There is a problem with the search bar: it covers both subjects and bookmarks lists, but only searchs in the bookmarks' one.
For example, if you type one of the subject name, nothing happens with it… it's not very logical! So, either the UI must be changed, or it must egally act in the subjects pane.

Conserving the actual UI, I see two possibilities of action:

It acts like a search bar:
It searchs independently in subjects and bookmarks, and show only what matches in each column. When you clic on an object (subject or bookmark), it resets the search (because if you click on a subject, you want to see what it contains; if you click an a bookmark… you want to do something with it; so conservating the search is in both case a non-sense).
I don't think it's very ergonomic, but it's coherent.

It acts like a filter bar:
The subjects pane shows both what matches directly and the subjects of the bookmarks which matches. The bookmarks part shows the bookmarks matching and the ones contained in the subjects matching. When you click on an object, you can "browse" normally, and clear the filter bar to do more things.
I think it's a very great solution, but certainly difficult to code.

Changing the UI:

The search bar is placed at the top of the bookmarks, and at the right of the subjects pane. The UI is so more or less the same as the history's window. Clicking on a subject resets the search (like in history).
It's a great solution.

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