When I read articles on my iPad in portrait mode, I like the screen to be as "clean" as possible. What I would like to see is that the article list (left or bottom) can be completely hidden. I don't need it when reading; I can swipe through all articles.
Yes, I already do that, but that's not what I call a clean interface. The Mr. Reader app is a good example of what I call "clean": only a very smal top and bottom bar with a light color that doesn't distract from the text.
I personally see no use for an article list when I'm in portrait mode. I, and maybe also many more people, go into portrait mode for reading and then don't really need to see the article list.