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Items: 17

1.

JBrowse: a dynamic web platform for genome visualization and analysis.

Buels R, Yao E, Diesh CM, Hayes RD, Munoz-Torres M, Helt G, Goodstein DM, Elsik CG, Lewis SE, Stein L, Holmes IH.

Genome Biol. 2016 Apr 12;17:66. doi: 10.1186/s13059-016-0924-1.

2.

Web Apollo: a web-based genomic annotation editing platform.

Lee E, Helt GA, Reese JT, Munoz-Torres MC, Childers CP, Buels RM, Stein L, Holmes IH, Elsik CG, Lewis SE.

Genome Biol. 2013 Aug 30;14(8):R93. doi: 10.1186/gb-2013-14-8-r93.

3.

Genoviz Software Development Kit: Java tool kit for building genomics visualization applications.

Helt GA, Nicol JW, Erwin E, Blossom E, Blanchard SG Jr, Chervitz SA, Harmon C, Loraine AE.

BMC Bioinformatics. 2009 Aug 25;10:266. doi: 10.1186/1471-2105-10-266.

4.

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets.

Nicol JW, Helt GA, Blanchard SG Jr, Raja A, Loraine AE.

Bioinformatics. 2009 Oct 15;25(20):2730-1. doi: 10.1093/bioinformatics/btp472. Epub 2009 Aug 4.

5.

RNA maps reveal new RNA classes and a possible function for pervasive transcription.

Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermüller J, Hofacker IL, Bell I, Cheung E, Drenkow J, Dumais E, Patel S, Helt G, Ganesh M, Ghosh S, Piccolboni A, Sementchenko V, Tammana H, Gingeras TR.

Science. 2007 Jun 8;316(5830):1484-8. Epub 2007 May 17.

6.

Transcriptional landscape of the human and fly genomes: nonlinear and multifunctional modular model of transcriptomes.

Willingham AT, Dike S, Cheng J, Manak JR, Bell I, Cheung E, Drenkow J, Dumais E, Duttagupta R, Ganesh M, Ghosh S, Helt G, Nix D, Piccolboni A, Sementchenko V, Tammana H, Kapranov P; ENCODE Genes And Transcripts Group, Gingeras TR.

Cold Spring Harb Symp Quant Biol. 2006;71:101-10.

PMID:
17480199
7.

Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays.

Kapranov P, Drenkow J, Cheng J, Long J, Helt G, Dike S, Gingeras TR.

Genome Res. 2005 Jul;15(7):987-97.

8.

Visualization techniques for genomic data.

Loraine AE, Helt GA.

Proc IEEE Comput Soc Bioinform Conf. 2002;1:321-6. Review.

PMID:
15838148
9.

Protein-based analysis of alternative splicing in the human genome.

Loraine AE, Helt GA, Cline MS, Siani-Rose MA.

Proc IEEE Comput Soc Bioinform Conf. 2002;1:118-24.

PMID:
15838129
10.

Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution.

Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G, Sementchenko V, Piccolboni A, Bekiranov S, Bailey DK, Ganesh M, Ghosh S, Bell I, Gerhard DS, Gingeras TR.

Science. 2005 May 20;308(5725):1149-54. Epub 2005 Mar 24.

11.

Exploring alternative transcript structure in the human genome using blocks and InterPro.

Loraine AE, Helt GA, Cline MS, Siani-Rose MA.

J Bioinform Comput Biol. 2003 Jul;1(2):289-306.

PMID:
15290774
12.

Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22.

Kampa D, Cheng J, Kapranov P, Yamanaka M, Brubaker S, Cawley S, Drenkow J, Piccolboni A, Bekiranov S, Helt G, Tammana H, Gingeras TR.

Genome Res. 2004 Mar;14(3):331-42.

13.

Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs.

Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, Kampa D, Piccolboni A, Sementchenko V, Cheng J, Williams AJ, Wheeler R, Wong B, Drenkow J, Yamanaka M, Patel S, Brubaker S, Tammana H, Helt G, Struhl K, Gingeras TR.

Cell. 2004 Feb 20;116(4):499-509.

14.
15.

An evaluation of ontology exchange languages for bioinformatics.

McEntire R, Karp P, Abernethy N, Benton D, Helt G, DeJongh M, Kent R, Kosky A, Lewis S, Hodnett D, Neumann E, Olken F, Pathak D, Tarczy-Hornoch P, Toldo L, Topaloglou T.

Proc Int Conf Intell Syst Mol Biol. 2000;8:239-50.

PMID:
10977085
16.

The genome sequence of Drosophila melanogaster.

Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, Sutton GG, Wortman JR, Yandell MD, Zhang Q, Chen LX, Brandon RC, Rogers YH, Blazej RG, Champe M, Pfeiffer BD, Wan KH, Doyle C, Baxter EG, Helt G, Nelson CR, Gabor GL, Abril JF, Agbayani A, An HJ, Andrews-Pfannkoch C, Baldwin D, Ballew RM, Basu A, Baxendale J, Bayraktaroglu L, Beasley EM, Beeson KY, Benos PV, Berman BP, Bhandari D, Bolshakov S, Borkova D, Botchan MR, Bouck J, Brokstein P, Brottier P, Burtis KC, Busam DA, Butler H, Cadieu E, Center A, Chandra I, Cherry JM, Cawley S, Dahlke C, Davenport LB, Davies P, de Pablos B, Delcher A, Deng Z, Mays AD, Dew I, Dietz SM, Dodson K, Doup LE, Downes M, Dugan-Rocha S, Dunkov BC, Dunn P, Durbin KJ, Evangelista CC, Ferraz C, Ferriera S, Fleischmann W, Fosler C, Gabrielian AE, Garg NS, Gelbart WM, Glasser K, Glodek A, Gong F, Gorrell JH, Gu Z, Guan P, Harris M, Harris NL, Harvey D, Heiman TJ, Hernandez JR, Houck J, Hostin D, Houston KA, Howland TJ, Wei MH, Ibegwam C, Jalali M, Kalush F, Karpen GH, Ke Z, Kennison JA, Ketchum KA, Kimmel BE, Kodira CD, Kraft C, Kravitz S, Kulp D, Lai Z, Lasko P, Lei Y, Levitsky AA, Li J, Li Z, Liang Y, Lin X, Liu X, Mattei B, McIntosh TC, McLeod MP, McPherson D, Merkulov G, Milshina NV, Mobarry C, Morris J, Moshrefi A, Mount SM, Moy M, Murphy B, Murphy L, Muzny DM, Nelson DL, Nelson DR, Nelson KA, Nixon K, Nusskern DR, Pacleb JM, Palazzolo M, Pittman GS, Pan S, Pollard J, Puri V, Reese MG, Reinert K, Remington K, Saunders RD, Scheeler F, Shen H, Shue BC, Sidén-Kiamos I, Simpson M, Skupski MP, Smith T, Spier E, Spradling AC, Stapleton M, Strong R, Sun E, Svirskas R, Tector C, Turner R, Venter E, Wang AH, Wang X, Wang ZY, Wassarman DA, Weinstock GM, Weissenbach J, Williams SM, WoodageT, Worley KC, Wu D, Yang S, Yao QA, Ye J, Yeh RF, Zaveri JS, Zhan M, Zhang G, Zhao Q, Zheng L, Zheng XH, Zhong FN, Zhong W, Zhou X, Zhu S, Zhu X, Smith HO, Gibbs RA, Myers EW, Rubin GM, Venter JC.

Science. 2000 Mar 24;287(5461):2185-95.

PMID:
10731132
17.

BioViews: Java-based tools for genomic data visualization.

Helt GA, Lewis S, Loraine AE, Rubin GM.

Genome Res. 1998 Mar;8(3):291-305.

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