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Items: 1 to 50 of 72

1.

Detecting gene subnetworks under selection in biological pathways.

Gouy A, Daub JT, Excoffier L.

Nucleic Acids Res. 2017 Sep 19;45(16):e149. doi: 10.1093/nar/gkx626.

2.

X-linked carriers of chronic granulomatous disease: Illness, lyonization, and stability.

Marciano BE, Zerbe CS, Falcone EL, Ding L, DeRavin SS, Daub J, Kreuzburg S, Yockey L, Hunsberger S, Foruraghi L, Barnhart LA, Matharu K, Anderson V, Darnell DN, Frein C, Fink DL, Lau KP, Long Priel DA, Gallin JI, Malech HL, Uzel G, Freeman AF, Kuhns DB, Rosenzweig SD, Holland SM.

J Allergy Clin Immunol. 2018 Jan;141(1):365-371. doi: 10.1016/j.jaci.2017.04.035. Epub 2017 May 18.

PMID:
28528201
3.

Detection of Pathways Affected by Positive Selection in Primate Lineages Ancestral to Humans.

Daub JT, Moretti S, Davydov II, Excoffier L, Robinson-Rechavi M.

Mol Biol Evol. 2017 Jun 1;34(6):1391-1402. doi: 10.1093/molbev/msx083. Erratum in: Mol Biol Evol. 2017 Jun 1;34(6):1549.

4.

Abnormal B-cell maturation in the bone marrow of patients with germline mutations in PIK3CD.

Dulau Florea AE, Braylan RC, Schafernak KT, Williams KW, Daub J, Goyal RK, Puck JM, Rao VK, Pittaluga S, Holland SM, Uzel G, Calvo KR.

J Allergy Clin Immunol. 2017 Mar;139(3):1032-1035.e6. doi: 10.1016/j.jaci.2016.08.028. Epub 2016 Sep 30. No abstract available.

5.

No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini.

Koutsovoulos G, Kumar S, Laetsch DR, Stevens L, Daub J, Conlon C, Maroon H, Thomas F, Aboobaker AA, Blaxter M.

Proc Natl Acad Sci U S A. 2016 May 3;113(18):5053-8. doi: 10.1073/pnas.1600338113. Epub 2016 Mar 24.

6.

267 Spanish Exomes Reveal Population-Specific Differences in Disease-Related Genetic Variation.

Dopazo J, Amadoz A, Bleda M, Garcia-Alonso L, Alemán A, García-García F, Rodriguez JA, Daub JT, Muntané G, Rueda A, Vela-Boza A, López-Domingo FJ, Florido JP, Arce P, Ruiz-Ferrer M, Méndez-Vidal C, Arnold TE, Spleiss O, Alvarez-Tejado M, Navarro A, Bhattacharya SS, Borrego S, Santoyo-López J, Antiñolo G.

Mol Biol Evol. 2016 May;33(5):1205-18. doi: 10.1093/molbev/msw005. Epub 2016 Jan 13.

7.

Treatment With Anakinra, a Recombinant IL-1 Receptor Antagonist, Unlikely to Induce Lasting Remission in Patients With CGD Colitis.

Hahn KJ, Ho N, Yockey L, Kreuzberg S, Daub J, Rump A, Marciano BE, Quezado M, Malech HL, Holland SM, Heller T, Zerbe CS.

Am J Gastroenterol. 2015 Jun;110(6):938-9. doi: 10.1038/ajg.2015.135. No abstract available.

PMID:
26052777
8.

Inference of Evolutionary Forces Acting on Human Biological Pathways.

Daub JT, Dupanloup I, Robinson-Rechavi M, Excoffier L.

Genome Biol Evol. 2015 May 13;7(6):1546-58. doi: 10.1093/gbe/evv083.

9.

Detection of convergent genome-wide signals of adaptation to tropical forests in humans.

Amorim CE, Daub JT, Salzano FM, Foll M, Excoffier L.

PLoS One. 2015 Apr 7;10(4):e0121557. doi: 10.1371/journal.pone.0121557. eCollection 2015.

10.

Bone marrow plasma cells are a primary source of serum HIV-1-specific antibodies in chronically infected individuals.

Montezuma-Rusca JM, Moir S, Kardava L, Buckner CM, Louie A, Kim LJ, Santich BH, Wang W, Fankuchen OR, Diaz G, Daub JR, Rosenzweig SD, Chun TW, Li Y, Braylan RC, Calvo KR, Fauci AS.

J Immunol. 2015 Mar 15;194(6):2561-8. doi: 10.4049/jimmunol.1402424. Epub 2015 Feb 13.

11.

Rfam: annotating families of non-coding RNA sequences.

Daub J, Eberhardt RY, Tate JG, Burge SW.

Methods Mol Biol. 2015;1269:349-63. doi: 10.1007/978-1-4939-2291-8_22.

PMID:
25577390
12.

Common severe infections in chronic granulomatous disease.

Marciano BE, Spalding C, Fitzgerald A, Mann D, Brown T, Osgood S, Yockey L, Darnell DN, Barnhart L, Daub J, Boris L, Rump AP, Anderson VL, Haney C, Kuhns DB, Rosenzweig SD, Kelly C, Zelazny A, Mason T, DeRavin SS, Kang E, Gallin JI, Malech HL, Olivier KN, Uzel G, Freeman AF, Heller T, Zerbe CS, Holland SM.

Clin Infect Dis. 2015 Apr 15;60(8):1176-83. doi: 10.1093/cid/ciu1154. Epub 2014 Dec 23.

13.

Cell-based computational modeling of vascular morphogenesis using Tissue Simulation Toolkit.

Daub JT, Merks RM.

Methods Mol Biol. 2015;1214:67-127. doi: 10.1007/978-1-4939-1462-3_6.

PMID:
25468600
14.

Rfam 12.0: updates to the RNA families database.

Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J, Finn RD.

Nucleic Acids Res. 2015 Jan;43(Database issue):D130-7. doi: 10.1093/nar/gku1063. Epub 2014 Nov 11.

15.

Widespread signals of convergent adaptation to high altitude in Asia and america.

Foll M, Gaggiotti OE, Daub JT, Vatsiou A, Excoffier L.

Am J Hum Genet. 2014 Oct 2;95(4):394-407. doi: 10.1016/j.ajhg.2014.09.002. Epub 2014 Sep 25.

16.

Patterns of positive selection in seven ant genomes.

Roux J, Privman E, Moretti S, Daub JT, Robinson-Rechavi M, Keller L.

Mol Biol Evol. 2014 Jul;31(7):1661-85. doi: 10.1093/molbev/msu141. Epub 2014 Apr 29.

17.

GATA2 deficiency: a protean disorder of hematopoiesis, lymphatics, and immunity.

Spinner MA, Sanchez LA, Hsu AP, Shaw PA, Zerbe CS, Calvo KR, Arthur DC, Gu W, Gould CM, Brewer CC, Cowen EW, Freeman AF, Olivier KN, Uzel G, Zelazny AM, Daub JR, Spalding CD, Claypool RJ, Giri NK, Alter BP, Mace EM, Orange JS, Cuellar-Rodriguez J, Hickstein DD, Holland SM.

Blood. 2014 Feb 6;123(6):809-21. doi: 10.1182/blood-2013-07-515528. Epub 2013 Nov 13.

18.

Evidence for polygenic adaptation to pathogens in the human genome.

Daub JT, Hofer T, Cutivet E, Dupanloup I, Quintana-Murci L, Robinson-Rechavi M, Excoffier L.

Mol Biol Evol. 2013 Jul;30(7):1544-58. doi: 10.1093/molbev/mst080. Epub 2013 Apr 26.

PMID:
23625889
19.

Abnormal nasal nitric oxide production, ciliary beat frequency, and Toll-like receptor response in pulmonary nontuberculous mycobacterial disease epithelium.

Fowler CJ, Olivier KN, Leung JM, Smith CC, Huth AG, Root H, Kuhns DB, Logun C, Zelazny A, Frein CA, Daub J, Haney C, Shelhamer JH, Bryant CE, Holland SM.

Am J Respir Crit Care Med. 2013 Jun 15;187(12):1374-81. doi: 10.1164/rccm.201212-2197OC.

20.

A cell-based model of extracellular-matrix-guided endothelial cell migration during angiogenesis.

Daub JT, Merks RM.

Bull Math Biol. 2013 Aug;75(8):1377-99. doi: 10.1007/s11538-013-9826-5. Epub 2013 Mar 15.

21.

Rfam 11.0: 10 years of RNA families.

Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A.

Nucleic Acids Res. 2013 Jan;41(Database issue):D226-32. doi: 10.1093/nar/gks1005. Epub 2012 Nov 3.

22.

Synthesis, spectroscopic properties, and electropolymerization of azulene dyads.

Nöll G, Daub J, Lutz M, Rurack K.

J Org Chem. 2011 Jun 17;76(12):4859-73. doi: 10.1021/jo200080v. Epub 2011 May 16.

PMID:
21506604
23.

Rfam: Wikipedia, clans and the "decimal" release.

Gardner PP, Daub J, Tate J, Moore BL, Osuch IH, Griffiths-Jones S, Finn RD, Nawrocki EP, Kolbe DL, Eddy SR, Bateman A.

Nucleic Acids Res. 2011 Jan;39(Database issue):D141-5. doi: 10.1093/nar/gkq1129. Epub 2010 Nov 9.

24.

Ecdysozoan mitogenomics: evidence for a common origin of the legged invertebrates, the Panarthropoda.

Rota-Stabelli O, Kayal E, Gleeson D, Daub J, Boore JL, Telford MJ, Pisani D, Blaxter M, Lavrov DV.

Genome Biol Evol. 2010 Jul 12;2:425-40. doi: 10.1093/gbe/evq030.

25.

The origins of apicomplexan sequence innovation.

Wasmuth J, Daub J, Peregrín-Alvarez JM, Finney CA, Parkinson J.

Genome Res. 2009 Jul;19(7):1202-13. doi: 10.1101/gr.083386.108. Epub 2009 Apr 10.

26.

Rfam: updates to the RNA families database.

Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A.

Nucleic Acids Res. 2009 Jan;37(Database issue):D136-40. doi: 10.1093/nar/gkn766. Epub 2008 Oct 25.

27.

The RNA WikiProject: community annotation of RNA families.

Daub J, Gardner PP, Tate J, Ramsköld D, Manske M, Scott WG, Weinberg Z, Griffiths-Jones S, Bateman A.

RNA. 2008 Dec;14(12):2462-4. doi: 10.1261/rna.1200508. Epub 2008 Oct 22.

28.

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
29.

Draft genome of the filarial nematode parasite Brugia malayi.

Ghedin E, Wang S, Spiro D, Caler E, Zhao Q, Crabtree J, Allen JE, Delcher AL, Guiliano DB, Miranda-Saavedra D, Angiuoli SV, Creasy T, Amedeo P, Haas B, El-Sayed NM, Wortman JR, Feldblyum T, Tallon L, Schatz M, Shumway M, Koo H, Salzberg SL, Schobel S, Pertea M, Pop M, White O, Barton GJ, Carlow CK, Crawford MJ, Daub J, Dimmic MW, Estes CF, Foster JM, Ganatra M, Gregory WF, Johnson NM, Jin J, Komuniecki R, Korf I, Kumar S, Laney S, Li BW, Li W, Lindblom TH, Lustigman S, Ma D, Maina CV, Martin DM, McCarter JP, McReynolds L, Mitreva M, Nutman TB, Parkinson J, Peregrín-Alvarez JM, Poole C, Ren Q, Saunders L, Sluder AE, Smith K, Stanke M, Unnasch TR, Ware J, Wei AD, Weil G, Williams DJ, Zhang Y, Williams SA, Fraser-Liggett C, Slatko B, Blaxter ML, Scott AL.

Science. 2007 Sep 21;317(5845):1756-60.

30.

An ionically driven molecular IMPLICATION gate operating in fluorescence mode.

Rurack K, Trieflinger C, Koval'chuck A, Daub J.

Chemistry. 2007;13(32):8998-9003.

PMID:
17705328
31.

Bond strength of direct and indirect bonded brackets after thermocycling.

Daub J, Berzins DW, Linn BJ, Bradley TG.

Angle Orthod. 2006 Mar;76(2):295-300.

PMID:
16539557
32.

Spectroelectrochemical investigation of a flavoprotein with a flavin-modified gold electrode.

Nöll G, Kozma E, Grandori R, Carey J, Schödl T, Hauska G, Daub J.

Langmuir. 2006 Feb 28;22(5):2378-83.

PMID:
16489832
33.
34.

Multiple switching and photogated electrochemiluminescence expressed by a dihydroazulene/boron dipyrromethene dyad.

Trieflinger C, Röhr H, Rurack K, Daub J.

Angew Chem Int Ed Engl. 2005 Oct 28;44(42):6943-7. No abstract available.

PMID:
16216044
35.

On the development of sensor molecules that display Fe(III)-amplified fluorescence.

Bricks JL, Kovalchuk A, Trieflinger C, Nofz M, Büschel M, Tolmachev AI, Daub J, Rurack K.

J Am Chem Soc. 2005 Oct 5;127(39):13522-9.

PMID:
16190715
36.

Homo-/heterotrinuclear mixed-valent oxo-centered iron/nickel clusters-Mössbauer studies on internal electron-exchange processes.

Saalfrank RW, Scheurer A, Reimann U, Hampel F, Trieflinger C, Büschel M, Daub J, Trautwein AX, Schünemann V, Coropceanu V.

Chemistry. 2005 Oct 7;11(20):5843-8.

PMID:
16041808
37.

"Turn ON/OFF your LOV light": boron-dipyrromethene-flavin dyads as biomimetic switches derived from the LOV domain.

Trieflinger C, Rurack K, Daub J.

Angew Chem Int Ed Engl. 2005 Apr 8;44(15):2288-91. No abstract available.

PMID:
15756697
38.

Selective calcium ion sensing with a bichromophoric squaraine foldamer.

Arunkumar E, Ajayaghosh A, Daub J.

J Am Chem Soc. 2005 Mar 9;127(9):3156-64.

PMID:
15740155
39.

A transcriptomic analysis of the phylum Nematoda.

Parkinson J, Mitreva M, Whitton C, Thomson M, Daub J, Martin J, Schmid R, Hall N, Barrell B, Waterston RH, McCarter JP, Blaxter ML.

Nat Genet. 2004 Dec;36(12):1259-67. Epub 2004 Nov 14.

PMID:
15543149
40.

Clinical applications of genetics in sporadic cancers.

Kwitkowski VE, Daub JR.

Semin Oncol Nurs. 2004 Aug;20(3):155-63. Review.

PMID:
15491025
41.

Structural modelling of optical and electrochemical properties of 4-aminodiphenylamines - optoelectronic studies on a polyaniline repeating unit.

Malval JP, Morand JP, Lapouyade R, Rettig W, Jonusauskas G, Oberlé J, Trieflinger C, Daub J.

Photochem Photobiol Sci. 2004 Oct;3(10):939-48. Epub 2004 Jun 25.

PMID:
15480485
42.

A genome sequence survey of the filarial nematode Brugia malayi: repeats, gene discovery, and comparative genomics.

Whitton C, Daub J, Quail M, Hall N, Foster J, Ware J, Ganatra M, Slatko B, Barrell B, Blaxter M.

Mol Biochem Parasitol. 2004 Oct;137(2):215-27.

PMID:
15383292
43.

DNA taxonomy of a neglected animal phylum: an unexpected diversity of tardigrades.

Blaxter M, Elsworth B, Daub J.

Proc Biol Sci. 2004 May 7;271 Suppl 4:S189-92.

44.

Signal sequence analysis of expressed sequence tags from the nematode Nippostrongylus brasiliensis and the evolution of secreted proteins in parasites.

Harcus YM, Parkinson J, Fernández C, Daub J, Selkirk ME, Blaxter ML, Maizels RM.

Genome Biol. 2004;5(6):R39. Epub 2004 May 18.

45.

Expressed sequence tags: medium-throughput protocols.

Whitton C, Daub J, Thompson M, Blaxter M.

Methods Mol Biol. 2004;270:75-92.

PMID:
15153623
46.

Construction of bacterial artificial chromosome libraries from the parasitic nematode Brugia malayi and physical mapping of the genome of its Wolbachia endosymbiont.

Foster JM, Kumar S, Ganatra MB, Kamal IH, Ware J, Ingram J, Pope-Chappell J, Guiliano D, Whitton C, Daub J, Blaxter ML, Slatko BE.

Int J Parasitol. 2004 May;34(6):733-46.

PMID:
15111095
47.

Redox-switchable squaraines with extended conjugation.

Büschel M, Ajayaghosh A, Arunkumar E, Daub J.

Org Lett. 2003 Aug 21;5(17):2975-8.

PMID:
12916959
48.

Abundant larval transcript-1 and -2 genes from Brugia malayi: diversity of genomic environments but conservation of 5' promoter sequences functional in Caenorhabditis elegans.

Gomez-Escobar N, Gregory WF, Britton C, Murray L, Corton C, Hall N, Daub J, Blaxter ML, Maizels RM.

Mol Biochem Parasitol. 2002 Nov-Dec;125(1-2):59-71.

PMID:
12467974
49.
50.

Metal- and ligand-directed one-pot syntheses, crystal structures, and properties of novel oxo-centered tetra- and hexametallic clusters.

Saalfrank RW, Reimann U, Göritz M, Hampel F, Scheurer A, Heinemann FW, Büschel M, Daub J, Schünemann V, Trautwein AX.

Chemistry. 2002 Aug 16;8(16):3614-9.

PMID:
12203287

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