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Items: 31

1.

Survival prediction in mesothelioma using a scalable Lasso regression model: instructions for use and initial performance using clinical predictors.

Kidd AC, McGettrick M, Tsim S, Halligan DL, Bylesjo M, Blyth KG.

BMJ Open Respir Res. 2018 Jan 30;5(1):e000240. doi: 10.1136/bmjresp-2017-000240. eCollection 2018.

2.

TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells.

Mariathasan S, Turley SJ, Nickles D, Castiglioni A, Yuen K, Wang Y, Kadel EE III, Koeppen H, Astarita JL, Cubas R, Jhunjhunwala S, Banchereau R, Yang Y, Guan Y, Chalouni C, Ziai J, Şenbabaoğlu Y, Santoro S, Sheinson D, Hung J, Giltnane JM, Pierce AA, Mesh K, Lianoglou S, Riegler J, Carano RAD, Eriksson P, Höglund M, Somarriba L, Halligan DL, van der Heijden MS, Loriot Y, Rosenberg JE, Fong L, Mellman I, Chen DS, Green M, Derleth C, Fine GD, Hegde PS, Bourgon R, Powles T.

Nature. 2018 Feb 22;554(7693):544-548. doi: 10.1038/nature25501. Epub 2018 Feb 14.

3.

Assessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome.

Wiberg RA, Halligan DL, Ness RW, Necsulea A, Kaessmann H, Keightley PD.

Genome Biol Evol. 2015 Aug 12;7(8):2432-44. doi: 10.1093/gbe/evv155.

4.

Recent Evolution in Rattus norvegicus Is Shaped by Declining Effective Population Size.

Deinum EE, Halligan DL, Ness RW, Zhang YH, Cong L, Zhang JX, Keightley PD.

Mol Biol Evol. 2015 Oct;32(10):2547-58. doi: 10.1093/molbev/msv126. Epub 2015 Jun 1.

5.

Analysis of Five Gene Sets in Chimpanzees Suggests Decoupling between the Action of Selection on Protein-Coding and on Noncoding Elements.

Santpere G, Carnero-Montoro E, Petit N, Serra F, Hvilsom C, Rambla J, Heredia-Genestar JM, Halligan DL, Dopazo H, Navarro A, Bosch E.

Genome Biol Evol. 2015 May 14;7(6):1490-505. doi: 10.1093/gbe/evv082.

6.

The relation between recombination rate and patterns of molecular evolution and variation in Drosophila melanogaster.

Campos JL, Halligan DL, Haddrill PR, Charlesworth B.

Mol Biol Evol. 2014 Apr;31(4):1010-28. doi: 10.1093/molbev/msu056. Epub 2014 Jan 30.

7.

Faster-X adaptive protein evolution in house mice.

Kousathanas A, Halligan DL, Keightley PD.

Genetics. 2014 Apr;196(4):1131-43. doi: 10.1534/genetics.113.158246. Epub 2013 Dec 20.

8.

Contributions of protein-coding and regulatory change to adaptive molecular evolution in murid rodents.

Halligan DL, Kousathanas A, Ness RW, Harr B, Eöry L, Keane TM, Adams DJ, Keightley PD.

PLoS Genet. 2013;9(12):e1003995. doi: 10.1371/journal.pgen.1003995. Epub 2013 Dec 5.

9.

Processing genome scale tabular data with wormtable.

Kelleher J, Ness RW, Halligan DL.

BMC Bioinformatics. 2013 Dec 5;14:356. doi: 10.1186/1471-2105-14-356.

10.

Estimation of the spontaneous mutation rate per nucleotide site in a Drosophila melanogaster full-sib family.

Keightley PD, Ness RW, Halligan DL, Haddrill PR.

Genetics. 2014 Jan;196(1):313-20. doi: 10.1534/genetics.113.158758. Epub 2013 Nov 8.

11.

Inference of site frequency spectra from high-throughput sequence data: quantification of selection on nonsynonymous and synonymous sites in humans.

Keightley PD, Halligan DL.

Genetics. 2011 Aug;188(4):931-40. doi: 10.1534/genetics.111.128355. Epub 2011 May 19.

12.

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
13.

Inference of mutation parameters and selective constraint in mammalian coding sequences by approximate Bayesian computation.

Keightley PD, Eöry L, Halligan DL, Kirkpatrick M.

Genetics. 2011 Apr;187(4):1153-61. doi: 10.1534/genetics.110.124073. Epub 2011 Feb 1.

14.

Positive and negative selection on noncoding DNA close to protein-coding genes in wild house mice.

Kousathanas A, Oliver F, Halligan DL, Keightley PD.

Mol Biol Evol. 2011 Mar;28(3):1183-91. doi: 10.1093/molbev/msq299. Epub 2010 Nov 8.

PMID:
21059791
15.

Evidence for pervasive adaptive protein evolution in wild mice.

Halligan DL, Oliver F, Eyre-Walker A, Harr B, Keightley PD.

PLoS Genet. 2010 Jan 22;6(1):e1000825. doi: 10.1371/journal.pgen.1000825.

16.

Patterns of DNA-sequence divergence between Drosophila miranda and D. pseudoobscura.

Marion de Procé S, Halligan DL, Keightley PD, Charlesworth B.

J Mol Evol. 2009 Dec;69(6):601-11. doi: 10.1007/s00239-009-9298-2. Epub 2009 Oct 27.

PMID:
19859648
17.

Distributions of selectively constrained sites and deleterious mutation rates in the hominid and murid genomes.

Eory L, Halligan DL, Keightley PD.

Mol Biol Evol. 2010 Jan;27(1):177-92. doi: 10.1093/molbev/msp219.

PMID:
19759235
18.

Analysis and implications of mutational variation.

Keightley PD, Halligan DL.

Genetica. 2009 Jun;136(2):359-69. doi: 10.1007/s10709-008-9304-4. Epub 2008 Jul 29. Review.

PMID:
18663587
19.

Effects of spontaneous mutation accumulation on sex ratio traits in a parasitoid wasp.

Pannebakker BA, Halligan DL, Reynolds KT, Ballantyne GA, Shuker DM, Barton NH, West SA.

Evolution. 2008 Aug;62(8):1921-35. doi: 10.1111/j.1558-5646.2008.00434.x. Epub 2008 Jun 3.

PMID:
18522711
20.

Evolution of genes and genomes on the Drosophila phylogeny.

Drosophila 12 Genomes Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N, Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y, Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q, Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W, Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I.

Nature. 2007 Nov 8;450(7167):203-18.

PMID:
17994087
21.
22.

Reduced efficacy of selection in regions of the Drosophila genome that lack crossing over.

Haddrill PR, Halligan DL, Tomaras D, Charlesworth B.

Genome Biol. 2007;8(2):R18.

23.

Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila.

Haag-Liautard C, Dorris M, Maside X, Macaskill S, Halligan DL, Houle D, Charlesworth B, Keightley PD.

Nature. 2007 Jan 4;445(7123):82-5. Erratum in: Nature. 2008 May 1;453(7191):128. Houle, David [added].

PMID:
17203060
24.
25.

Natural selection drives extremely rapid evolution in antiviral RNAi genes.

Obbard DJ, Jiggins FM, Halligan DL, Little TJ.

Curr Biol. 2006 Mar 21;16(6):580-5.

26.

Evolutionary constraints in conserved nongenic sequences of mammals.

Keightley PD, Kryukov GV, Sunyaev S, Halligan DL, Gaffney DJ.

Genome Res. 2005 Oct;15(10):1373-8.

27.

Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content.

Haddrill PR, Charlesworth B, Halligan DL, Andolfatto P.

Genome Biol. 2005;6(8):R67. Epub 2005 Jul 27.

28.
29.

Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila.

Halligan DL, Eyre-Walker A, Andolfatto P, Keightley PD.

Genome Res. 2004 Feb;14(2):273-9.

30.

Dominance and overdominance of mildly deleterious induced mutations for fitness traits in Caenorhabditis elegans.

Peters AD, Halligan DL, Whitlock MC, Keightley PD.

Genetics. 2003 Oct;165(2):589-99.

31.

How many lethal alleles?

Halligan DL, Keightley PD.

Trends Genet. 2003 Feb;19(2):57-9. Review.

PMID:
12547508

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