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Items: 20

1.

TRAP1 chaperone protein mutations and autoinflammation.

Standing AS, Hong Y, Paisan-Ruiz C, Omoyinmi E, Medlar A, Stanescu H, Kleta R, Rowcenzio D, Hawkins P, Lachmann H, McDermott MF, Eleftheriou D, Klein N, Brogan PA.

Life Sci Alliance. 2019 Dec 27;3(2). pii: e201900376. doi: 10.26508/lsa.201900376. Print 2020 Feb.

2.

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.

Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, Cetin Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Fernández JM, Gemovic B, Perovic VR, Davidović RS, Sumonja N, Veljkovic N, Asgari E, Mofrad MRK, Profiti G, Savojardo C, Martelli PL, Casadio R, Boecker F, Schoof H, Kahanda I, Thurlby N, McHardy AC, Renaux A, Saidi R, Gough J, Freitas AA, Antczak M, Fabris F, Wass MN, Hou J, Cheng J, Wang Z, Romero AE, Paccanaro A, Yang H, Goldberg T, Zhao C, Holm L, Törönen P, Medlar AJ, Zosa E, Borukhov I, Novikov I, Wilkins A, Lichtarge O, Chi PH, Tseng WC, Linial M, Rose PW, Dessimoz C, Vidulin V, Dzeroski S, Sillitoe I, Das S, Lees JG, Jones DT, Wan C, Cozzetto D, Fa R, Torres M, Warwick Vesztrocy A, Rodriguez JM, Tress ML, Frasca M, Notaro M, Grossi G, Petrini A, Re M, Valentini G, Mesiti M, Roche DB, Reeb J, Ritchie DW, Aridhi S, Alborzi SZ, Devignes MD, Koo DCE, Bonneau R, Gligorijević V, Barot M, Fang H, Toppo S, Lavezzo E, Falda M, Berselli M, Tosatto SCE, Carraro M, Piovesan D, Ur Rehman H, Mao Q, Zhang S, Vucetic S, Black GS, Jo D, Suh E, Dayton JB, Larsen DJ, Omdahl AR, McGuffin LJ, Brackenridge DA, Babbitt PC, Yunes JM, Fontana P, Zhang F, Zhu S, You R, Zhang Z, Dai S, Yao S, Tian W, Cao R, Chandler C, Amezola M, Johnson D, Chang JM, Liao WH, Liu YW, Pascarelli S, Frank Y, Hoehndorf R, Kulmanov M, Boudellioua I, Politano G, Di Carlo S, Benso A, Hakala K, Ginter F, Mehryary F, Kaewphan S, Björne J, Moen H, Tolvanen MEE, Salakoski T, Kihara D, Jain A, Šmuc T, Altenhoff A, Ben-Hur A, Rost B, Brenner SE, Orengo CA, Jeffery CJ, Bosco G, Hogan DA, Martin MJ, O'Donovan C, Mooney SD, Greene CS, Radivojac P, Friedberg I.

Genome Biol. 2019 Nov 19;20(1):244. doi: 10.1186/s13059-019-1835-8.

3.

TOPAZ: asymmetric suffix array neighbourhood search for massive protein databases.

Medlar A, Holm L.

BMC Bioinformatics. 2018 Jul 31;19(1):278. doi: 10.1186/s12859-018-2290-3.

4.

AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination.

Medlar AJ, Törönen P, Holm L.

Nucleic Acids Res. 2018 Jul 2;46(W1):W479-W485. doi: 10.1093/nar/gky359.

5.

PANNZER2: a rapid functional annotation web server.

Törönen P, Medlar A, Holm L.

Nucleic Acids Res. 2018 Jul 2;46(W1):W84-W88. doi: 10.1093/nar/gky350.

6.

HaploForge: a comprehensive pedigree drawing and haplotype visualization web application.

Tekman M, Medlar A, Mozere M, Kleta R, Stanescu H.

Bioinformatics. 2017 Dec 15;33(24):3871-3877. doi: 10.1093/bioinformatics/btx510.

PMID:
28961780
7.

Opportunities and challenges in metabarcoding approaches for helminth community identification in wild mammals.

Aivelo T, Medlar A.

Parasitology. 2018 Apr;145(5):608-621. doi: 10.1017/S0031182017000610. Epub 2017 May 23. Review.

PMID:
28534454
8.

Autoinflammatory periodic fever, immunodeficiency, and thrombocytopenia (PFIT) caused by mutation in actin-regulatory gene WDR1.

Standing AS, Malinova D, Hong Y, Record J, Moulding D, Blundell MP, Nowak K, Jones H, Omoyinmi E, Gilmour KC, Medlar A, Stanescu H, Kleta R, Anderson G, Nanthapisal S, Gomes SM, Klein N, Eleftheriou D, Thrasher AJ, Brogan PA.

J Exp Med. 2017 Jan;214(1):59-71. doi: 10.1084/jem.20161228. Epub 2016 Dec 19.

9.

Robust multi-group gene set analysis with few replicates.

Mishra PP, Medlar A, Holm L, Törönen P.

BMC Bioinformatics. 2016 Dec 9;17(1):526.

10.

Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization.

Veidenberg A, Medlar A, Löytynoja A.

Mol Biol Evol. 2016 Apr;33(4):1126-30. doi: 10.1093/molbev/msv333. Epub 2015 Dec 3.

PMID:
26635364
11.

Tracking year-to-year changes in intestinal nematode communities of rufous mouse lemurs (Microcebus rufus).

Aivelo T, Medlar A, Löytynoja A, Laakkonen J, Jernvall J.

Parasitology. 2015 Jul;142(8):1095-107. doi: 10.1017/S0031182015000438. Epub 2015 Apr 20.

PMID:
25892063
12.

Séance: reference-based phylogenetic analysis for 18S rRNA studies.

Medlar A, Aivelo T, Löytynoja A.

BMC Evol Biol. 2014 Nov 30;14:235. doi: 10.1186/s12862-014-0235-7.

13.

Nephrocalcinosis (enamel renal syndrome) caused by autosomal recessive FAM20A mutations.

Jaureguiberry G, De la Dure-Molla M, Parry D, Quentric M, Himmerkus N, Koike T, Poulter J, Klootwijk E, Robinette SL, Howie AJ, Patel V, Figueres ML, Stanescu HC, Issler N, Nicholson JK, Bockenhauer D, Laing C, Walsh SB, McCredie DA, Povey S, Asselin A, Picard A, Coulomb A, Medlar AJ, Bailleul-Forestier I, Verloes A, Le Caignec C, Roussey G, Guiol J, Isidor B, Logan C, Shore R, Johnson C, Inglehearn C, Al-Bahlani S, Schmittbuhl M, Clauss F, Huckert M, Laugel V, Ginglinger E, Pajarola S, Spartà G, Bartholdi D, Rauch A, Addor MC, Yamaguti PM, Safatle HP, Acevedo AC, Martelli-Júnior H, dos Santos Netos PE, Coletta RD, Gruessel S, Sandmann C, Ruehmann D, Langman CB, Scheinman SJ, Ozdemir-Ozenen D, Hart TC, Hart PS, Neugebauer U, Schlatter E, Houillier P, Gahl WA, Vikkula M, Bloch-Zupan A, Bleich M, Kitagawa H, Unwin RJ, Mighell A, Berdal A, Kleta R.

Nephron Physiol. 2012;122(1-2):1-6. doi: 10.1159/000349989. Epub 2013 Feb 23.

14.

Phospholipase A2 receptor (PLA2R1) sequence variants in idiopathic membranous nephropathy.

Coenen MJ, Hofstra JM, Debiec H, Stanescu HC, Medlar AJ, Stengel B, Boland-Augé A, Groothuismink JM, Bockenhauer D, Powis SH, Mathieson PW, Brenchley PE, Kleta R, Wetzels JF, Ronco P.

J Am Soc Nephrol. 2013 Mar;24(4):677-83. doi: 10.1681/ASN.2012070730. Epub 2013 Feb 21.

15.

Mutations in the autoregulatory domain of β-tubulin 4a cause hereditary dystonia.

Hersheson J, Mencacci NE, Davis M, MacDonald N, Trabzuni D, Ryten M, Pittman A, Paudel R, Kara E, Fawcett K, Plagnol V, Bhatia KP, Medlar AJ, Stanescu HC, Hardy J, Kleta R, Wood NW, Houlden H.

Ann Neurol. 2013 Apr;73(4):546-53. doi: 10.1002/ana.23832. Epub 2013 Feb 19.

16.

SwiftLink: parallel MCMC linkage analysis using multicore CPU and GPU.

Medlar A, Głowacka D, Stanescu H, Bryson K, Kleta R.

Bioinformatics. 2013 Feb 15;29(4):413-9. doi: 10.1093/bioinformatics/bts704. Epub 2012 Dec 13.

PMID:
23239673
17.

Linkage analysis confirms heterogeneity of hereditary gingival fibromatosis.

Nibali L, Medlar A, Stanescu H, Kleta R, Darbar U, Donos N.

Oral Dis. 2013 Jan;19(1):100-5. doi: 10.1111/j.1601-0825.2012.01965.x. Epub 2012 Jul 31.

PMID:
22849749
18.

Genetic testing in renal disease.

Bockenhauer D, Medlar AJ, Ashton E, Kleta R, Lench N.

Pediatr Nephrol. 2012 Jun;27(6):873-83. doi: 10.1007/s00467-011-1865-2. Epub 2011 May 27. Review.

PMID:
21617915
19.

Risk HLA-DQA1 and PLA(2)R1 alleles in idiopathic membranous nephropathy.

Stanescu HC, Arcos-Burgos M, Medlar A, Bockenhauer D, Kottgen A, Dragomirescu L, Voinescu C, Patel N, Pearce K, Hubank M, Stephens HA, Laundy V, Padmanabhan S, Zawadzka A, Hofstra JM, Coenen MJ, den Heijer M, Kiemeney LA, Bacq-Daian D, Stengel B, Powis SH, Brenchley P, Feehally J, Rees AJ, Debiec H, Wetzels JF, Ronco P, Mathieson PW, Kleta R.

N Engl J Med. 2011 Feb 17;364(7):616-26. doi: 10.1056/NEJMoa1009742.

20.

Cystinosis and mickey mouse.

Medlar A, Kleta R.

Nephrol Dial Transplant. 2010 Apr;25(4):1032-3. doi: 10.1093/ndt/gfp648. Epub 2009 Dec 3. No abstract available.

PMID:
19959600

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