Answers.Body: <p>There are very many examples of Markov chains in the life sciences. They are foundational models for many applications:</p>
  <ul>
  <li>dynamic programming (<a href="https://ics.uci.edu/%7Exhx/courses/CS284A-F08/lectures/CS284A_BLAST.pdf" rel="nofollow noreferrer">sequence alignment</a>)</li>
  <li>Hidden Markov Models (<a href="https://noble.gs.washington.edu/proj/segway/manuscript/description.pdf" rel="nofollow noreferrer">genomic segmentation</a>, <a href="http://hmmer.org/" rel="nofollow noreferrer">motif finding</a>, or <a href="http://hmmer.org/" rel="nofollow noreferrer">alignment</a>)</li>
  <li>population clustering (<a href="https://web.stanford.edu/group/pritchardlab/publications/pdfs/PritchardEtAl00.pdf" rel="nofollow noreferrer">STRUCTURE</a>)</li>
  <li>phylogenetics MCMC (<a href="https://beast.community/" rel="nofollow noreferrer">BEAST</a>)</li>
  <li><a href="https://academic.oup.com/bib/article/8/2/109/221633?login=false" rel="nofollow noreferrer">MCMC is rife</a> throughout bioinformatics in general</li>
  </ul>
  <p>There are a huge number of publications using Markov Chain based methods in the life sciences, including in recent years, see for example the results of this pubmed search:</p>
  <p><a href="https://i.sstatic.net/JRdS9c2C.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/JRdS9c2C.png" alt="PubMed screenshot of markov chain search" /></a></p>
  <p>It might help to get more information about what you mean when you write about Markov Chains, because clearly 2 different answerers have come up with very different answers! Is there more info on what your students are interested in?</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-12-13T17:03:31.390Z
Answers.LastActivityDate: 2024-12-13T17:03:31.390Z
Answers.UserDisplayName: Maximilian Press
Body: <p>I am a mathematician setting up an Research Experience for Undergrads (REU) course for next semester. Students have background in modeling with ordinary differential equations (population growth models, predator-prey relations, neuron firing models; stability analysis of linear and nonlinear systems, stable limit cycles). They have expressed interest in learning about Markov Chains, so I'm currently preparing some material on probability and textbook applications of Markov Chains techniques in the life sciences. I'm having more trouble identifying recent-ish peer reviewed important publications where Markov Chain techniques are used in a substantial way for important questions in biology or medicine. Any field of bio/med works, I just want to come up with a few recent (i.e. last decade), impactful examples of how these techniques are relevant.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-12-13T18:34:19.703Z
Comments.Text: @M__ if you have a really coherent writeup on BEAST to help OP I do think that would be valuable, given my treatment was extremely shallow and wide rather than narrow and deep. My main concern is that I think it's a mischaracterization to say that MCs are not used much in biology, so I'm trying to make sure that we have the examples to allow OP to explore if they so desire!
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-12-13T20:03:52.870Z
Comments.Text: @MaximilianPress :-( it's the end of the week and I'm exhausted. I'll see if I regain any energy next week.
Comments.UserDisplayName: M__
Tags: <hidden-markov-models>
Title: request for peer reviewed articles using Markov Chains
ThreadText: # request for peer reviewed articles using Markov Chains
  
  (Asked by: username_0 on 2024-12-11)
  
  I am a mathematician setting up an Research Experience for Undergrads (REU) course for next semester. Students have background in modeling with ordinary differential equations (population growth models, predator-prey relations, neuron firing models; stability analysis of linear and nonlinear systems, stable limit cycles). They have expressed interest in learning about Markov Chains, so I'm currently preparing some material on probability and textbook applications of Markov Chains techniques in the life sciences. I'm having more trouble identifying recent-ish peer reviewed important publications where Markov Chain techniques are used in a substantial way for important questions in biology or medicine. Any field of bio/med works, I just want to come up with a few recent (i.e. last decade), impactful examples of how these techniques are relevant.
  
  **Tags:** hidden-markov-models
  
  > **Comments:**
  > **username_1**: @username_2 if you have a really coherent writeup on BEAST to help OP I do think that would be valuable, given my treatment was extremely shallow and wide rather than narrow and deep. My main concern is that I think it's a mischaracterization to say that MCs are not used much in biology, so I'm trying to make sure that we have the examples to allow OP to explore if they so desire!  
  > **username_2**: @username_1 :-( it's the end of the week and I'm exhausted. I'll see if I regain any energy next week.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2024-12-13. Score: 2
  
  There are very many examples of Markov chains in the life sciences. They are foundational models for many applications:
  
  * dynamic programming ([sequence alignment](https://ics.uci.edu/%7Exhx/courses/CS284A-F08/lectures/CS284A_BLAST.pdf))
  * Hidden Markov Models ([genomic segmentation](https://noble.gs.washington.edu/proj/segway/manuscript/description.pdf), [motif finding](http://hmmer.org/), or [alignment](http://hmmer.org/))
  * population clustering ([STRUCTURE](https://web.stanford.edu/group/pritchardlab/publications/pdfs/PritchardEtAl00.pdf))
  * phylogenetics MCMC ([BEAST](https://beast.community/))
  * [MCMC is rife](https://academic.oup.com/bib/article/8/2/109/221633?login=false) throughout bioinformatics in general
  
  There are a huge number of publications using Markov Chain based methods in the life sciences, including in recent years, see for example the results of this pubmed search:
  
  [![PubMed screenshot of markov chain search](https://i.sstatic.net/JRdS9c2C.png)](https://i.sstatic.net/JRdS9c2C.png)
  
  It might help to get more information about what you mean when you write about Markov Chains, because clearly 2 different answerers have come up with very different answers! Is there more info on what your students are interested in?
  
  
  ---
  
  