Jack Chen, Associate Professor

Department of Molecular Biology and Biochemistry
Simon Fraser University

1. Janes et al., 2015. A comparative study of RNA-seq analysis strategies. (Briefings in Bioinformatics)
2. Jonkers and Lis, 2015. Getting up to speed with transcription elongation by RNA polymerase II. (Nature Reviews Molecular Cell Biology)
3. Blumenthal et al., 2015. Operon and non-operon gene clusters in the C. elegans genome.(WormBase)
4. Laurent et al., 2015. The Landscape of long noncoding RNA classification. (TIG)
5. Rehman et al., 2015. Modulation of alternative splicing by anticancer drugs. (WIREs RNA)
6. Szafranski and Kramer, 2015. It's a bit over, is that ok? The subtle surplus from tandem alternative splicing. (RNA Biology)
   Notes: Reviewed TASS, which is the second largest alternative splicing class in mammals. TASS can occur at the 5' or 3' splicing site. TASS is called NAGNAG 3' splice site if it occurs at the 3' splice site.
   
7. de Klerk et al., 2015. Alternative mRNA transcription, processing, and translation: insights from RNA sequencing. (TIG)
8. Miura et al., 2014. Alternative polyadenylation in the nervous system: To what lengths will 3' UTR extensions take us? (BioEssays)
9. de Klerk et al., 2014. RNA sequencing: from tag-based profiling to resolving complete transcript structure. (Cellular and Molecular Life Sciences)
10. Saliba et al., 2014. Single-cell RNA-seq: advances and future challenges. (NAR)
11. Sterne-Weiler and Sanford, 2014. Exon identity crisis: disease-causing mutations that disrupt the splicing code. (Genome Biology)
12. Irimia and Roy, 2014. Origin of Spliceosomal Introns and Alternative Splicing. (CSH Perspectives)
13. Fu and Ares, 2014. Context-dependent control of alternative splicing by RNA-binding proteins. (Nature Reviews Genetics)
14. Carstens, 2014. Networking in an Alternative Splicing World. (Molecular Cell)
15. Spieth et al., 2014. Overview of gene structure in C. elegans. (WormBook)
16. Han et al., 2014. Alternative applications for distinct RNA sequencing strategies. (Briefings in Bioinformatics)
17. Li et al., 2014. The emerging era of genomic data integration for analyzing splice isoform function. (TIG)
18. Zheng and Black, 2013. Alternative pre-mRNA splicing in neurons: growing up and extending its reach. (TIG)
19. Ulitsky and Bartel, 2013. lincRNAs: Genomics, Evolution, and Mechanisms. (Cell)
20. Mudge et al., 2013. Functional transcriptomics in the post-ENCODE era. (Genome Research)
    Notes: This article critically examines the definition of the concept gene. One recent definition is: A gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products (Gerstein et al., 2007). The complexity of human transcriptome manifests as alternative splicing within protein-coding genes and discovery of thousands of long noncoding RNAs.
    
21. Reddy et al., 2013. Complexity of the Alternative Splicing Landscape in Plants. (Plant Cell)
22. Barberan-Soler and Ragle, 2013. Alternative Splicing Regulation of Cancer-Related Pathways in Caenorhabditis elegans: An In Vivo Model System with a Powerful Reverse Genetics Toolbox. (International Journal of Cell Biology)
23. Kornblihtt et al., 2013. Alternative splicing: a pivotal step between eukaryotic transcription and translation. (Nature Reviews Molecular Cell Biology)
24. Pohl et al., 2013. Alternative splicing of mutually exclusive A review. (Biosystems)
25. Rinn and Chang, 2012. Genome Regulation by Long Noncoding RNAs. (Annual Reviews of Biochemistry)
26. Zahler, 2012. Pre-mRNA splicing and its regulation in Caenorhabditis elegans. (WormBook)
27. Ozsolak et al., 2011. RNA sequencing: advances, challenges and opportunities. (Nature Reviews Genetics)
28. Witten and Ule, 2011. Understanding splicing regulation through RNA splicing maps. (TIG)
29. Kalsotra and Cooper, 2011. Functional consequences of developmentally regulated alternative splicing. (Nature Reviews Genetics)
30. Calarco et al., 2011. Networking in a global world: Establishing functional connections between neural splicing regulators and their target transcripts. (RNA)
31. Hallegger et al., 2010. Alternative splicing: global insights. (FEBSJ)
32. Keren et al., 2010. Alternative splicing and evolution: diversification, exon definition and function. (Nature Reviews Genetics)
33. Licatalosi and Darnell, 2010. RNA processing and its regulation: global insights into biological networks. (Nature Reviews Genetics)
34. Nilsen and Graveley, 2010. Expansion of the eukaryotic proteome by alternative splicing. (Nature)
35. David and Manley, 2010. Alternative pre-mRNA splicing regulation in cancer: pathways and programs unhinged. (Genes and Development)
36. Chen and Manley, 2009. Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. (Nature Reviews Molecular Cell Biology)
37. Graveley et al., 2008. The haplo-spliceo-transcriptome: common variations in alternative splicing in the human population. (TIG)
38. David and Manley, 2008. The search for alternative splicing regulators: new approaches offer a path to a splicing code. (Genes and Development)
39. Barbazuk et al., 2008. Genome-wide analyses of alternative splicing in plants: Opportunities and challenges. (Genome Research)
40. Wang and Burge, 2008. Splicing regulation: From a parts list of regulatory elements to an integrated splicing code. (RNA)
41. Jeffares et al., 2008. Rapidly regulated genes are intron poor. (TIG)
42. Irimia et al., 2007. Coevolution of genomic intron number and splice sites. (TIG)
43. Carmel et al., 2007. Three distinct modes of intron dynamics in the evolution of eukaryotes. (Genome Research)
44. Coulombe-Huntington and Majewski, 2007. Characterization of intron loss events in mammals. (Genome Research)
45. Wang and Cooper, 2007. Splicing in disease: disruption of the splicing code and the decoding machinery. (Nature Reviews Genetics)
46. Reddy, 2007. Alternative Splicing of Pre-Messenger RNAs in Plants in the Genomic Era. (Annual Review of Plant Biology)
47. Rodrigues-Trelles et al., 2006. Origins and Evolution of Spliceosomal Introns. (Annual Reviews of Genetics)
48. Roy and Gilbert, 2006. The evolution of spliceosomal introns: patterns, puzzles and progress. (Nature Reviews Genetics)
49. Koonin, 2006. The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate?. (Biology Direct)
50. Jeffares et al., 2006. The biology of intron gain and loss. (TIG)
51. Blencowe, 2006. Alternative Splicing: New Insights from Global Analyses. (Cell)
52. Xing and Lee, 2006. Alternative splicing and RNA selection evolutionary consequences for eukaryotic genomes. (Nature Reviews Genetics)
53. Wang and Brendel, 2006. Genomewide comparative analysis of alternative splicing in plants. (PNAS)
54. Matlin et al., 2005. Understanding alternative splicing: towards a cellular code. (Nature Reviews Molecular Cell Biology)
55. Stamm et al., 2005. Function of alternative splicing. (Gene)
56. Pagani and Baralle, 2004. Genomic variants in exons and introns: identifying the splicing spoilers. (Nature Reviews Genetics)
57. Fu, 2004. Towards a Splicing Code. (Cell)
58. Ast, 2004. How did alternative splicing evolve? (Nature Reviews Genetics)
59. Black, 2003. MECHANISMS OF ALTERNATIVE PRE-MESSENGER RNA SPLICING. (Annual Review of Biochemistry)
60. Faustino and Cooper, 2005. Identification of Putative New Splicing Targets for ETR-3 Using Sequences Identified by Systematic Evolution of Ligands by Exponential Enrichment. (Mol Cell Biol)
61. Faustino and Cooper, 2003. Pre-mRNA splicing and human disease. (Genes and Development)
62. Ladd and Cooper, 2002. Finding signals that regulate alternative splicing in the postgenomic era. (Genome Biology)
63. Modrek and Lee, 2002. A genomic view of alternative splicing. (Nature Genetics)
64. Cartegni et al., 2002. Listening to silence and understanding nonsense: exonic mutations that affect splicing. (Nature Reviews Genetics)
65. Baker et al., 2001. Are Complex Behaviors Specified by Dedicated Regulatory Genes? Reasoning from Drosophila. (Cell)
    Notes: Alternative splicing dictates sex determination. RNA binding protein SXL is turned on in females, not males.
    
66. Lopez, 1998. ALTERNATIVE SPLICING OF PRE-mRNA: Developmental Consequences and Mechanisms of Regulation. (Annual Reviews of Genetics)
67. Blumenthal, 1995. Trans-splicing and polycistronic transcription in Caenohabditis elegans. (TIG)
68. Green, 1991. Biochemical mechanisms of constitutive and regulated pre-mRNA splicing. (Annu. Rev. Cell Biol.)
69. Padgett et al., 1986. Splicing of messenger RNA precursors. (Ann. Rev. Biochem)
70. Cavalier-Smith, 1985. Selfish DNA and the origin of introns. (Nature)

1. Beadell and Hagg, 2015. Evolutionary Dynamics of GLD-1mRNA Complexes in Caenorhabditis Nematodes. (Genome Biology and Evolution)
2. Calahorro et al., 2015. Analysis of splice variants for the C.elegans orthologue of human neuroligin reveals a developmentally regulated transcript. (Gene Expression Patterns)
3. Mathews et al., 2015. Unusual Regulation of Splicing of the Cholinergic Locus in Caenorhabditis elegans. (Genetics)
4. Ragle et al., 2015. Coordinated tissue-specific regulation of adjacent alternative 3' splice sites in C. elegans. (Genome Research)
   Notes: Focused on NAGNAG alternative splicing.
   
5. Stoeckius et al., 2014. Global characterization of the oocyte-to-embryo transition in Caenorhabditis elegans uncovers a novel mRNA clearance mechanism. (EMBO)
6. Grun et al., 2014. Conservation of mRNA and Protein Expression during Development of C. elegans. (Cell Reports)
   Notes: Compared gene/protein expression in C. elegans and C. briggsae.
   
7. Kuwasako et al., 2014. RBFOX and SUP-12 sandwich a G base to cooperatively regulate tissue-specific splicing. (Nature Structural and Molecular Biology)
8. Mackereth, 2014. Splicing factor SUP-12 and the molecular complexity of apparent cooperativity. (Worm)
9. Kuroyanagi et al., 2014. Comprehensive analysis of mutually exclusive alternative splicing in C. elegans. (Worm)
   Notes: Validated 29 ME exon clusters in 27 genes that are mutually spliced in C. elegans. These predictions were initially done by Ramani et al., 2011 (Genome Research).
   
10. Barberan-Soler et al., 2014. Co-option of the piRNA Pathway for Germline-Specific Alternative Splicing of C. elegans TOR. (Cell Report)
11. Norris et al., 2014. A Pair of RNA-Binding Proteins Controls Networks of Splicing Events Contributing to Specialization of Neural Cell Types. (Molecular Cell)
    Notes: Cell(neuron)-specific alternative splicing.
    
12. Glauser, 2014. The multiplicity of alternative splicing decisions in Caenorhabditis elegans is linked to specific intronic regulatory motifs and minisatellites. (BMC Genomics)
    Notes: Introduced terms including SASS, MASS.
    
13. Saito et al., 2013. The transcription start site landscape of C. elegans. (Genome Research)
    Notes: This study captured TSS by lowing the temperature for C. elegans growth and nuclear isolation.
    
14. Stadler and Fire, 2013. Conserved Translatome Remodeling in Nematode Species Executing a Shared Developmental Transition. (PLoS Genetics)
15. Kuroyanagi, 2013. Switch-like regulation of tissue-specific alternative pre-mRNA processing patterns revealed by customized fluorescence reporters. (Worm)
16. Kuroyanagi et al., 2013. Position-dependent and neuron-specific splicing regulation by the CELF family RNA-binding protein UNC-75 in Caenorhabditis elegans. (NAR)
17. Levin et al., 2012. Developmental Milestones Punctuate Gene Expression in the Caenorhabditis Embryo. (Developmental Cell)
18. Uyar et al., 2012. RNA-seq analysis of the C. briggsae transcriptome. (Genome Research)
19. Maxwell et al., 2012. Nutritional control of mRNA isoform expression during developmental arrest and recovery in C. elegans. (Genome Research)
20. Nam and Bartel, 2012. Long noncoding RNAs in C. elegans. (Genome Research)
21. Ohno et al., 2012. Muscle-Specific Splicing Factors ASD-2 and SUP-12 Cooperatively Switch Alternative Pre-mRNA Processing Patterns of the ADF/Cofilin Gene in Caenorhabditis elegans. (PLoS Genetics)
22. Allen et al, 2011. A global analysis of C. elegans trans-splicing. (Genome Research)
23. Jan et al., 2011. Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs. (Nature)
24. Lamm et al., 2011. Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome. (Genome Research)
25. Spencer et al., 2011. A spatial and temporal map of C. elegans gene expression. (Genome Research)
26. Ramani et al., 2011. Genome-wide analysis of alternative splicing in Caenorhabditis elegans. (Genome Research)
    Notes: This is arguably the most comprehensive RNA-seq and alternative splicing studies on C. elegans. Trans-splicing was not examined in this project.
    
27. Glauser et al., 2011. Intragenic alternative splicing coordination is essential for Caenorhabditis elegans slo-1 gene function. (PNAS)
    Notes: Coordinated alternative splicing events. A mutation was found to distrupt a UAAAUC intronic cis-regulatory element.
    
28. Barberan-Soler et al., 2011. Co-regulation of alternative splicing by diverse splicing factors in Caenorhabditis elegans. (NAR)
29. Glauser et al., 2011. Intragenic alternative splicing coordination is essential for Caenorhabditis elegans slo-1 gene function. (PNAS)
30. Johnson et al., 2011. Alternatively spliced domains interact to regulate BK potassium channel gating. (PNAS)
31. Ma et al., 2011. In vivo effects on intron retention and exon skipping by the U2AF large subunit and SF1/BBP in the nematode Caenorhabditis elegans. (RNA)
32. Mangone et al., 2010. The Landscape of C. elegans 3'UTRs. (Science)
33. Gerstein et al., 2010. Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project. (Science)
34. Ramani et al., 2009. High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans. (Genome Biology)
35. Hillier et al., 2009. Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. (Genome Research)
    Notes: This is the first and a very comprehensive RNA-seq study on C. elegans. Found many "genlets", which suggests genes that have not been annotated.
    
36. Barberan-Soler et al., 2009. Global analysis of alternative splicing uncovers developmental regulation of nonsense-mediated decay in C. elegans. (RNA)
37. Kabat et al., 2009. HRP-2, the Caenorhabditis elegans Homolog of Mammalian Heterogeneous Nuclear Ribonucleoproteins Q and R, Is an Alternative Splicing Factor That Binds to UCUAUC Splicing Regulatory Elements. (JBC)
38. Ohno et al., 2008. STAR family RNA-binding protein ASD-2 regulates developmental switching of mutually exclusive alternative splicing in vivo. (Genes and Development)
39. Barreran-Soler and Zahler, 2008. Alternative Splicing Regulation During C. elegans Development: Splicing Factors as Regulated Targets. (PLoS Genetics)
40. Barberan-Soler and Zahler, 2008. Alternative Splicing and the Steady-State Ratios of mRNA Isoforms Generated by It Are under Strong Stabilizing Selection in Caenorhabditis elegans. (MBE)
41. Shin et al., 2008. Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags. (BMC Biology)
42. Shan and Walthall, 2008. Copulation in C. elegans males requires a nuclear hormone receptor. (Developmental Biology)
43. Irimia et al., 2008. Widespread Evolutionary Conservation of Alternatively Spliced Exons in Caenorhabditis. (MBE)
44. Rukov et al., 2007. High Qualitative and Quantitative Conservation of Alternative Splicing in Caenorhabditis elegans and Caenorhabditis briggsae. (MBE)
45. Kuroyanagi et al., 2007. The Fox-1 Family and SUP-12 Coordinately Regulate Tissue-Specific Alternative Splicing In Vivo. (Mol Cell Biol)
46. Fox et al., 2007. The embryonic muscle transcriptome of Caenorhabditis elegans. (Genome Biology)
47. Kabat et al., 2006. Intronic Alternative Splicing Regulators Identified by Comparative Genomics in Nematodes. (PLoS Computational Biology)
48. Kuroyanagi et al., 2006. Transgenic alternative-splicing reporters reveal tissue-specific expression profiles and regulation mechanisms in vivo. (Nature Methods)
49. Oberstrass et al., 2005. Structure of PTB Bound to RNA: Specific Binding and Implications for Splicing Regulation. (Science)
50. Goodman et al., 2003. Alternative splicing affecting a novel domain in the C. elegans EGL-15 FGF receptor confers functional specificity. (Development)
51. Jin et al., 2003. A vertebrate RNA-binding protein Fox-1 regulates tissue-specific splicing via the pentanucleotide GCAUG. (EMBO)
52. Castillo-Davis et al., 2002. Selection for short introns in highly expressed genes. (Nature Genetics)
53. Farrer et al., 2002. Analysis of the role of Caenorhabditis elegans GC-AG introns in regulated splicing. (NAR)
54. Spike et al., 2002. MEC-8 regulates alternative splicing of unc-52 transcripts in C. elegans hypodermal cells. (Development)
55. Zorio et al., 1999. Both subunits of U2AF recognize the 3' splice site in Caenorhabditis elegans. (Nature)
56. Sibley et al., 1999. Genetic Identification, Sequence, and Alternative Splicing of the Caenorhabditis elegans c 2(IV) Collagen Gene. (JCB)
57. Aroin et al., 1993. Splicing in Caenorhabditis elegans does not require an AG at the 3' splice acceptor site. (Mol Cell Biol)
58. McCombie et al., 1992. Caenorhabditis elegans expressed sequence tags identify gene families and potential disease gene homologues. (Nature Genetics)

1. Yang et al., 2015. RNA-Seq Uncovers SNPs and Alternative Splicing Events in Asian Lotus (Nelumbo nucifera). (PLoS ONE)
2. Huang et al., 2015. Comparative transcriptomics uncovers alternative splicing changes and signatures of selection from maize improvement. (BMC Genomics)
3. Wu et al., 2014. Comprehensive Analysis of Alternative Splicing in Digitalis purpurea by Strand-Specific RNA-Seq. (PLoS ONE)
4. Tack et al., 2014. Transcriptome Analysis Indicates Considerable Divergence in Alternative Splicing Between Duplicated Genes in Arabidopsis thaliana. (Genetics)
5. Thatcher et al., 2014. Genome-Wide Analysis of Alternative Splicing in Zea mays: Landscape and Genetic Regulation. (Plant Cell)
6. Wang et al., 2014. RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications. (BMC Plant Biology)
7. Shen et al., 2014. Global Dissection of Alternative Splicing in Paleopolyploid Soybean. (Plant Cell)
8. Sha et al., 2011. Large-scale sequencing of normalized full-length cDNA library of soybean seed at different developmental stages and analysis of the gene expression profiles based on ESTs. (Molecular Biology Reports)
9. Uwezawa et al., 2008. Sequencing and Analysis of Approximately 40 000 Soybean cDNA Clones from a Full-Length-Enriched cDNA Library. (DNA Research)

1. Xu et al., 2015. Full-length transcriptome sequences and splice variants obtained by a combination of sequencing platforms applied to different root tissues of Salvia miltiorrhiza and tanshinone biosynthesis. (The Plant Journal)
2. Scruggs et al., 2015. Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin. (Molecular Cell)
   Notes: This new study applied the method "Start-seq" to probe transcription start sites.
   
3. Pelechano et al., 2015. Genome-wide identification of transcript start and end sites by transcript isoform sequencing. (Nature Protocols)
4. Busch and Hertel, 2015. Splicing predictions reliably classify different types of alternative splicing. (RNA)
5. Lareau and Brenner, 2015. Regulation of Splicing Factors by Alternative Splicing and NMD Is Conserved between Kingdoms Yet Evolutionarily Flexible. (MBE)
6. Wang et al., 2015. Species-Specific Exon Loss in Human Transcriptomes. (MBE)
7. Mele et al., 2015. The human transcriptome across tissues and individuals. (Science)
8. Rivas et al., 2015. Effect of predicted protein-truncating genetic variants on the human transcriptome. (Science)
9. Merkin et al., 2015. Origins and Impacts of New Mammalian Exons. (Cell Reports)
10. Abubucker et al., 2014. Identification and characterization of alternative splicing in parasitic nematode transcriptomes. (Parasites and Vectors)
11. Brown et al., 2014. Diversity and dynamics of the Drosophila transcriptome. (Nature)
12. Chen et al., 2014. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. (Genome Research)
13. Gerstein et al., 2014. Comparative analysis of the transcriptome across distant species. (Nature)
14. Tilgner et al., 2014. Defining a personal, allele-specific, and single-molecule long-read transcriptome. (PNAS)
15. Au and Sebastiano, 2014. The transcriptome of human pluripotent stem cells. (Current Opinion in Genetics and Development)
16. Schreiner et al., 2014. Targeted Combinatorial Alternative Splicing Generates Brain Region-Specific Repertoires of Neurexins. (Neuron)
17. Treutlein et al., 2014. Cartography of neurexin alternative splicing mapped by single-molecule long-read mRNA sequencing. (PNAS)
    Notes: Evaluated the value of PacBao sequencing in constructing full-length transcripts.
    
18. Adadey, 2014. Analysis of coordinated skipped exon pairs using single molecule sequencing technology. (MIT Ph.D. thesis)
    Notes: Applied PacBio SMRT sequencing technology to capture full-length transcripts. Focused on identifying correlated exon skipping.
    
19. Xiong et al., 2014. The human splicing code reveals new insights into the genetic determinants of disease. (Science)
    News and views: Guigo and Valcarcel, 2014. Prescribing splicing. (Science)
    
20. Wang et al., 2014. Alternative splicing at GYNNGY 5' splice sites: more noise, less regulation. (NAR)
21. Marinov et al., 2014. From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing. (Genome Research)
    Notes: This work applied SMRT sequencing technology.
    
22. Hamid and Makeyev, 2014. Regulation of mRNA abundance by polypyrimidine tract-binding protein-controlled alternate 5' splice site choice. (PLoS Genetics)
23. Szafranski et al., 2014. Physiological state co-regulates thousands of mammalian mRNA splicing events at tandem splice sites and alternative exons. (NAR)
24. Sharon et al., 2013. A single-molecule long-read survey of the human transcriptome. (Nature Biotechnology)
25. Ubby et al., 2013. TMEM16A alternative splicing coordination in breast cancer. (Molecular Cancer)
26. Rodriguez et al., 2013. APPRIS: annotation of principal and alternative splice isoforms. (NAR)
27. Barbosa-Morais et al., 2012. The Evolutionary Landscape of Alternative Splicing in Vertebrate Species. (Science)
28. Merkin et al., 2012. Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues. (Science)
29. Trapnell et al., 2013.Differential analysis of gene regulation at transcript resolution with RNA-seq. (Nature Biotechnology)
30. Bradley et al., 2012. Alternative Splicing of RNA Triplets Is Often Regulated and Accelerates Proteome Evolution. (PLoS Biology)
31. Anders et al., 2012. Detecting differential usage of exons from RNA-seq data. (Genome Research)
32. Gurskaya et al., 2012. Analysis of alternative splicing of cassette exons at single-cell level using two fluorescent proteins. (NAR)
33. Graveley et al., 2011. The developmental transcriptome of Drosophila melanogaster. (Nature)
34. Cherbas et al., 2011. The transcriptional diversity of 25 Drosophila cell lines. (Genome Research)
35. Luco et al., 2010. Regulation of Alternative Splicing by Histone Modifications. (Science)
36. Barash et al., 2010. Deciphering the splicing code. (Nature)
37. Core et al., 2008. Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters. (Science)
    Notes: Gene Expression--Where to Start? (Science)
    Notes: This study described a new method called GRO-seq.
38. Wang et al., 2008. Alternative isoform regulation in human tissue transcriptomes. (Nature)
    Notes: This is a comprehensive study of alternative splicing in human. 92-94% of human genes undergo alternative splicing, 86% with minor isoform frequency of 15% or more.
    
39. Castle et al., 2008. Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines. Nature Genetics.
40. Zhou and Lou, 2008. Repression of Prespliceosome Complex Formation at Two Distinct Steps by Fox-1/Fox-2 Proteins. (Mol Cell Biol)
41. Yeo et al., 2007. Discovery and Analysis of Evolutionarily Conserved Intronic Splicing Regulatory Elements. (PLoS Genetics)
42. Ule et al., 2006. An RNA map predicting Nova-dependent splicing regulation. (Nature)
43. Zhang and Chasin, 2006. Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons. (PNAS)
44. Fededa et al., 2005. A Polar Mechanism Coordinates Different Regions of Alternative Splicing within a Single Gene. (Molecular Cell)
    Notes: Described a case of coordinated alternative splicing.
    
45. Graveley, 2005. Mutually Exclusive Splicing of the Insect Dscam Pre-mRNA Directed by Competing Intronic RNA Secondary Structures. (Cell)
    Preview: Smith, 2005. Alternative Splicing! When Two is a Crowd. (Cell)
    
46. Ohler et al., 2005. Recognition of Unknown Conserved Alternatively Spliced Exons. (PLoS Computational Biology)
47. Hiller 2004. Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity. (Nature Genetics)
48. Yeo et al., 2004. Variation in alternative splicing across human tissues. (Genome Biology)
49. Modrek and Lee, 2003. Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. (Nature Genetics)
50. Johnson et al., 2003. Genome-Wide Survey of Human Alternative Pre-mRNA Splicing with Exon Junction Microarrays. (Science)
51. Sorek and Ast, 2003. Intronic Sequences Flanking Alternatively Spliced Exons Are Conserved Between Human and Mouse. (Genome Research)
52. Fairbrother et al., 2002. Predictive Identification of Exonic Splicing Enhancers in Human Genes. (Science)
53. Schmucker et al., 2000. Drosophila Dscam Is an Axon Guidance Receptor Exhibiting Extraordinary Molecular Diversity. (Cell)

1. Trinity, 2013. A Tutorial: De novo RNA-Seq Assembly and Analysis Using Trinity and EdgeR. (Online Protocol)
2. Haas et al., 2013. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. (Nature Protocol)
   Notes: This article desicrbed step-by-step procedure for running Trinity, a de novo transcriptome assembly program.
   
3. Trapnell et al., 2012. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. (Nature Protocols)
   Notes: This articles describes a protocol how to use the popular reference-based transcriptome assembly program suite called Tuxedo.
   
4. Grabherr et al., 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. (Nature Biotechnology)
   Notes: Described a popular de novo transcriptome assembly program program Trinity, which consists of three programs: Inchworm, Chrysalis, and Butterfly.