StatAlign: An Extendable Software Package for Joint Bayesian Estimation of Alignments and Evolutionary Trees. (1)
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Novák A, Miklós I, Lyngsø R, Hein J (0)
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PubMed: "Bioinformatics"[Jou... (0)
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Related Articles StatAlign: An Extendable Software Package for Joint Bayesian Estimation of Alignments and Evolutionary Trees. Bioinformatics. 2008 Aug 27; Authors: Novák A, Miklós I, Lyngsø R, Hein J MOTIVATION: Bayesian analysis is one of the most popular methods in phylogenetic inference. The most commonly used methods fix a single multiple alignment and consider only substitutions as phylogenetically informative mutations, though alignments and phylogenies should be inferred jointly as insertions and deletions also carry informative ...
The Joys of DIY Dynamic Programming (2)
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Keith Robison (1)
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Omics! Omics! (1)
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For nearly the first decade of my bioinformatics career I carried around a dirty little secret -- well, at least at times I felt it was one. I had coded many things, I could explain many algorithms, but I had never coded a dynamic programming alignment algorithm -- the core to so much I did. I had slightly hacked one version (just to have it do an all-all comparison of a database, doing each possible ...
Empirical profile mixture models for phylogenetic reconstruction. (1)
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Quang LS, Gascuel O, Lartillot N (0)
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Related Articles Empirical profile mixture models for phylogenetic reconstruction. Bioinformatics. 2008 Aug 21; Authors: Quang LS, Gascuel O, Lartillot N MOTIVATION: Previous studies have shown that accounting for sitespecific amino acid replacement patterns using mixtures of stationary probability profiles offers a promising approach for improving the robustness of phylogenetic reconstructions in the presence of saturation. However, such profile mixture models were introduced only in a Bayesian context, and are not yet available in a Maximum ...
Seeder: Discriminative Seeding DNA Motif Discovery. (1)
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Fauteux F, Blanchette M, Strömvik MV (0)
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Related Articles Seeder: Discriminative Seeding DNA Motif Discovery. Bioinformatics. 2008 Aug 21; Authors: Fauteux F, Blanchette M, Strömvik MV MOTIVATION: The computational identification of transcription factor binding sites is a major challenge in bioinformatics and an important complement to experimental approaches. RESULTS: We describe a novel, exact discriminative seeding DNA motif discovery algorithm designed for fast and reliable prediction of cis-regulatory elements in eukaryotic promoters. The algorithm is tested on biological benchmark data and shown ...
Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores. (1)
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Bogojeska J, Alexa A, Altmann A, Lengauer T, Rahnenführer J (0)
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Related Articles Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores. Bioinformatics. 2008 Aug 20; Authors: Bogojeska J, Alexa A, Altmann A, Lengauer T, Rahnenführer J SUMMARY: In genetics, many evolutionary pathways can be modeled by the ordered accumulation of permanent changes. Mixture models of mutagenetic trees have been used to describe disease progression in cancer and in HIV. In cancer, progression is modeled by the accumulation of chromosomal gains and losses ...
More genetics in high school than medical school? (1)
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Isaac Kohane (0)
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Countway Library of Medicine - Director's Blog (0)
1 week, 6 days
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This highly amusing story about fish that are not what they are said to be, should be a sobering wake-up call to medical schools. Here we read about students using third parties to DNA sequence and then taxonomize samples they procured in restaurants and groceries. In the article we read of high-school students (who are not necessarily interested in careers in science) whose scientific literacy with regard to genetics would put many physicians to shame. ...
PUBMETH.ORG (1)
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ITFP: an integrated platform of mammalian transcription factors. (1)
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Zheng G, Tu K, Yang Q, Xiong Y, Wei C, Xie L, Zhu Y, Li Y (0)
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Related Articles ITFP: an integrated platform of mammalian transcription factors. Bioinformatics. 2008 Aug 19; Authors: Zheng G, Tu K, Yang Q, Xiong Y, Wei C, Xie L, Zhu Y, Li Y SUMMARY: Investigation of transcription factors (TFs) and their downstream regulated genes (targets) is a significant issue in post genome era, which can provide a brand new vision for some vital biological process. However, information of TFs and their targets in mammalian is far from ...
Markov model plus k-word distributions: A synergy that produces novel statistical measures for sequence comparison. (1)
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Dai Q, Yang Y, Wang T (0)
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Related Articles Markov model plus k-word distributions: A synergy that produces novel statistical measures for sequence comparison. Bioinformatics. 2008 Aug 18; Authors: Dai Q, Yang Y, Wang T MOTIVATION: Many proposed statistical measures can efficiently compare biological sequences to further infer their structures, functions and evolutionary information. They are related in spirit because all the ideas for sequence comparison try to use the information on the k-word distributions, Markov model or both. Motivated by adding ...
Is a knol a scientific publishing platform? (2)
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peanutbutter (0)
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peanutbutter (0)
2 weeks, 2 days
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Image via CrunchBase, source unknown Google has recently released knol, which most people are calling Google’s version of Wikipedia. The main difference between a knol and a wikipedia article is that a knol has associated authorship or ownership against an article. This factor has caused some issues an outcries focusing on the merits of the wisdom of crowds verses the merits of single individuals and the whole ethos if information dissemination on the Web. (There ...
SciFoo: scientific fireworks (The Seven Stones) (2)
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Thomas (0)
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The Seven Stones (0)
2 weeks, 3 days
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In his list of eight 'generative' values (Better Than Free), Kevin Kelly includes 'embodiment'–the actual physical realization of an item or event which could be otherwise freely distributed over the web. While we are all 'hyperlinked' on the Internet, the value of those unique qualities that cannot be generated or "copied" on the web is dramatically increased. The type of intense emulation and shared excitement sparked at the recent Science Foo Camp (SciFoo 2008), organized ...
The Synergizer service for translating gene, protein, and other biological identifiers. (1)
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Berriz GF, Roth FP (0)
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Related Articles The Synergizer service for translating gene, protein, and other biological identifiers. Bioinformatics. 2008 Aug 12; Authors: Berriz GF, Roth FP SUMMARY: The Synergizer is a freely available web service that provides translations of biological database identifiers. It is accessible both programmatically and interactively. AVAILABILITY: The Synergizer is freely available to all users interactively via a web application and programmatically via a web service. Clients implementing the Synergizer application programming interface (API) are also ...
MotifVoter: a novel ensemble method for fine-grained integration of generic motif finders. (1)
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Wijaya E, Yiu SM, Son NT, Kanagasabai R, Sung WK (0)
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Related Articles MotifVoter: a novel ensemble method for fine-grained integration of generic motif finders. Bioinformatics. 2008 Aug 12; Authors: Wijaya E, Yiu SM, Son NT, Kanagasabai R, Sung WK MOTIVATION: Locating transcription factor binding sites (motifs) is a key step in understanding gene regulation. Based on Tompa's benchmark study, the performance of current de novo motif finders is far from satisfactory (with sensitivity </= 0:222 and precision </= 0:307). The same study also shows that ...
SeqMap : mapping massive amount of oligonucleotides to the genome. (1)
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Jiang H, Wong WH (0)
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Related Articles SeqMap : mapping massive amount of oligonucleotides to the genome. Bioinformatics. 2008 Aug 12; Authors: Jiang H, Wong WH SUMMARY: SeqMap is a tool for mapping large amount of short sequences to the genome. It is designed for finding all the places in a reference genome where each sequence may come from. This task is essential to the analysis of data from ultra high throughput sequencing machines. With a carefully designed index-filtering algorithm ...
Cancer outlier detection based on likelihood ratio test. (1)
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Hu J (0)
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Related Articles Cancer outlier detection based on likelihood ratio test. Bioinformatics. 2008 Aug 12; Authors: Hu J MOTIVATION: Microarray experiments can be used to help study the role of chromosomal translocation in cancer development through cancer outlier detection. The aim is to identify genes that are up- or down-regulated in a subset of cancer samples in comparison to normal samples. RESULTS: We propose a likelihood-based approach which targets detecting the change of point in mean ...
Comparison of algorithms for pre-processing of SELDI-TOF mass spectrometry data. (1)
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Cruz-Marcelo A, Guerra R, Vannucci M, Li Y, Lau CC, Man TK (0)
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Related Articles Comparison of algorithms for pre-processing of SELDI-TOF mass spectrometry data. Bioinformatics. 2008 Aug 11; Authors: Cruz-Marcelo A, Guerra R, Vannucci M, Li Y, Lau CC, Man TK MOTIVATION: Surface enhanced laser desorption and ionization (SELDI) time of flight (TOF) is a mass spectrometry (MS) technology. The key features in a mass spectrum are its peaks. In order to locate the peaks and quantify their intensities several pre-processing steps are required. Though different approaches ...
A word about databases (1)
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Jason Stajich (0)
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The Hyphal Tip: Fungal Genomes and Comparative Genomics (0)
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Report concludes that a fungal genome database is of "the highest priority". This is the title as listed in PubMed for this article from Future Medicine about the AAM report on charting future needs and avenues of research on the fungal kingdom. The need for a comprehensive database for information about fungi, starting at least with systematic collections of genomic and transcript data, is highlighted as a major need. Really and sort of new database ...
WikiPathways - the challenge of community curation (1)
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Joerg Kurt Wegner (2)
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Mining Drug Space (2)
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"But as the influx and complexity of biological data continue to grow, so will the challenge of organizing and maintaining these databases.Fortunately, the biology community can provide an answer that will scale with the challenge: community curation." [DOI 10.1371/journal.pbio.0060184]WikiPathways follows the concept of a community based data curation principle. So, they follow the same strategy of tools likeWikiProteinsEcoliWikiThe database is available as SubVersion repository (SVN) in the GenMAPP Pathway Markup Language (GPML) format. For a ...
Robust and Efficient Identification of Biomarkers by Classifying Features on Graphs. (1)
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Hwang T, Sicotte H, Tian Z, Wu B, Kocher JP, Wigle DA, Kumar V, Kuang R (0)
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Related Articles Robust and Efficient Identification of Biomarkers by Classifying Features on Graphs. Bioinformatics. 2008 Jul 24; Authors: Hwang T, Sicotte H, Tian Z, Wu B, Kocher JP, Wigle DA, Kumar V, Kuang R MOTIVATION: A central problem in biomarker discovery from large-scale gene expression or single nucleotide polymorphism (SNP) data is the computational challenge of taking into account the dependence among all the features. Methods that ignore the dependence usually identify non-reproducible biomarkers across ...
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