*  Third-generation RNA-sequencing analysis: graph alignment and transcript assembly with long reads
A common analysis workflow of RNA-sequencing (RNA-seq) data consists of mapping the sequencing reads to a reference genome, ... Third-generation RNA-sequencing analysis: graph alignment and transcript assembly with long reads. Visa fullständig post ... Third-generation RNA-sequencing analysis: graph alignment and transcript assembly with long reads. ... The first part of this thesis focuses on the analysis of short-read RNA-seq data. As short-read mapping is an already well- ...
  https://helda.helsinki.fi/handle/10138/228812?locale-attribute=sv
*  Protein and RNA multiple sequence alignment, protein secondary structure prediction, trees, sub-family and function analysis...
Protein and RNA multiple sequence alignment, protein secondary structure prediction, trees, sub-family and function analysis ... Protein and RNA multiple sequence alignment, protein secondary structure prediction, trees, sub-family and function analysis ... Day 2 focuses on using Jalview for RNA sequence analysis, and also integrating cDNA and protein analysis and covers more ... Jalview hands-on training course is for anyone who works with sequence data and multiple sequence alignments from proteins, RNA ...
  http://www.jalview.org/training/training-courses/Protein-and-RNA-multiple-sequence-alignment-protein-secondary-structure
*  PhD Alumni | UMD Department of Computer Science
RNA-Sequencing Analysis: Read Alignment and Discovery Reconstruction of Fusion Transcripts Steven Salzberg ... Efficient analysis of Generalized Stochastic Petri Nets Satish Kumar Tripathi Hung Edward 2005 Managing Uncertainty and ... Automated Analysis of MPEG Compressed Video Azriel Rosenfeld Kushner Todd 1982 A theoretical model of interprocessor ... Computational Analysis of Intelligent Agents: Social and Strategic Settings Ahuja Narendra 1979 Connectedness Properties of ...
  https://www.cs.umd.edu/community/alumni/phd?field_graduation_year_value%5Bvalue%5D=&combine=&order=uid&sort=asc&page=1
*  Computational Biology: Genomes, Networks, Evolution | Electrical Engineering and Computer Science | MIT OpenCourseWare
... biological sequence analysis, hidden Markov models, gene finding, RNA folding, sequence alignment, genome assembly Networks: ... gene expression analysis, regulatory motifs, graph algorithms, scale-free networks, network motifs, network evolution Evolution ... Genomes: biological sequence analysis, hidden Markov models, gene finding, RNA folding, sequence alignment, genome assembly ... Networks: gene expression analysis, regulatory motifs, graph algorithms, scale-free networks, network motifs, network evolution ...
  http://dspace.mit.edu/bitstream/handle/1721.1/103560/6-047-fall-2008/contents/index.htm?sequence=242
*  St Andrews 2017 One Day Workshop | jalview.org
Jalview Multiple Sequence Alignment and Analysis Workshop for investigating structure and function of protein, RNA and DNA. ... "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench". Bioinformatics25 (9) 1189-1191 doi: 10.1093/ ... RNA and DNA sequence data. The course provides training in loading, editing, annotating and saving alignments, viewing 3D ... What is Jalview: Jalview is a free protein and nucleic acid sequence alignment visualisation software, with easy-to-use editing ...
  http://www.jalview.org/training/training-courses/St-Andrews-2017-One-Day-Workshop
*  Computer Science Course Descriptions - 2012-2014 Graduate Catalog - UT Dallas
Biological sequence analysis, gene finding, RNA folding, protein folding, sequence alignment, genome assembly, comparative ... sequence alignment and gene finding). Biological databases, data analysis and management. Prerequisite: Knowledge equivalent to ... CS 6359 (SE 6359) Object-Oriented Analysis and Design (3 semester hours) Analysis and practice of modern tools and concepts ... SE 6359 (CS 6359) Object-Oriented Analysis and Design (3 semester hours) Analysis and practice of modern tools and concepts ...
  http://www.utdallas.edu/ogs/CAT2012/ECS/CS/coursedescriptions_cs.htm
*  Computer Science Course Descriptions - 2010-2012 Graduate Catalog - UT Dallas
Biological sequence analysis, gene finding, RNA folding, protein folding, sequence alignment, genome assembly, comparative ... sequence alignment and gene finding). Biological databases, data analysis and management. (3-0) T. CS 6333 Algorithms in ... Major topics include: sequence alignment for determining similarity between proteins and genes; properties of similarities and ... CS 6359 (SE 6359) Object-Oriented Analysis and Design (3 semester hours) Analysis and practice of modern tools and concepts ...
  http://www.utdallas.edu/ogs/CAT2010/ECS/CS/coursedescriptions_cs.htm
*  Plus it
Multiple Sequence Alignments and RNA Secondary Structure Analysis. Multiple sequence alignments were performed using the ... Sequence Conservation Analysis. We used Phast (v1.4) for identifying evolutionarily conserved elements in a multiple alignment ... Small RNA Analysis. Seedlings were collected and processed with TRIzol (Invitrogen). RNA gel blots were performed with 6 to 12 ... MIR166 MIRNAs Have Specific Patterns of Sequence Conservation. The observation that the conservation of sequence and RNA ...
  http://www.plantcell.org/content/29/6/1248
*  Bionews] BIRD 2008 call for posters
RNA Structure and Function . Proteomics . Sequence Analysis & Alignment . SNPs and Haplotyping . System Biology and Modelling ... Machine learning and data analysis . Gene Expression/regulation & Microarrays . MicroRNA and RNAi . Molecular Diagnostics and ...
  http://www.bio.net/bionet/mm/bionews/2007-July/006117.html
*  In silico discovery of human natural anti... & related info | Mendeley
Molecular Sequence Data. *Proteome/*genetics. *RNA, Antisense/*genetics. *Sequence Alignment/*methods. *Sequence Analysis, RNA ... RESULTS: We have identified 568 NATs from human RefSeq RNA sequences. Among them, 403 NATs are reported for the first time, and ... According to the pairing region of a sense and antisense RNA pair, hNATs are divided into 6 classes, of which about 87% involve ... Combined with endogenous micro RNAs, hNATs could be regarded as a special group of transcripts contributing to the complex ...
  https://www.mendeley.com/research-papers/silico-discovery-human-natural-antisense-transcripts/
*  Training | jalview.org
Protein, RNA and DNA multiple sequence alignment and functional analysis workshop using Jalview. On 9.15am - 5.00pm Friday 14th ... RNA and DNA multiple sequence alignment and functional analysis' workshop.. The course is suitable for both Jalview novices and ... Jalview Sequence Alignment and Analysis Workshop. On Thursday 23rd November, Jim Procter and Suzanne Duce ran the fourth ... "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench". Bioinformatics25 (9) 1189-1191 doi: 10.1093/ ...
  http://www.jalview.org/taxonomy/term/3
*  Frontiers | Micropathogen Community Analysis in Hyalomma rufipes via High-Throughput Sequencing of Small RNAs | Frontiers in...
The sRNA deep-sequencing approach used in this analysis provides an intuitive method to survey micropathogen prevalence in ... As part of this analysis, a phylogenetic tree was constructed to display the relationships among the homologous sequences that ... As part of this analysis, a phylogenetic tree was constructed to display the relationships among the homologous sequences that ... Illumina HiSeq2000 technology was utilized to perform deep sequencing of small RNAs (sRNAs) extracted from field-collected H. ...
  https://www.frontiersin.org/articles/10.3389/fcimb.2017.00374/full
*  Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families - Current Protocols
... coding RNA (ncRNA) sequences identified in a wide variety of organisms ... Phylogeny‐aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 320:1632‐1635. doi: ... doi: 10.1261/rna.2750811.. Bauer, M., Klau, G.W., and Reinert, K. 2007. Accurate multiple sequence‐structure alignment of RNA ... RNA 17:1204‐1212. doi: 10.1261/rna.2753211.. Rost, B. 1999. Twilight zone of protein sequence alignments. Protein Eng. 12:85‐94 ...
  http://www.currentprotocols.com/WileyCDA/CPUnit/refId-bi1213.html?quicktabs_cp=cited
*  WN 2018 | STATS 547 - Probabilistic Modeling in Bioinformatics | Section 001
Analysis of DNA/RNA and protein sequence data. Algorithms for sequence alignment, statistical analysis of similarity scores, ... multiple sequence alignment, sequence comparison, and structure prediction. Analysis of expression array data. For more ... This course covers topics in Biological Sequence Analysis. Probabilistic models of proteins and nucleic acids. ... The syllabi do not necessarily reflect the assignments, sequence of course materials, and/or course expectations that the ...
  http://www.lsa.umich.edu/cg/cg_detail.aspx?content=2170STATS547001&termArray=w_18_2170
*  Shortest path vs. Sum-of-Pairs. The graph shows the MCC | Open-i
The graph shows the MCC score over 120 (5!) permutations order of the five sequences of the glmS dataset that was used in Table ... RNA, Untranslated/chemistry*/genetics*. *Sequence Alignment/methods*. *Sequence Analysis, RNA/methods*. *Software* ... Bottom Line: We also show that RNA secondary structures can be compared very rapidly by a simple string Edit-Distance algorithm ... Bottom Line: We also show that RNA secondary structures can be compared very rapidly by a simple string Edit-Distance algorithm ...
  https://openi.nlm.nih.gov/detailedresult.php?img=PMC2147038_1471-2105-8-366-6&req=4
*  CSC 2417 -- Algorithms for Genome Sequence Analysis
De novo transcriptome sequencing Presenter: Ilya Sutskever Slides. * April 4th NOTE UNUSUAL DATE -- micro RNAs & Datastorage ... Compressed Sequence Alignment Presenter: Vlad Yanovsky * April 9th -- HCI & Other. Hawkeye Assembly Viewer Presenter: Justin Ho ... DNA Sequencing. Shotgun sequencing * January 23rd -- Mapping Reads, Long & Short. Q-gram filtering techniques Presenter: Joe ... Analysis of Next Generation Sequencing Data. Winter 2008 Classes: W 11-1 in Bahen 025 ...
  http://www.cs.utoronto.ca/~brudno/csc2431/index.html
*  Itinerant Bioinformaticist: 2015
Topics include (a) genomes: sequence analysis, gene finding, RNA folding, genome alignment and assembly, database search; (b) ... Topics include: genome sequencing; functional landscape of the human genome (genes, gene regulation, repeats, RNA genes, ... Transcript structure analysis, Differential Expression, Significance Testing. Small and Large regulatory RNAs: lincRNA, miRNA, ... Amortized Analysis. Competitive Analysis. Network Flow. van Emde Boas Data Structure. Disjoint Sets Data Structures. P vs. NP. ...
  http://itinerantbioinformaticist.blogspot.jp/2015/
*  Jalview Glasgow 2016 One Day Workshop | jalview.org
Protein, RNA and DNA multiple sequence alignment and functional analysis workshop using Jalview ... "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench". Bioinformatics25 (9) 1189-1191 doi: 10.1093/ ... to provide training in how to use Jalview multiple sequence alignment visualisation program to visualise proteins, RNA and DNA ... RNA and DNA sequence data. The course will involve presentations, hands-on exercises and demonstrations. Plus, there are ...
  http://www.jalview.org/training/training-courses/Jalview-Glasgow-2016-One-Day-Workshop
*  Decreased cohesin in the brain leads to defective synapse development and anxiety-related behavior | JEM
Read alignment and transcriptome processing. RNA-sequencing data analysis was performed with TopHat2 version 2.0.9 (Kim et al ... All RNA-sequencing experiments were run on an Illumina HiSeq-2000, and RNA samples were sequenced with four replicates for P1 ... RNA extraction, cDNA library preparation, and RNA-sequencing. Total RNA was extracted from mouse cortex. The cDNA library was ... RNA was prepared from the P1 cortices of Smc3+/+ or Smc3+/− mice, and gene expression levels were analyzed by RNA-sequencing. ...
  http://jem.rupress.org/content/early/2017/04/12/jem.20161517
*  1206 December-2006 | www.caims.ca
Protein & RNA Structure and Function. * Proteomics. * Sequence Analysis & Alignment. * SNPs and Haplotyping. * Systems Biology ... Sequence analysis. Paper submission must be made electronically by following the instructions at. http://www.easychair.org/ ... Risk analysis and risk management. * Security and Privacy in Pervasive and Ubiquitous Computing. * Security for Grid Computing ... Formal analysis of security properties. * Information warfare. * Internet and web security. * Intrusion detection and ...
  http://www.caims.ca/node/283
*  0806 August-2006 | www.caims.ca
Protein & RNA Structure and Function. * Proteomics. * Sequence Analysis & Alignment. * SNPs and Haplotyping. * Systems Biology ... analysis, interval analysis, logical approaches (e.g. provers), or other. methods,. * proving geometric theorems with logical ... Intelligence Analysis. Sensor Network Applications. Social Network Analysis. Application Case Studies. Other Novel Applications ... 7.2 Nonlinear analysis of EEG and MEG. 7.3 Chaotic dynamics of nerve cells. 8. Applications. 8.1 Economics and finance. 8.2 Bio ...
  http://www.caims.ca/node/280
*  Alignment-free sequence analysis - Wikipedia
Molecular sequence and structure data of DNA, RNA, and proteins, gene expression profiles or microarray data, metabolic pathway ... alignment-free sequence analysis approaches to molecular sequence and structure data provide alternatives over alignment-based ... Sequence analysis Multiple sequence alignment Phylogenomics Bioinformatics Metagenomics Next-generation sequencing Population ... The pioneering approaches for sequence analysis were based on sequence alignment either global or local, pairwise or multiple ...
  https://en.wikipedia.org/wiki/Alignment-free_sequence_analysis
*  Human Microbiome Project - Wikipedia
... a web-based RNA alignment tool; WebMGA, a customizable web server for fast metagenomic sequence analysis; and DNACLUST, a tool ... Stombaugh, J.; Widmann, J.; McDonald, D.; Knight, R. (2011). "Boulder ALignment Editor (ALE): A web-based RNA alignment tool". ... Wu, S.; Zhu, Z.; Fu, L.; Niu, B.; Li, W. (2011). "WebMGA: A customizable web server for fast metagenomic sequence analysis". ... The project also financed deep sequencing of bacterial 16S rRNA sequences amplified by polymerase chain reaction from human ...
  https://en.wikipedia.org/wiki/Human_Microbiome_Project
*  EMBL Advanced Course in Analysis of Short Read Sequencing Data: post #1
127 AimsThe course will cover all processing steps in the analysis of ChIP-Seq and RNA-Seq experiments: base calling, alignment ... region identification, integrative bioinformatic and statistical analysis. It will be a m... ... EMBL Advanced Course in Analysis of Short Read Sequencing Data - posted in Conference and Workshop: Location & Date: EMBL ... The course will cover all processing steps in the analysis of ChIP-Seq and RNA-Seq experiments: base calling, alignment, region ...
  http://www.protocol-online.org/forums/topic/6988-embl-advanced-course-in-analysis-of-short-read-sequencing-data/
*  Statistical Analyses of Next Generation Sequence Data: A Partial Overview
In high-throughput resequencing of large genomes SOLiD is more accurate than Illumina whereas for RNA sequence analysis (RNA- ... Ultrafast and memory efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25. [PMC free ... Keywords: DNA, Sequencing, Deep sequencing, High throughput, Sequence reads, RNA, ChIP-seq, Intensities ... Jiang and Wong (2009) used statistical inference of isoform expression using high throughput RNA sequencing (RNA-Seq) data by ...
  http://pubmedcentralcanada.ca/pmcc/articles/PMC2989618/