2011
Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP et al.
The UCSC Genome Browser database: update 2011.
Nucleic Acids Res 2011 Jan;39(Database issue):D876-82.
George AD, Tenenbaum SA
Web-based tools for studying RNA structure and function.
Methods Mol Biol 2011;703:67-86.
Hubisz MJ, Lin MF, Kellis M, Siepel A
Error and error mitigation in low-coverage genome assemblies.
PLoS One 2011 Feb 14;6(2):e17034.
Jain R, Devine T, George AD, Chittur SV, Baroni TE, Penalva LO, Tenenbaum SA
RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling.
Methods Mol Biol 2011;703:247-63.
Lin MF, Jungreis I, Kellis M
PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions.
Bioinformatics 2011 Jul 1;27(13):i275-82.
Raney BJ, Cline MS, Rosenbloom KR, Dreszer TR, Learned K, Barber GP, Meyer LR, Sloan CA et al.
ENCODE whole-genome data in the UCSC genome browser (2011 update).
Nucleic Acids Res 2011 Jan;39(Database issue):D871-5.
Salimullah M, Sakai M, Plessy C, Carninci P
NanoCAGE: a high-resolution technique to discover and interrogate cell transcriptomes.
Cold Spring Harb Protoc 2011 Jan 1;2011(1):pdb.prot5559.
2010
Adli M, Zhu J, Bernstein BE
Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors.
Nat Methods 2010 Aug;7(8):615-8.
Blahnik KR, Dou L, O'Geen H, McPhillips T, Xu X, Cao AR, Iyengar S, Nicolet CM et al.
Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data.
Nucleic Acids Res 2010 Jan;38(3):e13.
Ernst J, Kellis M
Discovery and characterization of chromatin states for systematic annotation of the human genome.
Nat Biotechnol 2010 Aug;28(8):817-25.
Goren A, Ozsolak F, Shoresh N, Ku M, Adli M, Hart C, Gymrek M, Zuk O et al.
Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA.
Nat Methods 2010 Jan;7(1):47-9.
Hung JH, Whitfield TW, Yang TH, Hu Z, Weng Z, DeLisi C
Identification of functional modules that correlate with phenotypic difference: the influence of network topology.
Genome Biol 2010;11(2):R23.
Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D
BigWig and BigBed: enabling browsing of large distributed datasets.
Bioinformatics 2010 Sep 1;26(17):2204-7.
Kokocinski F, Harrow J, Hubbard T
AnnoTrack--a tracking system for genome annotation.
BMC Genomics 2010 Oct 5;11:538.
Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, Ariyaratne PN, Mohamed YB et al.
ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing.
Genome Biol 2010;11(2):R22.
Mariotti M, Guigó puigó R
Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes.
Bioinformatics 2010 Nov 1;26(21):2656-63.
Plessy C, Bertin N, Takahashi H, Simone R, Salimullah M, Lassmann T, Vitezic M, Severin J et al.
Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan.
Nat Methods 2010 Jul;7(7):528-34.
Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE et al.
The UCSC Genome Browser database: update 2010.
Nucleic Acids Res 2010 Jan;38(Database issue):D613-9.
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ et al.
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
Nat Biotechnol 2010 May;28(5):511-5.
Underwood JG, Uzilov AV, Katzman S, Onodera CS, Mainzer JE, Mathews DH, Lowe TM, Salama SR et al.
FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing.
Nat Methods 2010 Dec;7(12):995-1001.
Zerbino DR
Using the Velvet de novo assembler for short-read sequencing technologies.
Curr Protoc Bioinformatics 2010 Sep;Chapter 11:Unit 11.5.
2009
Amid C, Rehaume LM, Brown KL, Gilbert JG, Dougan G, Hancock RE, Harrow JL
Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.
BMC Genomics 2009 Dec 15;10:606.
Fullwood MJ, Ruan Y
ChIP-based methods for the identification of long-range chromatin interactions.
J Cell Biochem 2009 May 1;107(1):30-9.
Fullwood MJ, Wei CL, Liu ET, Ruan Y
Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses.
Genome Res 2009 Apr;19(4):521-32.
George AD, Tenenbaum SA
Informatic resources for identifying and annotating structural RNA motifs.
Mol Biotechnol 2009 Feb;41(2):180-93.
Giresi PG, Lieb JD
Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements).
Methods 2009 Jul;48(3):233-9.
Hesselberth JR, Chen X, Zhang Z, Sabo PJ, Sandstrom R, Reynolds AP, Thurman RE, Neph S et al.
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting.
Nat Methods 2009 Apr;6(4):283-9.
Kuhn RM, Karolchik D, Zweig AS, Wang T, Smith KE, Rosenbloom KR, Rhead B, Raney BJ et al.
The UCSC Genome Browser Database: update 2009.
Nucleic Acids Res 2009 Jan;37(Database issue):D755-61.
Lajoie BR, van Berkum NL, Sanyal A, Dekker J
My5C: web tools for chromosome conformation capture studies.
Nat Methods 2009 Oct;6(10):690-1.
Lam HY, Khurana E, Fang G, Cayting P, Carriero N, Cheung KH, Gerstein MB
Pseudofam: the pseudogene families database.
Nucleic Acids Res 2009 Jan;37(Database issue):D738-43.
Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR et al.
Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Science 2009 Oct 9;326(5950):289-93.
Lu DV, Brown RH, Arumugam M, Brent MR
Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner.
Bioinformatics 2009 Jul 1;25(13):1587-93.
Pepke S, Wold B, Mortazavi A
Computation for ChIP-seq and RNA-seq studies.
Nat Methods 2009 Nov;6(11 Suppl):S22-32.
Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM et al.
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.
Genome Res 2009 Jul;19(7):1316-23.
Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M et al.
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.
Nat Biotechnol 2009 Jan;27(1):66-75.
2008
Boyle AP, Guinney J, Crawford GE, Furey TS
F-Seq: a feature density estimator for high-throughput sequence tags.
Bioinformatics 2008 Nov 1;24(21):2537-8.
Djebali S, Kapranov P, Foissac S, Lagarde J, Reymond A, Ucla C, Wyss C, Drenkow J et al.
Efficient targeted transcript discovery via array-based normalization of RACE libraries.
Nat Methods 2008 Jul;5(7):629-35.
Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, Diekhans M, Giardine B, Harte RA et al.
The UCSC Genome Browser Database: 2008 update.
Nucleic Acids Res 2008 Jan;36(Database issue):D773-9.
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B
Mapping and quantifying mammalian transcriptomes by RNA-Seq.
Nat Methods 2008 Jul;5(7):621-8.
Tress ML, Wesselink JJ, Frankish A, López G, Goldman N, Löytynoja A, Massingham T, Pardi F et al.
Determination and validation of principal gene products.
Bioinformatics 2008 Jan 1;24(1):11-7.
Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A et al.
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data.
Nat Methods 2008 Sep;5(9):829-34.
Wilming LG, Gilbert JG, Howe K, Trevanion S, Hubbard T, Harrow JL
The vertebrate genome annotation (Vega) database.
Nucleic Acids Res 2008 Jan;36(Database issue):D753-60.