Taivosalo, A., T. Kriščiunaite, A. Seiman, N. Part, I. Stulova, and R. Vilu. (2018). Comprehensive analysis of proteolysis during 8 months of ripening of high-cooked Old Saare cheese. J. Dairy Sci. 101:944-967.


Hälvin-Tanilas, Kristel. (2017) Assessment of bioavailable B vitamin content in food using in vitro digestibility assay and LC-MS SIDA. Analytical and Bioanalytical Chemistry

K. Adamberg, K. Kolk, M. Jaagura, R. Vilu, S. Adamberg. (2017) The composition and metabolism of faecal microbiota is specifically modulated by different dietary polysaccharides and mucin: an isothermal microcalorimetry study. Beneficial Microbes: 9 (1)

Concetta Panebianco, Kaarel Adamberg, Signe Adamberg, Chiara Saracino, Madis Jaagura, Kaia Kolk, Anna Grazia Di Chio, Paolo Graziano, Raivo Vilu, Valerio Pazienza. (2017). Engineered Resistant-Starch (ERS) Diet Shapes Colon Microbiota Profile in Parallel with the Retardation of Tumor Growth in In Vitro and In Vivo Pancreatic Cancer Models. Nutrients 2017, 9(4), 331; doi:10.3390/nu9040331


Bondarenko, Olesja M; Ivask, Angela; Kahru, Anne; Vija, Heiki; Titma, Tiina; Visnapuu, Meeri; Joost, Urmas; Pudova, Ksenia; Adamberg, Signe; Visnapuu, Triinu; Alamäe, Tiina. (2016). Bacterial polysaccharide levan as stabilizing, non-toxic and functional coating material for microelement-nanoparticles. Carbohydrate Polymers, 136, 710−720, j.carbpol.2015.09.093.

Viiard, E.; Bessmeltseva, M.; Simm, J.; Talve, T.; Aaspõllu, A; Paalme, T.; Sarand, I. (2016). Diversity and Stability of Lactic Acid Bacteria in Rye Sourdoughs of Four Bakeries with Different Propagation Parameters. PLoS ONE, e0148325, 10.1371/journal.pone.0148325.

Kaspar Kevvai, Mary-Liis Kütt, Ildar Nisamedtinov and Toomas Paalme (2016). Simultaneous utilization of ammonia, free amino acids and peptides during fermentative growth of Saccharomyces cerevisiae. Journal of the institute of brewing

Seisonen, S.; Vene, K.; Koppel, K. (2016). The current practice in the application of chemometrics for correlation of sensory and gas chromatographic data. Food Chemistry, 210 (1), 530−540, 10.1016/j.foodchem.2016.04.134.

Mardo, Karin; Visnapuu, Triinu; Aasamets, Anneli; Viigand, Katrin; Bondarenko, Olesja; Vija, Heiki; Adamberg Kaarel; Adamberg, Signe; Alamäe, Tiina. (2016). Enzymatic synthesis and ways of further treatment of fructooligosaccharides and polymeric levan for prebiotic efficiency studies. In: ELSEVIER, S122−123.

Objartel Mart, Tamm Martti, Kraft Kadri, Annus Paul, Land Raul (2016). Fat prediction in minced meat with low-cost BIA spectrometer. In: Abstract Book: 16th International Conference on Electrical Bio- Impedance (ICEBI) and the 17th Conference on Electrical Impedance Tomography (EIT) 2016 [ilmumas].


Stulova I, Kabanova N, Krisciunaite T, Adamberg K, Laht TM, and Vilu R (2015) Microcalorimetric study of the growth of Streptococcus thermophilus in renneted milk. Front. Microbiol., available online

Adamberg K, Valgepea K and Vilu R (2015) Advanced continuous cultivation methods for systems microbiology. Society for General Microbiology, available online

Peebo, K., Valgepea, K., Maser, A., Nahku, R., Adamberg, K., & Vilu, R. Proteome reallocation in Escherichia coli with increasing specific growth rate. Mol. BioSyst., 2015, 11, 1184 – 1193. doi:10.1039/C4MB00721B

Seisonen, S., Kivima, E., Vene K. 2015. Characterization of the aroma profile of different honeys and corresponding flowers using solid phase microextraction and gas chromatography-mass spectrometry/olfactometry. Food Chemistry, 169, 34–40

Aller K, Adamberg K, Reile I, Timarova V, Peebo K, and Vilu R (2015) Excess of threonine compared to serine promotes threonine aldolase activity in Lactococcus lactis IL1403. Microbiol., available online

Valgepea K, Peebo K, Adamberg K, and Vilu R (2015) Lean-proteome strains – next step in metabolic engineering. Front. Bioeng. Biotechnol., available online

Esquerré T, Moisan A, Chiapello H, Arike L, Vilu R, Gaspin C, Cocaign-Bousquet M and Girbal L (2015) Genome-wide investigation of mRNA lifetime determinants in Escherichia coli cells cultured at different growth rates. BMC Genomics, 16, 275


Aller K, Adamberg K, Timarova V, Seiman A, Feštšenko D and Vilu R (2014) Nutritional requirements and media development for Lactococcus lactis IL1403., Appl. Microbiol. Biotechnol., 98, 13, 5871-5881

Adamberg S, Sumeri I, Uusna R, Ambalam P, Kondepudi KK, Adamberg K, Wadström T, Ljungh Å (2014). Survival and synergistic growth of mixed cultures of bifidobacteria and lactobacilli combined with prebiotic oligosaccharides in a gastrointestinal tract simulator. Microbial Ecology in Health & Disease, 25: 23062 –

Lahtvee PJ, Seiman A, Arike L, Adamberg K, Vilu R (2014) Protein turnover forms one of the highest maintenance costs in Lactococcus lactis. Microbiology, 160:1501-1512.
Paalme T, Kevvai K, Vilbaste A, Hälvin K, and Nisamedtinov I (2014) Uptake and accumulation of B-group vitamers in Saccharomyces cerevisiae in ethanol-stat fed-batch culture. World J. Microbiol. Biotechnol., 30, 9, 2351-2359

Peebo K, Valgepea K, Nahku R, Riis G, Õun M, Adamberg K, and Vilu R (2014) Coordinated activation of PTA-ACS and TCA cycles strongly reduces overflow metabolism of acetate in Escherichia coli. Appl. Microbiol. Biotechnol., 98, 11, 5131-5143

Abner K, Aaviksaar T, Adamberg K, and Vilu R (2014) Single-cell model of prokaryotic cell cycle. J. Theor. Biol. 341, 78–87

Bessmeltseva M, Viiard E, Simm J, Paalme T, and Sarand I (2014) Evolution of Bacterial Consortia in Spontaneously Started Rye Sourdoughs during Two Months of Daily Propagation. PLoS One 9, 4, e95449

Kütt M-L, Stagsted J (2014) Caseins from bovine colostrum and milk strongly bind piscidin-1, an antimicrobial peptide from fish. International Journal of Biological Macromolecules 70, 364–372

Hälvin K, Nisamedtinov I, and Paalme T (2014) Comparison of different extraction methods to determine free and bound forms of B-group vitamins in quinoa. Anal Bioanal Chem. available online

Kevvai K, Kütt M-L, Nisamedtinov I, and Paalme T (2014) Utilization of (15)N-labelled yeast hydrolysate in Lactococcus lactis IL1403 culture indicates co-consumption of peptide-bound and free amino acids with simultaneous efflux of free amino acids. Antonie Van Leeuwenhoek 105, 3, 511–522

Erm S, Adamberg K, and Vilu R (2014) Multiplying steady-state culture in multi-reactor system. Bioprocess Biosyst. Eng., 27 (11), 2361-2370.


Stulova I, Kabanova N, Krišciunaite T, Taivosalo A, Laht T-M, and Vilu R (2013) Fermentation of reconstituted milk by Streptococcus thermophilus: Effect of irradiation on skim milk powder. Int. Dairy J. 31, 2, 139–149

Kabanova N, Stulova I, and Vilu R (2013) Microcalorimetric study of growth of Lactococcus lactis IL1403 at low glucose concentration in liquids and solid agar gels. Thermochim. Acta 559, 69–75

Viiard E, Mihhalevski A, Rühka T, Paalme T, and Sarand I (2013) Evaluation of the microbial community in industrial rye sourdough upon continuous back-slopping propagation revealed Lactobacillus helveticus as the dominant species. J. Appl. Microbiol. 114, 2, 404–412

Vene K, Seisonen S, Koppel K, Leitner E, and Paalme T (2013) A Method for GC–Olfactometry Panel Training. Chemosens. Percept.

Valgepea K, Adamberg K, Seiman A, and Vilu R (2013) Escherichia coli achieves faster growth by increasing catalytic and translation rates of proteins. Mol. Biosyst. 9, 2344–2358

Pey J, Valgepea K, Rubio A, Beasley JE, and Planes FJ (2013) Integrating gene and protein expression data with genome-scale metabolic networks to infer functional pathways. BMC Syst. Biol. 7, 1, 134

Hälvin K, Paalme T, and Nisamedtinov I (2013) Comparison of different extraction methods for simultaneous determination of B complex vitamins in nutritional yeast using LC/MS-TOF and stable isotope dilution assay. Anal. Bioanal. Chem. 405, 4, 1213–1222

Mihhalevski A, Nisamedtinov I, Hälvin K, Ošeka A, and Paalme T (2013) Stability of B-complex vitamins and dietary fiber during rye sourdough bread production. J. Cereal Sci. 57, 1, 30–38


Sumeri I, Adamberg S, Uusna R, Sarand I, and Paalme T (2012) Survival of cheese bacteria in a gastrointestinal tract simulator. Int. Dairy J. 25, 1, 36–41

Mihhalevski A, Heinmaa I, Traksmaa R, Pehk T, Mere A, and Paalme T (2012) Structural Changes of Starch during Baking and Staling of Rye Bread. J. Agric. Food Chem., 60, 34, 8492–8500

Krišciunaite T, Stulova I, Taivosalo A, Laht T-M, and Vilu R (2012) Composition and renneting properties of raw bulk milk in Estonia. Int. Dairy J. 23, 1, 45–52

Kabanova N, Stulova I, and Vilu R (2012) Microcalorimetric study of the growth of bacterial colonies of Lactococcus lactis IL1403 in agar gels. Food Microbiol. 29, 1, 67–79

Orumets K, Kevvai K, Nisamedtinov I, Tamm T, and Paalme T (2012) YAP1 over-expression in Saccharomyces cerevisiae enhances glutathione accumulation at its biosynthesis and substrate availability levels. Biotechnol. J. 7, 4, 566–568

Arike L, Valgepea K, Peil L, Nahku R, Adamberg K, and Vilu R (2012) Comparison and applications of label-free absolute proteome quantification methods on Escherichia coli. J. Proteomics 75, 17, 5437–5448

Adamberg K, Seiman A, and Vilu R (2012) Increased Biomass Yield of Lactococcus lactis by Reduced Overconsumption of Amino Acids and Increased Catalytic Activities of Enzymes. PLoS One 7, 10


Kaseleht K, Paalme T, Mihhalevski A, and Sarand I (2011) Analysis of volatile compounds produced by different species of lactobacilli in rye sourdough using multiple headspace extraction. Int. J. Food Sci. Technol. 46, 9, 1940–1946

Koppel K, Timberg L, Salumets A, and Paalme T (2011) Possibility for a Strawberry Jam Sensory Standard. J. Sens. Stud. 26, 1, 71–80

Koppel K, Chambers IV E, and Chambers DH (2011) Flavour and Acceptance of Estonian Cheeses. Agron. Res. 9, 2, 409–414

Krišciunaite T, Stulova I, Kabanova N, Laht T-M, and Vilu R (2011) The effect of hydrogen peroxide on the growth of thermophilic lactic starter and acid gelation of UHT milk. Int. Dairy J. 21, 4, 239–246

Nisamedtinov I, Kevvai K, Orumets K, Arike L, Sarand I, Korhola M, and Paalme T (2011) Metabolic changes underlying the higher accumulation of glutathione in Saccharomyces cerevisiae mutants. Appl. Microbiol. Biotechnol. 89, 4, 1029–1037

Timberg L, Kuldjärv R, Koppel K, and Paalme T (2011) Rainbow Trout Composition and Fatty Acid Content in Estonia. Agron. Res. 9, 2, 495–500

Timberg L, Koppel K, Kuldjärv R, and Paalme T (2011) Sensory and Chemical Properties of Baltic Sprat (Sprattus sprattus balticus) and Baltic Herring (Clupea harengus membras) in Different Catching Seasons. Agron. Res. 9, 2, 489–494

Vázquez-Araújo L, Koppel K, Chambers IV E, Adhikari K, and Carbonell-Barrachina AA (2011) Instrumental and sensory aroma profile of pomegranate juices from the USA: differences between fresh and commercial juice. Flavour Fragr. J. 26, 2, 129–138

Mihhalevski A, Sarand I, Viiard E, Salumets A, and Paalme T (2011) Growth characterization of individual rye sourdough bacteria by isothermal microcalorimetry. J. Appl. Microbiol. 110, 2, 529–540

Kaseleht K, Leitner E, and Paalme T (2011) Determining aroma-active compounds in Kama flour using SPME-GC/MS and GC-olfactometry. Flavour Fragr. J. 26, 2, 122–128

Stulova I, Kabanova N, Krišciunaite T, Laht T-M, and Vilu R (2011) The Effect of Milk Heat Treatment on the Growth Characteristics of Lactic Acid Bacteria. Agron. Res. 9, 2, 473–478

Nahku R, Peebo K, Valgepea K, Barrick JE, Adamberg K, and Vilu R (2011) Stock culture heterogeneity rather than new mutational variation complicates short-term cell physiology studies of Escherichia coli K-12 MG1655 in continuous culture. Microbiology 157, 9, 2604–2610

Lahtvee P-J, Adamberg K, Arike L, Nahku R, Aller K, and Vilu R (2011) Multi-omics approach to study the growth efficiency and amino acid metabolism in Lactococcus lactis at various specific growth rates. Microb. Cell Fact. 10, 12

Kaseleht K, Paalme T, and Nisamedtinov I (2011) Quantitative Analysis of Acetaldehyde in Foods Consumed by Children using SPME / GC-MS (Tof), On-fiber Derivatization and Deuterated Acetaldehyde as an Internal Standard. Agron. Res. 9, 2, 395–401

Kaseleht K, Paalme T, and Nisamedtinov I (2011) Quantitative Analysis of Acetaldehyde in Foods Consumed by Children using SPME / GC-MS (Tof), On-fiber Derivatization and Deuterated Acetaldehyde as an Internal Standard. Agron. Res. 9, 2, 395–401


Sumeri I, Arike L, Stekolstsikova J, Uusna R, Adamberg S, Adamberg K, and Paalme T (2010) Effect of stress pretreatment on survival of probiotic bacteria in gastrointestinal tract simulator. Appl. Microbiol. Biotechnol. 86, 6, 1925–1931

Koppel K, and Chambers IV E (2010) Development and Application of a Lexicon To Describe the Flavor of Pomegranate Juice. J. Sens. Stud. 25, 6, 819–837

Spitsmeister M, Adamberg K, and Vilu R (2010) UPLC/MS based method for quantitative determination of fatty acid composition in Gram-negative and Gram-positive bacteria. J. Microbiol. Methods 82, 3, 288–295

Stulova I, Adamberg S, Krišciunaite T, Kampura M, Blank L, and Laht T-M (2010) Microbiological quality of raw milk produced in Estonia. Lett. Appl. Microbiol. 51, 6, 683–690

Nahku R, Valgepea K, Lahtvee P-J, Erm S, Abner K, Adamberg K, and Vilu R (2010) Specific growth rate dependent transcriptome profiling of Escherichia coli K12 MG1655 in accelerostat cultures. J. Biotechnol. 145, 1, 60–65

Nisamedtinov I, Kevvai K, Orumets K, Rautio JJ, and Paalme T (2010) Glutathione accumulation in ethanol-stat fed-batch culture of Saccharomyces cerevisiae with a switch to cysteine feeding. Appl. Microbiol. Biotechnol. 87, 1, 175–183

Valgepea K, Adamberg K, Nahku R, Lahtvee P-J, Arike L, and Vilu R (2010) Systems biology approach reveals that overflow metabolism of acetate in Escherichia coli is triggered by carbon catabolite repression of acetyl-CoA synthetase. BMC Syst. Biol. 4, 166


Lahtvee P-J, Valgepea K, Nahku R, Abner K, Adamberg K, and Vilu R (2009) Steady state growth space study of Lactococcus lactis in D-stat cultures. Antonie Van Leeuwenhoek 96, 487–496

Adamberg K, Lahtvee P-J, Valgepea K, Abner K, and Vilu R (2009) Quasi steady state growth of Lactococcus lactis in glucose-limited acceleration stat (A-stat) cultures. Antonie Van Leeuwenhoek 95, 3, 219–226

Kabanova N, Kazarjan A, Stulova I, and Vilu R (2009) Microcalorimetric study of growth of Lactococcus lactis IL1403 at different glucose concentrations in broth. Thermochim. Acta 496, 1-2, 87–92


Sumeri I, Arike L, Adamberg K, and Paalme T (2008) Single bioreactor gastrointestinal tract simulator for study of survival of probiotic bacteria. Appl. Microbiol. Biotechnol. 80, 2, 317–324

Nisamedtinov I, Lindsey GG, Karreman R, Orumets K, Koplimaa M, Kevvai K, and Paalme T (2008) The response of the yeast Saccharomyces cerevisiae to sudden vs. gradual changes in environmental stress monitored by expression of the stress response protein Hsp12p. FEMS Yeast Res. 8, 6, 829–838


Kasemets K, Nisamedtinov I, Laht T-M, Abner K, and Paalme T (2007) Growth characteristics of Saccharomyces cerevisiae S288C in changing environmental conditions: auxo-accelerostat study. Antonie Van Leeuwenhoek 92, 1, 109–128


Paalme T, Nisamedtinov I, Abner K, Laht T-M, Drews M, and Pehk T (2006) Application of 13C-[2] – and 13C-[1,2] acetate in metabolic labelling studies of yeast and insect cells. Antonie Van Leeuwenhoek 89, 3-4, 443–457


Kaspar Kevvai, “Applications of 15N-labeled Yeast Hydrolysates in Metabolic Studies of Lactococcus Lactis and Saccharomyces Cerevisiae”

Kadri Aller, “Development and Applications of Chemically Defined Media for Lactic Acid Bacteria.” 2016

Kaspar Valgepea, “Absolute Quantitative Multi-omics Characterization of Specific Growth Rate-dependent Metabolism of Escherichia coli.” 2014

Kristel Hälvin, “Determination of B-group Vitamins in Food Using an LC-MS Stable Isotope Dilution Assay.” 2014.

Ene Viiard, “Diversity and Stability of Lactic Acid Bacteria During Rye Sourdough Propagation.” 2014.

Irina Stulova, “The Effects of Milk Composition and Treatment on the Growth of Lactic Acid Bacteria.” 2013.

Natalja Kabanova, “Development of a Microcalorimetric Method for the Study of Fermentation Processes.” 2013.

Tiina Krisciunaite, “A Study of Milk Coagulability.” 2013.

Anna Traksmaa, “Rye sourdough fermentation and bread stability.” 2012.

Loreida Timberg, “Spice-Cured Sprats Ripening, Sensory Parameters Development, and Quality Indicators.” 2012.

Liisa Arike, “Quantitative Proteomics of Escherichia coli: From Relative to Absolute Scale.” 2012.

Petri-Jaan Lahtvee, “Quantitative omics-level analysis of growth rate dependent energy metabolism in Lactococcus lactis.” 2012.

Ranno Nahku, “Validation of critical factors for the quantitative characterization of bacterial physiology in accelerostat cultures.” 2012.

Kerti Orumets, “Molecular mechanisms controlling intracellular glutathione levels in baker’s yeast Saccharomyces cerevisiae and a random mutagenized glutathione over-accumulating isolate.” 2012.

Kristel Vene, “Identification of Aroma Compounds in Food Using SPME-GC/MS and GC-Olfactometry.” 2012.

Ingrid Sumeri, “The Study of Probiotic Bacteria in Human Gastrointestinal Tract Simulator.” 2011.

Kadri Koppel, “Food Category Appraisal Using Sensory Methods.” 2011.