204 posts · 155,749 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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- June 19, 2013
- 09:11 AM
- 16 views
Video Tip of the Week: ENCODE ChIP-Seq Significance Tool
We’ve been doing training and workshops on the UCSC Genome Browser for 10 years now. It’s a tremendous tool that has to be a foundational item in your toolkit in genomics. But–there may be times when you want to examine some of the data that you can find there in another way, with a different [...]... Read more »
Auerbach, R., Chen, B., & Butte, A. (2013) Relating Genes to Function: Identifying Enriched Transcription Factors using the ENCODE ChIP-Seq Significance Tool. Bioinformatics. DOI: 10.1093/bioinformatics/btt316
- June 12, 2013
- 09:31 AM
- 31 views
Video Tip of the Week: TrioVis for family genome data sets
I’m always interested in new strategies to visualize data. So when I saw discussion about a tool to help analyze family genomic data, I went to have a look. TrioVis is a new software tool that offers nice visualization and filtering strategies for exploring parent and child trio data sets. These data sets will become [...]... Read more »
Sakai, R., Sifrim, A., Vande Moere, A., & Aerts, J. (2013) TrioVis: a visualization approach for filtering genomic variants of parent-child trios. Bioinformatics. DOI: 10.1093/bioinformatics/btt267
- June 6, 2013
- 08:07 AM
- 12 views
What’s the Answer? (CNVs vs SVs)
BioStar is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those items or discussions here [...]... Read more »
Scherer, S., Lee, C., Birney, E., Altshuler, D., Eichler, E., Carter, N., Hurles, M., & Feuk, L. (2007) Challenges and standards in integrating surveys of structural variation. Nature Genetics, 39(7s). DOI: 10.1038/ng2093
- May 29, 2013
- 09:33 AM
- 58 views
Video Tip of the Week: QIIME for Quantitative Insights Into Microbial Ecology
The other day I was watching scientists in my twittersphere discuss things they were observing at the American Society for Microbiology meeting (#ASM2013 for more chatter). I like to see what kinds of tools are being discussed at meetings–and twitter is quite useful for that–and this particular tweet caught my eye: True RT @phylogenomics: I [...]... Read more »
Caporaso, J., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F., Costello, E., Fierer, N., Peña, A., Goodrich, J., Gordon, J.... (2010) QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7(5), 335-336. DOI: 10.1038/nmeth.f.303
- May 22, 2013
- 09:32 AM
- 65 views
Video Tip of the Week: Canary Database for sentinels of human health
Recently we attended the Medical Library Association conference (#MLAnet13). Librarians are working so hard to wrangle information into usable forms, and to generate new connections among data types to reveal new information and leads for further studies. I ♥ librarians. In one of the sessions I attended on Medical Informatics, I heard several great talks. One [...]... Read more »
Rabinowitz, P., Scotch, M., & Conti, L. (2010) Animals as Sentinels: Using Comparative Medicine To Move Beyond the Laboratory. ILAR Journal, 51(3), 262-267. DOI: 10.1093/ilar.51.3.262
Rabinowitz, P., Gordon, Z., Holmes, R., Taylor, B., Wilcox, M., Chudnov, D., Nadkarni, P., & Dein, F. (2005) Animals as Sentinels of Human Environmental Health Hazards: An Evidence-Based Analysis. EcoHealth, 2(1), 26-37. DOI: 10.1007/s10393-004-0151-1
Rabinowitz, P., Cullen, M., & Lake, H. (1999) Wildlife as sentinels for human health hazards: a review of study designs. Journal of Environmental Medicine, 1(4), 217-223. DOI: 10.1002/jem.33
- May 15, 2013
- 09:33 AM
- 64 views
Video Tip of the Week: Influenza Research Database (IRD)
It may not be traditionally what you think of as flu season, but lately there’s been a great deal of talk about some viruses that are concerning public health officials and infectious disease specialists. You might have heard of the H7N9 situation in China, and the NCoV virus in France that made headlines. But researchers [...]... Read more »
Squires, R., Noronha, J., Hunt, V., García-Sastre, A., Macken, C., Baumgarth, N., Suarez, D., Pickett, B., Zhang, Y., Larsen, C.... (2012) Influenza Research Database: an integrated bioinformatics resource for influenza research and surveillance. Influenza and Other Respiratory Viruses, 6(6), 404-416. DOI: 10.1111/j.1750-2659.2011.00331.x
Pickett, B., Sadat, E., Zhang, Y., Noronha, J., Squires, R., Hunt, V., Liu, M., Kumar, S., Zaremba, S., Gu, Z.... (2011) ViPR: an open bioinformatics database and analysis resource for virology research. Nucleic Acids Research, 40(D1). DOI: 10.1093/nar/gkr859
- May 1, 2013
- 09:17 AM
- 84 views
Video Tip of the Week: My Cancer Genome
There are a lot of cancer database resources out there. Most of the ones we’ve focused on have been the data repository types. TCGA, ICGC, CaBIG, COSMIC, Cancer Genome Workbench, UCSC Cancer Genomic Browser, and of course big repositories like GEO. Researchers will need these sources of data to locate key alterations in cancer cells [...]... Read more »
Swanton, C. (2012) My Cancer Genome: a unified genomics and clinical trial portal. The Lancet Oncology, 13(7), 668-669. DOI: 10.1016/S1470-2045(12)70312-1
Yeh, P., Chen, H., Andrews, J., Naser, R., Pao, W., & Horn, L. (2013) DNA-Mutation Inventory to Refine and Enhance Cancer Treatment (DIRECT): A Catalog of Clinically Relevant Cancer Mutations to Enable Genome-Directed Anticancer Therapy. Clinical Cancer Research, 19(7), 1894-1901. DOI: 10.1158/1078-0432.CCR-12-1894
- April 24, 2013
- 09:32 AM
- 71 views
Video Tip of the Week: Cancer Atlas roadmap
I’ve talked a lot about how much I am interested in seeing new visualization strategies for working with the volumes of data was have today–which are certainly not going to stop flowing in. But a more basic level of this is even just locating and navigating to find the data sets you might want to [...]... Read more »
Robbins, D., Gruneberg, A., Deus, H., Tanik, M., & Almeida, J. (2013) A self-updating road map of The Cancer Genome Atlas. Bioinformatics. DOI: 10.1093/bioinformatics/btt141
The Cancer Genome Atlas (TCGA) Research Network. (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature, 455(7216), 1061-1068. DOI: 10.1038/nature07385
- April 23, 2013
- 11:43 AM
- 88 views
Creating the reference genome
In our workshops around the world on the UCSC Genome Browser, we talk at the very beginning about the framework for the organization of the data in the graphical representation. We describe that the reference genome–the official released genome–for a species provides the genome coordinates, or positions, that allows the rest of the data to [...]... Read more »
Zody, M., Jiang, Z., Fung, H., Antonacci, F., Hillier, L., Cardone, M., Graves, T., Kidd, J., Cheng, Z., Abouelleil, A.... (2008) Evolutionary toggling of the MAPT 17q21.31 inversion region. Nature Genetics, 40(9), 1076-1083. DOI: 10.1038/ng.193
- April 17, 2013
- 09:38 AM
- 132 views
Video Tip of the Week: Sharing #H7N9 data at GISAID.org with EpiFlu™
This week’s video Tip of the Week offers you a quick tour of GISAID’s resources and their EpiFlu™ database. This is the database you might be hearing about in the news—the one to which researchers submit the new H7N9 influenza sequence data that they are collecting. Originally this initiative was seeded as the “Global Initiative [...]... Read more »
Bogner, P., Capua, I., Cox, N., Lipman, D., & others, . (2006) A global initiative on sharing avian flu data. Nature, 442(7106), 981-981. DOI: 10.1038/442981a
Butler, D. (2013) Urgent search for flu source. Nature, 496(7444), 145-146. DOI: 10.1038/496145a
Gao, R., Cao, B., Hu, Y., Feng, Z., Wang, D., Hu, W., Chen, J., Jie, Z., Qiu, H., Xu, K.... (2013) Human Infection with a Novel Avian-Origin Influenza A (H7N9) Virus. New England Journal of Medicine, 2147483647. DOI: 10.1056/NEJMoa1304459
- April 10, 2013
- 09:31 AM
- 103 views
Video Tip of the Week: Introductory Cheminformatics
This week’s tip of the week is a bit afield from what we usually cover. But sometimes I see that people are looking for cheminformatics materials from our site, and this resource that I learned about recently seems like a terrific effort to wrangle some of the basics and foundations of cheminformatics (or, as David [...]... Read more »
Wild, D. (2009) Grand challenges for cheminformatics. Journal of Cheminformatics, 1(1), 1. DOI: 10.1186/1758-2946-1-1
- April 8, 2013
- 11:25 AM
- 151 views
Genetic privacy webinar series continues
There have been a number of heated discussions about genetic privacy recently. Lately the discussion of the Henrietta Lacks (HeLa) genome paper erupted into wide-ranging awareness of some of the issues and complexities around genome data and family relationships. The paper by Yaniv Erlich’s team about re-identification of study participants using genealogy site details also [...]... Read more »
Presidential Commission for the Study of Bioethical Issues. (2012) Privacy and Progress in Whole Genome Sequencing. www.bioethics.gov. info:other/
Gymrek, M., McGuire, A., Golan, D., Halperin, E., & Erlich, Y. (2013) Identifying Personal Genomes by Surname Inference. Science, 339(6117), 321-324. DOI: 10.1126/science.1229566
- April 3, 2013
- 09:32 AM
- 123 views
Video Tip of the Week: Phytozome and the Peach Genome
We’ve laughed in the past about a “genome of the day” because there are so many projects each week that we want to explore, and it’s hard to keep up. But recently I wanted to have a look at the peach genome project, because–well, peaches! And the summary papers are nice. But generally I want [...]... Read more »
Verde, I., Abbott, A., Scalabrin, S., Jung, S., Shu, S., Marroni, F., Zhebentyayeva, T., Dettori, M., Grimwood, J., Cattonaro, F.... (2013) The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nature Genetics. DOI: 10.1038/ng.2586
Goodstein, D., Shu, S., Howson, R., Neupane, R., Hayes, R., Fazo, J., Mitros, T., Dirks, W., Hellsten, U., Putnam, N.... (2011) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Research, 40(D1). DOI: 10.1093/nar/gkr944
- March 27, 2013
- 09:45 AM
- 142 views
Video Tip of the Week: Enzyme Portal and User-Centered Design
This week’s video tip of the week introduces you to Enzyme Portal, an interface to explore data about these important proteins, from the EBI. In the video, Jenny Cham–one of the authors of the paper below–takes you through the main features of their newly designed resource. I learned about the new effort from this blog [...]... Read more »
de Matos, P., Cham, J., Cao, H., Alcántara, R., Rowland, F., Lopez, R., & Steinbeck, C. (2013) The Enzyme Portal: A case study in applying user-centred design methods in bioinformatics. BMC Bioinformatics, 14(1), 103. DOI: 10.1186/1471-2105-14-103
- March 20, 2013
- 09:13 AM
- 171 views
Video Tip of the Week: figshare + GenoCAD = outreach
For this week’s video tip of the week, I’m going to highlight the services of figshare. Figshare is a terrific resource for storing data, posters, paper, slides, code, movies, and more. Nearly any sort of digital item that you may be creating as part of your research or research communications projects can be uploaded to [...]... Read more »
Singh, J. (2011) FigShare. Journal of Pharmacology and Pharmacotherapeutics, 2(2), 138. DOI: 10.4103/0976-500X.81919
Cai, Y., Wilson, M., & Peccoud, J. (2010) GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs. Nucleic Acids Research, 38(8), 2637-2644. DOI: 10.1093/nar/gkq086
- March 13, 2013
- 10:23 AM
- 152 views
Protip: check the genome of your cell line. HeLa cells are “strikingly aberrant”
This is a paper I’ve been waiting for: the analysis of the HeLa genome. I was aware of a lot of issues with the cell lines and missing or duplicated regions from the ENCODE data that was coming along some time ago: Mining the “big data” is…fascinating. And necessary. People may be familiar with HeLa [...]... Read more »
Landry1 JJM, Pyl1 PT, Rausch T, Zichner T, Tekkedil1 MM, Stütz AM, Jauch A, Aiyar RS, Pau G, Delhomme N.... (2013) The Genomic and Transcriptomic Landscape of a HeLa Cell Line. G3. info:/10.1534/g3.113.005777
- February 27, 2013
- 09:12 AM
- 167 views
Video Tip of the Week: NetGestalt
For this week’s tip we highlight a new tool, NetGestalt, which offers some interesting visualization strategies for large-scale biological data in the context of pathways. I see a lot of need for this, and am pleased to be introduced to this tool. (And they have Venns! I ♥ Venns!) I found out about it from [...]... Read more »
Zhang, B., Kirov, S., & Snoddy, J. (2005) WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Research, 33(Web Server). DOI: 10.1093/nar/gki475
- February 23, 2013
- 06:02 PM
- 222 views
Spanking #ENCODE
While I was on the road last week–ironically to do a workshops including one on ENCODE data in the UCSC Genome Browser, a conflama erupted over a new paper that was published essentially spanking the ENCODE team for some of the claims they made. Some of the first notes I saw: Wow – brutal (IMO [...]... Read more »
Graur, D., Zheng, Y., Price, N., Azevedo, R., Zufall, R., & Elhaik, E. (2013) On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biology and Evolution. DOI: 10.1093/gbe/evt028
Rosenbloom, K., Sloan, C., Malladi, V., Dreszer, T., Learned, K., Kirkup, V., Wong, M., Maddren, M., Fang, R., Heitner, S.... (2012) ENCODE Data in the UCSC Genome Browser: year 5 update. Nucleic Acids Research, 41(D1). DOI: 10.1093/nar/gks1172
- February 20, 2013
- 08:25 AM
- 119 views
Video Tip of the Week: ENCODE Data at UCSC (reminder)
This week’s tip of the week is a reminder: go and watch the ENCODE tutorial that is sponsored by the UCSC Genome Browser’s ENCODE team. There now just one week of free access left. For a number of years a team at the UCSC Genome Browser group was designated as the DCC, or Data Coordination [...]... Read more »
Rosenbloom, K., Sloan, C., Malladi, V., Dreszer, T., Learned, K., Kirkup, V., Wong, M., Maddren, M., Fang, R., Heitner, S.... (2012) ENCODE Data in the UCSC Genome Browser: year 5 update. Nucleic Acids Research, 41(D1). DOI: 10.1093/nar/gks1172
- February 18, 2013
- 01:43 PM
- 193 views
Human Genome Project perspectives in 2013: webinar series
In recognition of another decade-based anniversary (and they actually joke in the first session about how it’s always possible to find a 10-year something to celebrate on this topic), the NHGRI is hosting a series of talks and a day-long event to celebrate where we came from, and where we are going, with genome data. [...]... Read more »
WATSON, J., & CRICK, F. (1953) Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid. Nature, 171(4356), 737-738. DOI: 10.1038/171737a0
Lander, E., Linton, L., Birren, B., Nusbaum, C., Zody, M., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W.... (2001) Initial sequencing and analysis of the human genome. Nature, 409(6822), 860-921. DOI: 10.1038/35057062
Marshall, E. (2001) Bermuda Rules: Community Spirit, With Teeth. Science, 291(5507), 1192-1192. DOI: 10.1126/science.291.5507.1192
Collins, F., Morgan, M., & Patrionos, A. (2003) The Human Genome Project: Lessons from Large-Scale Biology. Science, 300(5617), 286-290. DOI: 10.1126/science.1084564
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