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Mixed Markov models.
Fridman A. Fridman A. Proc Natl Acad Sci U S A. 2003 Jul 8;100(14):8092-6. doi: 10.1073/pnas.0731829100. Epub 2003 Jun 26. Proc Natl Acad Sci U S A. 2003. PMID: 12829802 Free PMC article.
In this article, we study the analytical and computational properties of mixed Markov models. In particular, we show that positive mixed models have a local Markov property that is equivalent to their global factorization. We also describe a computationally efficien …
In this article, we study the analytical and computational properties of mixed Markov models. In particular, we show that positive mi …
Mapping the timescale of suicidal thinking.
Coppersmith DDL, Ryan O, Fortgang RG, Millner AJ, Kleiman EM, Nock MK. Coppersmith DDL, et al. Proc Natl Acad Sci U S A. 2023 Apr 25;120(17):e2215434120. doi: 10.1073/pnas.2215434120. Epub 2023 Apr 18. Proc Natl Acad Sci U S A. 2023. PMID: 37071683 Free PMC article.
We found that suicidal thinking changes rapidly. Both descriptive statistics and Markov-switching models indicated that elevated states of suicidal thinking lasted on average 1 to 3 h. ...
We found that suicidal thinking changes rapidly. Both descriptive statistics and Markov-switching models indicated that elevated stat …
Selectivity filter modalities and rapid inactivation of the hERG1 channel.
Miranda WE, DeMarco KR, Guo J, Duff HJ, Vorobyov I, Clancy CE, Noskov SY. Miranda WE, et al. Proc Natl Acad Sci U S A. 2020 Feb 11;117(6):2795-2804. doi: 10.1073/pnas.1909196117. Epub 2020 Jan 24. Proc Natl Acad Sci U S A. 2020. PMID: 31980532 Free PMC article.
The human ether-a-go-go-related gene (hERG1) channel conducts small outward K(+) currents that are critical for cardiomyocyte membrane repolarization. ...Overall, our findings provide an understanding of the molecular mechanisms controlling selective transport in K( …
The human ether-a-go-go-related gene (hERG1) channel conducts small outward K(+) currents that are critical for cardiomyocyte membran …
Discovery of a hidden transient state in all bromodomain families.
Raich L, Meier K, Günther J, Christ CD, Noé F, Olsson S. Raich L, et al. Proc Natl Acad Sci U S A. 2021 Jan 26;118(4):e2017427118. doi: 10.1073/pnas.2017427118. Proc Natl Acad Sci U S A. 2021. PMID: 33468647 Free PMC article.
While the general structure of BDs is well known, their dynamical features and their interplay with other macromolecules are poorly understood, hampering the rational design of potent and selective inhibitors. Here, we combine extensive molecular dynamics simulations, Markov …
While the general structure of BDs is well known, their dynamical features and their interplay with other macromolecules are poorly understo …
Ion-triggered selectivity in bacterial sodium channels.
Furini S, Domene C. Furini S, et al. Proc Natl Acad Sci U S A. 2018 May 22;115(21):5450-5455. doi: 10.1073/pnas.1722516115. Epub 2018 May 7. Proc Natl Acad Sci U S A. 2018. PMID: 29735669 Free PMC article.
Although this liquid-like environment looks optimal for rapid conduction of Na(+), it seems incompatible with efficient discrimination between similar ion species, such as Na(+) and K(+), through steric effects. Here extensive molecular dynamics simulations, combined with …
Although this liquid-like environment looks optimal for rapid conduction of Na(+), it seems incompatible with efficient discrimination betwe …
Compositional and thermal state of the lower mantle from joint 3D inversion with seismic tomography and mineral elasticity.
Deng X, Xu Y, Hao S, Ruan Y, Zhao Y, Wang W, Ni S, Wu Z. Deng X, et al. Proc Natl Acad Sci U S A. 2023 Jun 27;120(26):e2220178120. doi: 10.1073/pnas.2220178120. Epub 2023 Jun 20. Proc Natl Acad Sci U S A. 2023. PMID: 37339202 Free PMC article.
In this study, we inverted for the 3D chemical composition and thermal state of the lower mantle based on seismic tomography and mineral elasticity data by employing a Markov chain Monte Carlo framework. The results show a silica-enriched lower mantle with a Mg/Si ratio le …
In this study, we inverted for the 3D chemical composition and thermal state of the lower mantle based on seismic tomography and mineral ela …
Evaporation Study of an Ionic Liquid with a Double-Charged Cation.
Chilingarov NS, Zhirov MS, Shmykova AM, Martynova EA, Glukhov LM, Chernikova EA, Kustov LM, Markov VY, Ioutsi VA, Sidorov LN. Chilingarov NS, et al. J Phys Chem A. 2018 May 17;122(19):4622-4627. doi: 10.1021/acs.jpca.8b02488. Epub 2018 May 7. J Phys Chem A. 2018. PMID: 29684267
This decomposition does not affect the vaporization characteristics of [C(3)(MIm)(2)(2+)][Tf(2)N(-)](2), which were established to be as follows. The vaporization enthalpy (550 K) is equal to (155.5 3.2) kJ.mol(-1); the saturated vapor pressure is described by the equation …
This decomposition does not affect the vaporization characteristics of [C(3)(MIm)(2)(2+)][Tf(2)N(-)](2), which were established to be as fol …
Full molecular trajectories of RNA polymerase at single base-pair resolution.
Righini M, Lee A, Cañari-Chumpitaz C, Lionberger T, Gabizon R, Coello Y, Tinoco I Jr, Bustamante C. Righini M, et al. Proc Natl Acad Sci U S A. 2018 Feb 6;115(6):1286-1291. doi: 10.1073/pnas.1719906115. Epub 2018 Jan 19. Proc Natl Acad Sci U S A. 2018. PMID: 29351994 Free PMC article.
Using this instrument, we implemented a protocol that synthesizes single base-pair trajectories, which are used to test a Large State Space Hidden Markov Model algorithm to recover their individual steps. We then used this algorithm on real transcription data obtained in t …
Using this instrument, we implemented a protocol that synthesizes single base-pair trajectories, which are used to test a Large State Space …
Reconstructing dynamic microRNA-regulated interaction networks.
Schulz MH, Pandit KV, Lino Cardenas CL, Ambalavanan N, Kaminski N, Bar-Joseph Z. Schulz MH, et al. Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):15686-91. doi: 10.1073/pnas.1303236110. Epub 2013 Aug 28. Proc Natl Acad Sci U S A. 2013. PMID: 23986498 Free PMC article.
We developed the MIRna Dynamic Regulatory Events Miner (mirDREM), a probabilistic modeling method that uses input-output hidden Markov models to reconstruct dynamic regulatory networks that explain how temporal gene expression is jointly regulated by miRNAs and transcripti …
We developed the MIRna Dynamic Regulatory Events Miner (mirDREM), a probabilistic modeling method that uses input-output hidden Markov …
Structural basis of action for a human ether-a-go-go-related gene 1 potassium channel activator.
Perry M, Sachse FB, Sanguinetti MC. Perry M, et al. Proc Natl Acad Sci U S A. 2007 Aug 21;104(34):13827-32. doi: 10.1073/pnas.0703934104. Epub 2007 Aug 10. Proc Natl Acad Sci U S A. 2007. PMID: 17693551 Free PMC article.
Activation of human ether-a-go-go-related gene 1 (hERG1) K(+) channels mediates cardiac action potential repolarization. ...These findings define a putative binding site for RPR and confirm the importance of an interaction between the S4-S5 linker and the S6 domain in elec …
Activation of human ether-a-go-go-related gene 1 (hERG1) K(+) channels mediates cardiac action potential repolarization. ...These fin …
22 results