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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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


"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.


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.

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