
@ARTICLE{Dunn2013,
	isbn = "2050-084X", 
	abstract = "Ribosomes can read through stop codons in a regulated manner, elongating rather than terminating the nascent peptide. Stop codon readthrough is essential to diverse viruses, and phylogenetically predicted to occur in a few hundred genes in Drosophila melanogaster, but the importance of regulated readthrough in eukaryotes remains largely unexplored. Here, we present a ribosome profiling assay (deep sequencing of ribosome-protected mRNA fragments) for Drosophila melanogaster, and provide the first genome-wide experimental analysis of readthrough. Readthrough is far more pervasive than expected: the vast majority of readthrough events evolved within D. melanogaster and were not predicted phylogenetically. The resulting C-terminal protein extensions show evidence of selection, contain functional subcellular localization signals, and their readthrough is regulated, arguing for their importance. We further demonstrate that readthrough occurs in yeast and humans. Readthrough thus provides general mechanisms both to regulate gene expression and function, and to add plasticity to the proteome during evolution.", 
	number = 0, 
	year = 2013, 
	author = "Dunn, Joshua G and Foo, Catherine K and Belletier, Nicolette G and Gavis, Elizabeth R and Weissman, Jonathan S", 
	location = "http://dx.doi.org/10.7554/elife.01179", 
	journal = "Elife", 
	volume = 2, 
	address = "California Institute of Quantitative Biosciences, San Francisco, United States.", 
	pages = "e01179", 
	doi = "10.7554/elife.01179",
	url = "http://view.ncbi.nlm.nih.gov/pubmed/24302569", 
	title = "Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster", 
}

@ARTICLE{FieldsRodriguez2015,
    title = {A {Regression}-{Based} {Analysis} of {Ribosome}-{Profiling} {Data} {Reveals} a {Conserved} {Complexity} to {Mammalian} {Translation}},
    volume = {60},
    issn = {1097-2765},
    url = "http://www.cell.com/article/S1097276515009053/abstract",
    doi = "10.1016/j.molcel.2015.11.013",
    abstract = "A fundamental goal of genomics is to identify the complete set of expressed proteins. Automated annotation strategies rely on assumptions about protein-coding sequences (CDSs), e.g., they are conserved, do not overlap, and exceed a minimum length. However, an increasing number of newly discovered proteins violate these rules. Here we present an experimental and analytical framework, based on ribosome profiling and linear regression, for systematic identification and quantification of translation. Application of this approach to lipopolysaccharide-stimulated mouse dendritic cells and HCMV-infected human fibroblasts identifies thousands of novel CDSs, including micropeptides and variants of known proteins, that bear the hallmarks of canonical translation and exhibit translation levels and dynamics comparable to that of annotated CDSs. Remarkably, many translation events are identified in both mouse and human cells even when the peptide sequence is not conserved. Our work thus reveals an unexpected complexity to mammalian translation suited to provide both conserved regulatory or protein-based functions.",
    language = "English",
    number = 5,
    urldate = {2015-12-08},
    journal = "Molecular Cell",
    author = "Fields, Alexander P. and Rodriguez, Edwin H. and Jovanovic, Marko and Stern-Ginossar, Noam and Haas, Brian J. and Mertins, Philipp and Raychowdhury, Raktima and Hacohen, Nir and Carr, Steven A. and Ingolia, Nicholas T. and Regev, Aviv and Weissman, Jonathan S.",
    month = "Mar",
    year = 2015,
    pages = "816-827",
}

@ARTICLE{Ingolia2009,
	isbn = "1095-9203", 
	abstract = "Techniques for systematically monitoring protein translation have lagged far behind methods for measuring messenger RNA (mRNA) levels. Here, we present a ribosome-profiling strategy that is based on the deep sequencing of ribosome-protected mRNA fragments and enables genome-wide investigation of translation with subcodon resolution. We used this technique to monitor translation in budding yeast under both rich and starvation conditions. These studies defined the protein sequences being translated and found extensive translational control in both determining absolute protein abundance and responding to environmental stress. We also observed distinct phases during translation that involve a large decrease in ribosome density going from early to late peptide elongation as well as widespread regulated initiation at non-adenine-uracil-guanine (AUG) codons. Ribosome profiling is readily adaptable to other organisms, making high-precision investigation of protein translation experimentally accessible.", 
	number = 5924, 
	month = "Apr", 
	year = 2009, 
	author = {Ingolia, Nicholas T and Ghaemmaghami, Sina and Newman, John R S and Weissman, Jonathan S}, 
	journal = "Science", 
	volume = 324, 
	address = "Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, and California Institute for Quantitative Biosciences, San Francisco, CA 94158, USA. ingolia@cmp.ucsf.edu", 
	pages = "218-23", 
	url = "http://view.ncbi.nlm.nih.gov/pubmed/19213877", 
	title = "Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling",
	doi = "10.1126/science.1168978",
}

@article{Ingolia2011,
	isbn = "1097-4172", 
	abstract = "The ability to sequence genomes has far outstripped approaches for deciphering the information they encode. Here we present a suite of techniques, based on ribosome profiling (the deep sequencing of ribosome-protected mRNA fragments), to provide genome-wide maps of protein synthesis as well as a pulse-chase strategy for determining rates of translation elongation. We exploit the propensity of harringtonine to cause ribosomes to accumulate at sites of translation initiation together with a machine learning algorithm to define protein products systematically. Analysis of translation in mouse embryonic stem cells reveals thousands of strong pause sites and unannotated translation products. These include amino-terminal extensions and truncations and upstream open reading frames with regulatory potential, initiated at both AUG and non-AUG codons, whose translation changes after differentiation. We also define a class of short, polycistronic ribosome-associated coding RNAs (sprcRNAs) that encode small proteins. Our studies reveal an unanticipated complexity to mammalian proteomes.", 
	number = 4, 
	month = "Nov", 
	year = 2011, 
	author = "Ingolia, Nicholas T and Lareau, Liana F and Weissman, Jonathan S", 
	doi = "10.1016/j.cell.2011.10.002", 
	journal = "Cell", 
	volume = 147, 
	address = "Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA. ingolia@ciwemb.edu", 
	pages = "789-802", 
	url = "http://view.ncbi.nlm.nih.gov/pubmed/22056041", 
	title = "Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes", 
}

@article{Kent2010,
	isbn = {1367-4811}, 
	abstract = "BigWig and BigBed files are compressed binary indexed files containing data at several resolutions that allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser. The visualization is implemented using a multi-layered software approach that takes advantage of specific capabilities of web-based protocols and Linux and UNIX operating systems files, R trees and various indexing and compression tricks. As a result, only the data needed to support the current browser view is transmitted rather than the entire file, enabling fast remote access to large distributed data sets.",
	number = 17,
	month = "Sep",
	year = 2010,
	author = "Kent, W J and Zweig, A S and Barber, G and Hinrichs, A S and Karolchik, D", 
	journal = "Bioinformatics", 
	volume = 26,
	address = "Center for Biomolecular Science and Engineering, School of Engineering, University of California, Santa Cruz (UCSC), Santa Cruz, CA 95064, USA.", 
	pages = {2204-7},
	url = "http://view.ncbi.nlm.nih.gov/pubmed/20639541", 
	title = "BigWig and BigBed: enabling browsing of large distributed datasets",
	doi = "10.1093/bioinformatics/btq351" 
}

@article{Rouskin2014,
	isbn = "1476-4687", 
	abstract = "RNA has a dual role as an informational molecule and a direct effector of biological tasks. The latter function is enabled by RNA's ability to adopt complex secondary and tertiary folds and thus has motivated extensive computational and experimental efforts for determining RNA structures. Existing approaches for evaluating RNA structure have been largely limited to in vitro systems, yet the thermodynamic forces which drive RNA folding in vitro may not be sufficient to predict stable RNA structures in vivo. Indeed, the presence of RNA-binding proteins and ATP-dependent helicases can influence which structures are present inside cells. Here we present an approach for globally monitoring RNA structure in native conditions in vivo with single-nucleotide precision. This method is based on in vivo modification with dimethyl sulphate (DMS), which reacts with unpaired adenine and cytosine residues, followed by deep sequencing to monitor modifications. Our data from yeast and mammalian cells are in excellent agreement with known messenger RNA structures and with the high-resolution crystal structure of the Saccharomyces cerevisiae ribosome. Comparison between in vivo and in vitro data reveals that in rapidly dividing cells there are vastly fewer structured mRNA regions in vivo than in vitro. Even thermostable RNA structures are often denatured in cells, highlighting the importance of cellular processes in regulating RNA structure. Indeed, analysis of mRNA structure under ATP-depleted conditions in yeast shows that energy-dependent processes strongly contribute to the predominantly unfolded state of mRNAs inside cells. Our studies broadly enable the functional analysis of physiological RNA structures and reveal that, in contrast to the Anfinsen view of protein folding whereby the structure formed is the most thermodynamically favourable, thermodynamics have an incomplete role in determining mRNA structure in vivo.", 
	number = "7485", 
	month = "Jan", 
	year = 2014, 
	author = "Rouskin, Silvi and Zubradt, Meghan and Washietl, Stefan and Kellis, Manolis and Weissman, Jonathan S", 
	journal = "Nature", 
	volume = 505, 
	address = "Department of Cellular and Molecular Pharmacology, California Institute of Quantitative Biology, Center for RNA Systems Biology, Howard Hughes Medical Institute, University of California, San Francisco, California 94158, USA.", 
	pages = "701-5", 
	url = "http://view.ncbi.nlm.nih.gov/pubmed/24336214", 
	title = "Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo",
	doi = "10.1038/nature12894", 
}

@ARTICLE{flybaseRef,
	isbn = "1362-4962", 
	abstract = "FlyBase (http://flybase.org) is the leading database and web portal for genetic and genomic information on the fruit fly Drosophila melanogaster and related fly species. Whether you use the fruit fly as an experimental system or want to apply Drosophila biological knowledge to another field of study, FlyBase can help you successfully navigate the wealth of available Drosophila data. Here, we review the FlyBase web site with novice and less-experienced users of FlyBase in mind and point out recent developments stemming from the availability of genome-wide data from the modENCODE project. The first section of this paper explains the organization of the web site and describes the report pages available on FlyBase, focusing on the most popular, the Gene Report. The next section introduces some of the search tools available on FlyBase, in particular, our heavily used and recently redesigned search tool QuickSearch, found on the FlyBase homepage. The final section concerns genomic data, including recent modENCODE (http://www.modencode.org) data, available through our Genome Browser, GBrowse.", 
	number = "Database issue", 
	month = "Jan", 
	year = 2012, 
	author = "McQuilton, Peter and St Pierre, Susan E and Thurmond, Jim and Flybase Consortium", 
	location = "http://dx.doi.org/10.1093/nar/gkr1030", 
	journal = "Nucleic Acids Res", 
	volume = 40, 
	address = "Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.", 
	pages = "D706-14", 
	url = "http://view.ncbi.nlm.nih.gov/pubmed/22127867", 
	title = "FlyBase 101--the basics of navigating FlyBase", 
	doi = "10.1093/nar/gkr1030"
}

@ARTICLE{sgdRef,
	isbn = "1362-4962", 
	abstract = "The Saccharomyces Genome Database (SGD, http://www.yeastgenome.org) is the community resource for the budding yeast Saccharomyces cerevisiae. The SGD project provides the highest-quality manually curated information from peer-reviewed literature. The experimental results reported in the literature are extracted and integrated within a well-developed database. These data are combined with quality high-throughput results and provided through Locus Summary pages, a powerful query engine and rich genome browser. The acquisition, integration and retrieval of these data allow SGD to facilitate experimental design and analysis by providing an encyclopedia of the yeast genome, its chromosomal features, their functions and interactions. Public access to these data is provided to researchers and educators via web pages designed for optimal ease of use.", 
	number = "Database issue", 
	month = "Jan", 
	year = 1012, 
	author = "Cherry, J Michael and Hong, Eurie L and Amundsen, Craig and Balakrishnan, Rama and Binkley, Gail and Chan, Esther T and Christie, Karen R and Costanzo, Maria C and Dwight, Selina S and Engel, Stacia R and Fisk, Dianna G and Hirschman, Jodi E and Hitz, Benjamin C and Karra, Kalpana and Krieger, Cynthia J and Miyasato, Stuart R and Nash, Rob S and Park, Julie and Skrzypek, Marek S and Simison, Matt and Weng, Shuai and Wong, Edith D", 
	journal = "Nucleic Acids Res", 
	volume = 40, 
	address = "Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA. cherry@stanford.edu", 
	pages = "D700-5", 
	url = "http://view.ncbi.nlm.nih.gov/pubmed/22110037", 
	title = "Saccharomyces Genome Database: the genomics resource of budding yeast"
}

@ARTICLE{Nagalakshmi2008,
	number = 5881, 
	year = 2008, 
	author = "Nagalakshmi, Ugrappa and Wang, Zhong and Waern, Karl and Shou, Chong and Raha, Debasish and Gerstein, Mark and Snyder, Michael", 
	location = "http://dx.doi.org/10.1126/science.1158441", 
	journal = "Science", 
	volume = 320, 
	pages = "1344-9", 
	doi = "10.1126/science.1158441", 
	title = "The transcriptional landscape of the yeast genome defined by RNA sequencing."
}

@ARTICLE{Yassour2009,
	isbn = "1091-6490", 
	abstract = "Defining the transcriptome, the repertoire of transcribed regions encoded in the genome, is a challenging experimental task. Current approaches, relying on sequencing of ESTs or cDNA libraries, are expensive and labor-intensive. Here, we present a general approach for ab initio discovery of the complete transcriptome of the budding yeast, based only on the unannotated genome sequence and millions of short reads from a single massively parallel sequencing run. Using novel algorithms, we automatically construct a highly accurate transcript catalog. Our approach automatically and fully defines 86 percent of the genes expressed under the given conditions, and discovers 160 previously undescribed transcription units of 250 bp or longer. It correctly demarcates the 5' and 3' UTR boundaries of 86 and 77 percent of expressed genes, respectively. The method further identifies 83 percent of known splice junctions in expressed genes, and discovers 25 previously uncharacterized introns, including 2 cases of condition-dependent intron retention. Our framework is applicable to poorly understood organisms, and can lead to greater understanding of the transcribed elements in an explored genome.", 
	number = 9, 
	month = "Mar", 
	year = 2009, 
	author = "Yassour, Moran and Kaplan, Tommy and Fraser, Hunter B and Levin, Joshua Z and Pfiffner, Jenna and Adiconis, Xian and Schroth, Gary and Luo, Shujun and Khrebtukova, Irina and Gnirke, Andreas and Nusbaum, Chad and Thompson, Dawn-Anne and Friedman, Nir and Regev, Aviv", 
	journal = "Proc Natl Acad Sci U S A", 
	volume = 106, 
	address = "School of Computer Science and Engineering, The Hebrew University, Jerusalem, 91904, Israel.", 
	pages = "3264-9", 
	url = "http://view.ncbi.nlm.nih.gov/pubmed/19208812", 
	title = "Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing"
}

@article{Jan2014,
	isbn = "1095-9203", 
	abstract = "Localized protein synthesis is a fundamental mechanism for creating distinct subcellular environments. Here we developed a generalizable proximity-specific ribosome profiling strategy that enables global analysis of translation in defined subcellular locations. We applied this approach to the endoplasmic reticulum (ER) in yeast and mammals. We observed the large majority of secretory proteins to be cotranslationally translocated, including substrates capable of posttranslational insertion in vitro. Distinct translocon complexes engaged nascent chains at different points during synthesis. Whereas most proteins engaged the ER immediately after or even before signal sequence (SS) emergence, a class of Sec66-dependent proteins entered with a looped SS conformation. Finally, we observed rapid ribosome exchange into the cytosol after translation termination. These data provide insights into how distinct translocation mechanisms act in concert to promote efficient cotranslational recruitment.", 
	number = 6210, 
	month = "Nov", 
	year = 2014, 
	author = "Jan, Calvin H and Williams, Christopher C and Weissman, Jonathan S", 
	journal = "Science", 
	volume = 346, 
	pages = "1257521", 
	url = "http://view.ncbi.nlm.nih.gov/pubmed/25378630", 
	doi = "10.1126/science.1257521",
	title = "Principles of ER cotranslational translocation revealed by proximity-specific ribosome profiling", 
}

@article{Oh2011,
	isbn = "1097-4172", 
	abstract = "As nascent polypeptides exit ribosomes, they are engaged by a series of processing, targeting, and folding factors. Here, we present a selective ribosome profiling strategy that enables global monitoring of when these factors engage polypeptides in the complex cellular environment. Studies of the Escherichia coli chaperone trigger factor (TF) reveal that, though TF can interact with many polypeptides, β-barrel outer-membrane proteins are the most prominent substrates. Loss of TF leads to broad outer-membrane defects and premature, cotranslational protein translocation. Whereas in vitro studies suggested that TF is prebound to ribosomes waiting for polypeptides to emerge from the exit channel, we find that in vivo TF engages ribosomes only after ~100 amino acids are translated. Moreover, excess TF interferes with cotranslational removal of the N-terminal formyl methionine. Our studies support a triaging model in which proper protein biogenesis relies on the fine-tuned, sequential engagement of processing, targeting, and folding factors.", 
	number = 6, 
	month = "Dec", 
	year = 2011, 
	author = "Oh, Eugene and Becker, Annemarie H and Sandikci, Arzu and Huber, Damon and Chaba, Rachna and Gloge, Felix and Nichols, Robert J and Typas, Athanasios and Gross, Carol A and Kramer, Günter and Weissman, Jonathan S and Bukau, Bernd", 
	doi = "10.1016/j.cell.2011.10.044", 
	journal = "Cell", 
	volume = 147, 
	address = "Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA.", 
	pages = "1295-308", 
	url = "http://view.ncbi.nlm.nih.gov/pubmed/22153074", 
	title = "Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo", 
}

@article{Gilbert2014,
	isbn = "1097-4172", 
	abstract = "While the catalog of mammalian transcripts and their expression levels in different cell types and disease states is rapidly expanding, our understanding of transcript function lags behind. We present a robust technology enabling systematic investigation of the cellular consequences of repressing or inducing individual transcripts. We identify rules for specific targeting of transcriptional repressors (CRISPRi), typically achieving 90-99 percent knockdown with minimal off-target effects, and activators (CRISPRa) to endogenous genes via endonuclease-deficient Cas9. Together they enable modulation of gene expression over a ∼1,000-fold range. Using these rules, we construct genome-scale CRISPRi and CRISPRa libraries, each of which we validate with two pooled screens. Growth-based screens identify essential genes, tumor suppressors, and regulators of differentiation. Screens for sensitivity to a cholera-diphtheria toxin provide broad insights into the mechanisms of pathogen entry, retrotranslocation and toxicity. Our results establish CRISPRi and CRISPRa as powerful tools that provide rich and complementary information for mapping complex pathways.", 
	number = 3, 
	month = "Oct", 
	year = 2014, 
	author = "Gilbert, Luke A and Horlbeck, Max A and Adamson, Britt and Villalta, Jacqueline E and Chen, Yuwen and Whitehead, Evan H and Guimaraes, Carla and Panning, Barbara and Ploegh, Hidde L and Bassik, Michael C and Qi, Lei S and Kampmann, Martin and Weissman, Jonathan S", 
	journal = "Cell", 
	volume = 159, 
	address = "Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA.", 
	pages = "647-61", 
	url = "http://view.ncbi.nlm.nih.gov/pubmed/25307932",
	doi = "10.1016/j.cell.2014.09.029",
	title = "Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation", 
}

@article{Stern-Ginossar2012,
	number = 6110, 
	year = 2012, 
	author = "Stern-Ginossar, Noam and Weisburd, Ben and Michalski, Annette and Le, Vu Thuy Khanh and Hein, Marco Y and Huang, Sheng-Xiong and Ma, Ming and Shen, Ben and Qian, Shu-Bing and Hengel, Hartmut and Mann, Matthias and Ingolia, Nicholas T and Weissman, Jonathan S", 
	journal = "Science", 
	volume = 338, 
	pages = "1088-93", 
	doi = "10.1126/science.1227919", 
	title = "Decoding human cytomegalovirus", 
}

@article{Anders2010,
	isbn = "1465-6914", 
	abstract = "High-throughput sequencing assays such as RNA-Seq, ChIP-Seq or barcode counting provide quantitative readouts in the form of count data. To infer differential signal in such data correctly and with good statistical power, estimation of data variability throughout the dynamic range and a suitable error model are required. We propose a method based on the negative binomial distribution, with variance and mean linked by local regression and present an implementation, DESeq, as an R/Bioconductor package.", 
	number = 10, 
	year = 2010, 
	author = "Anders, Simon and Huber, Wolfgang", 
	journal = "Genome Biol", 
	volume = 11, 
	address = "European Molecular Biology Laboratory, Mayerhofstraße 1, 69117 Heidelberg, Germany. sanders@fs.tum.de", 
	pages = "R106", 
	url = "http://view.ncbi.nlm.nih.gov/pubmed/20979621", 
	title = "Differential expression analysis for sequence count data", 
}

@article{Anders2013,
	isbn = "1750-2799", 
	abstract = "RNA sequencing (RNA-seq) has been rapidly adopted for the profiling of transcriptomes in many areas of biology, including studies into gene regulation, development and disease. Of particular interest is the discovery of differentially expressed genes across different conditions (e.g., tissues, perturbations) while optionally adjusting for other systematic factors that affect the data-collection process. There are a number of subtle yet crucial aspects of these analyses, such as read counting, appropriate treatment of biological variability, quality control checks and appropriate setup of statistical modeling. Several variations have been presented in the literature, and there is a need for guidance on current best practices. This protocol presents a state-of-the-art computational and statistical RNA-seq differential expression analysis workflow largely based on the free open-source R language and Bioconductor software and, in particular, on two widely used tools, DESeq and edgeR. Hands-on time for typical small experiments (e.g., 4-10 samples) can be <1 h, with computation time <1 d using a standard desktop PC.", 
	number = 9, 
	month = "Sep", 
	year = 2013, 
	author = "Anders, Simon and McCarthy, Davis J and Chen, Yunshun and Okoniewski, Michal and Smyth, Gordon K and Huber, Wolfgang and Robinson, Mark D", 
	journal = "Nat Protoc", 
	volume = 8, 
	address = "Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.", 
	pages = "1765-86", 
	url = "http://view.ncbi.nlm.nih.gov/pubmed/23975260", 
	title = "Count-based differential expression analysis of RNA sequencing data using R and Bioconductor", 
}

@article{Benjamini1995,
	number = 1, 
    year = 1995,
	author = "Benjamini, Yoav and Hochberg, Yosef", 
	journal = "Journal of the Royal Statistical Society. Series B (Methodological)", 
	volume = 57, 
	pages = "289-300", 
	title = "Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing", 
}

@article{Love2014,
	isbn = "1474-760X", 
	abstract = "In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html webcite.", 
	number = 12, 
	year = 2014, 
	author = "Love, Michael I and Huber, Wolfgang and Anders, Simon", 
	journal = "Genome Biol", 
	volume = 15, 
	pages = 550, 
	url = "http://view.ncbi.nlm.nih.gov/pubmed/25516281", 
	doi = "10.1186/s13059-014-0550-8",
	title = "Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2", 
}

@article{Rodriguez2013,
    author = "Rodriguez, Jose Manuel and Maietta, Paolo and Ezkurdia, Iakes and Pietrelli, Alessandro and Wesselink, Jan-Jaap and Lopez, Gonzalo and Valencia, Alfonso and Tress, Michael L.", 
    title = "APPRIS: annotation of principal and alternative splice isoforms",
    volume = 41, 
    number = "D1", 
    pages = "D110-D117", 
    year = 2013, 
    doi = "10.1093/nar/gks1058", 
    abstract ="Here, we present APPRIS (http://appris.bioinfo.cnio.es), a database that houses annotations of human splice isoforms. APPRIS has been designed to provide value to manual annotations of the human genome by adding reliable protein structural and functional data and information from cross-species conservation. The visual representation of the annotations provided by APPRIS for each gene allows annotators and researchers alike to easily identify functional changes brought about by splicing events. In addition to collecting, integrating and analyzing reliable predictions of the effect of splicing events, APPRIS also selects a single reference sequence for each gene, here termed the principal isoform, based on the annotations of structure, function and conservation for each transcript. APPRIS identifies a principal isoform for 85\% of the protein-coding genes in the GENCODE 7 release for ENSEMBL. Analysis of the APPRIS data shows that at least 70\% of the alternative (non-principal) variants would lose important functional or structural information relative to the principal isoform.", 
    URL = "http://nar.oxfordjournals.org/content/41/D1/D110.abstract",
    eprint = "http://nar.oxfordjournals.org/content/41/D1/D110.full.pdf+html",
    journal = "Nucleic Acids Research",
}

