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bibliography.bib
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@article{guha1998approximation,
title={Approximation algorithms for connected dominating sets},
author={Guha, Sudipto and Khuller, Samir},
journal={Algorithmica},
volume={20},
number={4},
pages={374--387},
year={1998},
publisher={Springer}
}
@article{chan2012approximation,
title={Approximation algorithms for maximum independent set of pseudo-disks},
author={Chan, Timothy M and Har-Peled, Sariel},
journal={Discrete \& Computational Geometry},
volume={48},
number={2},
pages={373--392},
year={2012},
publisher={Springer}
}
@article{erlebach2005polynomial,
title={Polynomial-time approximation schemes for geometric intersection graphs},
author={Erlebach, Thomas and Jansen, Klaus and Seidel, Eike},
journal={SIAM Journal on Computing},
volume={34},
number={6},
pages={1302--1323},
year={2005},
publisher={SIAM}
}
@article{bafna1996nonoverlapping,
title={Nonoverlapping local alignments (weighted independent sets of axis-parallel rectangles)},
author={Bafna, Vineet and Narayanan, Babu and Ravi, R},
journal={Discrete Applied Mathematics},
volume={71},
number={1-3},
pages={41--53},
year={1996},
publisher={Elsevier}
}
@article{chandra2001greedy,
title={Greedy local improvement and weighted set packing approximation},
author={Chandra, Barun and Halld{\'o}rsson, Magn{\'u}s M},
journal={Journal of Algorithms},
volume={39},
number={2},
pages={223--240},
year={2001},
publisher={Elsevier}
}
@inproceedings{berman2000d,
title={A d/2 approximation for maximum weight independent set in d-claw free graphs},
author={Berman, Piotr},
booktitle={Scandinavian Workshop on Algorithm Theory},
pages={214--219},
year={2000},
organization={Springer}
}
@article{newman2004fast,
title={Fast algorithm for detecting community structure in networks},
author={Newman, Mark EJ},
journal={Physical review E},
volume={69},
number={6},
pages={066133},
year={2004},
publisher={APS}
}
@article{clauset2004finding,
title={Finding community structure in very large networks},
author={Clauset, Aaron and Newman, Mark EJ and Moore, Cristopher},
journal={Physical review E},
volume={70},
number={6},
pages={066111},
year={2004},
publisher={APS}
}
@article{blondel2008fast,
title={Fast unfolding of communities in large networks},
author={Blondel, Vincent D and Guillaume, Jean-Loup and Lambiotte, Renaud and Lefebvre, Etienne},
journal={Journal of statistical mechanics: theory and experiment},
volume={2008},
number={10},
pages={P10008},
year={2008},
publisher={IOP Publishing}
}
@article{kaminker2002transposable,
title={The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective},
author={Kaminker, Joshua S and Bergman, Casey M and Kronmiller, Brent and Carlson, Joseph and Svirskas, Robert and Patel, Sandeep and Frise, Erwin and Wheeler, David A and Lewis, Suzanna E and Rubin, Gerald M and others},
journal={Genome biology},
volume={3},
number={12},
pages={research0084--1},
year={2002},
publisher={BioMed Central}
}
@article{koren2012hybrid,
title={Hybrid error correction and de novo assembly of single-molecule sequencing reads},
author={Koren, Sergey and Schatz, Michael C and Walenz, Brian P and Martin, Jeffrey and Howard, Jason T and Ganapathy, Ganeshkumar and Wang, Zhong and Rasko, David A and McCombie, W Richard and Jarvis, Erich D and others},
journal={Nature biotechnology},
volume={30},
number={7},
pages={693},
year={2012},
publisher={Nature Publishing Group}
}
@article{she2004structure,
title={The structure and evolution of centromeric transition regions within the human genome},
author={She, Xinwei and Horvath, Julie E and Jiang, Zhaoshi and Liu, Ge and Furey, Terrence S and Christ, Laurie and Clark, Royden and Graves, Tina and Gulden, Cassy L and Alkan, Can and others},
journal={Nature},
volume={430},
number={7002},
pages={857},
year={2004},
publisher={Nature Publishing Group}
}
@article{skaletsky2003male,
title={The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes},
author={Skaletsky, Helen and Kuroda-Kawaguchi, Tomoko and Minx, Patrick J and Cordum, Holland S and Hillier, LaDeana and Brown, Laura G and Repping, Sjoerd and Pyntikova, Tatyana and Ali, Johar and Bieri, Tamberlyn and others},
journal={Nature},
volume={423},
number={6942},
pages={825},
year={2003},
publisher={Nature Publishing Group}
}
@article{riethman2004mapping,
title={Mapping and initial analysis of human subtelomeric sequence assemblies},
author={Riethman, Harold and Ambrosini, Anthony and Castaneda, Carlos and Finklestein, Jeffrey and Hu, Xue-Lan and Mudunuri, Uma and Paul, Sheila and Wei, Jun},
journal={Genome research},
volume={14},
number={1},
pages={18--28},
year={2004},
publisher={Cold Spring Harbor Lab}
}
@article{alkan2007organization,
title={Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data},
author={Alkan, Can and Ventura, Mario and Archidiacono, Nicoletta and Rocchi, Mariano and Sahinalp, S Cenk and Eichler, Evan E},
journal={PLoS computational biology},
volume={3},
number={9},
pages={e181},
year={2007},
publisher={Public Library of Science}
}
@article{rudd2004analysis,
title={Analysis of the centromeric regions of the human genome assembly},
author={Rudd, M Katharine and Willard, Huntington F},
journal={Trends in genetics},
volume={20},
number={11},
pages={529--533},
year={2004},
publisher={Elsevier}
}
@article{myers2000whole,
title={A whole-genome assembly of Drosophila},
author={Myers, Eugene W and Sutton, Granger G and Delcher, Art L and Dew, Ian M and Fasulo, Dan P and Flanigan, Michael J and Kravitz, Saul A and Mobarry, Clark M and Reinert, Knut HJ and Remington, Karin A and others},
journal={Science},
volume={287},
number={5461},
pages={2196--2204},
year={2000},
publisher={American Association for the Advancement of Science}
}
@book{peterson2013plant,
title={Plant transposable elements: methods and protocols},
author={Peterson, Thomas Allen and Peterson, Thomas Allen},
year={2013},
publisher={Springer}
}
@article{ummat2014resolving,
title={Resolving complex tandem repeats with long reads},
author={Ummat, Ajay and Bashir, Ali},
journal={Bioinformatics},
volume={30},
number={24},
pages={3491--3498},
year={2014},
publisher={Oxford University Press}
}
@article{horvath2000mosaic,
title={The mosaic structure of human pericentromeric DNA: a strategy for characterizing complex regions of the human genome},
author={Horvath, Juliann E and Schwartz, Stuart and Eichler, Evan E},
journal={Genome research},
volume={10},
number={6},
pages={839--852},
year={2000},
publisher={Cold Spring Harbor Lab}
}
@article{han2010mite,
title={MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences},
author={Han, Yujun and Wessler, Susan R},
journal={Nucleic acids research},
volume={38},
number={22},
pages={e199--e199},
year={2010},
publisher={Oxford University Press}
}
@article{shen2009detect,
title={Detect overlapping and hierarchical community structure in networks},
author={Shen, Huawei and Cheng, Xueqi and Cai, Kai and Hu, Mao-Bin},
journal={Physica A: Statistical Mechanics and its Applications},
volume={388},
number={8},
pages={1706--1712},
year={2009},
publisher={Elsevier}
}
@article{palla2005uncovering,
title={Uncovering the overlapping community structure of complex networks in nature and society},
author={Palla, Gergely and Der{\'e}nyi, Imre and Farkas, Ill{\'e}s and Vicsek, Tam{\'a}s},
journal={Nature},
volume={435},
number={7043},
pages={814},
year={2005},
publisher={Nature Publishing Group}
}
@article{xie2013overlapping,
title={Overlapping community detection in networks: The state-of-the-art and comparative study},
author={Xie, Jierui and Kelley, Stephen and Szymanski, Boleslaw K},
journal={Acm computing surveys (csur)},
volume={45},
number={4},
pages={43},
year={2013},
publisher={ACM}
}
@article{kannan2004clusterings,
title={On clusterings: Good, bad and spectral},
author={Kannan, Ravi and Vempala, Santosh and Vetta, Adrian},
journal={Journal of the ACM (JACM)},
volume={51},
number={3},
pages={497--515},
year={2004},
publisher={ACM}
}
@article{brandes2007engineering,
title={Engineering graph clustering: Models and experimental evaluation},
author={Brandes, Ulrik and Gaertler, Marco and Wagner, Dorothea},
journal={ACM Journal of Experimental Algorithmics},
volume={12},
number={1.1},
pages={1--26},
year={2007}
}
@article{tomita2006worst,
title={The worst-case time complexity for generating all maximal cliques and computational experiments},
author={Tomita, Etsuji and Tanaka, Akira and Takahashi, Haruhisa},
journal={Theoretical Computer Science},
volume={363},
number={1},
pages={28--42},
year={2006},
publisher={Elsevier}
}
@inproceedings{zhang2005genome,
title={Genome-scale computational approaches to memory-intensive applications in systems biology},
author={Zhang, Yun and Abu-Khzam, Faisal N and Baldwin, Nicole E and Chesler, Elissa J and Langston, Michael A and Samatova, Nagiza F},
booktitle={Supercomputing, 2005. Proceedings of the ACM/IEEE SC 2005 Conference},
pages={12--12},
year={2005},
organization={IEEE}
}
@article{brandes2001faster,
title={A faster algorithm for betweenness centrality},
author={Brandes, Ulrik},
journal={Journal of mathematical sociology},
volume={25},
number={2},
pages={163--177},
year={2001},
publisher={Taylor \& Francis}
}
@article{guy2000genomic,
title={Genomic sequence and transcriptional profile of the boundary between pericentromeric satellites and genes on human chromosome arm 10q},
author={Guy, J and Spalluto, C and McMurray, A and Hearn, T and Crosier, M and Viggiano, L and Miolla, V and Archidiacono, N and Rocchi, M and Scott, C and others},
journal={Human molecular genetics},
volume={9},
number={13},
pages={2029--2042},
year={2000},
publisher={Oxford University Press}
}