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Method: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification
- Manuel Tardaguila,
- Lorena de la Fuente,
- Cristina Marti,
- Cécile Pereira,
- Francisco Jose Pardo-Palacios,
- Hector del Risco,
- Marc Ferrell,
- Maravillas Mellado,
- Marissa Macchietto,
- Kenneth Verheggen,
- Mariola Edelmann,
- Iakes Ezkurdia,
- Jesus Vazquez,
- Michael Tress,
- Ali Mortazavi,
- Lennart Martens,
- Susana Rodriguez-Navarro,
- Victoria Moreno-Manzano,
- and Ana Conesa
Genome Res. March 2018 28: 396-411; Published in Advance February 9, 2018, doi:10.1101/gr.222976.117
...transcripts, even in well-annotated mammalian species. The advances in sequencing technology have created a need for studies and tools that can characterize these novel variants. Here, we present SQANTI, an automated pipeline for the classification of long-read transcripts that can assess the quality of data...
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LETTER: Clustering of DNA Sequences in Human Promoters
- Peter C. FitzGerald,
- Andrey Shlyakhtenko,
- Alain A. Mir,
- and Charles Vinson
Genome Res. August 2004 14: 1562-1574; Published in Advance July 15, 2004, doi:10.1101/gr.1953904
...a core promoter requirement for cAMP responsiveness. Mol. Cell 11 : 1101 –1108. ↵ Davuluri, R.V., Suzuki, Y., Sugano, S., and Zhang, M.Q. 2000 . CART classification of human 5′ UTR sequences. Genome Res. 10 : 1807 –1816. ↵ Dynan, W.S. and Tjian, R. 1985 . Control of eukaryotic messenger RNA synthesis...
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Research: Conserved non-AUG uORFs revealed by a novel regression analysis of ribosome profiling data
- Pieter Spealman,
- Armaghan W. Naik,
- Gemma E. May,
- Scott Kuersten,
- Lindsay Freeberg,
- Robert F. Murphy,
- and Joel McManus
Genome Res. February 2018 28: 214-222; Published in Advance December 18, 2017, doi:10.1101/gr.221507.117
...Bioinformatics 8: 295. ↵Davuluri RV, Suzuki Y, Sugano S, Zhang MQ. 2000. CART classification of human 5′ UTR sequences. Genome Res 10: 1807–1816. ↵Dujon B. 2006. Yeasts illustrate the molecular mechanisms of eukaryotic evolution. Trends Genet 22: 375–387. ↵Edgar RC. 2004. MUSCLE: multiple sequence alignment...
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Methods: A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data—A case study using E2F1
- Victor X. Jin,
- Alina Rabinovich,
- Sharon L. Squazzo,
- Roland Green,
- and Peggy J. Farnham
Genome Res. December 2006 16: 1585-1595; Published in Advance October 19, 2006, doi:10.1101/gr.5520206
...that were found at a higher frequency near the E2F1 PWMs in the E2F1 target promoter set than near the E2F1 PWMs in the nontarget set, using a P -value &lt; 0.05. These PWMs were then used as predictor variables to construct a classification and regression tree (CART) model. For each Δ value, we constructed...
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LETTER: Distribution and Characterization of Regulatory Elements in the Human Genome
- Jacek Majewski and
- Jurg Ott
Genome Res. December 1, 2002 12: 1827-1836; doi:10.1101/gr.606402
.... Opin. Genet. Dev. 5 : 309 – 314 . ↵ Davuluri R.V. , Suzuki Y. , Sugano S. , Zhang M.Q. ( 2000 ) CART classification of human 5′ UTR sequences. Genome Res. 10 : 1807 – 1816 . ↵ Deutsch M. , Long M. ( 1999 ) Intron-exon structures of eukaryotic model organisms. Nucleic Acids Res. 27 : 3219 – 3228...
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LETTER: Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches
- Victor X. Jin,
- Henriette O’Geen,
- Sushma Iyengar,
- Roland Green,
- and Peggy J. Farnham
Genome Res. June 2007 17: 807-817; doi:10.1101/gr.6006107
...classification, we defined the regions as upstream of a gene (between −100 kb and +1), overlapping with the transcription start site, within a transcribed region (without distinguishing between exons and introns), and within 100 kb downstream from the 3′-UTR (Supplemental Fig. 3A). If a site fell in between two...
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LETTER: The mouse genome: Experimental examination of gene predictions and transcriptional start sites
- Sujit Dike,
- Vivekanand S. Balija,
- Lidia U. Nascimento,
- Zhenyu Xuan,
- Jacqueline Ou,
- Theresa Zutavern,
- Lance E. Palmer,
- Greg Hannon,
- Michael Q. Zhang,
- and W. Richard McCombie
Genome Res. December 2004 14: 2424-2429; doi:10.1101/gr.3158304
...., Sasaki, D., et al. 2003 . Targeting a complex transcriptome: The construction of the mouse full-length cDNA encyclopedia. Genome Res. 13 : 1273 -1289. ↵ Davuluri, R.V., Suzuki, Y., Sugano, S., and Zhang, M.Q. 2000 . CART classification of human 5′ UTR sequences. Genome Res. 10 : 1807 -1816. ↵ Davuluri, R...
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REVIEW: Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques
- Laura Elnitski,
- Victor X. Jin,
- Peggy J. Farnham,
- and Steven J.M. Jones
Genome Res. December 2006 16: 1455-1464; Published in Advance October 19, 2006, doi:10.1101/gr.4140006
...of a weight matrix model, which incorporates prior knowledge of PWMs, with statistical classification methods to identify the TFBSs. To illustrate this point, a CART model ( c lassification a nd r egression t ree) has been used to identify estrogen receptor α target genes ( Jin et al. 2004 ), and a MARS model...
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ARTICLE: The Genexpress Index: a resource for gene discovery and the genic map of the human genome.
- R Houlgatte,
- R Mariage-Samson,
- S Duprat,
- A Tessier,
- S Bentolila,
- B Lamy,
- and C Auffray
Genome Res. October 1995 5: 272-304; doi:10.1101/gr.5.3.272
...signatures over 5750 distinct human gene transcripts. About half of these genes have been assigned to specific chromosomes utilizing 2733 eSTS markers, the polymerase chain reaction, and DNA from human-rodent somatic cell hybrids. Sequence and clone clustering and a functional classification together...

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