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Inferring biophysical models of evolution from genome-wide patterns of codon usage [article]

Willow B. Kion-Crosby, Michael Manhart, Alexandre V. Morozov
2019 bioRxiv   pre-print
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

Willow B. Kion-Crosby, Alexandre V. Morozov
2018 Physical Review Letters  
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]

Bozena Mika-Gospodorz, Suparat Giengkam, Alexander Westermann, Jantana Wongsantichon, Willow B. Kion-Crosby, Suthida Chuenklin, Loo Chien Wang, Piyanate Sunyakumthorn, Radoslaw Sobota, Selvakumar Subbian, Joerg Vogel, Lars Barquist (+1 others)
2019 bioRxiv   pre-print
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

Willow B. Kion-Crosby
2019
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

Michael Manhart, Willow Kion-Crosby, Alexandre V. Morozov
2015 Journal of Chemical Physics  
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]

Alejandro V. Cano, Joshua L. Payne
2020 bioRxiv   pre-print
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]

Andrea Cavagna, Antonio Culla, Xiao Feng, Irene Giardina, Tomás S. Grigera, Willow Kion-Crosby, Stefania Melillo, Giulia Pisegna, Lorena Postiglione, Pablo Villegas
2021 arXiv   pre-print
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

Bozena Mika-Gospodorz, Suparat Giengkam, Alexander J. Westermann, Jantana Wongsantichon, Willow Kion-Crosby, Suthida Chuenklin, Loo Chien Wang, Piyanate Sunyakumthorn, Radoslaw M. Sobota, Selvakumar Subbian, Jörg Vogel, Lars Barquist (+1 others)
2020 Nature Communications  
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

Humna Awan, Eric Gawiser
2020 Zenodo  
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)  
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

Aditya Ballal
2022
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

John Bonini
2020
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

Michael Manhart, Michael Manhart, Michael Manhart, Alexandre Morozov
unpublished
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