Reading and Resources - Computational Biology </head> <body bgcolor="#B2DBFC"> <table> <tr style="text-align: center"><td><a href="index.html"><img src="images/logo2.png" style="border:none" alt="logo"></a></td> <td> <h3>Computational Molecular Biology, aka Algorithms for Computational Biology</h3> <a href="index.html">Home</a> * <a href="syllabus.html">Syllabus</a> * <a href="course-information.html">Course Information</a> * <a href="reading-and-resources.html">Readings and Resources</a> * <a href="office-hours.html">Lecturers,TAs, office hours</a> * <a href="homework-submission.html">Homework Submission</a> * <a href="collaboration.html">Collaboration Policy</a> </td> </tr> </table> <h1>Reading and other resources</h1> <h2>General approach</h2> <p>This is a graduate course that is intended to accommodate students with diverse backgrounds in computer science and biology. Therefore, I expect you to be resourceful about finding the reading materials that are most appropriate for you. Do not just sit and wait for me to tell you what to read - if there is a term or concept you don't understand or want to understand better, try searching on <a href="google.com">Google</a>, going to the <a href="http://www.library.wustl.edu/">library</a> to get a reference book, or looking up a review article in <a href="http://www4.ncbi.nlm.nih.gov/PubMed">Pubmed</a>. I will do my best to provide you with starting points and key terms/concepts that will allow you to look things up quickly.</p> <h2>Textbook for selected topics</h2> <p>Parts of the course and the outside reading are based on the text: </p> <p><i><a href="http://www.genetics.wustl.edu/eddy/publications/cupbook.html">Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids</a></i> by Durbin, Eddy, Krogh, and Mitchison is a required text. It is available at Amazon and other fine websites- it has not been ordered specifically by the Washington University bookstore.</p> <p>A reference that may occasionally be useful is <i>Genomes</i>, 2<sup>nd</sup> Edition, By T.A. Brown is a useful reference. It is available <a href="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=genomes.TOC&depth=2">online</a>.</p> <p>Homeworks will require programming in C, on UNIX systems. A large number of books on C and UNIX are available. Find ones that suit your style. For short, clear, and authoritative, I recommend: </p> <p><a href="http://www.amazon.com/exec/obidos/tg/detail/-/0131103628/qid=1029943361/sr=8-1/ref=sr_8_1/104-1498855-9214357?s=books&n=507846"><em>The C Programming Language</em></a> </p> <p style='margin-left:.5in'>B.W. Kernighan and D.M. Ritchie. 1988. </p> <p><a href="http://www.amazon.com/exec/obidos/tg/detail/-/013937468X/qid=1029943193/sr=8-1/ref=sr_8_1/104-1498855-9214357?s=books&n=507846"><em>Unix C Shell Field Guide</em> </a></p> <p style='margin-left:.5in'>G. Anderson and P. Anderson. 1986.</p> <h2>Reference for general biology background</h2> <p>I strongly suggest that, if your background in molecular biology is limited, you purchase or otherwise get access to a serious introductory textbook on molecular biology or cell and molecular biology. There are a number of good ones around, and it doesn't much matter which one you use --- they all contain pretty much the same basic facts. I will not refer to these explicitly in lecture, but I suggest you read a few choice chapters. For example, I use</p> <p><a href="http://www.whfreeman.com/lodish/">Molecular Cell Biology, by Harvey Lodish, et al., 4<sup>th</sup> Edition. New York: W.H. Freeman and Company.</a></p> <p><b><a href="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowSection&rid=mcb">NEW</b> The full text is available through PubMed!</a></b></p> <p>This book is expensive but everyone interested enough to take this course should own this book or one like it. There is a good supplementary <a href="http://www.whfreeman.com/lodish/">website for the book</a>, but looking at the site is no substitute for owning the book. I would particularly recommend the following chapters:</p> <ul> <li>Chapter 1: The Dynamic Cell</li> <li>Chapter 4: Nucleic Acids, the Genetic Cod, and the Synthesis of Macromolecules</li> <li>Chapter 7: Recombinant DNA and Genomics</li> <li>Chapter 9: Molecular Structure of Genes and Chromosomes</li> <li>Chapter 11: RNA Processing, Nuclear Transport, and Transcriptional Control</li> </ul> <p>Also of interest, though less central to the lecture topics, are:</p> <ul> <li>Chapter 6: Manipulating Cells and Viruses in Culture</li> <li>Chapter 8: Genetic Analysis in Cell Biology</li> <li>Chapter 10: Regulation of Transcription Initiation</li> </ul> <h3>Online resources for biology background</h3> <p>There are vast treasure troves of biology information, including complete courses, available for free on the web. For example, I just typed "molecular biology textbooks" into Google and the top hit was <a href="http://www.cellbio.com/courses.html">this valuable page</a>. I have checked out one site linked from it, which I can recommend: <a href="http://web.mit.edu/esgbio/www/">the MIT online biology textbook.</a> However, I still think it is worth having your own hardcopy molecular biology text, as it will provide lots more information and probably better indexing.</p> <h2>Journal papers</h2> <h3>Papers with direct relation to lectures</h3> <p>A number of lectures will be based on specific journal papers. Here is a list that will probably grow as the semester progresses, with links to online copies where possible.</p> <p><a href="Literature/PhredI.pdf">Ewing, B, Hillier, L, Wendl, MC, & Green, P (1998). Base-calling of automated sequencer traces using Phred. I. Accuracy Assessment. Genome Research, 8, 175-185.</a></p> <p><a href="Literature/PhredII.pdf">Ewing, B & Green, P (1998). Base-calling of automated sequencer traces using Phred. II. Error Probabilities. Genome Research, 8, 186-194.</a></p> <p><a href="Literature/Burge%20Thesis.pdf">Burge, C. 1997. Identification of Genes in Human Genomic DNA. Stanford University, Stanford, CA.</a><br /> (This is actually a dissertation but it is the best available source on HMM Gene Finding.)</p> <h2>Online journals</h2> <p>Many journals provide all their articles on line. Some are free to anyone and many others are free if you access them through the <a href="http://library.wustl.edu/fulltext/ej.html">library's Full Text Sources list</a>. One of the most important for this class is <a href="http://www.genome.org/contents-by-date.0.shtml">Genome Research</a> -- It is well worth browsing.</p> </body> </html>