200 posts · 151,786 views
On the OpenHelix blog you will find a genomics resources news portal with daily postings about genomics and bioinformatics resources, genomics news and research, science and more. Our goal is to keep you, the researcher, informed about the overwhelming amount of genomics data out there and how to access it through the tools, databases and resources that are publicly available to you.
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- December 14, 2011
- 09:05 AM
- 3,317 views
Video Tip of the Week: Big Changes to NCBI’s Genome Resources
NCBI was created in 1988 and has maintained the GenBank database for years. They also provide many computational resources and data retrieval systems for many types of biological data. As such they know all too well how quickly the data that biologists collect has changed and expanded. As uses for various data types have been [...]... Read more »
Tatusova, T., Karsch-Mizrachi, I., & Ostell, J. (1999) Complete genomes in WWW Entrez: data representation and analysis. Bioinformatics, 15(7), 536-543. DOI: 10.1093/bioinformatics/15.7.536
Barrett, T., Clark, K., Gevorgyan, R., Gorelenkov, V., Gribov, E., Karsch-Mizrachi, I., Kimelman, M., Pruitt, K., Resenchuk, S., Tatusova, T.... (2011) BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata. Nucleic Acids Research. DOI: 10.1093/nar/gkr1163
Sayers, E., Barrett, T., Benson, D., Bolton, E., Bryant, S., Canese, K., Chetvernin, V., Church, D., DiCuccio, M., Federhen, S.... (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research. DOI: 10.1093/nar/gkr1184
- December 12, 2011
- 10:40 AM
- 2,964 views
Why don’t users employ workflows for “big data”? I know why.
Yesterday a tweet to a great post came across the ethers, and ever since I read it I knew I had to write this post. Here’s the original nugget:
RT @ctitusbrown: (my) thoughts on data intensive science & workflows: http://bit.ly/tWXSnx
It is a post about why end users are not adopting workflows which could really help them in this eScience world we find ourselves in, and as we keep moving forward with giant data sets and “big data” projects. And some other points about........ 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 4, 2010
- 12:38 AM
- 2,629 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
- September 23, 2009
- 08:45 AM
- 1,895 views
Tip of the week: JBrowse, a game changer?
In most of software and database development the changes that are coming along all the time seem to be tweaks and polishes on the existing strategies. Every so often, though, there’s a big shift in the strategy or mechanism. This week the JBrowse paper I read made me realize that is now firmly underway. Today’s tip of the week will introduce JBrowse, and here I’ll describe some of the reasons this is a game changer.... Read more »
Skinner, M., Uzilov, A., Stein, L., Mungall, C., & Holmes, I. (2009) JBrowse: A next-generation genome browser. Genome Research, 19(9), 1630-1638. DOI: 10.1101/gr.094607.109
- July 22, 2008
- 10:03 PM
- 1,883 views
Another Wiki, WikiPathways
PLoS Biology reports today on WikiPathway. The paper entitled “WikiPathways: Pathway editing for the people,” announces a new wiki for the ‘public curation’ of pathway data. The authors argue that
 The exponential growth of diverse types of biological data presents the research community with an unprecedented challenge to keep the flood of biological data as accessible, ... Read more »
Alexander Pico, Thomas Kelder, Martijn P van Iersel, Kristina Hanspers, Bruce R Conklin, & Chris Evelo. (2008) WikiPathways: Pathway Editing for the People. PLoS Biology, 6(7). DOI: 10.1371/journal.pbio.0060184
- April 6, 2009
- 09:15 AM
- 1,773 views
Gene expression and SNPs…very neat stuff
by Mary in OpenHelix
A question on the blog last week got me going through my old posts, because I was sure that I had done one on a database of SNP effects on gene expression. But it turned out that was in my memory, but still in the draft posts for the blog….
I had come across the work [...]... Read more »
Heinzen, E., Ge, D., Cronin, K., Maia, J., Shianna, K., Gabriel, W., Welsh-Bohmer, K., Hulette, C., Denny, T., & Goldstein, D. (2008) Tissue-Specific Genetic Control of Splicing: Implications for the Study of Complex Traits. PLoS Biology, 6(12). DOI: 10.1371/journal.pbio.1000001
- March 24, 2010
- 01:01 AM
- 1,739 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
- February 16, 2011
- 09:11 AM
- 1,677 views
Tip of the Week: Melina II for promoter analysis
by Mary in OpenHelix
One of the most frequently-asked questions we get when we are out doing workshops is: how do I find motifs in promoters, and what can I do with them to find more information? Just last Friday we were asked this again at the workshops we did at USC. So for this week’s tip of the week I’m going to show one of the tools I recommend for that purpose–Melina II. (I also recommended the MEME Suite and VISTA‘s rVISTA features as well, but for this tip I’ll focus on Melin........ Read more »
Okumura, T., Makiguchi, H., Makita, Y., Yamashita, R., & Nakai, K. (2007) Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions. Nucleic Acids Research, 35(Web Server). DOI: 10.1093/nar/gkm362
- December 15, 2010
- 01:34 AM
- 1,631 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
- March 18, 2009
- 06:34 AM
- 1,629 views
Tip of the Week: TDR Targets Database
by Jennifer in OpenHelix
For today’s tip, I would like to introduce you to the TDR Targets Database, which seeks “… to exploit the availability of diverse datasets to facilitate the identification and prioritization of drug targets in pathogens causing neglected diseases.” I found out about this database this past weekend as I was catching up on my [...]... Read more »
Agüero, F., Al-Lazikani, B., Aslett, M., Berriman, M., Buckner, F., Campbell, R., Carmona, S., Carruthers, I., Chan, A., Chen, F.... (2008) Genomic-scale prioritization of drug targets: the TDR Targets database. Nature Reviews Drug Discovery, 7(11), 900-907. DOI: 10.1038/nrd2684
- November 20, 2009
- 10:51 AM
- 1,605 views
Corn: 85% not corn, and missing big pieces
by Mary in OpenHelix
So I’m all excited about the genome festival that I’m seeing, related to the publication of the new sequence version of corn. You can access the main paper in Science, and there’s a very neat diagram in figure 1 that is like looking across time at the sequence data and into the corn nebula. But the thing that cracked me up was this line from the abstract:
Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the ........ Read more »
Springer, N., Ying, K., Fu, Y., Ji, T., Yeh, C., Jia, Y., Wu, W., Richmond, T., Kitzman, J., Rosenbaum, H.... (2009) Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content. PLoS Genetics, 5(11). DOI: 10.1371/journal.pgen.1000734
Schnable, P., Ware, D., Fulton, R., Stein, J., Wei, F., Pasternak, S., Liang, C., Zhang, J., Fulton, L., Graves, T.... (2009) The B73 Maize Genome: Complexity, Diversity, and Dynamics. Science, 326(5956), 1112-1115. DOI: 10.1126/science.1178534
- May 26, 2010
- 08:34 AM
- 1,577 views
Tip of the Week: The Cancer Genome Workbench
In today’s tip I’d like to introduce you to the Cancer Genome Workbench, or CGWB. The workbench gathers cancer information from a wide variety of projects including Johns Hopkins University and GlaxoSmithKline Cancer Cell Line Genomic Profiling Data, NCI’s Therapeutically Applicable Research to Generate Effective Treatment (TARGET), NHGRI’s Tumor Sequencing Project (TSP), The Cancer Genome Atlas (TCGA), and the Sanger Center’s COSMIC initiative and presents the cum........ Read more »
Zhang, J., Finney, R., Rowe, W., Edmonson, M., Yang, S., Dracheva, T., Jen, J., Struewing, J., & Buetow, K. (2007) Systematic analysis of genetic alterations in tumors using Cancer Genome WorkBench (CGWB). Genome Research, 17(7), 1111-1117. DOI: 10.1101/gr.5963407
- August 26, 2010
- 04:55 PM
- 1,538 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
- January 5, 2011
- 08:45 AM
- 1,531 views
Tip of the Week: SKIPPY predicting variants w/ splicing affects
More and more disease-causing mutations are being identified in exonic splicing regulatory sequences (ESRs). These disease effects can result from ESR mutations that cause exon skipping in functionally diverse genes. In today’s tip I’d like to introduce you to a tool designed to detect exon variants that modulate splicing. The tool is named SKIPPY and has been developed and is maintained by groups in the Genomic Functional Analysis research section of the NHGRI.
At the end of the ........ Read more »
Woolfe, A., Mullikin, J., & Elnitski, L. (2010) Genomic features defining exonic variants that modulate splicing. Genome Biology, 11(2). DOI: 10.1186/gb-2010-11-2-r20
Cline, M., & Karchin, R. (2010) Using bioinformatics to predict the functional impact of SNVs. Bioinformatics. DOI: 10.1093/bioinformatics/btq695
- March 30, 2011
- 01:07 AM
- 1,529 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
- March 28, 2011
- 09:15 AM
- 1,491 views
Protein Structure Analysis – How Far We’ve Come!
The team here at OpenHelix has recently updated our sponsored tutorials on two excellent structural biology resources, the RCSB Protein Data Bank (PBD) and the PSI-Nature Structural Biology Knowledgebase (PSI SBKB). Because the tutorials are sponsored by these resources they are free for anyone to view and download in full. You can access our training materials for the resources at our RCSB PDB landing page, or our PSI SBKB landing page. I’m very happy with both tutorial suites, so please........ Read more »
Berman, H. (2000) The Protein Data Bank. Nucleic Acids Research, 28(1), 235-242. DOI: 10.1093/nar/28.1.235
Berman, H., Westbrook, J., Gabanyi, M., Tao, W., Shah, R., Kouranov, A., Schwede, T., Arnold, K., Kiefer, F., Bordoli, L.... (2009) The protein structure initiative structural genomics knowledgebase. Nucleic Acids Research, 37(Database). DOI: 10.1093/nar/gkn790
Doolittle, R. (2010) The Roots of Bioinformatics in Protein Evolution. PLoS Computational Biology, 6(7). DOI: 10.1371/journal.pcbi.1000875
Miller, M. (2010) The early years of retroviral protease crystal structures. Biopolymers, 94(4), 521-529. DOI: 10.1002/bip.21387
- January 13, 2010
- 08:17 AM
- 1,479 views
Tip of the Week: iceLogo for conserved sequence display
by Mary in OpenHelix
I’ve always been a fan of clever graphical displays that convey key data points. They can be so effective when done well. And from way back when I was first exposed to the logo-style histogram displays for conserved promoter sequences they’ve always struck me as particularly suited to this method. Usually for ease-of-use I’ve gone to WebLogo. It’s easy, and quick to use. But recently I learned of another tool that provides the logos and has a bit more to it. T........ Read more »
Colaert, N., Helsens, K., Martens, L., Vandekerckhove, J., & Gevaert, K. (2009) Improved visualization of protein consensus sequences by iceLogo. Nature Methods, 6(11), 786-787. DOI: 10.1038/nmeth1109-786
- May 21, 2010
- 09:22 AM
- 1,453 views
Tomatoes On My Mind
I’ve got tomatoes on my mind, so summer must be coming. It seems every where I turn, I’m being reminded of tomatoes. Not the grocery store/hot house kind, but the fresh farmer’s market/back yard-grown kind with juice and flavor so plentiful that it runs down your arms and onto the sunny porch floor where [...]... Read more »
Ruzicka, D., Barrios-Masias, F., Hausmann, N., Jackson, L., & Schachtman, D. (2010) Tomato root transcriptome response to a nitrogen-enriched soil patch. BMC Plant Biology, 10(1), 75. DOI: 10.1186/1471-2229-10-75
- November 3, 2010
- 09:15 AM
- 1,443 views
Tip of the Week: VISTA Enhancer Browser
by Mary in OpenHelix
At the recent (and excellent) Beyond the Genome 2010 conference, Len Pennachio gave a talk about the VISTA Enhancer Browser that reminded me how much I have always liked this project. It’s the kind of project I’d do if I had a lab: it takes the computational data we’ve been accumulating + developmental biology bench techniques = cool new insights into the function of conserved regions of the genome that we previously didn’t know much about.
The foundation of the project ........ Read more »
Visel, A., Blow, M., Li, Z., Zhang, T., Akiyama, J., Holt, A., Plajzer-Frick, I., Shoukry, M., Wright, C., Chen, F.... (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature, 457(7231), 854-858. DOI: 10.1038/nature07730
Visel, A., Minovitsky, S., Dubchak, I., & Pennacchio, L. (2007) VISTA Enhancer Browser--a database of tissue-specific human enhancers. Nucleic Acids Research, 35(Database). DOI: 10.1093/nar/gkl822
- December 9, 2009
- 07:45 AM
- 1,437 views
Tip of the Week: GRAIL for prioritizing SNPs
by Mary in OpenHelix
Perusing my copy of Nature Genetics last week, I was flipping through the pages and noticed an unusual graphic. I looked at it a little closer and was convinced it was one of the Spirographs that I used to make as a kid. (Remember those? I always liked that….) I looked a little bit closer and realized it was somewhat more informative than the Spirographs I used to draw. This represented the relationships between genes, based on the literature. Hmmm….how did they do this, ex........ Read more »
Raychaudhuri, S., Plenge, R., Rossin, E., Ng, A., , ., Purcell, S., Sklar, P., Scolnick, E., Xavier, R., Altshuler, D.... (2009) Identifying Relationships among Genomic Disease Regions: Predicting Genes at Pathogenic SNP Associations and Rare Deletions. PLoS Genetics, 5(6). DOI: 10.1371/journal.pgen.1000534
Raychaudhuri, S., Thomson, B., Remmers, E., Eyre, S., Hinks, A., Guiducci, C., Catanese, J., Xie, G., Stahl, E., Chen, R.... (2009) Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk. Nature Genetics, 41(12), 1313-1318. DOI: 10.1038/ng.479
Medland, S., Nyholt, D., Painter, J., McEvoy, B., McRae, A., Zhu, G., Gordon, S., Ferreira, M., Wright, M., & Henders, A. (2009) Common Variants in the Trichohyalin Gene Are Associated with Straight Hair in Europeans. The American Journal of Human Genetics, 85(5), 750-755. DOI: 10.1016/j.ajhg.2009.10.009
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