TY - JOUR AU - Wang, E. AU - Sandberg, R. AU - Luo, S. AU - Khrebtukova, I. AU - Zhang, L. AU - Mayr, C. PY - 2008 DA - 2008// TI - Alternative isoform regulation in human tissue transcriptomes JO - Nature VL - 456 UR - https://doi.org/10.1038/nature07509 DO - 10.1038/nature07509 ID - Wang2008 ER - TY - JOUR AU - Pan, Q. AU - Shai, O. AU - Lee, L. AU - Frey, B. AU - Blencowe, B. PY - 2008 DA - 2008// TI - Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing JO - Nat Genet VL - 40 UR - https://doi.org/10.1038/ng.259 DO - 10.1038/ng.259 ID - Pan2008 ER - TY - JOUR AU - Graveley, B. PY - 2001 DA - 2001// TI - Alternative splicing: Increasing diversity in the proteomic world JO - Trends in Genet VL - 17 UR - https://doi.org/10.1016/S0168-9525(00)02176-4 DO - 10.1016/S0168-9525(00)02176-4 ID - Graveley2001 ER - TY - JOUR AU - Martin, J. AU - Wang, Z. PY - 2011 DA - 2011// TI - Next-generation transcriptome assembly JO - Nature Rev Genet VL - 12 UR - https://doi.org/10.1038/nrg3068 DO - 10.1038/nrg3068 ID - Martin2011 ER - TY - JOUR AU - Trapnell, C. AU - Williams, B. AU - Pertea, G. AU - Mortazavi, A. AU - Kwan, G. AU - van Baren, M. PY - 2010 DA - 2010// TI - Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation JO - Nat Biotechnol VL - 28 UR - https://doi.org/10.1038/nbt.1621 DO - 10.1038/nbt.1621 ID - Trapnell2010 ER - TY - JOUR AU - Guttman, M. AU - Garber, M. AU - Levin, J. AU - Donaghey, J. AU - Robison, J. AU - Adiconis, X. PY - 2010 DA - 2010// TI - Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs JO - Nat Biotechnol VL - 28 UR - https://doi.org/10.1038/nbt.1633 DO - 10.1038/nbt.1633 ID - Guttman2010 ER - TY - JOUR AU - Li, W. AU - Feng, J. AU - Jiang, T. PY - 2011 DA - 2011// TI - IsoLasso: a LASSO regression approach to RNA-Seq based transcriptome assembly JO - J Comput Biol VL - 18 UR - https://doi.org/10.1089/cmb.2011.0171 DO - 10.1089/cmb.2011.0171 ID - Li2011 ER - TY - JOUR AU - Li, J. AU - Jiang, C. AU - Brown, J. AU - Huang, H. AU - Bickel, P. PY - 2011 DA - 2011// TI - Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation JO - Proc Natl Acad Sci USA VL - 108 UR - https://doi.org/10.1073/pnas.1113972108 DO - 10.1073/pnas.1113972108 ID - Li2011 ER - TY - JOUR AU - Florea, L. AU - Di Francesco, V. AU - Miller, J. AU - Turner, R. AU - Yao, A. AU - Harris, M. PY - 2005 DA - 2005// TI - Gene and alternative splicing annotation with AIR JO - Genome Res VL - 15 UR - https://doi.org/10.1101/gr.2889405 DO - 10.1101/gr.2889405 ID - Florea2005 ER - TY - JOUR AU - Heber, S. AU - Alekseyev, M. AU - Sze, S. H. AU - Tang, H. AU - Pevzner, P. PY - 2002 DA - 2002// TI - Splicing graphs and EST assembly prroblem JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.suppl_1.S181 DO - 10.1093/bioinformatics/18.suppl_1.S181 ID - Heber2002 ER - TY - JOUR AU - Trapnell, C. AU - Hendrickson, D. G. AU - Savageau, M. AU - Goff, L. AU - Rinn, J. L. AU - Pachter, L. PY - 2013 DA - 2013// TI - Differential analysis of gene regulation at transcript resolution with RNA-seq JO - Nat Biotechnol VL - 31 UR - https://doi.org/10.1038/nbt.2450 DO - 10.1038/nbt.2450 ID - Trapnell2013 ER - TY - JOUR AU - Li, B. AU - Dewey, C. PY - 2011 DA - 2011// TI - RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome JO - BMC Bioinformatics VL - 12 UR - https://doi.org/10.1186/1471-2105-12-323 DO - 10.1186/1471-2105-12-323 ID - Li2011 ER - TY - JOUR AU - Feige, U. PY - 1998 DA - 1998// TI - A threhshold of ln n for approximating Set Cover JO - J ACM VL - 45 UR - https://doi.org/10.1145/285055.285059 DO - 10.1145/285055.285059 ID - Feige1998 ER - TY - JOUR AU - Wheeler, D. AU - Church, D. AU - Federhen, S. AU - Lash, A. AU - Madden, T. AU - Pontius, J. PY - 2003 DA - 2003// TI - Database resources of the National Center for Biotechnology JO - Nucl Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg033 DO - 10.1093/nar/gkg033 ID - Wheeler2003 ER - TY - CHAP AU - Florea, L. AU - Song, L. AU - Salzberg, S. L. PY - 2013 DA - 2013// TI - Thousands of novel exon skipping events discovered in transcripts from sixteen human tissues BT - BMC Genomics ID - Florea2013 ER - TY - JOUR AU - Griebel, T. AU - Zacher, B. AU - Ribeca, P. AU - Raineri, E. AU - Lacroix, V. AU - Guigisó, R. PY - 2012 DA - 2012// TI - Modelling and simulating generic RNA-Seq experiments with the flux simulator JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gks666 DO - 10.1093/nar/gks666 ID - Griebel2012 ER - TY - JOUR AU - Trapnell, C. AU - Pachter, L. AU - Salzberg, S. PY - 2009 DA - 2009// TI - TopHat: discovering splice junctions with RNA-Seq JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp120 DO - 10.1093/bioinformatics/btp120 ID - Trapnell2009 ER -