@ARTICLE{Kim2013-vg,
  title       = {{TopHat2}: accurate alignment of transcriptomes in the
                 presence of insertions, deletions and gene fusions},
  author      = "Kim, Daehwan and Pertea, Geo and Trapnell, Cole and Pimentel,
                 Harold and Kelley, Ryan and Salzberg, Steven L",
  affiliation = "Center for Bioinformatics and Computational Biology,
                 University of Maryland, College Park, MD, 20742, USA.
                 infphilo@umiacs.umd.edu.",
  journal     = "Genome Biol.",
  volume      =  14,
  number      =  4,
  pages       = "R36",
  month       =  "25~" # apr,
  year        =  2013,
  url         = "http://dx.doi.org/10.1186/gb-2013-14-4-r36",
  issn        = "1465-6906",
  pmid        = "23618408",
  doi         = "10.1186/gb-2013-14-4-r36"
}
@ARTICLE{Langmead2012-bs,
  title     = {Fast gapped-read alignment with Bowtie 2},
  author    = "Langmead, Ben and Salzberg, Steven L",
  journal   = "Nat. Methods",
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  number    =  4,
  pages     = "357--359",
  month     =  apr,
  year      =  2012,
  url       = "http://dx.doi.org/10.1038/nmeth.1923",
  issn      = "1548-7091",
  pmid      = "22388286",
  doi       = "10.1038/nmeth.1923"
}
@ARTICLE{Howard2013-fq,
  title       = {High-throughput {RNA} sequencing of pseudomonas-infected
                 Arabidopsis reveals hidden transcriptome complexity and novel
                 splice variants},
  author      = "Howard, Brian E and Hu, Qiwen and Babaoglu, Ahmet Can and
                 Chandra, Manan and Borghi, Monica and Tan, Xiaoping and He,
                 Luyan and Winter-Sederoff, Heike and Gassmann, Walter and
                 Veronese, Paola and Heber, Steffen",
  affiliation = "Department of Computer Science, North Carolina State
                 University, Raleigh, North Carolina, United States of America.",
  journal     = "PLoS One",
  volume      =  8,
  number      =  10,
  pages       = "e74183",
  month       =  "1~" # oct,
  year        =  2013,
  url         = "http://dx.doi.org/10.1371/journal.pone.0074183",
  issn        = "1932-6203",
  pmid        = "24098335",
  doi         = "10.1371/journal.pone.0074183",
  pmc         = "PMC3788074"
}
@ARTICLE{Li2009-oc,
  title   = {Fast and accurate short read alignment with {Burrows-Wheeler}
             transform},
  author  = "Li, H and Durbin, R",
  journal = "Bioinformatics",
  volume  =  25,
  number  =  14,
  pages   = "1754--1760",
  month   =  jul,
  year    =  2009,
  url     = "http://dx.doi.org/10.1093/bioinformatics/btp324",
  issn    = "1367-4803",
  pmid    = "19451168",
  doi     = "10.1093/bioinformatics/btp324"
}
@ARTICLE{Li2013-oy,
  title         = {Aligning sequence reads, clone sequences and assembly
                   contigs with {BWA-MEM}},
  author        = "Li, Heng",
  journal       = "arXiv [q-bio.GN]",
  month         =  03,
  year          =  2013,
  url           = "http://arxiv.org/abs/1303.3997",
  archivePrefix = "arXiv",
  eprint        = "1303.3997",
  primaryClass  = "q-bio.GN",
  arxivid       = "1303.3997"
}
@ARTICLE{Liao2013-bn,
  title       = {The Subread aligner: fast, accurate and scalable read mapping
                 by seed-and-vote},
  author      = "Liao, Yang and Smyth, Gordon K and Shi, Wei",
  affiliation = "Division of Bioinformatics, The Walter and Eliza Hall
                 Institute of Medical Research, 1G Royal Parade, Parkville,
                 Victoria 3052, Australia.",
  journal     = "Nucleic Acids Res.",
  volume      =  41,
  number      =  10,
  pages       = "e108",
  month       =  "4~" # apr,
  year        =  2013,
  url         = "http://dx.doi.org/10.1093/nar/gkt214",
  issn        = "0305-1048",
  pmid        = "23558742",
  doi         = "10.1093/nar/gkt214",
  pmc         = "PMC3664803"
}
@MISC{Girke2014-oy,
  title       = {{systemPipeR}: {NGS} workflow and report generation
                 environment},
  author      = "Girke, Thomas",
  institution = "UC Riverside",
  month       =  "28~" # jun,
  year        =  2014,
  url         = "https://github.com/tgirke/systemPipeR"
}
@ARTICLE{Lawrence2013-kt,
  title       = {Software for computing and annotating genomic ranges},
  author      = "Lawrence, Michael and Huber, Wolfgang and Pag\`{e}s, Herv\'{e}
                 and Aboyoun, Patrick and Carlson, Marc and Gentleman, Robert
                 and Morgan, Martin T and Carey, Vincent J",
  affiliation = "Bioinformatics and Computational Biology, Genentech, Inc.,
                 South San Francisco, California, United States of America.
                 michafla@gene.com",
  journal     = "PLoS Comput. Biol.",
  volume      =  9,
  number      =  8,
  pages       = "e1003118",
  month       =  "8~" # aug,
  year        =  2013,
  url         = "http://dx.doi.org/10.1371/journal.pcbi.1003118",
  issn        = "1553-734X",
  pmid        = "23950696",
  doi         = "10.1371/journal.pcbi.1003118",
  pmc         = "PMC3738458"
}
@ARTICLE{Robinson2010-uk,
  title   = {edgeR: a Bioconductor package for differential expression analysis
             of digital gene expression data},
  author  = "Robinson, M D and McCarthy, D J and Smyth, G K",
  journal = "Bioinformatics",
  volume  =  26,
  number  =  1,
  pages   = "139--140",
  month   =  jan,
  year    =  2010,
  url     = "http://dx.doi.org/10.1093/bioinformatics/btp616",
  issn    = "1367-4803",
  pmid    = "19910308",
  doi     = "10.1093/bioinformatics/btp616"
}
@ARTICLE{Love2014-sh,
  title   = {Moderated estimation of fold change and dispersion for {RNA-seq}
             data with {DESeq2}},
  author  = "Love, Michael and Huber, Wolfgang and Anders, Simon",
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  volume  =  15,
  number  =  12,
  pages   = "550",
  year    =  2014,
  url     = "http://genomebiology.com/2014/15/12/550",
  issn    = "1465-6906",
  doi     = "10.1186/s13059-014-0550-8"
}
@ARTICLE{McKenna2010-ql,
  title       = {The Genome Analysis Toolkit: a {MapReduce} framework for
                 analyzing next-generation {DNA} sequencing data},
  author      = "McKenna, Aaron and Hanna, Matthew and Banks, Eric and
                 Sivachenko, Andrey and Cibulskis, Kristian and Kernytsky,
                 Andrew and Garimella, Kiran and Altshuler, David and Gabriel,
                 Stacey and Daly, Mark and DePristo, Mark A",
  affiliation = "Program in Medical and Population Genetics, The Broad
                 Institute of Harvard and MIT, Cambridge, Massachusetts 02142,
                 USA.",
  journal     = "Genome Res.",
  volume      =  20,
  number      =  9,
  pages       = "1297--1303",
  month       =  "19~" # jul,
  year        =  2010,
  url         = "http://dx.doi.org/10.1101/gr.107524.110",
  issn        = "1088-9051",
  pmid        = "20644199",
  doi         = "10.1101/gr.107524.110",
  pmc         = "PMC2928508"
}
@ARTICLE{Li2011-ll,
  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",
  month   =  "1~" # nov,
  year    =  2011,
  url     = "http://bioinformatics.oxfordjournals.org/content/27/21/2987.abstract",
  issn    = "1367-4803",
  doi     = "10.1093/bioinformatics/btr509"
}
@ARTICLE{Wu2010-iq,
  title   = {Fast and {SNP-tolerant} detection of complex variants and splicing
             in short reads},
  author  = "Wu, T D and Nacu, S",
  journal = "Bioinformatics",
  volume  =  26,
  number  =  7,
  pages   = "873--881",
  month   =  apr,
  year    =  2010,
  url     = "http://dx.doi.org/10.1093/bioinformatics/btq057",
  issn    = "1367-4803",
  pmid    = "20147302",
  doi     = "10.1093/bioinformatics/btq057"
}
@ARTICLE{Zhang2008-pc,
  title   = {Model-based analysis of {ChIP-Seq} ({MACS})},
  author  = "Zhang, Y and Liu, T and Meyer, C A and Eeckhoute, J and Johnson, D
             S and Bernstein, B E and Nussbaum, C and Myers, R M and Brown, M
             and Li, W and Liu, X S",
  journal = "Genome Biol.",
  volume  =  9,
  number  =  9,
  year    =  2008,
  url     = "http://dx.doi.org/10.1186/gb-2008-9-9-r137",
  issn    = "1465-6906",
  pmid    = "18798982",
  doi     = "10.1186/gb-2008-9-9-r137"
}

@ARTICLE{Yu2015-xu,
  title       = {{ChIPseeker}: an {R/Bioconductor} package for {ChIP} peak
                 annotation, comparison and visualization},
  author      = "Yu, Guangchuang and Wang, Li-Gen and He, Qing-Yu",
  affiliation = "Key Laboratory of Functional Protein Research of Guangdong
                 Higher Education Institutes, College of Life Science and
                 Technology, Jinan University, Guangzhou 510632, China, State
                 Key Laboratory of Emerging Infectious Diseases, School of
                 Public Health, The University of Hong Kong, Hong Kong SAR,
                 China and. Guangdong Information Center, Guangzhou 510031,
                 China. Key Laboratory of Functional Protein Research of
                 Guangdong Higher Education Institutes, College of Life Science
                 and Technology, Jinan University, Guangzhou 510632, China.",
  journal     = "Bioinformatics",
  volume      =  31,
  number      =  14,
  pages       = "2382--2383",
  month       =  "15~" # jul,
  year        =  2015,
  url         = "http://dx.doi.org/10.1093/bioinformatics/btv145",
  issn        = "1367-4803, 1367-4811",
  pmid        = "25765347",
  doi         = "10.1093/bioinformatics/btv145"
}

@ARTICLE{Zhu2010-zo,
  title       = {{ChIPpeakAnno}: a Bioconductor package to annotate {ChIP-seq}
                 and {ChIP-chip} data},
  author      = "Zhu, Lihua J and Gazin, Claude and Lawson, Nathan D and
                 Pag\`{e}s, Herv\'{e} and Lin, Simon M and Lapointe, David S
                 and Green, Michael R",
  affiliation = "Program in Gene Function and Expression, University of
                 Massachusetts Medical School, Worcester, Massachusetts 01605,
                 USA. julie.zhu@umassmed.edu",
  journal     = "BMC Bioinformatics",
  volume      =  11,
  pages       = "237",
  month       =  "11~" # may,
  year        =  2010,
  url         = "http://dx.doi.org/10.1186/1471-2105-11-237",
  issn        = "1471-2105",
  pmid        = "20459804",
  doi         = "10.1186/1471-2105-11-237",
  pmc         = "PMC3098059"
}

@ARTICLE{Juntawong2014-ny,
  title       = {Translational dynamics revealed by genome-wide profiling of
                 ribosome footprints in Arabidopsis},
  author      = "Juntawong, Piyada and Girke, Thomas and Bazin, J\'{e}r\'{e}mie
                 and Bailey-Serres, Julia",
  affiliation = "Center for Plant Cell Biology and Department of Botany and
                 Plant Sciences, University of California, Riverside, CA 92521.",
  journal     = "Proc. Natl. Acad. Sci. U. S. A.",
  volume      =  111,
  number      =  1,
  pages       = "E203--12",
  month       =  "7~" # jan,
  year        =  2014,
  url         = "http://dx.doi.org/10.1073/pnas.1317811111",
  annote      = "PMID: 24367078",
  keywords    = "alternative splicing; long intergenic noncoding RNA; ribosome
                 profiling; translational efficiency; uORF",
  issn        = "0027-8424, 1091-6490",
  pmid        = "24367078",
  doi         = "10.1073/pnas.1317811111",
  pmc         = "PMC3890782"
}
@ARTICLE{Ingolia2009-cb,
  title   = {Genome-wide analysis in vivo of translation with nucleotide
             resolution using ribosome profiling},
  author  = "Ingolia, N T and Ghaemmaghami, S and Newman, J R and Weissman, J S",
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  pages   = "218--223",
  month   =  apr,
  year    =  2009,
  url     = "http://dx.doi.org/10.1016/j.ymeth.2009.03.016",
  issn    = "0036-8075",
  pmid    = "19213877",
  doi     = "10.1016/j.ymeth.2009.03.016"
}
@ARTICLE{Aspden2014-uu,
  title       = {Extensive translation of small Open Reading Frames revealed by
                 {Poly-Ribo-Seq}},
  author      = "Aspden, Julie L and Eyre-Walker, Ying Chen and Phillips, Rose
                 J and Amin, Unum and Mumtaz, Muhammad Ali S and Brocard,
                 Michele and Couso, Juan-Pablo",
  affiliation = "School of Life Sciences, University of Sussex, Brighton,
                 United Kingdom. School of Life Sciences, University of Sussex,
                 Brighton, United Kingdom. School of Life Sciences, University
                 of Sussex, Brighton, United Kingdom. School of Life Sciences,
                 University of Sussex, Brighton, United Kingdom. School of Life
                 Sciences, University of Sussex, Brighton, United Kingdom.
                 School of Life Sciences, University of Sussex, Brighton,
                 United Kingdom. School of Life Sciences, University of Sussex,
                 Brighton, United Kingdom.",
  journal     = "Elife",
  volume      =  3,
  pages       = "e03528",
  month       =  "21~" # aug,
  year        =  2014,
  url         = "http://dx.doi.org/10.7554/eLife.03528",
  keywords    = "biochemistry; d. melanogaster; evolutionary biology; genomics;
                 non-coding RNAs; small open reading Frames; transmembrane
                 peptides",
  issn        = "2050-084X",
  pmid        = "25144939",
  doi         = "10.7554/eLife.03528",
  pmc         = "PMC4359375"
}
@ARTICLE{Ingolia2011-fc,
  title   = {Ribosome profiling of mouse embryonic stem cells reveals the
             complexity and dynamics of mammalian proteomes},
  author  = "Ingolia, N T and Lareau, L F and Weissman, J S",
  journal = "Cell",
  volume  =  147,
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  pages   = "789--802",
  month   =  "11~" # nov,
  year    =  2011,
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  issn    = "0092-8674, 1097-4172;0092-8674",
  pmid    = "22056041",
  doi     = "10.1016/j.cell.2011.10.002"
}
@ARTICLE{Juntawong2015-ru,
  title       = {Ribosome profiling: a tool for quantitative evaluation of
                 dynamics in {mRNA} translation},
  author      = "Juntawong, Piyada and Hummel, Maureen and Bazin, Jeremie and
                 Bailey-Serres, Julia",
  affiliation = "Center for Plant Cell Biology and Department of Botany and
                 Plant Sciences, University of California, Riverside, CA,
                 92521, USA.",
  journal     = "Methods Mol. Biol.",
  volume      =  1284,
  pages       = "139--173",
  year        =  2015,
  url         = "http://dx.doi.org/10.1007/978-1-4939-2444-8_7",
  issn        = "1064-3745, 1940-6029",
  pmid        = "25757771",
  doi         = "10.1007/978-1-4939-2444-8\_7"
}

@ARTICLE{Ma2016-cw,
  title       = "{Cell culture-based profiling across mammals reveals DNA repair
                 and metabolism as determinants of species longevity}",
  author      = "Ma, Siming and Upneja, Akhil and Galecki, Andrzej and Tsai,
                 Yi-Miau and Burant, Charles F and Raskind, Sasha and Zhang,
                 Quanwei and Zhang, Zhengdong D and Seluanov, Andrei and
                 Gorbunova, Vera and Clish, Clary B and Miller, Richard A and
                 Gladyshev, Vadim N",
  affiliation = "Division of Genetics, Department of Medicine, Brigham and
                 Women's Hospital, Harvard Medical School, Boston, United
                 States. Division of Genetics, Department of Medicine, Brigham
                 and Women's Hospital, Harvard Medical School, Boston, United
                 States. Department of Pathology, University of Michigan
                 Medical School, Ann Arbor, United States. Department of
                 Pathology, University of Michigan Medical School, Ann Arbor,
                 United States. Department of Internal Medicine, University of
                 Michigan Medical School, Ann Arbor, United States. Department
                 of Internal Medicine, University of Michigan Medical School,
                 Ann Arbor, United States. Department of Genetics, Albert
                 Einstein College of Medicine, Bronx, United States. Department
                 of Genetics, Albert Einstein College of Medicine, Bronx,
                 United States. Department of Biology, University of Rochester,
                 Rochester, United States. Department of Biology, University of
                 Rochester, Rochester, United States. Broad Institute,
                 Cambridge, United States. Department of Pathology, University
                 of Michigan Medical School, Ann Arbor, United States. Division
                 of Genetics, Department of Medicine, Brigham and Women's
                 Hospital, Harvard Medical School, Boston, United States.",
  journal     = "Elife",
  volume      =  5,
  month       =  "22~" # nov,
  year        =  2016,
  url         = "http://dx.doi.org/10.7554/eLife.19130",
  keywords    = "cell biology; evolutionary biology; genomics; human; mouse;
                 rat; rhesus macaque",
  language    = "en",
  issn        = "2050-084X",
  pmid        = "27874830",
  doi         = "10.7554/eLife.19130"
}

@ARTICLE{Lamb2006-uv,
  title   = "{The Connectivity Map: using gene-expression signatures to connect
             small molecules, genes, and disease}",
  author  = "Lamb, J and Crawford, E D and Peck, D and Modell, J W and Blat, I
             C and Wrobel, M J and Lerner, J and Brunet, J P and Subramanian, A
             and Ross, K N and Reich, M and Hieronymus, H and Wei, G and
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             Carr, S A and Lander, E S and Golub, T R",
  journal = "Science",
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  number  =  5795,
  pages   = "1929--1935",
  month   =  sep,
  year    =  2006,
  url     = "http://dx.doi.org/10.1126/science.1132939",
  issn    = "0036-8075",
  pmid    = "17008526",
  doi     = "10.1126/science.1132939"
}
@ARTICLE{Peters2015-fc,
  title       = {The transcriptional landscape of age in human peripheral blood},
  author      = "Peters, Marjolein J and Joehanes, Roby and Pilling, Luke C and
                 Schurmann, Claudia and Conneely, Karen N and Powell, Joseph
                 and Reinmaa, Eva and Sutphin, George L and ..., ... and Johnson, Andrew D",
  journal     = "Nat. Commun.",
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  month       =  "22~" # oct,
  year        =  2015,
  url         = "http://dx.doi.org/10.1038/ncomms9570",
  issn        = "2041-1723",
  pmid        = "26490707",
  doi         = "10.1038/ncomms9570",
  pmc         = "PMC4639797"
}

@MISC{Sood2015-pb,
  title   = {A novel multi-tissue {RNA} diagnostic of healthy ageing relates to
             cognitive health status},
  author  = "Sood, Sanjana and Gallagher, Iain and Lunnon, Katie and Rullman,
             Eric and Keohane, Aoife and Crossland, Hannah and Phillips, Bethan
             and Cederholm, Tommy and Jensen, Thomas and van Loon, Luc and
             Lannfelt, Lars and Kraus, William and Atherton, Philip and Howard,
             Robert and Gustafsson, Thomas and Hodges, Angela and Timmons,
             James",
  journal = "Genome Biology",
  volume  =  16,
  number  =  1,
  pages   = "185",
  year    =  2015,
  url     = "http://genomebiology.com/2015/16/1/185",
  issn    = "1474-760X",
  doi     = "10.1186/s13059-015-0750-x"
}

@ARTICLE{Tacutu2013-so,
  title       = "{Human Ageing Genomic Resources: integrated databases and tools
                 for the biology and genetics of ageing}",
  author      = "Tacutu, Robi and Craig, Thomas and Budovsky, Arie and Wuttke,
                 Daniel and Lehmann, Gilad and Taranukha, Dmitri and Costa,
                 Joana and Fraifeld, Vadim E and de Magalh{\~a}es, Jo{\~a}o
                 Pedro",
  affiliation = "Integrative Genomics of Ageing Group, Institute of Integrative
                 Biology, University of Liverpool, Liverpool L69 7ZB, UK.",
  journal     = "Nucleic Acids Res.",
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  month       =  jan,
  year        =  2013,
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  language    = "en",
  issn        = "0305-1048, 1362-4962",
  pmid        = "23193293",
  doi         = "10.1093/nar/gks1155",
  pmc         = "PMC3531213"
}

@ARTICLE{Craig2015-wz,
  title       = "{The Digital Ageing Atlas: integrating the diversity of
                 age-related changes into a unified resource}",
  author      = "Craig, Thomas and Smelick, Chris and Tacutu, Robi and Wuttke,
                 Daniel and Wood, Shona H and Stanley, Henry and Janssens,
                 Georges and Savitskaya, Ekaterina and Moskalev, Alexey and
                 Arking, Robert and de Magalh{\~a}es, Jo{\~a}o Pedro",
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  month       =  jan,
  year        =  2015,
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  language    = "en",
  issn        = "0305-1048, 1362-4962",
  pmid        = "25232097",
  doi         = "10.1093/nar/gku843",
  pmc         = "PMC4384002"
}
@UNPUBLISHED{Sergushichev2016-ms,
  title    = "{An algorithm for fast preranked gene set enrichment analysis
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  language = "en",
  doi      = "10.1101/060012"
}
@ARTICLE{Subramanian2005-sn,
  title   = "{Gene set enrichment analysis: a knowledge-based approach for
             interpreting genome-wide expression profiles}",
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             Ebert, B L and Gillette, M A and Paulovich, A and Pomeroy, S L and
             Golub, T R and Lander, E S and Mesirov, J P",
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  issn    = "0027-8424",
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  doi     = "10.1073/pnas.0506580102",
  pmc     = "PMC1239896"
}
@ARTICLE{Barger2017-au,
  title       = "{Identification of tissue-specific transcriptional markers of
                 caloric restriction in the mouse and their use to evaluate
                 caloric restriction mimetics}",
  author      = "Barger, Jamie L and Vann, James M and Cray, Nicole L and Pugh,
                 Thomas D and Mastaloudis, Angela and Hester, Shelly N and
                 Wood, Steven M and Newton, Michael A and Weindruch, Richard
                 and Prolla, Tomas A",
  affiliation = "LifeGen Technologies LLC, Madison, WI, USA. Center for
                 Anti-Aging Research, NSE Products, Inc., Provo, UT, USA.
                 Departments of Statistics and of Biostatistics and Medical
                 Informatics, University of Wisconsin, Madison, WI, USA.
                 Department of Medicine, SMPH, University of Wisconsin,
                 Madison, WI, USA. Geriatric Research, Education and Clinical
                 Center, William S. Middleton Memorial Veterans Hospital,
                 Madison, WI, USA. Departments of Genetics and Medical
                 Genetics, University of Wisconsin, Madison, WI, USA.",
  journal     = "Aging Cell",
  volume      =  16,
  number      =  4,
  pages       = "750--760",
  month       =  aug,
  year        =  2017,
  url         = "http://dx.doi.org/10.1111/acel.12608",
  keywords    = "aging; biomarkers; caloric restriction; gene expression; mouse",
  language    = "en",
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