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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/41493?offset=570</link>
	<atom:link href="https://bioinformaticsonline.com/related/41493?offset=570" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44626/meta-transcriptomics-dynamic-world-of-rna-in-diverse-environments</guid>
	<pubDate>Wed, 31 Jul 2024 02:40:49 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44626/meta-transcriptomics-dynamic-world-of-rna-in-diverse-environments</link>
	<title><![CDATA[Meta-Transcriptomics: Dynamic World of RNA in Diverse Environments]]></title>
	<description><![CDATA[<p>Meta-transcriptomics combines high-throughput sequencing technologies with computational biology to profile the RNA content of a sample. This technique allows researchers to capture a snapshot of gene expression and metabolic activities across diverse microbial communities, such as those found in soil, water, and the human gut.</p><p><strong>Key Components</strong></p><ol>
<li>
<p><strong>Sample Collection</strong>: Meta-transcriptomics begins with the collection of environmental samples. These samples are often complex, containing a wide range of microorganisms.</p>
</li>
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<p><strong>RNA Extraction</strong>: RNA is extracted from the sample, which includes mRNA, rRNA, tRNA, and other non-coding RNAs. This step is crucial as it determines the quality and representativeness of the data.</p>
</li>
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<p><strong>Sequencing</strong>: High-throughput RNA sequencing (RNA-seq) technologies are used to obtain sequences of the RNA transcripts. This step provides a vast amount of data on the RNA molecules present in the sample.</p>
</li>
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<p><strong>Data Analysis</strong>: Computational tools and bioinformatics methods are employed to process and analyze the sequencing data. This involves mapping RNA sequences to reference genomes or transcriptomes, identifying expressed genes, and quantifying their abundance.</p>
</li>
<li>
<p><strong>Functional Annotation</strong>: The functional roles of identified transcripts are inferred based on known gene functions, allowing researchers to understand the metabolic and ecological functions of the microbial community.</p>
</li>
</ol><p><strong>Applications</strong></p><ol>
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<p><strong>Environmental Monitoring</strong>: Meta-transcriptomics can be used to monitor the health and functional status of ecosystems. For example, it can help assess the impact of pollution on microbial communities by revealing changes in gene expression related to stress response and degradation processes.</p>
</li>
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<p><strong>Microbiome Research</strong>: In human health, meta-transcriptomics offers insights into the gut microbiome&rsquo;s functional state. It helps in understanding how microbial communities interact with their host, how they respond to dietary changes, and their role in health and disease.</p>
</li>
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<p><strong>Biotechnology</strong>: The technique can aid in the discovery of novel enzymes and bioactive compounds by profiling microbial communities in extreme environments or industrial processes.</p>
</li>
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<p><strong>Disease Pathogenesis</strong>: By analyzing RNA profiles from disease-associated environments, researchers can uncover pathogen-host interactions and identify potential targets for therapeutic interventions.</p>
</li>
</ol><p><strong>Challenges</strong></p><ol>
<li>
<p><strong>Complexity of Data</strong>: The sheer volume and complexity of data generated by meta-transcriptomics can be overwhelming. Effective data management and advanced computational tools are required to extract meaningful insights.</p>
</li>
<li>
<p><strong>Sampling Bias</strong>: Environmental samples can be heterogeneous, and RNA extraction methods may introduce biases, potentially affecting the accuracy of the results.</p>
</li>
<li>
<p><strong>Reference Databases</strong>: Incomplete or biased reference databases can hinder the accurate functional annotation of transcripts, especially when studying novel or poorly characterized organisms.</p>
</li>
</ol><p><strong>Future Directions</strong></p><p>Meta-transcriptomics is a rapidly evolving field, with ongoing advancements in sequencing technologies and bioinformatics. Future research may focus on improving data integration, developing more comprehensive reference databases, and enhancing our understanding of microbial community dynamics in various environments. As these challenges are addressed, meta-transcriptomics will continue to provide valuable insights into the functional roles of microorganisms and their interactions within ecosystems.</p><p><strong>Conclusion</strong></p><p>Meta-transcriptomics represents a powerful tool for exploring the functional aspects of microbial communities in their natural environments. By capturing a snapshot of gene expression and metabolic activities, this approach offers a deeper understanding of ecological interactions, health implications, and biotechnological potentials. As technology and methodologies advance, meta-transcriptomics is poised to make significant contributions to our knowledge of the microbial world.</p>]]></description>
	<dc:creator>Abhi</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/27459/tools-for-searching-repeats-and-palindromic-sequences</guid>
	<pubDate>Sat, 21 May 2016 22:32:25 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/27459/tools-for-searching-repeats-and-palindromic-sequences</link>
	<title><![CDATA[Tools for Searching Repeats And Palindromic Sequences]]></title>
	<description><![CDATA[<p>What are genomic interspersed repeats?</p><p>In the mid 1960's scientists discovered that many genomes contain stretches of highly repetitive DNA sequences ( see Reassociation Kinetics Experiments, and C-Value Paradox ). These sequences were later characterized and placed into five categories:</p><p><strong>Simple Repeats</strong> - Duplications of simple sets of DNA bases (typically 1-5bp) such as A, CA, CGG etc.<br /><strong>Tandem Repeats</strong> - Typically found at the centromeres and telomeres of chromosomes these are duplications of more complex 100-200 base sequences.<br /><strong>Segmental Duplications</strong> - Large blocks of 10-300 kilobases which are that have been copied to another region of the genome.<br /><strong>Interspersed Repeats</strong><br />Processed Pseudogenes, Retrotranscripts, SINES - Non-functional copies of RNA genes which have been reintegrated into the genome with the assitance of a reverse transcriptase.<br />DNA Transposons<br />Retrovirus Retrotransposons<br />Non-Retrovirus Retrotransposons ( LINES )</p><p>Currently up to 50% of the human genome is repetitive in nature and as improvements are made in detection methods this number is expected to increase.</p><p>On the other hand; In genetics, the term palindrome refers to a sequence of nucleotides along a DNA (deoxyribonucleic acid) or RNA (ribonucleic acid) strand that contains the same series of nitrogenous bases regardless from which direction the strand is analyzed. Akin to a language palindrome&mdash;wherein a word or phrase is spelled the same left-to-right as right-to-left (e.g., the word RADAR or the phrase "able was I ere I saw elba")&mdash;with genetic palindromes it does not matter whether the nucleic acid strand is read starting from the 3' (three prime) end or the 5' (five prime) end of the strand.</p><p>Recent research on palindromes centers on understanding palindrome formation during gene amplification. Other studies have attempted to relate palindrome formation to molecular mechanisms involved in double stranded breaks and in the formation of inverted repeats. Assisted by high speed computers, other groups of scientists link palindrome formation to the conservation of genetic information.</p><p>Related to the direction of transcription by RNA polymerase, DNA strands have upstream and downstream terminus defined by differing chemical groups at each end. The ends of each strand of DNA or RNA are termed the 5' (phosphate bound to the 5' position carbon) and 3' (phosphate bound to the 3' carbon) ends to indicate a polarity within the molecule. Using the letters A, T, C, G, to represent the nitrogenous bases adenine, thymine, cytosine, and guanine found in DNA, and the letters A, U, C, G to represent the nitrogenous bases adenine, uracil, cytosine, guanine found in RNA (Note that uracil in RNA replaces the thymine found in DNA), geneticists usually represent DNA by a series of base codes (e.g., 5' AATCGGATTGCA 3'). The base codes are usually arranged from the 5' end to the 3' end.</p><p>Because of specific base pairing in DNA (i.e., adenine (A) always bonds with (thymine (T) and cytosine (C) always bonds with guanine (G)) the complimentary stand to the sequence 5' AATCGGATTGCA 3' would be 3' TTAGCCTAACGT 5'.</p><p>With palindromes the sequences on the complimentary strands read the same in either direction. For example, a sequence of 5' GAATTC3' on one strand would be complimented by a 3' CTTAAG 5' strand. In either case, when either strand is read from the 5' prime end the sequence is GAATTC. Another example of a palindrome would be the sequence 5' CGAAGC 3' that, when reversed, still reads CGAAGC.</p><p>Palindromes are important sequences within nucleic acids. Often they are the site of binding for specific enzymes (e.g., restriction endobucleases) designed to cut the DNA strands at specific locations (i.e., at palindromes).</p><p>Palindromes may arise from brakeage and chromosomal inversions that form inverted repeats that compliment each other. When a palindrome results from an inversion, it is often referred to as an inverted repeat. For example, the sequence 5' CGAAGC 3', if inverted (reversed 180&deg;), still reads CGAAGC.</p><p>The <a href="http://emboss.open-bio.org/">European Molecular Biology Open Software Suite (EMBOSS)</a> includes some basic tools for finding tandem repeats and inverted repeats (see <a href="http://emboss.open-bio.org/html/use/apbs06.html#GroupsAppsTableNucleicrepeatsR6">B.6.22. Applications in group Nucleic:repeats</a>). There are many on-line services providing the EMBOSS tools, for example:</p><ul>
<li>Wageningen Bioinformatics Webportal <a href="http://emboss.bioinformatics.nl/">EMBOSS explorer</a></li>
<li><a href="http://mobyle.pasteur.fr/">Mobyle@Pasteur</a></li>
<li><a href="http://wsembnet.vital-it.ch/">Soaplab2 Web Services at Vital-IT</a></li>
</ul><p>For more sophisticated repeat finding you will want to look at tools using <a href="http://www.girinst.org/repbase/">Repbase</a> for example:</p><ul>
<li>CENSOR
<ul>
<li><a href="http://www.girinst.org/censor/">CENSOR@GIRI</a></li>
<li><a href="http://www.ebi.ac.uk/Tools/so/censor/">CENSOR@EMBL-EBI</a></li>
</ul>
</li>
<li><a href="http://www.repeatmasker.org/">RepeatMasker</a></li>
<li><a href="http://mummer.sourceforge.net/">MUMmer</a>&nbsp;(scan_for_match)</li>
<li><a href="http://emboss.bioinformatics.nl/cgi-bin/emboss/palindrome">Emboss Palindrome</a></li>
</ul><p>Other nucleotide repeat finding methods found by a couple of web searches:</p><ul>
<li><a href="http://tandem.bu.edu/trf/trf.html">Tandem Repeats Finder</a></li>
<li><a href="http://selab.janelia.org/recon.html">RECON</a></li>
<li><a href="http://www.yandell-lab.org/software/repeatrunner.html">RepeatRunner</a></li>
<li><a href="http://bibiserv.techfak.uni-bielefeld.de/reputer/">REPuter</a></li>
<li><a href="http://210.212.215.200/IMEX/index.html">Imperfect Microsatellite Extractor (IMEx)</a></li>
<li><a href="http://www.imtech.res.in/raghava/srf/">Spectral Repeat Finder (SRF)</a></li>
<li><a href="http://zlab.bu.edu/repfind/form.html">REPFIND</a></li>
<li><a href="http://crispr.u-psud.fr/Server/CRISPRfinder.php">CRISPRfinder</a></li>
<li><a href="http://grail.lsd.ornl.gov/grailexp/">GrailEXP</a></li>
<li><a href="http://alggen.lsi.upc.edu/recerca/search/frame-search.html">CONREPP</a></li>
<li><a href="http://www.biophp.org/minitools/find_palindromes/demo.php%20"><span>find_palindromes</span></a></li>
<li><a href="http://insilico.ehu.eus/palindromes/"><span>Palindrome</span></a></li>
<li><a href="http://emboss.bioinformatics.nl/cgi-bin/emboss/palindrome">EMBOSS Palindrome</a></li>
<li><a href="http://bioinfo.cs.technion.ac.il/projects/Engel-Freund/new.html">Palindrome Search</a></li>
</ul>]]></description>
	<dc:creator>Radha Agarkar</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/44364/genbank-release-2570-is-now-available</guid>
	<pubDate>Wed, 23 Aug 2023 00:23:23 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/44364/genbank-release-2570-is-now-available</link>
	<title><![CDATA[GenBank release 257.0 is now available!]]></title>
	<description><![CDATA[<p><span>GenBank release 257.0 is now available! This release has 25.10 trillion bases and 3.69 billion records. Learn more:&nbsp;https://ncbiinsights.ncbi.nlm.nih.gov/2023/08/21/genbank-release-257/</span><a href="https://ow.ly/zHbV50PBE5o"><br /></a></p><p><a href="https://www.ncbi.nlm.nih.gov/genbank/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=genbank-release-20230821">GenBank</a>&nbsp;release 257.0 (8/15/2023) is now available on the&nbsp;<a href="https://ftp.ncbi.nlm.nih.gov/genbank/">NCBI FTP site</a>. This release has 25.10 trillion bases and 3.69 billion records.</p><p><strong>The current release has:</strong></p><ul>
<li>246,119,175 traditional records containing 2,112,058,517,945 base pairs of sequence data</li>
<li>2,631,493,489 WGS records containing 22,294,446,104,543 base pairs of sequence data</li>
<li>686,271,945 bulk-oriented TSA records containing 646,176,166,908 base pairs of sequence data</li>
<li>124,421,006 bulk-oriented TLS records containing 48,289,699,026 base pairs of sequence data</li>
</ul>]]></description>
	<dc:creator>Neel</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37788/s-plot2-creates-an-interactive-two-dimensional-heatmap-of-sequences</guid>
	<pubDate>Fri, 28 Sep 2018 05:36:19 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37788/s-plot2-creates-an-interactive-two-dimensional-heatmap-of-sequences</link>
	<title><![CDATA[S-plot2: creates an interactive, two-dimensional heatmap of sequences]]></title>
	<description><![CDATA[<p><span>S-plot2 creates an interactive, two-dimensional heatmap capturing the similarities and dissimilarities in nucleotide usage between genomic sequences (partial or complete). In S-plot2, whole eukaryotic chromosomes and smaller prokaryotic genomes can be efficiently compared. The tool includes functionality to extract, analyze, and automate BLAST queries of regions of interest within the heatmap. This facilitates the investigation of quickly evolving coding regions, novel coding regions, and laterally transferred elements.</span></p>
<p><span>http://www.putonti-lab.com/uploads/4/5/3/0/45307835/s-plot2_tutorial.pdf</span></p>
<p><span>http://journals.sagepub.com/doi/pdf/10.1177/1176934318797354</span></p><p>Address of the bookmark: <a href="https://bitbucket.org/lkalesinskas/splot" rel="nofollow">https://bitbucket.org/lkalesinskas/splot</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38678/upho-scripts-for-homology-and-orthology-assessment-from-genomic-sequences</guid>
	<pubDate>Mon, 14 Jan 2019 10:36:42 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38678/upho-scripts-for-homology-and-orthology-assessment-from-genomic-sequences</link>
	<title><![CDATA[UPhO: Scripts for homology and orthology assessment from genomic sequences.]]></title>
	<description><![CDATA[<p>UPhO finds orthologs with and without inparalogs from input gene family trees. Refer to the Documentation.pdf for more detailed explanations on its usage, installation and dependencies. Type UPhO.py -h for help.</p>
<p>The only input requierement for UPhO is a tree (or trees) in Newick format in which the leaves are named with a species idenfifier, a field separator, and sequence identifier. By default, the field separator is the character "|" but custom delimiters can be defined. Examples of trees to test UPhO are provided in the TestData folder.</p><p>Address of the bookmark: <a href="https://github.com/ballesterus/UPhO" rel="nofollow">https://github.com/ballesterus/UPhO</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/42296/igblast-117-is-now-available-with-improved-identification-of-productive-v-gene-sequences</guid>
	<pubDate>Sun, 01 Nov 2020 16:52:58 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/42296/igblast-117-is-now-available-with-improved-identification-of-productive-v-gene-sequences</link>
	<title><![CDATA[IgBLAST 1.17 is now available with improved identification of productive V gene sequences]]></title>
	<description><![CDATA[<p>A new release of&nbsp;<a href="https://go.usa.gov/x7WMc" target="_blank">IgBLAST</a>&nbsp;(1.17), the popular package for classifying and analyzing immunoglobulin and T cell receptor sequences, is now available on the&nbsp;<a href="https://go.usa.gov/x7WMc" target="_blank">web</a>&nbsp;and from the&nbsp;<a href="https://ftp.ncbi.nih.gov/blast/executables/igblast/release/LATEST" target="_blank">FTP site</a>. The updated package is better at identifying productive V gene sequences. We added a new field , &ldquo;V frame shift&rdquo;, to the IgBLAST output to indicate whether the V gene translation frame contains a frame-shift. We have also updated the definition of a productive V(D)J sequence to now exclude those with internal frame shifts.</p><p>See the&nbsp;<a href="https://ncbi.github.io/igblast/" target="_blank">new IgBLAST manual</a>&nbsp;on the NCBI GitHub site for more information on setting up and running IgBLAST.</p><p>If you have any questions or concerns, please email us at&nbsp;<a href="mailto:blast-help@ncbi.nlm.nih.gov" target="_blank">blast-help@ncbi.nlm.nih.gov</a></p><p>&nbsp;</p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44479/doubletrouble-identify-duplicated-genes-from-whole-genome-protein-sequences-and-classify</guid>
	<pubDate>Tue, 05 Mar 2024 00:23:49 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44479/doubletrouble-identify-duplicated-genes-from-whole-genome-protein-sequences-and-classify</link>
	<title><![CDATA[doubletrouble: identify duplicated genes from whole-genome protein sequences and classify]]></title>
	<description><![CDATA[<p><span>doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). Transposon-derived duplicates (TRD) can be further subdivided into rTRD (retrotransposon-derived duplication) and dTRD (DNA transposon-derived duplication). If users want a simpler classification scheme, duplicates can also be classified into SD- and SSD-derived (small-scale duplication) gene pairs. Besides classifying gene pairs, users can also classify genes, so that each gene is assigned a unique mode of duplication. Users can also calculate substitution rates per substitution site (i.e., Ka and Ks) from duplicate pairs, find peaks in Ks distributions with Gaussian Mixture Models (GMMs), and classify gene pairs into age groups based on Ks peaks.</span></p><p>Address of the bookmark: <a href="https://bioconductor.org/packages/release/bioc/html/doubletrouble.html" rel="nofollow">https://bioconductor.org/packages/release/bioc/html/doubletrouble.html</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/poll/view/19921/which-of-the-followings-are-the-best-place-to-study-bioinformatics</guid>
	<pubDate>Sun, 28 Dec 2014 00:20:30 -0600</pubDate>
	<link>https://bioinformaticsonline.com/poll/view/19921/which-of-the-followings-are-the-best-place-to-study-bioinformatics</link>
	<title><![CDATA[Which of the followings are the best place to study Bioinformatics ?]]></title>
	<description><![CDATA[<p>Bioinformatics is a major growth area and qualified Bioinformaticians are in high demand. An explosion in biological data has resulted from genome projects, next generation sequencing and other 'omics' techniques. Bioinformatics provides the tools to analyse and exploit such data sets.<br /><br />Can you please suggest me the best place to study bioinformatics ( Grad/PostGrad).</p>]]></description>
	<dc:creator>Reshma Khatun</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/21257/bioinformatics-phds-cover-letter</guid>
	<pubDate>Mon, 16 Feb 2015 12:48:52 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/21257/bioinformatics-phds-cover-letter</link>
	<title><![CDATA[Bioinformatics PhDs - Cover Letter]]></title>
	<description><![CDATA[<p><strong>Overview</strong><br />The reception your cover letter will receive is more varied and unpredictable than the other elements of your application packet.&nbsp; Some readers, especially at large research universities, will skip it entirely, and focus instead on more direct indicators of your academic achievements and potential: the CV, letters, and writing sample.&nbsp; Most often, however, your cover letter works in tandem with your CV, and represents your best opportunity to communicate directly with your target audience prior to an interview.<br /><br />The cover letter should not simply repeat the information contained in the CV; rather it should elaborate and frame the aspects of your academic training and background that you want search committee members to have uppermost in their minds as they consider your candidacy.&nbsp; At a minimum, it should contain a clear statement of your research and teaching interests, and how your qualifications match the requirements of the job description. Many disciplines have their own conventions and protocols for application materials including the cover letter. Be sure to show a draft of your letter to your chair or the department's placement advisor.<br /><br />There is no perfect or even preferred style of cover letter save that tone should be that of a confident professional.&nbsp; Departments aren't interested in hiring graduate students (they already have enough of those).&nbsp; They are looking for serious scholars/teachers who will make interesting, congenial, and productive colleagues. While it is probably not a good use of your time to tailor your letter for each opening, you will probably need at least two base versions that emphasize different elements (You would not want to use the same cover letter to apply to Oberlin as UC Irvine). You may want to customize the letters for the three to five jobs most attractive to you.<br /><br />Your cover letter should not exceed a page and a half or two at the most.&nbsp; No one will read a four-page letter, and your apparent inability to communicate your credentials in a concise manner is not to your advantage. Every line of your letter should serve a demonstrable purpose. Some people have gotten excellent jobs with a brief, boilerplate letter containing no more than a short intro, a paragraph on their research, and a couple of sentences on their teaching. Others use letters that discuss in very specific terms how they, their research, and their teaching would "fit" within the existing department and institutional setting. The choice of style is up to you, and should reflect what makes you feel most comfortable and most positive about your credentials.<br /><br />There are, however, circumstances where a longer, more annotated version is more likely to be helpful. The issues you should take into account when making this decision are:<br /><br />&nbsp;&nbsp;&nbsp; The size of the department/institution<br />&nbsp;&nbsp;&nbsp; The extent to which your research is mainstream and its significance readily apparent<br />&nbsp;&nbsp;&nbsp; The extent to which your qualifications diverge from those mentioned in the job ad<br />&nbsp;&nbsp;&nbsp; The extent to which the institution to which you are applying differs from UC Berkeley and the relative importance of teaching versus research<br />&nbsp;&nbsp;&nbsp; Unusual circumstances or career paths<br /><br />Size matters. The larger the department, the less detailed your letter needs to be.&nbsp; If there are already six people working in your sub-field, they can assess and translate the significance of your work to others in the department.&nbsp; If, however, you will be the only history of science person or the only physical anthropologist in the department, the search committee and others will likely need more help from you to understand the import of your work.&nbsp; Remember, if they are searching for your specialty they are understaffed in your area, and even if there is more than one person in your sub-field she/he may be on leave or otherwise uninvolved in the search.<br /><br />Similarly, smaller departments are more likely to be concerned than larger ones about the specific courses you are prepared to teach.&nbsp; If there are certain core courses your position needs to cover, make it unambiguously clear that you are prepared to do so even if you haven't taught them already.<br /><br />As a rule of thumb, the more your profile diverges from the specifics of the job description (or the norm, such that it exists), the more likely you will want to say more about why you are nonetheless a strong candidate.&nbsp; By doing so you can turn a question mark into an advantage.&nbsp; Highlight your strengths, and if you have time perform a little research on the department (see below) so you can explain how you would add to the department in ways that they might otherwise not have considered.&nbsp; Job descriptions are not always etched in stone. If you're very interested in the job, call the department and ask to speak to someone on the search committee.&nbsp; If that's too intimidating, call the departmental assistant or secretary. They can at least tell you if it&rsquo;s a new position or replacement which in turn can indicate whether they really need someone who can teach The Politics of Southern Africa or if Middle Eastern Politics would do just as well.&nbsp; They may well be willing to sacrifice a course in an area that the ad specified in order to get the extra teaching experience or innovative research that you have to offer, but only if you give them the opportunity and explain what they'd get in return.<br /><br />&nbsp;If you've taken an unusually long time to finish because you spent three years learning a new language in order to prepare for two years of original research or some other factor that enriches what you have to offer as a teacher or a scholar, let them know about it.&nbsp; Learning a new language, for example, is an indicator of your commitment to serious scholarship.&nbsp; Think of a way to put a positive valence on an aspect of your CV that you believe is likely to raise questions or doubts.<br /><br />As hard as it may be for not-yet-employed-but-soon-to-be academics like yourselves to believe, there are some individuals and departments that are intimidated by you and your institutional pedigree.&nbsp; There are many fine schools and departments that are convinced that every Berkeley graduate student is only interested in a position at Harvard, Princeton, or (hold your nose) Stanford.&nbsp; If it is a small liberal arts college, they may also assume that you view teaching and advising undergraduates strictly as a necessary evil. Ergo, why interview someone who will either look down their nose at us, and/or desert us for greener pastures as soon as their third book has been published and Yale comes calling.&nbsp; They often don't seem to realize that Berkeley graduate students are sincerely interested in a wide range of academic settings for a variety of reasons personal and professional, and, perhaps more to the point, Yale rarely "comes calling."&nbsp; An even greater burden of proof exists if a quick scan of your CV reveals that your all of your experience in higher education has occurred in a large, elite, research-oriented setting. How can you overcome this potential obstacle especially if you're very interested in a school that you have reason to believe may be suspicious of Berkeley PhDs?<br /><br />It's probably not advisable to write in a cover letter that they shouldn't be intimidated by lil' old you (i.e., "I'm really not very good; in fact, my advisor says I'm her worst graduate student in twenty years."), but there are ways to indicate a sincere interest in their department.&nbsp; One means is to do a little research, and briefly discuss how you might fit into the department and the institutional community-at-large.&nbsp; There are numerous articles written by faculty about the search process that state explicitly the positive impact it can have on their impression of a candidate to see evidence that that he/she has taken the time to learn something about them. Researching a department and its associated programs/research centers has never been easier.&nbsp; Virtually all colleges and universities are online, and their web addresses can be easily located using Education/Universities link.<br /><br />A second way to address fears of imminent flight is to provide evidence of ties to the area, the university, or lifestyle.&nbsp;&nbsp; If you are from the Midwest, have family nearby, or even if you just spent an enjoyable summer there, add a line about it and your desire to return to your cover letter for Purdue or Wayne State.&nbsp; If you did your undergraduate work at a similar type of institution, draw their attention to that link.&nbsp; Don't assume that they will notice where you got your BA on your CV, and make the connection.<br /><br />If you are applying to small, liberal arts colleges, don't just list the courses you've taught with a line of boilerplate about how important you take your teaching responsibilities to be. These days, a good, small college has a list price of about $30,000 a year, and close contact with people like you is one of their key selling points to parents and potential students. You are expected to be more than a lecturer, and your ability to convey your recognition of that fact and a sincere interest in working closely with students matters. Advising, participating in non-academic activities, watching your students grow and mature inside the classroom and out (and having an influence on that process) can be among the most rewarding aspects of the profession.&nbsp; If you value these broader elements of being a professor, let them know. In particular, if your own experience has been limited to large universities, think about describing an episode where you had a positive impact on the development of a student and the satisfaction you derived from helping him or her. At many small colleges, and large universities (including Berkeley) as well, one of the most significant pedagogical trends is fostering greater student involvement in faculty research.&nbsp; If you can articulate how this might occur for you and their students in a brief but thoughtful manner, it can alleviate some of the concerns occasioned by your Berkeley background.<br /><br />Your letter typically will have four segments: the introduction, research, teaching, and the closing.<br /><br /><strong>Introduction</strong><br />Be sure to identify the position you are applying for by rank and sub-field in the first sentence or two.&nbsp; It is not uncommon for departments to be engaged in more than one search in a given year, and large departments may have more than one in your sub-field.&nbsp; If it is an open rank position and you are applying as an assistant professor, in most cases you and your record of accomplishments will not be directly compared with those of more experienced candidates applying for it at the associate or full professor level.&nbsp; Rather, applicants are assessed based on where they are in their career path, and you have every chance of successfully competing against them.<br /><br />If you have finished, mention it up front. If not, state when you expect to file - no later than June 2003.&nbsp; Many readers will view your optimistic prediction with a skeptical eye, and anything you can say that makes the claim appear more credible (e.g., "I have written and my chair has reviewed four of the six chapters.") can help mitigate their concerns.&nbsp; You can put such a statement in the introduction or wait until you discuss the dissertation itself.<br /><br />If your discipline holds its annual meeting in the summer or early fall (i.e., before application deadlines) and you had an excellent conference interview, make reference to it in the cover letter including the names of the faculty with whom you spoke.&nbsp; By the time people actually start to read files, months may have passed and even the strongest of impressions can fade.&nbsp; But they can be rehabilitated and revived, especially if you can remind them of a specific strength, ability, or issue that seemed particularly salient during the interview.<br />Research<br />Unless you are applying to a school that cares only about your teaching (increasingly rare), a description of your research generally follows next.&nbsp; The challenge here is not simply to describe your research, but to frame it in terms of your sub-field and discipline. The search committee, hasn't lived, eaten and breathed Post-Edwardian Hermeneutics for the past five years the way you have. And they haven't been there every step of the torturous process like your friends and significant others. So forgive them for not immediately recognizing your research at first blush for the path-breaking work that it is.<br /><br />Departments want to know that in hiring you, they are adding someone who will make a future contribution to the discipline and enhance the reputation of the department. However, they are often ill-equipped to understand exactly how that will be true in your particular case. Many disciplines are sufficiently broad that leading or cutting-edge research in one sub-field is barely intelligible to those in others.&nbsp; In addition, when you became a candidate for the short list, your file will be read by department members outside your specialty, and, oftentimes later on in the process, by individuals outside your discipline as well. You need to describe the forest in which your tree resides, and explain why it matters in terms of the broader trends and issues within your discipline. Obviously, if your work is focused on one of the classic conundrums of your field, much less in the way of providing perspective is necessary than if you are addressing an emergent issue or employing an unconventional approach.<br /><br />If your research is particularly novel or cutting-edge, any markers of broader acceptance by other, more established scholars or scholarly organs in your field can ameliorate possible concerns about its relevance and potential importance.&nbsp; In discussing your work, note the recognition it has received in the form of competitive grants, awards, publications in refereed journals, and/or presentations at major conferences.<br /><br />It is also important to mention where you expect your research to go after the completion of your dissertation and the publications that will flow from it.&nbsp; They, especially at research-oriented institutions, want to know at least in broad terms where you expect to go from here.&nbsp; They want to see evidence of a scholarly agenda that extends beyond the dissertation.&nbsp; You don't need to have pages written or titles blocked out, but you need to tell them in a paragraph, (two at the most) about what questions intrigue you, and how you expect to go about finding the answers to them.&nbsp; These questions for future research may have been generated by the findings of your dissertation, unusual data uncovered during your fieldwork, or interesting side issues that you were forced to put off in order to keep your dissertation taut and focused.&nbsp; Think twice about mentioning future projects that appear entirely unrelated to your current work. Departments will want you to be firmly established in one area before you go off into another.<br /><br />The relative importance of teaching versus research is a continuous and not a discrete variable.&nbsp; Even schools that emphasize teaching in their job listing will generally want evidence of scholarly engagement and publishing potential. It is a very competitive market for students out there, and virtually all institutions are under pressure to sell themselves via the quality of their faculty to the limited number of good students in the applicant pool.&nbsp; A good marker for the relative importance of teaching versus research is the teaching load.&nbsp; An institution with a 3-2 teaching load (a total of five courses taught per two-semester year) will expect more in the way of and value research more highly than one with a 3-3 load.<br /><br />If you work in a capital-intensive area, mention your track record of gaining grants and other sources of external funding.<br /><strong>Teaching</strong><br />In a similar fashion, the more the institution you are applying to diverges from Berkeley and the more your profile differs from the job description, the more expansive you should be in talking about your teaching and what you have to offer their students.&nbsp; If you have won a teaching award at Berkeley, don't make them wait until they read your CV to discover that fact.<br /><br />For letters sent to large universities where you will be expected to teach large, lecture courses and graduate seminars, little is needed except to convey that you have the necessary experience and/or background.&nbsp; Since the dominant pedagogical style is the same as that found at Berkeley, it will be assumed that you will be able to do the same for them.<br /><br />If you have TA'd some of the courses that (based on the job description) you would be expected to offer, let them know.&nbsp; If you have not had that opportunity, but your fields and research fall within the domain of the job description, you may want to add a line about how well prepared you are to teach such courses based on your training and research.<br /><br />If your profile does not correspond exactly to the description found in the job announcement, but you believe that you could nonetheless teach the required courses, explain the basis for your confidence. What strength would you bring to the department that would more than make up for your "otherness"?&nbsp; Departments may decide that they don't "need" another conventional European historian if you can convince them that you can handle the core courses and offer something new that they don't currently cover as well. In this case especially, think about doing some research so you can speak in more specific terms about how you would fit into and enhance the department's offerings. Help them visualize how you would strengthen them as a department.<br /><br />Small colleges will want to know that you are able to teach on a more intimate basis and are prepared to take the time to do it well. If you give them three generic lines about how "important" you consider your teaching responsibilities, don't expect much of a positive response.&nbsp; Spend a couple of paragraphs describing your teaching experience and philosophy, and how you would take advantage of the opportunity to create you own courses.<br /><br />If you've had the opportunity to design and teach your own course, tell them, briefly, how you went about it and the choices you made. Don't just say you're a good teacher, tell them why. Look over your teaching evaluations and pick out one or two consistent strengths to highlight. Drawing on your experience, talk about how you engage students and enhance their skills (especially writing) and intellectual development.<br /><br />For good, small colleges, the quality of the teaching offered to students is their stock-in- trade.&nbsp; Even the most research-oriented, small colleges take teaching undergraduates very seriously. You need to demonstrate that you take it seriously as well, and can talk about it using more than vague generalities and shop-worn cliches.<br />Closing/Enclosures<br />Wrap it up quickly.&nbsp; If you are going to be traveling for any significant portion of the job search season be sure to let them know how they can contact you (email, cellphone and/or a Pacific Bell message center account are particularly good options).<br /><br />Before closing, include a sentence where you list the materials you have enclosed (e.g., CV, dissertation abstract, transcripts, teaching statement/portfolio, writing samples, etc.) and are having sent separately (letters of recommendation).&nbsp; You will often be assembling multiple packets at the same time (as in midnight October 14th, midnight November 14th, etc.) for jobs that ask for different combinations of enclosures.&nbsp; In addition to telling them what they should have received, it serves as a handy list for you to check before sealing the envelope.<br /><br />Should you send a writing sample, even if they haven't asked for one? Unless the norm in your discipline is to never send more than they ask for, if you've been smart and have already run off thirty copies at two cents per page (that's only sixty cents for a thirty page chapter) by all means send it.&nbsp; That way it's in the file should someone become interested in you and want to read more.</p>]]></description>
	<dc:creator>Martin Jones</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/22044/binc-sample-question-paper</guid>
	<pubDate>Thu, 16 Apr 2015 09:12:39 -0500</pubDate>
	<link>https://bioinformaticsonline.com/file/view/22044/binc-sample-question-paper</link>
	<title><![CDATA[BINC Sample Question Paper !!!]]></title>
	<description><![CDATA[<p>BINC sample question paper for round ONE.</p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/22044" length="1260" type="text/plain" />
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