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Items: 48

1.

Identification of functional long non-coding RNAs in C. elegans.

Akay A, Jordan D, Navarro IC, Wrzesinski T, Ponting CP, Miska EA, Haerty W.

BMC Biol. 2019 Feb 18;17(1):14. doi: 10.1186/s12915-019-0635-7.

PMID:
30777050
2.

A gene expression signature in developing Purkinje cells predicts autism and intellectual disability co-morbidity status.

Clifford H, Dulneva A, Ponting CP, Haerty W, Becker EBE.

Sci Rep. 2019 Jan 24;9(1):485. doi: 10.1038/s41598-018-37284-1.

3.

A quantitative framework for characterizing the evolutionary history of mammalian gene expression.

Chen J, Swofford R, Johnson J, Cummings BB, Rogel N, Lindblad-Toh K, Haerty W, Palma FD, Regev A.

Genome Res. 2019 Jan;29(1):53-63. doi: 10.1101/gr.237636.118. Epub 2018 Dec 14.

PMID:
30552105
4.

The evolutionary dynamics of microRNAs in domestic mammals.

Penso-Dolfin L, Moxon S, Haerty W, Di Palma F.

Sci Rep. 2018 Nov 19;8(1):17050. doi: 10.1038/s41598-018-34243-8.

5.

Aequatus: an open-source homology browser.

Thanki AS, Soranzo N, Herrero J, Haerty W, Davey RP.

Gigascience. 2018 Nov 1;7(11). doi: 10.1093/gigascience/giy128.

6.

Adaptation and conservation insights from the koala genome.

Johnson RN, O'Meally D, Chen Z, Etherington GJ, Ho SYW, Nash WJ, Grueber CE, Cheng Y, Whittington CM, Dennison S, Peel E, Haerty W, O'Neill RJ, Colgan D, Russell TL, Alquezar-Planas DE, Attenbrow V, Bragg JG, Brandies PA, Chong AY, Deakin JE, Di Palma F, Duda Z, Eldridge MDB, Ewart KM, Hogg CJ, Frankham GJ, Georges A, Gillett AK, Govendir M, Greenwood AD, Hayakawa T, Helgen KM, Hobbs M, Holleley CE, Heider TN, Jones EA, King A, Madden D, Graves JAM, Morris KM, Neaves LE, Patel HR, Polkinghorne A, Renfree MB, Robin C, Salinas R, Tsangaras K, Waters PD, Waters SA, Wright B, Wilkins MR, Timms P, Belov K.

Nat Genet. 2018 Aug;50(8):1102-1111. doi: 10.1038/s41588-018-0153-5. Epub 2018 Jul 2.

7.

Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions.

Bailey PC, Schudoma C, Jackson W, Baggs E, Dagdas G, Haerty W, Moscou M, Krasileva KV.

Genome Biol. 2018 Feb 19;19(1):23. doi: 10.1186/s13059-018-1392-6.

8.

GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline.

Thanki AS, Soranzo N, Haerty W, Davey RP.

Gigascience. 2018 Mar 1;7(3):1-10. doi: 10.1093/gigascience/giy005.

9.

Alpha-synuclein induces the unfolded protein response in Parkinson's disease SNCA triplication iPSC-derived neurons.

Heman-Ackah SM, Manzano R, Hoozemans JJM, Scheper W, Flynn R, Haerty W, Cowley SA, Bassett AR, Wood MJA.

Hum Mol Genet. 2017 Nov 15;26(22):4441-4450. doi: 10.1093/hmg/ddx331.

10.

Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination.

Tamiru M, Natsume S, Takagi H, White B, Yaegashi H, Shimizu M, Yoshida K, Uemura A, Oikawa K, Abe A, Urasaki N, Matsumura H, Babil P, Yamanaka S, Matsumoto R, Muranaka S, Girma G, Lopez-Montes A, Gedil M, Bhattacharjee R, Abberton M, Kumar PL, Rabbi I, Tsujimura M, Terachi T, Haerty W, Corpas M, Kamoun S, Kahl G, Takagi H, Asiedu R, Terauchi R.

BMC Biol. 2017 Sep 19;15(1):86. doi: 10.1186/s12915-017-0419-x.

11.

Identification of genetic variants affecting vitamin D receptor binding and associations with autoimmune disease.

Gallone G, Haerty W, Disanto G, Ramagopalan SV, Ponting CP, Berlanga-Taylor AJ.

Hum Mol Genet. 2017 Jun 1;26(11):2164-2176. doi: 10.1093/hmg/ddx092.

12.

Whole-exome sequencing of 228 patients with sporadic Parkinson's disease.

Sandor C, Honti F, Haerty W, Szewczyk-Krolikowski K, Tomlinson P, Evetts S, Millin S, Keane T, McCarthy SA, Durbin R, Talbot K, Hu M, Webber C, Ponting CP, Wade-Martins R.

Sci Rep. 2017 Jan 24;7:41188. doi: 10.1038/srep41188.

13.

Separation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq.

Macaulay IC, Teng MJ, Haerty W, Kumar P, Ponting CP, Voet T.

Nat Protoc. 2016 Nov;11(11):2081-103. doi: 10.1038/nprot.2016.138. Epub 2016 Sep 29.

PMID:
27685099
14.

Identification of molecular signatures specific for distinct cranial sensory ganglia in the developing chick.

Patthey C, Clifford H, Haerty W, Ponting CP, Shimeld SM, Begbie J.

Neural Dev. 2016 Jan 27;11:3. doi: 10.1186/s13064-016-0057-y.

15.

Evolutionary Consequences of Male Driven Sexual Selection and Sex-Biased Fitness Modifications in Drosophila melanogaster and Members of the simulans Clade.

Jagadeeshan S, Haerty W, Moglinicka M, Ahuja A, De Vito S, Singh RS.

Int J Evol Biol. 2015;2015:756269. doi: 10.1155/2015/756269. Epub 2015 Sep 1.

16.

Microglia recapitulate a hematopoietic master regulator network in the aging human frontal cortex.

Wehrspaun CC, Haerty W, Ponting CP.

Neurobiol Aging. 2015 Aug;36(8):2443.e9-2443.e20. doi: 10.1016/j.neurobiolaging.2015.04.008. Epub 2015 Apr 25. Review.

17.

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes.

Macaulay IC, Haerty W, Kumar P, Li YI, Hu TX, Teng MJ, Goolam M, Saurat N, Coupland P, Shirley LM, Smith M, Van der Aa N, Banerjee R, Ellis PD, Quail MA, Swerdlow HP, Zernicka-Goetz M, Livesey FJ, Ponting CP, Voet T.

Nat Methods. 2015 Jun;12(6):519-22. doi: 10.1038/nmeth.3370. Epub 2015 Apr 27.

PMID:
25915121
19.

Genome-wide discovery of human splicing branchpoints.

Mercer TR, Clark MB, Andersen SB, Brunck ME, Haerty W, Crawford J, Taft RJ, Nielsen LK, Dinger ME, Mattick JS.

Genome Res. 2015 Feb;25(2):290-303. doi: 10.1101/gr.182899.114. Epub 2015 Jan 5.

20.

RBFOX and PTBP1 proteins regulate the alternative splicing of micro-exons in human brain transcripts.

Li YI, Sanchez-Pulido L, Haerty W, Ponting CP.

Genome Res. 2015 Jan;25(1):1-13. doi: 10.1101/gr.181990.114.

21.

The genomic substrate for adaptive radiation in African cichlid fish.

Brawand D, Wagner CE, Li YI, Malinsky M, Keller I, Fan S, Simakov O, Ng AY, Lim ZW, Bezault E, Turner-Maier J, Johnson J, Alcazar R, Noh HJ, Russell P, Aken B, Alföldi J, Amemiya C, Azzouzi N, Baroiller JF, Barloy-Hubler F, Berlin A, Bloomquist R, Carleton KL, Conte MA, D'Cotta H, Eshel O, Gaffney L, Galibert F, Gante HF, Gnerre S, Greuter L, Guyon R, Haddad NS, Haerty W, Harris RM, Hofmann HA, Hourlier T, Hulata G, Jaffe DB, Lara M, Lee AP, MacCallum I, Mwaiko S, Nikaido M, Nishihara H, Ozouf-Costaz C, Penman DJ, Przybylski D, Rakotomanga M, Renn SCP, Ribeiro FJ, Ron M, Salzburger W, Sanchez-Pulido L, Santos ME, Searle S, Sharpe T, Swofford R, Tan FJ, Williams L, Young S, Yin S, Okada N, Kocher TD, Miska EA, Lander ES, Venkatesh B, Fernald RD, Meyer A, Ponting CP, Streelman JT, Lindblad-Toh K, Seehausen O, Di Palma F.

Nature. 2014 Sep 18;513(7518):375-381. doi: 10.1038/nature13726. Epub 2014 Sep 3.

22.

Considerations when investigating lncRNA function in vivo.

Bassett AR, Akhtar A, Barlow DP, Bird AP, Brockdorff N, Duboule D, Ephrussi A, Ferguson-Smith AC, Gingeras TR, Haerty W, Higgs DR, Miska EA, Ponting CP.

Elife. 2014 Aug 14;3:e03058. doi: 10.7554/eLife.03058. Review.

23.

No gene in the genome makes sense except in the light of evolution.

Haerty W, Ponting CP.

Annu Rev Genomics Hum Genet. 2014;15:71-92. doi: 10.1146/annurev-genom-090413-025621. Epub 2014 Apr 24.

PMID:
24773316
24.

Increased substitution rates surrounding low-complexity regions within primate proteins.

Lenz C, Haerty W, Golding GB.

Genome Biol Evol. 2014 Mar;6(3):655-65. doi: 10.1093/gbe/evu042.

25.

Mutations within lncRNAs are effectively selected against in fruitfly but not in human.

Haerty W, Ponting CP.

Genome Biol. 2013 May 27;14(5):R49. doi: 10.1186/gb-2013-14-5-r49.

26.

The African coelacanth genome provides insights into tetrapod evolution.

Amemiya CT, Alföldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch I, Manousaki T, Schneider I, Rohner N, Organ C, Chalopin D, Smith JJ, Robinson M, Dorrington RA, Gerdol M, Aken B, Biscotti MA, Barucca M, Baurain D, Berlin AM, Blatch GL, Buonocore F, Burmester T, Campbell MS, Canapa A, Cannon JP, Christoffels A, De Moro G, Edkins AL, Fan L, Fausto AM, Feiner N, Forconi M, Gamieldien J, Gnerre S, Gnirke A, Goldstone JV, Haerty W, Hahn ME, Hesse U, Hoffmann S, Johnson J, Karchner SI, Kuraku S, Lara M, Levin JZ, Litman GW, Mauceli E, Miyake T, Mueller MG, Nelson DR, Nitsche A, Olmo E, Ota T, Pallavicini A, Panji S, Picone B, Ponting CP, Prohaska SJ, Przybylski D, Saha NR, Ravi V, Ribeiro FJ, Sauka-Spengler T, Scapigliati G, Searle SM, Sharpe T, Simakov O, Stadler PF, Stegeman JJ, Sumiyama K, Tabbaa D, Tafer H, Turner-Maier J, van Heusden P, White S, Williams L, Yandell M, Brinkmann H, Volff JN, Tabin CJ, Shubin N, Schartl M, Jaffe DB, Postlethwait JH, Venkatesh B, Di Palma F, Lander ES, Meyer A, Lindblad-Toh K.

Nature. 2013 Apr 18;496(7445):311-6. doi: 10.1038/nature12027.

27.

Rapid evolution of Beta-keratin genes contribute to phenotypic differences that distinguish turtles and birds from other reptiles.

Li YI, Kong L, Ponting CP, Haerty W.

Genome Biol Evol. 2013;5(5):923-33. doi: 10.1093/gbe/evt060.

28.

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage.

Shaffer HB, Minx P, Warren DE, Shedlock AM, Thomson RC, Valenzuela N, Abramyan J, Amemiya CT, Badenhorst D, Biggar KK, Borchert GM, Botka CW, Bowden RM, Braun EL, Bronikowski AM, Bruneau BG, Buck LT, Capel B, Castoe TA, Czerwinski M, Delehaunty KD, Edwards SV, Fronick CC, Fujita MK, Fulton L, Graves TA, Green RE, Haerty W, Hariharan R, Hernandez O, Hillier LW, Holloway AK, Janes D, Janzen FJ, Kandoth C, Kong L, de Koning AP, Li Y, Literman R, McGaugh SE, Mork L, O'Laughlin M, Paitz RT, Pollock DD, Ponting CP, Radhakrishnan S, Raney BJ, Richman JM, St John J, Schwartz T, Sethuraman A, Spinks PQ, Storey KB, Thane N, Vinar T, Zimmerman LM, Warren WC, Mardis ER, Wilson RK.

Genome Biol. 2013 Mar 28;14(3):R28. doi: 10.1186/gb-2013-14-3-r28.

29.

Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome.

Young RS, Marques AC, Tibbit C, Haerty W, Bassett AR, Liu JL, Ponting CP.

Genome Biol Evol. 2012;4(4):427-42. doi: 10.1093/gbe/evs020. Epub 2012 Mar 8.

30.

Is speciation accompanied by rapid evolution? Insights from comparing reproductive and nonreproductive transcriptomes in Drosophila.

Jagadeeshan S, Haerty W, Singh RS.

Int J Evol Biol. 2011;2011:595121. doi: 10.4061/2011/595121. Epub 2011 Aug 22.

31.

The LysR-type PcaQ protein regulates expression of a protocatechuate-inducible ABC-type transport system in Sinorhizobium meliloti.

Maclean AM, Haerty W, Golding GB, Finan TM.

Microbiology. 2011 Sep;157(Pt 9):2522-33. doi: 10.1099/mic.0.050542-0. Epub 2011 Jun 23.

PMID:
21700663
32.

Increased polymorphism near low-complexity sequences across the genomes of Plasmodium falciparum isolates.

Haerty W, Golding GB.

Genome Biol Evol. 2011;3:539-50. doi: 10.1093/gbe/evr045. Epub 2011 May 21.

33.

Low-complexity sequences and single amino acid repeats: not just "junk" peptide sequences.

Haerty W, Golding GB.

Genome. 2010 Oct;53(10):753-62. doi: 10.1139/g10-063. Review.

PMID:
20962881
34.

Genome-wide evidence for selection acting on single amino acid repeats.

Haerty W, Golding GB.

Genome Res. 2010 Jun;20(6):755-60. doi: 10.1101/gr.101246.109. Epub 2010 Jan 7.

35.
36.

Similar selective factors affect both between-gene and between-exon divergence in Drosophila.

Haerty W, Golding B.

Mol Biol Evol. 2009 Apr;26(4):859-66. doi: 10.1093/molbev/msp006. Epub 2009 Jan 15.

PMID:
19150804
37.

Comparative analysis of function and interaction of transcription factors in nematodes: extensive conservation of orthology coupled to rapid sequence evolution.

Haerty W, Artieri C, Khezri N, Singh RS, Gupta BP.

BMC Genomics. 2008 Aug 27;9:399. doi: 10.1186/1471-2164-9-399.

38.
39.

Evolution in the fast lane: rapidly evolving sex-related genes in Drosophila.

Haerty W, Jagadeeshan S, Kulathinal RJ, Wong A, Ravi Ram K, Sirot LK, Levesque L, Artieri CG, Wolfner MF, Civetta A, Singh RS.

Genetics. 2007 Nov;177(3):1321-35.

40.

Association between levels of coding sequence divergence and gene misregulation in Drosophila male hybrids.

Artieri CG, Haerty W, Singh RS.

J Mol Evol. 2007 Dec;65(6):697-704. Epub 2007 Nov 20.

PMID:
18026889
41.

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
42.
43.
44.
45.

Reproductive isolation in natural populations of Drosophila melanogaster from Brazzaville (Congo).

Haerty W, Jallon JM, Rouault J, Bazin C, Capy P.

Genetica. 2002 Nov;116(2-3):215-24.

PMID:
12555780
46.

[Generalized gas gangrene infection with rhabdomyloysis following cholecystectomy].

Haerty W, Schelling G, Haller M, Schönfelder R, Maiwald G, Nerlich A, Kohz P, Grabein B, Briegel J.

Anaesthesist. 1997 Mar;46(3):207-10. German.

PMID:
9163265
47.

Organ selection in intensive care: transplantation of a liver allograft, including calcified cyst of Echinococcus granularis.

Bein T, Haerty W, Haller M, Forst H, Pratschke E.

Intensive Care Med. 1993;19(3):182. No abstract available.

PMID:
8315130
48.

[Metastatic malignant glucagonoma].

Haerty W, Schraudolph M, Nerlich A.

Pathologe. 1992 Jul;13(4):224-7. German. No abstract available.

PMID:
1508861

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