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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/32465?offset=10</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44734/data-visualization-in-bioinformatics-useful-and-eye-catching-plots-for-data-analysis</guid>
	<pubDate>Sat, 14 Dec 2024 12:41:53 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44734/data-visualization-in-bioinformatics-useful-and-eye-catching-plots-for-data-analysis</link>
	<title><![CDATA[Data Visualization in Bioinformatics: Useful and Eye-Catching Plots for Data Analysis]]></title>
	<description><![CDATA[<p>Data visualization is a cornerstone of bioinformatics, enabling researchers to interpret complex datasets effectively. With a plethora of data types&mdash;genomic sequences, expression profiles, protein interactions, and more&mdash;the right visualizations can make or break an analysis. This blog highlights some of the most useful and visually compelling plots for bioinformatics data analysis, along with tools to create them.</p><h4><strong>1. Heatmaps: Exploring Patterns in High-Dimensional Data</strong></h4><p>Heatmaps are a go-to visualization for representing high-dimensional datasets, such as gene expression or metabolomics data. They use color gradients to display data intensity, making patterns and clusters easily detectable.</p><ul>
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<p><strong>Applications</strong>: Gene expression analysis, pathway enrichment, methylation studies.</p>
</li>
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<p><strong>Tools</strong>: Seaborn (Python), ComplexHeatmap (R), Morpheus (web-based).</p>
</li>
</ul><p><strong>Tip</strong>: Add dendrograms to visualize clustering of rows and columns for hierarchical relationships.</p><h4><strong>2. Volcano Plots: Highlighting Differential Features</strong></h4><p>Volcano plots are indispensable for identifying significantly differentially expressed genes or proteins. They plot the log2 fold change against &ndash;log10(p-value), making it easy to spot statistically significant changes.</p><ul>
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<p><strong>Applications</strong>: RNA-seq, proteomics, and metabolomics.</p>
</li>
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<p><strong>Tools</strong>: ggplot2 (R), EnhancedVolcano (R), Plotly (Python).</p>
</li>
</ul><p><strong>Tip</strong>: Use color to highlight significant features and label key genes or proteins.</p><h4><strong>3. PCA Plots: Reducing Complexity with Principal Component Analysis</strong></h4><p>Principal Component Analysis (PCA) plots are used to reduce dimensionality and uncover trends or clusters in data. They provide insights into sample variability and grouping.</p><ul>
<li>
<p><strong>Applications</strong>: Transcriptomics, metabolomics, microbiome studies.</p>
</li>
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<p><strong>Tools</strong>: scikit-learn + Matplotlib (Python), prcomp (R), ClustVis (web-based).</p>
</li>
</ul><p><strong>Tip</strong>: Annotate clusters with metadata to enhance interpretability.</p><h4><strong>4. Manhattan Plots: Genome-Wide Association Studies</strong></h4><p>Manhattan plots visualize p-values across the genome, making it easy to identify significant associations in genome-wide studies. They resemble city skylines, with the highest peaks indicating loci of interest.</p><ul>
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<p><strong>Applications</strong>: GWAS, QTL mapping.</p>
</li>
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<p><strong>Tools</strong>: qqman (R), Matplotlib (Python).</p>
</li>
</ul><p><strong>Tip</strong>: Use alternating colors for chromosomes and highlight significant SNPs for clarity.</p><h4><strong>5. Circular Plots (Circos): Visualizing Genomic Relationships</strong></h4><p>Circular plots are ideal for visualizing relationships across the genome, such as structural variations, gene duplications, or synteny.</p><ul>
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<p><strong>Applications</strong>: Comparative genomics, structural variation studies.</p>
</li>
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<p><strong>Tools</strong>: Circos (standalone), Rcircos (R), pyCircos (Python).</p>
</li>
</ul><p><strong>Tip</strong>: Keep the plot clean and avoid overcrowding to maintain readability.</p><h4><strong>6. Sankey Diagrams: Tracking Data Flows</strong></h4><p>Sankey diagrams visualize flows or relationships between categories, often used to track changes in gene expression or pathway enrichment across conditions.</p><ul>
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<p><strong>Applications</strong>: Pathway analysis, gene set enrichment analysis.</p>
</li>
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<p><strong>Tools</strong>: Plotly (Python), networkD3 (R).</p>
</li>
</ul><p><strong>Tip</strong>: Use gradients or distinct colors to highlight key transitions.</p><h4><strong>7. Network Graphs: Mapping Interactions</strong></h4><p>Network graphs represent relationships between entities, such as protein-protein interactions or gene regulatory networks. Nodes represent entities, and edges represent relationships.</p><ul>
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<p><strong>Applications</strong>: Systems biology, interactomics.</p>
</li>
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<p><strong>Tools</strong>: Cytoscape (standalone), igraph (R), NetworkX (Python).</p>
</li>
</ul><p><strong>Tip</strong>: Use edge thickness or node size to represent interaction strength or centrality.</p><h4><strong>8. Violin Plots: Visualizing Data Distribution</strong></h4><p>Violin plots combine a boxplot with a density plot, showing the distribution and variability of data.</p><ul>
<li>
<p><strong>Applications</strong>: Single-cell RNA-seq, quantitative trait analysis.</p>
</li>
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<p><strong>Tools</strong>: Seaborn (Python), ggplot2 (R).</p>
</li>
</ul><p><strong>Tip</strong>: Split violins by groups for side-by-side comparisons.</p><h4><strong>9. Time-Series Plots: Monitoring Changes Over Time</strong></h4><p>Time-series plots display changes in variables across time points, useful for tracking gene expression dynamics or metabolic fluxes.</p><ul>
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<p><strong>Applications</strong>: Time-course experiments, cell cycle studies.</p>
</li>
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<p><strong>Tools</strong>: Matplotlib (Python), ggplot2 (R).</p>
</li>
</ul><p><strong>Tip</strong>: Smooth the data to highlight trends while avoiding overfitting.</p><h4><strong>10. Genome Tracks: Visualizing Genomic Features</strong></h4><p>Genome tracks display multiple layers of genomic data, such as gene annotations, sequencing coverage, and epigenetic marks.</p><ul>
<li>
<p><strong>Applications</strong>: ChIP-seq, ATAC-seq, whole-genome sequencing.</p>
</li>
<li>
<p><strong>Tools</strong>: IGV (standalone), pyGenomeTracks (Python).</p>
</li>
</ul><p><strong>Tip</strong>: Stack related tracks for direct comparisons.</p><h4><strong>11. UpSet Plots: Visualizing Set Intersections</strong></h4><p>UpSet plots are a powerful alternative to Venn diagrams for visualizing intersections between multiple datasets.</p><ul>
<li>
<p><strong>Applications</strong>: Overlap analysis for gene sets, pathways, or variants.</p>
</li>
<li>
<p><strong>Tools</strong>: UpSetR (R), ComplexUpset (Python).</p>
</li>
</ul><p><strong>Tip</strong>: Use bar plots to represent the size of each intersection for added clarity.</p><h4><strong>12. Ridge Plots: Comparing Distributions</strong></h4><p>Ridge plots visualize the distributions of multiple datasets, stacked for easy comparison.</p><ul>
<li>
<p><strong>Applications</strong>: Transcriptomics, single-cell RNA-seq.</p>
</li>
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<p><strong>Tools</strong>: ggridges (R), Matplotlib (Python).</p>
</li>
</ul><p><strong>Tip</strong>: Use transparency and consistent scaling for better readability.</p><h4><strong>13. Chord Diagrams: Visualizing Connections Between Groups</strong></h4><p>Chord diagrams illustrate relationships between categories, such as shared genes between pathways or overlaps in regulatory elements.</p><ul>
<li>
<p><strong>Applications</strong>: Pathway overlap, synteny, co-expression networks.</p>
</li>
<li>
<p><strong>Tools</strong>: Circlize (R), Holoviews (Python).</p>
</li>
</ul><p><strong>Tip</strong>: Use distinct colors for each group to emphasize relationships.</p><h4><strong>14. Treemaps: Hierarchical Data Representation</strong></h4><p>Treemaps visualize hierarchical data as nested rectangles, with area proportional to data size.</p><ul>
<li>
<p><strong>Applications</strong>: Ontology enrichment, pathway analysis.</p>
</li>
<li>
<p><strong>Tools</strong>: Treemapify (R), Plotly (Python).</p>
</li>
</ul><p><strong>Tip</strong>: Use colors to represent additional variables, like significance or enrichment scores.</p><h4><strong>15. T-SNE/UMAP Plots: Dimensionality Reduction for Clustering</strong></h4><p>T-SNE and UMAP plots are great for visualizing high-dimensional data in two dimensions while preserving local or global structure.</p><ul>
<li>
<p><strong>Applications</strong>: Single-cell transcriptomics, clustering analyses.</p>
</li>
<li>
<p><strong>Tools</strong>: scikit-learn (Python), Seurat (R).</p>
</li>
</ul><p><strong>Tip</strong>: Combine with metadata annotations for better cluster interpretation.</p><h4><strong>Bringing It All Together</strong></h4><p>The choice of visualization can significantly impact the insights gained from bioinformatics data. By selecting plots tailored to your data type and analysis goals, you can effectively communicate your findings and make your research more impactful. Whether you&rsquo;re a seasoned bioinformatician or a beginner, mastering these visualizations will elevate your analyses and presentations.</p>]]></description>
	<dc:creator>LEGE</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/10664/dna-replication-process-3d-animation</guid>
	<pubDate>Sat, 10 May 2014 04:41:22 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/10664/dna-replication-process-3d-animation</link>
	<title><![CDATA[DNA Replication Process [3D Animation]]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/27TxKoFU2Nw" frameborder="0" allowfullscreen></iframe>See an organised list of all the animations: http://doctorprodigious.wordpress.com/hd-animations/]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/14011/dynamic-chromosome-breakpoints</guid>
	<pubDate>Wed, 13 Aug 2014 18:38:10 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/14011/dynamic-chromosome-breakpoints</link>
	<title><![CDATA[Dynamic chromosome breakpoints !!!]]></title>
	<description><![CDATA[<p>Cell division involves the distribution of identical genetic material, DNA, to two daughters&rsquo; cells. During this process, duplicated deoxyribonucleic acid (DNA) goes through a condensation and decondensation process. This is followed by nuclear envelope dissolution, mitotic spindle assembly, migration of the sister chromatid pairs to the metaphase plate, division and segregation of identical sets of chromosomes into daughter nuclei and nuclear envelope reformation.</p><p>The vital metaphase stage of cell division, when the sister chromatids migrated to the centre and lined up in a row, and pulled apart using attached microtubules in such a way that half the DNA ends up in each daughter cell. However, before the mitotic spindle‐mediated movement gets start and pulled DNA apart, the chromosomes are free to undergo <strong>recombination </strong>which involves the exchange of genetic material either between multiple chromosomes or between different regions of the same chromosome.</p><p><img src="http://www.sciencelearn.org.nz/var/sciencelearn/storage/images/contexts/uniquely-me/sci-media/images/chromosomes-crossing-over/464438-1-eng-NZ/Chromosomes-crossing-over.jpg" alt="image" width="504" height="342" style="border: 0px; border: 0px;"></p><p>During recombination, the precise breakage of each strand, exchange between the strands, and sealing of the resulting recombined molecules happens. The &ldquo;<strong>chromosomal breakpoints</strong>&rdquo; refers to these places where they break. Mostly, this process occurs with a high degree of accuracy at high frequency in both eukaryotic and prokaryotic cells. But occasionally this &ldquo;break and sealing/ break and reattach&rdquo; process goes wrong and the reattachment happens in the wrong place which usually create disaster (with few exceptions).These chromosome disaster or abnormalities involve the gain, loss or rearrangement of visible amounts of genetic material during cell division. These abnormalities are of two type, the first one is numerical abnormalities &nbsp;where severe disorders are caused by the loss or gain of whole chromosomes, which affect the copy number of hundreds or even thousands of genes. The second are structural abnormalities which can be unbalanced or balanced. The former are similar to numerical abnormalities in that genetic material is either gained or lost. The natural defects in chromosome segregation are linked to cancer and several genetic diseases (http://en.wikipedia.org/wiki/List_of_genetic_disorders). Therefore, the enzymes involved in regulating cell division are still the attractive drug targets for many diseases.</p><p>&nbsp;</p><p>&nbsp;</p><p><img src="http://upload.wikimedia.org/wikipedia/commons/4/4a/Chromosomal_translocations.svg" alt="image" width="424" height="331" style="border: 0px; border: 0px;"></p><p>&nbsp;</p><p>Apart from certain chromosome abnormalities, these &ldquo;crossing over&rdquo; of segments of maternal and paternal chromosomes to form hybrid chromosomes have some evolutionary importance and considered as a driver of genetic variation. Moreover, the chromosome breakage in evolution is considered to be non-random in nature(http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020014). In addition the study of breakpoint regions and non-breakpoint (stable) regions of chromosomes indicates both the regions evolved in distinctly different ways ( http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675965/). These breakage may lead to genetic diseases or participate to chromosomal rearranmgnets and contributed in development of new species.</p><p>I will try to explain the genome hotspots/Evolutionary Breakpoint Regions(EBRs)/fragile regions/weak fragments/&nbsp; in my next blog.</p><p><strong>Software for recombination detection:</strong></p><p><strong>RAT</strong> http://cbr.jic.ac.uk/dicks/software/RAT/</p><p><strong>Breakpointer</strong> https://github.com/ruping/Breakpointer</p><p><strong>DRP</strong> http://web.cbio.uct.ac.za/~darren/rdp.html</p><p><strong>RB-finder</strong> http://www.ncbi.nlm.nih.gov/pubmed/18707535</p><p><strong>LDhat2.0</strong> http://ldhat.sourceforge.net/LDhat2.0/instructions.shtml</p><p><strong>Reference:</strong></p><p>http://www.nature.com/scitable/topicpage/genetic-recombination-514#</p><p>Image: Wikipedia , sciencelearn.org.nz</p><p><strong>Recommended Articles:</strong></p><p>http://www.friendshipcircle.org/blog/2012/05/22/13-chromosomal-disorders-youve-never-heard-of/</p><p>http://web.udl.es/usuaris/e4650869/docencia/segoncicle/genclin98/recursos_classe_%28pdf%29/revisionsPDF/chromosyndromes.pdf</p><p>http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2775595/table/T2/</p><p>http://learn.genetics.utah.edu/content/disorders/chromosomal/</p><p>http://www.ncert.nic.in/html/learning_basket/biology/cc&amp;cd.pdf</p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/920/bioinformatics-algorithms</guid>
	<pubDate>Tue, 16 Jul 2013 03:35:15 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/920/bioinformatics-algorithms</link>
	<title><![CDATA[Bioinformatics Algorithms]]></title>
	<description><![CDATA[<p>An algorithm is a computable set of steps to achieve a desired result.</p><p>We use algorithms every day. For example, a recipe for baking a cake is an algorithm. Most programs, with the exception of some artificial intelligence applications, consist of algorithms. Inventing elegant algorithms -- algorithms that are simple and require the fewest steps possible -- is one of the principal challenges in programming. An algorithm is a description of a procedure which terminates with a result. In other words an algorithm is a set of instructions, sometimes called a procedure or a function, that is used to perform a certain task. This can be a simple process, such as adding two numbers together, or a complex function, such as adding effects to an image. For example, in order to sharpen a digital photo, the algorithm would need to process each pixel in the image and determine which ones to change and how much to change them in order to make the image look sharper.</p><p>In mathematics, computer science, and related subjects, an algorithm is an effective method for solving a problem using a finite sequence of instructions. Algorithms are used for calculation, data processing, and many other fields.<br />Each algorithm is a list of well-defined instructions for completing a task. Starting from an initial state, the instructions describe a computation that proceeds through a well-defined series of successive states, eventually terminating in a final ending state. The transition from one state to the next is not necessarily deterministic; some algorithms, known as randomized algorithms, incorporate randomness.</p><p><strong>History</strong></p><p>The origin of the term comes from the ancients. The concept becomes more precise with the use of variables in mathematics. Algorithm in the sense of what is now used by computers appeared as soon as first mechanical engines were invented.<br />The word algorithm comes from the name of the 9th century Persian Muslim mathematician Abu Abdullah Muhammad ibn Musa Al-Khwarizmi. The word algorism originally referred only to the rules of performing arithmetic using Hindu-Arabic numerals but evolved via European Latin translation of Al-Khwarizmi's name into algorithm by the 18th century. The use of the word evolved to include all definite procedures for solving problems or performing tasks.<br />The algorithm of Archimedes gives an approximation of the Pi number.<br />Eratosthenes has defined an algorithim for retrieving prime numbers.<br />Averro&egrave;s (1126-1198) was using algorithmic methods for calculations.<br />Adelard de Bath (12 th) introduces the algorismus term, from Al-Khwarizmi.<br />During the 1800's up to the mid-1900's:<br /><br />- George Boole (1847) has invented the binary algebra, the basis of computers. Actually he has unified logic and calculation in a common symbolism.<br /><br />- Gottlob Frege (1879) formula language's, that is a lingua characterica, a language written with special symbols, "for pure thought", that is free from rhetorical embellishments... constructed from specific symbols that are manipulated according to definite rules.<br /><br />- Giuseppe Peano (1888) It's The principles of arithmetic, presented by a new method was the first attempt at an axiomatization of mathematics in a symbolic language.<br /><br />- Alfred North Whitehead and Bertrand Russell in their Principia Mathematica (1910-1913) has further simplified and amplified the work of Frege.<br /><br />- Kurt Go&euml;del (1931) cites the paradox of the liar that completely reduces rules of recursion to numbers.<br /><br />The concept of algorithm was formalized in 1936 through Alan Turing's Turing machines and Alonzo Church's lambda calculus, which in turn formed the foundation of computer science.<br />Stephen C. Kleene (1943) defined his now-famous thesis known as the "Church-Turing Thesis". In this context:<br /><br />" Algorithmic theories... In setting up a complete algorithmic theory, what we do is to describe a procedure, performable for each set of values of the independent variables, which procedure necessarily terminates and in such manner that from the outcome we can read a definite answer, "yes" or "no," to the question, "is the predicate value true?"</p><p><strong>Classification</strong></p><p><strong>Classification by purpose</strong></p><p>Each algorithm has a goal, for example, the purpose of the Quick Sort algorithm is to sort data in ascending or descending order. But the number of goals is infinite, and we have to group them by kind of purposes:</p><p><strong>Classification by implementation</strong></p><p>An algorithm may be implemeted according to different basical principles.</p><ul>
<li>Recursive or iterative</li>
</ul><p>A recursive algorithm is one that calls itself repeatedly until a certain condition matches. It is a method common to functional programming.&nbsp;<br />Iterative algorithms use repetitive constructs like loops.<br />Some problems are better suited for one implementation or the other. For example, the towers of hanoi problem is well understood in recursive implementation. Every recursive version has an iterative equivalent iterative, and vice versa.</p><ul>
<li>Logical or procedural</li>
</ul><p>An algorithm may be viewed as controlled logical deduction.&nbsp;<br />A logic component expresses the axioms which may be used in the computation and a control component determines the way in which deduction is applied to the axioms.&nbsp;<br />This is the basis of the logic programming. In pure logic programming languages the control component is fixed and algorithms are specified by supplying only the logic component.</p><ul>
<li>Serial or parallel</li>
</ul><p>Algorithms are usually discussed with the assumption that computers execute one instruction of an algorithm at a time. This is a serial algorithm, as opposed to parallel algorithms, which take advantage of computer architectures to process several instructions at once. They divide the problem into sub-problems and pass them to several processors. Iterative algorithms are generally parallelizable. Sorting algorithms can be parallelized efficiently.</p><ul>
<li>Deterministic or non-deterministic</li>
</ul><p>Deterministic algorithms solve the problem with a predefined process whereas non-deterministic algorithm must perform guesses of best solution at each step through the use of heuristics.<br /><br /><strong>Classification by design paradigm</strong></p><p>A design paradigm is a domain in research or class of problems that requires a dedicated kind of algorithm:</p><ul>
<li>Divide and conquer</li>
</ul><p>A divide and conquer algorithm repeatedly reduces an instance of a problem to one or more smaller instances of the same problem (usually recursively), until the instances are small enough to solve easily. One such example of divide and conquer is merge sorting. Sorting can be done on each segment of data after dividing data into segments and sorting of entire data can be obtained in conquer phase by merging them.<br />The binary search algorithm is an example of a variant of divide and conquer called decrease and conquer algorithm, that solves an identical subproblem and uses the solution of this subproblem to solve the bigger problem.</p><ul>
<li>Dynamic programming</li>
</ul><p>The shortest path in a weighted graph can be found by using the shortest path to the goal from all adjacent vertices.&nbsp;<br />When the optimal solution to a problem can be constructed from optimal solutions to subproblems, using dynamic programming avoids recomputing solutions that have already been computed.&nbsp;<br />- The main difference with the "divide and conquer" approach is, subproblems are independent in divide and conquer, where as the overlap of subproblems occur in dynamic programming.&nbsp;<br />- Dynamic programming and memoization go together. The difference with straightforward recursion is in caching or memoization of recursive calls. Where subproblems are independent, this is useless. By using memoization or maintaining a table of subproblems already solved, dynamic programming reduces the exponential nature of many problems to polynomial complexity.</p><ul>
<li>The greedy method</li>
</ul><p>A greedy algorithm is similar to a dynamic programming algorithm, but the difference is that solutions to the subproblems do not have to be known at each stage. Instead a "greedy" choice can be made of what looks the best solution for the moment.&nbsp;<br />The most popular greedy algorithm is finding the minimal spanning tree as given by Kruskal.</p><ul>
<li>Linear programming</li>
</ul><p>The problem is expressed as a set of linear inequalities and then an attempt is made to maximize or minimize the inputs. This can solve many problems such as the maximum flow for directed graphs, notably by using the simplex algorithm.&nbsp;<br />A complex variant of linear programming is called integer programming, where the solution space is restricted to all integers.</p><ul>
<li>Reduction also called transform and conquer</li>
</ul><p>Solve a problem by transforming it into another problem. A simple example: finding the median in an unsorted list is first translating this problem into sorting problem and finding the middle element in sorted list. The main goal of reduction is finding the simplest transformation possible.</p><ul>
<li>Using graphs</li>
</ul><p>Many problems, such as playing chess, can be modeled as problems on graphs. A graph exploration algorithms are used.&nbsp;<br />This category also includes the search algorithms and backtracking.<br /><br /><strong>The probabilistic and heuristic paradigm</strong></p><ul>
<li>Probabilistic</li>
</ul><p>Those that make some choices randomly.</p><ul>
<li>Genetic</li>
</ul><p>Attempt to find solutions to problems by mimicking biological evolutionary processes, with a cycle of random mutations yielding successive generations of "solutions". Thus, they emulate reproduction and "survival of the fittest".</p><ul>
<li>Heuristic</li>
</ul><p>Whose general purpose is not to find an optimal solution, but an approximate solution where the time or resources to find a perfect solution are not practical.</p><p><strong>Classification by complexity</strong></p><p>Some algorithms complete in linear time, and some complete in exponential amount of time, and some never complete.</p><p><strong>Algorithms resources on net.</strong></p><p><a href="http://www.cs.uga.edu/~cai/courses/compbio/2008fall/bookchapters/Chapter08/Ch08_GraphsDNAseq.pdf">Graph Algorithms in Bioinformatics</a></p><p><a href="http://zikuladevs.com/notes/Part%20II%20Revision/Bio_Alg_Descriptions[1].pdf">Bioinformatics Algorithms Description</a></p><p><a href="http://users.aims.ac.za/~marshall/BioinformaticsCourse.html">Bioinformatics Algorithms Course Page</a></p><p><a href="http://www.cybertory.org/downloads/bae/BioinformaticsAlgorithmsExcelDoc.pdf">Bioinformatics Algorithm Demonstrations</a></p><p><a href="http://www.cse.sc.edu/~maxal/csce590b/Lect01-02.pdf">Introduction to Bioinformatics Algorithms Lectures 1-2 by Dr. Max Alekseyev USC, 2009</a></p><p><a href="http://lectures.molgen.mpg.de/online_lectures.html">Online Lectures on Bioinformatics</a></p><p><a href="http://www.ks.uiuc.edu/Training/Tutorials/science/bioinformatics-tutorial/bioinformatics.pdf.bak">Sequence Alignment Algorithms</a></p><p><a href="http://www.avatar.se/molbioinfo2001/seqali-dyn.html">Algorithm for sequence alignment: dynamic programming</a></p><p><a href="http://www.4tphi.net/~awalters/PI/pi.pdf">Network Protocol Analysis using Bioinformatics Algorithms</a></p><p><strong>Bioinformatics Algorithms Links</strong></p><p><strong>Dynamic Programming</strong></p><p>Particularly good sites...</p><p>&bull;<a href="http://www.cis.upenn.edu/~sahuguet/MSA/">http://www.cis.upenn.edu/~sahuguet/MSA/</a><br />&bull;<a href="http://www.blc.arizona.edu/courses/bioinformatics/align.html">http://www.blc.arizona.edu/courses/bioinformatics/align.html</a><br />&bull;<a href="http://www.cs.monash.edu.au/~lloyd/tildeStrings/Notes/DPA.html">http://www.cs.monash.edu.au/~lloyd/tildeStrings/Notes/DPA.html</a><br />&bull;<a href="http://www.cs.orst.edu/~schut/cs325/dynamic.htm">http://www.cs.orst.edu/~schut/cs325/dynamic.htm</a><br />&bull;<a href="http://www.catalase.com/dprog.htm">http://www.catalase.com/dprog.htm</a><br />&bull;<a href="http://bioweb.ncsa.uiuc.edu/~bioph490/BIOPH2.html#SEQUENCE_COMP">http://bioweb.ncsa.uiuc.edu/~bioph490/BIOPH2.html#SEQUENCE_COMP</a><br />&bull;<a href="http://www.qucis.queensu.ca/home/cisc365/javascript/dp1/index.html">http://www.qucis.queensu.ca/home/cisc365/javascript/dp1/index.html</a><br />Other sites...<br />&bull;<a href="http://bioweb.ncsa.uiuc.edu/~bioph490/dynamic_programming_demo.html">http://bioweb.ncsa.uiuc.edu/~bioph490/dynamic_programming_demo.html</a><br />&bull;<a href="http://www.qucis.queensu.ca/home/cisc365/365overheads.html">http://www.qucis.queensu.ca/home/cisc365/365overheads.html</a><br />&bull;<a href="http://www.qucis.queensu.ca/home/cisc365/dp/dp.p01.html">http://www.qucis.queensu.ca/home/cisc365/dp/dp.p01.html</a><br />&bull;<a href="http://www.dgp.toronto.edu/csc270/tut_dp.html">http://www.dgp.toronto.edu/csc270/tut_dp.html</a><br />&bull;<a href="http://queue.ieor.berkeley.edu/~jshu/knapsack/DP/dp.html">http://queue.ieor.berkeley.edu/~jshu/knapsack/DP/dp.html</a><br />&bull;<a href="http://mat.gsia.cmu.edu/classes/dynamic/dynamic.html">http://mat.gsia.cmu.edu/classes/dynamic/dynamic.html</a><br />&bull;<a href="http://www.cs.sandia.gov/~scistra/class_3">http://www.cs.sandia.gov/~scistra/class_3</a><br />&bull;<a href="http://levine.sscnet.ucla.edu/Econ101/dynamic.htm">http://levine.sscnet.ucla.edu/Econ101/dynamic.htm</a><br />&bull;<a href="http://mat.gsia.cmu.edu/classes/stoch_dynamic/stoch_dynamic.html">http://mat.gsia.cmu.edu/classes/stoch_dynamic/stoch_dynamic.html</a><br />&bull;<a href="http://mat.gsia.cmu.edu/classes/dynamic/node8.html">http://mat.gsia.cmu.edu/classes/dynamic/node8.html</a><br />&bull;<a href="http://www.maths.mu.oz.au/~moshe/dp/bibl/bibliography.html">http://www.maths.mu.oz.au/~moshe/dp/bibl/bibliography.html</a><br />&bull;<a href="http://cartan.gmd.de/PAPER/ismb95/ismb_html.html">http://cartan.gmd.de/PAPER/ismb95/ismb_html.html</a><br />&bull;<a href="http://screwdriver.bu.edu/bibliography/dynamic_programming.htm">http://screwdriver.bu.edu/bibliography/dynamic_programming.htm</a><br />&bull;<a href="http://www.norvig.com/design-patterns/">http://www.norvig.com/design-patterns/</a><br />&bull;<a href="http://tome.cbs.univ-montp1.fr/htmltxt/Doc/manual/node137.html">http://tome.cbs.univ-montp1.fr/htmltxt/Doc/manual/node137.html</a><br />&bull;<a href="http://poem.princeton.edu/~verdu/dynamic.html">http://poem.princeton.edu/~verdu/dynamic.html</a><br />&bull;<a href="http://www.orca1.com/opushelpweb/opusDynamic_Programming.html">http://www.orca1.com/opushelpweb/opusDynamic_Programming.html</a><br />&bull;<a href="http://screwdriver.bu.edu/cn760-lectures/l7/index.htm">http://screwdriver.bu.edu/cn760-lectures/l7/index.htm</a><br />&bull;<a href="http://www.ms.unimelb.edu.au/~moshe/dp/dp.html">http://www.ms.unimelb.edu.au/~moshe/dp/dp.html</a><br />&bull;<a href="http://mat.gsia.cmu.edu/ORCS/0255.html">http://mat.gsia.cmu.edu/ORCS/0255.html</a><br />&bull;<a href="http://aae.wisc.edu/e703/notes/a13dynpr.htm">http://aae.wisc.edu/e703/notes/a13dynpr.htm</a><br />&bull;<a href="http://bioweb.pasteur.fr/docs/modeller/node137.html">http://bioweb.pasteur.fr/docs/modeller/node137.html</a><br />&bull;<a href="http://www2.uwindsor.ca/~lama/my470/ddynamic.htm">http://www2.uwindsor.ca/~lama/my470/ddynamic.htm</a><br />&bull;<a href="http://students.ceid.upatras.gr/~papagel/project/ex5_6_1.htm">http://students.ceid.upatras.gr/~papagel/project/ex5_6_1.htm</a><br />&bull;<a href="http://www.cs.sunysb.edu/~algorith/lectures-good/node12.html">http://www.cs.sunysb.edu/~algorith/lectures-good/node12.html</a><br />&bull;<a href="http://www.cs.sunysb.edu/~algorith/lectures-good/node12.html">http://www.cs.sunysb.edu/~algorith/lectures-good/node12.html</a><br />&bull;<a href="http://www.utdallas.edu/~scniu/documents/7315.htm">http://www.utdallas.edu/~scniu/documents/7315.htm</a><br />&bull;<a href="http://www.ii.uib.no/~pinar/seminar/larry.html">http://www.ii.uib.no/~pinar/seminar/larry.html</a><br />&bull;<a href="http://www.deakin.edu.au/~gecole/books.html">http://www.deakin.edu.au/~gecole/books.html</a><br />&bull;<a href="http://www.cseg.engr.uark.edu/~wessels/algs/notes/dynamic.html">http://www.cseg.engr.uark.edu/~wessels/algs/notes/dynamic.html</a><br />&bull;<a href="http://www.csc.liv.ac.uk/~ped/teachadmin/algor/dyprog.html">http://www.csc.liv.ac.uk/~ped/teachadmin/algor/dyprog.html</a><br />&bull;<a href="http://www.eli.sdsu.edu/courses/fall96/cs660/notes/dynamicProg/dynamicProg.html">http://www.eli.sdsu.edu/courses/fall96/cs660/notes/dynamicProg/dynamicProg.html</a><br />&bull;<a href="http://www.cs.indiana.edu/l/www/ftp/techreports/TR514.html">http://www.cs.indiana.edu/l/www/ftp/techreports/TR514.html</a><br />&bull;<a href="http://www.cs.brandeis.edu/~mairson/poems/node3.html">http://www.cs.brandeis.edu/~mairson/poems/node3.html</a><br />&bull;<a href="http://www.cis.tu-graz.ac.at/igi/oaich/animations/Dynamic2.html">http://www.cis.tu-graz.ac.at/igi/oaich/animations/Dynamic2.html</a><br />&bull;<a href="http://bioweb.ncsa.uiuc.edu/~workshop/">http://bioweb.ncsa.uiuc.edu/~workshop/</a></p><p><br />Smith Waterman<br />&bull;<a href="http://genome-www.stanford.edu/Saccharomyces/help/sw_alignment.html">http://genome-www.stanford.edu/Saccharomyces/help/sw_alignment.html</a><br />&bull;<a href="http://genome-www.stanford.edu/Saccharomyces/help/sw_details.html">http://genome-www.stanford.edu/Saccharomyces/help/sw_details.html</a><br />&bull;<a href="http://www.stanford.edu/~sntaylor/bioc218/final.htm">http://www.stanford.edu/~sntaylor/bioc218/final.htm</a><br />&bull;<a href="http://www.maths.tcd.ie/~lily/pres2/sld009.htm">http://www.maths.tcd.ie/~lily/pres2/sld009.htm</a><br />&bull;<a href="http://bioweb.ncsa.uiuc.edu/~workshop/Lab_3/Smith-Waterman.htm">http://bioweb.ncsa.uiuc.edu/~workshop/Lab_3/Smith-Waterman.htm</a><br />&bull;<a href="http://www.tigem.it/LOCAL/SW/threshold.html">http://www.tigem.it/LOCAL/SW/threshold.html</a><br />&bull;<a href="http://sgbcd.weizmann.ac.il/genweb/help/smith-waterman.html">http://sgbcd.weizmann.ac.il/genweb/help/smith-waterman.html</a><br />&bull;<a href="http://cbrg.ethz.ch/ServerBooklet/section2_3_5.html">http://cbrg.ethz.ch/ServerBooklet/section2_3_5.html</a><br />Needleman &amp; Wunsch<br />&bull;<a href="http://www.maths.tcd.ie/~lily/pres2/sld003.htm">http://www.maths.tcd.ie/~lily/pres2/sld003.htm</a><br />&bull;<a href="http://acer.gen.tcd.ie/~amclysag/nwswat.html">http://acer.gen.tcd.ie/~amclysag/nwswat.html</a><br />&bull;<a href="http://www.nada.kth.se/~erikw/thesis/chapter2_3.html">http://www.nada.kth.se/~erikw/thesis/chapter2_3.html</a><br />&bull;<a href="http://www.irbm.it/irbm-course95/gb/docs/amps/subsection3_6_1.html">http://www.irbm.it/irbm-course95/gb/docs/amps/subsection3_6_1.html</a><br />&bull;<a href="http://www.ibc.wustl.edu/~zuker/Bio-5495/align-html/node3.html">http://www.ibc.wustl.edu/~zuker/Bio-5495/align-html/node3.html</a></p><p><strong>General (NW vs. SW vs. HMM, etc.)</strong></p><p>&bull;<a href="http://www.maths.tcd.ie/~lily/pres2/">http://www.maths.tcd.ie/~lily/pres2/</a><br />&bull;<a href="http://acer.gen.tcd.ie/~amclysag/nwswat.html">http://acer.gen.tcd.ie/~amclysag/nwswat.html</a><br />&bull;<a href="http://laguerre.psc.edu/biomed/TUTORIALS/SEQUENCE/MULTIPLE/tutorial.html">http://laguerre.psc.edu/biomed/TUTORIALS/SEQUENCE/MULTIPLE/tutorial.html</a><br />&bull;<a href="http://www.cse.ucsc.edu/research/compbio/">http://www.cse.ucsc.edu/research/compbio/</a></p><p><strong>Hmms</strong></p><p>&bull;<a href="http://www.medmicro.mds.qmw.ac.uk/HMMER/main.html">http://www.medmicro.mds.qmw.ac.uk/HMMER/main.html</a><br />&bull;<a href="http://alfredo.wustl.edu/ismb96/abs/p02.html">http://alfredo.wustl.edu/ismb96/abs/p02.html</a><br />&bull;<a href="http://www.cse.ucsc.edu/research/compbio/html_format_papers/hughkrogh96/cabios.html">http://www.cse.ucsc.edu/research/compbio/html_format_papers/hughkrogh96/cabios.html</a><br />&bull;<a href="http://wwwsyseng.anu.edu.au/~jason/hmmlinks.html">http://wwwsyseng.anu.edu.au/~jason/hmmlinks.html</a><br />&bull;<a href="http://www.breadfan.com/markov.html">http://www.breadfan.com/markov.html</a><br />&bull;<a href="http://cslu.cse.ogi.edu/HLTsurvey/ch1node34.html">http://cslu.cse.ogi.edu/HLTsurvey/ch1node34.html</a><br />&bull;<a href="http://www.ibc.wustl.edu/service/hmmalign/glocal.html">http://www.ibc.wustl.edu/service/hmmalign/glocal.html</a><br />&bull;<a href="http://www.cse.ucsc.edu/research/compbio/html_format_papers/ismb94/node5.html">http://www.cse.ucsc.edu/research/compbio/html_format_papers/ismb94/node5.html</a><br />&bull;<a href="http://www.iscs.nus.edu.sg/~luakt/ic3222/lecture/nlp18new/index.htm">http://www.iscs.nus.edu.sg/~luakt/ic3222/lecture/nlp18new/index.htm</a><br />&bull;<a href="http://www.cse.ucsc.edu/research/compbio/sam.html">http://www.cse.ucsc.edu/research/compbio/sam.html</a>&nbsp;SAM Software for HMMs</p><p><strong>Genetic Algorithms</strong><br /><br />&bull;<a href="http://www.staff.uiuc.edu/~carroll/ga.html">http://www.staff.uiuc.edu/~carroll/ga.html</a><br />&bull;<a href="http://kal-el.ugr.es/gags.html">http://kal-el.ugr.es/gags.html</a><br />&bull;<a href="http://kal-el.ugr.es/~jmerelo/GAJS.html">http://kal-el.ugr.es/~jmerelo/GAJS.html</a><br />&bull;<a href="http://www.genetic-programming.org/">http://www.genetic-programming.org/</a><br />&bull;<a href="http://www.iitk.ac.in/kangal/deb_tut.shtml">http://www.iitk.ac.in/kangal/deb_tut.shtml</a></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/4314/postdocs-positions-in-computer-science-in-helsinki-finland</guid>
  <pubDate>Fri, 06 Sep 2013 10:11:19 -0500</pubDate>
  <link></link>
  <title><![CDATA[PostDocs positions in computer science in HELSINKI, FINLAND]]></title>
  <description><![CDATA[
<p>Several university departments in the Helsinki region, Finland, are looking for postdoctoral researchers in the field of computer science and information technology. Jobs are available at:<br />·       Helsinki Institute for Information Technology HIIT, Aalto University and University of Helsinki, http://www.hiit.fi<br />·       Department of Computer Science, University of Helsinki, http://www.cs.helsinki.fi<br />·       Department of Information and Computer Science, Aalto University, http://ics.aalto.fi<br />·       Department of Computer Science and Engineering, Aalto University, http://cse.aalto.fi<br />·       Department of Mathematics and Statistics, University of Helsinki, http://mathstat.helsinki.fi/english/<br /> <br />Why Helsinki?<br />The collaborating Aalto University and University of Helsinki form a leading hub of computer science and modelling, including Machine learning, Data mining, Algorithms, Computational Logic, Cloud computing, Distributed computing, Human-centric ubiquitous ICT, Bioinformatics, etc.<br />Helsinki region is a safe, pleasant and attractive place to live in, with well-functioning services such as public transport etc. Finland has a comprehensive social security and health care system, including exceptionally good parental leaves, and children's day care services.<br /> <br />Positions are offered in:<br />Algorithm engineering (String Algorithms group)<br />Algorithmic bioinformatics (Genome-Scale Algorithmics group)<br />Automated reasoning and search, especially propositional logic (Computational Logic group)<br />Computational astrophysics and/or data analysis (Computational Methods and Data Analysis for Astrophysics group)<br />Computational biology and statistical methods in bioinformatics (Computational Systems Biology group)<br />Computational creativity and data mining (Discovery group)<br />Dynamic and large-scale networked systems (Data Communications Software group)<br />Intelligent multimodal information access (Content-Based Image and Information Retrieval Group)<br />Machine learning and neuroscience (Statistical Machine Learning group)<br />Machine learning for structured data (Kernel Machines, Pattern Analysis and Computational Biology group)<br />Machine learning methods for infectious disease epidemiology (Bayesian Statistics Group)<br />Probabilistic modeling and machine learning (Complex Systems Computation group)<br />Statistical machine learning (Statistical Machine Learning group)<br />Analysing ubiquitous sensor data (HIIT-Wide Focus Area)<br />Interactive visualization (HIIT-Wide Focus Area)<br />Affective computing and BCI (HIIT-Wide Focus Area)<br />Intelligent user interfaces and/or recommender systems (HIIT-Wide Focus Area)<br />Information retrieval and HCI (HIIT-Wide Focus Area)<br />Machine learning and data analysis, especially information retrieval, HCI, text and context data (HIIT-Wide Focus Area)<br />Probabilistic modeling and data analysis for bioinformatics (HIIT-Wide Focus Area)</p>

<p>More at http://www.hiit.fi/postdoc-call-2013</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/5220/paolo-ruggerone-lab</guid>
  <pubDate>Tue, 01 Oct 2013 14:15:53 -0500</pubDate>
  <link></link>
  <title><![CDATA[Paolo Ruggerone Lab]]></title>
  <description><![CDATA[
<p>Efflux pumps (RND family)</p>

<p>Functioning of efflux systems in Gram-negative bacteria<br />Determinants of the compound-efflux system interactions<br />Action of inhibitors on efflux systems<br />Structural and dynamical features of the efflux systems</p>

<p>TatA<br />Assembly of the TatA system<br />Study of the dynamical features of the charge zipper</p>

<p>Methods<br />Setup of a kinetic Monte Carlo (KMC) scheme to study the flux of antibiotics through porins and efflux systems<br />Setup of protocol to integrate MD results in a ligand-based approach</p>

<p>Viral inhibitors<br />Interactions of selected compounds with RNA-dependent RNA polymerases (RdRps) of HCV and BVDV<br />Assessment of the role of mutations in RdRps<br />Antimicrobial peptides</p>

<p>Interactions of antimicrobial peptides with membranes: structure and dynamics<br />Interactions between antimicrobial peptides in the presence of different membranes<br />Protein-protein interactions<br />Effects of mutations</p>

<p>Lab Page<br />http://www.dsf.unica.it/~paolo/Site/Home.html</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/19631/rosalind-bioinformatics-problems</guid>
	<pubDate>Thu, 18 Dec 2014 10:32:48 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/19631/rosalind-bioinformatics-problems</link>
	<title><![CDATA[Rosalind Bioinformatics problems !!!]]></title>
	<description><![CDATA[<p>Rosalind is a platform for learning bioinformatics and programming through problem solving. <a href="http://rosalind.info/problems/list-view/">Take a tour</a> to get the hang of how Rosalind works.</p>
<p>http://rosalind.info/problems/list-view/</p><p>Address of the bookmark: <a href="http://rosalind.info/problems/list-view/" rel="nofollow">http://rosalind.info/problems/list-view/</a></p>]]></description>
	<dc:creator>Abhi</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/4210/uni-computing-bergen-norway</guid>
  <pubDate>Tue, 03 Sep 2013 18:40:50 -0500</pubDate>
  <link></link>
  <title><![CDATA[Uni Computing Bergen Norway]]></title>
  <description><![CDATA[
<p>Info on Uni Computing (Webpage: http://www.bccs.uni.no/) :</p>

<p>Uni Computing (formerly Uni BCCS) is a department of Uni Research, affiliated with the University of Bergen.</p>

<p>5 groups in this lab works on computational resources, methods, algorithms, and software.</p>

<p>Following two bioinformatics groups are:</p>

<p>The Computational Biology Unit (CBU) provides education and research in bioinformatics focused on functional genomics.</p>

<p>The Computational Ecology Unit (CEU) is basically deal with population fluctuations, behavioural patterns and the ways life cycles emerge.</p>
]]></description>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/25993/hoffman-lab</guid>
  <pubDate>Tue, 12 Jan 2016 02:47:41 -0600</pubDate>
  <link></link>
  <title><![CDATA[Hoffman Lab]]></title>
  <description><![CDATA[
<p>They develop machine learning techniques to better understand chromatin biology. These models and algorithms transform high-dimensional functional genomics data into interpretable patterns and lead to new biological insight.</p>

<p>https://www.pmgenomics.ca/hoffmanlab/</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/13226/you-and-your-friend-have-similar-dna</guid>
	<pubDate>Sun, 27 Jul 2014 20:44:05 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/13226/you-and-your-friend-have-similar-dna</link>
	<title><![CDATA[You and your friend have similar DNA !!!]]></title>
	<description><![CDATA[<p>New research out of Massachusetts claims that people often choose friends that are similar to them in genetics and they are more accurate than you might suppose. A study published on PNAS&nbsp;http://www.pnas.org/content/111/Supplement_3/10796.full found that people are apt to pick friends who are genetically similar to themselves - so much so that friends tend to be as alike at the genetic level as a person's fourth cousin.</p><div style="text-align: center;"><img src="http://i.kinja-img.com/gawker-media/image/upload/s--CwLwHa43--/18fbmlokxcmqcjpg.jpg" alt="image" width="300" height="271" style="border: 0px; border: 0px;"></div><p>Scientists with a long-running Framingham Heart Study looked at 1,932 people (examination of about 1.5 million markers of genetic variations), comparing unrelated friends to unrelated strangers. They found that friends shared about 1% of their genes &mdash; a percentage much higher than those shared with strangers.This new findings made it clear that people have more DNA in common with those who are selected as friends than with strangers in the same population.&nbsp;</p><p>The genes that lined up the most were olfactory genes, which deal with smell. The ones that lined up the least were immune system genes. The researchers weren't sure why that happened :/. Olfactory genes might be a straightforward explanation: People who like the same smells tend to be drawn to similar environments, where they meet others with the same tendencies.</p><p>Reference:</p><p>http://www.pnas.org/content/111/Supplement_3/10796.full</p><p>Image : http://i.kinja-img.com</p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

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