\begin{thebibliography}{27}
\providecommand{\natexlab}[1]{#1}
\providecommand{\url}[1]{\texttt{#1}}
\expandafter\ifx\csname urlstyle\endcsname\relax
  \providecommand{\doi}[1]{doi: #1}\else
  \providecommand{\doi}{doi: \begingroup \urlstyle{rm}\Url}\fi

\bibitem[Ajtai et~al.(1983)Ajtai, Koml\'{o}s, and
  Szemer{\'e}di]{cit:opt_sort_netw}
M.~Ajtai, J.~Koml\'{o}s, and E.~Szemer{\'e}di.
\newblock An 0(n log n) sorting network.
\newblock In \emph{Proceedings of the Fifteenth Annual ACM Symposium on Theory
  of Computing}, STOC '83, pages 1--9, New York, NY, USA, 1983. ACM.
\newblock ISBN 0-89791-099-0.
\newblock \doi{10.1145/800061.808726}.
\newblock URL \url{http://doi.acm.org/10.1145/800061.808726}.

\bibitem[Alam(2009)]{cit:genet_alg}
Nahid Alam.
\newblock Implementation of genetic algorithms in fpga-based reconfigurable
  computing systems.
\newblock 2009.
\newblock URL
  \url{https://tigerprints.clemson.edu/all_theses/618/?utm_source=tigerprints.clemson.edu%2Fall_theses%2F618&utm_medium=PDF&utm_campaign=PDFCoverPages}.

\bibitem[Batcher(1968)]{cit:bitonic}
K.~E. Batcher.
\newblock Sorting networks and their applications.
\newblock In \emph{Proceedings of the April 30--May 2, 1968, Spring Joint
  Computer Conference}, AFIPS '68 (Spring), pages 307--314, New York, NY, USA,
  1968. ACM.
\newblock \doi{10.1145/1468075.1468121}.
\newblock URL \url{http://doi.acm.org/10.1145/1468075.1468121}.

\bibitem[Che et~al.(2008)Che, Li, Sheaffer, Skadron, and Lach]{cit:compare_GPU}
S.~Che, J.~Li, J.~W. Sheaffer, K.~Skadron, and J.~Lach.
\newblock Accelerating compute-intensive applications with gpus and fpgas.
\newblock In \emph{2008 Symposium on Application Specific Processors}, pages
  101--107, June 2008.
\newblock \doi{10.1109/SASP.2008.4570793}.

\bibitem[Chodowiec and Gaj(2003)]{cit:FPGA_AES}
Pawe{\l} Chodowiec and Kris Gaj.
\newblock Very compact fpga implementation of the aes algorithm.
\newblock In Colin~D. Walter, {\c{C}}etin~K. Ko{\c{c}}, and Christof Paar,
  editors, \emph{Cryptographic Hardware and Embedded Systems - CHES 2003},
  pages 319--333, Berlin, Heidelberg, 2003. Springer Berlin Heidelberg.
\newblock ISBN 978-3-540-45238-6.

\bibitem[Chrysos et~al.(2012)Chrysos, Sotiriades, Rousopoulos, Dollas,
  Papadopoulos, Kirmitzoglou, Promponas, Theocharides, Petihakis, Lagnel,
  Vavylis, and Kotoulas]{cit:bio_paper}
G.~Chrysos, E.~Sotiriades, C.~Rousopoulos, A.~Dollas, A.~Papadopoulos,
  I.~Kirmitzoglou, V.~Promponas, T.~Theocharides, G.~Petihakis, J.~Lagnel,
  P.~Vavylis, and G.~Kotoulas.
\newblock Opportunities from the use of fpgas as platforms for bioinformatics
  algorithms.
\newblock In \emph{2012 IEEE 12th International Conference on Bioinformatics
  Bioengineering (BIBE)}, pages 559--565, Nov 2012.
\newblock \doi{10.1109/BIBE.2012.6399733}.

\bibitem[Cormen and Leiserson(2009)]{cit:alg_intro}
Thomas~H. Cormen and Charles~E. Leiserson.
\newblock \emph{Introduction to algorithms, 3rd edition}.
\newblock The MIT Press, 2009.

\bibitem[Demaine(2002)]{cit:dem_survey}
Erik Demaine.
\newblock Cache-oblivious algorithms and data structures.
\newblock \emph{EEF Summer School on Massive Data Sets}, 2002.

\bibitem[Grozea et~al.(2010)Grozea, Bankovic, and Laskov]{cit:GPU_compare_sort}
Cristian Grozea, Zorana Bankovic, and Pavel Laskov.
\newblock \emph{FPGA vs. Multi-core CPUs vs. GPUs: Hands-On Experience with a
  Sorting Application}, pages 105--117.
\newblock Springer Berlin Heidelberg, Berlin, Heidelberg, 2010.
\newblock ISBN 978-3-642-16233-6.
\newblock \doi{10.1007/978-3-642-16233-6_12}.
\newblock URL \url{https://doi.org/10.1007/978-3-642-16233-6_12}.

\bibitem[Guo et~al.(2004)Guo, Najjar, Vahid, and Vissers]{cit:why_faster}
Zhi Guo, Walid Najjar, Frank Vahid, and Kees Vissers.
\newblock A quantitative analysis of the speedup factors of fpgas over
  processors.
\newblock In \emph{Proceedings of the 2004 ACM/SIGDA 12th International
  Symposium on Field Programmable Gate Arrays}, FPGA '04, pages 162--170, New
  York, NY, USA, 2004. ACM.
\newblock ISBN 1-58113-829-6.
\newblock \doi{10.1145/968280.968304}.
\newblock URL \url{http://doi.acm.org/10.1145/968280.968304}.

\bibitem[Hagerup(1998)]{cit:word_ram}
Torben Hagerup.
\newblock Sorting and searching on the word ram.
\newblock In Michel Morvan, Christoph Meinel, and Daniel Krob, editors,
  \emph{STACS 98}, pages 366--398, Berlin, Heidelberg, 1998. Springer Berlin
  Heidelberg.
\newblock ISBN 978-3-540-69705-3.

\bibitem[Harper(1977)]{cit:synch_circ}
L.~H. Harper.
\newblock An $n \log n$ lower bound on synchronous combinational complexity.
\newblock \emph{Proceedings of the American Mathematical Society}, 64\penalty0
  (2):\penalty0 300--306, 1977.
\newblock ISSN 00029939, 10886826.
\newblock URL \url{http://www.jstor.org/stable/2041447}.

\bibitem[Huffstetler(2018)]{cit:intel_combined_xeon}
Jennifer Huffstetler.
\newblock Intel processors and fpgas-better together, May 2018.
\newblock URL
  \url{https://itpeernetwork.intel.com/intel-processors-fpga-better-together/}.

\bibitem[Hussain et~al.(2011)Hussain, Benkrid, Seker, and
  Erdogan]{cit:FPGA_k-means}
H.~M. Hussain, K.~Benkrid, H.~Seker, and A.~T. Erdogan.
\newblock Fpga implementation of k-means algorithm for bioinformatics
  application: An accelerated approach to clustering microarray data.
\newblock In \emph{2011 NASA/ESA Conference on Adaptive Hardware and Systems
  (AHS)}, pages 248--255, June 2011.
\newblock \doi{10.1109/AHS.2011.5963944}.

\bibitem[Karatsuba and Ofman(1962)]{cit:karatsuba}
A.~Karatsuba and Yu. Ofman.
\newblock Multiplication of many-digital numbers by automatic computers.
\newblock In \emph{Dokl. Akad. Nauk SSSR}, volume 145, pages 293--294, 1962.
\newblock URL \url{http://mi.mathnet.ru/dan26729}.

\bibitem[Karkooti et~al.(2005)Karkooti, Cavallaro, and
  Dick]{cit:FPGA_matrix_inv}
M.~Karkooti, J.~R. Cavallaro, and C.~Dick.
\newblock Fpga implementation of matrix inversion using qrd-rls algorithm.
\newblock In \emph{Conference Record of the Thirty-Ninth Asilomar Conference
  onSignals, Systems and Computers, 2005.}, pages 1625--1629, October 2005.
\newblock \doi{10.1109/ACSSC.2005.1600043}.

\bibitem[Ma et~al.(2014)Ma, Agrawal, and Chamberlain]{cit:model_GPU}
Lin Ma, Kunal Agrawal, and Roger~D. Chamberlain.
\newblock A memory access model for highly-threaded many-core architectures.
\newblock \emph{Future Generation Computer Systems}, 30:\penalty0 202 -- 215,
  2014.
\newblock ISSN 0167-739X.
\newblock \doi{https://doi.org/10.1016/j.future.2013.06.020}.
\newblock URL
  \url{http://www.sciencedirect.com/science/article/pii/S0167739X13001349}.
\newblock Special Issue on Extreme Scale Parallel Architectures and Systems,
  Cryptography in Cloud Computing and Recent Advances in Parallel and
  Distributed Systems, ICPADS 2012 Selected Papers.

\bibitem[Mahram(2013)]{cit:bio_thesis}
Atabak Mahram.
\newblock Fpga acceleration of sequence analysis tools in bioinformatics, 2013.
\newblock URL \url{https://open.bu.edu/handle/2144/11126}.

\bibitem[Reed(2003)]{cit:rand_tree_height}
Bruce Reed.
\newblock The height of a random binary search tree.
\newblock \emph{J. ACM}, 50\penalty0 (3):\penalty0 306--332, May 2003.
\newblock ISSN 0004-5411.
\newblock \doi{10.1145/765568.765571}.
\newblock URL \url{http://doi.acm.org/10.1145/765568.765571}.

\bibitem[Romoth et~al.(2017)Romoth, Porrmann, and Rückert]{cit:uses_FPGA}
Johannes Romoth, Mario Porrmann, and Ulrich Rückert.
\newblock {Survey of FPGA applications in the period 2000 – 2015 (Technical
  Report)}, 2017.

\bibitem[Sklavos(2015)]{cit:RAM_speed}
Dustin Sklavos.
\newblock Ddr3 vs. ddr4: Raw bandwidth by the numbers, Sep 2015.
\newblock URL
  \url{https://www.techspot.com/news/62129-ddr3-vs-ddr4-raw-bandwidth-numbers.html}.

\bibitem[Strassen(1969)]{cit:strassen}
Volker Strassen.
\newblock Gaussian elimination is not optimal.
\newblock \emph{Numer. Math.}, 13\penalty0 (4):\penalty0 354--356, August 1969.
\newblock ISSN 0029-599X.
\newblock \doi{10.1007/BF02165411}.
\newblock URL \url{http://dx.doi.org/10.1007/BF02165411}.

\bibitem[van Rooij and Bodlaender(2011)]{cit:alg_dom_set}
Johan~M.M. van Rooij and Hans~L. Bodlaender.
\newblock Exact algorithms for dominating set.
\newblock \emph{Discrete Applied Mathematics}, 159\penalty0 (17):\penalty0 2147
  -- 2164, 2011.
\newblock ISSN 0166-218X.
\newblock \doi{https://doi.org/10.1016/j.dam.2011.07.001}.
\newblock URL
  \url{http://www.sciencedirect.com/science/article/pii/S0166218X11002393}.

\bibitem[Vitter(2008)]{cit:book_low_bnd}
Jeffrey~Scott Vitter.
\newblock Algorithms and data structures for external memory.
\newblock \emph{Found. Trends Theor. Comput. Sci.}, 2\penalty0 (4):\penalty0
  54--63, January 2008.
\newblock ISSN 1551-305X.
\newblock \doi{10.1561/0400000014}.
\newblock URL \url{http://dx.doi.org/10.1561/0400000014}.

\bibitem[Vollmer(1999)]{cit:circuit_book}
Heribert Vollmer.
\newblock \emph{Introduction to Circuit Complexity: A Uniform Approach}.
\newblock Springer-Verlag, Berlin, Heidelberg, 1999.
\newblock ISBN 3540643109.

\bibitem[Woeginger(2003)]{cit:exp_survey}
Gerhard~J. Woeginger.
\newblock Combinatorial optimization - eureka, you shrink!
\newblock chapter Exact Algorithms for NP-hard Problems: A Survey, pages
  185--207. Springer-Verlag New York, Inc., New York, NY, USA, 2003.
\newblock ISBN 3-540-00580-3.
\newblock URL \url{http://dl.acm.org/citation.cfm?id=885909.885927}.

\bibitem[Zwick and Gupta(1996)]{cit:simulate_tm}
Uri Zwick and Anupam Gupta.
\newblock Concrete complexity lecture notes, lecture 3, 1996.
\newblock URL \url{www.cs.tau.ac.il/~zwick/circ-comp-new/two.ps}.

\end{thebibliography}
