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Items: 23

1.

Data Science Solution to Event Prediction in Outsourced Clinical Trial Models.

Dalevi D, Lovick S, Mann H, Metcalfe PD, Spencer S, Hollis S, Ruau D.

Stud Health Technol Inform. 2015;216:1065.

PMID:
26262364
2.

Combining evidence of preferential gene-tissue relationships from multiple sources.

Guo J, Hammar M, Oberg L, Padmanabhuni SS, Bjäreland M, Dalevi D.

PLoS One. 2013 Aug 12;8(8):e70568. doi: 10.1371/journal.pone.0070568. eCollection 2013.

3.

ERBB3 is a marker of a ganglioneuroblastoma/ganglioneuroma-like expression profile in neuroblastic tumours.

Wilzén A, Krona C, Sveinbjörnsson B, Kristiansson E, Dalevi D, Øra I, De Preter K, Stallings RL, Maris J, Versteeg R, Nilsson S, Kogner P, Abel F.

Mol Cancer. 2013 Jul 8;12(1):70. doi: 10.1186/1476-4598-12-70.

4.

A 6-gene signature identifies four molecular subgroups of neuroblastoma.

Abel F, Dalevi D, Nethander M, Jörnsten R, De Preter K, Vermeulen J, Stallings R, Kogner P, Maris J, Nilsson S.

Cancer Cell Int. 2011 Apr 14;11:9. doi: 10.1186/1475-2867-11-9.

5.

Estimating DNA coverage and abundance in metagenomes using a gamma approximation.

Hooper SD, Dalevi D, Pati A, Mavromatis K, Ivanova NN, Kyrpides NC.

Bioinformatics. 2010 Feb 1;26(3):295-301. doi: 10.1093/bioinformatics/btp687. Epub 2009 Dec 14.

6.

Bridging the gap between systems biology and medicine.

Clermont G, Auffray C, Moreau Y, Rocke DM, Dalevi D, Dubhashi D, Marshall DR, Raasch P, Dehne F, Provero P, Tegner J, Aronow BJ, Langston MA, Benson M.

Genome Med. 2009 Sep 29;1(9):88. doi: 10.1186/gm88.

7.

ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes.

Kristiansson E, Hugenholtz P, Dalevi D.

Bioinformatics. 2009 Oct 15;25(20):2737-8. doi: 10.1093/bioinformatics/btp508. Epub 2009 Aug 20.

PMID:
19696045
8.

Testing of chromosomal clumping of gene properties.

Fernandez-Ricaud L, Dalevi D, Blomberg A, Nerman O.

Stat Appl Genet Mol Biol. 2009;8:Article 19. doi: 10.2202/1544-6115.1428. Epub 2009 Feb 26.

PMID:
19341353
9.

Integration of phenotypic metadata and protein similarity in Archaea using a spectral bipartitioning approach.

Hooper SD, Anderson IJ, Pati A, Dalevi D, Mavromatis K, Kyrpides NC.

Nucleic Acids Res. 2009 Apr;37(7):2096-104. doi: 10.1093/nar/gkp075. Epub 2009 Feb 17.

10.

Annotation of metagenome short reads using proxygenes.

Dalevi D, Ivanova NN, Mavromatis K, Hooper SD, Szeto E, Hugenholtz P, Kyrpides NC, Markowitz VM.

Bioinformatics. 2008 Aug 15;24(16):i7-13. doi: 10.1093/bioinformatics/btn276.

PMID:
18689842
11.

A molecular study of microbe transfer between distant environments.

Hooper SD, Raes J, Foerstner KU, Harrington ED, Dalevi D, Bork P.

PLoS One. 2008 Jul 9;3(7):e2607. doi: 10.1371/journal.pone.0002607.

12.

Expected gene-order distances and model selection in bacteria.

Dalevi D, Eriksen N.

Bioinformatics. 2008 Jun 1;24(11):1332-8. doi: 10.1093/bioinformatics/btn111. Epub 2008 Apr 1.

PMID:
18381402
13.

Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite.

Warnecke F, Luginbühl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT, Cayouette M, McHardy AC, Djordjevic G, Aboushadi N, Sorek R, Tringe SG, Podar M, Martin HG, Kunin V, Dalevi D, Madejska J, Kirton E, Platt D, Szeto E, Salamov A, Barry K, Mikhailova N, Kyrpides NC, Matson EG, Ottesen EA, Zhang X, Hernández M, Murillo C, Acosta LG, Rigoutsos I, Tamayo G, Green BD, Chang C, Rubin EM, Mathur EJ, Robertson DE, Hugenholtz P, Leadbetter JR.

Nature. 2007 Nov 22;450(7169):560-5.

PMID:
18033299
14.

Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool.

Dalevi D, Desantis TZ, Fredslund J, Andersen GL, Markowitz VM, Hugenholtz P.

BMC Bioinformatics. 2007 Oct 18;8:402.

15.

IMG/M: a data management and analysis system for metagenomes.

Markowitz VM, Ivanova NN, Szeto E, Palaniappan K, Chu K, Dalevi D, Chen IM, Grechkin Y, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Hugenholtz P, Kyrpides NC.

Nucleic Acids Res. 2008 Jan;36(Database issue):D534-8. Epub 2007 Oct 11.

16.

Identification of putative regulatory upstream ORFs in the yeast genome using heuristics and evolutionary conservation.

Cvijović M, Dalevi D, Bilsland E, Kemp GJ, Sunnerhagen P.

BMC Bioinformatics. 2007 Aug 8;8:295.

17.

Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.

DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL.

Appl Environ Microbiol. 2006 Jul;72(7):5069-72.

18.

A new order estimator for fixed and variable length Markov models with applications to DNA sequence similarity.

Dalevi D, Dubhashi D, Hermansson M.

Stat Appl Genet Mol Biol. 2006;5:Article8. Epub 2006 Mar 17.

PMID:
16646872
19.

Bayesian classifiers for detecting HGT using fixed and variable order markov models of genomic signatures.

Dalevi D, Dubhashi D, Hermansson M.

Bioinformatics. 2006 Mar 1;22(5):517-22. Epub 2006 Jan 10.

PMID:
16403797
20.

Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting.

Samuelsson J, Dalevi D, Levander F, Rögnvaldsson T.

Bioinformatics. 2004 Dec 12;20(18):3628-35. Epub 2004 Aug 5.

PMID:
15297302
21.

Measuring genome divergence in bacteria: a case study using chlamydian data.

Dalevi DA, Eriksen N, Eriksson K, Andersson SG.

J Mol Evol. 2002 Jul;55(1):24-36.

PMID:
12165840
22.

Discovering the dynamics of microbial genomes.

Dalevi D, Andersson SG.

IEEE Eng Med Biol Mag. 2001 Jul-Aug;20(4):55-60. No abstract available.

PMID:
11494770
23.

A multiple-outgroup approach to resolving division-level phylogenetic relationships using 16S rDNA data.

Dalevi D, Hugenholtz P, Blackall LL.

Int J Syst Evol Microbiol. 2001 Mar;51(Pt 2):385-91.

PMID:
11321083

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