Great question. While everyone has their schools of thought; both methods have their benefits. I tend to favor flat architecture with targeted cross linking. I guess you could call it a hybrid strategy. I begin with a totally flat architecture and silo where it makes sense for the rankings and the navigation for the user. It's all about logical grouping and don't forget the pages must all be link-worthy on their own. If the pages are all strong enough to generate links the problem tends to take care of itself.
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RE: Site Architecture: Cross Linking vs. Siloing
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RE: What would be a good way to drive traffic to a temporary post - job posting / classified ad?
Twitter - Facebook - Leverage your social channels - Industry contacts - I think SEOMOZ may offer a jobs posting location. If not it's not a bad idea. Hope this helps.
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RE: How much javascript does Googlebot read
I would say yes they are cloaked links. I would suggest using HTML links only for maximum juice and to not anger the Googlebot. Serving different content to the user with and without javascript is a no-no. As for your crawl budget - best practice is to use a nofollow tag on the link and a noindex on the target page if you don't want it in the SERPS.
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RE: Link Building PR versus topic
Both are desirable. I'd personally go with Domain authority and Page Authority over relevance if I had to choose. Links from monster news sites, mash-ups and other high traffic sites really pack a wallop. Need Proof - go to the Keyword Difficulty tool and check the top ranking sites for a series of terms. We have found some result listings that have little to no relevance but massive domain authority which carries the day.
FYI Use the Mozbar plugin when logged in to get more accurate data than PR. Or if you're getting really down and dirty go with The SEOMoz Linkscape Tool and run an advanced report by site links.
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RE: What is the best practice for changing a url of an existing page
Best practices is using the 301 redirect method - permanent
http://httpd.apache.org/docs/2.0/mod/mod_alias.html#redirect
You can also contact the link webmaster/s if possible to let them know that the page has changed url.
For added stability and to let Google know you should rebuild your sitemap to reflect the change as well.
In addition run Xenu or Screaming Frog to find all your internal linking locations to avoid missing the buried internal links.
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RE: Link Acquisition - PA vs PR
PageRank is an outdated stat. Google doesn't update it very much (if at all) anymore so you're looking at outdated data if you use PR. Page Authority on the other hand is calculated much more frequently. One other metric which you can get (and should heavily consider) from the updated SEOMoz Toolbar for Firefox or Chrome is Domain Authority.
Rand Just did a great Whiteboard Friday Video on Link Acquisition called Competitive Link Analysis Tips.
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RE: 100 Words per category
I don't think it's the quantity so much as the quality. EGOL alluded to this. Semantic processing of keywords in relation to other keywords in a context relevant to the search term is key. We have examples of this where our site beats much larger and authoritative sites on long tail keyword phrases even with their brand name included. This is as a direct result of the number of ways the keyword is used in relation to other keywords.
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RE: Best tools to find topics (not keywords) to write about?
The tried and true methods are keyword research and those you mentioned but to your question, I have always found that observation and opinion posts work very well for us. Whether you observe your industry, your city, your coworkers, your backyard, your commute to work, all are good idea generators. It pays to throw out the old preconceptions and just let it come. Sometimes the harder I try to create content, the harder it is. Forget the box let alone thinking outside of it. Reading is also very helpful. Read all you can about your field and your hobbies. Sometimes a connection happens when least expected. You could actually build out this Q and A and make it a topic to write about.
Happy writing