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Items: 1 to 50 of 65

1.

Cross-sectional survey of health management and prevalence of vector-borne diseases, endoparasites and ectoparasites in Samoan dogs.

Carslake RJ, Hill KE, Sjölander K, Hii SF, Prattley D, Acke E.

Aust Vet J. 2017 Dec;95(12):462-468. doi: 10.1111/avj.12647.

PMID:
29243242
2.

Standardized benchmarking in the quest for orthologs.

Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, Lecompte O, von Mering C, Xenarios I, Sjölander K, Jensen LJ, Martin MJ, Muffato M; Quest for Orthologs consortium, Gabaldón T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C.

Nat Methods. 2016 May;13(5):425-30. doi: 10.1038/nmeth.3830. Epub 2016 Apr 4.

3.

The COMBREX project: design, methodology, and initial results.

Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, Kasif S.

PLoS Biol. 2013;11(8):e1001638. doi: 10.1371/journal.pbio.1001638. Epub 2013 Aug 27. No abstract available.

4.

The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification.

Afrasiabi C, Samad B, Dineen D, Meacham C, Sjölander K.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W242-8. doi: 10.1093/nar/gkt399. Epub 2013 May 18.

5.

The interface of protein structure, protein biophysics, and molecular evolution.

Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S.

Protein Sci. 2012 Jun;21(6):769-85. doi: 10.1002/pro.2071. Epub 2012 Apr 23. Review.

6.

Distribution and properties of the genes encoding the biosynthesis of the bacterial cofactor, pyrroloquinoline quinone.

Shen YQ, Bonnot F, Imsand EM, RoseFigura JM, Sjölander K, Klinman JP.

Biochemistry. 2012 Mar 20;51(11):2265-75. doi: 10.1021/bi201763d. Epub 2012 Mar 9.

7.

Ortholog identification in the presence of domain architecture rearrangement.

Sjölander K, Datta RS, Shen Y, Shoffner GM.

Brief Bioinform. 2011 Sep;12(5):413-22. doi: 10.1093/bib/bbr036. Epub 2011 Jun 28. Review.

8.

ModBase, a database of annotated comparative protein structure models, and associated resources.

Pieper U, Webb BM, Barkan DT, Schneidman-Duhovny D, Schlessinger A, Braberg H, Yang Z, Meng EC, Pettersen EF, Huang CC, Datta RS, Sampathkumar P, Madhusudhan MS, Sjölander K, Ferrin TE, Burley SK, Sali A.

Nucleic Acids Res. 2011 Jan;39(Database issue):D465-74. doi: 10.1093/nar/gkq1091. Epub 2010 Nov 19.

9.

Arabidopsis thaliana PGR7 encodes a conserved chloroplast protein that is necessary for efficient photosynthetic electron transport.

Jung HS, Okegawa Y, Shih PM, Kellogg E, Abdel-Ghany SE, Pilon M, Sjölander K, Shikanai T, Niyogi KK.

PLoS One. 2010 Jul 21;5(7):e11688. doi: 10.1371/journal.pone.0011688.

10.

SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction.

Hagopian R, Davidson JR, Datta RS, Samad B, Jarvis GR, Sjölander K.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W29-34. doi: 10.1093/nar/gkq298. Epub 2010 Apr 29.

11.

Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase.

Gaudet P, Lane L, Fey P, Bridge A, Poux S, Auchincloss A, Axelsen K, Braconi Quintaje S, Boutet E, Brown P, Coudert E, Datta RS, de Lima WC, de Oliveira Lima T, Duvaud S, Farriol-Mathis N, Ferro Rojas S, Feuermann M, Gateau A, Hinz U, Hulo C, James J, Jimenez S, Jungo F, Keller G, Lemercier P, Lieberherr D, Moinat M, Nikolskaya A, Pedruzzi I, Rivoire C, Roechert B, Schneider M, Stanley E, Tognolli M, Sjölander K, Bougueleret L, Chisholm RL, Bairoch A.

Database (Oxford). 2009;2009:bap016. Epub 2009 Oct 15.

12.

Getting started in structural phylogenomics.

Sjölander K.

PLoS Comput Biol. 2010 Jan 29;6(1):e1000621. doi: 10.1371/journal.pcbi.1000621. No abstract available.

13.

Active site prediction using evolutionary and structural information.

Sankararaman S, Sha F, Kirsch JF, Jordan MI, Sjölander K.

Bioinformatics. 2010 Mar 1;26(5):617-24. doi: 10.1093/bioinformatics/btq008. Epub 2010 Jan 14.

14.

ResBoost: characterizing and predicting catalytic residues in enzymes.

Alterovitz R, Arvey A, Sankararaman S, Dallett C, Freund Y, Sjölander K.

BMC Bioinformatics. 2009 Jun 27;10:197. doi: 10.1186/1471-2105-10-197.

15.

INTREPID: a web server for prediction of functionally important residues by evolutionary analysis.

Sankararaman S, Kolaczkowski B, Sjölander K.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W390-5. doi: 10.1093/nar/gkp339. Epub 2009 May 13.

16.

Berkeley PHOG: PhyloFacts orthology group prediction web server.

Datta RS, Meacham C, Samad B, Neyer C, Sjölander K.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W84-9. doi: 10.1093/nar/gkp373. Epub 2009 May 12.

17.

INTREPID--INformation-theoretic TREe traversal for Protein functional site IDentification.

Sankararaman S, Sjölander K.

Bioinformatics. 2008 Nov 1;24(21):2445-52. doi: 10.1093/bioinformatics/btn474. Epub 2008 Sep 6.

18.

Basic protein sequence analysis.

Krishnamurthy N, Sjölander KV.

Curr Protoc Protein Sci. 2005 Sep;Chapter 2:Unit 2.11. doi: 10.1002/0471140864.ps0211s41.

PMID:
18429280
19.

Phylogenomic inference of protein molecular function.

Krishnamurthy N, Sjölander K.

Curr Protoc Bioinformatics. 2005 Oct;Chapter 6:Unit 6.9. doi: 10.1002/0471250953.bi0609s11.

PMID:
18428751
20.

Basic protein sequence analysis.

Krishnamurthy N, Sjölander KV.

Curr Protoc Mol Biol. 2005 May;Chapter 19:Unit 19.5. doi: 10.1002/0471142727.mb1905s70.

PMID:
18265355
21.

The Generation Challenge Programme comparative plant stress-responsive gene catalogue.

Wanchana S, Thongjuea S, Ulat VJ, Anacleto M, Mauleon R, Conte M, Rouard M, Ruiz M, Krishnamurthy N, Sjolander K, van Hintum T, Bruskiewich RM.

Nucleic Acids Res. 2008 Jan;36(Database issue):D943-6. Epub 2007 Oct 11.

22.

Automated protein subfamily identification and classification.

Brown DP, Krishnamurthy N, Sjölander K.

PLoS Comput Biol. 2007 Aug;3(8):e160.

23.

Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis.

Glanville JG, Kirshner D, Krishnamurthy N, Sjölander K.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W27-32. Epub 2007 May 8.

24.
25.

Arabidopsis downy mildew resistance gene RPP27 encodes a receptor-like protein similar to CLAVATA2 and tomato Cf-9.

Tör M, Brown D, Cooper A, Woods-Tör A, Sjölander K, Jones J D G, Holub E B.

Plant Physiol. 2007 Feb;143(2):1079. No abstract available.

26.
27.

Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA).

Leebens-Mack J, Vision T, Brenner E, Bowers JE, Cannon S, Clement MJ, Cunningham CW, dePamphilis C, deSalle R, Doyle JJ, Eisen JA, Gu X, Harshman J, Jansen RK, Kellogg EA, Koonin EV, Mishler BD, Philippe H, Pires JC, Qiu YL, Rhee SY, Sjölander K, Soltis DE, Soltis PS, Stevenson DW, Wall K, Warnow T, Zmasek C.

OMICS. 2006 Summer;10(2):231-7. Review.

28.

Functional classification using phylogenomic inference.

Brown D, Sjölander K.

PLoS Comput Biol. 2006 Jun 30;2(6):e77. Review. No abstract available.

29.

Phylogenomic analysis of the receptor-like proteins of rice and Arabidopsis.

Fritz-Laylin LK, Krishnamurthy N, Tör M, Sjölander KV, Jones JD.

Plant Physiol. 2005 Jun;138(2):611-23.

30.

Proteome analysis of the rice etioplast: metabolic and regulatory networks and novel protein functions.

von Zychlinski A, Kleffmann T, Krishnamurthy N, Sjölander K, Baginsky S, Gruissem W.

Mol Cell Proteomics. 2005 Aug;4(8):1072-84. Epub 2005 May 18.

31.

Subfamily hmms in functional genomics.

Brown D, Krishnamurthy N, Dale JM, Christopher W, Sjölander K.

Pac Symp Biocomput. 2005:322-33.

32.

Molecular characterization of proteolytic cleavage sites of the Pseudomonas syringae effector AvrRpt2.

Chisholm ST, Dahlbeck D, Krishnamurthy N, Day B, Sjolander K, Staskawicz BJ.

Proc Natl Acad Sci U S A. 2005 Feb 8;102(6):2087-92. Epub 2005 Jan 31.

33.

Predicted hexameric structure of the Agrobacterium VirB4 C terminus suggests VirB4 acts as a docking site during type IV secretion.

Middleton R, Sjölander K, Krishnamurthy N, Foley J, Zambryski P.

Proc Natl Acad Sci U S A. 2005 Feb 1;102(5):1685-90. Epub 2005 Jan 24.

34.

Functional analysis of Avr9/Cf-9 rapidly elicited genes identifies a protein kinase, ACIK1, that is essential for full Cf-9-dependent disease resistance in tomato.

Rowland O, Ludwig AA, Merrick CJ, Baillieul F, Tracy FE, Durrant WE, Fritz-Laylin L, Nekrasov V, Sjölander K, Yoshioka H, Jones JD.

Plant Cell. 2005 Jan;17(1):295-310. Epub 2004 Dec 14.

35.

Characterization of tick-borne encephalitis virus from Estonia.

Golovljova I, Vene S, Sjölander KB, Vasilenko V, Plyusnin A, Lundkvist A.

J Med Virol. 2004 Dec;74(4):580-8.

PMID:
15484275
36.

From endonucleases to transcription factors: evolution of the AP2 DNA binding domain in plants.

Magnani E, Sjölander K, Hake S.

Plant Cell. 2004 Sep;16(9):2265-77. Epub 2004 Aug 19.

37.
38.

The Arabidopsis thaliana chloroplast proteome reveals pathway abundance and novel protein functions.

Kleffmann T, Russenberger D, von Zychlinski A, Christopher W, Sjölander K, Gruissem W, Baginsky S.

Curr Biol. 2004 Mar 9;14(5):354-62.

39.

COACH: profile-profile alignment of protein families using hidden Markov models.

Edgar RC, Sjölander K.

Bioinformatics. 2004 May 22;20(8):1309-18. Epub 2004 Feb 12.

PMID:
14962937
40.

A comparison of scoring functions for protein sequence profile alignment.

Edgar RC, Sjölander K.

Bioinformatics. 2004 May 22;20(8):1301-8. Epub 2004 Feb 12.

PMID:
14962936
41.

Phylogenomic inference of protein molecular function: advances and challenges.

Sjölander K.

Bioinformatics. 2004 Jan 22;20(2):170-9. Review.

PMID:
14734307
42.

Hantavirus infections in Spain: analysis of sera from the general population and from patients with pneumonia, renal disease and hepatitis.

Lledó L, Klingström J, Gegúndez MI, Plyusnina A, Vapalahti O, Saz JV, Beltrán M, Sjölander KB, Vaheri A, Plyusnin A, Lundkvist A.

J Clin Virol. 2003 Aug;27(3):296-307.

PMID:
12878094
43.

SATCHMO: sequence alignment and tree construction using hidden Markov models.

Edgar RC, Sjölander K.

Bioinformatics. 2003 Jul 22;19(11):1404-11.

PMID:
12874053
44.
45.

Hantaviruses in Estonia.

Golovljova I, Sjölander KB, Lindegren G, Vene S, Vasilenko V, Plyusnin A, Lundkvist A.

J Med Virol. 2002 Dec;68(4):589-98.

PMID:
12376968
46.

Rodent host specificity of European hantaviruses: evidence of Puumala virus interspecific spillover.

Klingström J, Heyman P, Escutenaire S, Sjölander KB, De Jaegere F, Henttonen H, Lundkvist A.

J Med Virol. 2002 Dec;68(4):581-8.

PMID:
12376967
47.

Serological divergence of Dobrava and Saaremaa hantaviruses: evidence for two distinct serotypes.

Sjölander KB, Golovljova I, Vasilenko V, Plyusnin A, Lundkvist A.

Epidemiol Infect. 2002 Feb;128(1):99-103.

48.

Modifying the cellular transport of DNA-based vaccines alters the immune response to hantavirus nucleocapsid protein.

Bucht G, Sjölander KB, Eriksson S, Lindgren L, Lundkvist A, Elgh F.

Vaccine. 2001 Jul 16;19(28-29):3820-9.

PMID:
11427253
49.

The sequence of the human genome.

Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigó R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X.

Science. 2001 Feb 16;291(5507):1304-51. Erratum in: Science 2001 Jun 5;292(5523):1838.

PMID:
11181995
50.

Evidence of Puumala Hantavirus infection in red foxes (Vulpes vulpes) in Belgium.

Escutenaire S, Pastoret PP, Sjölander KB, Heyman P, Brochier B, Lundkvist A.

Vet Rec. 2000 Sep 23;147(13):365-6. No abstract available.

PMID:
11083049

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