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METHODS: Mining SNPs From EST Databases
- Leslie Picoult-Newberg,
- Trey E. Ideker,
- Mark G. Pohl,
- Scott L. Taylor,
- Miriam A. Donaldson,
- Deborah A. Nickerson,
- and Michael Boyce-Jacino
Genome Res. February 1, 1999 9: 167-174; doi:10.1101/gr.9.2.167
...Mining SNPs From EST Databases Leslie Picoult-Newberg 1 , 3 , Trey E. Ideker 2 , Mark G. Pohl 1 , Scott L. Taylor 2 , Miriam A. Donaldson 1 , Deborah A. Nickerson 2 , and Michael Boyce-Jacino 1 1Orchid...
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RESOURCE: A global assembly of cotton ESTs
- Joshua A. Udall,
- Jordan M. Swanson,
- Karl Haller,
- Ryan A. Rapp,
- Michael E. Sparks,
- Jamie Hatfield,
- Yeisoo Yu,
- Yingru Wu,
- Caitriona Dowd,
- Aladdin B. Arpat,
- Brad A. Sickler,
- Thea A. Wilkins,
- Jin Ying Guo,
- Xiao Ya Chen,
- Jodi Scheffler,
- Earl Taliercio,
- Ricky Turley,
- Helen McFadden,
- Paxton Payton,
- Natalya Klueva,
- Randell Allen,
- Deshui Zhang,
- Candace Haigler,
- Curtis Wilkerson,
- Jinfeng Suo,
- Stefan R. Schulze,
- Margaret L. Pierce,
- Margaret Essenberg,
- HyeRan Kim,
- Danny J. Llewellyn,
- Elizabeth S. Dennis,
- David Kudrna,
- Rod Wing,
- Andrew H. Paterson,
- Cari Soderlund,
- and Jonathan F. Wendel
Genome Res. March 2006 16: 441-450; Published in Advance February 14, 2006, doi:10.1101/gr.4602906
...survey of ∼42,000 fiber ESTs based on a single fiber library from diploid G. arboreum (A ) proved extremely useful for identifying genes, and led to the development of a 70-mer oligonucleotide cotton fiber microarray. A more thorough description of the Gossypium transcriptome, involving a wide array...
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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
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RESOURCE: Single Nucleotide Polymorphisms Associated With Rat Expressed Sequences
- Victor Guryev,
- Eugene Berezikov,
- Rainer Malik,
- Ronald H.A. Plasterk,
- and Edwin Cuppen
Genome Res. July 2004 14: 1438-1443; doi:10.1101/gr.2154304
.... ↵ Picoult-Newberg, L., Ideker, T.E., Pohl, M.G., Taylor, S.L., Donaldson, M.A., Nickerson, D.A., and Boyce-Jacino, M. 1999 . Mining SNPs from EST databases. Genome Res. 9 : 167 –174. ↵ Ramensky, V., Bork, P., and Sunyaev, S. 2002 . Human non-synonymous SNPs: Server and survey. Nucleic Acids Res. 30 : 3894...
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Research: RNA editing in the human ENCODE RNA-seq data
- Eddie Park,
- Brian Williams,
- Barbara J. Wold,
- and Ali Mortazavi
Genome Res. September 2012 22: 1626-1633; doi:10.1101/gr.134957.111
...based on data from the GM12878 lymphoblastoid cell line RNA-seq data has been mined for known SNPs in expressed genes to study allele-specific expression (Montgomery et al. 2010). While sequence variants in RNA-seq that are not in the are RNA 5Corresponding author E-mail ali.mortazavi@uci.edu Article...
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Methods: Targeted screening of cis-regulatory variation in human haplotypes
- Dominique J. Verlaan,
- Bing Ge,
- Elin Grundberg,
- Rose Hoberman,
- Kevin C.L. Lam,
- Vonda Koka,
- Joana Dias,
- Scott Gurd,
- Nicolas W. Martin,
- Hans Mallmin,
- Olof Nilsson,
- Eef Harmsen,
- Ken Dewar,
- Tony Kwan,
- and Tomi Pastinen
Genome Res. January 2009 19: 118-127; Published in Advance October 29, 2008, doi:10.1101/gr.084798.108
...and its effect on disease . Nature 452 : 423 – 428 . ↵ Ge, B. , Gurd, S. , Gaudin, T. , Dore, C. , Lepage, P. , Harmsen, E. , Hudson, T.J. , Pastinen, T. ( 2005 ) Survey of allelic expression using EST mining . Genome Res. 15 : 1584 – 1591 . ↵ Gimelbrant, A. , Hutchinson, J.N. , Thompson, B.R. , Chess, A...
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ARTICLE: Allele-specific gene expression patterns in primary leukemic cells reveal regulation of gene expression by CpG site methylation
- Lili Milani,
- Anders Lundmark,
- Jessica Nordlund,
- Anna Kiialainen,
- Trond Flaegstad,
- Gudmundur Jonmundsson,
- Jukka Kanerva,
- Kjeld Schmiegelow,
- Kevin L. Gunderson,
- Gudmar Lönnerholm,
- and Ann-Christine Syvänen
Genome Res. January 2009 19: 1-11; Published in Advance November 7, 2008, doi:10.1101/gr.083931.108
...Allele-specific gene expression patterns in primary leukemic cells reveal regulation of gene expression by CpG site methylation Lili Milani 1 , Anders Lundmark 1 , Jessica Nordlund 1 , Anna Kiialainen 1 , Trond Flaegstad 2 , 8...
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Letter: Exon-trapping mediated by the human retrotransposon SVA
- Dustin C. Hancks,
- Adam D. Ewing,
- Jesse E. Chen,
- Katsushi Tokunaga,
- and Haig H. Kazazian, Jr
Genome Res. November 2009 19: 1983-1991; Published in Advance July 27, 2009, doi:10.1101/gr.093153.109
...performed a computational survey to identify splicing events. We focused on splicing events involving the 228 SVA elements present in intronic regions oriented in the same direction as the surrounding gene. EST databases (Boguski et al. 1993) were mined for uniquely aligned sequences with evidence...
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Methods: Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs
- Bastien Chevreux,
- Thomas Pfisterer,
- Bernd Drescher,
- Albert J. Driesel,
- Werner E.G. Müller,
- Thomas Wetter,
- and Sándor Suhai
Genome Res. June 2004 14: 1147-1159; Published in Advance May 12, 2004, doi:10.1101/gr.1917404
...Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs Bastien Chevreux 1 , 7 , Thomas Pfisterer 2 , Bernd Drescher 3 , Albert J. Driesel 4 , Werner E.G. Müller 5 , Thomas...
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LETTER: An Ordered Comparative Map of the Cattle and Human Genomes
- Mark R. Band,
- Joshua H. Larson,
- Mark Rebeiz,
- Cheryl A. Green,
- D. Wayne Heyen,
- Jena Donovan,
- Ryan Windish,
- Chad Steining,
- Prapti Mahyuddin,
- James E. Womack,
- and Harris A. Lewin
Genome Res. September 1, 2000 10: 1359-1368; doi:10.1101/gr.145900
...77843, USA Abstract A cattle–human whole-genome comparative map was constructed using parallel radiation hybrid (RH) mapping in conjunction with EST sequencing, database mining for unmapped cattle genes, and a predictive bioinformatics approach (COMPASS) for targeting specific homologous...

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