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Items: 1 to 50 of 65

1.

The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata.

Armaleo D, Müller O, Lutzoni F, Andrésson ÓS, Blanc G, Bode HB, Collart FR, Dal Grande F, Dietrich F, Grigoriev IV, Joneson S, Kuo A, Larsen PE, Logsdon JM Jr, Lopez D, Martin F, May SP, McDonald TR, Merchant SS, Miao V, Morin E, Oono R, Pellegrini M, Rubinstein N, Sanchez-Puerta MV, Savelkoul E, Schmitt I, Slot JC, Soanes D, Szövényi P, Talbot NJ, Veneault-Fourrey C, Xavier BB.

BMC Genomics. 2019 Jul 23;20(1):605. doi: 10.1186/s12864-019-5629-x.

2.

Pseudomonas fluorescens increases mycorrhization and modulates expression of antifungal defense response genes in roots of aspen seedlings.

Shinde S, Zerbs S, Collart FR, Cumming JR, Noirot P, Larsen PE.

BMC Plant Biol. 2019 Jan 3;19(1):4. doi: 10.1186/s12870-018-1610-0.

3.

Modeling the Pseudomonas Sulfur Regulome by Quantifying the Storage and Communication of Information.

Larsen PE, Zerbs S, Laible PD, Collart FR, Korajczyk P, Dai Y, Noirot P.

mSystems. 2018 Jun 19;3(3). pii: e00189-17. doi: 10.1128/mSystems.00189-17. eCollection 2018 May-Jun.

4.

Pseudomonas fluorescens Transportome Is Linked to Strain-Specific Plant Growth Promotion in Aspen Seedlings under Nutrient Stress.

Shinde S, Cumming JR, Collart FR, Noirot PH, Larsen PE.

Front Plant Sci. 2017 Mar 21;8:348. doi: 10.3389/fpls.2017.00348. eCollection 2017.

5.

Transport capabilities of environmental Pseudomonads for sulfur compounds.

Zerbs S, Korajczyk PJ, Noirot PH, Collart FR.

Protein Sci. 2017 Apr;26(4):784-795. doi: 10.1002/pro.3124. Epub 2017 Feb 10.

6.

Multi-Omics Approach Identifies Molecular Mechanisms of Plant-Fungus Mycorrhizal Interaction.

Larsen PE, Sreedasyam A, Trivedi G, Desai S, Dai Y, Cseke LJ, Collart FR.

Front Plant Sci. 2016 Jan 19;6:1061. doi: 10.3389/fpls.2015.01061. eCollection 2015.

7.

Live Cell Discovery of Microbial Vitamin Transport and Enzyme-Cofactor Interactions.

Anderson LN, Koech PK, Plymale AE, Landorf EV, Konopka A, Collart FR, Lipton MS, Romine MF, Wright AT.

ACS Chem Biol. 2016 Feb 19;11(2):345-54. doi: 10.1021/acschembio.5b00918. Epub 2015 Dec 22.

PMID:
26669591
8.

Predicting Ecological Roles in the Rhizosphere Using Metabolome and Transportome Modeling.

Larsen PE, Collart FR, Dai Y.

PLoS One. 2015 Sep 2;10(9):e0132837. doi: 10.1371/journal.pone.0132837. eCollection 2015.

9.

Using metabolomic and transportomic modeling and machine learning to identify putative novel therapeutic targets for antibiotic resistant Pseudomonad infections.

Larsen PE, Collart FR, Dai Y.

Conf Proc IEEE Eng Med Biol Soc. 2014;2014:314-7. doi: 10.1109/EMBC.2014.6943592.

PMID:
25569960
10.

Predicting bacterial community assemblages using an artificial neural network approach.

Larsen P, Dai Y, Collart FR.

Methods Mol Biol. 2015;1260:33-43. doi: 10.1007/978-1-4939-2239-0_3.

PMID:
25502374
11.

Modeling forest ecosystem responses to elevated carbon dioxide and ozone using artificial neural networks.

Larsen PE, Cseke LJ, Miller RM, Collart FR.

J Theor Biol. 2014 Oct 21;359:61-71. doi: 10.1016/j.jtbi.2014.05.047. Epub 2014 Jun 10.

PMID:
24928153
12.

Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-coumaric acid and related aromatic acids.

Tan K, Chang C, Cuff M, Osipiuk J, Landorf E, Mack JC, Zerbs S, Joachimiak A, Collart FR.

Proteins. 2013 Oct;81(10):1709-26. doi: 10.1002/prot.24305. Epub 2013 Jul 23.

13.

Characterization of transport proteins for aromatic compounds derived from lignin: benzoate derivative binding proteins.

Michalska K, Chang C, Mack JC, Zerbs S, Joachimiak A, Collart FR.

J Mol Biol. 2012 Nov 2;423(4):555-75. doi: 10.1016/j.jmb.2012.08.017. Epub 2012 Aug 25.

14.

BowStrap v1.0: Assigning statistical significance to expressed genes using short-read transcriptome data.

Larsen PE, Collart FR.

BMC Res Notes. 2012 Jun 7;5:275. doi: 10.1186/1756-0500-5-275.

15.

Biophysical and structural characterization of a sequence-diverse set of solute-binding proteins for aromatic compounds.

Pietri R, Zerbs S, Corgliano DM, Allaire M, Collart FR, Miller LM.

J Biol Chem. 2012 Jul 6;287(28):23748-56. doi: 10.1074/jbc.M112.352385. Epub 2012 May 10.

16.

Environment sensing and response mediated by ABC transporters.

Giuliani SE, Frank AM, Corgliano DM, Seifert C, Hauser L, Collart FR.

BMC Genomics. 2011 Jun 15;12 Suppl 1:S8. doi: 10.1186/1471-2164-12-S1-S8.

17.

Using next generation transcriptome sequencing to predict an ectomycorrhizal metabolome.

Larsen PE, Sreedasyam A, Trivedi G, Podila GK, Cseke LJ, Collart FR.

BMC Syst Biol. 2011 May 13;5:70. doi: 10.1186/1752-0509-5-70.

18.

Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset.

Larsen PE, Collart FR, Field D, Meyer F, Keegan KP, Henry CS, McGrath J, Quinn J, Gilbert JA.

Microb Inform Exp. 2011 Jun 14;1(1):4. doi: 10.1186/2042-5783-1-4.

19.

Using deep RNA sequencing for the structural annotation of the Laccaria bicolor mycorrhizal transcriptome.

Larsen PE, Trivedi G, Sreedasyam A, Lu V, Podila GK, Collart FR.

PLoS One. 2010 Jul 6;5(7):e9780. doi: 10.1371/journal.pone.0009780.

20.

Bacterial systems for production of heterologous proteins.

Zerbs S, Frank AM, Collart FR.

Methods Enzymol. 2009;463:149-68. doi: 10.1016/S0076-6879(09)63012-3. Review.

PMID:
19892172
21.

Crystal structures of YkuI and its complex with second messenger cyclic Di-GMP suggest catalytic mechanism of phosphodiester bond cleavage by EAL domains.

Minasov G, Padavattan S, Shuvalova L, Brunzelle JS, Miller DJ, Baslé A, Massa C, Collart FR, Schirmer T, Anderson WF.

J Biol Chem. 2009 May 8;284(19):13174-84. doi: 10.1074/jbc.M808221200. Epub 2009 Feb 24.

22.

Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization.

Pinchuk GE, Rodionov DA, Yang C, Li X, Osterman AL, Dervyn E, Geydebrekht OV, Reed SB, Romine MF, Collart FR, Scott JH, Fredrickson JK, Beliaev AS.

Proc Natl Acad Sci U S A. 2009 Feb 24;106(8):2874-9. doi: 10.1073/pnas.0806798106. Epub 2009 Feb 5.

23.

Functional assignment of solute-binding proteins of ABC transporters using a fluorescence-based thermal shift assay.

Giuliani SE, Frank AM, Collart FR.

Biochemistry. 2008 Dec 30;47(52):13974-84. doi: 10.1021/bi801648r.

PMID:
19063603
24.

"System 48" high-throughput cloning and protein expression analysis.

Abdullah JM, Joachimiak A, Collart FR.

Methods Mol Biol. 2009;498:117-27. doi: 10.1007/978-1-59745-196-3_8.

25.

Addressing Shewanella oneidensis "cytochromome": the first step towards high-throughput expression of cytochromes c.

Londer YY, Giuliani SE, Peppler T, Collart FR.

Protein Expr Purif. 2008 Nov;62(1):128-37. doi: 10.1016/j.pep.2008.06.014. Epub 2008 Jul 8.

PMID:
18657620
26.

Efficient site-specific labeling of proteins via cysteines.

Kim Y, Ho SO, Gassman NR, Korlann Y, Landorf EV, Collart FR, Weiss S.

Bioconjug Chem. 2008 Mar;19(3):786-91. doi: 10.1021/bc7002499. Epub 2008 Feb 15.

27.

Crystal structure of an apo form of Shigella flexneri ArsH protein with an NADPH-dependent FMN reductase activity.

Vorontsov II, Minasov G, Brunzelle JS, Shuvalova L, Kiryukhina O, Collart FR, Anderson WF.

Protein Sci. 2007 Nov;16(11):2483-90.

28.

Development of BIATECH-54 standard mixtures for assessment of protein identification and relative expression.

Kolker E, Hogan JM, Higdon R, Kolker N, Landorf E, Yakunin AF, Collart FR, van Belle G.

Proteomics. 2007 Oct;7(20):3693-8. Review.

PMID:
17890649
29.

The 2.2 A resolution crystal structure of Bacillus cereus Nif3-family protein YqfO reveals a conserved dimetal-binding motif and a regulatory domain.

Godsey MH, Minasov G, Shuvalova L, Brunzelle JS, Vorontsov II, Collart FR, Anderson WF.

Protein Sci. 2007 Jul;16(7):1285-93.

30.

New vectors for co-expression of proteins: structure of Bacillus subtilis ScoAB obtained by high-throughput protocols.

Stols L, Zhou M, Eschenfeldt WH, Millard CS, Abdullah J, Collart FR, Kim Y, Donnelly MI.

Protein Expr Purif. 2007 Jun;53(2):396-403. Epub 2007 Feb 6.

PMID:
17363272
31.

Bacterial expression strategies for human angiogenesis proteins.

Dieckman LJ, Zhang W, Rodi DJ, Donnelly MI, Collart FR.

J Struct Funct Genomics. 2006 Mar;7(1):23-30.

PMID:
16688392
32.

Primary structure-based function characterization of BRCT domain replicates in BRCA1.

Chen Y, Borowicz S, Fackenthal J, Collart FR, Myatt E, Moy S, Babnigg G, Wilton R, Boernke WE, Schiffer M, Stevens FJ, Olopade OI.

Biochem Biophys Res Commun. 2006 Jun 23;345(1):188-96. Epub 2006 Apr 21.

PMID:
16677609
33.

An expression vector tailored for large-scale, high-throughput purification of recombinant proteins.

Donnelly MI, Zhou M, Millard CS, Clancy S, Stols L, Eschenfeldt WH, Collart FR, Joachimiak A.

Protein Expr Purif. 2006 Jun;47(2):446-54. Epub 2006 Jan 30.

34.

Automated purification of recombinant proteins: combining high-throughput with high yield.

Lin CT, Moore PA, Auberry DL, Landorf EV, Peppler T, Victry KD, Collart FR, Kery V.

Protein Expr Purif. 2006 May;47(1):16-24. Epub 2005 Dec 15.

PMID:
16406573
35.

Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations.

Kolker E, Picone AF, Galperin MY, Romine MF, Higdon R, Makarova KS, Kolker N, Anderson GA, Qiu X, Auberry KJ, Babnigg G, Beliaev AS, Edlefsen P, Elias DA, Gorby YA, Holzman T, Klappenbach JA, Konstantinidis KT, Land ML, Lipton MS, McCue LA, Monroe M, Pasa-Tolic L, Pinchuk G, Purvine S, Serres MH, Tsapin S, Zakrajsek BA, Zhu W, Zhou J, Larimer FW, Lawrence CE, Riley M, Collart FR, Yates JR 3rd, Smith RD, Giometti CS, Nealson KH, Fredrickson JK, Tiedje JM.

Proc Natl Acad Sci U S A. 2005 Feb 8;102(6):2099-104. Epub 2005 Jan 31.

36.

Efficient recognition of protein fold at low sequence identity by conservative application of Psi-BLAST: application.

Stevens FJ, Kuemmel C, Babnigg G, Collart FR.

J Mol Recognit. 2005 Mar-Apr;18(2):150-7.

PMID:
15593246
37.

Crystal structure of Bacillus subtilis YdaF protein: a putative ribosomal N-acetyltransferase.

Brunzelle JS, Wu R, Korolev SV, Collart FR, Joachimiak A, Anderson WF.

Proteins. 2004 Dec 1;57(4):850-3. No abstract available.

38.

In vivo biotinylated proteins as targets for phage-display selection experiments.

Scholle MD, Collart FR, Kay BK.

Protein Expr Purif. 2004 Sep;37(1):243-52.

PMID:
15294305
39.

Genome-scale expression of proteins from Bacillus subtilis.

Moy S, Dieckman L, Schiffer M, Maltsev N, Yu GX, Collart FR.

J Struct Funct Genomics. 2004;5(1-2):103-9.

PMID:
15263849
40.

Express primer tool for high-throughput gene cloning and expression.

Yoon JR, Laible PD, Gu M, Scott HN, Collart FR.

Biotechniques. 2002 Dec;33(6):1328-33.

41.

A new vector for high-throughput, ligation-independent cloning encoding a tobacco etch virus protease cleavage site.

Stols L, Gu M, Dieckman L, Raffen R, Collart FR, Donnelly MI.

Protein Expr Purif. 2002 Jun;25(1):8-15.

PMID:
12071693
42.

High throughput methods for gene cloning and expression.

Dieckman L, Gu M, Stols L, Donnelly MI, Collart FR.

Protein Expr Purif. 2002 Jun;25(1):1-7.

PMID:
12071692
43.

Differential signatures of bacterial and mammalian IMP dehydrogenase enzymes.

Zhang R, Evans G, Rotella F, Westbrook E, Huberman E, Joachimiak A, Collart FR.

Curr Med Chem. 1999 Jul;6(7):537-43.

PMID:
10390599
44.

Characteristics and crystal structure of bacterial inosine-5'-monophosphate dehydrogenase.

Zhang R, Evans G, Rotella FJ, Westbrook EM, Beno D, Huberman E, Joachimiak A, Collart FR.

Biochemistry. 1999 Apr 13;38(15):4691-700.

PMID:
10200156
45.
46.

Isosteric analogues of nicotinamide adenine dinucleotide derived from furanfurin, thiophenfurin, and selenophenfurin as mammalian inosine monophosphate dehydrogenase (type I and II) inhibitors.

Franchetti P, Cappellacci L, Perlini P, Jayaram HN, Butler A, Schneider BP, Collart FR, Huberman E, Grifantini M.

J Med Chem. 1998 May 7;41(10):1702-7.

PMID:
9572896
47.

Cloning and characterization of the gene encoding IMP dehydrogenase from Arabidopsis thaliana.

Collart FR, Osipiuk J, Trent J, Olsen GJ, Huberman E.

Gene. 1996 Oct 3;174(2):217-20.

PMID:
8890737
48.

Cloning, characterization and sequence comparison of the gene coding for IMP dehydrogenase from Pyrococcus furiosus.

Collart FR, Osipiuk J, Trent J, Olsen GJ, Huberman E.

Gene. 1996 Oct 3;174(2):209-16.

PMID:
8890736
49.

Interferon-independent activation of (2'-5') oligoadenylate synthetase in Friend erythroleukemia cell variants exposed to HMBA.

Salzberg S, Heller A, Zou JP, Collart FR, Huberman E.

J Cell Sci. 1996 Jun;109 ( Pt 6):1517-26.

50.

Recombinant human inosine monophosphate dehydrogenase type I and type II proteins. Purification and characterization of inhibitor binding.

Hager PW, Collart FR, Huberman E, Mitchell BS.

Biochem Pharmacol. 1995 May 11;49(9):1323-9.

PMID:
7763314

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