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Best matches for D’haeseleer P[au]:

What are DNA sequence motifs? D'haeseleer P et al. Nat Biotechnol. (2006)

Genome Sequence of the Historical Clinical Isolate Burkholderia pseudomallei PHLS 6. D'haeseleer P et al. Genome Announc. (2016)

Proteomic Profiling of <i>Burkholderia thailandensis</i> During Host Infection Using Bio-Orthogonal Noncanonical Amino Acid Tagging (BONCAT). Franco M et al. Front Cell Infect Microbiol. (2018)

Search results

Items: 44

1.

Encapsulin carrier proteins for enhanced expression of antimicrobial peptides.

Lee TH, Carpenter TS, D'haeseleer P, Savage DF, Yung MC.

Biotechnol Bioeng. 2019 Nov 10. doi: 10.1002/bit.27222. [Epub ahead of print]

PMID:
31709513
2.

Combining multiple functional annotation tools increases coverage of metabolic annotation.

Griesemer M, Kimbrel JA, Zhou CE, Navid A, D'haeseleer P.

BMC Genomics. 2018 Dec 19;19(1):948. doi: 10.1186/s12864-018-5221-9.

3.

Proteomic Profiling of Burkholderia thailandensis During Host Infection Using Bio-Orthogonal Noncanonical Amino Acid Tagging (BONCAT).

Franco M, D'haeseleer PM, Branda SS, Liou MJ, Haider Y, Segelke BW, El-Etr SH.

Front Cell Infect Microbiol. 2018 Oct 23;8:370. doi: 10.3389/fcimb.2018.00370. eCollection 2018.

4.

Metagenomic analysis of intertidal hypersaline microbial mats from Elkhorn Slough, California, grown with and without molybdate.

D'haeseleer P, Lee JZ, Prufert-Bebout L, Burow LC, Detweiler AM, Weber PK, Karaoz U, Brodie EL, Glavina Del Rio T, Tringe SG, Bebout BM, Pett-Ridge J.

Stand Genomic Sci. 2017 Nov 15;12:67. doi: 10.1186/s40793-017-0279-6. eCollection 2017.

5.

Genome Sequence of the Historical Clinical Isolate Burkholderia pseudomallei PHLS 6.

D'haeseleer P, Johnson SL, Davenport KW, Chain PS, Schoeniger J, Ray D, Sinha A, Williams KP, Peña J, Branda SS, El-Etr S.

Genome Announc. 2016 Jun 30;4(3). pii: e00649-16. doi: 10.1128/genomeA.00649-16.

6.

Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw.

Simmons CW, Reddy AP, D'haeseleer P, Khudyakov J, Billis K, Pati A, Simmons BA, Singer SW, Thelen MP, VanderGheynst JS.

Biotechnol Biofuels. 2014 Dec 31;7(1):495. doi: 10.1186/s13068-014-0180-0. eCollection 2014.

7.

Phylogenomically guided identification of industrially relevant GH1 β-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry.

Heins RA, Cheng X, Nath S, Deng K, Bowen BP, Chivian DC, Datta S, Friedland GD, D'Haeseleer P, Wu D, Tran-Gyamfi M, Scullin CS, Singh S, Shi W, Hamilton MG, Bendall ML, Sczyrba A, Thompson J, Feldman T, Guenther JM, Gladden JM, Cheng JF, Adams PD, Rubin EM, Simmons BA, Sale KL, Northen TR, Deutsch S.

ACS Chem Biol. 2014 Sep 19;9(9):2082-91. doi: 10.1021/cb500244v. Epub 2014 Jul 17.

8.

Discovery and characterization of ionic liquid-tolerant thermophilic cellulases from a switchgrass-adapted microbial community.

Gladden JM, Park JI, Bergmann J, Reyes-Ortiz V, D'haeseleer P, Quirino BF, Sale KL, Simmons BA, Singer SW.

Biotechnol Biofuels. 2014 Jan 29;7(1):15. doi: 10.1186/1754-6834-7-15.

9.

Discovery of two novel β-glucosidases from an Amazon soil metagenomic library.

Bergmann JC, Costa OY, Gladden JM, Singer S, Heins R, D'haeseleer P, Simmons BA, Quirino BF.

FEMS Microbiol Lett. 2014 Feb;351(2):147-55. doi: 10.1111/1574-6968.12332. Epub 2013 Dec 16.

10.

Discovery of microorganisms and enzymes involved in high-solids decomposition of rice straw using metagenomic analyses.

Reddy AP, Simmons CW, D'haeseleer P, Khudyakov J, Burd H, Hadi M, Simmons BA, Singer SW, Thelen MP, Vandergheynst JS.

PLoS One. 2013 Oct 25;8(10):e77985. doi: 10.1371/journal.pone.0077985. eCollection 2013.

11.

Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron.

Deangelis KM, D'Haeseleer P, Chivian D, Simmons B, Arkin AP, Mavromatis K, Malfatti S, Tringe S, Hazen TC.

Stand Genomic Sci. 2013 Feb 25;7(3):382-98. doi: 10.4056/sigs.3377516. eCollection 2013.

12.

Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass.

D'haeseleer P, Gladden JM, Allgaier M, Chain PS, Tringe SG, Malfatti SA, Aldrich JT, Nicora CD, Robinson EW, Paša-Tolić L, Hugenholtz P, Simmons BA, Singer SW.

PLoS One. 2013 Jul 19;8(7):e68465. doi: 10.1371/journal.pone.0068465. Print 2013.

13.

Rapid countermeasure discovery against Francisella tularensis based on a metabolic network reconstruction.

Chaudhury S, Abdulhameed MD, Singh N, Tawa GJ, D'haeseleer PM, Zemla AT, Navid A, Zhou CE, Franklin MC, Cheung J, Rudolph MJ, Love J, Graf JF, Rozak DA, Dankmeyer JL, Amemiya K, Daefler S, Wallqvist A.

PLoS One. 2013 May 21;8(5):e63369. doi: 10.1371/journal.pone.0063369. Print 2013.

14.

From soil to structure, a novel dimeric β-glucosidase belonging to glycoside hydrolase family 3 isolated from compost using metagenomic analysis.

McAndrew RP, Park JI, Heins RA, Reindl W, Friedland GD, D'haeseleer P, Northen T, Sale KL, Simmons BA, Adams PD.

J Biol Chem. 2013 May 24;288(21):14985-92. doi: 10.1074/jbc.M113.458356. Epub 2013 Apr 11.

15.

Glycoside hydrolases from a targeted compost metagenome, activity-screening and functional characterization.

Dougherty MJ, D'haeseleer P, Hazen TC, Simmons BA, Adams PD, Hadi MZ.

BMC Biotechnol. 2012 Jul 3;12:38. doi: 10.1186/1472-6750-12-38.

16.

Complete genome sequence of Thioalkalivibrio sp. K90mix.

Muyzer G, Sorokin DY, Mavromatis K, Lapidus A, Foster B, Sun H, Ivanova N, Pati A, D'haeseleer P, Woyke T, Kyrpides NC.

Stand Genomic Sci. 2011 Dec 31;5(3):341-55. doi: 10.4056/sigs.2315092. Epub 2011 Dec 23.

17.

A thermophilic ionic liquid-tolerant cellulase cocktail for the production of cellulosic biofuels.

Park JI, Steen EJ, Burd H, Evans SS, Redding-Johnson AM, Batth T, Benke PI, D'haeseleer P, Sun N, Sale KL, Keasling JD, Lee TS, Petzold CJ, Mukhopadhyay A, Singer SW, Simmons BA, Gladden JM.

PLoS One. 2012;7(5):e37010. doi: 10.1371/journal.pone.0037010. Epub 2012 May 23.

18.

Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus.

Khudyakov JI, D'haeseleer P, Borglin SE, Deangelis KM, Woo H, Lindquist EA, Hazen TC, Simmons BA, Thelen MP.

Proc Natl Acad Sci U S A. 2012 Aug 7;109(32):E2173-82. doi: 10.1073/pnas.1112750109. Epub 2012 May 14.

19.

Application of phenotypic microarrays to environmental microbiology.

Borglin S, Joyner D, DeAngelis KM, Khudyakov J, D'haeseleer P, Joachimiak MP, Hazen T.

Curr Opin Biotechnol. 2012 Feb;23(1):41-8. doi: 10.1016/j.copbio.2011.12.006. Epub 2012 Jan 2. Review.

20.

Complete genome sequence of "Enterobacter lignolyticus" SCF1.

Deangelis KM, D'Haeseleer P, Chivian D, Fortney JL, Khudyakov J, Simmons B, Woo H, Arkin AP, Davenport KW, Goodwin L, Chen A, Ivanova N, Kyrpides NC, Mavromatis K, Woyke T, Hazen TC.

Stand Genomic Sci. 2011 Oct 15;5(1):69-85. doi: 10.4056/sigs.2104875. Epub 2011 Sep 23.

21.

Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume.

Lu Z, Deng Y, Van Nostrand JD, He Z, Voordeckers J, Zhou A, Lee YJ, Mason OU, Dubinsky EA, Chavarria KL, Tom LM, Fortney JL, Lamendella R, Jansson JK, D'haeseleer P, Hazen TC, Zhou J.

ISME J. 2012 Feb;6(2):451-60. doi: 10.1038/ismej.2011.91. Epub 2011 Aug 4.

22.

Identification of biofilm matrix-associated proteins from an acid mine drainage microbial community.

Jiao Y, D'haeseleer P, Dill BD, Shah M, Verberkmoes NC, Hettich RL, Banfield JF, Thelen MP.

Appl Environ Microbiol. 2011 Aug;77(15):5230-7. doi: 10.1128/AEM.03005-10. Epub 2011 Jun 17.

23.

Complete genome sequence of "Thioalkalivibrio sulfidophilus" HL-EbGr7.

Muyzer G, Sorokin DY, Mavromatis K, Lapidus A, Clum A, Ivanova N, Pati A, d'Haeseleer P, Woyke T, Kyrpides NC.

Stand Genomic Sci. 2011 Feb 14;4(1):23-35. doi: 10.4056/sigs.1483693.

24.

Deep-sea oil plume enriches indigenous oil-degrading bacteria.

Hazen TC, Dubinsky EA, DeSantis TZ, Andersen GL, Piceno YM, Singh N, Jansson JK, Probst A, Borglin SE, Fortney JL, Stringfellow WT, Bill M, Conrad ME, Tom LM, Chavarria KL, Alusi TR, Lamendella R, Joyner DC, Spier C, Baelum J, Auer M, Zemla ML, Chakraborty R, Sonnenthal EL, D'haeseleer P, Holman HY, Osman S, Lu Z, Van Nostrand JD, Deng Y, Zhou J, Mason OU.

Science. 2010 Oct 8;330(6001):204-8. doi: 10.1126/science.1195979. Epub 2010 Aug 24.

25.

Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community.

Allgaier M, Reddy A, Park JI, Ivanova N, D'haeseleer P, Lowry S, Sapra R, Hazen TC, Simmons BA, VanderGheynst JS, Hugenholtz P.

PLoS One. 2010 Jan 21;5(1):e8812. doi: 10.1371/journal.pone.0008812.

26.

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.

Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D'haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, Eisen JA.

Nature. 2009 Dec 24;462(7276):1056-60. doi: 10.1038/nature08656.

27.

Complete genome sequence of Slackia heliotrinireducens type strain (RHS 1).

Pukall R, Lapidus A, Nolan M, Copeland A, Glavina Del Rio T, Lucas S, Chen F, Tice H, Cheng JF, Chertkov O, Bruce D, Goodwin L, Kuske C, Brettin T, Detter JC, Han C, Pitluck S, Pati A, Mavrommatis K, Ivanova N, Ovchinnikova G, Chen A, Palaniappan K, Schneider S, Rohde M, Chain P, D'haeseleer P, Göker M, Bristow J, Eisen JA, Markowitz V, Kyrpides NC, Klenk HP, Hugenholtz P.

Stand Genomic Sci. 2009 Nov 22;1(3):234-41. doi: 10.4056/sigs.37633.

28.

Complete genome sequence of Halogeometricum borinquense type strain (PR3).

Malfatti S, Tindall BJ, Schneider S, Fähnrich R, Lapidus A, Labuttii K, Copeland A, Glavina Del Rio T, Nolan M, Chen F, Lucas S, Tice H, Cheng JF, Bruce D, Goodwin L, Pitluck S, Anderson I, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, D'haeseleer P, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Chain P.

Stand Genomic Sci. 2009 Sep 24;1(2):150-9. doi: 10.4056/sigs.23264.

29.

Complete genome sequence of Saccharomonospora viridis type strain (P101).

Pati A, Sikorski J, Nolan M, Lapidus A, Copeland A, Glavina Del Rio T, Lucas S, Chen F, Tice H, Pitluck S, Cheng JF, Chertkov O, Brettin T, Han C, Detter JC, Kuske C, Bruce D, Goodwin L, Chain P, D'haeseleer P, Chen A, Palaniappan K, Ivanova N, Mavromatis K, Mikhailova N, Rohde M, Tindall BJ, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.

Stand Genomic Sci. 2009 Sep 24;1(2):141-9. doi: 10.4056/sigs.20263.

30.

Complete genome sequence of Sanguibacter keddieii type strain (ST-74).

Ivanova N, Sikorski J, Sims D, Brettin T, Detter JC, Han C, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Chen F, Lucas S, Tice H, Cheng JF, Bruce D, Goodwin L, Pitluck S, Pati A, Mavromatis K, Chen A, Palaniappan K, D'haeseleer P, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Göker M, Pukall R, Klenk HP, Kyrpides NC.

Stand Genomic Sci. 2009 Sep 24;1(2):110-8. doi: 10.4056/sigs.16197.

31.

Complete genome sequence of Cryptobacterium curtum type strain (12-3).

Mavrommatis K, Pukall R, Rohde C, Chen F, Sims D, Brettin T, Kuske C, Detter JC, Han C, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Tice H, Cheng JF, Bruce D, Goodwin L, Pitluck S, Ovchinnikova G, Pati A, Ivanova N, Chen A, Palaniappan K, Chain P, D'haeseleer P, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Rohde M, Klenk HP, Kyrpides NC.

Stand Genomic Sci. 2009 Sep 24;1(2):93-100. doi: 10.4056/sigs.12260.

32.

Complete genome sequence of Kytococcus sedentarius type strain (541).

Sims D, Brettin T, Detter JC, Han C, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Chen F, Lucas S, Tice H, Cheng JF, Bruce D, Goodwin L, Pitluck S, Ovchinnikova G, Pati A, Ivanova N, Mavrommatis K, Chen A, Palaniappan K, D'haeseleer P, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Schneider S, Göker M, Pukall R, Kyrpides NC, Klenk HP.

Stand Genomic Sci. 2009 Jul 20;1(1):12-20. doi: 10.4056/sigs.761.

33.

Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10).

Lapidus A, Pukall R, Labuttii K, Copeland A, Del Rio TG, Nolan M, Chen F, Lucas S, Tice H, Cheng JF, Bruce D, Goodwin L, Pitluck S, Rohde M, Göker M, Pati A, Ivanova N, Mavrommatis K, Chen A, Palaniappan K, D'haeseleer P, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.

Stand Genomic Sci. 2009 Jul 20;1(1):3-11. doi: 10.4056/sigs.492.

34.

Microbial genotype-phenotype mapping by class association rule mining.

Tamura M, D'haeseleer P.

Bioinformatics. 2008 Jul 1;24(13):1523-9. doi: 10.1093/bioinformatics/btn210. Epub 2008 May 8.

35.

How does DNA sequence motif discovery work?

D'haeseleer P.

Nat Biotechnol. 2006 Aug;24(8):959-61. Review. No abstract available.

PMID:
16900144
36.

Deciphering principles of transcription regulation in eukaryotic genomes.

Nguyen DH, D'haeseleer P.

Mol Syst Biol. 2006;2:2006.0012. Epub 2006 Apr 18.

37.

What are DNA sequence motifs?

D'haeseleer P.

Nat Biotechnol. 2006 Apr;24(4):423-5.

PMID:
16601727
38.

Estimating and improving protein interaction error rates.

D'haeseleer P, Church GM.

Proc IEEE Comput Syst Bioinform Conf. 2004:216-23.

PMID:
16448015
39.

How does gene expression clustering work?

D'haeseleer P.

Nat Biotechnol. 2005 Dec;23(12):1499-501. Review.

PMID:
16333293
40.

Closing the circle of osmoregulation.

D'haeseleer P.

Nat Biotechnol. 2005 Aug;23(8):941-2. No abstract available.

PMID:
16082361
41.

From annotated genomes to metabolic flux models and kinetic parameter fitting.

Segrè D, Zucker J, Katz J, Lin X, D'haeseleer P, Rindone WP, Kharchenko P, Nguyen DH, Wright MA, Church GM.

OMICS. 2003 Fall;7(3):301-16.

PMID:
14583118
42.

Automated modelling of signal transduction networks.

Steffen M, Petti A, Aach J, D'haeseleer P, Church G.

BMC Bioinformatics. 2002 Nov 1;3:34.

43.

Genetic network inference: from co-expression clustering to reverse engineering.

D'haeseleer P, Liang S, Somogyi R.

Bioinformatics. 2000 Aug;16(8):707-26.

PMID:
11099257
44.

Linear modeling of mRNA expression levels during CNS development and injury.

D'haeseleer P, Wen X, Fuhrman S, Somogyi R.

Pac Symp Biocomput. 1999:41-52.

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