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Items: 1 to 20 of 61

1.

Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding.

Cannistraci CV, Alanis-Lobato G, Ravasi T.

Bioinformatics. 2013 Jul 1;29(13):i199-209. doi: 10.1093/bioinformatics/btt208.

2.

Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales.

Faircloth BC, McCormack JE, Crawford NG, Harvey MG, Brumfield RT, Glenn TC.

Syst Biol. 2012 Oct;61(5):717-26. doi: 10.1093/sysbio/sys004. Epub 2012 Jan 9.

PMID:
22232343
3.

MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S.

Mol Biol Evol. 2011 Oct;28(10):2731-9. doi: 10.1093/molbev/msr121. Epub 2011 May 4.

4.

Unexpected complexity of the reef-building coral Acropora millepora transcription factor network.

Ryu T, Mavromatis CH, Bayer T, Voolstra CR, Ravasi T.

BMC Syst Biol. 2011 Apr 28;5:58. doi: 10.1186/1752-0509-5-58.

5.

Positive and negative selection in murine ultraconserved noncoding elements.

Halligan DL, Oliver F, Guthrie J, Stemshorn KC, Harr B, Keightley PD.

Mol Biol Evol. 2011 Sep;28(9):2651-60. doi: 10.1093/molbev/msr093. Epub 2011 Apr 8.

PMID:
21478460
6.

Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes.

Cannistraci CV, Ravasi T, Montevecchi FM, Ideker T, Alessio M.

Bioinformatics. 2010 Sep 15;26(18):i531-9. doi: 10.1093/bioinformatics/btq376.

7.

An SNP in an ultraconserved regulatory element affects Dlx5/Dlx6 regulation in the forebrain.

Poitras L, Yu M, Lesage-Pelletier C, Macdonald RB, Gagné JP, Hatch G, Kelly I, Hamilton SP, Rubenstein JL, Poirier GG, Ekker M.

Development. 2010 Sep;137(18):3089-97. doi: 10.1242/dev.051052. Epub 2010 Aug 11.

8.

GeneCards Version 3: the human gene integrator.

Safran M, Dalah I, Alexander J, Rosen N, Iny Stein T, Shmoish M, Nativ N, Bahir I, Doniger T, Krug H, Sirota-Madi A, Olender T, Golan Y, Stelzer G, Harel A, Lancet D.

Database (Oxford). 2010 Aug 5;2010:baq020. doi: 10.1093/database/baq020.

9.

The Amphimedon queenslandica genome and the evolution of animal complexity.

Srivastava M, Simakov O, Chapman J, Fahey B, Gauthier ME, Mitros T, Richards GS, Conaco C, Dacre M, Hellsten U, Larroux C, Putnam NH, Stanke M, Adamska M, Darling A, Degnan SM, Oakley TH, Plachetzki DC, Zhai Y, Adamski M, Calcino A, Cummins SF, Goodstein DM, Harris C, Jackson DJ, Leys SP, Shu S, Woodcroft BJ, Vervoort M, Kosik KS, Manning G, Degnan BM, Rokhsar DS.

Nature. 2010 Aug 5;466(7307):720-6. doi: 10.1038/nature09201.

10.

The dynamic genome of Hydra.

Chapman JA, Kirkness EF, Simakov O, Hampson SE, Mitros T, Weinmaier T, Rattei T, Balasubramanian PG, Borman J, Busam D, Disbennett K, Pfannkoch C, Sumin N, Sutton GG, Viswanathan LD, Walenz B, Goodstein DM, Hellsten U, Kawashima T, Prochnik SE, Putnam NH, Shu S, Blumberg B, Dana CE, Gee L, Kibler DF, Law L, Lindgens D, Martinez DE, Peng J, Wigge PA, Bertulat B, Guder C, Nakamura Y, Ozbek S, Watanabe H, Khalturin K, Hemmrich G, Franke A, Augustin R, Fraune S, Hayakawa E, Hayakawa S, Hirose M, Hwang JS, Ikeo K, Nishimiya-Fujisawa C, Ogura A, Takahashi T, Steinmetz PR, Zhang X, Aufschnaiter R, Eder MK, Gorny AK, Salvenmoser W, Heimberg AM, Wheeler BM, Peterson KJ, Böttger A, Tischler P, Wolf A, Gojobori T, Remington KA, Strausberg RL, Venter JC, Technau U, Hobmayer B, Bosch TC, Holstein TW, Fujisawa T, Bode HR, David CN, Rokhsar DS, Steele RE.

Nature. 2010 Mar 25;464(7288):592-6. doi: 10.1038/nature08830. Epub 2010 Mar 14.

11.

Are "ultraconserved" genetic elements really indispensable?

Gross L.

PLoS Biol. 2007 Sep;5(9):e253. doi: 10.1371/journal.pbio.0050253. Epub 2007 Sep 4. No abstract available.

12.

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.

Ostlund G, Schmitt T, Forslund K, Köstler T, Messina DN, Roopra S, Frings O, Sonnhammer EL.

Nucleic Acids Res. 2010 Jan;38(Database issue):D196-203. doi: 10.1093/nar/gkp931. Epub 2009 Nov 5.

13.

Short ultraconserved promoter regions delineate a class of preferentially expressed alternatively spliced transcripts.

Rödelsperger C, Köhler S, Schulz MH, Manke T, Bauer S, Robinson PN.

Genomics. 2009 Nov;94(5):308-16. doi: 10.1016/j.ygeno.2009.07.005. Epub 2009 Aug 4.

14.

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Langmead B, Trapnell C, Pop M, Salzberg SL.

Genome Biol. 2009;10(3):R25. doi: 10.1186/gb-2009-10-3-r25. Epub 2009 Mar 4.

15.

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.

Huang da W, Sherman BT, Lempicki RA.

Nat Protoc. 2009;4(1):44-57. doi: 10.1038/nprot.2008.211.

16.

Algorithm of OMA for large-scale orthology inference.

Roth AC, Gonnet GH, Dessimoz C.

BMC Bioinformatics. 2008 Dec 4;9:518. doi: 10.1186/1471-2105-9-518. Erratum in: BMC Bioinformatics.2009;10. doi:10.1186/1471-2105-10-220.

17.

Large number of ultraconserved elements were already present in the jawed vertebrate ancestor.

Wang J, Lee AP, Kodzius R, Brenner S, Venkatesh B.

Mol Biol Evol. 2009 Mar;26(3):487-90. doi: 10.1093/molbev/msn278. Epub 2008 Dec 3.

PMID:
19052148
18.

Identification and characterization of new long conserved noncoding sequences in vertebrates.

Sakuraba Y, Kimura T, Masuya H, Noguchi H, Sezutsu H, Takahasi KR, Toyoda A, Fukumura R, Murata T, Sakaki Y, Yamamura M, Wakana S, Noda T, Shiroishi T, Gondo Y.

Mamm Genome. 2008 Oct-Dec;19(10-12):703-12. doi: 10.1007/s00335-008-9152-7. Epub 2008 Nov 18.

PMID:
19015917
19.

Ultraconserved elements: analyses of dosage sensitivity, motifs and boundaries.

Chiang CW, Derti A, Schwartz D, Chou MF, Hirschhorn JN, Wu CT.

Genetics. 2008 Dec;180(4):2277-93. doi: 10.1534/genetics.108.096537. Epub 2008 Oct 28.

20.

NCBI Reference Sequences: current status, policy and new initiatives.

Pruitt KD, Tatusova T, Klimke W, Maglott DR.

Nucleic Acids Res. 2009 Jan;37(Database issue):D32-6. doi: 10.1093/nar/gkn721. Epub 2008 Oct 16.

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