Mary

140 posts · 67,371 views

OpenHelix
140 posts

Sort by Latest Post, Most Popular

View by Condensed, Full

  • July 23, 2014
  • 09:38 AM
  • 48 views

Video Tip of the Week: Nowomics, set up alert feeds for new data

by Mary in OpenHelix

Yeah, I know you know. There’s a lot of genomics and proteomics data coming out every day–some of it in the traditional publication route, but some of it isn’t–and it’s only getting harder and harder to wrangle the useful information to access the signal from the noise.  I can remember when merely looking through the […]... Read more »

Acland A., T. Barrett, J. Beck, D. A. Benson, C. Bollin, E. Bolton, S. H. Bryant, K. Canese, D. M. Church, & K. Clark. (2014) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 42(D1). DOI: http://dx.doi.org/10.1093/nar/gkt1146  

  • July 22, 2014
  • 09:08 AM
  • 55 views

A History of Bioinformatics (told from the Year 2039)

by Mary in OpenHelix

A week or so back I was watching the chatter around the #ISMB / #BOSC2014 meeting, and saw a number of amusing and intriguing comments about Titus Brown’s keynote talk. [embedded tweets] You can see a lot of chatter about it in the Storify. I was delighted to soon see this follow up...... Read more »

  • July 16, 2014
  • 09:37 AM
  • 76 views

Video Tip of the Week: VectorBase, for invertebrate vectors of human pathogens

by Mary in OpenHelix

I wish I had been clever enough to coordinate this week’s Video Tip of the Week with “Mosquito Week” a couple of months back. There was a bunch of chatter at that time about this infographic that was released by Bill Gates, which illustrated the contribution of various human-killing species. The mosquito was deemed: The […]... Read more »

Megy K., D. Lawson, D. Campbell, E. Dialynas, D. S. T. Hughes, G. Koscielny, C. Louis, R. M. MacCallum, S. N. Redmond, & A. Sheehan. (2012) VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics. Nucleic Acids Research, 40(D1). DOI: http://dx.doi.org/10.1093/nar/gkr1089  

  • July 9, 2014
  • 09:37 AM
  • 84 views

Video Tip of the Week: Google Genomics, API and GAbrowse

by Mary in OpenHelix

This week’s video tip comes to us from Google–it’s about their participation in the “Global Alliance for Genomics and Health” coalition. Global Alliance is aimed at developing genomic data standards for interoperability, and they’ve been working on creating the framework (some background links below in the references will provide further details). It has over 170 […]... Read more »

  • July 3, 2014
  • 09:59 AM
  • 119 views

What’s the Answer? (mutation nomenclature)

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 »

  • July 2, 2014
  • 09:36 AM
  • 96 views

Video Tip of the Week: NCBI Variation Viewer

by Mary in OpenHelix

The folks at NCBI recently hosted a webinar that covered a number of resources: GTR, ClinVar, and MedGen. It was a nice introduction to these resources using a case study of exploring information about a 9-year-old child who needed to get clearance for participation in sports. So they follow the course of some details about […]... Read more »

Landrum M. J., G. R. Riley, W. Jang, W. S. Rubinstein, D. M. Church, & D. R. Maglott. (2014) ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Research, 42(D1). DOI: http://dx.doi.org/10.1093/nar/gkt1113  

  • June 25, 2014
  • 09:37 AM
  • 129 views

Video Tip of the Week: Leukemia outcome predictions challenge

by Mary in OpenHelix

Although I had other tips in the pipeline, I’m bumping this one up because it is time sensitive. It’s about a competition (or challenge, as they describe it) to use data from cases of leukemia to model make predictions about the outcomes, which could help drive treatment decisions someday. It is called the Acute Myeloid […]... Read more »

Boutros Paul C, Kyle Ellrott, Thea C Norman, Kristen K Dang, Yin Hu, Michael R Kellen, Christine Suver, J Christopher Bare, Lincoln D Stein, & Paul T Spellman. (2014) Global optimization of somatic variant identification in cancer genomes with a global community challenge. Nature Genetics, 46(4), 318-319. DOI: http://dx.doi.org/10.1038/ng.2932  

  • June 19, 2014
  • 09:37 AM
  • 99 views

What’s The Answer? (explosion of careers)

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 »

  • June 18, 2014
  • 09:38 AM
  • 115 views

Video Tip of the Week: e-PathGen, Using Genomics to Support Public Health

by Mary in OpenHelix

Recently I saw the Director of Public Health Genomics for the CDC tweet about a resource that was new to me, ePathGen, Pathogen Genomics for Epidemiology. This is an area that I’m glad to see getting attention. My undergrad degree was in microbiology, and certainly the most memorable class I had in college was about pathogenic […]... Read more »

  • June 12, 2014
  • 09:43 AM
  • 65 views

What’s the Answer? (aligning isoforms)

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 »

  • June 11, 2014
  • 09:36 AM
  • 108 views

Video Tip of the Week: InterMine for complex queries

by Mary in OpenHelix

We’ve been fans of InterMine for a long time. We did a tip-of-the-week in a while ago that highlighted ways that this software can be used to mine from big data projects of many types. The generic framework of InterMine can be customized for use at different projects–today I’ll include videos from the FlyMine installation […]... Read more »

Smith Richard N, Aleksic Jelena, Butano Daniela, Carr Adrian, Contrino Sergio, Hu Fengyuan, Lyne Mike, Lyne Rachel, Kalderimis Alex, & Rutherford Kim. (2012) InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data. Bioinformatics (Oxford, England). DOI: 10.1093/bioinformatics/bts577  

Lyne Rachel, Smith Richard, Rutherford Kim, Wakeling Matthew, Varley Andrew, Guillier Francois, Janssens Hilde, Ji Wenyan, Mclaren Peter, & North Philip. (2012) FlyMine: an integrated database for Drosophila and Anopheles genomics. Genome biology. PMID: 17615057  

Balakrishnan Rama, Park Julie, Karra Kalpana, Hitz Benjamin C, Binkley Gail, Hong Eurie L, Sullivan Julie, Micklem Gos, & Cherry J Michael. (2012) YeastMine--an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit. Database : the journal of biological databases and curation. PMID: 22434830  

Sullivan Julie, Karra Kalpana, Moxon Sierra A T, Vallejos Andrew, Motenko Howie, Wong J D, Aleksic Jelena, Balakrishnan Rama, Binkley Gail, & Harris Todd. (2013) InterMOD: integrated data and tools for the unification of model organism research. Scientific reports, 3( 1802 1802). PMID: 23652793  

  • May 28, 2014
  • 09:42 AM
  • 109 views

Video Tip of the Week: New UCSC “stacked” wiggle track view

by Mary in OpenHelix

This week’s video tip shows you a new way to look at the multiWig track data at the UCSC Genome Browser. A new option has recently been released (see 06 May 2014), a “stacked” view, and it’s a handy way to look at the data with a new strategy. But I’ll admit it took me […]... Read more »

Kent W J, Zweig A S, Barber G, Hinrichs A S, & Karolchik D. (2010) BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics (Oxford, England). PMID: 20639541  

Karolchik Donna, Barber Galt P, Casper Jonathan, Clawson Hiram, Cline Melissa S, Diekhans Mark, Dreszer Timothy R, Fujita Pauline A, Guruvadoo Luvina, & Haeussler Maximilian. (2013) The UCSC Genome Browser database: 2014 update. Nucleic acids research. PMID: 24270787  

The ENCODE Project Consortium, Bernstein Bradley E, Birney Ewan, Dunham Ian, Green Eric D, Gunter Chris, & Snyder Michael. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature. PMID: 22955616  

  • May 21, 2014
  • 09:33 AM
  • 129 views

Video Tip of the Week: PhenX, standardizing phenotype measurements

by Mary in OpenHelix

This week’s tip is actually sort of a mega-tip. It’s not just one video–it’s a series of videos that the GeneticAlliance has provided (and there are more to come) with the theme: “Managing the Mass of Measures: Real People’s Real Data Made Useful”. It is part of their Standards and Tools webinar series that is […]... Read more »

Hamilton C. M., Strader L. C., Pratt J. G., Maiese D., Hendershot T., Kwok R. K., Hammond J. A., Huggins W., Jackman D., & Pan H. (2011) The PhenX Toolkit: Get the Most From Your Measures. American Journal of Epidemiology, 174(3), 253-260. DOI: 10.1093/aje/kwr193  

  • May 14, 2014
  • 09:42 AM
  • 124 views

Video Tip of the Week: PheGenI, Phenotype-Genotype Integrator

by Mary in OpenHelix

The hunt for variations in genes and genomes has been both fruitful and frustrating. We can see genome variations in a variety of ways, but we can’t always connect them with a phenotype easily. And vice versa, of course. Another problem is that the kinds of data that we want to mine for further analysis […]... Read more »

Ramos Erin M, Hoffman Douglas, Junkins Heather A, Maglott Donna, Phan Lon, Sherry Stephen T, Feolo Mike, & Hindorff Lucia A. (2013) Phenotype–Genotype Integrator (PheGenI): synthesizing genome-wide association study (GWAS) data with existing genomic resources. European Journal of Human Genetics, 22(1), 144-147. DOI: 10.1038/ejhg.2013.96  

  • April 30, 2014
  • 08:49 AM
  • 108 views

Video Tip of the Week: canEvolve

by Mary in OpenHelix

Frequently when we go to a site to do workshops, we get requests about other workshops that they might host at their site. Last week at the workshop we did (UCSC Genome Browser, GenoCAD), I was asked again about tools for cancer genomics–such as TCGA and ICGC. This is a pretty common request, and I’ve […]... Read more »

Samur Mehmet Kemal, Yan Zhenyu, Wang Xujun, Cao Qingyi, Munshi Nikhil C., Li Cheng, Shah Parantu K., & Colak Dilek. (2013) canEvolve: A Web Portal for Integrative Oncogenomics. PLoS ONE, 8(2). DOI: 10.1371/journal.pone.0056228.s004  

  • April 23, 2014
  • 09:36 AM
  • 153 views

Video Tip of the Week: Atlas of Cancer Signaling Networks

by Mary in OpenHelix

Last week I highlighted a software tool that lets you customize maps of molecular interactions, and navigate around at various resolutions to explore. It’s called NaviCell, and it seems to offer a lot of opportunity for folks to develop helpful maps related to their research. This week I’m going to note that this same team […]... Read more »

Kuperstein Inna, Cohen David PA, Pook Stuart, Viara Eric, Calzone Laurence, Barillot Emmanuel, & Zinovyev Andrei. (2013) NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. BMC Systems Biology, 7(1), 100. DOI: 10.1186/1752-0509-7-100  

  • April 17, 2014
  • 09:39 AM
  • 223 views

What’s the Answer? (new Biostars interface)

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 »

Parnell Laurence D., Lindenbaum Pierre, Shameer Khader, Dall'Olio Giovanni Marco, Swan Daniel C., Jensen Lars Juhl, Cockell Simon J., Pedersen Brent S., Mangan Mary E., & Miller Christopher A. (2011) BioStar: An Online Question . PLoS Computational Biology, 7(10). DOI: 10.1371/journal.pcbi.1002216.g002  

  • April 16, 2014
  • 09:37 AM
  • 221 views

Video Tip of the Week: NaviCell for custom interaction maps for systems biology

by Mary in OpenHelix

The onslaught of sequence data from a whole range of species and tissues continues, and certainly will for a long time. But moving from there to the level of understanding the interactions among the genes that contribute to the structures, behaviors, and phenotypes of the systems requires other types of supporting software. NaviCell is a […]... Read more »

Kuperstein Inna, Cohen David PA, Pook Stuart, Viara Eric, Calzone Laurence, Barillot Emmanuel, & Zinovyev Andrei. (2013) NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. BMC Systems Biology, 7(1), 100. DOI: 10.1186/1752-0509-7-100  

Funahashi A., Matsuoka Y., Jouraku A., Morohashi M., Kikuchi N., & Kitano H. (2008) CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks. Proceedings of the IEEE, 96(8), 1254-1265. DOI: 10.1109/JPROC.2008.925458  

  • April 10, 2014
  • 09:14 AM
  • 288 views

What’s The Answer? (1000 Genomes signatures)

by Mary in OpenHelix

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 »

Pybus M., Dall'Olio G. M., Luisi P., Uzkudun M., Carreno-Torres A., Pavlidis P., Laayouni H., Bertranpetit J., & Engelken J. (2013) 1000 Genomes Selection Browser 1.0: a genome browser dedicated to signatures of natural selection in modern humans. Nucleic Acids Research, 42(D1). DOI: 10.1093/nar/gkt1188  

  • April 2, 2014
  • 09:37 AM
  • 179 views

Video Tip of the Week: EuPathDB

by Mary in OpenHelix

I love pathogens and parasites. Really, I do. I mean–not up very close. But their astonishing range and cleverness often earns my respect. How these small organisms can wreak havoc on larger systems, inveigle the larger organisms to fly, carry, or ship them around during appropriate points in their life cycle, and to cloak themselves […]... Read more »

Aurrecoechea C., Brestelli J., Brunk B. P., Fischer S., Gajria B., Gao X., Gingle A., Grant G., Harb O. S., & Heiges M. (2009) EuPathDB: a portal to eukaryotic pathogen databases. Nucleic Acids Research, 38(Database). DOI: 10.1093/nar/gkp941  

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.

Register Now

Research Blogging is powered by SMG Technology.

To learn more, visit seedmediagroup.com.