Yang EW, Bahn JH, Hsiao EY, Tan BX, Sun Y, Fu T, Zhou B, Van Nostrand EL, Pratt GA, Freese P, Wei X, Quinones-Valdez G, Urban AE, Graveley BR, Burge CB, Yeo GW, Xiao X. Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA. Nat Commun. 2019 Mar 22;10(1):1338. doi: 10.1038/s41467-019-09292-w.
Gonen N, Sabath N, Burge CB, Shalgi R. Widespread PERK-dependent repression of ER targets in response to ER stress. Sci Rep. 2019 Mar 13;9(1):4330. doi: 10.1038/s41598-019-38705-5.
Rohani N, Hao L, Alexis MS, Joughin BA, Krismer K, Moufarrej MN, Soltis AR, Lauffenburger DA, Yaffe MB, Burge CB, Bhatia SN, Gertler FB. Acidification of tumor at stromal boundaries drives transcriptome alterations associated with aggressive phenotypes. Cancer Res. 2019 Feb 12. pii: canres.1604.2018. doi: 10.1158/0008-5472.CAN-18-1604.
2018
Sudmant P, Lee H, Dominguez D, Heiman M, Burge CB (2018) Widespread Accumulation of Ribosome Associated Isolated 3' UTRs in Neuronal Cell Populations of the Aging Brain . Cell Reports. Volume 25 Issue 9, 27 November 2018, Pages 2447-2456. e4 (Open Access)
Pai AA, Paggi JM, Yan P, Adelman K, and Burge CB. Numerous recursive sites contribute to accuracy of splicing in long introns in flies. PLoS Genet 14(8): e1007588. (Open Access)
Dominguez D, Freese P, Maria Alexis M, Su A, Hochman M, Palden T, Bazile C, Lambert NJ, Van Nostrand EL, Pratt GA, Yeo GW, Graveley BR, and Burge CB (2018).
Sequence, Structure, and Context Preferences of Human RNA Binding Proteins. Mol. Cell 70, 854-867. (Open Access)
Murphy PA, Butty VL, Boutz PL, Begum S, Kimble AL, Sharp PA, Burge CB, Hynes RO. (2018).
Alternative RNA splicing in the endothelium mediated in part by Rbfox2 regulates the arterial response to low flow.
eLife e29494.
2017
Vidaki M, Drees F, Saxena T, Lanslots E, Taliaferro MJ, Tatarakis A, Burge CB, Wang ET, Gertler FB. (2017).
A Requirement for Mena, an Actin Regulator, in Local mRNA Translation in Developing Neurons.
Neuron 95(3):608-622.
Pai AA, Henriques T, McCue K, Burkholder A, Adelman K and Burge CB. (2017). The Kinetics of pre-mRNA splicing in the Drosphila genome and the influence of gene architecture. eLife e32537.
2016
Conway AE, Van Nostrand EL, Pratt GA, Aigner S, Wilbert ML, Sundararaman B, Freese P, Lambert NJ, Sathe S, Liang TY, Essex A, Landais S, Burge CB, Jones DL, Yeo GW. Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival. Cell reports, 15, 666-679, 2016.
Kapeli K, Pratt GA, Vu AQ, Hutt KR, Martinez FJ, Sundararaman B, Batra R, Freese P, Lambert NJ, Huelga SC, Chun SJ, Liang TY, Chang J, Donohue JP, Shiue L, Zhang J, Zhu H, Cambi F, Kasarskis E, Hoon S, Ares MJr, Burge CB, Ravits J, Rigo F, Yeo GW. Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses. Nature communications, 7, 12143, 2016.
Pai AA, Baharian G, Page Sabourin A, Brinkworth JF, Nedelec Y, Foley JW, Grenier JC, Siddle KJ, Dumaine A, Yotova V, Johnson Z, Landford RE, Burge CB, Barreiro LB, (2016) Widespread Shortening of 3' Untranslated Regions and Increased Exon Inclusion Are Evolutionarily Conserved Features of Innate Immune Responses to Infection. PLoS Genet 12(9): e1006338. doi:10.1371/journal.pgen.1006338
Martinez FJ, Pratt GA, Van Nostrand EL, BatraR, Huelga SC, Kapeli K, Freese P, Chun SJ, Ling K, Gelboin-Burkhart C, Fijany L, Wang HC, Nussbacher JK, Broski SM, Kim HJ, Lardelli R, Sundararaman B, Donohue JP, Javaherian A, Lykke-Andersen J, Finkbeiner S, Bennett F, Ares M, Burge CB, Taylor JP, Rigo F, Yeo GW, (2016) Protein-RNA Networks Regulated by Normal andALS-Associated Mutant HNRNPA2B1 in the NervousSystem Neuron 92, 1–16 http://dx.doi.org/10.1016/j.neuron.2016.09.050
Taliaferro JM, Lambert NJ, Sudmant PH, Dominguez D, Merkin JJ, Alexis MS, Bazile C, Burge CB (2016). RNA sequence context effects measured in vitro predict in vivo protein binding and regulation. Mol Cell 2016 Oct 20;64(2):294-306. doi: 10.1016/j.molcel.2016.08.035. Epub 2016 Oct 6.
Gould G, Paggi J, Yuchun G, Phizicky D, Zinshteyn B, Wang ET, Gilbert W, Gifford D, Burge CB. (2016). Identification of new branch points and unconventional introns in saccharomyces cerevisiae. Published in Advance, RNA 2016. 10.1261/rna.057216.116
Taliaferro JM, Vidaki M, Oliveira R, Olson S, Zhan L, Saxena T, Wang ET, Graveley BR, Gertler FB, Swanson MS, Burge CB. (2016). Distal alternative last exons localize mRNAs to neural projections. Mol. Cell 62, 1-13. doi: 10.1016/j.molcel.2016.01.020. Epub 2016 Feb 18.
2015
Sudmant PH, Alexis MS, Burge CB. (2015). Meta-analysis of RNA-seq expression data across species, tissues and studies. Genome Biol. 16, 287.
Wang ET, Ward AJ, Cherone J, Wang TT, Giudice J, Treacy D, Freese P, Lambert NJ, Saxena T, Cooper TA, Burge CB. (2015). Antagonistic regulation of mRNA expression and splicing by CELF and MBNL proteins. Genome Res. 25, 858-71.
Merkin JJ, Chen P, Alexis MS Hautaniemi SK, Burge CB (2015). Origins and impacts of new mammalian exons. Cell Reports 10, 1-14.(Open Access)
Katz Y, Wang ET, Silterra J, Schwartz S, Wong B, Thorvaldsdottir H, Robinson JT, Mesirov JP, Airoldi EM, Burge CB (2015). Quantitative visualization of alternative exon expression from RNA-seq data. Bioinformatics. pii: btv034 (Pub ahead of print)
2014
Katz Y, Li F, Lambert N, Sokol E, Tam WL, Cheng A, Airoldi E, Lengner C, Gupta P, Yu Z, Jaenisch R, Burge C. (2014). Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state eLife 2014;10.7554/eLife.03915
Taliaferro JM, Wang ET, Burge CB (2014). Genomic analysis of mRNA localization. RNA Biol 11, 1040-50. (Review).
Cheng AW, Shi J, Wong P, Luo KL, Trepman P, Wang ET, Choi H, Burge CB, Lodish HF (2014). Muscleblind-like 1 (Mbnl1) regulates pre-mRNA alternative splicing during terminal erythropoiesis. Blood 124:598-610.
Aijö T, Butty V, Chen Z, Salo V, Tripathi S, Burge CB, Lahesmaa R, Lähdesmäki H. (2014). Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation. Bioinformatics 30, 1113-1120.
Shalgi R, Hurt JA, Lindquist S, Burge CB. (2014). Widespread Inhibition of Posttranscriptional Splicing Shapes the Cellular Transcriptome following Heat Shock. Cell Reports 7, 1362-70.
Lambert N, Robertson A, Jangi M, McGeary S, Sharp PA, Burge CB. (2014). RNA Bind-n-Seq: Quantitative Assessment of the Sequence and Structural Binding Specificity of RNA Binding Proteins. Mol. Cell 54, 887-900.
Giudice J, Xia Z, Wang ET, Scavuzzo MA, Ward AJ, Kalsotra A, Wang W, Wehrens XH, Burge CB, Li W, Cooper TA. (2014). Alternative splicing regulates vesicular trafficking genes in cardiomyocytes during postnatal heart development. Nature Commun. 5:3603.
Spies N, Burge CB, Bartel DP. (2013). 3' UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts. Genome Res. 23, 2078-90.
Almada AE, Wu X, Kriz AJ, Burge CB, Sharp PA. (2013). Promoter directionality is controlled by U1 snRNP and polyadenylation signals. Nature 499, 360-3.
Han H, Irimia M, Ross PJ, Sung HK, Alipanahi B, David L, Golipour A, Gabut M, Michael IP, Nachman EN, Wang E, Trcka D, Thompson T, O'Hanlon D, Slobodeniuc V, Barbosa-Morais NL, Burge CB, Moffat J, Frey BJ, Nagy A, Ellis J, Wrana JL, Blencowe BJ. (2013). MBNL proteins repress ES-cell-specific alternative splicing and reprogramming. Nature 498, 241-45.
Hurt JA, Robertson DA, Burge CB. (2013). Global analyses of UPF1 binding and function reveals expanded scope of nonsense-mediated mRNA decay. Genome Res. 23, 1636-50.
Ji, X, Zhou, Y, Pandit, S, Huang, J, Li, H, Lin, CY., Xiao, ., Burge, CB, and Fu, X-D. (2013). SR Proteins Collaborate with 7SK and Promoter-Associated Nascent RNA to Release Paused Polymerase. Cell 153, 855-868.
Klattenhoff CA, Scheuermann JC, Surface LE, Bradley RK, Fields PA, Steinhauser ML,Ding H,Butty VL, Torrey L, Haas S, Abo R, Tabebordbar M, Lee RT, Burge CB, and Boyer LA. (2013). Braveheart, a Long Noncoding RNA Required for CardiovascularLineage Commitment. Cell 152, 1-14.
Shalgi R, Hurt JA, Krykbaeva I, Taipale M, Lindquist S, Burge CB. (2013). Widespread regulation of translation by elongation pausing in heat shock. Mol. Cell 49, 439-452.
Wang Y, Xiao X, Zhang J, Choudhury R, Robertson A, Li K, Ma M, Burge CB, Wang Z. (2013). A complex network of factors with overlapping affinities represses splicing through intronic elements. NSMB 20, 36-45.
2012
Merkin J, Russell C, Chen P, Burge CB. (2012). Evolutionary dynamics of gene and isoform regulation in mammalian tissues. Science 338, 1593-9. Abstract Reprint Full Text
Loven J, Orlando DA, Sigova AA, Lin CY, Rahl PB, Burge CB, Levens DL, Lee TI, Young RA. (2012). Revisiting global gene expression analysis. Cell 151, 476-482. (Primer).
Lin CY, Lovén J, Rahl PB, Paranal RM, Burge CB, Bradner JE, Lee TI, Young RA. (2012). Transcriptional Amplification in Tumor Cells with Elevated c-Myc. Cell 151, 56-67.
Wang ET, Cody NA, Jog S, Biancollela M, Wang TT, Treacy DJ, Luo S, Schroth GP, Housman DE, Reddy S, Lécuyer E, Burge CB. (2012). Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins. Cell 150, 710-724. PMCID: PMC3428802
Anderson, ES, Lin, CH, Xiao, X, Stoilov, P, Burge, CB, Black, DL. (2012). The cardiotonic steroid digitoxin regulates alternative splicing through depletion of the splicing factors SRSF3 and TRA2B. RNA 18, 1041-9. Open Access
Bradley, RK, Merkin, J, Lambert, NJ, Burge, CB. (2012). Alternative Splicing of RNA Triplets is Often Regulated and Accelerates Proteome Evolution. PLoS Biol. 10, e1001229. Open Access
2011
Zheng, G X.Y, Ravi, A., Gould, GM, Burge, CB, Sharp, PA. (2011). Genome-Wide Impact of A Recently Expanded MicroRNA Cluster in Mouse. PNAS USA 108, 15804-9.
Shapiro IM, Cheng AW, Flytzanis NC, Balsamo M, Condeelis JS, Oktay MH, Burge CB and Gertler FB. (2011). An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype. PLoS Genet. 7, e1002218. Open Access
Nutiu R, Friedman RC, Luo S, Khrebtukova I, Silva D, Li R, Zhan L, Schroth GP, Burge CB. (2011). Direct visualization of DNA affinity landscapes using a sequencing instrument. Nature Biotech. 29, 659-664.
Zheng GXY, Ravi A, Calabrese JM, Medeiros LA, Kirak O, Dennis L, Jaenisch R, Burge CB, Sharp PA. (2011). A Latent Pro-survival Function for the Mir-290-295 Cluster in Mouse Embryonic Stem Cells. PLoS Genet. 7(5):e1002054. Full Text
Bandyopadhyay S, Friedman RC, Marquez RT, Keck K, Kong B, Icardi MS, Brown, KE, Burge CB, Schmidt W, Wang Y, McCaffrey AP. (2011). Hepatitis C Virus Infection and Hepatic Stellate Cell Activation Down-regulate miR-29: miR-29 Over-expression Reduces Hepatitis C Viral Abundance In Culture. J. Infectious Disease 203, 1753-1762.
2010
Bland CS, Wang ET, Vu A, David MP, Castle JC, Johnson JM, Burge CB, Cooper TA. (2010). Global regulation of alternative splicing during myogenic differentiation. Nucleic Acids Res. 38, 7651-64.
Katz Y, Wang ET, Airoldi EM, Burge CB. (2010). Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nature Methods 7, 1009-1015 .
Ramskold D, Wang ET, Burge CB, Sandberg R. (2009). An abundance of ubuquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comp Biol 5:e1000598.
Spies N, Nielsen CB, Padgett RA, Burge CB. (2009). Biased chromatin signatures around polyadenylation sites and exons. Mol Cell 36, 245-254. Full Texte Full Text at Mol Cell
Xiao X, Wang Z, Jang M, Nutiu R, Wang ET, Burge CB. (2009). Splice site strength–dependent activity and genetic buffering by poly-G runs. Nature Struct Mol Biol 16, 1094-1100.
Friedman, RC, Farh KK, Burge, CB, Bartel, DP. (2009). Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 19, 92-105. Open Access.
2008
Kalsotra, A, Xiao X, Ward A, Castle J, Johnson JM., Burge CB, Cooper TA. (2008). A post natal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart. PNAS 105, 20333-20338.
Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. (2008). Alternative Isoform Regulation in Human Tissue Transcriptomes. Nature 456, 470-476. Full Text
Friedman BA, Stadler MB, Shomron N, Ding Y, Burge CB. (2008). Ab initio identification of functionally interacting pairs of cis-regulatory elements. Genome Research 18, 1643-1651.
Sandberg R, Neilson JR, Sarma A, Sharp PA, Burge CB. (2008). Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites. Science 320, 1643-1647. AbstractxtFull Text
Wang Z, Burge CB. (2008). Splicing regulation: From a parts list of regulatory elements to an integrated splicing code. RNA 14, 802-813.
Boyerinas B, Park S-M, Shomron N, Hedegaard MM, Vinther J, Andersen JS, Feig C, Xu J, Burge CB, Peter, ME. (2008). Identification of let-7 regulated oncofetal genes. Cancer Res. 68, 2587-2591.
2007
Xiao X., Wang Z., Jang M. and Burge CB. (2007). Coevolutionary Networks of Splicing cis-Regulatory Elements. PNAS104, 18583-18588.
Nielsen CB, Shomron N, Sandberg R, Hornstein E, Burge C.B. (2007). Determinants of Targeting by Endogenous and Exogenous MicroRNAs and siRNAs. RNA 13, 1894-1910.
Giorgi C, Yeo GW, Stone ME, Katz DB, Burge C, Turrigiano G, Moore MJ. (2007). The EJC Factor eIF4AIII Modulates Synaptic Strength and Neuronal Protein Expression. Cell 130, 179-91.
Neilson, JR, Zheng, GXY., Burge, CB, Sharp, PA. (2007). Dynamic regulation of miRNA expression in ordered stages of cellular development.Genes Dev. 21, 578-89.
Ruvinsky I, Ohler U, Burge CB, Ruvkun, G.
(2007). Detection of broadly expressed neuronal genes in C. elegans. Dev. Biol. 302, 617-626.
Ibrahim EC, Hims MM, Shomron N,
Burge CB, Slaugenhaupt SA, Reed R. (2007). Weak Definition of IKBKAP exon 20 leads to aberrant
splicing in familial dysautonomia.Hum Mutat. 28, 41-53.
2006
Stadler M B, Shomron N, Yeo G,
Schneider A, Xiao X, Burge CB. (2006). Inference of Splicing Regulatory Activities
by Sequence Neighborhood Analysis. PLoS Genet.2, e191.
Wang Z, Xiao X, Van Nostrand E,
Burge CB. (2006). General and specific functions of exonic splicing silencers in splicing
control. Mol. Cell23, 61-70.
Yahyanejad M, Burge CB, Kardar M. (2006). Untangling
influences of hydrophobicity on protein sequences and structures. Proteins62, 1101-6.
Holste D, Huo G, Tung V,
Burge CB. (2006). HOLLYWOOD: a comparative relational database of alternative
splicing.Nucl. Acids Res.34, D56-62.
2005
Farh KK, Grimson A, Jan C, Lewis
BP, Johnston WK, Lim LP, Burge CB, Bartel DP (2005). The widespread
impact of mammalian microRNAs on mRNA repression and evolution.Science310, 1817-1821.
Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD. (2005). A transcriptional response to replication
status mediated by the conserved bacterial replication protein DnaA. PNAS
102, 12932-12937. PDF (Open Access).
Han K, Yeo G, An P, Burge CB, Grabowski PJ. (2005). A combinatorial code for splicing silencing: UAGG and
GGGG motifs. PLoS Biol.3, e158. PDF (Open Access).
Lewis BP, Burge CB, Bartel DP. (2005). Conserved seed pairing, often flanked by adenosines, indicates
that thousands of human genes are microRNA targets. Cell120,
15-20.
Ohler U, Shomron, N, Burge, CB. (2005). Recognition of unknown conserved alternatively spliced exons. PLoS Comp.
Biol.1, e15:0001-0010. PDF (Open
Access).
Pfarr N, Prawitt D, Kirschfink
M, Schroff C, Knuf M, Habermehl P, Mannhardt W, Zepp F, Fairbrother W,
Loos M, Burge CB, Pohlenz J. (2005). Linking C5 deficiency to an exonic
splicing enhancer mutation. J. Immunol.174, 4172-4177.
Yeo G, Van Nostrand E, Holste
D, Poggio T, Burge CB. (2005). Identification and analysis of alternative
splicing events conserved in human and mouse.Proc. Natl. Acad. Sci. USA
102, 2850-2855.
PDF (Open Access).
Padgett RA, Burge CB. (2005). Splice sites. In: Encyclopedia of Life Sciences.
John Wiley & Sons, Ltd: Chichester http://www.els.net/
2004
Eng L, Coutinho G, Nahas S, Yeo
G, Tanouye R, Babaei M, Dork T, Burge C, Gatti RA. (2004). Nonclassical
splicing mutations in the coding and noncoding regions of the ATM gene: maximum entropy
estimates of splice junction strengths. Hum. Mutat.23, 67-76.
Fairbrother WG, Holste D,
Burge CB, Sharp PA. (2004). Single nucleotide polymorphism-based validation
of exonic splicing enhancers. PLoS Biol.2(9), e268: 1-8. PDF at PLoS Biology web site.
Fairbrother, WG, Yeo G, Yeh
R-F, Goldstein P, Mawson M, Sharp PA, Burge CB. (2004). RESCUE-ESE
identifies candidate exonic splicing enhancers in vertebrate exons.Nucl. Acids
Res.32, W187-W190. PubMed Abstract and links to full text
Nielsen CB*, Friedman B*,
Birren B, Burge CB, Galagan JE. (2004). Patterns of intron gain and loss in
fungi. PLoS Biol.2, e422. PDF (Open Access).
Ohler U, Yekta S, Lim LP,
Bartel DP, Burge CB. (2004). Patterns of flanking sequence conservation and a
characteristic upstream motif for microRNA gene identification.RNA10,
1309-1322.
Seneff S, Wang C, Burge CB. (2004). Gene structure prediction using an orthologous gene of known exon-intron
structure. Appl. Bioinformatics3, 81-90.
Wang Z, Rolish ME, Yeo G,
Tung V, Mawson M, Burge CB. (2004). Systematic identification and analysis of
exonic splicing silencers.Cell119, 831-845.
Yeo G*, Holste D*, Kreiman, G,
Burge CB. (2004). Variation in alternative splicing across human tissues.
Genome Biol.5, R74. PDF (Open
Access).
Yeo G, Hoon S, Venkatesh B,
Burge CB. (2004). Variation in sequence and organization of splicing regulatory
elements in vertebrate genes. Proc. Natl. Acad. Sci. USA101,
15700-15705. PDF (Open Access).
Yeo G, Burge CB. (2004).
Maximum entropy modeling of short sequence motifs with applications to RNA splicing
signals.J. Comp. Biol.11, 377-394.
* These authors contributed
equally.
2003
Ambros V, Bartel B, Bartel DP,
Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones
S, Marshall M, Matzke M, Ruvkun G, Tuschl T. (2003). A uniform system for
microRNA annotation. RNA9, 277-279.
Arndt PF, Burge CB, Hwa
T. (2003). DNA sequence evolution with neighbor-dependent mutation. J. Comp.
Biol.10, 313-322.
Katz L, Burge CB. (2003).
Widespread selection for local RNA structure in coding regions of bacterial genes.
Genome Res.13, 2042-2051.
Lewis BP*, Shih I-h*,
Jones-Rhoades MW, Bartel DP, Burge CB. (2003). Prediction of mammalian
microRNA targets.Cell115, 787-798.
Yeo G, Burge CB. (2003).
Maximum entropy modeling of short sequence motifs with applications to RNA splicing
signals. in Proceedings of the 7th Annual International Conference on Computational
Molecular Biology (RECOMB03), W. Miller et al., eds., pp. 322-331 (ACM Press,
New York).
* These authors contributed
equally.
2002
Arndt PF, Burge CB, Hwa T.
(2002). DNA sequence evolution with neighbor-dependent mutation. in Proceedings of the
6th Annual International Conference on Computational Molecular Biology
(RECOMB02), G. Meyer et al., eds., ACM Press, New York, pp. 32-38.
Crollius HR, Jaillon O, Bernot
A, Pelletier E, Dasilva C, Bouneau L, Burge C, Yeh R-F, Quetier F,
Saurin W, Weissenbach J. (2002). Genome-wide comparisons between human and
tetraodon. Ernst Schering Res. Found Workshop 36, 11-29.
Fairbrother W*, Yeh R-F*,
Sharp PA, Burge CB. (2002). Predictive identification of exonic splicing
enhancers in human genes. Science297, 1007-1013. PDF at Science web site.
Burge, CB. (2001). Chipping away at
the transcriptome.Nature Genet.27, 4-6.
Das M*, Burge CB*, Park E.,
Colinas J, Pelletier J. (2001). Assessment of the total number of human
transcription units.Genomics77, 71-78.
International Human Genome
Sequencing Consortium (2001). Initial sequencing and analysis of the human genome.
Nature409, 860-921.
Lim LP, Burge CB. (2001). A computational analysis of sequence features involved in recognition of short introns. Proc. Natl. Acad. Sci. USA98, 1119311198.
Yeh R-F, Lim LP, Burge CB. (2001) Computational inference of homologous gene structures in the human genome. Genome Res.11, 803-816.