Filters








45,094 Hits in 9.1 sec

Studying the Evolution of Promoter Sequences: A Waiting Time Problem

Sarah Behrens, Martin Vingron
2010 Journal of Computational Biology  
emerges at random in a promoter sequence?  ...  and (2) How does the composition of a TF binding site affect this waiting time?  ...  Á p x n À 1 , x n : (3) 2.1.2. Modelling the time evolution of the promoter sequence. The promoter sequence evolution (X 1 (t), . . . , X n (t)) t!  ... 
doi:10.1089/cmb.2010.0084 pmid:21128851 pmcid:PMC3119604 fatcat:hb2bjqvfyfc5rlwutrrtik3fxi

The waiting time problem in a model hominin population

John Sanford, Wesley Brewer, Franzine Smith, John Baumgardner
2015 Theoretical Biology and Medical Modelling  
Conclusion: We show that the waiting time problem is a significant constraint on the macroevolution of the classic hominin population.  ...  When natural selection had successfully amplified an instance of the target string to the point of fixation, the experiment was halted, and the waiting time statistics were tabulated.  ...  Evolution often needs a specific fix to a specific problem, and that fix must be timely in order to retain relevance.  ... 
doi:10.1186/s12976-015-0016-z pmid:26376851 pmcid:PMC4573302 fatcat:tbpomqgyhjemzguvdv5svugltu

Waiting for regulatory sequences to appear

Richard Durrett, Deena Schmidt
2007 The Annals of Applied Probability  
Here, we will show that for words of length 6, the average waiting time is 100,000 years, while for words of length 8, the waiting time has mean 375,000 years when there is a 7 out of 8 letter match in  ...  the population consensus sequence (an event of probability roughly 5/16) and has mean 650 million years when there is not.  ...  We would like to thank Eric Siggia for pointing out the problem in Stone and Wray (2001) . Andrew D.  ... 
doi:10.1214/105051606000000619 fatcat:baiigrepfbhaxdtrfzjoihc7ze

Genome sequences of Halobacterium species

Wailap Victor Ng, Brian R. Berquist, James A. Coker, Melinda Capes, Timothy H. Wu, Priya DasSarma, Shiladitya DasSarma
2008 Genomics  
However, after a wait of nearly 8 years, the paper by Pfeiffer et al. reporting the genome sequence of R-1 published in a recent issue of Genomics [18] is, unfortunately, extremely disappointing because  ...  Whether that is a result of evolution inside or outside a laboratory setting is unknown, but it is certainly not a result of misassembly of the Halobacterium sp. strain NRC-1 genome sequence.  ... 
doi:10.1016/j.ygeno.2008.04.005 pmid:18538726 fatcat:kgiqf54pcfe4vh4jp7bhutsngi

Coding Sequences: A History of Sequence Comparison Algorithms as a Scientific Instrument

Hallam Stevens
2011 Perspectives on Science  
By treating this software as a kind of scientiªc instrument used to examine sets of biological objects, the paper shows how algorithms have been used as different sorts of tools and appropriated for different  ...  Sequence comparison algorithms are sophisticated pieces of software that compare and match identical or similar regions of DNA, RNA, or protein sequence.  ...  Those interested in studying sequence no longer had to conªne themselves to problems of molecular evolution-what can 278 Coding sequences 28.  ... 
doi:10.1162/posc_a_00042 fatcat:wogni66rd5a5pdwke6fxtjixri

The "Sequencing" Fallacy

Thomas Carothers
2007 Journal of Democracy  
In the second half of the 1990s, a counterreaction emerged to the heady enthusiasm about democracy and democracy promotion that flourished during the peak years of democracy's "third wave" in the late  ...  , these different accounts coalesced around a central argument that appealed to what might be called the need for democratic sequencing.  ...  Don't Wait for the Rule of Law The idea of sequencing rests on a mistaken two-part premise: that a significant number of autocrats can and will act as generators of rule-oflaw development and state-building  ... 
doi:10.1353/jod.2007.0002 fatcat:nzirxm6fbncahnw3rvoxphqapa

The Sequencing "Fallacy"

Edward D. Mansfield, Jack L. Snyder
2007 Journal of Democracy  
In the second half of the 1990s, a counterreaction emerged to the heady enthusiasm about democracy and democracy promotion that flourished during the peak years of democracy's "third wave" in the late  ...  , these different accounts coalesced around a central argument that appealed to what might be called the need for democratic sequencing.  ...  Don't Wait for the Rule of Law The idea of sequencing rests on a mistaken two-part premise: that a significant number of autocrats can and will act as generators of rule-oflaw development and state-building  ... 
doi:10.1353/jod.2007.0047 fatcat:6ytt6nyfefhbtkgpnp7dkvbeum

Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution

Rick Durrett, Deena Schmidt
2008 Genetics  
In particular, we examine the waiting time for a pair of mutations, the first of which inactivates an existing transcription factor binding site and the second of which creates a new one.  ...  Results of Nowak and collaborators concerning the onset of cancer due to the inactivation of tumor suppressor genes give the distribution of the time until some individual in a population has experienced  ...  Both authors were partially supported by a National Science Foundation/National Institutes of General Medical Sciences grant (DMS 0201037).  ... 
doi:10.1534/genetics.107.082610 pmid:18791261 pmcid:PMC2581952 fatcat:lo6fcm2s4jc7lgyumuq4y5hj5i

Whole Genome Sequencing [chapter]

Joergen Schlundt
2019 Encyclopedia of Gerontology and Population Aging  
The rapid development of technologies to sequences DNA and RNA is bringing down the cost of genomic sequencing and at the same time increasing the accuracy of the outcome.  ...  But it does not stop there: After initial studies found that you can change the average weight of groups of mice by changing their gut microorganisms, a number of studies have looked further into this  ... 
doi:10.1007/978-3-319-69892-2_943-1 fatcat:xswwsp6kdbh6bndy65zfgrfabm

Tool-path problem in direct energy deposition metal-additive manufacturing: sequence strategy generation

M. Murua, A. Suarez, D. Galar, R. Santana
2020 IEEE Access  
The tool-path problem has been extensively studied in manufacturing technologies, as it has a considerable impact on production time.  ...  Additive manufacturing is one of these technologies; it takes time to fabricate parts, so the selection of optimal tool-paths is critical.  ...  the objectives of distance and waiting time.  ... 
doi:10.1109/access.2020.2994748 fatcat:dvwarqbfgjbw5pw42dhb6wrvka

Learning Sequences: Their Existence, Effect, and Evolution

Christopher B. Bingham, Jason P. Davis
2012 Academy of Management Journal  
Our core contribution is an emergent theoretical framework that develops the concept of learning sequences. We find that learning sequences exist and are influenced by initial conditions.  ...  We also find that learning sequences evolve in fundamentally distinct ways over time and with repeated use.  ...  Davis (jasond@mit.edu) is an assistant professor of strategy at the Sloan School of Management at the Massachusetts Institute of Technology.  ... 
doi:10.5465/amj.2009.0331 fatcat:m44ci2xhjfbzzhg7of43z2rnyy

A Review of Prediction and Optimization for Sequence-Driven Scheduling in Job Shop Flexible Manufacturing Systems

Prita Meilanitasari, Seung-Jun Shin
2021 Processes  
current challenges and future directions to promote the feasibility and usability of the relevant research.  ...  Current challenges are summarized as follows: less consideration of uncertainty factors causes a gap between the reality and the derived schedules; the use of stationary dispatching rules is limited to  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/pr9081391 fatcat:r3p5bzdlvnf2lnm6ymxq3vjcsm

Reconstructing the Dynamics of HIV Evolution within Hosts from Serial Deep Sequence Data

Art F. Y. Poon, Luke C. Swenson, Evelien M. Bunnik, Diana Edo-Matas, Hanneke Schuitemaker, Angélique B. van 't Wout, P. Richard Harrigan, Christophe Fraser
2012 PLoS Computational Biology  
We used the known dates of sampling to directly estimate rates of evolution and to map ancestral mutations to a reconstructed timeline in units of days.  ...  We observed highly patient-specific distributions and time-scales of mutation accumulation, implying that the role of a fitness valley is contingent on the genotype of the transmitted variant.  ...  Wrote the paper: AFYP.  ... 
doi:10.1371/journal.pcbi.1002753 pmid:23133358 pmcid:PMC3486858 fatcat:4a2qeabbabf3jhp36so7g6uvlq

Comparisons of bi-objective genetic algorithms for hybrid flowshop scheduling with sequence-dependent setup times

S.M. Mousavi, M. Zandieh, M. Amiri
2012 International Journal of Production Research  
A B S T R A C T Multi-criteria sequence dependent setup times scheduling problems exist almost everywhere in real modern manufacturing world environments.  ...  Accordingly, by recognizing the research gaps, a large number of recommendations for further study have been proposed.  ...  effects of sequence-dependent setup times and limited waiting time.  ... 
doi:10.1080/00207543.2010.543178 fatcat:ch5qv36nyjedvojvytrmjh6wpu

Thousands of human sequences provide deep insight into single genomes

Deanna M. Church
2020 Nature  
that promote the process.  ...  The larger sample size means that gene length is less of a problem in the gnomAD analysis, but even so, the authors could not definitively assess pLoF frequency in the 30% of genes that were expected to  ... 
doi:10.1038/d41586-020-01485-4 pmid:32461645 fatcat:jtendlcxcvhtfe4q7mux4rxgaq
« Previous Showing results 1 — 15 out of 45,094 results