Recommendations for YA with brainy protagonists

My almost-14-year-old daughter is currently into books with brainy lead characters. She particularly likes characters with interests in math, science, or programming, but any kind of braininess is okay. She likes character-driven books, or plot-driven books with very well developed characters. Mature themes are fine.

Her current favorite is Mr Penumbra's 24 Hour bookstore. She's read and loved everything by John Green. She has read Alan Bradley's Flavia series but it's not her favorite, because she prefers contemporary.

Suggestions? Thanks in advance!

Okay, rummaging around in my YA fiction tag:

A Wrinkle in Time, of course.
Empress of the World
Juniper, Gentian, and Rosemary
Magic or Madness
Surviving the Applewhites
The Westing Game
The Curious Incident of the Dog In the Night-time

I read most of these from about the ages of 12-16 myself. I guess I liked brainy protagonists at that age too.

I would recommend For the Win by Cory Doctorow, which is a fascinating YA novel about online economies. It's really long but so worth it.

Other cerebral recommendations:
Nothing by Janne Teller (very philosophical)
Marcelo in the Real World by Francisco X. Stork (narrated by an autistic boy who is fascinated by music and religion)
The Freak Observer by Blythe Woolston (about a girl very interested in science)
How to Say Goodbye in Robot by Natalie Standiford (amazing and smart characters)

The Austin Series by Madeleine L'Engle would be an excellent series. http://www.librarything.com/series/Chronos%252FThe+Austins%3A+Chronological+Orde...

Edit to add: If she likes fantasy, or is open to some really well written fantasy with strong characters, I would also recommend anything by Tamora Pierce. In particular, the Circle of Magic quartet has some elements of science in them. (Its been a while, but the 4 main characters each have a different elemental magic and have to understand how that element affects the world around it).

For something in the vein of Mr. Penumbra's 24-Hour Bookstore, maybe Emily Arsenault's The Broken Teaglass? It's an adult literary mystery, and similar to Mr. Penumbra has a pair of younger adults solving a mystery using their specialized knowledge and access (in this case, the mystery is set at a dictionary publisher).

The first book that came to mind was The Astonishing Life of Octavian Nothing, Traitor to the Nation -- but if she prefers contemporary, that's out.

Evolution, Me, and Other Freaks of Nature by Robin Brande was pretty good.
The Disreputable History of Frankie Landau-Banks by E. Lockhart is a lot of fun.
So is Into the Wild Nerd Yonder by Julie Halpern.
The Opposite of Hallelujah by Anna Jarzab is less fun, more thoughtful, but the main character is a science geek.
No and Me by Delphine de Vigan has a gifted 13-year-old as the main character.

That's all I have for now. Hope some of these appeal to her!

Oh yeah, one more: Fat Cat by Robin Brande. It's about a girl who goes on a "Caveman" diet as part of a project for her advanced science class. When this results in her losing a bunch of weight and guys start getting interested in her, she turns this situation into a kind of science experiment too.

These are great suggestions. Thank you all so much! I've handed the list off to my daughter, and she is happily browsing and buying. :)

Honey, Baby, Sweetheart by Deb Caletti has a smart girl who falls for a bad boy. I read very little chick lit but she had me laughing out loud. I also enjoyed Caletti's The Nature of Jade.

My first thought is www.wake by Robert Sawyer as the whole concept is quite interesting. It's adult scifi that crosses over to teen readers because the main character is a 14 or 15 year old blind girl. Quite contemporary.

Other books:
Genesis by Bernard Beckett - set in the future but would be of interest.
August by Bernard Beckett - also set in a near future
Sophie's World by Jostein Gaarder - philosophy

more fast paced YA thrillers -
Brainjack by Brian Falkner - hacking
Erebos by Ursula Poznanski - computers

The Orson Scott Card Ender's books: Ender's Game, Ender's Shadow and another one are about a genius kid.

Someday, Angeline.

Oh, and the City of Ember series

Maybe have her try the perks of being a wallflower, thirteen reasons why, Pushing the Limits, Cinder, and origin. Some may be a bit of a stretch, but I think all are great.

Brainy lead characters (and one of them is a girl) in OUT by M.J.Schwarz

The Young Wizards series by Diane Duane, first book is So You Want to be a Wizard.

I recommend the The Mysterious Benedict Society by Trenton Lee. It has plenty of twists and turns and you have to pay very good attention or else you'll miss things! Its full of likable and dislikable geniuses that have to complete many difficult tasks.

Teagan from The Goblin Wars trilogy by Kersten Hamilton is incredibly intelligent (her goal is to get into the veterinary science program at Cornell). Cath from Fangirl by Rainbow Rowell is a gifted writer.