Neves, L., Ferreira, R., Oliveira, R., Alves, M.M. (2010) Influence of innoculum acclimation in the biodegradation rate and estimated biodegradability of cow manure, food waste and oil. Environmental Engineering and Management Journal 9 (3), 327-334.

Neves, L. (2009) Anaerobis Co-digestion of Organic Wastes PhD Thesis (University of Minho) http://hdl.handle.net/1822/9875

Sarraguça, M.C., Paulo, A., Alves, M.M., Dias, A.M.A., Lopes, J.A., Ferreira, E.C. (2009) Quantitative monitoring of an activated sludge reactor using on-line UV-visible and near infrared spectroscopy. Analytical and Bioanalytical Chemistry 395(4), 1159-1166.

Raposo, F., de la Rubia, M.A., Borja, R., Alaiz, M., Beltrán, J., Cavinato, C., Clinckspoor, M., Demirer, G., Diamadopoulos, E., Helmreich, B., Jenicek, P., Martí, N., Méndez, R., Noguerol, J., Pereira, F., Picard, S., Torrijos, M. (2009) An interlaboratory study as useful tool for proficiency testing of chemical oxygen demand measurements using solid substrates and liquid samples with high suspended solid content. Talanta 80(1), 329-337.

Alves, M.M., Pereira, M.A., Sousa, D.Z., Cavaleiro, A.J., Picavet, M., Smidt, H., Stams, A.J.M. (2009) Waste-lipids to energy: how to optimize methane production from long chain fatty acids (LCFA). Microbial Biotechnology 2(5), 538-550.

Neves, L., Oliveira, R., Alves, M.M. (2009) Fate of LCFA in the Co-Digestion of Cow-Manure, Food Waste and Discontinuous Addition of Oil Water Research 43, 5142-510.

Costa, J.C., Moita, I., Ferreira, E.C., Alves, M.M. (2009) Morphology and physiology of anaerobic granular sludge exposed to organic solvents Journal of Hazardous Materials 167, (1-3) 393-398

Costa, J.C., Alves, M.M., Ferreira, E.C. (2009) A chemometric tool to monitor high-rate anaerobic granular sludge reactors during load and toxic disturbances. Biochemical Engineering Journal In press (doi:10.1016/j.bej.2008.12.006)

Angelidaki, I., Alves, M.M., Bolzonella D., Borzacconi L., Campos L., Guwy A.J., Kalyuzhnyi S., Jenicek P., van Lier J.B. (2009) Defining the biomethane potential (BMP) of solid organic wastes and energy crops: a proposed protocol for batch assays. Water Science and Technology 59.5, 927-934.

Cavaleiro, A.J., Salvador, A.F., Alves, J.I., Alves, M.M. (2009) Continuous High Rate Anaerobic Treatment of Lipid-Rich Wastewaters is Possible Applying a Step Feeding Start-up. Environmental Science and Technology 43(8), 2931-2936.

Sousa, D.Z., Balk, M., Alves, M.M., Schink, B., McInerney, M.J., Smidt, H., Plugge, C.M., Stams, A.J.M. (2009) Degradation of long-chain fatty acids by sulfate-reducing and methanogenic communities. Handbook of Hydrocarbon and Lipid Microbiology. Timmis, Kenneth N. (Ed.).

Sousa, D.Z., Smidt, H., Alves, M.M., Stams, A.J.M. (2009) Ecophysiology of syntrophic communities that degrade saturated and unsaturated long-chain fatty acids. FEMS microbiology ecology 68 (3) 257-272.

Oliveira, C.S., Ordaz, A., Alves, M.M., Ferreira, E.C., Thalasso, F. (2009) Determination of kinetic and stoichiometric parameters of Pseudomonas putida F1 by chemostat and in situ pulse respirometry. Chemical Product and Process Modeling 4(2), Article 2.

Costa, J.C., Alves, M.M., Ferreira, E.C. (2009) Principal Component Analysis and quantitative image analysis to predict effects of toxics in anaerobic granular sludge. Bioresource Technology 100(3), 1180-1185.

Sousa, D.Z., Alves, J.I., Alves, M.M., Smidt, H., Stams, A.J.M. (2009) Effect of sulfate on methanogenic communities that degrade unsaturated and saturated long chain fatty acids (LCFA). Environmental Microbiology 11(1), 68-80.

Abreu, A.A., Danko, A.S., Costa, J.C., Ferreira, E.C., Alves, M.M. (2009) Inoculum type response to different pHs on biohydrogen production from L-arabinose, a component of hemicellulosic biopolymers. International Journal of Hydrogen Energy 34(4), 1744–1751.

Van der Zee, F.P., Cervantes, F.J. (2009) Impact and application of electron shuttles on the redox (bio)transformation of contaminants: A review. Biotechnology Advances 27(3), 256–277.

Neves, L., Oliveira, R., Alves, M.M. (2009) Co-digestion of cow manure, food waste and intermittent input of fat. Bioresource Technology 100, 1957-1962.

Costa, J.C., Moita, I., Abreu, A.A., Ferreira, E.C., Alves, M.M. (2009) Advanced Monitoring of High Rate Anaerobic Reactors through Quantitative Image analysis of granular sludge and Multivariate Statistical Analysis. Biotechnology and Bioengineering 102:2, 445-456.

Neves, L., Pereira, M.A., Mota, M., Alves, M.M. (2009) Detection and quantification of long chain fatty acids in liquid and solid samples and its relevance to understand anaerobic digestion of lipids. Bioresource Technology 100, 91-96.

Danko, A.S., Pinheiro F., Abreu, A.A., Alves, M.M. (2008) Effect of methanogenic inhibitors, inocula type, and temperature on biohydrogen production from food components. Environmental Engineering and Management Journal 7:5, 531-536.

Cirne, D.G., Van der Zee, F.P., Fernandez-Polanco, M., Fernandez-Polanco, F. (2008) Control of sulphide during anaerobic treatment of S-containing wastewaters by adding limited amounts of oxygen or nitrate. Reviews in Environmental Science and Biotechnology 7:2, 93-105.

Sousa, D.Z., Pereira, M.A., Alves, J.I., Smidt, H., Stams, A.J.M., Alves, M.M. (2008) Anaerobic microbial LCFA degradation in bioreactors. Water Science and Technology 57;3, 439-444.

Dias, A.M.A., Moita, I., Páscoa, R., Alves, M.M., Lopes, J.A., Ferreira, E.C. (2008) Activated sludge process monitoring through in-situ NIR spectral analysis. Water Science and Technology 57:10, 1643-1650.

Danko, A.S., Abreu, A.A., Alves, M.M. (2008) Effect of arabinose concentration on dark fermentation hydrogen production using different mixed cultures. International Journal of Hydrogen Energy 33, 4527-4532.

Harrelkas F., Paulo, A., Alves, M.M., Khadir, L., Zahraa, O., Pons, M.-N., Van der Zee, F.P. (2008) Photocatalytic and combined anaerobic-photocatalytic treatment of textile dyes. Chemosphere 72:11, 1816-1822.

Gonçalves, M., Alves, M.M., Correia J. P., Marques I. P. (2008) Electrooxidation as the anaerobic pre-treatment of fats: oleate conversion using RuO2 and IrO2 based anodes. Bioresource technology 99, 8207-8211.

Cavaleiro, A.J., Pereira, M.A., Alves, M.M. (2008) Enhancement of methane production from Long Chain Fatty Acid based effluents. Bioresource Technology 99:10, 4086-4095.

Ordaz, A., Oliveira, C.S., Aguilar, R., Carrión, M., Ferreira, E.C., Alves, M.M., Thalasso, F. (2008) Kinetic and stoichiometric parameters estimation in a nitrifying bubble column through "in-situ" pulse respirometry. Biotechnology and Bioengineering 100:1, 94-102.

Neves, L., Gonçalo, E., Oliveira, R., Alves, M.M. (2008) Influence of composition on the biomethanation potential of restaurant waste at mesophilic temperatures. Waste Management 28:6, 965-972.

Costa, J.C. (2008) Supervision of transient anaerobic granular sludge process through quantitative image analysis and multivariate statistical techniques. PhD Thesis (University of Minho) http://hdl.handle.net/1822/8504

Pires, O.C. (2008) Sistemas inteligentes para monitorização e controlo de processos integrados de tratamento biológico de efluentes. PhD Thesis (University of Minho) http://hdl.handle.net/1822/7690

Sousa, D.Z., Smidt, H., Alves, M.M., Stams, A.J.M. (2007) Syntrophomonas zehnderi sp. nov., an anaerobe that degrades long chain fatty acids in co-culture with Methanobacterium formicicum. International Journal of Systematic and Evolutionary Microbiology 57, 609-615.

Costa, J.C., Abreu, A.A., Ferreira E.C., Alves, M.M. (2007) Quantitative image analysis as a diagnostic tool for monitoring structural changes of anaerobic granular sludge during detergent shock loads. Biotechnology and Bioengineering 98:1, 60-68.

Abreu, A.A., Costa, J.C., Araya-Kroff, P., Ferreira, E.C., Alves, M.M. (2007) Quantitative image analysis as a diagnostic tool for identifying structural changes during a revival process of anaerobic granular sludge. Water Research 41:7, 1473-1480.

Sousa, D.Z., Pereira, M.A., Stams, A.J.M., Alves, M.M., Smidt H. (2007) Methanogenic communities involved in anaerobic degradation of unsaturated or saturated long chain fatty acids (LCFA). Applied Environmental Microbiology 73:4, 1054-1064.

Cirne, D.G., Paloumet, X., Björnsson, L., Alves, M.M., Mattiasson, B. (2007) Influence of lipid concentration on the hydrolysis and biomethanation of lipid-rich wastes. Renewable Energy 32:6, 965-975.

Sousa, D.Z., Pereira, M.A., Smidt H., Stams, A.J.M., Alves, M.M. (2007) Molecular assessment of complex microbial communities degrading long chain fatty acids (LCFA) in methanogenic bioreactors. FEMS Microbiology Ecology 60:2, 252-265.

Sousa, D.Z. (2007) Ecology and physiology of anaerobic microbial communities that degrade long chain fatty acids. PhD Thesis (University of Minho) http://hdl.handle.net/1822/6287

Araya-Kroff, P. (2007) Quantitative image analysis as a diagnostic tool for identifying structural changes of anaerobic granular sludge. PhD Thesis (University of Minho) http://hdl.handle.net/1822/8576

Gonçalves, M., Bastos, E., Alves, M.M., Correia, J.P., Marques, I.P. (2006) Effect of electrochemical treatment of oleic acid on anaerobic digestion. Environmental Technology 27:11, 1289-1295.

Pires, O.C., Palma, C., Costa, J.C., Moita, I., Alves, M.M., Ferreira, E.C. (2006) Knowledge-based fuzzy system for diagnosis and control of an integrated biological wastewater treatment process. Water Science and Technology 53:4/5, 313–320.

Cirne, D., Björnsson, L., Alves, M.M., Mattiasson, B. (2006) Effects of bioaugmentation by anaerobic lipolytic bacteria on anaerobic digestion of lipid-rich waste. Journal of Chemical Technology and Biotechnology 81:11, 1745-1752.

Neves, L., Oliveira, R., Alves, M.M. (2006) Enhancement of methane production from barley waste. Biomass and Bioenergy 30, 599-603.

Neves, L., Oliveira, R., Alves, M.M. (2006) Anaerobic co-digestion of coffee waste and sewage sludge. Waste Management 26:2, 176-181.

Pereira, M.A., Pires, O.C., Mota, M., Alves, M.M. (2005) Anaerobic biodegradation of oleic and palmitic acids: Evidence of mass transfer limitations caused by long chain fatty acid accumulation onto the anaerobic sludge. Biotechnology and Bioengineering 92:1, 15-23.

Gonçalves, M., Joyce, A., Alves, M.M., Correia J.P., Marques, I. P. (2005) Anodic oxidation of oleate for wastewater treatment. Desalination 185:1-3, 351-355.

Pereira, M.A., Sousa, D.Z., Mota, M., Alves, M.M. (2004) Mineralization of LCFA associated to anaerobic sludge: kinetics, enhancement of methanogenic activity and effect of VFA. Biotechnology & Bioengineering 88:4, 502-511.

Araya-Kroff, P., Amaral, A.L., Neves, L., Ferreira, E.C., Pons, M.-N., Mota, M., Alves, M.M. (2004) Development of image analysis techniques as a tool to detect and quantify morphological changes in anaerobic sludge: I - application to a granulation process. Biotechnology & Bioengineering 87:2, 184-193.

Amaral, A.L., Pereira, M.A., da Motta, M., Pons M.-N., Mota, M., Ferreira, E.C., Alves, M.M. (2004) Development of image analysis techniques as a tool to detect and quantify morphological changes in anaerobic sludge: II – application to a granule deterioration process triggered by the contact with oleic acid. Biotechnology & Bioengineering 87:2, 194-199.

Neves, L., Oliveira, R., Alves, M.M. (2004) Influence of inoculum activity on the bio-methanization of a kitchen waste under different waste/inoculum ratios. Process Biochemistry 39:12, 2019-2024.

Pereira, M.A., Cavaleiro, A.J., Mota, M., Alves, M.M. (2003) Accumulation of LCFA onto anaerobic sludge under steady state and shock loading conditions: effect on acetogenic and methanogenic activity. Water Science and Technology 48:6, 33-40.

Pereira, M.A., Roest, R., Stams, A.J.M., Akkermans, A.D.L., Amaral, A.L., Pons, M.-N., Ferreira, E.C., Mota, M., Alves, M.M. (2003) Image analysis, methanogenic activity measurements and molecular biological techniques to monitor granular sludge from an EGSB reactor fed with oleic acid. Water Science and Technology 47:5, 181-188.

Pereira, M.A. (2003) Anaerobic biodegradation of long chain fatty acids - biomethanisation of biomass-associated LCFA as a challenge for the anaerobic treatment of effluents with high lipid-LCFA content. PhD Thesis (University of Minho) http://hdl.handle.net/1822/4650

Pereira, M.A., Roest, K., Stams, A.J.M., Mota, M., Alves, M.M., Akkermans, A. (2002) Molecular monitoring of microbial diversity of two EGSB reactors treating oleic acid. FEMS Microbiology Ecology 41:2, 95-103.

Pereira, M.A., Pires, O.C., Mota, M., Alves, M.M. (2002) Anaerobic degradation of oleic acid by suspended and granular sludge: identification of palmitate as a key intermediate. Water Science and Technology 45:10, 139-144.

Pereira, M.A., Mota, M., Alves, M.M. (2002) Operation of an anaerobic filter and an EGSB reactor for the treatment of oleic-acid based effluents: influence of inoculum quality. Process Biochemistry 37:9, 1025-1031.

Ribeiro, N.J., Pires, O.C., Mota, M., Ferreira, E.C., Alves, M.M. (2001) Influence of up-flow velocity on the performance of an anaerobic filter under oleic acid overloads. Biotechnology Letters 23:22, 1833-1839.

Pereira, M.A., Mota, M., Alves, M.M. (2001) Degradation of Oleic Acid in Anaerobic Filters: Effect of Inoculum Acclimatization and Biomass Recirculation. Water Environment Research 73:5, 612-621.

Teixeira, P., Alves, M.M., Oliveira, R. (2001) Hydraulic characteristics of an anoxic rotating biological contactor. Influence of the biofilm. Environmental Technology 22, 1169-1175.

Cavaleiro, A.J., Alves, M.M., Mota, M. (2001) Microbial and operational response of an anaerobic fixed bed digester to oleic acid overloads. Process Biochemistry 37:4, 387-394.

Alves, M.M., Mota Vieira, J.A., Álvares Pereira, R.M., Pereira, M.A., Mota, M. (2001) Effects of Lipids and Oleic Acid on Biomass Development in Anaerobic Fixed Bed Reactors. Part I: biofilm growth and activity. Water Research 35:1, 255-263.

Alves, M.M., Mota Vieira, J.A., Álvares Pereira, R.M., Pereira, M.A., Mota, M. (2001) Effects of Lipids and oleic Acid on Biomass Development in Anaerobic Fixed Bed Reactors. Part II: Oleic acid toxicity and biodegradability. Water Research 35:1, 264-270.

Alves, M.M., Cavaleiro, A.J., Ferreira, E.C., Amaral, A.L., Mota, M., da Motta, M., Vivier, H., Pons, M.-N. (2000) Characterization by Image Analysis of Anaerobic Sludge under Shock Conditions. Water Science and Technology 41:12, 207-214.

Alves, M.M., Ferreira, E.C., Amaral, A.L., Pereira, M.A., Novais, J.M., Mota M. (2000) Staged and non-staged anaerobic filters: performance in relation with the physical and biological characteristics of microbial aggregates. Journal of Chemical Technology & Biotechnology 75, 601-609.

Araya, P., Chamy, R., Mota, M., Alves, M.M. (2000) Biodegradability and toxicity of styrene in the anaerobic digestion process. Biotechnology Letters 22, 1477-1481.

Pereira, M.A., Alves, M.M., Azeredo, J., Mota, M., Oliveira, R. (2000) Influence of physico-chemical properties of pororus microcarriers on the adhesion of an anaerobic consortium. Journal of Industrial Microbiology & Biotechnology 24, 181-186.

Alves, M.M., Pereira, M.A., Polanco, F., Novais, J.M., Mota, M. (1999) A new device to select microcarriers for biomass immobilization: application to an anaerobic consortium. Water Environment Research 71:2, 209-217.

Alves, M.M. (1998) Estudo e caracterização de digestores anaeróbios de leito fixo PhD Thesis (University of Minho) http://hdl.handle.net/1822/2580

Alves, M.M., Bellouti, M., Pereira, M.A., Álvares Pereira, M.R., Mota Vieira, J.A., Novais, J.M., Mota, M. (1998) A new method to study interactions between biomass and packing material in anaerobic filters. Biotechnology Techniques 12:4, 277-283.

Alves, M.M., Pereira, M.A., Mota, M., Novais, J.M., Colleran, E. (1998) Staged and non-staged anaerobic filters: Microbial activity stratification, hidrodynamic behaviour and performance. Journal of Chemical Technology & Biotechnology 73, 99-108.

Bellouti, M., Alves, M.M., Novais, J.M., Mota M. (1997) Flocs vs Granules: Differentiation by Fractal Dimension. Water Research 31:5, 1227-1231