http://www.bios.unc.edu/~weisun/teach/RNA-seq_pipeline.pdf
ArrayExpressHTS R/Bioconductor based Package (EMBL)
http://www.ebi.ac.uk/Tools/rwiki/
Gene Pattern - Broad Institute (web-based), uses Cufflinks
http://www.broadinstitute.org/cancer/software/genepattern/modules/RNA-seq/
Thursday, November 29, 2012
DEXSeq
Detecting differential usage of exons from RNA-seq data
RNA-Seq is a powerful tool for the study of alternative splicing and other
forms of alternative isoform expression. Understanding the regulation of
these processes requires sensitive and specific detection of differential iso-
form abundance in comparisons between conditions, cell types or tissues.
We present DEXSeq, a statistical method to test for differential exon usage
in RNA-Seq data. DEXSeq employs generalized linear models and offers re-
liable control of false discoveries by taking biological variation into account.
DEXSeq detects genes, and in many cases specific exons, that are subject to
differential exon usage with high sensitivity. We demonstrate the versatility
of DEXSeq by applying it to several data sets. The method facilitates the
study of regulation and function of alternative exon usage on a genome-wide
scale. An implementation of DEXSeq is available as an R/Bioconductor
package.
http://genome.cshlp.org/content/early/2012/06/21/gr.133744.111.full.pdf+html
http://watson.nci.nih.gov/bioc_mirror/packages/2.9/bioc/html/DEXSeq.html
HTSeq: Analysing high-throughput sequencing data with Python
http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html
RNA-Seq is a powerful tool for the study of alternative splicing and other
forms of alternative isoform expression. Understanding the regulation of
these processes requires sensitive and specific detection of differential iso-
form abundance in comparisons between conditions, cell types or tissues.
We present DEXSeq, a statistical method to test for differential exon usage
in RNA-Seq data. DEXSeq employs generalized linear models and offers re-
liable control of false discoveries by taking biological variation into account.
DEXSeq detects genes, and in many cases specific exons, that are subject to
differential exon usage with high sensitivity. We demonstrate the versatility
of DEXSeq by applying it to several data sets. The method facilitates the
study of regulation and function of alternative exon usage on a genome-wide
scale. An implementation of DEXSeq is available as an R/Bioconductor
package.
http://genome.cshlp.org/content/early/2012/06/21/gr.133744.111.full.pdf+html
http://watson.nci.nih.gov/bioc_mirror/packages/2.9/bioc/html/DEXSeq.html
HTSeq: Analysing high-throughput sequencing data with Python
http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html
Analysis of the bread wheat genome using whole-genome shotgun sequencing.
http://www.sciencedaily.com/releases/2012/11/121128143545.htm
Rachel Brenchley, Manuel Spannagl, Matthias Pfeifer, Gary L. A. Barker, Rosalinda D’Amore, Alexandra M. Allen, Neil McKenzie, Melissa Kramer, Arnaud Kerhornou, Dan Bolser, Suzanne Kay, Darren Waite, Martin Trick, Ian Bancroft, Yong Gu, Naxin Huo, Ming-Cheng Luo, Sunish Sehgal, Bikram Gill, Sharyar Kianian, Olin Anderson, Paul Kersey, Jan Dvorak, W. Richard McCombie, Anthony Hall, Klaus F. X. Mayer, Keith J. Edwards, Michael W. Bevan, Neil Hall. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature, 2012; 491 (7426): 705 DOI: 10.1038/nature11650
The wheat genome is five times the size of the human genome, giving it a complexity that makes it difficult to study.
Bread wheat (Triticum aestivum) is a globally important crop, accounting for 20 per cent of the calories consumed by humans. Major efforts are underway worldwide to increase wheat production by extending genetic diversity and analysing key traits, and genomic resources can accelerate progress. But so far the very large size and polyploid complexity of the bread wheat genome have been substantial barriers to genome analysis. Here we report the sequencing of its large, 17-gigabase-pair, hexaploid genome using 454 pyrosequencing, and comparison of this with the sequences of diploid ancestral and progenitor genomes. We identified between 94,000 and 96,000 genes, and assigned two-thirds to the three component genomes (A, B and D) of hexaploid wheat. High-resolution synteny maps identified many small disruptions to conserved gene order. We show that the hexaploid genome is highly dynamic, with significant loss of gene family members on polyploidization and domestication, and an abundance of gene fragments. Several classes of genes involved in energy harvesting, metabolism and growth are among expanded gene families that could be associated with crop productivity. Our analyses, coupled with the identification of extensive genetic variation, provide a resource for accelerating gene discovery and improving this major crop.
Rachel Brenchley, Manuel Spannagl, Matthias Pfeifer, Gary L. A. Barker, Rosalinda D’Amore, Alexandra M. Allen, Neil McKenzie, Melissa Kramer, Arnaud Kerhornou, Dan Bolser, Suzanne Kay, Darren Waite, Martin Trick, Ian Bancroft, Yong Gu, Naxin Huo, Ming-Cheng Luo, Sunish Sehgal, Bikram Gill, Sharyar Kianian, Olin Anderson, Paul Kersey, Jan Dvorak, W. Richard McCombie, Anthony Hall, Klaus F. X. Mayer, Keith J. Edwards, Michael W. Bevan, Neil Hall. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature, 2012; 491 (7426): 705 DOI: 10.1038/nature11650
The wheat genome is five times the size of the human genome, giving it a complexity that makes it difficult to study.
Bread wheat (Triticum aestivum) is a globally important crop, accounting for 20 per cent of the calories consumed by humans. Major efforts are underway worldwide to increase wheat production by extending genetic diversity and analysing key traits, and genomic resources can accelerate progress. But so far the very large size and polyploid complexity of the bread wheat genome have been substantial barriers to genome analysis. Here we report the sequencing of its large, 17-gigabase-pair, hexaploid genome using 454 pyrosequencing, and comparison of this with the sequences of diploid ancestral and progenitor genomes. We identified between 94,000 and 96,000 genes, and assigned two-thirds to the three component genomes (A, B and D) of hexaploid wheat. High-resolution synteny maps identified many small disruptions to conserved gene order. We show that the hexaploid genome is highly dynamic, with significant loss of gene family members on polyploidization and domestication, and an abundance of gene fragments. Several classes of genes involved in energy harvesting, metabolism and growth are among expanded gene families that could be associated with crop productivity. Our analyses, coupled with the identification of extensive genetic variation, provide a resource for accelerating gene discovery and improving this major crop.
Tuesday, November 27, 2012
Wednesday, November 21, 2012
Comparative genomics
http://www.ornl.gov/sci/techresources/Human_Genome/faq/compgen.shtml
Indeed, below we show that about 40% of the human genome can be aligned confidently with the mouse genome.
In total, about 90.2% of the human genome and 93.3% of the mouse genome unambiguously reside within conserved syntenic segments.
What are the comparative genome sizes of humans and other organisms being studied?
http://www.nature.com/nature/journal/v420/n6915/full/nature01262.html Initial sequencing and comparative analysis of the mouse genomeNature 420, 520-562 (5 December 2002) | doi:10.1038/nature01262; Received 18 September 2002; Accepted 31 October 2002 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| The proportion of mouse genes with a single identifiable orthologue in the human genome seems to be approximately 80%. The proportion of mouse genes without any homologue currently detectable in the human genome (and vice versa) seems to be less than 1%. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Dozens of local gene family expansions have occurred in the mouse lineage. Most of these seem to involve genes related to reproduction, immunity and olfaction, suggesting that these physiological systems have been the focus of extensive lineage-specific innovation in rodents. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
In total, about 90.2% of the human genome and 93.3% of the mouse genome unambiguously reside within conserved syntenic segments.
Neuroscience movies
http://www.edfilmfest.org.uk/films/2011/neuroscience-at-the-movies-brainstorm
http://www.imdb.com/title/tt0085271/
Neuroscience at the Movies: Brainstorm
Douglas Trumbull / United States of America / 1983 / 106 mins
Christopher Walken, Natalie Wood, Louise Fletcher, Cliff Robertson, Jordan Christopher
In Natalie Woods’ last film, scientists have developed the Hat: a helmet that allows sensations to be read from a person’s brain and written to tape so that others can experience them.
This is great for rollercosters and sex but when scientist Walken is confronted with a tape recorded during someone’s death, he has to think twice before pressing play. Utilising Showscan special effects this is An undeniably stimulating film to kick off our Reel Science programme and ignite a discussion with Centre of Clinical Brain Sciences Professor Stephen Lawrie from the University of Edinburgh on the ethics and verity of neurological science in film.
http://www.imdb.com/title/tt0209144/
Memento chronicles two separate stories of Leonard, an ex-insurance investigator who can no longer build new memories, as he attempts to find the murderer of his wife, which is the last thing he remembers. One story line moves forward in time while the other tells the story backwards revealing more each time. Written by Scion013
Lorenzo's Oil
http://www.imdb.com/title/tt0104756/
A boy develops a disease so rare that nobody is working on a cure, so his father decides to learn all about it and tackle the problem himself.
http://faculty.washington.edu/chudler/moviesn.html
http://scienceboard.net/pdf/brain_flicks.pdf
http://www.imdb.com/title/tt0085271/
Neuroscience at the Movies: Brainstorm
Douglas Trumbull / United States of America / 1983 / 106 mins
Christopher Walken, Natalie Wood, Louise Fletcher, Cliff Robertson, Jordan Christopher
In Natalie Woods’ last film, scientists have developed the Hat: a helmet that allows sensations to be read from a person’s brain and written to tape so that others can experience them.
This is great for rollercosters and sex but when scientist Walken is confronted with a tape recorded during someone’s death, he has to think twice before pressing play. Utilising Showscan special effects this is An undeniably stimulating film to kick off our Reel Science programme and ignite a discussion with Centre of Clinical Brain Sciences Professor Stephen Lawrie from the University of Edinburgh on the ethics and verity of neurological science in film.
http://www.imdb.com/title/tt0209144/
Memento chronicles two separate stories of Leonard, an ex-insurance investigator who can no longer build new memories, as he attempts to find the murderer of his wife, which is the last thing he remembers. One story line moves forward in time while the other tells the story backwards revealing more each time. Written by Scion013
Lorenzo's Oil
http://www.imdb.com/title/tt0104756/
A boy develops a disease so rare that nobody is working on a cure, so his father decides to learn all about it and tackle the problem himself.
http://faculty.washington.edu/chudler/moviesn.html
http://scienceboard.net/pdf/brain_flicks.pdf
Cell and tissue types
http://en.wikipedia.org/wiki/Connective_tissue
Connective tissue (CT) is a fibrous tissue and the most diverse tissue.[1] It is one of the four traditional classes of tissues (the others being epithelial, muscle, and nervous tissue). CT is found throughout the body.
The special CT subtype includes cartilage,bone, adipose tissue, blood, hematopoietic tissue (tissue that makes blood cells), and lymphatic tissue, as well as the most abundant protein in mammals, Type-I collagen, which makes up about 25% of the total protein content of the mammalian body.
http://en.wikipedia.org/wiki/Muscle_tissue
Muscle tissue is one of four basic biological tissues present in animals. It is a soft tissue that composes muscles.
http://en.wikipedia.org/wiki/Nervous_tissue
Nervous tissue is the main component of the nervous system - the brain, spinal cord, and nerves-which regulates and controls body functions. It is composed of neurons, which transmit impulses, and the neuroglia cells, which assist propagation of the nerve impulse as well as provide nutrients to the neuron.
http://en.wikipedia.org/wiki/Epithelium
Epithelial tissues line the cavities and surfaces of structures throughout the body, and also form many glands. Functions of epithelial cells include secretion, selective absorption, protection, transcellular transport and detection of sensation. In Greek "epi" means, "on, upon," and "thele" meaning "nipple".
http://en.wikipedia.org/wiki/Neuron
A neuron (
/ˈnjʊərɒn/ newr-on; also known as a neurone or nerve cell) is an electricallyexcitable cell that processes and transmits information through electrical and chemical signals. A chemical signal occurs via a synapse, a specialized connection with other cells. http://en.wikipedia.org/wiki/Neuroglia
Glial cells, sometimes called neuroglia or simply glia (Greek γλία, γλοία "glue"; pronounced in English as either /ˈɡliːə/ or /ˈɡlaɪə/), are non-neuronal cells that maintainhomeostasis, form myelin, and provide support and protection for neurons in the brain, and for neurons in other parts of the nervous system such as in the autonomic nervous system.
Microglia - are specialized macrophages capable of phagocytosis that protect neurons of the central nervous system.
Macroglia
- CNS: Astrocytes ("star", many functions, blood-brain barrier, ion homeostasis, nutrient support), Oligodendrocytes ("few branches", insulate axons), Ependymal cells, Radial glia,
Friday, November 16, 2012
Bioinformatics salary
- http://education-portal.com/articles/Salary_and_Career_Info_for_Bioinformatics_Specialists.html
- http://www.simplyhired.com/a/salary/search/q-bioinformatics
- http://jobmeplz.com/bioinformatics-salary.html
- http://www.glassdoor.com/Hourly-Pay/Genome-Sciences-Centre-Computational-Biologist-Bioinformatics-Hourly-Pay-E198280_DAO.htm?filter.jobTitleExact=Computational+Biologist+-+Bioinformaticshttp://bioinformaticssalary.net/
- http://www.ccs.neu.edu/home/kevin/bioinf/employment.html
- http://www.wowjobs.ca/salary-bioinformatics+specialist
- http://www.the-scientist.com/?articles.view/articleNo/13893/title/Partners-in-Research--Competitors-in-Pay/
- http://www.the-scientist.com/?articles.view/articleNo/13205/title/Academia-or-Industry-/
- http://www.the-scientist.com/?articles.view/articleNo/13893/title/Partners-in-Research--Competitors-in-Pay/
- http://www.careercruising.com
- http://www.labspaces.net/blog/1317/Negotiating_Salary_in_Biotech
- http://www.jobs-salary.com/biomedical-engineer-salary.htm
DEseq
DEseq
http://www-huber.embl.de/users/anders/DESeq/
DESeq is an R package to analyse count data from high-throughput sequencing assays such as RNA-Seq and test for differential expression.
http://www-huber.embl.de/users/anders/DESeq/
DESeq is an R package to analyse count data from high-throughput sequencing assays such as RNA-Seq and test for differential expression.
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