, Tanase-Nicola S, Nemenman I.

J Stat Phys. 2011 Jul;144(2):367-378.

28.

Gain control in molecular information processing: lessons from neuroscience.

Nemenman I.

Phys Biol. 2012;9(2):026003. doi: 10.1088/1478-3975/9/2/026003. Epub 2012 Apr 4.

29.

Fitness in time-dependent environments includes a geometric phase contribution.

Tanase-Nicola S, Nemenman I.

J R Soc Interface. 2012 Jun 7;9(71):1354-62. doi: 10.1098/rsif.2011.0695. Epub 2011 Nov 23.

30.

Model cortical association fields account for the time course and dependence on target complexity of human contour perception.

Gintautas V, Ham MI, Kunsberg B, Barr S, Brumby SP, Rasmussen C, George JS, Nemenman I, Bettencourt LM, Kenyon GT.

PLoS Comput Biol. 2011 Oct;7(10):e1002162. doi: 10.1371/journal.pcbi.1002162. Epub 2011 Oct 6. Erratum in: PLoS Comput Biol. 2011 Oct;7(10). doi: 10.1371/annotation/35890214-d064-4b76-8bfc-5ac1ab07c8b8. Kenyon, Garret T [corrected to Kenyon, Garrett T].

31.

Information transduction capacity of noisy biochemical signaling networks.

Cheong R, Rhee A, Wang CJ, Nemenman I, Levchenko A.

Science. 2011 Oct 21;334(6054):354-8. doi: 10.1126/science.1204553. Epub 2011 Sep 15.

32.

Selected papers from the Fourth Annual q-bio Conference on Cellular Information Processing.

Nemenman I, Faeder JR, Hlavacek WS, Jiang Y, Wall ME, Zilman A.

Phys Biol. 2011 Oct;8(5):050301. doi: 10.1088/1478-3975/8/5/050301. Epub 2011 Aug 10.

PMID:
21832800
33.

Mass conservation and inference of metabolic networks from high-throughput mass spectrometry data.

Bandaru P, Bansal M, Nemenman I.

J Comput Biol. 2011 Feb;18(2):147-54. doi: 10.1089/cmb.2010.0222.

34.

Multivariate dependence and genetic networks inference.

Margolin AA, Wang K, Califano A, Nemenman I.

IET Syst Biol. 2010 Nov;4(6):428-40. doi: 10.1049/iet-syb.2010.0009.

PMID:
21073241
35.

Time-dependent corrections to effective rate and event statistics in Michaelis-Menten kinetics.

Sinitsyn NA, Nemenman I.

IET Syst Biol. 2010 Nov;4(6):409-15. doi: 10.1049/iet-syb.2010.0064.

PMID:
21073239
36.

The Third q-bio Conference on Cellular Information Processing.

Nemenman I, Hlavacek WS, Jiang Y, Wall ME, Zilman A.

IET Syst Biol. 2010 Nov;4(6):331-3. doi: 10.1049/iet-syb.2010.9133. No abstract available.

PMID:
21073232
37.

Mesoscopic statistical properties of multistep enzyme-mediated reactions.

de Ronde WH, Daniels BC, Mugler A, Sinitsyn NA, Nemenman I.

IET Syst Biol. 2009 Sep;3(5):429. doi: 10.1049/iet-syb.2008.0167.

PMID:
21028932
38.

Quantifying evolvability in small biological networks.

Mugler A, Ziv E, Nemenman I, Wiggins CH.

IET Syst Biol. 2009 Sep;3(5):379-87. doi: 10.1049/iet-syb.2008.0165.

39.

The simplicity of completion time distributions for common complex biochemical processes.

Bel G, Munsky B, Nemenman I.

Phys Biol. 2009 Dec 21;7(1):016003. doi: 10.1088/1478-3975/7/1/016003.

PMID:
20026876
40.

Specificity and completion time distributions of biochemical processes.

Munsky B, Nemenman I, Bel G.

J Chem Phys. 2009 Dec 21;131(23):235103. doi: 10.1063/1.3274803. Erratum in: J Chem Phys. 2012 May 28;136(20):209902.

PMID:
20025351
41.

Genome-wide identification of post-translational modulators of transcription factor activity in human B cells.

Wang K, Saito M, Bisikirska BC, Alvarez MJ, Lim WK, Rajbhandari P, Shen Q, Nemenman I, Basso K, Margolin AA, Klein U, Dalla-Favera R, Califano A.

Nat Biotechnol. 2009 Sep;27(9):829-39. doi: 10.1038/nbt.1563. Epub 2009 Sep 9.

42.

Adiabatic coarse-graining and simulations of stochastic biochemical networks.

Sinitsyn NA, Hengartner N, Nemenman I.

Proc Natl Acad Sci U S A. 2009 Jun 30;106(26):10546-51. doi: 10.1073/pnas.0809340106. Epub 2009 Jun 12.

43.

Serially regulated biological networks fully realise a constrained set of functions.

Mugler A, Ziv E, Nemenman I, Wiggins CH.

IET Syst Biol. 2008 Sep;2(5):313-22. doi: 10.1049/iet-syb:20080097.

PMID:
19045826
44.

Determinants of bistability in induction of the Escherichia coli lac operon.

Dreisigmeyer DW, Stajic J, Nemenman I, Hlavacek WS, Wall ME.

IET Syst Biol. 2008 Sep;2(5):293-303. doi: 10.1049/iet-syb:20080095.

PMID:
19045824
45.

Selected papers from the First q-bio Conference on Cellular Information Processing.

Nemenman I, Hlavacek WS, Edwards JS, Faeder JR, Jiang Y, Wall ME.

IET Syst Biol. 2008 Sep;2(5):203-5. doi: 10.1049/iet-syb:20089018. No abstract available.

PMID:
19045816
46.

Neural coding of natural stimuli: information at sub-millisecond resolution.

Nemenman I, Lewen GD, Bialek W, de Ruyter van Steveninck RR.

PLoS Comput Biol. 2008 Mar 7;4(3):e1000025. doi: 10.1371/journal.pcbi.1000025.

47.

Universal geometric theory of mesoscopic stochastic pumps and reversible ratchets.

Sinitsyn NA, Nemenman I.

Phys Rev Lett. 2007 Nov 30;99(22):220408. Epub 2007 Nov 30.

PMID:
18233271
48.

Q-bio 2007: a watershed moment in modern biology.

Edwards JS, Faeder JR, Hlavacek WS, Jiang Y, Nemenman I, Wall ME.

Mol Syst Biol. 2007;3:148. Epub 2007 Dec 4. No abstract available.

49.

Optimal signal processing in small stochastic biochemical networks.

Ziv E, Nemenman I, Wiggins CH.

PLoS One. 2007 Oct 24;2(10):e1077.

50.

Reconstruction of metabolic networks from high-throughput metabolite profiling data: in silico analysis of red blood cell metabolism.

Nemenman I, Escola GS, Hlavacek WS, Unkefer PJ, Unkefer CJ, Wall ME.

Ann N Y Acad Sci. 2007 Dec;1115:102-15. Epub 2007 Oct 9.

PMID:
17925356

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