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Science
Whitepapers and theory behind decentralized systems
Bitcoin whitepaper by Satoshi Nakamoto - also available as an AudioBook
Enabling Blockchain Innovations with Pegged Sidechains
The Bitcoin Lightning Network by Joseph Poon and Thaddeus Dryja
The Bitcoin Backbone Protocol by Juan A Garay, Aggelos Kiayias and Nikos Leonardos
Bitcoin-NG: A Scalable Blockchain Protocol by Ittay Eyal, Adem Efe Gencer, Emin Gun Sirer and Robbert van Renesse
Eclipse Attacks on Bitcoin’s Peer-to-Peer Network by Ethan Heilman, Alison Kendler, Aviv Zohar and Sharon Goldberg
Does Governance Have a Role in Pricing? Cross-Country Evidence from Bitcoin Markets by Robert Viglione
Bitcoin in Islamic Banking and Finance by Charles W Evans
SoK: Research Perspectives and Challenges for Bitcoin and Cryptocurrencies by Joseph Bonneau, Andrew Miller, Jeremy Clark, Arvind Narayanan, Joshua A. Kroll and Edward W Felten
NuBits whitepaper by Jordan Lee
Peercoin - Peer-to-Peer Crypto-Currency with Proof-of-Stake by Sunny King and Scott Nadal
FoldingCoin whitepaper by Robert Ross and James Sewell
Analysis of the Cryptocurrency Marketplace by Alexander Heid
Ethereum whitepaper by Vitalik Buterin
Ethereum yellowpaper by Gavin Wood
Notes on Scalable Blockchain Protocols by Vitalik Buterin
Vitalik Buterin has also written a series of technical articles on the Ethereum blog
IBM adept whitepaper early release
Plasma: Scalable Autonomous Smart Contracts by Joseph Poon and Vitalik Buterin
NXT Whitepaper
Factom - Business Processes Secured by Immutable Audit Trails on the Blockchain
Steem: An incentivized, blockchain-based, public content platform.
The tangle by Serguei Popov
Stratis Whitepaper by Chris Trew, Guy Brandon and Nicolas Dorier
Decentralized autonomous organization to automate governance by Christoph Jentzsch (slock.it)
Decentralized value distribution system for blockchain based applications by BackFeed
An economic system for blockchain based applications by BackFeed
Digix’s whitepaper:The Gold Standard in Crypto Assets by Anthony C. Eufemio, Kai C. Chng and Shaun Djie
Augur: a Decentralized, Open-Source Platform for Prediction Markets by Dr. Jack Peterson and Joseph Krug
Gnosis whitepaper
IPFS - Content Addressed, Versioned, P2P File System by Juan Benet
Storj - A Peer-to-Peer Cloud Storage Network by Shawn Wilkinson
MetaDisk - A Blockchain-Based Decentralized File Storage Application by Shawn Wilkinson and Jim Lowry
Filecoin - A Cryptocurrency Operated File Storage Network
Democratizing Content Publication with Coral by Michael J. Freedman, Eric Freudenthal, and David Mazières
Escaping the Evils of Centralized Control with self-certifying pathnames by David Mazières and M. Frans Kaashock
Sia: Simple Decentralized Storage by David Vorick and Luke Champine
TrueBit - A scalable verification solution for blockchains by Jason Teutsch and Christian Reitwießner
Golem whitepaper
CryptoNote v 2.0 by Nicolas van Saberhagen
Zcash Protocol Specification by Daira Hopwood, Sean Bowe, Taylor Hornby and Nathan Wilcox
Zerocash: Decentralized Anonymous Payments from Bitcoin by Eli Ben-Sasson et al.
Kademlia: A Peer-to-peer Information System Based on the XOR Metric by Petar Maymounkov and David Mazieres
Ledger Journal - a peer-reviewed journal focused on cryptocurrency and blockchain technology. It is an open access journal, all content is available under a Creative Commons license.