SCarborSNV.bib

%Similar tools
@article{monovar,
  title={Monovar: single-nucleotide variant detection in single cells},
  author={Zafar, Hamim and Wang, Yong and Nakhleh, Luay and Navin, Nicholas and Chen, Ken},
  journal={Nature methods},
  volume={13},
  number={6},
  pages={505},
  year={2016},
  publisher={Nature Publishing Group}
}

@article{sciphi,
  title={Single-cell mutation identification via phylogenetic inference},
  author={Singer, Jochen and Kuipers, Jack and Jahn, Katharina and Beerenwinkel, Niko},
  journal={Nature communications},
  volume={9},
  number={1},
  pages={5144},
  year={2018},
  publisher={Nature Publishing Group}
}

@book{BSA,
  title={Biological sequence analysis: probabilistic models of proteins and nucleic acids},
  author={Durbin, Richard and Eddy, Sean R and Krogh, Anders and Mitchison, Graeme},
  year={1998},
  publisher={Cambridge university press}
}

@article{NJ,
title={The neighbor-joining method: a new method for reconstructing phylogenetic trees.},
author={Saitou, Naruya and Nei, Masatoshi},
journal={Molecular biology and evolution},
volume={4},
number={4},
pages={406--425},
year={1987}
}


%Bio background
@book{EmperorMaladies,
  title={The emperor of all maladies: a biography of cancer},
  author={Mukherjee, Siddhartha},
  year={2010},
  publisher={Simon and Schuster}
}

@article{bigbang,
    title={A Big Bang model of human colorectal tumor growth},
    author={Sottoriva, Andrea and Kang, Haeyoun and Ma, Zhicheng and Graham, Trevor A and Salomon, Matthew P and Zhao, Junsong and Marjoram, Paul and Siegmund, Kimberly and Press, Michael F and Shibata, Darryl and others},
    journal={Nature genetics},
    volume={47},
    number={3},
    pages={209},
    year={2015},
    publisher={Nature Publishing Group}
}

@article{metastatic,
  title={The evolutionary history of lethal metastatic prostate cancer},
  author={Gundem, Gunes and Van Loo, Peter and Kremeyer, Barbara and Alexandrov, Ludmil B and Tubio, Jose MC and Papaemmanuil, Elli and Brewer, Daniel S and Kallio, Heini ML and H{\"o}gn{\"a}s, Gunilla and Annala, Matti and others},
  journal={Nature},
  volume={520},
  number={7547},
  pages={353},
  year={2015},
  publisher={Nature Publishing Group}
}

@article{21breasts,
  title={The life history of 21 breast cancers},
  author={Nik-Zainal, Serena and Van Loo, Peter and Wedge, David C and Alexandrov, Ludmil B and Greenman, Christopher D and Lau, King Wai and Raine, Keiran and Jones, David and Marshall, John and Ramakrishna, Manasa and others},
  journal={Cell},
  volume={149},
  number={5},
  pages={994--1007},
  year={2012},
  publisher={Elsevier}
}

@article{21breasts2,
    title={Mutational processes molding the genomes of 21 breast cancers},
    author={Nik-Zainal, Serena and Alexandrov, Ludmil B and Wedge, David C and Van Loo, Peter and Greenman, Christopher D and Raine, Keiran and Jones, David and Hinton, Jonathan and Marshall, John and Stebbings, Lucy A and others},
    journal={Cell},
    volume={149},
    number={5},
    pages={979--993},
    year={2012},
    publisher={Elsevier}
}


@article{greaves2012clonal,
  title={Clonal evolution in cancer},
  author={Greaves, Mel and Maley, Carlo C},
  journal={Nature},
  volume={481},
  number={7381},
  pages={306},
  year={2012},
  publisher={Nature Publishing Group}
}

@article{merlo2006cancer,
  title={Cancer as an evolutionary and ecological process},
  author={Merlo, Lauren MF and Pepper, John W and Reid, Brian J and Maley, Carlo C},
  journal={Nature reviews cancer},
  volume={6},
  number={12},
  pages={924},
  year={2006},
  publisher={Nature Publishing Group}
}

@article{aneuploidy,
title={Aneuploidy and cancer},
author={Rajagopalan, Harith and Lengauer, Christoph},
journal={Nature},
volume={432},
number={7015},
pages={338},
year={2004},
publisher={Nature Publishing Group}
}

%Sequencing
@article{sequencesequencers,
    title={The sequence of sequencers: The history of sequencing DNA},
    author={Heather, James M and Chain, Benjamin},
    journal={Genomics},
    volume={107},
    number={1},
    pages={1--8},
    year={2016},
    publisher={Elsevier}
}

@article{massivelyparallel,
    title={Massively parallel sequencing: the next big thing in genetic medicine},
    author={Tucker, Tracy and Marra, Marco and Friedman, Jan M},
    journal={The American Journal of Human Genetics},
    volume={85},
    number={2},
    pages={142--154},
    year={2009},
    publisher={Elsevier}
}

@article{SCSadvance,
    title={Advances and applications of single-cell sequencing technologies},
    author={Wang, Yong and Navin, Nicholas E},
    journal={Molecular cell},
    volume={58},
    number={4},
    pages={598--609},
    year={2015},
    publisher={Elsevier}
}

@article{scprimer,
  title={Single-cell sequencing},
  author={Nawy, Tal},
  journal={Nature methods},
  volume={11},
  number={1},
  pages={18},
  year={2013},
  publisher={Nature Publishing Group}
}

@article{clonevol,
    title={ClonEvol: clonal ordering and visualization in cancer sequencing},
    author={Dang, HX and White, BS and Foltz, SM and Miller, CA and Luo, Jingqin and Fields, RC and Maher, CA},
    journal={Annals of oncology},
    volume={28},
    number={12},
    pages={3076--3082},
    year={2017},
    publisher={Oxford University Press}
}

@article{onecelltime,
    title={Cancer genomics: one cell at a time},
    author={Navin, Nicholas E},
    journal={Genome biology},
    volume={15},
    number={8},
    pages={452},
    year={2014},
    publisher={BioMed Central}
}

@article{rnaseq,
    title={RNA-Seq: a revolutionary tool for transcriptomics},
    author={Wang, Zhong and Gerstein, Mark and Snyder, Michael},
    journal={Nature reviews genetics},
    volume={10},
    number={1},
    pages={57},
    year={2009},
    publisher={Nature Publishing Group}
}

@article{cellity,
    title={Classification of low quality cells from single-cell RNA-seq data},
    author={Ilicic, Tomislav and Kim, Jong Kyoung and Kolodziejczyk, Aleksandra A and Bagger, Frederik Otzen and McCarthy, Davis James and Marioni, John C and Teichmann, Sarah A},
    journal={Genome biology},
    volume={17},
    number={1},
    pages={29},
    year={2016},
    publisher={BioMed Central}
}

@book{biochemistry,
title={Biochemistry},
author={Berg, J.M. and Tymoczko, J.L. and Stryer, L.},
isbn={9780716787242},
lccn={2005052751},
series={Biochemistry (Berg)},
url={https://books.google.es/books?id=Uhm\_ngEACAAJ},
year={2007},
publisher={W. H. Freeman}
}

@article{gao2016punctuated,
  title={Punctuated copy number evolution and clonal stasis in triple-negative breast cancer},
  author={Gao, Ruli and Davis, Alexander and McDonald, Thomas O and Sei, Emi and Shi, Xiuqing and Wang, Yong and Tsai, Pei-Ching and Casasent, Anna and Waters, Jill and Zhang, Hong and others},
  journal={Nature genetics},
  volume={48},
  number={10},
  pages={1119},
  year={2016},
  publisher={Nature Publishing Group}
}

@article{greenman2007patterns,
title={Patterns of somatic mutation in human cancer genomes},
author={Greenman, Christopher and Stephens, Philip and Smith, Raffaella and Dalgliesh, Gillian L and Hunter, Christopher and Bignell, Graham and Davies, Helen and Teague, Jon and Butler, Adam and Stevens, Claire and others},
journal={Nature},
volume={446},
number={7132},
pages={153},
year={2007},
publisher={Nature Publishing Group}
}

@article{alexandrov2013signatures,
    title={Signatures of mutational processes in human cancer},
    author={Alexandrov, Ludmil B and Nik-Zainal, Serena and Wedge, David C and Aparicio, Samuel AJR and Behjati, Sam and Biankin, Andrew V and Bignell, Graham R and Bolli, Niccolo and Borg, Ake and B{\o}rresen-Dale, Anne-Lise and others},
    journal={Nature},
    volume={500},
    number={7463},
    pages={415},
    year={2013},
    publisher={Nature Publishing Group}
}

@article{JC,
title={Evolution of protein molecules},
author={Jukes, Thomas H and Cantor, Charles R and others},
journal={Mammalian protein metabolism},
volume={3},
number={21},
pages={132},
year={1969},
publisher={New York}
}

@article{neutralevoltumour,
  title={Identification of neutral tumor evolution across cancer types},
  author={Williams, Marc J and Werner, Benjamin and Barnes, Chris P and Graham, Trevor A and Sottoriva, Andrea},
  journal={Nature genetics},
  volume={48},
  number={3},
  pages={238},
  year={2016},
  publisher={Nature Publishing Group}
}

@article{numcells,
  title={Does the cell number $10^9$ still really fit one gram of tumor tissue?},
  author={Del Monte, Ugo},
  journal={Cell Cycle},
  volume={8},
  number={3},
  pages={505--506},
  year={2009},
  publisher={Taylor \& Francis}
}

@article{yachida,
  title={Distant metastasis occurs late during the genetic evolution of pancreatic cancer},
  author={Yachida, Shinichi and Jones, Si{\^a}n and Bozic, Ivana and Antal, Tibor and Leary, Rebecca and Fu, Baojin and Kamiyama, Mihoko and Hruban, Ralph H and Eshleman, James R and Nowak, Martin A and others},
  journal={Nature},
  volume={467},
  number={7319},
  pages={1114},
  year={2010},
  publisher={Nature Publishing Group}
}

@article{listatistical,
    title={A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data},
    author={Li, Heng},
    journal={Bioinformatics},
    volume={27},
    number={21},
    pages={2987--2993},
    year={2011},
    publisher={Oxford University Press}
}

@article{ledurbin,
  title={{SNP} detection and genotyping from low-coverage sequencing data on multiple diploid samples},
  author={Le, Si Quang and Durbin, Richard},
  journal={Genome research},
  volume={21},
  number={6},
  pages={952--960},
  year={2011},
  publisher={Cold Spring Harbor Lab}
}

@article{negedge,
    title={A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates.},
    author={Kuhner, Mary K and Felsenstein, Joseph},
    journal={Molecular biology and evolution},
    volume={11},
    number={3},
    pages={459--468},
    year={1994}
}

RFmetric, TreeCmp
@article{RFmetric,
  title={Comparison of phylogenetic trees},
  author={Robinson, David F and Foulds, Leslie R},
  journal={Mathematical biosciences},
  volume={53},
  number={1-2},
  pages={131--147},
  year={1981},
  publisher={Elsevier}
}

@article{TreeCmp,
  title={TreeCmp: comparison of trees in polynomial time},
  author={Bogdanowicz, Damian and Giaro, Krzysztof and Wr{\'o}bel, Borys},
  journal={Evolutionary Bioinformatics},
  volume={8},
  pages={EBO--S9657},
  year={2012},
  publisher={SAGE Publications Sage UK: London, England}
}

@article{BWAMEM,
  title={Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM},
  author={Li, Heng},
  journal={arXiv preprint arXiv:1303.3997},
  year={2013}
}

@article{missingNJ,
  title={A weighted least-squares approach for inferring phylogenies from incomplete distance matrices},
  author={Makarenkov, Vladimir and Lapointe, Fran{\c{c}}ois-Joseph},
  journal={Bioinformatics},
  volume={20},
  number={13},
  pages={2113--2121},
  year={2004},
  publisher={Oxford University Press}
}

@article{samtools,
  title={The sequence alignment/map format and SAMtools},
  author={Li, Heng and Handsaker, Bob and Wysoker, Alec and Fennell, Tim and Ruan, Jue and Homer, Nils and Marth, Gabor and Abecasis, Goncalo and Durbin, Richard},
  journal={Bioinformatics},
  volume={25},
  number={16},
  pages={2078--2079},
  year={2009},
  publisher={Oxford University Press}
}

@article{gatk1,
  title={A framework for variation discovery and genotyping using next-generation DNA sequencing data},
  author={DePristo, Mark A and Banks, Eric and Poplin, Ryan and Garimella, Kiran V and Maguire, Jared R and Hartl, Christopher and Philippakis, Anthony A and Del Angel, Guillermo and Rivas, Manuel A and Hanna, Matt and others},
  journal={Nature genetics},
  volume={43},
  number={5},
  pages={491},
  year={2011},
  publisher={Nature Publishing Group}
}

@article{gatk2,
  title={From FastQ data to high-confidence variant calls: the genome analysis toolkit best practices pipeline},
  author={Van der Auwera, Geraldine A and Carneiro, Mauricio O and Hartl, Christopher and Poplin, Ryan and Del Angel, Guillermo and Levy-Moonshine, Ami and Jordan, Tadeusz and Shakir, Khalid and Roazen, David and Thibault, Joel and others},
  journal={Current protocols in bioinformatics},
  volume={43},
  number={1},
  pages={11--10},
  year={2013},
  publisher={Wiley Online Library}
}

@article{DATA,
  title={Clonal evolution in breast cancer revealed by single nucleus genome sequencing},
  author={Wang, Yong and Waters, Jill and Leung, Marco L and Unruh, Anna and Roh, Whijae and Shi, Xiuqing and Chen, Ken and Scheet, Paul and Vattathil, Selina and Liang, Han and others},
  journal={Nature},
  volume={512},
  number={7513},
  pages={155},
  year={2014},
  publisher={Nature Publishing Group}
}

%UNUSED:
@article{sciclone,
  title={Sci{C}lone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution},
  author={Miller, Christopher A and White, Brian S and Dees, Nathan D and Griffith, Malachi and Welch, John S and Griffith, Obi L and Vij, Ravi and Tomasson, Michael H and Graubert, Timothy A and Walter, Matthew J and others},
  journal={PLoS computational biology},
  volume={10},
  number={8},
  pages={e1003665},
  year={2014},
  publisher={Public Library of Science}
}