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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/4962?offset=40</link>
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	<description><![CDATA[]]></description>
	
	
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/35752/hejnol-group</guid>
  <pubDate>Thu, 22 Feb 2018 16:02:53 -0600</pubDate>
  <link></link>
  <title><![CDATA[Hejnol Group]]></title>
  <description><![CDATA[
<p>The group studies a broad range of animal taxa using morphological and molecular tools to unravel the evolution and development of animal organ systems.</p>

<p>To understand the evolution of the biodiversity seen on planet earth is one of the major goals in biology. How animals explored new habitats from only being confined to the marine environment and the how the forms diversified is still one of the most tremendous questions to be answered.</p>

<p>http://www.sars.no/research/HejnolGrp.php</p>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/38551/gupta-lab</guid>
  <pubDate>Sat, 29 Dec 2018 13:18:31 -0600</pubDate>
  <link></link>
  <title><![CDATA[Gupta Lab]]></title>
  <description><![CDATA[
<p>Work include (i) understanding the evolutionary relationships among different prokaryotic and eukaryotic organisms; (ii) Understanding the cellular functions of these lineage-specific signature proteins as well as lineage-specific conserved inserts and deletions in important housekeeping proteins by genetic and biochemical studies; (iii) Development of novel diagnostic methods (PCR based and immunological) for identification of different groups of organisms based upon these signature proteins and conserved indels; (iv) The use of these lineage-specific probes with predicitive ability to identify/explore the presence of different groups of organisms in metagenomic sequences from various environments.</p>

<p>https://fhs.mcmaster.ca/gupta-lab/index.html</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/42794/tmrca-calculator</guid>
	<pubDate>Wed, 03 Feb 2021 05:07:30 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42794/tmrca-calculator</link>
	<title><![CDATA[TMRCA Calculator]]></title>
	<description><![CDATA[<p><span>This program calculates the probability that two people have a certain number of generations between them, based on the standard&nbsp;</span><em>infinite alleles</em><span>&nbsp;formula of Walsh. It calculates both the probability of being at an exact number of generations back to the Most Recent Common Ancestor (MRCA) of a certain pair of people and the cumulative probability that the actual number of generations is less than a certain value. Note that the convention using generations is changed from an earlier version of this calculator which used "transmission events". It can list both result types in a table or graph. In either case the horizontal axis stops at the point where the cumulative probability reaches 95% or 10 generations, whichever is longer, or an absolute max of 50,000. Beyond 90% the calculation becomes inaccurate.</span></p>
<p>https://clandonaldusa.org/index.php/tmrca-calculator</p><p>Address of the bookmark: <a href="https://clandonaldusa.org/index.php/tmrca-calculator" rel="nofollow">https://clandonaldusa.org/index.php/tmrca-calculator</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43806/genomicus-genome-browser-that-enables-users-to-navigate-in-genomes-in-several-dimensions</guid>
	<pubDate>Mon, 28 Feb 2022 23:27:37 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43806/genomicus-genome-browser-that-enables-users-to-navigate-in-genomes-in-several-dimensions</link>
	<title><![CDATA[Genomicus: genome browser that enables users to navigate in genomes in several dimensions]]></title>
	<description><![CDATA[<p>Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.</p>
<p>Once a query gene has been entered, it is displayed in its genomic context in parallel to the genomic context of all its orthologous and paralogous copies in all the other sequenced metazoan genomes. Moreover, Genomicus stores and displays the predicted ancestral genome structure in all the ancestral species within the phylogenetic range of interest.</p>
<p>All the data on extant species displayed in this browser are from&nbsp;<a href="http://www.ensembl.org/">Ensembl</a>.</p>
<p><br><strong>Summary statistics of Genomicus version 105.01:</strong><span>&nbsp;(view species tree in&nbsp;</span><a href="https://www.genomicus.bio.ens.psl.eu/genomicus-105.01/data/SpeciesTree.pdf">pdf</a><span>&nbsp;or&nbsp;</span><a href="https://www.genomicus.bio.ens.psl.eu/genomicus-105.01/data/SpeciesTree.nwk">newick</a><span>)</span><br><br></p>
<table id="introstats">
<tbody>
<tr><th>Number of extant species</th>
<td>200</td>
</tr>
<tr><th>Number of extant genes</th>
<td>4303993</td>
</tr>
<tr><th>&nbsp;</th></tr>
<tr><th>Number of ancestral species</th>
<td>196</td>
</tr>
<tr><th>Number of ancestral genes</th>
<td>4624213</td>
</tr>
<tr><th>Number of ancestral synteny blocks</th>
<td>83342<br><br></td>
</tr>
</tbody>
</table><p>Address of the bookmark: <a href="https://www.genomicus.bio.ens.psl.eu/genomicus-105.01/cgi-bin/search.pl" rel="nofollow">https://www.genomicus.bio.ens.psl.eu/genomicus-105.01/cgi-bin/search.pl</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44773/genetic-basis-of-tail-loss-evolution</guid>
	<pubDate>Tue, 04 Mar 2025 12:12:36 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44773/genetic-basis-of-tail-loss-evolution</link>
	<title><![CDATA[Genetic basis of tail-loss evolution]]></title>
	<description><![CDATA[<p>The paper <em>"On the genetic basis of tail-loss evolution in humans and apes (https://www.nature.com/articles/s41586-024-07095-8)"</em>, published in <em>Nature</em>, investigates the genetic mechanisms that led to the loss of tails in humans and apes. The study suggests that a specific genetic mutation, involving the insertion of an <em>Alu</em> element (a type of transposable DNA sequence), played a critical role in the evolutionary transition from tailed primates to tailless hominoids.</p><h3><strong>Key Findings of the Study:</strong></h3><ol>
<li>
<p><strong>Alu Insertion and Tail Loss:</strong><br /> The researchers discovered an <em>Alu</em>-mediated genetic change in a common ancestor of modern apes and humans. This change disrupted the normal function of a gene involved in tail development, leading to the suppression of tail formation.</p>
</li>
<li>
<p><strong>Gene Disruption Mechanism:</strong><br /> The <em>Alu</em> insertion was found within a regulatory region of the <em>TBXT</em> gene (also known as <em>T</em> or <em>Brachyury</em>), which is crucial for tail development in vertebrates. This insertion likely altered the gene's expression patterns, leading to tail reduction over evolutionary time.</p>
</li>
<li>
<p><strong>Functional Evidence from Model Organisms:</strong><br /> To test their hypothesis, the researchers introduced similar genetic modifications in mice. The modified mice exhibited shortened or absent tails, supporting the idea that the identified mutation played a role in tail loss in hominoids.</p>
</li>
<li>
<p><strong>Evolutionary Implications:</strong><br /> The findings suggest that small, random genomic changes&mdash;such as transposable element insertions&mdash;can have profound effects on body morphology. This study provides evidence that mobile DNA elements (like <em>Alu</em>) can drive major evolutionary transitions.</p>
</li>
<li>
<p><strong>Relevance to Human Evolution:</strong><br /> Understanding the genetic basis of tail loss helps in reconstructing the evolutionary history of hominins (the lineage that includes humans and our extinct relatives). It also sheds light on how genetic variations contribute to anatomical diversity among primates.</p>
</li>
</ol><h3><strong>Significance of the Study:</strong></h3><p>This research highlights the role of transposable elements in shaping evolutionary traits and provides a concrete genetic explanation for a defining characteristic of humans and great apes. It also demonstrates how mutations in regulatory regions of developmental genes can lead to significant anatomical changes.</p>]]></description>
	<dc:creator>LEGE</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/4043/what-is-bioinformatics</guid>
	<pubDate>Wed, 28 Aug 2013 06:53:05 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/4043/what-is-bioinformatics</link>
	<title><![CDATA[What is Bioinformatics?]]></title>
	<description><![CDATA[<iframe src="http://player.vimeo.com/video/71581534?byline=0" width="" height="" frameborder="0" webkitAllowFullScreen allowFullScreen></iframe>Illustration and Animation: Rachel Robinson Script: Tiffany Trent Voice-over: Kris Monger Sound: Glisten Carefully by Guennadi Malyshevski]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/33629/list-of-universities-offering-bachelor-master-or-phd-bioinformatics-degree-in-malaysia</guid>
	<pubDate>Thu, 22 Jun 2017 01:34:02 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/33629/list-of-universities-offering-bachelor-master-or-phd-bioinformatics-degree-in-malaysia</link>
	<title><![CDATA[List of universities offering Bachelor,  Master or PhD bioinformatics degree in Malaysia]]></title>
	<description><![CDATA[<p>Bioinformatics is a newly emerging interdisciplinary research area, which may be defined as the ―interface between biological and computational sciences. Most of the Bioinformatics work that is done can be described as analyzing biological data, although a growing number of projects deal with the organization of biological information. The global Bioinformatics industry has grown at a double-digit growth rate in the past and is expected to follow the same pattern in the next four years. US remains the largest market in the world, but Asia-Pacific countries, particularly India and China, are witnessing the fastest growth and are anticipated to emerge as the dominating forces in future. The Comparison of Bioinformatics Industry between Malaysia, India and other countries&nbsp;are discussed in this&nbsp;<span>http://ijbssnet.com/journals/Vol.%202_No._10;_June_2011/11.pdf paper.</span></p><p>Bioinformatics is full of opportunities. The sector is poised to open new avenues for the other related sectors also. But the biggest opportunity area in the Bioinformatics market will be in the drug discovery sector. Reduction of both the cost and time taken to discover a new drug due to fast development in the Bioinformatics tools and software zone is also making drug discovery an attractive field to venture in. Malaysian bioinformatics growth and future are discuss in this https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723929/ paper.&nbsp;Keeping all such inportance in mind, following universities in Malaysia offering bioinformatics cources:</p><p><strong>3 program(s) at AIMST University<strong>, Malaysia</strong></strong></p><p>Master of Science in Biotechnology (MSc) - Bioinformatics by Research</p><p>Master of Science (M.Sc) in Medical Microbiology (Bioinformatics) by Research</p><p>Doctor of Philosophy in Biotechnology (PhD) - Bioinformatics by Research</p><p>&nbsp;</p><p><strong>1 program(s) at INTI International University and Colleges<strong>, Malaysia</strong></strong></p><p>American Degree Transfer Program (Biosciences) in Bioinformatics</p><p>&nbsp;</p><p><strong>3 program(s) at Management and Science University (MSU)<strong>, Malaysia</strong></strong></p><p>Master in Bioinformatics (By Research)</p><p>PhD in Bioinformatics</p><p>Bachelor in Bioinformatics (Hons)</p><p>&nbsp;</p><p><strong>1 program(s) at Multimedia University (MMU)<strong>, Malaysia</strong></strong></p><p>Bachelor of Science (Honours) Bioinformatics</p><p>&nbsp;</p><p><strong>1 program(s) at Universiti Industri Selangor (UNISEL) Bestari Jaya Campus<strong>, Malaysia</strong></strong></p><p>Bachelor of Bioinformatics (Hons)</p><p>&nbsp;</p><p><strong>2 program(s) at Universiti Malaysia Sabah (UMS)<strong>, Malaysia</strong></strong></p><p>PhD - Doctor of Philosophy in Bioinformatics (By Research)</p><p>MSc - Master of Science in Bioinformatics (By Research)</p><p>&nbsp;</p><p><strong>6 program(s) at Universiti Putra Malaysia (UPM)<strong>, Malaysia</strong></strong></p><p>MSc - Master of Science in Bioinformatics by Research</p><p>Master of Science in Bioinformatics and System Biology by Research</p><p>Master of Science (M.Sc) in Bioinformatics and Systems Biology (With Thesis)</p><p>PhD - Doctor of Philosophy in Bioinformatics by Research</p><p>PhD - Doctor of Philosophy in Bioinformatics and Systems Biology (With Thesis)</p><p>PhD - Doctor of Philosophy in Bioinformatics and System Biology by Research</p><p>&nbsp;</p><p><strong>1 program(s) at Universiti Selangor (UNISEL)<strong>, Malaysia</strong></strong></p><p>Bachelor of Bioinformatics (Hons)</p><p>&nbsp;</p><p><strong>3 program(s) at Universiti Teknologi Malaysia (UTM)<strong>, Malaysia</strong></strong></p><p>M.Sc - Master of Science (Bioscience) in Bioinformatics Research Group (BIRG) By Research</p><p>PhD - Doctor of Philosophy (Bioscience) in Bioinformatics Research Group (BIRG) By Research</p><p>Bachelor of Computer Science (BioInformatics)</p><p>&nbsp;</p><p><strong>4 program(s) at University of Malaya (UM)<strong>, Malaysia</strong></strong></p><p>MSc - Master of Science in Bioinformatics by Research</p><p>Master in Bioinformatics by Coursework</p><p>PhD - Doctor of Philosophy in Bioinformatics by Research</p><p>Bachelor of Science (BSc) in Bioinformatics</p><p>&nbsp;</p><p><strong>3 program(s) at Perdana University<strong>, Malaysia</strong></strong></p><p>Master in Bioinformatics (By Research)</p><p>PhD in Bioinformatics</p><p>Bachelor in Bioinformatics (Hons)</p><p>&nbsp;</p><p><strong>3 program(s) at&nbsp;Monash University, Malaysia</strong></p><p>Master in Bioinformatics (By Research)</p><p>PhD in Bioinformatics</p><p>Bachelor in Bioinformatics (Hons)</p><p>&nbsp;</p><p><span>The real bioinformatics scope lies if there are research labs which work in this field. One has to take account of that. If so then try to get information of those labs and visit them to get a hang of the work they pursue. For detail Bioinformatics in Malaysia: Hope, Initiative, Effort, Reality, and Challenges are discussed in&nbsp;<span>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723929/ paper.</span></span></p>]]></description>
	<dc:creator>sahabuddin</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/45316/from-genes-to-algorithms-the-ai-revolution-in-bioinformatics</guid>
	<pubDate>Wed, 16 Sep 2026 02:23:40 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/45316/from-genes-to-algorithms-the-ai-revolution-in-bioinformatics</link>
	<title><![CDATA[From Genes to Algorithms: The AI Revolution in Bioinformatics]]></title>
	<description><![CDATA[<p>Imagine waking up to a message from your doctor saying your genetic profile has been analyzed and a small change in your DNA has been found that could raise your risk for a certain disease. Instead of being alarmed, you learn that the condition was caught early and your genetic information can help doctors find treatments that might work better for you. Not long ago, this would have seemed like science fiction. But thanks to the rapid progress of artificial intelligence (AI) and bioinformatics, it is becoming more realistic. Bioinformatics brings together biology, computer science, mathematics, and statistics to collect, manage, and analyze biological data. As new technologies produce huge amounts of genomic, transcriptomic, proteomic, and clinical data, traditional methods often cannot keep up. AI is now playing a bigger role in bioinformatics, helping researchers find patterns, make predictions, and understand biological systems in ways that were once out of reach.</p><p>Modern sequencing technologies have turned biology into a data-heavy science. The human genome has about three billion DNA base pairs, and sequencing can produce massive datasets quickly. Bioinformatics helps organize and interpret this information, allowing scientists to compare genomes, find genes, spot genetic differences, study gene expression, and understand diseases at the molecular level. Now, AI is changing how these datasets are analyzed. Machine learning and deep learning can find complex patterns in biological data and make predictions using large datasets. Rather than following only set rules, AI systems can learn from data and help researchers solve tough biological problems.</p><p>A key example of AI in bioinformatics is predicting protein structures. Proteins are vital for many functions in living things, and their three-dimensional shapes are closely tied to what they do. For a long time, figuring out these structures in the lab was slow and difficult. AI-based tools like AlphaFold have shown that deep learning can predict protein structures with impressive accuracy. These advances help speed up biological research and give scientists useful predictions to support their experiments. This shift means bioinformatics is moving from just analyzing biological data to predicting how biology works and designing new solutions.</p><p>AI is also expected to greatly influence drug discovery. Traditionally, developing a new drug is a long and costly process that involves finding biological targets, searching for possible drug molecules, testing how well they work, studying their properties, and running many experiments. AI can help researchers analyze large chemical and biological datasets, predict how molecules might interact with targets, find promising compounds, and estimate properties of drug candidates. Generative AI can even help design new molecules to test in the lab. This does not mean lab experiments will go away, but AI can help researchers focus on the best options and possibly speed up some parts of drug development.</p><p>Personalized medicine is another area where AI-driven bioinformatics could make a big difference. Each person has a unique mix of genetic, molecular, environmental, and lifestyle factors, so people with the same disease might respond differently to the same treatment. Bioinformatics lets researchers study individual biological data, and AI can combine many types of information, like genetic data, gene expression, protein levels, medical images, clinical records, and drug responses. In the future, this could help doctors look beyond just the disease and focus on the specific biology of each patient. This would support more personalized ways to diagnose, assess risk, and choose treatments.</p><p>As AI becomes more common, the job of bioinformaticians will likely change. Instead of spending most of their time on repetitive computer tasks, they may focus more on creating research questions, understanding AI results, checking predictions, and linking computer findings to lab experiments. Future professionals will need to know about molecular biology, genetics, statistics, programming, machine learning, data science, databases, and computational biology. But technical skills alone will not be enough. Being able to ask good scientific questions and carefully judge computer results will be even more important, since AI can make predictions, but scientists must decide if those predictions make sense and can be proven in the lab.</p><p>Even with its great potential, using AI in bioinformatics comes with big challenges. AI systems rely on the quality and variety of the data they are trained on. Biological and clinical datasets can have missing information, technical errors, inconsistent measurements, and may not represent all groups equally. A model that works well on one dataset might not work as well on another group or in a different setting. That is why data quality, proper validation, transparency, reproducibility, and careful model development are crucial for the future of AI in bioinformatics. Researchers also need to think about genetic privacy, data ownership, security, and using personal biological information responsibly. These concerns are especially important when AI predictions are used in healthcare.</p><p>The lab of the future may look very different from today&rsquo;s. Researchers might use AI to review scientific papers, find research questions, analyze large datasets, come up with ideas, and predict which experiments will be most helpful. Automated lab systems could then run these experiments, create new data, and send the results back to computer models. This would create a cycle of making guesses, predicting, experimenting, collecting data, and learning. This approach could speed up scientific discovery by helping researchers explore questions more efficiently. Bioinformatics could become a key link between computer predictions and real lab experiments.</p><p>In the end, the future of bioinformatics with AI will not be about replacing people with machines. It will be about humans and AI working together. Computers can handle huge amounts of biological data and spot patterns that a single person could not. But humans bring scientific understanding, creativity, critical thinking, ethical judgment, and the ability to see the bigger picture. AI might find a pattern in millions of genomes, but scientists need to figure out why it matters. An AI model could suggest a new drug, but researchers must check if it is safe and works well. A computer might find a genetic change, but doctors have to decide what it means for a real patient.</p><p>The future of bioinformatics is closely tied to the future of AI. As biological data grows and AI models get better, bioinformatics may shift from mainly analyzing data to predicting biological processes, designing new molecules, speeding up experiments, and supporting personalized healthcare. For students and researchers, this is an exciting chance to work where biology and technology meet. The most successful people will not just be those who use the latest AI tools, but those who understand biology well enough to ask good questions and judge the answers carefully. The future will not be about AI versus humans, but about people and AI working together to understand life in ways we never could before. The next big discovery may come from this partnership between a biological question, a computer model, a lab experiment, and human curiosity.</p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/42958/claus-peter-stelzer-lab</guid>
  <pubDate>Mon, 15 Mar 2021 15:24:41 -0500</pubDate>
  <link></link>
  <title><![CDATA[Claus-Peter Stelzer Lab]]></title>
  <description><![CDATA[
<p>Interested in various topics at the intersection of ecology and evolution. In my research I use rotifers as model organisms for experimental studies at the individual and population level. Rotifers are ideally suited for this, because populations of thousands can be kept in small containers in the lab, while single individuals can still be handled conveniently. </p>

<p>More at https://www.uibk.ac.at/limno/personnel/stelzer/index.html.en#research</p>
]]></description>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/5254/mike-ritchie-lab</guid>
  <pubDate>Wed, 02 Oct 2013 15:25:45 -0500</pubDate>
  <link></link>
  <title><![CDATA[Mike Ritchie Lab]]></title>
  <description><![CDATA[
<p>Mike Ritchie Lab primary research focus is the detection of susceptibility genes for common diseases such as cancer, diabetes, hypertension, and cardiovascular disease, among others. The approaches will involve the development and application of new statistical methods with a focus on the detection of gene-gene interactions associated with human disease.</p>

<p>Gene expression and protein expression patterns between normal and non-normal tissues is a growing area of research that may lead to the identification of candidate genes for understanding the etiology of common, complex diseases. </p>

<p>Lab homepage @ http://ritchielab.psu.edu/ritchielab/</p>
]]></description>
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