35 posts · 18,672 views
OpenHelix
35 posts
Sort by Latest Post, Most Popular
View by Condensed, Full
- May 21, 2012
- 04:50 PM
- 38 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
- 48 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
- 81 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 23, 2012
- 10:29 AM
- 98 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 17, 2012
- 01:30 PM
- 155 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
- 124 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
- 166 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
- 184 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
- 139 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 7, 2012
- 09:32 AM
- 215 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 15, 2012
- 09:36 AM
- 270 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
- 308 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 23, 2012
- 10:15 AM
- 315 views
The Genomics Landscape circa 2012 lecture by Eric Green (with video)
There is a course running right now at NHGRI that is covering a timely set of genomics aspects. Called Current Topics in Genome Analysis 2012 (CTGA), it’s going to hit a great series of aspects of the current landscape–and offer a look at the future–in genomics.
On the course page you can download the slides, and watch the YouTube videos of the lecture. I had a chance to watch the first one so far, and I’ll summarize it below. But be sure to check back to the Genome.gov YouTube page or the course page to explore them all as they come along. Here’s the first one, which is important to set the frame for the series.... 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 19, 2011
- 11:30 AM
- 283 views
Got a genome transcriptome. Now what?
I was catching up on some mailing list reading last week when I saw an unusual item come across the UCSC discussion mailing list. Someone who is in the process of obtaining genome and transcriptome sequence for a new project asked the UCSC group for guidance on what to do with it. It’s actually a [...]... Read more »
Xu, X., Nagarajan, H., Lewis, N., Pan, S., Cai, Z., Liu, X., Chen, W., Xie, M., Wang, W., Hammond, S.... (2011) The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line. Nature Biotechnology, 29(8), 735-741. DOI: 10.1038/nbt.1932
Klimke, W., O'Donovan, C., White, O., Brister, J., Clark, K., Fedorov, B., Mizrachi, I., Pruitt, K., & Tatusova, T. (2011) Solving the Problem: Genome Annotation Standards before the Data Deluge. Standards in Genomic Sciences, 5(1), 168-193. DOI: 10.4056/sigs.2084864
- December 19, 2011
- 11:30 AM
- 352 views
Got a genome and transcriptome. Now what?
I was catching up on some mailing list reading last week when I saw an unusual item come across the UCSC discussion mailing list. Someone who is in the process of obtaining genome and transcriptome sequence for a new project asked the UCSC group for guidance on what to do with it. It’s actually a question we’ve been hearing a lot in workshops–people are considering grants for this sort of project, or have plans for a brand new sequencer that’s arrived at their site. I thought other people might consider these recommendations useful information too, so I’m re-posting it here:... Read more »
Xu, X., Nagarajan, H., Lewis, N., Pan, S., Cai, Z., Liu, X., Chen, W., Xie, M., Wang, W., Hammond, S.... (2011) The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line. Nature Biotechnology, 29(8), 735-741. DOI: 10.1038/nbt.1932
Klimke, W., O'Donovan, C., White, O., Brister, J., Clark, K., Fedorov, B., Mizrachi, I., Pruitt, K., & Tatusova, T. (2011) Solving the Problem: Genome Annotation Standards before the Data Deluge. Standards in Genomic Sciences, 5(1), 168-193. DOI: 10.4056/sigs.2084864
- December 12, 2011
- 10:40 AM
- 1,249 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 what we need in workflows. We’re big fans of workflows and have talked about them in the past....... 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
- December 7, 2011
- 09:34 AM
- 420 views
Video tip of the week: VarSifter for identifying key sequence variations
Recently many of the bioinformatics tweeps I follow were excited about the tool called VarSifter. Here’s the notice that I saw: RT @yokofakun: http://www.youtube.com/watch?v=I7azpqTWFuM Jamie Teer describes VarSifter, an interactive GUI tool for handing/quering/filtering VCFs #ngs I just had a chance to watch the video, and now I can see why they were impressed! Over [...]... Read more »
Robinson, J., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E., Getz, G., & Mesirov, J. (2011) Integrative genomics viewer. Nature Biotechnology, 29(1), 24-26. DOI: 10.1038/nbt.1754
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. DOI: 10.1093/nar/gkr1055
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & , . (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16), 2078-2079. DOI: 10.1093/bioinformatics/btp352
- November 23, 2011
- 09:24 AM
- 559 views
Video Tip of the Week: BioMart’s new central portal
BioMart is widely-used data management open-source software, with an interface that enables end-users to generate complex and customized queries across many types and sources of biological data. It’s part of the GMOD tool kit, and many project teams that have big data have chosen the BioMart software to organize and make their data available to [...]... Read more »
Kasprzyk, A. (2011) BioMart: driving a paradigm change in biological data management. Database. DOI: 10.1093/database/bar049
Zhang, J., Haider, S., Baran, J., Cros, A., Guberman, J., Hsu, J., Liang, Y., Yao, L., & Kasprzyk, A. (2011) BioMart: a data federation framework for large collaborative projects. Database. DOI: 10.1093/database/bar038
Guberman, J., Ai, J., Arnaiz, O., Baran, J., Blake, A., Baldock, R., Chelala, C., Croft, D., Cros, A., Cutts, R.... (2011) BioMart Central Portal: an open database network for the biological community. Database. DOI: 10.1093/database/bar041
Haider, S., Ballester, B., Smedley, D., Zhang, J., Rice, P., & Kasprzyk, A. (2009) BioMart Central Portal--unified access to biological data. Nucleic Acids Research, 37(Web Server). DOI: 10.1093/nar/gkp265
- November 7, 2011
- 11:32 AM
- 468 views
Getting help with bioinformatics questions online
There are thousands of bioinformatics databases, servers, algorithms, and apps in the bioinformatics ecosystem. Even though we are immersed in this environment ourselves, it seems that every day there’s something new, and in every workshop we do someone brings us an issue they have which requires some sort of tool that we haven’t explored yet–some [...]... Read more »
Parnell, L., Lindenbaum, P., Shameer, K., Dall'Olio, G., Swan, D., Jensen, L., Cockell, S., Pedersen, B., Mangan, M., Miller, C.... (2011) BioStar: An Online Question . PLoS Computational Biology, 7(10). DOI: 10.1371/journal.pcbi.1002216
Dall'Olio, G., Marino, J., Schubert, M., Keys, K., Stefan, M., Gillespie, C., Poulain, P., Shameer, K., Sugar, R., Invergo, B.... (2011) Ten Simple Rules for Getting Help from Online Scientific Communities. PLoS Computational Biology, 7(9). DOI: 10.1371/journal.pcbi.1002202
- November 2, 2011
- 09:20 AM
- 560 views
Video Tip of the Week: MizBee Synteny Browser
In my last tip of the week I was really pleased about the opportunity to see the data from a paper set up in a custom GBrowse, but it also reminded me of the limitations of some current strategies for visualization that we are facing. In that case one of the things that I wanted [...]... Read more »
Meyer, M., Munzner, T., & Pfister, H. (2009) MizBee: A Multiscale Synteny Browser. IEEE Transactions on Visualization and Computer Graphics, 15(6), 897-904. DOI: 10.1109/TVCG.2009.167
Meyer, M., Munzner, T., DePace, A., & Pfister, H. (2010) MulteeSum: A Tool for Comparative Spatial and Temporal Gene Expression Data. IEEE Transactions on Visualization and Computer Graphics, 16(6), 908-917. DOI: 10.1109/TVCG.2010.137
Meyer, M., Wong, B., Styczynski, M., Munzner, T., & Pfister, H. (2010) Pathline: A Tool For Comparative Functional Genomics. Computer Graphics Forum, 29(3), 1043-1052. DOI: 10.1111/j.1467-8659.2009.01710.x
topics
join us!
Do you write about peer-reviewed research in your blog? Use ResearchBlogging.org to make it easy for your readers — and others from around the world — to find your serious posts about academic research.
If you don't have a blog, you can still use our site to learn about fascinating developments in cutting-edge research from around the world.
