Mary

171 posts · 79,691 views

OpenHelix
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  • December 18, 2014
  • 09:36 AM
  • 37 views

What’s the Answer? (FANTOM5 promoter atlas)

by Mary in OpenHelix

Biostars 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 Biostars 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 »

Forrest Alistair R. R., Michael Rehli, J. Kenneth Baillie, Michiel J. L. de Hoon, Vanja Haberle, Timo Lassmann, Ivan V. Kulakovskiy, Marina Lizio, Masayoshi Itoh, & Robin Andersson. (2014) A promoter-level mammalian expression atlas. Nature, 507(7493), 462-470. DOI: http://dx.doi.org/10.1038/nature13182  

Severin Jessica, Jayson Harshbarger, Hideya Kawaji, Carsten O Daub, Yoshihide Hayashizaki, Nicolas Bertin, & Alistair R R Forrest. (2014) Interactive visualization and analysis of large-scale sequencing datasets using ZENBU. Nature Biotechnology, 32(3), 217-219. DOI: http://dx.doi.org/10.1038/nbt.2840  

  • December 17, 2014
  • 09:38 AM
  • 50 views

Video Tip of the Week: yEd Graph Editor for visualizing pathways and networks

by Mary in OpenHelix

This week’s video tip of the week closes out a series that began last month. I started to explore one gene co-expression tool, which led me to another tool for visualization, and so on. This week’s tool is the final piece that you need to know about if you want to create the kind of […]... Read more »

  • December 11, 2014
  • 09:39 AM
  • 61 views

What’s the Answer? (tidy data format)

by Mary in OpenHelix

Biostars 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 Biostars 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 »

Wickham Hadley Wickham. (2014) Tidy Data. Journal of Statistical Software, 59(10). info:other/JSSOBK:v59i10

  • December 10, 2014
  • 09:38 AM
  • 72 views

Video Tip of the Week: “Virtually Immune” computational immune system modeling

by Mary in OpenHelix

This week’s video tip of the week is the next in a series. It began when I took a look at GeneFriends, and their option to output the data for use in BioLayout Express3D. So of course we had to then take a look at BioLayout. While I was exploring BioLayout, I came across Virtually […]... Read more »

  • December 8, 2014
  • 10:47 AM
  • 56 views

Oxford plots from the gibbon genome paper

by Mary in OpenHelix

A while back I talked about the software in the gibbon genome paper. I went through to try to pull out as much of the software as I could as sort of a catalog of a representative genome project. Of course, there was a lot in there. Some of it, though, consisted of unpublished code. […]... Read more »

Carbone Lucia, R. Alan Harris, Sante Gnerre, Krishna R. Veeramah, Belen Lorente-Galdos, John Huddleston, Thomas J. Meyer, Javier Herrero, Christian Roos, Bronwen Aken.... (2014) Gibbon genome and the fast karyotype evolution of small apes. Nature, 513(7517), 195-201. DOI: http://dx.doi.org/10.1038/nature13679  

  • December 3, 2014
  • 09:38 AM
  • 27 views

Video Tip of the Week: BioLayout Express3D for network visualizations

by Mary in OpenHelix

My previous Video Tip of the Week highlighted the GeneFriends tool. With GeneFriends you can search for co-expression of genes in RNA-seq data sets. But you can take these results further and visualize them with the BioLayout Express3D tool, so I wanted to bring more details about BioLayout in this tip since we haven’t covered […]... Read more »

  • November 26, 2014
  • 07:12 AM
  • 95 views

Thanksgiving week, light posting. One holiday genome (cranberries).

by Mary in OpenHelix

There’s nobody reading the blog this week each year, everyone is traveling or napping, at least in the US. So I’ll just bring a holiday genome I came across recently. Cranberries. This fruit is one of very few native North American fruits that are widely cultivated. I went looking to see if a genome paper […]... Read more »

  • November 25, 2014
  • 01:18 PM
  • 129 views

Oy. I worry about this with cell line studies a lot. Mis-IDed contaminated.

by Mary in OpenHelix

Via NCBI Announce mailing list: NCBI BioSample includes curated list of over 400 known misidentified and contaminated cell lines The NCBI BioSample database now includes a curated list of over 400 known misidentified and contaminated cell lines. Scientists should check this list before they start working with a new cell line to see if that cell line […]... Read more »

American Type Culture Collection Standards Development Organization Workgroup ASN-0002. (2010) Cell line misidentification: the beginning of the end. Nature Reviews Cancer, 10(6), 441-448. DOI: http://dx.doi.org/10.1038/nrc2852  

  • November 19, 2014
  • 09:50 AM
  • 120 views

Video Tip of the Week: GeneFriends

by Mary in OpenHelix

It was just a little tweet, with hardly any information about the function or purpose of the resource mentioned. But the cute name drove a lot of people to take a look at GeneFriends from our blog recently, so I figured it was worth highlighting this tool as our Video Tip of the Week. So […]... Read more »

  • November 12, 2014
  • 08:08 AM
  • 144 views

Video Tip of the Week: UpSet about genomics Venn Diagrams?

by Mary in OpenHelix

Who can forget the Banana Venn? It was one of the most talked-about visualizations in genomics that I’m aware of. A new concept in data visualization: the Venn/banana diagram. MT @phylogenomics http://t.co/xjitNDNl — Iddo Friedberg (@iddux) July 19, 2012 Banana? RT @phylogenomics: Perhaps the best genomics Venn diagram ever #Bananas #NotSureWhatItMeansButDontCare http://t.co/xMV25GBG — Brian Kent […]... Read more »

D’Hont Angélique, Jean-Marc Aury, Franc-Christophe Baurens, Françoise Carreel, Olivier Garsmeur, Benjamin Noel, Stéphanie Bocs, Gaëtan Droc, Mathieu Rouard, & Corinne Da Silva. (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature, 488(7410), 213-217. DOI: http://dx.doi.org/10.1038/nature11241  

Lex Alexander , Gehlenborg Nils , Strobelt Hendrik , Vuillemot Romain Vuillemot, & Pfister Hanspeter . (2014) UpSet: Visualization of Intersecting Sets. IEEE Transactions on Visualization and Computer Graphics (InfoVis '14). info:other/TBD

Gibbs Richard A., Michael L. Metzker, Donna M. Muzny, Erica J. Sodergren, Steven Scherer, Graham Scott, David Steffen, Kim C. Worley, Paula E. Burch, & Geoffrey Okwuonu. (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature, 428(6982), 493-521. DOI: http://dx.doi.org/10.1038/nature02426  

  • November 10, 2014
  • 09:48 AM
  • 107 views

Genome Editing with CRISPR-Cas9, nifty animation

by Mary in OpenHelix

I saw this come across my twitter feed the other day, and as a nice Friday afternoon diversion I posted it to Google+. I was surprised how popular it was. So I thought–hey, I have a blog too. Let’s put it there…. So grab some coffee and watch, a nice gentle way to get your […]... Read more »

Platt Randall J., Sidi Chen, Yang Zhou, Michael J. Yim, Lukasz Swiech, Hannah R. Kempton, James E. Dahlman, Oren Parnas, Thomas M. Eisenhaure, Marko Jovanovic.... (2014) CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling. Cell, 159(2), 440-455. DOI: http://dx.doi.org/10.1016/j.cell.2014.09.014  

  • November 5, 2014
  • 09:47 AM
  • 105 views

Video Tip of the Week: Genome Browser in a Box

by Mary in OpenHelix

We’ve been doing UCSC Genome Browser training workshops for a decade now. We’ve seen all sorts of situations–from places that had terrific bioinformatics and IT support, to places where the attendees had no idea if anyone provided support at their institution. Ironically, sometimes the places with little support were big-name research places where all the […]... Read more »

Haeussler M., B. J. Raney, A. S. Hinrichs, H. Clawson, A. S. Zweig, D. Karolchik, J. Casper, M. L. Speir, D. Haussler, & W. J. Kent. (2014) Navigating protected genomics data with UCSC Genome Browser in a Box. Bioinformatics. DOI: http://dx.doi.org/10.1093/bioinformatics/btu712  

  • October 29, 2014
  • 09:46 AM
  • 115 views

Video Tip of the Week: PaleoBioDB, for your paleobiology searches

by Mary in OpenHelix

Yeah, I know, it’s not genomics–but it’s the history of life on this planet–right?  The Paleobiology Database has been keeping records of this ancient biology for a while now, and they have some really nice tools to explore the fossil records and resources that have become available. It’s also interesting to me to see the […]... Read more »

Varela Sara, González-Hernández Javier, Sgarbi Luciano, Marshall Charles, Uhen Mark, Peters Shanan, & McClennen Michael. (2014) paleobioDB: an R package for downloading, visualizing and processing data from the Paleobiology Database. Ecography. DOI: 10.1111/ecog.01154  

  • October 22, 2014
  • 09:46 AM
  • 124 views

Video Tip of the Week: SeqMonk

by Mary in OpenHelix

Always on the lookout for effective visualization tools, I recently came across a series of videos about the SeqMonk software. It’s not software that I had used before, so I wanted to look at the videos, and then try it out. It downloaded quickly, offered me an extensive list of genomes to load up, and […]... Read more »

  • October 15, 2014
  • 09:46 AM
  • 136 views

Video Tip of the Week: MedGen, GTR, and ClinVar

by Mary in OpenHelix

The terrific folks at NCBI have been increasing their outreach with a series of webinars recently. I talked about one of them not too long ago, and I mentioned that when I found the whole webinar I’d highlight that. This recording is now available, and if you are interested in using these medical genetics resources, […]... Read more »

Acland A., R. Agarwala, T. Barrett, J. Beck, D. A. Benson, C. Bollin, E. Bolton, S. H. Bryant, K. Canese, D. M. Church.... (2013) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 42(D1). DOI: http://dx.doi.org/10.1093/nar/gkt1146  

  • October 8, 2014
  • 06:49 AM
  • 144 views

Video Tip of the Week: UCSC #Ebola Genome Portal

by Mary in OpenHelix

Although I had other tips in my queue already, over the last week I’ve seen a lot of talk about the new Ebola virus portal from the UCSC Genome Browser team. And it struck me that researchers who have worked primarily on viral sequences may not be as familiar with the functions of the UCSC […]... Read more »

Karolchik D., G. P. Barber, J. Casper, H. Clawson, M. S. Cline, M. Diekhans, T. R. Dreszer, P. A. Fujita, L. Guruvadoo, M. Haeussler.... (2013) The UCSC Genome Browser database: 2014 update. Nucleic Acids Research, 42(D1). DOI: http://dx.doi.org/10.1093/nar/gkt1168  

  • October 6, 2014
  • 11:18 AM
  • 132 views

Bioinformatics tools extracted from a typical mammalian genome project [supplement]

by Mary in OpenHelix

This is Table 1 that accompanies the full blog post: Bioinformatics tools extracted from a typical mammalian genome project. See the main post for the details and explanation. The table is too long to keep in the post, but I wanted it to be web-searchable. A copy also resides at FigShare: http://dx.doi.org/10.6084/m9.figshare.1194867 Software tool/object/item/resource access […]... Read more »

Carbone Lucia, R. Alan Harris, Sante Gnerre, Krishna R. Veeramah, Belen Lorente-Galdos, John Huddleston, Thomas J. Meyer, Javier Herrero, Christian Roos, Bronwen Aken.... (2014) Gibbon genome and the fast karyotype evolution of small apes. Nature, 513(7517), 195-201. DOI: http://dx.doi.org/10.1038/nature13679  

  • October 6, 2014
  • 11:12 AM
  • 137 views

Bioinformatics tools extracted from a typical mammalian genome project

by Mary in OpenHelix

In this extended blog post, I describe my efforts to extract the information about bioinformatics-related items from a recent genome sequencing paper, and the larger issues this raises in the field. It’s long, and it’s something of a hybrid between a blog post and a paper format, just to give it some structure for my […]... Read more »

Carbone Lucia, R. Alan Harris, Sante Gnerre, Krishna R. Veeramah, Belen Lorente-Galdos, John Huddleston, Thomas J. Meyer, Javier Herrero, Christian Roos, Bronwen Aken.... (2014) Gibbon genome and the fast karyotype evolution of small apes. Nature, 513(7517), 195-201. DOI: http://dx.doi.org/10.1038/nature13679  

  • October 1, 2014
  • 09:46 AM
  • 176 views

Video Tip of the Week: MEGA, Molecular Evolutionary Genetics Analysis

by Mary in OpenHelix

This week’s tip of the week highlights the MEGA tools–MEGA is a collection of tools that perform Molecular Evolutionary Genetics Analysis. MEGA tools are not new–they’ve been developed and supported over many years. In fact, on their landing page you can see the first reference to MEGA was in 1994. How much computing were you […]... Read more »

  • September 25, 2014
  • 09:46 AM
  • 219 views

What’s the Answer? (domain and lollipop mutation diagrams)

by Mary in OpenHelix

Biostars 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 Biostars 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 »

Gao J., U. Dogrusoz, G. Dresdner, B. Gross, S. O. Sumer, Y. Sun, A. Jacobsen, R. Sinha, E. Larsson, & E. Cerami. (2013) Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal. Science Signaling, 6(269). DOI: http://dx.doi.org/10.1126/scisignal.2004088  

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