8th Cell Cyclist Newsletter

B2UzV4VIUAA6yj_Just before leaving for a weekend at the ‘2015 KI Neuroscience PhD Ski Conference’ in Norway I’d like to share with you a new round of science-related resources:

1. Let’s start with two interesting special issues in Frontiers Genetics/Oncology on molecular cancer mechanisms and therapeutic implications: “Cancer-associated defects in the DNA damage response: drivers for malignant transformation and potential therapeutic targets.” and “Molecular mechanisms of cellular stress responses in cancer and their therapeutic implications.”
http://journal.frontiersin.org/researchtopic/2492 and http://journal.frontiersin.org/researchtopic/1922

2. According to a study in PlosOne writing a grant proposal takes on average 116 PI hours. I wonder if PI hours are longer or shorter than PhD or Postdoc hours. However the time spent writing was not related to whether the grant was funded – ‘To Apply or Not to Apply: A Survey Analysis of Grant Writing Costs and Benefits’ http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118494

3. For all of you doing flow cytometry, BD provides an excellent resource on optimal buffer conditions and antibody concentrations for a range of surface markers and intracellular staining. http://cytobank.org/facselect/

4. Finally upon request and since I couldn’t find anything on the internet, the code for a very basic ImageJ macro to crop a cell tracked from live-cell imaging into a separate stack. Good for analysis or simply to show a representative cell. (As WordPress doesn’t support upload of all file types I had to paste the code into a word document. Just copy&paste into a text file and change the file ending to *.ijm for ImageJ macros.)
SingleCellStack

Cheers,
Erik

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7th Cell Cyclist Newsletter

health-mortality-research-spendSome time has passed since the last post, with me being busy doing science. But I also collected some helpful and/or resources to share with you. Btw, I really appreciate when people send suggestions and feedback. Thanks a lot. And here we go:

1. No matter if you want to do a simple Student’s t-test or a Three-way ANOVA, Nature provides a very nice collection of basic and advanced statistic resources for scientists.
http://www.nature.com/collections/qghhqm

2. Again at Nature they provide a nice and extensive protocol exchange of currently 2623 laboratory protocols. Everything from microscopy, basic and advance protein biochemistry, cloning, stem cells, cell cycle and DNA damage, ChIP, flow cytometry … you name it.
http://www.nature.com/protocolexchange/protocols

3. ‘Cancer kills almost a third of us, and yet we spend less than £5 per person per year researching it.’ – Sciencogram breaks down the money invested in science stacked up against the challenges tackled. Something to think about.
http://scienceogram.org/

4. Some helpful advise when dealing with unfavorable reviews of your paper – How to convince referees and respond to reviews
http://exchanges.wiley.com/blog/2015/01/22/cooperation-not-confrontation-how-to-convince-referees-and-respond-to-reviews/

5. And if arguing doesn’t help, maybe this can cheer you up if your paper got rejected – A list of significant scientific papers that got rejected. Many of these discoveries have even been awarded with the Nobel prize later.
https://majesticforest.wordpress.com/2014/08/15/papers-that-triumphed-over-their-rejections/

Cheers,
Erik

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6th Cell Cyclist Newsletter

Dear Cell Cyclists,Screen Shot 2015-02-05 at 4.29.14 PM

Time flies by when you’re doing science. And so I have some sciency resources to share with you again.

1. A recent paper suggests that culturing cells alters their epigenetic and transcriptional profile within as early as three days.
http://genomebiology.com/2015/16/1/11/abstract

2. There is a whole volume from ‘Methods in Molecular Biology’ devoted to advanced fluorescence microscopy techniques including all your favorite acronyms – TIRF, FRET, FLIM, FRAP, SIM, STED…
http://link.springer.com/book/10.1007%2F978-1-4939-2080-8

3. A very good read for PhD students, post-docs (and PIs) – ‘What is the best publication strategy in science?’
http://www.smartsciencecareer.com/best-publication-strategy-in-science/

4. Talking about publishing. This recent analysis suggests a growing impact of ‘Non-Elite Journals’, as they continuously increase their fraction of publications, citations and top-cited papers.
http://arxiv.org/pdf/1410.2217.pdf

Cheers,
Erik

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5th Cell Cyclist Newsletter

Dear Cell Cyclists,
B7AR-v5IEAAp7O8.jpg_large
Thanks to the many that signed up for this newsletter.
Here are some fresh articles and resources that got me interested during the last two weeks:

1. CRISPR has already revolutionized genome engineering and many are working to establish the technique in their lab. Addgene offers some really nice resources on the topic – guides, protocols, trouble-shooting and of course lots of plasmids. (btw, I’d bet a case of beer on a Nobel prize for CRISPR within the next five years)
http://www.addgene.org/CRISPR/planning-your-experiment/

2. There is frequent discussion in our lab discussions about cancer type prevalence. Case numbers, survival rates, trends and statistics from the US can be found at:
http://seer.cancer.gov/statfacts/html/breast.html

3. Ever wondered about who ‘invented’ the journal club? – The history of Journal Clubs
http://blogs.plos.org/absolutely-maybe/sciences-water-coolers-turning-up-the-volume-on-journal-clubs/

4. For all those that have biology PhD or are working on it the picture on top provides a nice overview of the current job landscape in academia and industry. And if you want to know how your chances are to obtain one of these precious faculty positions have a look at Science Magazine’s PI-predictor:
http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2014_06_02/caredit.a1400136

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4th Cell Cyclist Newsletter

B6Xs1qYCcAEnVkXHappy New Year Cell Cyclists! And of course also to the people studying other interesting stuff. Hope you had a nice Christmas break and that  2015 is going to be an awesome science year for all of you.

But let’s get to recent sciency things that I stumbled upon:

1. A must-read for all fluorescence microscopist – The Microscopy Blog from the director of the imaging facility at UCSF. I really like the monthly roundup of recent microscopy papers.
http://nic.ucsf.edu/blog/

2. A resource list of all the genes/proteins involved in DNA damage and repair.
http://sciencepark.mdanderson.org/labs/wood/dna_repair_genes.html

3. Talking about DNA repair, Nico Dantuma from CMB lately got featured at ‘The people behind science’. Read his and other interviews at:
http://www.peoplebehindthescience.com/dr-nico-dantuma/

4. Andrei Chagin, group leader at FiFa developed the Author Scientific Contribution (ASC) Index – A simple and clever improvement of the impact factor. Thanks Julian for the tip!
http://asc.conzept.se/

5. Finally, a recent paper in science suggests that at least two thirds of cancers cases can be explained simply by the number of cell division in the respective tissue during a lifetime. Thus most cancers are the result of biological bad luck and cannot be prevented.
http://www.sciencemag.org/content/347/6217/78.abstract

Cheers,
Erik

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3rd Cell Cyclist Newsletter

Hello Cell Cyclists,Screen Shot 2015-01-08 at 11.54.01 AM

Here come some helpful microscopy resources and other sciency things that got me interested in the last weeks:

1. A very handy complete ‎fluorescent protein table. Great way to help pick your next tag for your protein, or double check the conditions of the one you already have:
http://nic.ucsf.edu/FPvisualization/

2. A guide on choosing compatible fluorescent proteins for multicolor imaging:
http://blog.addgene.org/choosing-your-fluorescent-proteins-for-multi-color-imaging

3. A review on the new low-fluorescence DMEM for microscopy from Life Techologies (Fluorobrite DMEM). Including example movies:
http://nic.ucsf.edu/blog/?p=1343

4. A paper using stochastic modeling to estimate how many people who cite a paper have actually read it:
https://www.complex-systems.com/pdf/14-3-5.pdf

5. A scientific search engine that provides you with a list of experts, patents, companies etc. that work with your technology, method or protein of interest:
https://en.expernova.com/

Cheers,
Erik

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2nd Cell Cyclist Newsletter

Hello cell cyclists,
Here are the sciency things that got me interested in the last two weeks:

1. At antibodypedia you can find data on almost 1.5 million antibodies. This includes WBs, IFs, FACS plots and paper references. A really helpful tool:
http://www.antibodypedia.com/

2. An online tool that helps you find the appropriate journal for your manuscript by searching the keywords in the title and abstract. It includes a good overview of impact and open access availability:
http://www.journalguide.com/

3. If you want to know what people discuss about your papers on F1000, Google+ and Twitter you can now check your Altmetrics (alternative metrics) simply using your ORCID (Open Researcher and Contributor ID):
http://altmetric-orcid-profiles.herokuapp.com/0000-0002-2176-3248

4. With some of you I already I shared parts of the ‘Ten simple rules’ series from PLoS. There is lots of interesting article including Ten simple rules for…
…writing research papers
…better figures
…reviewers
…successful collaborations
…building and maintaining a scientific reputation
…writing a review
…getting grants
…getting published

Check it out at: http://www.ploscollections.org/article/browse/issue/info%3Adoi%2F10.1371%2Fissue.pcol.v03.i01

Cheers,
Erik

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1st Cell Cyclist Newsletter

Hello cell cyclists,nature_top_100_papers_infographicV2_30.10.14
So this is the first ‘official’ newsletter. I’ll see how it goes and if I find regularly interesting things. I appreciate any input/feedback.
So here we go:

1. Nature Methods selected the 10 methods that impacted biology the most in the last 10 years. I guess it’s worth keeping an eye on these as the revolution is still ongoing:
http://www.nature.com/nmeth/journal/v11/n10/full/nmeth1014-1000.html

2. In line, Nature explored the 100 most-cited papers of all time and they are mainly about new methods:
http://www.nature.com/news/the-top-100-papers-1.16224?WT.ec_id=NATURE-20141030

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