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Items: 1 to 20 of 70

1.

Local DNA topography correlates with functional noncoding regions of the human genome.

Parker SC, Hansen L, Abaan HO, Tullius TD, Margulies EH.

Science. 2009 Apr 17;324(5925):389-92. doi: 10.1126/science.1169050. Epub 2009 Mar 12.

2.
3.

An expansive human regulatory lexicon encoded in transcription factor footprints.

Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, Johnson AK, Maurano MT, Humbert R, Rynes E, Wang H, Vong S, Lee K, Bates D, Diegel M, Roach V, Dunn D, Neri J, Schafer A, Hansen RS, Kutyavin T, Giste E, Weaver M, Canfield T, Sabo P, Zhang M, Balasundaram G, Byron R, MacCoss MJ, Akey JM, Bender MA, Groudine M, Kaul R, Stamatoyannopoulos JA.

Nature. 2012 Sep 6;489(7414):83-90. doi: 10.1038/nature11212.

4.

Analysis of sequence conservation at nucleotide resolution.

Asthana S, Roytberg M, Stamatoyannopoulos J, Sunyaev S.

PLoS Comput Biol. 2007 Dec;3(12):e254. doi: 10.1371/journal.pcbi.0030254. Epub 2007 Nov 14.

5.

Fast-evolving noncoding sequences in the human genome.

Bird CP, Stranger BE, Liu M, Thomas DJ, Ingle CE, Beazley C, Miller W, Hurles ME, Dermitzakis ET.

Genome Biol. 2007;8(6):R118.

6.

Evolution of conserved secondary structures and their function in transcriptional regulation networks.

Xie HB, Irwin DM, Zhang YP.

BMC Genomics. 2008 Nov 2;9:520. doi: 10.1186/1471-2164-9-520.

7.

Personal and population genomics of human regulatory variation.

Vernot B, Stergachis AB, Maurano MT, Vierstra J, Neph S, Thurman RE, Stamatoyannopoulos JA, Akey JM.

Genome Res. 2012 Sep;22(9):1689-97. doi: 10.1101/gr.134890.111.

8.

8.2% of the Human genome is constrained: variation in rates of turnover across functional element classes in the human lineage.

Rands CM, Meader S, Ponting CP, Lunter G.

PLoS Genet. 2014 Jul 24;10(7):e1004525. doi: 10.1371/journal.pgen.1004525. eCollection 2014 Jul.

9.

Thermodynamic Additivity for Impacts of Base-Pair Substitutions on Association of the Egr-1 Zinc-Finger Protein with DNA.

Chattopadhyay A, Zandarashvili L, Luu RH, Iwahara J.

Biochemistry. 2016 Nov 29;55(47):6467-6474. Epub 2016 Nov 11.

10.

Close sequence comparisons are sufficient to identify human cis-regulatory elements.

Prabhakar S, Poulin F, Shoukry M, Afzal V, Rubin EM, Couronne O, Pennacchio LA.

Genome Res. 2006 Jul;16(7):855-63. Epub 2006 Jun 12.

11.

Purifying selection maintains highly conserved noncoding sequences in Drosophila.

Casillas S, Barbadilla A, Bergman CM.

Mol Biol Evol. 2007 Oct;24(10):2222-34. Epub 2007 Jul 23.

PMID:
17646256
12.

Distribution and intensity of constraint in mammalian genomic sequence.

Cooper GM, Stone EA, Asimenos G; NISC Comparative Sequencing Program, Green ED, Batzoglou S, Sidow A.

Genome Res. 2005 Jul;15(7):901-13. Epub 2005 Jun 17.

13.
14.

Construction of a genome-scale structural map at single-nucleotide resolution.

Greenbaum JA, Pang B, Tullius TD.

Genome Res. 2007 Jun;17(6):947-53.

15.

DNA shape, genetic codes, and evolution.

Parker SC, Tullius TD.

Curr Opin Struct Biol. 2011 Jun;21(3):342-7. doi: 10.1016/j.sbi.2011.03.002. Epub 2011 Mar 23. Review.

16.

Evolutionary constraint in flanking regions of avian genes.

Künstner A, Nabholz B, Ellegren H.

Mol Biol Evol. 2011 Sep;28(9):2481-9. doi: 10.1093/molbev/msr066. Epub 2011 Apr 4.

PMID:
21393603
17.

The sequence of the human genome.

Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigó R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X.

Science. 2001 Feb 16;291(5507):1304-51. Erratum in: Science 2001 Jun 5;292(5523):1838.

PMID:
11181995
18.

A genome-wide screen for noncoding elements important in primate evolution.

Bush EC, Lahn BT.

BMC Evol Biol. 2008 Jan 23;8:17. doi: 10.1186/1471-2148-8-17.

19.

Natural Selection and Functional Potentials of Human Noncoding Elements Revealed by Analysis of Next Generation Sequencing Data.

Jha P, Lu D, Xu S.

PLoS One. 2015 Jun 8;10(6):e0129023. doi: 10.1371/journal.pone.0129023. eCollection 2015.

20.

Ultraconservation identifies a small subset of extremely constrained developmental enhancers.

Visel A, Prabhakar S, Akiyama JA, Shoukry M, Lewis KD, Holt A, Plajzer-Frick I, Afzal V, Rubin EM, Pennacchio LA.

Nat Genet. 2008 Feb;40(2):158-60. doi: 10.1038/ng.2007.55. Epub 2008 Jan 6.

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