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  • microarray data analysis
    30 2010 Short courses on microarray March 12 2007 This is a collection of papers so far 2398 papers excluding the unpublished preprints with emphasis on analysis of microarray a k a DNA chip expression data Papers on microarray technology itself are not usually in Also these topics are not really covered using microarray data to infer regulatory networks using microarray for promoter analysis using microarray to detect DNA copy numbers using microarray for genotyping Gradually I will add papers on gene sets which is a system biology topics and RNA seq which is related to NGS review networks database application affymetrix protein General reviews on microarray may be included Analysis of gene network only some These papers are on microarray related databases Papers on results of microarray expriments only some Affymetrix oligo chips only Protein chips This page was selected as a webpick of the day April 20 2000 by BioMedNet Online Magazine HMS Beagle SEE ALSO http en wikipedia org wiki DNA microarray wikipedia entry of microarray http garfield library upenn edu histcomp index microarray html Science Citation analysis on microarray papers using the HISTCITE program http www camda duke edu CAMDA Critical Assessment of Microarray Data Analysis

    Original URL path: http://linkage.rockefeller.edu/microarray/ (2012-11-26)
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  • DNA correlations: front page
    possibility of theoretical research based on combinatorix sic and the theory of numbers I have a feeling this can be done What do you think George Gamow 1904 1968 in a letter to Watson and Crick 1953 From the point of view of the theory of information the works of Shakespeare with the same number of letters and signs aligned at random by a monkey would have the same value It is this lack of definition of the value of information that makes it difficult to use in biology What could be considered as objective in the Shakespearean information that would distinguish it from the monkey s information Essentially the transmissibility The value of influence therefore of evolution Jacques Monod 1910 1976 notesbook 1959 Whereas ordinary mortals are content to mimic others creative geniuses are condemned to plagiarize themselves is my shorter albeit inarticulate version of what Van Veen said in Ada by Vladimir Nobokov Indeed it seems that vaunted geniuses seldom invented more than one modus operandi during their lifetimes and even civilization has largely been dependent upon plagiarizing a small number of creative works e g the multitudes of Gothic churches can be viewed as pan European plagiarism of the abbey church of St Denis and or the cathedral at Sens This is not surprising for new genes sensu stricto has seldom been invented Evolution rather relies on palgiarizing an old and tested theme the mechanism of evolution by gene duplication this principle of repetitious recurrence pervades both the construction of coding sequences in the genome which can be regarded as being representative of nature and musical composition which can be regarded as the most abstract and therefore the most intellectual expression of nature Susumu Ohno 1928 2000 and Midori Ohno Immunogenetics 24 71 78 1986 Searching for

    Original URL path: http://linkage.rockefeller.edu/dnacorr/ (2012-11-26)
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  • Entrez-PubMed
    names as smith jc Initials are optional Enter journal titles in full or as MEDLINE abbreviations Use the Journals Database to find journal titles PubMed a service of the National Library of Medicine provides access to over 12 million MEDLINE citations back to the mid 1960 s and additional life science journals PubMed includes links to many sites providing full text articles and other related resources Bookshelf Additions New PubMed

    Original URL path: http://linkage.rockefeller.edu/search_entrez.html (2012-11-26)
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  • GUI for linkage
    Matise J Ott Using web browsers as the graphical user interface for linkage analysis abstract Am J Hum Genet supplement to vol 59 page A307 1996 for beta testers How do I use it Fill out information on the first page then click continue to page 2 If you want to prepare yourself with the questions ahead check the page a summary of all questions to be asked Fill out information on the second page then click continue to page 3 Fill out information on the third page then click the show the datafile There are two options for displaying the datafile either see the datafile with comments or without You can switch between these two options by clicking back on your web browser change the choice then click show the datafile again When you are finished click the File Save As on your web browser type in the name of the file to be saved You are done For users who know PREPLINK well For binary factor locus type we restrict the number of binary factors to be equal to the number of alleles You can input multiple lines in one window but lines are separated by semicolons For

    Original URL path: http://linkage.rockefeller.edu/gui/webpreplink.html (2012-11-26)
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  • fastlink readme: optimize for maxhap
    program ofm c can be modified to handle it by changing the constant INFO LINE KEY near the beginning of ofm c OFM does not require that the locus file be called datafile dat If the lcp produced script includes multiple runs OFM assumes that they are all runs of the same program but the alleles used in each run may vary If the alleles vary from run to run then OFM figures out the allele product for each run and uses the largest product as the optimized value of maxhap For now OFM is specific to UNIX To compile on AIX IBM s version of UNIX add the flags D POSIX SOURCE D XOPEN SOURCE to EXTRAFLAGS in Makefile USAGE Before beginning a run on a data set move to the directory where the data pedigree file and data file and script produced by lcp reside Once there execute the program with the following command line ofm target script source dir Makefile The arguments to this program are target the desired target to remake it must be one of the valid targets specified in the program or void which will NOT remake any target Valid targets for sequential FASTLINK include installfast installslow ilink slowilink linkmap slowlinkmap mlink slowmlink ofm can also be used with the targets for parallel FASTLINK see README parallel script is the script file which will perform the analysis on the data you wish to optimize your code for source dir the directory where the source code is located Makefile the name of the Makefile which should be in the source dir If either Makefile or source dir are not specified on the command line compiled in constants will be used If these constants do not represent files available then the user will be notified of

    Original URL path: http://linkage.rockefeller.edu/soft/fastlink/fl_ofm.html (2012-11-26)
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  • Why Traverse the Pedigree
    The issue of loops is discussed in detail in the accompanying document Loops in FASTLINK The reason for the term traversal is that it is natural to update the conditional genotype probabilities for one family at a time This raises a major question when updating the conditional genotype probability for members of some nuclear family what should we condition on besides A nuclear family consists of two parents and all the children which they produced together Some geneticists use the term full sibship to mean the same thing as what I am calling nuclear family A valid traversal sequence is a sequence of visits to nuclear families done in such a way that Each nuclear family has one visit during which the genotype probabilities of one of its members are updated conditional on the genotypes of the other members of the nuclear family which have been in turn conditioned on other individuals and The nesting of the conditionals is such that at the last update the proband s genotype probabilities are updated indirectly conditional on the observed data for the rest of the pedigree and Elston and Stewart made the fundamental observation that under some conditions to be specified below it is sufficient to condition the update of a given nuclear family on all of its descendant nuclear families When arriving at a new nuclear family the probabilities of the parent that connects up the tree are updated conditional on the spouse the children and The children already are conditioned on any descendants further down in the tree Such an upward traversal sequence will work if There is exactly one nuclear family T at the top generation Every other nuclear family has exactly one parent who is a direct descendant of the two parents in family T and one parent

    Original URL path: http://linkage.rockefeller.edu/soft/traverse/node2.html (2012-11-26)
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  • Nuclear Family Graph
    the LINKAGE algorithm allow for some arbitrary orderings in the nuclear family visits It is possible to correctly implement the Elston Stewart algorithm to visit the nuclear families in orders which are absolutely impossible with LINKAGE no matter how LINKAGE makes its free choices For example in a pedigree that satisfies the 4 conditions above and has multiple nuclear families at each generation but the topmost the generation by generation traversal sequences proposed above as possible for the Elston Stewart algorithm are not possible in LINKAGE This will be illustrated with an example below Since I am trained in graph algorithms I prefer to think of the pedigree with the following auxiliary graph which I call the nuclear family graph First let s assume that there are no multiple marriages In this graph each nuclear family becomes a vertex and two vertices are adjacent i e connected by an undirected edge if their nuclear families share an individual which is a parent in one family and a child in the other The case of multiple marriages is subtle We call a nuclear family a multiple marriage if one of its parents parented offspring with multiple distinct mates both of whom

    Original URL path: http://linkage.rockefeller.edu/soft/traverse/node3.html (2012-11-26)
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  • Edge Labels
    edge w r t x and a down edge w r t y if the shared individual is a parent in nuclear family x and a child in nuclear family y In the case of f multiple marriages the edges between them are down edges w r t the first f multiple marriage for a given individual and up edges w r t to all the other f multiple marriages

    Original URL path: http://linkage.rockefeller.edu/soft/traverse/node4.html (2012-11-26)
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