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- January 25, 2012
- 10:09 AM
- 33 views
Video Tip of the Week: Biological Sequence Analysis I @ NIH
Well, more than a tip, a lecture. We haven’t done a tip today, we are in grant application process (time limiting) and this is an excellent video we’d like for more to see. Mary posted the first lecture, The Genomic Landscape circa 2012, in a series given at NIH. As the course description mentions, “The lectures [...]... Read more »
Green, E., Guyer, M., Green, E., Guyer, M., Manolio, T., & Peterson, J. (2011) Charting a course for genomic medicine from base pairs to bedside. Nature, 470(7333), 204-213. DOI: 10.1038/nature09764
- December 21, 2011
- 10:15 AM
- 240 views
Video Tip of the Week: eggNOG for the holidays (or to explore orthologous genes)
Who can resist a nice cup of eggnog for the holidays (especially with added brandy). I know I can’t. I make my grandpa’s recipe every December and, considering it uses tons of sugar, eggs, heavy cream and alcohol and that 1/2 & 1/2 is the lightest ingredient, only December.
Oh, that’s not what this tip is about, it’s about database of orthologous groups of genes, eggNOG. We’ve mentioned eggNOG before several times, but only in passing or in relation (orthologous?........ Read more »
Powell, S., Szklarczyk, D., Trachana, K., Roth, A., Kuhn, M., Muller, J., Arnold, R., Rattei, T., Letunic, I., Doerks, T.... (2011) eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Research. DOI: 10.1093/nar/gkr1060
- November 30, 2011
- 08:25 AM
- 258 views
Video Tip of the Week: Phosida, a post-translational modification database
Over 2 years ago I did a tip of the week on Phosida. Phosida is a database of phosphorylation, acetylation, and N-glycosylation data. Since the last tip, Phosida has undergone significant growth and some changes, including the addition of much more data (80,000 phosphorylation, acetylation and N-glycosylated sites from 9 different species) and tools (prediction and [...]... Read more »
Gnad, F., Gunawardena, J., & Mann, M. (2010) PHOSIDA 2011: the posttranslational modification database. Nucleic Acids Research, 39(Database). DOI: 10.1093/nar/gkq1159
- November 16, 2011
- 08:09 AM
- 336 views
Video Tip of the Week: MapMi, automated mapping of microRNA loci
Today’s video tip of the week is on MapMi. This tool is found at EBI and was developed by the Enright lab. The purpose of this tool is a computational system for mapping of miRNAs within and across species. As the abstract of their recent paper says: Currently miRBase is their primary repository, providing annotations [...]... Read more »
Guerra-Assuncao, J., & Enright, A. (2010) MapMi: automated mapping of microRNA loci. BMC Bioinformatics, 11(1), 133. DOI: 10.1186/1471-2105-11-133
- September 7, 2011
- 09:42 AM
- 500 views
Tip of the Week: Plant comparative genomics using Plaza
Plaza, a resource for plant comparative genomics, has a lot more than meets the eye at first. Currently the database has comparative tools and data for nearly 2 dozen plants including monocots, dicots, mosses and algae. There are some obvious tools and data from the homepage, but I suggest you take a look at the [...]... Read more »
Proost, S., Van Bel, M., Sterck, L., Billiau, K., Van Parys, T., Van de Peer, Y., & Vandepoele, K. (2009) PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants. THE PLANT CELL ONLINE, 21(12), 3718-3731. DOI: 10.1105/tpc.109.071506
- August 17, 2011
- 09:06 AM
- 463 views
Tip of the Week: CoGe (comparing genomes) revisited
I did a tip on CoGe’s tool, GeVo about two years ago and we’ve had a guest post about CoGe from Eric Lyons, the lead developer of CoGe just over a year ago. In our ongoing and occasional quest to keep our tips fresh (and move them to SciVee), I’ve decided to revisit CoGe and [...]... Read more »
Tang, H., Lyons, E., Pedersen, B., Schnable, J., Paterson, A., & Freeling, M. (2011) Screening synteny blocks in pairwise genome comparisons through integer programming. BMC Bioinformatics, 12(1), 102. DOI: 10.1186/1471-2105-12-102
- March 30, 2011
- 01:07 AM
- 751 views
Tip of the Week: MetaPhoOrs, orthology and paralogy predictions
The researchers and developers at PhylomeDB haven’t rested on their laurels. I did a tip of the week on PhylomeDB 3 months ago and not too long ago I was checking over there and found the team had created another useful database and analysis tool, MetaPhoOrs. What is MetaPhoOrs? To quote from the homepage:
MetaPhOrs is a public repository of phylogeny-based orthology and paralogy predictions that were computed using resources available in seven popular homology prediction services (Phylome........ Read more »
Pryszcz, L., Huerta-Cepas, J., & Gabaldon, T. (2010) MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score. Nucleic Acids Research, 39(5). DOI: 10.1093/nar/gkq953
- December 15, 2010
- 01:34 AM
- 920 views
Tip of the Week: RepTar, a database of miRNA target sites
microRNAs have become a rich source of research as they probably have a huge effect on gene expression and disease. The human genome may encode over 1,000 miRNAs that target over half of our genes. They might be implicated in a lot of common diseases (which not yet have been picked up in GWAS studies?). They are a fascinating area of biology that has only come of it’s on in the last decade. As such, the number of databases to catalog miRNAs is large. Today’s tip is on a new one, RepT........ Read more »
Elefant, N., Berger, A., Shein, H., Hofree, M., Margalit, H., & Altuvia, Y. (2010) RepTar: a database of predicted cellular targets of host and viral miRNAs. Nucleic Acids Research. DOI: 10.1093/nar/gkq1233
- December 6, 2010
- 08:00 AM
- 873 views
non-Traditional family structures and genomics
As I and my family await our 23andme kit to scan our genomes, family history has come back to the forefront of my thoughts. I used to be very fascinated by my own genealogy, and with adopted children, the concepts of descent, biology and culture have taken adjusted meanings for me. It’s why we have a ‘family map’ instead of a ‘family tree’. The difference between our cultural genealogy and our genetic genealogy has been become quite clear to me. Obtaining our family........ Read more »
Burns McGrath, B., & Edwards, K. (2009) When Family Means More (or Less) Than Genetics: The Intersection of Culture, Family, and Genomics. Journal of Transcultural Nursing, 20(3), 270-277. DOI: 10.1177/1043659609334931
- August 26, 2010
- 04:55 PM
- 922 views
Galaxy, a stride towards reproducible computational research
Galaxy started out as a very useful tool to do genomics research that was reproducible and sharable. One of my pet peeves in reading research papers that use genomic analysis or online genomics resources is the materials and methods sections. Often the methods and parameters used are mentioned only in a very cursory manner, if [...]... Read more »
Goecks, J., Nekrutenko, A., Taylor, J., & Galaxy Team, T. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biology, 11(8). DOI: 10.1186/gb-2010-11-8-r86
- May 18, 2010
- 04:35 PM
- 654 views
Personal Genomics, tipping points and a personal perspective
Please indulge a long post from a personal perspective, what genomics is about to do for _me_. This is information that many, if not all, of our readers already know. I’ve been researching and working in either experimental biology or genomics for over 20 years. Ever since the beginning of the Human Genome Project , which coincidently started the same year I started my Ph.D. program, into my postdoctoral research at EMBL and now my work at OpenHelix, I’ve known that someday personal........ Read more »
Ashley, E., Butte, A., Wheeler, M., Chen, R., Klein, T., Dewey, F., Dudley, J., Ormond, K., Pavlovic, A., & Morgan, A. (2010) Clinical assessment incorporating a personal genome. The Lancet, 375(9725), 1525-1535. DOI: 10.1016/S0140-6736(10)60452-7
- May 4, 2010
- 12:38 AM
- 2,012 views
Personal Genomics, clinical assessment and online resources
The Lancet paper, Clinical assessment incorporating a personal genome, has held my fascination this weekend (yes, I read it at the beach). Mary posted Friday and again Saturday on the paper and related NPR segment. It feels to me to be a seminal paper, though I do agree with Daniel at Genetic Future, there are a lot there we still don’t know. A large portion of the variation is in non-coding regions, and thus predictions and propensities are hard to come by with the available analysis. In ........ Read more »
Ashley, E., Butte, A., Wheeler, M., Chen, R., Klein, T., Dewey, F., Dudley, J., Ormond, K., Pavlovic, A., & Morgan, A. (2010) Clinical assessment incorporating a personal genome. The Lancet, 375(9725), 1525-1535. DOI: 10.1016/S0140-6736(10)60452-7
- March 24, 2010
- 01:01 AM
- 1,095 views
Tip of the Week: Genomicus and genome evolution
Today’s tip is on Genomicus. Genomicus is a great tool to visualize gene duplication, synteny and genome evolution. The search and display interfaces are quite straightforward, and there are lots of great features (viewing ancestral gene information, links out to resources, different views of phylogenies, etc) in the tool. This video is only a short introduction. You can delve deeper into the tool with the help and documentation, including an 11 minute video.
There is also a recent (adva........ Read more »
Muffato, M., Louis, A., Poisnel, C., & Roest Crollius, H. (2010) Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes. Bioinformatics. DOI: 10.1093/bioinformatics/btq079
- November 16, 2009
- 05:52 PM
- 495 views
(re)Funding Databases II
So, I wrote about defunding resources and briefly mentioned a paper in Database about funding (or ‘re’funding) databases and resources. I’d like to discuss this a bit further. The paper, by Chandras et. al, discusses how databases and, to use their term, Biological Resource Centers (BRCs) are to maintain financial viability.
Let me state first, I completely agree with their premise, that databases and resources have become imperative. The earlier model of “publication of ........ Read more »
Chandras, C., Weaver, T., Zouberakis, M., Smedley, D., Schughart, K., Rosenthal, N., Hancock, J., Kollias, G., Schofield, P., & Aidinis, V. (2009) Models for financial sustainability of biological databases and resources. Database. DOI: 10.1093/database/bap017
- October 20, 2009
- 01:23 PM
- 942 views
Transcription Start Sites, databases and tools
A recent paper in PLoS One finds hundreds of new putative transcription start sites (TSS): PLoS ONE: Genome-Wide Identification of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in E. coli. I found the paper interesting, and a good example of how high-throughput studies and genomics can advance our understanding of biology and work in concert with experimental biology, while at the same time dumping a whole lot of new data in our laps.
I’d like to point out so........ Read more »
Mendoza-Vargas, A., Olvera, L., Olvera, M., Grande, R., Vega-Alvarado, L., Taboada, B., Jimenez-Jacinto, V., Salgado, H., Juárez, K., Contreras-Moreira, B.... (2009) Genome-Wide Identification of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in E. coli. PLoS ONE, 4(10). DOI: 10.1371/journal.pone.0007526
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