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Inferring biophysical models of evolution from genome-wide patterns of codon usage
[article]
2019
bioRxiv
pre-print
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We illustrate this point using 6 Arg codons as a representative example ( Fig. 2A,B ). ...
(c) Ratios of the two selection coefficients from (a) and (b), shown as box-and-whisker plots for each organism. ...
doi:10.1101/578815
fatcat:djyqk4hdbvazbptpkrkmwv2umy
Rapid Bayesian Inference of Global Network Statistics Using Random Walks
2018
Physical Review Letters
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2017 pre-print arXiv:1712.00804v1 fatcat:lpbx23lzgrcarir35tqve42xqeOther Versions
K x , ) q Kx x e −qx , (6) where B(K x , ) = 1 0 dq x q Kx x e −qx K x ! ...
Fig. 3(b) shows how the estimate of the total number of Wikipedia pages evolves as K p increases. ...
doi:10.1103/physrevlett.121.038301
pmid:30085804
fatcat:ezc3qr3ixrfmpopatia3pm4o6i
Dual RNA-seq provides insight into the biology of the neglected intracellular human pathogen Orientia tsutsugamushi
[article]
2019
bioRxiv
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B. Clinical observation score of mice 12 days post-infection. ...
B. Clinical observation score of mice 12 days post infection
, Supp. ...
doi:10.1101/743641
fatcat:vkapb4scvbc3zlrzftzc6bxmku
First-passage dynamics of random walks on complex and mutational codon networks
2019
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In (b)-(d), all values were grouped into 100 bins. ...
We illustrate this point using 6 Arg codons as a representative example (Fig. 6.1A,B). ...
doi:10.7282/t3-d4p2-8h52
fatcat:dx6n6bbnijfabfoy5r2vsrfrau
Path statistics, memory, and coarse-graining of continuous-time random walks on networks
2015
Journal of Chemical Physics
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Manhart, Kion-Crosby, and Morozov J. Chem. ...
Phys. 143, 214106 (2015)
Manhart, Kion-Crosby, and Morozov
(3) std ,t(3) std and kurtosisl(4) std ,t (4) std of length and time, all as functions of β. ...
time by taking derivatives of its generating functions: To express these in terms of the length and waiting time moments, we use Faà di Bruno's formula for derivatives of composite functions: 37 where B ...
doi:10.1063/1.4935968
pmid:26646868
pmcid:PMC4703372
fatcat:67tvsb4xrjc65ikynx5rjeoyde
Mutation bias interacts with composition bias to influence adaptive evolution
[article]
2020
bioRxiv
pre-print
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Modeling evolution using the probability of fixation: History and Michael Manhart, Willow Kion-Crosby, and Alexandre V. Morozov. Path statistics, memory, and coarse-graining Andreas Wagner. ...
was calculated as 439 O A, B = |C| min(| A|, |B|) , (6) where A and B are multisets -sets that permit multiple instances of an element. ...
doi:10.1101/2020.02.20.957217
fatcat:f6gepm3ub5bwhgpwbwwxhrgpt4
Marginal speed confinement resolves the conflict between correlation and control in natural flocks of birds
[article]
2021
arXiv
pre-print
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After these manipulations we get the distribution P ({s,v a }) = Ω({s,v a }) e −βH ds Dv Ω({s ,v b }) e −βH (S14) with a = 0 and Dv ≡ b =0 dv b . ...
B, vol. 64, pp. 451-456, 08 2008. [7] P. Romanczuk and L. ...
arXiv:2101.09748v2
fatcat:27naxijtlrg6hbkfe4qgifx54q
Dual RNA-seq of Orientia tsutsugamushi informs on host-pathogen interactions for this neglected intracellular human pathogen
2020
Nature Communications
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HUVEC = human umbilical vein endothelial cell. b Growth curve showing replication of Ot in cultured HUVEC cells. ...
Fig. 7 7 Karp is more virulent than UT176 in a mouse infection model. a Weight change over 12 days of infection. b Clinical observation score of mice 12 days post infection. ...
doi:10.1038/s41467-020-17094-8
pmid:32620750
fatcat:cazonyd7onhw5lg5wxue63nh5e
Probing Dark Energy with Large Galaxy Surveys: Systematics Quantification & Mitigation
2020
Zenodo
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I have also been very lucky to have met some of the most incredible graduate students: Willow Kion-Crosby, who made life as I knew it so much more palatable and gave me the treasure of a camaraderie, who ...
Similarly, w B i = q AB i for observed Type-A while w B i = q BB i for observed Type-B. Also note that N tot = N A obs + N B obs = N A true + N B true . ...
doi:10.5281/zenodo.3764151
fatcat:gtmcyodj7rc2fivm2lstycdymi
ASSOCIATION INTELLIGENCE
1853
BMJ (Clinical Research Edition)
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B. ...
Mather, of Ashtonle-Willows. JounmuL for May Gth.
have had ample time and opportunity for considering its provi-
sions and expressing their feelings and opinions thereupon. ...
doi:10.1136/bmj.s3-1.28.611
fatcat:lwtpehfidfczzeqawxdjdbpfzm
Evolution and stochastic dynamics in complex systems
2022
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Next, I would also like to thank all my colleagues Willow Kion-Crosby, Unab Javed, Ted Malliaris and Jesus Rives for helping me with my work and some interesting random discussions. ...
Weekly calls with Willow for the Community Detection project helped us shape the project. ...
Thus the term (n i , |n s ) ≈ 0 and P B (n i , |n s ) ≈ P N (n i , log( +1)|n s ). Thus, P B out ( ) = P N out (log( +1)) where P out ( ) = n j ∈C j P (n j , |n s ) and C is the community of n s . ...
doi:10.7282/t3-e6cw-v287
fatcat:5u3e3emrezgffe6itbiok4yywi
Materials design from first principles: methods, models, and tools
2020
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Kion-Crosby, Ghanashyam Khanal, Ian Laflotte, and Caitlin Carpenter. ...
physics department who have made my time here much more enjoyable including Colin Rylands, David Walter, Sean Burcher, Raghav Kunnawalkam-Elayavalli, John Wu, Kartheik Iyer, Jesse Rivera, Jesus Rives, Willow ...
doi:10.7282/t3-v1ys-9h98
fatcat:2tqlom3hvva53m2aemdpp5sx7u
BIOPHYSICS AND STOCHASTIC PROCESSES IN MOLECULAR EVOLUTION ABSTRACT OF THE DISSERTATION BIOPHYSICS AND STOCHASTIC PROCESSES IN MOLECULAR EVOLUTION
unpublished
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The many students in the biophysics group during my time here -Manjul Apratim, Aatish Bhatia, Rǎzvan Chereji, Adel Dayarian, Dai Wei, Bill Flynn, Allan Haldane, Dave Hassan, Pasha Khromov, Willow Kion-Crosby ...
are then given by k A→B = λ/(2π A ) and k B→A = λ/(2π B ). ...
We also note that for two matrices A and B, This can easily be proved by multiplying both sides by A − B. ...
fatcat:tzx6k557yvdptcbdj7jl6xcm4i