Reading academic papers on the iPhone

I frequently want to read academic papers while on the go. They're usually in PDF format, so I sync them to my iPhone with iBooks.

The problem is that most of the papers I want to read are in a two-column format that's extremely difficult to read on the phone's screen - I have to zoom in on a column, scroll down, then scroll up to the top of the next column and repeat.

Is there any software that will "flatten" out the PDF? I love Instapaper for web-based information; something that could turn a two-column PDF into a long stream of text and images would be great.

Goodreader for the iphone extracts text and images and fits them to your iphone screen and can be customized to your liking.

Calibre can be used to manage eBook libraries including PDF, and has the tools to transform them to other formats, including re-flow of text.

For academic papers I would recommend Papers by Mekentosj.

The app is available for iOS and Mac, so you can read, annotate or mark your papers on the go and have all papers in sync with your Mac. At home you can easily work with your papers, because Papers is also reference management software and gives the ability to directly search within your papers and cite within Word, Pages and several other editors.

I have the iOS and the Mac app and I love it.