Boutard M, Ettwiller L, Cerisy T, Alberti A, Labadie K, Salanoubat M, Schildkraut I, Tolonen AC (2016)
Global repositioning of transcription start sites in a plant-fermenting bacterium
Nature Communications 7:13783 | DOI: 10.1038/ncomms13783.

Tolonen AC, Cerisy T, El-Sayyed H, Boutard M, Salanoubat M, Church GM (2015)
Fungal lysis by a soil bacterium fermenting cellulose
Environmental Microbiology 17(8):2618-27. DOI: 10.1111/1462-2920.12495.

Tolonen AC, Zuroff TR, Ramya M, Boutard M, Cerisy T, Curtis WR (2015)
Physiology, genomics, and pathway engineering of an ethanol-tolerant strain of Clostridium phytofermentans
Applied and Environmental Microbiology DOI: 10.1128/AEM.00619-1.

Petit E, Coppi MV, Hayes JC, Tolonen AC, Warnick T, Latouf WG, Amisano D, Biddle A, Mukherjee S, Ivanova N, Lykidis A, Land M, Hauser L, Kyrpides N, Henrissat B, Lau J, Schnell DJ, Church GM, Leschine SB, Blanchard JL (2015)
Genome and transcriptome of Clostridium phytofermentans, catalyst for the direct conversion of plant feedstocks to fuels
PLOS One DOI: 10.1371/journal.pone.0118285

Boutard M, Cerisy T, Nogue PY, Alberti A, Weissenbach J, Salanoubat M, Tolonen AC (2014)
Functional diversity of carbohydrate-active enzymes enabling a bacterium to ferment plant biomass
PLOS Genetics DOI: 10.1371/journal.pgen.1004773

Tolonen AC, Haas W (2014)
Quantitative proteomics using reductive dimethylation for stable isotope labeling
Journal of Visualized Experiments Issue 89. DOI: 10.3791/51416.

Tolonen AC, Petit E, Blanchard JL, Warnick T, Leschine SB (2013)
Technologies to study plant biomass fermentation using the model bacterium Clostridium phytofermentans
Royal Society of Chemistry Energy and Environment Series 10. DOI:10.1039/9781849734738-00114.

Isaacs FJ, Carr PA, Wang HH, Lajoie MJ, Sterling B, Kraal L, Tolonen AC, Gianoulis T, Goodman D, Reppas NB, Emig CJ, Bang D, Hwang SJ, Jewett MC, Jacobson JM, Church GM (2011)
Precise manipulation of chromosomes in vivo enables genome-wide codon replacement
Science 333(6040):348-53.

Tolonen AC, Haas W, Chilaka AC, Aach J, Gygi SP, Church GM (2011)
Proteome-wide systems analysis of a cellulosic biofuel producing microbe
Nature-EMBO Molecular Systems biology 7:461. free article

Tolonen AC, Chilaka AC, Church GM (2009)
Targeted gene inactivation in Clostridium phytofermentans shows that cellulose degradation requires the family 9 hydrolase Cphy3367
Molecular Microbiology 74(6): 1300-13. free article

Frangeul L, Quillardet P, Castets AM, Humbert JF, Matthijs HC, Cortez D, Tolonen A, Zhang CC, Gribaldo S, Kehr JC, Zilliges Y, Ziemert N, Becker S, Talla E, Latifi A, Billault A, Lepelletier A, Dittmann E, Bouchier C, de Marsac NT (2008)
Highly plastic genome of Microcystis aeruginosa PCC7806, a ubiquitous toxic freshwater cyanobacterium
BMC Genomics 9: 274

Tolonen AC, Liszt GB, Hess WR (2006)
Genetic manipulation of Prochlorococcus MIT9313: GFP expression on an RSF1010 plasmid and Tn5 transposition
Applied and Environmental Microbiology. 72(12): 7607-13. free article

Tolonen AC, Aach J, Lindell D, Johnson ZI, Rector T, Steen R, Church GM, Chisholm SW (2006)
Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability
Nature-EMBO Molecular Systems Biology Oct 2006 doi:10.1038. free article

Tolonen AC (2005)
Prochlorococcus genetic transformation and the genomics of nitrogen metabolism
Ph.D. Thesis MIT, Cambridge MA USA

Lindell D, Sullivan MB, Johnson ZI, Tolonen AC, Rohwer F, and Chisholm SW (2004)
Transfer of photosynthetic genes to and from Prochlorococcus viruses
Proceedings of the National Academy of Sciences (101): 11013-11018.

Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, Arellano A, Coleman M, Hauser L, Hess WR, Johnson ZI, Land M, Lindell D, Post AF, Regala W, Shah M, Shaw SL, Steglich C, Sullivan MB, Ting CS, Tolonen A, Webb EA, Zinser ER, Chisholm SW (2003)
Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation
Nature 424 (6952): 1042-1047.

Lee SS, Kennedy S, Tolonen AC, Ruvkun G (2003)
DAF-16 target genes that control C. elegans life-span and metabolism
Science 300 (5619): 644-647.

Tolonen AC, Albeanu DF, Corbett JF, Handley H, Henson C, Malik P (2002)
Optimized in situ construction of oligomers on an array surface
Nucleic Acids Research 30 (20) e107 free article