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% Wood2014-vs
@ARTICLE{kraken,
title = "Kraken: ultrafast metagenomic sequence classification using exact
alignments",
author = "Wood, Derrick E and Salzberg, Steven L",
journal = "Genome Biol.",
volume = 15,
number = 3,
pages = "R46",
month = mar,
year = 2014,
url = "http://dx.doi.org/10.1186/gb-2014-15-3-r46",
language = "en",
issn = "1465-6906",
pmid = "24580807",
doi = "10.1186/gb-2014-15-3-r46",
pmc = "PMC4053813"
}
% Yang2002-sx
@ARTICLE{Yang:2002ty,
title = "Normalization for {cDNA} microarray data: a robust composite
method addressing single and multiple slide systematic
variation",
author = "Yang, Yee Hwa and Dudoit, Sandrine and Luu, Percy and Lin,
David M and Peng, Vivian and Ngai, John and Speed, Terence P",
affiliation = "Department of Statistics, Helen Wills Neuroscience Institute,
University of California, Berkeley, CA 94720-3860, USA.",
journal = "Nucleic Acids Res.",
volume = 30,
number = 4,
pages = "e15",
month = feb,
year = 2002,
url = "https://www.ncbi.nlm.nih.gov/pubmed/11842121",
language = "en",
issn = "0305-1048, 1362-4962",
pmid = "11842121",
pmc = "PMC100354"
}
% Love2016-ht
@ARTICLE{Love:2015kw,
title = "{RNA-Seq} workflow: gene-level exploratory analysis and
differential expression",
author = "Love, Michael I and Anders, Simon and Kim, Vladislav and Huber,
Wolfgang",
journal = "F1000Res.",
volume = 4,
month = nov,
year = 2016,
url = "https://f1000research.com/articles/4-1070/v2/pdf",
doi = "10.12688/f1000research.7035.2"
}
% Dobin2013-hr
@ARTICLE{STAR,
title = "{STAR}: ultrafast universal {RNA-seq} aligner",
author = "Dobin, Alexander and Davis, Carrie A and Schlesinger, Felix
and Drenkow, Jorg and Zaleski, Chris and Jha, Sonali and
Batut, Philippe and Chaisson, Mark and Gingeras, Thomas R",
affiliation = "Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
dobin@cshl.edu",
journal = "Bioinformatics",
volume = 29,
number = 1,
pages = "15--21",
month = jan,
year = 2013,
url = "http://dx.doi.org/10.1093/bioinformatics/bts635",
language = "en",
issn = "1367-4803, 1367-4811",
pmid = "23104886",
doi = "10.1093/bioinformatics/bts635",
pmc = "PMC3530905"
}
% Dobin2016-qj
@ARTICLE{Dobin:2016kq,
title = "Optimizing {RNA-Seq} Mapping with {STAR}",
author = "Dobin, Alexander and Gingeras, Thomas R",
affiliation = "Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring
Harbor, NY, 11746, USA. dobin@cshl.edu. Cold Spring Harbor
Laboratory, One Bungtown Road, Cold Spring Harbor, NY, 11746,
USA.",
journal = "Methods Mol. Biol.",
volume = 1415,
pages = "245--262",
year = 2016,
url = "http://dx.doi.org/10.1007/978-1-4939-3572-7_13",
language = "en",
issn = "1064-3745, 1940-6029",
pmid = "27115637",
doi = "10.1007/978-1-4939-3572-7\_13"
}
% Kolde2015-dy
@MANUAL{pheatmap,
title = "pheatmap: Pretty Heatmaps",
author = "Kolde, Raivo",
year = 2015,
url = "https://CRAN.R-project.org/package=pheatmap"
}
% Andrews2010-fq
@MANUAL{fastqc,
title = "{FastQC}: a quality control tool for high throughput sequence data",
author = "Andrews, Simon",
year = 2010,
url = "http://www.bioinformatics.babraham.ac.uk/projects/fastq"
}
% Conesa2016-uj
@ARTICLE{Conesa:2016du,
title = "A survey of best practices for {RNA-seq} data analysis",
author = "Conesa, Ana and Madrigal, Pedro and Tarazona, Sonia and
Gomez-Cabrero, David and Cervera, Alejandra and McPherson,
Andrew and Szcze{\'s}niak, Micha{\l} Wojciech and Gaffney,
Daniel J and Elo, Laura L and Zhang, Xuegong and Mortazavi,
Ali",
affiliation = "Institute for Food and Agricultural Sciences, Department of
Microbiology and Cell Science, University of Florida,
Gainesville, FL, 32603, USA. aconesa@ufl.edu. Centro de
Investigaci{\'o}n Pr{\'\i}ncipe Felipe, Genomics of Gene
Expression Laboratory, 46012, Valencia, Spain.
aconesa@ufl.edu. Wellcome Trust Sanger Institute, Wellcome
Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
pm12@sanger.ac.uk. Wellcome Trust-Medical Research Council
Cambridge Stem Cell Institute, Anne McLaren Laboratory for
Regenerative Medicine, Department of Surgery, University of
Cambridge, Cambridge, CB2 0SZ, UK. pm12@sanger.ac.uk. Centro
de Investigaci{\'o}n Pr{\'\i}ncipe Felipe, Genomics of Gene
Expression Laboratory, 46012, Valencia, Spain. Department of
Applied Statistics, Operations Research and Quality,
Universidad Polit{\'e}cnica de Valencia, 46020, Valencia,
Spain. Unit of Computational Medicine, Department of Medicine,
Karolinska Institutet, Karolinska University Hospital, 171 77,
Stockholm, Sweden. Center for Molecular Medicine, Karolinska
Institutet, 17177, Stockholm, Sweden. Unit of Clinical
Epidemiology, Department of Medicine, Karolinska University
Hospital, L8, 17176, Stockholm, Sweden. Science for Life
Laboratory, 17121, Solna, Sweden. Systems Biology Laboratory,
Institute of Biomedicine and Genome-Scale Biology Research
Program, University of Helsinki, 00014, Helsinki, Finland.
School of Computing Science, Simon Fraser University, Burnaby,
V5A 1S6, BC, Canada. Department of Bioinformatics, Institute
of Molecular Biology and Biotechnology, Adam Mickiewicz
University in Pozna{\'n}, 61-614, Pozna{\'n}, Poland. Wellcome
Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton,
Cambridge, CB10 1SA, UK. Turku Centre for Biotechnology,
University of Turku and {\AA}bo Akademi University, FI-20520,
Turku, Finland. Key Lab of Bioinformatics/Bioinformatics
Division, TNLIST and Department of Automation, Tsinghua
University, Beijing, 100084, China. School of Life Sciences,
Tsinghua University, Beijing, 100084, China. Department of
Developmental and Cell Biology, University of California,
Irvine, Irvine, CA, 92697-2300, USA. ali.mortazavi@uci.edu.
Center for Complex Biological Systems, University of
California, Irvine, Irvine, CA, 92697, USA.
ali.mortazavi@uci.edu.",
journal = "Genome Biol.",
volume = 17,
pages = "13",
month = jan,
year = 2016,
url = "http://dx.doi.org/10.1186/s13059-016-0881-8",
language = "en",
issn = "1465-6906",
pmid = "26813401",
doi = "10.1186/s13059-016-0881-8",
pmc = "PMC4728800"
}
% Li2012-jp
@ARTICLE{Li:2012cx,
title = "Volcano plots in analyzing differential expressions with
{mRNA} microarrays",
author = "Li, Wentian",
affiliation = "The Robert S. Boas Center for Genomics and Human Genetics, The
Feinstein Institute for Medical Research, North Shore LIJ
Health System, Manhasset, 350 Community Drive, NY 11030, USA.
wtli2012@gmail.com",
journal = "J. Bioinform. Comput. Biol.",
volume = 10,
number = 6,
pages = "1231003",
month = dec,
year = 2012,
url = "http://dx.doi.org/10.1142/S0219720012310038",
language = "en",
issn = "0219-7200, 1757-6334",
pmid = "23075208",
doi = "10.1142/S0219720012310038"
}
% RStudio_Team2016-pf
@MANUAL{RStudio,
title = "{RStudio}: Integrated Development Environment for {R}",
author = "{RStudio Team}",
year = 2016,
url = "http://www.rstudio.com/",
address = "Boston, MA",
organization = "RStudio, Inc."
}
% Zhang2014-af
@ARTICLE{PEAR,
title = "{PEAR}: a fast and accurate Illumina {Paired-End} reAd mergeR",
author = "Zhang, Jiajie and Kobert, Kassian and Flouri, Tom{\'a}{\v s}
and Stamatakis, Alexandros",
affiliation = "The Exelixis Lab, Scientific Computing Group, Heidelberg
Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35,
D-69118 Heidelberg, Graduate School for Computing in Medicine
and Life Sciences, Institut f{\"u}r Neuro- und Bioinformatik,
University of L{\"u}beck, 23538 L{\"u}beck and Karlsruhe
Institute of Technology, Institute for Theoretical
Informatics, Postfach 6980, 76128 Karlsruhe, Germany.",
journal = "Bioinformatics",
volume = 30,
number = 5,
pages = "614--620",
month = mar,
year = 2014,
url = "http://dx.doi.org/10.1093/bioinformatics/btt593",
language = "en",
issn = "1367-4803, 1367-4811",
pmid = "24142950",
doi = "10.1093/bioinformatics/btt593",
pmc = "PMC3933873"
}
% Pimentel2017-qf
@ARTICLE{sleuth,
title = "Differential analysis of {RNA-seq} incorporating
quantification uncertainty",
author = "Pimentel, Harold and Bray, Nicolas L and Puente, Suzette and
Melsted, P{\'a}ll and Pachter, Lior",
affiliation = "Department of Computer Science, University of California,
Berkeley, Berkeley, California, USA. Innovative Genomics
Institute and Department of Molecular \&Cell Biology,
University of California, Berkeley, Berkeley, California, USA.
Department of Statistics, University of California, Berkeley,
Berkeley, California, USA. Faculty of Industrial Engineering,
Mechanical Engineering and Computer Science, University of
Iceland, Reykjav{\'\i}k, Iceland. Division of Biology and
Biological Engineering, Caltech, Pasadena, California, USA.",
journal = "Nat. Methods",
volume = 14,
number = 7,
pages = "687--690",
month = jul,
year = 2017,
url = "http://dx.doi.org/10.1038/nmeth.4324",
language = "en",
issn = "1548-7091, 1548-7105",
pmid = "28581496",
doi = "10.1038/nmeth.4324"
}
% Soneson2016-tu
@ARTICLE{tximport,
title = "Differential analyses for {RNA-seq}: transcript-level estimates
improve gene-level inferences",
author = "Soneson, Charlotte and Love, Michael I and Robinson, Mark D",
journal = "F1000Res.",
volume = 4,
month = dec,
year = 2016,
url = "https://f1000research.com/articles/4-1521/v1/pdf",
doi = "10.12688/f1000research.7563.1"
}
% Staedtler2013-ya
@ARTICLE{Staedtler:2013eg,
title = "Robust and tissue-independent gender-specific transcript
biomarkers",
author = "Staedtler, Frank and Hartmann, Nicole and Letzkus, Martin and
Bongiovanni, Sandrine and Scherer, Andreas and Marc, Philippe
and Johnson, Keith J and Schumacher, Martin M",
affiliation = "Novartis Institutes for BioMedical Research (NIBR), Biomarker
Development, Basel, Switzerland. Frank.Staedtler@novartis.com",
journal = "Biomarkers",
volume = 18,
number = 5,
pages = "436--445",
month = aug,
year = 2013,
url = "http://dx.doi.org/10.3109/1354750X.2013.811538",
language = "en",
issn = "1354-750X, 1366-5804",
pmid = "23829492",
doi = "10.3109/1354750X.2013.811538"
}
% Patro2014-qz
@ARTICLE{sailfish,
title = "Sailfish enables alignment-free isoform quantification from
{RNA-seq} reads using lightweight algorithms",
author = "Patro, Rob and Mount, Stephen M and Kingsford, Carl",
affiliation = "Lane Center for Computational Biology, School of Computer
Science, Carnegie Mellon University, Pittsburgh, Pennsylvania,
USA. 1] Department of Cell Biology and Molecular Genetics,
University of Maryland, College Park, Maryland, USA. [2]
Center for Bioinformatics and Computational Biology,
University of Maryland, College Park, Maryland, USA.",
journal = "Nat. Biotechnol.",
volume = 32,
number = 5,
pages = "462--464",
month = may,
year = 2014,
url = "http://dx.doi.org/10.1038/nbt.2862",
language = "en",
issn = "1087-0156, 1546-1696",
pmid = "24752080",
doi = "10.1038/nbt.2862",
pmc = "PMC4077321"
}
% Patro2017-pi
@ARTICLE{salmon,
title = "Salmon provides fast and bias-aware quantification of
transcript expression",
author = "Patro, Rob and Duggal, Geet and Love, Michael I and Irizarry,
Rafael A and Kingsford, Carl",
affiliation = "Department of Computer Science, Stony Brook University, Stony
Brook, New York, USA. DNAnexus, Mountain View, California,
USA. Department of Biostatistics and Computational Biology,
Dana-Farber Cancer Institute, Cambridge, Massachusetts, USA.
Department of Biostatistics, Harvard T.H. Chan School of
Public Health, Cambridge, Massachusetts, USA. Computational
Biology Department, Carnegie Mellon University, Pittsburgh,
Pennsylvania, USA.",
journal = "Nat. Methods",
volume = 14,
number = 4,
pages = "417--419",
month = apr,
year = 2017,
url = "http://dx.doi.org/10.1038/nmeth.4197",
language = "en",
issn = "1548-7091, 1548-7105",
pmid = "28263959",
doi = "10.1038/nmeth.4197"
}
% Liao2014-js
@ARTICLE{featureCounts,
title = "featureCounts: an efficient general purpose program for
assigning sequence reads to genomic features",
author = "Liao, Yang and Smyth, Gordon K and Shi, Wei",
affiliation = "Bioinformatics Division, The Walter and Eliza Hall Institute
of Medical Research, 1G Royal Parade, Parkville, VIC 3052,
Department of Computing and Information Systems and Department
of Mathematics and Statistics, The University of Melbourne,
Parkville, VIC 3010, Australia.",
journal = "Bioinformatics",
volume = 30,
number = 7,
pages = "923--930",
month = apr,
year = 2014,
url = "http://dx.doi.org/10.1093/bioinformatics/btt656",
language = "en",
issn = "1367-4803, 1367-4811",
pmid = "24227677",
doi = "10.1093/bioinformatics/btt656"
}
% Van_den_Berge2017-xy
@UNPUBLISHED{VandenBerge:2017fe,
title = "A general and powerful stage-wise testing procedure for
differential expression and differential transcript usage",
author = "Van den Berge, Koen and Soneson, Charlotte and Robinson, Mark D
and Clement, Lieven",
journal = "bioRxiv",
pages = "109082",
month = feb,
year = 2017,
url = "http://www.biorxiv.org/content/early/2017/02/16/109082",
language = "en",
doi = "10.1101/109082"
}
% Cui2003-rn
@ARTICLE{Cui:2003kh,
title = "Statistical tests for differential expression in {cDNA}
microarray experiments",
author = "Cui, Xiangqin and Churchill, Gary A",
affiliation = "The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine
04609, USA.",
journal = "Genome Biol.",
volume = 4,
number = 4,
pages = "210",
month = mar,
year = 2003,
url = "https://www.ncbi.nlm.nih.gov/pubmed/12702200",
language = "en",
issn = "1465-6906",
pmid = "12702200",
pmc = "PMC154570"
}
% Langaas:2005vn
@ARTICLE{Langaas2005-zl,
title = "Estimating the Proportion of True Null Hypotheses, with
Application to {DNA} Microarray Data",
author = "Langaas, Mette and Lindqvist, Bo Henry and Ferkingstad, Egil",
journal = "J. R. Stat. Soc. Series B Stat. Methodol.",
publisher = "[Royal Statistical Society, Wiley]",
volume = 67,
number = 4,
pages = "555--572",
year = 2005,
url = "http://www.jstor.org/stable/3647644",
issn = "1369-7412, 1467-9868"
}
% Love2014-sq
@ARTICLE{DESeq2,
title = "Moderated estimation of fold change and dispersion for {RNA-seq}
data with {DESeq2}",
author = "Love, Michael I and Huber, Wolfgang and Anders, Simon",
journal = "Genome Biol.",
volume = 15,
number = 12,
pages = "550",
year = 2014,
url = "http://dx.doi.org/10.1186/s13059-014-0550-8",
language = "en",
issn = "1465-6906",
pmid = "25516281",
doi = "10.1186/s13059-014-0550-8",
pmc = "PMC4302049"
}
% Benjamini1995-de
@ARTICLE{Benjamini:1995ws,
title = "Controlling the False Discovery Rate: A Practical and Powerful
Approach to Multiple Testing",
author = "Benjamini, Yoav and Hochberg, Yosef",
journal = "J. R. Stat. Soc. Series B Stat. Methodol.",
publisher = "[Royal Statistical Society, Wiley]",
volume = 57,
number = 1,
pages = "289--300",
year = 1995,
url = "http://www.jstor.org/stable/2346101",
issn = "1369-7412, 0035-9246"
}
% Kolde2015-vr
@ARTICLE{GOsummaries,
title = "{GOsummaries}: an {R} Package for Visual Functional Annotation of
Experimental Data",
author = "Kolde, Raivo and Vilo, Jaak",
journal = "F1000Res.",
volume = 4,
month = aug,
year = 2015,
url = "https://f1000research.com/articles/4-574/v1/pdf",
doi = "10.12688/f1000research.6925.1"
}
% Ward1963-xf
@ARTICLE{WardJr:1963eu,
title = "Hierarchical grouping to optimize an objective function",
author = "Ward, Jr, Joe H",
journal = "Journal of the American Statistical Association",
publisher = "Taylor \& Francis",
volume = 58,
number = 301,
pages = "236--244",
year = 1963,
url = "http://www.tandfonline.com/doi/abs/10.1080/01621459.1963.10500845",
doi = "10.1080/01621459.1963.10500845"
}
% Pantano2017-qp
@MANUAL{DEGreport,
title = "{DEGreport}: Report of {DEG} analysis",
author = "Pantano, Lorena",
year = 2017,
url = "https://bioconductor.org/packages/release/bioc/html/DEGreport.html",
doi = "10.18129/B9.bioc.DEGreport"
}
% Hilbe2011-wh
@BOOK{Hilbe:2011ua,
title = "{Negative Binomial Regression}",
author = "Hilbe, Joseph M",
publisher = "Cambridge University Press",
month = mar,
year = 2011,
url = "https://market.android.com/details?id=book-0Q_ijxOEBjMC",
language = "en",
isbn = "9780521198158"
}
% Karyagyna2010-cx
@ARTICLE{Karyagyna:2010th,
title = "{Probe-Level} Universal Search ({PLUS}) algorithm for gender
differentiation in affymetrix datasets",
author = "Karyagyna, Anna S and Vassiliev, Michail O and Ershova, Anna S
and Nurtdinov, Ramil N and Lossev, Ilya S",
affiliation = "NF Gamaleya Research Institute of Epidemiology and
Microbiology, Russian Academy of Medical Sciences, Institute
of Agricultural Biotechnology, Moscow, Russia.
akaryagina@gmail.com",
journal = "J. Bioinform. Comput. Biol.",
volume = 8,
number = 3,
pages = "553--577",
month = jun,
year = 2010,
url = "https://www.ncbi.nlm.nih.gov/pubmed/20556862",
language = "en",
issn = "0219-7200, 1757-6334",
pmid = "20556862",
doi = "10.1142/S0219720010004823"
}
% Wickham2009-si
@BOOK{ggplot2,
title = "ggplot2: Elegant Graphics for Data Analysis",
author = "Wickham, Hadley",
publisher = "Springer New York",
series = "Use R",
year = 2009,
url = "https://link.springer.com/book/10.1007%2F978-0-387-98141-3",
isbn = "9780387981406, 9780387981413",
doi = "10.1007/978-0-387-98141-3"
}
% Robinson2010-np
@ARTICLE{Robinson:2010dd,
title = "A scaling normalization method for differential expression
analysis of {RNA-seq} data",
author = "Robinson, Mark D and Oshlack, Alicia",
affiliation = "Bioinformatics Division, Walter and Eliza Hall Institute, 1G
Royal Parade, Parkville, Australia. mrobinson@wehi.edu.au",
journal = "Genome Biol.",
volume = 11,
number = 3,
pages = "R25",
month = mar,
year = 2010,
url = "http://dx.doi.org/10.1186/gb-2010-11-3-r25",
language = "en",
issn = "1465-6906",
pmid = "20196867",
doi = "10.1186/gb-2010-11-3-r25",
pmc = "PMC2864565"
}
% Jolliffe2002-jz
@BOOK{Jolliffe:2002wx,
title = "{Principal component analysis}",
author = "Jolliffe, Ian",
publisher = "Wiley Online Library",
year = 2002
}
% Wickham2007-lr
@ARTICLE{reshape2,
title = "Reshaping data with the reshape package",
author = "Wickham, Hadley",
journal = "J. Stat. Softw.",
volume = 21,
number = 12,
pages = "1--20",
year = 2007
}
% Cox1987-dw
@ARTICLE{Cox:1987fu,
title = "Parameter Orthogonality and Approximate Conditional Inference",
author = "Cox, D R and Reid, N",
journal = "J. R. Stat. Soc. Series B Stat. Methodol.",
publisher = "[Royal Statistical Society, Wiley]",
volume = 49,
number = 1,
pages = "1--39",
year = 1987,
url = "http://www.jstor.org/stable/2345476",
issn = "1369-7412, 0035-9246"
}
% Li2014-ll
@ARTICLE{Li:2014fv,
title = "Using volcano plots and regularized-chi statistics in genetic
association studies",
author = "Li, Wentian and Freudenberg, Jan and Suh, Young Ju and Yang,
Yaning",
affiliation = "The Robert S. Boas Center for Genomics and Human Genetics, The
Feinstein Institute for Medical Research, North Shore LIJ
Health System, 350 Community Drive, Manhasset, NY 11030, USA.
Electronic address: wtli2012@gmail.com. The Robert S. Boas
Center for Genomics and Human Genetics, The Feinstein
Institute for Medical Research, North Shore LIJ Health System,
350 Community Drive, Manhasset, NY 11030, USA. Department of
Biostatistics, School of Medicine, Inha University, Incheon,
South Korea. Department of Statistics and Finance, University
of Science and Technology of China, Anhui, 230026 Hefei,
China.",
journal = "Comput. Biol. Chem.",
volume = 48,
pages = "77--83",
month = feb,
year = 2014,
url = "http://dx.doi.org/10.1016/j.compbiolchem.2013.02.003",
language = "en",
issn = "1476-9271, 1476-928X",
pmid = "23602812",
doi = "10.1016/j.compbiolchem.2013.02.003"
}
% Wang2009-dt
@ARTICLE{Wang:2009di,
title = "{RNA-Seq}: a revolutionary tool for transcriptomics",
author = "Wang, Zhong and Gerstein, Mark and Snyder, Michael",
affiliation = "Department of Molecular, Cellular and Developmental Biology,
Yale University, 219 Prospect Street, New Haven, Connecticut
06520, USA.",
journal = "Nat. Rev. Genet.",
volume = 10,
number = 1,
pages = "57--63",
month = jan,
year = 2009,
url = "http://dx.doi.org/10.1038/nrg2484",
language = "en",
issn = "1471-0056, 1471-0064",
pmid = "19015660",
doi = "10.1038/nrg2484",
pmc = "PMC2949280"
}
% Okonechnikov2016-us
@ARTICLE{qualimap,
title = "Qualimap 2: advanced multi-sample quality control for
high-throughput sequencing data",
author = "Okonechnikov, Konstantin and Conesa, Ana and
Garc{\'\i}a-Alcalde, Fernando",
affiliation = "Department of Molecular Biology, Max Planck Institute for
Infection Biology, D-10117, Berlin, Germany. Genomics of Gene
Expression Lab, Centro de Investigaci{\'o}n Pr{\'\i}ncipe
Felipe, 46012, Valencia, Spain and Microbiology and Cell
Science Department, Institute for Food and Agricultural
Research, University of Florida at Gainesville, FL 32611-0700,
USA.",
journal = "Bioinformatics",
volume = 32,
number = 2,
pages = "292--294",
month = jan,
year = 2016,
url = "http://dx.doi.org/10.1093/bioinformatics/btv566",
language = "en",
issn = "1367-4803, 1367-4811",
pmid = "26428292",
doi = "10.1093/bioinformatics/btv566",
pmc = "PMC4708105"
}
% Martin2011-nx
@ARTICLE{cutadapt,
title = "Cutadapt removes adapter sequences from high-throughput
sequencing reads",
author = "Martin, Marcel",
journal = "EMBnet.journal",
volume = 17,
number = 1,
pages = "10--12",
month = may,
year = 2011,
url = "http://journal.embnet.org/index.php/embnetjournal/article/view/200",
language = "en",
issn = "2226-6089, 2226-6089",
pmid = "1000006697",
doi = "10.14806/ej.17.1.200"
}
% Craciun2016-ha
@ARTICLE{Craciun2016,
title = "{RNA} Sequencing Identifies Novel Translational Biomarkers of
Kidney Fibrosis",
author = "Craciun, Florin L and Bijol, Vanesa and Ajay, Amrendra K and
Rao, Poornima and Kumar, Ramya K and Hutchinson, John and
Hofmann, Oliver and Joshi, Nikita and Luyendyk, James P and
Kusebauch, Ulrike and Moss, Christopher L and Srivastava,
Anand and Himmelfarb, Jonathan and Waikar, Sushrut S and
Moritz, Robert L and Vaidya, Vishal S",
affiliation = "Renal Division, Department of Medicine and. Department of
Pathology, Brigham and Women's Hospital, Boston,
Massachusetts; Department of Biostatistics and. Department of
Pathology and Diagnostic Investigation, Michigan State
University, East Lansing, Michigan; Institute for Systems
Biology, Seattle, Washington; Kidney Research Institute,
University of Washington, Seattle, Washington; and. Renal
Division, Department of Medicine and Department of
Environmental Health, Harvard T.H. Chan School of Public
Health, Boston, Massachusetts; Harvard Program in Therapeutic
Sciences, Harvard Medical School, Boston, Massachusetts
vvaidya@bwh.harvard.edu.",
journal = "J. Am. Soc. Nephrol.",
volume = 27,
number = 6,
pages = "1702--1713",
month = jun,
year = 2016,
url = "http://dx.doi.org/10.1681/ASN.2015020225",
language = "en",
issn = "1046-6673, 1533-3450",
pmid = "26449608",
doi = "10.1681/ASN.2015020225",
pmc = "PMC4884105"
}
% Yu2012-ae
@ARTICLE{Yu2012,
title = "clusterProfiler: an {R} package for comparing biological
themes among gene clusters",
author = "Yu, Guangchuang and Wang, Li-Gen and Han, Yanyan and He,
Qing-Yu",
affiliation = "Institute of Life and Health Engineering, Key Laboratory of
Functional Protein Research of Guangdong Higher Education
Institutes, Jinan University, Guangzhou, People's Republic of
China.",
journal = "OMICS",
volume = 16,
number = 5,
pages = "284--287",
month = may,
year = 2012,
url = "http://dx.doi.org/10.1089/omi.2011.0118",
language = "en",
issn = "1536-2310, 1557-8100",
pmid = "22455463",
doi = "10.1089/omi.2011.0118",
pmc = "PMC3339379"
}
% Daily2017-fj
@ARTICLE{Daily2017,
title = "Molecular, phenotypic, and sample-associated data to describe
pluripotent stem cell lines and derivatives",
author = "Daily, Kenneth and Ho Sui, Shannan J and Schriml, Lynn M and
Dexheimer, Phillip J and Salomonis, Nathan and Schroll, Robin
and Bush, Stacy and Keddache, Mehdi and Mayhew, Christopher
and Lotia, Samad and Perumal, Thanneer M and Dang, Kristen and
Pantano, Lorena and Pico, Alexander R and Grassman, Elke and
Nordling, Diana and Hide, Winston and Hatzopoulos, Antonis K
and Malik, Punam and Cancelas, Jose A and Lutzko, Carolyn and
Aronow, Bruce J and Omberg, Larsson",
affiliation = "Sage Bionetworks, Seattle, Washington 98109, USA. Department
of Biostatistics, Harvard T.H. Chan School of Public Health,
Boston, Massachusetts 02115, USA. Institute for Genome
Sciences and Department of Epidemiology and Public Health,
University of Maryland School of Medicine, Baltimore, Maryland
21201, USA. Department of Biomedical Informatics, Cincinnati
Children's Hospital, Cincinnati, Ohio 45229, USA. Division of
Experimental Hematology and Cancer Biology, Cincinnati
Children's Hospital, Cincinnati, Ohio 45229, USA. Division of
Human Genetics, Cincinnati Children's Hospital, Cincinnati,
Ohio 45229, USA. Division of Developmental Biology, Cincinnati
Children's Hospital, Cincinnati, Ohio 45229, USA. Gladstone
Institutes, San Francisco, California 94158, USA.
Translational Trials Development and Support Laboratory Field
Service, Cincinnati Children's Hospital, Cincinnati, Ohio
45229, USA. Cell Manipulation Laboratory, Cincinnati
Children's Hospital, Cincinnati, Ohio 45229, USA. Sheffield
Institute for Translational Neuroscience, University of
Sheffield, Sheffield S10 2HQ, UK. Harvard Stem Cell Institute,
Cambridge, Massachusetts 02138, USA. Departments of Medicine
and Cell and Developmental Biology, Division of Cardiovascular
Medicine, Vanderbilt University, Nashville, Tennessee 37232,
USA.",
journal = "Sci Data",
volume = 4,
pages = "170030",
month = mar,
year = 2017,
url = "http://dx.doi.org/10.1038/sdata.2017.30",
language = "en",
issn = "2052-4463",
pmid = "28350385",
doi = "10.1038/sdata.2017.30",
pmc = "PMC5369318"
}
% Andrews2010-fq
@MANUAL{Andrews2010,
title = "{FastQC}: a quality control tool for high throughput sequence data",
author = "Andrews, Simon",
year = 2010,
url = "http://www.bioinformatics.babraham.ac.uk/projects/fastq"
}
% Dudoit2002-sy
@ARTICLE{Dudoit2002,
title = "Statistical methods for identifying differentially expressed
genes in replicated {cDNA} microarray experiments",
author = "Dudoit, Sandrine and Yang, Yee Hwa and Callow, Matthew J and
Speed, Terence P",
journal = "Stat. Sin.",
publisher = "Institute of Statistical Science, Academia Sinica",
volume = 12,
number = 1,
pages = "111--139",
year = 2002,
url = "http://www.jstor.org/stable/24307038",
issn = "1017-0405, 1996-8507"
}
% Huber2002-sf
@ARTICLE{Huber2002,
title = "Variance stabilization applied to microarray data calibration
and to the quantification of differential expression",
author = "Huber, Wolfgang and von Heydebreck, Anja and S{\"u}ltmann,
Holger and Poustka, Annemarie and Vingron, Martin",
affiliation = "Department of Molecular Genome Analysis, German Cancer
Research Center, INF 280, Heidelberg, 69120, Germany.
w.huber@dkfz.de",
journal = "Bioinformatics",
volume = "18 Suppl 1",
pages = "S96--104",
year = 2002,
url = "https://www.ncbi.nlm.nih.gov/pubmed/12169536",
language = "en",
issn = "1367-4803",
pmid = "12169536"
}
% Li2015-iq
@ARTICLE{Li_norm_2015,
title = "Comparing the normalization methods for the differential
analysis of Illumina high-throughput {RNA-Seq} data",
author = "Li, Peipei and Piao, Yongjun and Shon, Ho Sun and Ryu, Keun Ho",
affiliation = "College of Electrical and Computer Engineering, Chungbuk
National University, Cheongju-si, South Korea.
lipeipei0611@gmail.com. College of Electrical and Computer
Engineering, Chungbuk National University, Cheongju-si, South
Korea. pyz@dblab.chungbuk.ac.kr. College of Electrical and
Computer Engineering, Chungbuk National University,
Cheongju-si, South Korea. shon0621@gmail.com. College of
Electrical and Computer Engineering, Chungbuk National
University, Cheongju-si, South Korea.
khryu@dblab.chungbuk.ac.kr.",
journal = "BMC Bioinformatics",
volume = 16,
pages = "347",
month = oct,
year = 2015,
url = "http://dx.doi.org/10.1186/s12859-015-0778-7",
language = "en",
issn = "1471-2105",
pmid = "26511205",
doi = "10.1186/s12859-015-0778-7",
pmc = "PMC4625728"
}
@ARTICLE{Robert2015-mj,
title = "Errors in {RNA-Seq} quantification affect genes of relevance
to human disease",
author = "Robert, Christelle and Watson, Mick",
affiliation = "The Roslin Institute and Royal (Dick) School of Veterinary
studies, University of Edinburgh, Easter Bush, EH25 9RG, UK.
christelle.robert@roslin.ed.ac.uk. Edinburgh Genomics, The
Roslin Institute, University of Edinburgh, Easter Bush, EH25
9RG, UK. mick.watson@roslin.ed.ac.uk.",
journal = "Genome Biol.",
volume = 16,
pages = "177",
month = sep,
year = 2015,
url = "http://dx.doi.org/10.1186/s13059-015-0734-x",
language = "en",
issn = "1465-6906",
pmid = "26335491",
doi = "10.1186/s13059-015-0734-x",
pmc = "PMC4558956"
}
% Morgan2017-dw
@MANUAL{SummarizedExperiment,
title = "{SummarizedExperiment}: {SummarizedExperiment} container",
author = "Morgan, Martin and Obenchain, Valerie and Hester, Jim and
Pag{\`e}s, Herv{\'e}",
year = 2017,
url = "http://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html",
doi = "10.18129/B9.bioc.SummarizedExperiment"
}
% Allaire2017-mf
@MANUAL{rmarkdown,
title = "rmarkdown: Dynamic Documents for {R}",
author = "Allaire, J J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan
and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins,
Aron and Hyndman, Rob and Arslan, Ruben",
year = 2017,
url = "https://CRAN.R-project.org/package=rmarkdown"
}
% Ewels2016-vh
@ARTICLE{MultiQC,
title = "{MultiQC}: summarize analysis results for multiple tools and
samples in a single report",
author = "Ewels, Philip and Magnusson, M{\aa}ns and Lundin, Sverker and
K{\"a}ller, Max",
affiliation = "Department of Biochemistry and Biophysics, Science for Life
Laboratory, Stockholm University, Stockholm 106 91, Sweden.
Department of Molecular Medicine and Surgery, Science for Life
Laboratory, Center for Molecular Medicine, Karolinska
Institutet, Stockholm, Sweden. Science for Life Laboratory,
School of Biotechnology, Division of Gene Technology, Royal
Institute of Technology, Stockholm, Sweden.",
journal = "Bioinformatics",
volume = 32,
number = 19,
pages = "3047--3048",
month = oct,
year = 2016,
url = "http://dx.doi.org/10.1093/bioinformatics/btw354",
language = "en",
issn = "1367-4803, 1367-4811",
pmid = "27312411",
doi = "10.1093/bioinformatics/btw354",
pmc = "PMC5039924"
}
% Huber2015-nw
@ARTICLE{Bioconductor,
title = "Orchestrating high-throughput genomic analysis with
Bioconductor",
author = "Huber, Wolfgang and Carey, Vincent J and Gentleman, Robert and
Anders, Simon and Carlson, Marc and Carvalho, Benilton S and
Bravo, Hector Corrada and Davis, Sean and Gatto, Laurent and
Girke, Thomas and Gottardo, Raphael and Hahne, Florian and
Hansen, Kasper D and Irizarry, Rafael A and Lawrence, Michael
and Love, Michael I and MacDonald, James and Obenchain,
Valerie and Ole{\'s}, Andrzej K and Pag{\`e}s, Herv{\'e} and
Reyes, Alejandro and Shannon, Paul and Smyth, Gordon K and
Tenenbaum, Dan and Waldron, Levi and Morgan, Martin",
affiliation = "European Molecular Biology Laboratory, Heidelberg, Germany. 1]
Channing Division of Network Medicine, Brigham and Women's
Hospital and Harvard Medical School, Boston, Massachusetts,
USA. [2] Harvard School of Public Health, Boston,
Massachusetts, USA. Genentech, South San Francisco,
California, USA. Computational Biology Program, Fred
Hutchinson Cancer Research Center, Seattle, Washington, USA.
Department of Medical Genetics, School of Medical Sciences,
State University of Campinas, Campinas, Brazil. Center for
Bioinformatics and Computational Biology, University of
Maryland, College Park, Maryland, USA. Center for Cancer
Research, National Cancer Institute, National Institutes of
Health, Bethesda, Maryland, USA. Department of Biochemistry,
University of Cambridge, Cambridge, UK. Institute for
Integrative Genome Biology, University of California,
Riverside, Riverside, California, USA. Vaccine and Infectious
Disease Division, Fred Hutchinson Cancer Research Center,
Seattle, Washington, USA. Novartis Institutes for Biomedical
Research, Basel, Switzerland. 1] McKusick-Nathans Institute of
Genetic Medicine, Johns Hopkins University, Baltimore,
Maryland, USA. [2] Department of Biostatistics, Johns Hopkins
University, Baltimore, Maryland, USA. 1] Harvard School of
Public Health, Boston, Massachusetts, USA. [2] Dana-Farber
Cancer Institute, Boston, Massachusetts, USA. Department of
Environmental and Occupational Health Sciences, University of
Washington, Seattle, Washington, USA. 1] Walter and Eliza Hall
Institute of Medical Research, Parkville, Victoria, Australia.
[2] Department of Mathematics and Statistics, University of
Melbourne, Parkville, Victoria, Australia. School of Urban
Public Health at Hunter College, City University of New York,
New York, New York, USA.",
journal = "Nat. Methods",
volume = 12,
number = 2,
pages = "115--121",
month = feb,
year = 2015,
url = "http://dx.doi.org/10.1038/nmeth.3252",
language = "en",
issn = "1548-7091, 1548-7105",
pmid = "25633503",
doi = "10.1038/nmeth.3252",
pmc = "PMC4509590"
}
@ARTICLE{Ewing1998-wj,
title = "Base-calling of automated sequencer traces using phred. I.
Accuracy assessment",
author = "Ewing, B and Hillier, L and Wendl, M C and Green, P",
affiliation = "Department of Molecular Biotechnology, University of
Washington, Seattle, Washington 98195-7730, USA.",
journal = "Genome Res.",
volume = 8,
number = 3,
pages = "175--185",