136 posts · 95,068 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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- May 21, 2012
- 04:50 PM
- 3 views
Francis Collins wants to put you on a chip.
Well, ok, not quite yet. But he thinks it’s coming. Have a look (and hang on to the end for you on a chip): [YouTube TEDMED talk here].
At a recent TEDMED session, Francis Collins gave a short talk about some ways forward in drug development. It’s just taking too long, and there are many hazards that affect the process today. He had a nice illustration of the pipeline that takes us from a bucketload of promising compounds –pre-clinical testing – clinical trials – 1 FDA approval if you are lucky, and have a billion dollars to spend on this.... Read more »
Collins, F. (2011) Reengineering Translational Science: The Time Is Right. Science Translational Medicine, 3(90), 90-90. DOI: 10.1126/scitranslmed.3002747
- May 16, 2012
- 09:31 AM
- 35 views
Video Tip of the Week: BindingDB for binding affinities
Recently when I was adding videos to our SciVee collection, I noticed that there was a set of new videos about BindingDB. This database has been around for a long time, and I was surprised to realize that we hadn’t covered it yet. And it certainly only grows more important to understand proteins and their binding partners–whether they are other proteins or chemical compounds that can be important effectors of health and disease.
For a decade now this database has been curated and maintained to provide access to information from publications that is often not easily accessible. As their homepage says today:
"BindingDB contains 832,773 binding data, for 5,765 protein targets and 362,123 small molecules."... Read more »
Liu T., Lin Y., Wen X., Jorissen R. N., & Gilson M. K. (2007) BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Research, 35(Database). DOI: 10.1093/nar/gkl999
- May 2, 2012
- 09:32 AM
- 74 views
Video tip of the week: Updated UCSC Genome Browser movie slides
The UCSC Genome Browser has been providing access to reference genomes and associated annotation data for many years now. If you go to the “archives” page you can see the old genomes all the way back to 2003. Check it out–you can find the teeny (but colorful) look at the human assembly from April 2003–and the rather small selection of tracks that were present then. Really–go have a quick look–and realize how much more we have now.
There are new species and new assemblies of the genomes over time, of course. New and updated annotation tracks. ... Read more »
Dreszer, T., Karolchik, D., Zweig, A., Hinrichs, A., Raney, B., Kuhn, R., Meyer, L., Wong, M., Sloan, C., Rosenbloom, K.... (2011) The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Research, 40(D1). DOI: 10.1093/nar/gkr1055
- April 25, 2012
- 08:00 AM
- 78 views
Video Tip of Week: Bioproject, it’s where to start finding data (hint, not the papers so much anymore))
A few months ago, Jennifer did a nice tip on on NCBI’s Genome Resources and the changes there. There she briefly mentioned Genome Project resource moving to a new home, BioProject, just about a year ago. Today, I’d like to give you a quick overview of BioProject. It was described in this year’s issue of [...]... Read more »
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, 40(D1). DOI: 10.1093/nar/gkr1163
- April 23, 2012
- 10:29 AM
- 89 views
“Regulatory and Epigenetic Landscapes of Mammalian Genomes”
In the series of talks from the Current Topics in Genome Analysis course from NHGRI, Laura Elnitski spoke on regulation and epigenetics. I’ll include some of my notes below, but be sure to check out the whole talk when you have a chance–and the slides are available for download from the CTGA page.
Dr. Elnitski frames the talk by indicating that we’ve been focusing on the roughly 2% of the genome that consists of protein-coding genes, but that there’s a lot more going on outside of that, and how much more there is to learn about other aspects of genome regulation.... 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
Hindorff, L., Sethupathy, P., Junkins, H., Ramos, E., Mehta, J., Collins, F., & Manolio, T. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proceedings of the National Academy of Sciences, 106(23), 9362-9367. DOI: 10.1073/pnas.0903103106
- April 18, 2012
- 10:00 AM
- 111 views
Video Tip of the Week – The Cell: An Image Library
Who says social media is a waste of time? Not me – my LinkedIn updates keep including announcements of the “Image of the week” from The Cell: An Image Library. For my tip this week I decided to follow up on that & check out the images available from this resource, & I’m glad I did. The Cell Image Library is brought to you by the The American Society for Cell Biology (ASCB), and contains thousands of images, time series and groups of images, videos and animations of cells in a variety of organisms. Images are organized by Cell Process, Cell Component, Cell Type, Organism and Recently added. You can browse images or do a basic search from the homepage, or perform advanced searches. The advanced search form allows users to query with keywords, and for image attributes, specific image licensing categories, biological categories, imaging techniques, or associated anatomy terms.... Read more »
Miller, K. (2010) Finding the key – cell biology and science education. Trends in Cell Biology, 20(12), 691-694. DOI: 10.1016/j.tcb.2010.08.008
- April 18, 2012
- 09:10 AM
- 37 views
Video Tip of the Week – The Cell: An Image Library
Who says social media is a waste of time? Not me – my LinkedIn updates keep including announcements of the “Image of the week” from The Cell: An Image Library. For my tip this week I decided to follow up on that & check out the images available from this resource, & I’m glad I did. [...]... Read more »
Miller, K. (2010) Finding the key – cell biology and science education. Trends in Cell Biology, 20(12), 691-694. DOI: 10.1016/j.tcb.2010.08.008
- April 17, 2012
- 01:30 PM
- 144 views
“Happy families are all alike; every unhappy family is unhappy in its own way.”
A few months back I was impressed with a paper that examined some serious chromosomal consequences that were possibly affecting cognitive development in some individuals. It struck me how important it was that something we haven’t had the tools to explore that effectively in the past–chromothripsis–was going to become more observed and better characterized. And it was going to offer at least some understanding in otherwise uncharacterized medical scenarios, which were hugely frustrating to affected families. These “genomic catastrophe” events might not be that common–but for the patients and their families, the effects are profound. And often unique. Recently “pulverized” chromosomes were also described in cancer cells. It’s hard to imagine how to fix massive restructurings of this sort.... Read more »
Liu, P., Erez, A., Nagamani, S., Dhar, S., Kołodziejska, K., Dharmadhikari, A., Cooper, M., Wiszniewska, J., Zhang, F., Withers, M.... (2011) Chromosome Catastrophes Involve Replication Mechanisms Generating Complex Genomic Rearrangements. Cell, 146(6), 889-903. DOI: 10.1016/j.cell.2011.07.042
Crasta, K., Ganem, N., Dagher, R., Lantermann, A., Ivanova, E., Pan, Y., Nezi, L., Protopopov, A., Chowdhury, D., & Pellman, D. (2012) DNA breaks and chromosome pulverization from errors in mitosis. Nature, 482(7383), 53-58. DOI: 10.1038/nature10802
Callaway, E. (2012) Gene hunt is on for mental disability. Nature, 484(7394), 302-303. DOI: 10.1038/484302a
- April 11, 2012
- 09:30 AM
- 117 views
Video Tip of the Week: A 3D Worm!
In this era of big data and computational tools, it’s easy to generate huge amounts of texty and statistical data that offers great insights into biology, and delivers leads to design experiments in actual organisms and cells. But the cell and developmental biologist in me still yearns for great visualization tools to explore the results, beyond rows and columns and p-values. I think that better visualizations of the -omics data is still one of the unmet needs in this arena, and I’ve talked about that more than once but most recently here.... Read more »
Yook, K., Harris, T., Bieri, T., Cabunoc, A., Chan, J., Chen, W., Davis, P., de la Cruz, N., Duong, A., Fang, R.... (2011) WormBase 2012: more genomes, more data, new website. Nucleic Acids Research, 40(D1). DOI: 10.1093/nar/gkr954
- April 8, 2012
- 09:55 AM
- 160 views
The data isn’t in the papers anymore. Again.
I know this is a topic I keep hammering on. But I’m not sure that it’s really grokked by a lot of people who are not as deep into the bioinformatics aspects of biology today. Or those who support biologists, such as publishers and librarians, who may not be as immersed in the daily software aspects.
There was a nice post by Ed Yong last week about a paper published on sticklebacks. There are several cool things about this paper–but one of them is merely the fact that we can use the next-generation sequencing technology we have to examine species that ways that we just couldn’t before. And Ed made the point that there wasn’t only one genome in this paper–there were 21 genome sequencing events in this paper... Read more »
Jones, F., Grabherr, M., Chan, Y., Russell, P., Mauceli, E., Johnson, J., Swofford, R., Pirun, M., Zody, M., White, S.... (2012) The genomic basis of adaptive evolution in threespine sticklebacks. Nature, 484(7392), 55-61. DOI: 10.1038/nature10944
- March 28, 2012
- 09:47 AM
- 177 views
Video Tip of the Week: Population Genetics Introduction
For additional details see our blog post at URL http://blog.openhelix.eu/?p=11488. Another session in the Current Topics in Genome Analysis 2012 course that has been organized by the NHGRI featured Lynn Jorde. Lynn delivered a lecture (about 1.5 hours long in total–but he makes you stand up at 1 hour to stretch ) that provides a nice and gentle introduction to population genetics.... Read more »
Moore, B., Hu, H., Singleton, M., De La Vega, F., Reese, M., & Yandell, M. (2011) Global analysis of disease-related DNA sequence variation in 10 healthy individuals: Implications for whole genome-based clinical diagnostics. Genetics in Medicine, 13(3), 210-217. DOI: 10.1097/GIM.0b013e31820ed321
Yandell, M., Huff, C., Hu, H., Singleton, M., Moore, B., Xing, J., Jorde, L., & Reese, M. (2011) A probabilistic disease-gene finder for personal genomes. Genome Research, 21(9), 1529-1542. DOI: 10.1101/gr.123158.111
- March 26, 2012
- 11:15 AM
- 138 views
Genomics Impact on Infectious Disease (with video)
As part of the The Genomics in Medicine Lecture Series from NHGRI, Jonathan Zenilman gave a lecture on various ways that new genome technology has aided in the ways that clinicians can diagnose, manage, and treat infectious disease. This lecture series is delivering a number of videos on various intersections of clinical medical situations and genomics, not just on the basic research in the field.... Read more »
Price, L., Liu, C., Melendez, J., Frankel, Y., Engelthaler, D., Aziz, M., Bowers, J., Rattray, R., Ravel, J., Kingsley, C.... (2009) Community Analysis of Chronic Wound Bacteria Using 16S rRNA Gene-Based Pyrosequencing: Impact of Diabetes and Antibiotics on Chronic Wound Microbiota. PLoS ONE, 4(7). DOI: 10.1371/journal.pone.0006462
- March 21, 2012
- 12:00 PM
- 155 views
Video Tip of the Week: TFBS using Mapper
The database and search tool I will focus on in this tip of the week is Mapper. Mapper uses TFBS from Transfac and Jasper and maps them to genomic locations for several species. Using “the search power of profile hidden Markov models (HMMs),” Mapper includes a database of pre-computed TFBS locations and an on-the-fly search engine for TBFS. Additionally, there is rSNPs, a nice handy tool designed to identify SNPs which have a significant effect on the score of a TFBS.... Read more »
Marinescu, V., Kohane, I., & Riva, A. (2005) MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes . BMC Bioinformatics, 6(1), 79. DOI: 10.1186/1471-2105-6-79
- March 14, 2012
- 09:40 AM
- 170 views
Video Tip of the Week: New Genetic Testing Registry (GTR) Resource
For more information, see our blog post at http://blog.openhelix.eu/?p=11439. In this movie we compare the new GTR resource from NCBI to other clinical resources that you may already be using, to answer why you may want to use the GTR.... Read more »
Pagon RA. (2006) GeneTests: an online genetic information resource for health care providers. Journal of the Medical Library Association : JMLA, 94(3), 343-8. PMID: 16888670
Mitchell JA, Fomous C, & Fun J. (2006) Challenges and strategies of the Genetics Home Reference. Journal of the Medical Library Association : JMLA, 94(3), 336-42. PMID: 16888669
Amberger, J., Bocchini, C., & Hamosh, A. (2011) A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®). Human Mutation, 32(5), 564-567. DOI: 10.1002/humu.21466
Aymé, S., & Schmidtke, J. (2007) Networking for rare diseases: a necessity for Europe. Bundesgesundheitsblatt - Gesundheitsforschung - Gesundheitsschutz, 50(12), 1477-1483. DOI: 10.1007/s00103-007-0381-9
- March 7, 2012
- 09:32 AM
- 207 views
Video tip of the week: Highlights [heh] of the Cannabis browser
Yeah, I couldn't resist. Stop groaning--lighten up! Ok, really, I'll stop now. The Cannabis genome project is an interesting exploration of an important plant genome, with a bunch of new data, and you can examine all of it in their browser. They are using a custom version of the UCSC Genome Browser, which we know is a great way to visualize and query data that might be important to you. In this week's tip we'll see some of the data and how you can interact with it.... Read more »
van Bakel, H., Stout, J., Cote, A., Tallon, C., Sharpe, A., Hughes, T., & Page, J. (2011) The draft genome and transcriptome of Cannabis sativa. Genome Biology, 12(10). DOI: 10.1186/gb-2011-12-10-r102
- February 29, 2012
- 09:17 AM
- 198 views
Video Tip of the Week: eGIFT, extracting gene information from text
eGIFT, as the tag line says, is a tool to extract gene information from text. It’s a tool that allows you to search for and explore terms and documents related to a gene or set of genes. There are many ways to search and explore eGIFT, find genes given a specific term, find terms related to a set of genes and more. How does the tool do this?... Read more »
Tudor, C., Schmidt, C., & Vijay-Shanker, K. (2010) eGIFT: Mining Gene Information from the Literature. BMC Bioinformatics, 11(1), 418. DOI: 10.1186/1471-2105-11-418
- February 22, 2012
- 10:09 AM
- 212 views
Video tip of the week: Updated Introductory Tutorial on the RCSB PDB
This post is part of OpenHelix's "Tip of the Week" blog feature. For today’s tip I am offering our full introductory tutorial on the RCSB PDB, which we completely updated to cover their Top Search Bar, PDB 101 education feature, and more. ... Read more »
Berman, H., & et al. (2000) The Protein Data Bank. Nucleic Acids Research, 28(1), 235-242. DOI: 10.1093/nar/28.1.235
Rose, P., Beran, B., Bi, C., Bluhm, W., Dimitropoulos, D., Goodsell, D., Prlic, A., Quesada, M., Quinn, G., Westbrook, J.... (2010) The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Research, 39(Database). DOI: 10.1093/nar/gkq1021
- February 15, 2012
- 09:36 AM
- 267 views
Video Tip of the Week: OMIA, Online Mendelian Inheritance in Animals
Many people are probably familiar with OMIM, Online Mendelian Inheritance in Man. It's one of the oldest online collections of human genetic traits around. But many people may not be aware that OMIM inspired OMIA--Online Mendelian Inheritance in Animals.
The team from the University of Sydney that develops and curates OMIA collects information on animal traits with a specific emphasis on non-laboratory animals and comparative biology. The species range is huge.... Read more »
Nicholas, F. (2003) Online Mendelian Inheritance in Animals (OMIA): a comparative knowledgebase of genetic disorders and other familial traits in non-laboratory animals. Nucleic Acids Research, 31(1), 275-277. DOI: 10.1093/nar/gkg074
Lenffer, J., Nicholas FW., Castle K., Rao A., Gregory S., Poidinger M., Mailman MD., & Ranganathan S. (2006) OMIA (Online Mendelian Inheritance in Animals): an enhanced platform and integration into the Entrez search interface at NCBI. Nucleic Acids Research, 34(90001). DOI: 10.1093/nar/gkj152
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, 40(D1). DOI: 10.1093/nar/gkr1184
- February 1, 2012
- 09:30 AM
- 303 views
Video Tip of the Week: SNPeffect 4.0
One of the most frequent questions we hear when we do workshops is: how to I find out if this SNP has an effect on my favorite protein? Well, that’s assuming it is a coding SNP. Of course, promoter SNPs and splicing SNPs and other features would be great to assess as well. Right now, though, the most mature tools are those that look at the effects of variation on the coding of the amino acids in proteins.... Read more »
De Baets, G., Van Durme, J., Reumers, J., Maurer-Stroh, S., Vanhee, P., Dopazo, J., Schymkowitz, J., & Rousseau, F. (2011) SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants. Nucleic Acids Research, 40(D1). DOI: 10.1093/nar/gkr996
- January 25, 2012
- 10:09 AM
- 289 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
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