The following papers refer to Bioengineering scientific publications at peer reviews journals by Researchers and PhD Students affiliated to MPP.

They are organized by year and author’s last name in 7 subthemes:

Bioprocess and Biomolecular Engineering


R. Gallardo, C. Faria, L.R. Rodrigues, M.A. Pereira, M.M. Alves "Anaerobic granular sludge as a biocatalyst for 1,3-propanediol production from glycerol in continuous bioreactors". Bioresource Technology 155() 28-33, 2014.


P.Ma, F. Varela, M. Magoch, A. R. Silva, A.L. Rosário, J. Brito, T.F. Oliveira, P. Nogly, M. Pessanha, M.Stelter, A. Kletzin, P. J.F. Henserson, M. Archer. "An Efficient Strategy for Small-Scale Screening and Production of Archaeal Membrane Transport Proteins in Escherichia Coli." Edited by Hendrik W. van Veen. PLoS ONE 8, no. 10 (October 7, 2013): e76913. doi:10.1371/journal.pone.0076913.


T. Barroso, R. Viveiros, M. Coelho, T. Casimiro, A.M. Botelho do Rego, A. Aguiar-Ricardo, “Influence of poly(N-isopropylacrylamide) and poly(N,N′-diethyl acrylamide) coatings on polysulfone/polyacrylonitrile-based membranes for protein separation”, Polymers for Advanced Technologies, 23(10), 1381–1393, 2012.

J.M. Dantas, L. Morgado, Y.Y. Londer, A.P. Fernandes, R.O. Louro, P.R. Pokkuluri, M. Schiffer, C.A. Salgueiro, “Pivotal role of the strictly conserved aromatic residue F15 in the cytochrome c 7 family”, JBIC Journal of Biological Inorganic Chemistry, 17(1), 11-24, 2012.

B.M. Fonseca, C.M. Paquete, C.A. Salgueiro, R.O. Louro, “The role of intramolecular interactions in the functional control of multiheme cytochromes c”, FEBS Letters, 586(5), 504–509, 2012.

G.A.L. Gonçalves, D.M. Bower, D.M.F. Prazeres, G.A. Monteiro, K.L.J. Prather, “Rational engineering of Escherichia coli strains for plasmid biopharmaceutical manufacturing”, Biotechnology Journal, 7(2), 251–261, 2012.

R.M. Tostões, S.B. Leite, M. Serra, J. Jensen, P. Björquist, M.J.T. Carrondo, C. Brito, P.M. Alves, “Human liver cell spheroids in extended perfusion bioreactor culture for repeated-dose drug testing”, Hepatology, 55(4), 1227–1236, 2012.

M. Temtem, T. Barroso, T. Casimiro, J.F. Mano, A. Aguiar-Ricardo, “Dual Stimuli Responsive Poly(N-isopropylacrylamide) Coated Chitosan Scaffolds for Controlled Release Prepared from a Non Residue Technology”, J. Supercrit. Fluids, 66, 398–404, 2012.


H. Águas, S.K. Ram , A. Araújo, D. Gaspar, A. Vicente, S.A. Filonovich, E. Fortunato, R. Martins, I. Ferreira, “Silicon thin film solar cells on commercial tiles”, Energy Environ. Sci., 4, 4620-4632, 2011.

T. Barroso, M. Temtem, T. Casimiro, A. Aguiar-Ricardo, “Antifouling performance of polyacrilonitrile-based membranes: from green synthesis to application”, J. Supercrit. Fluids, 56, 312-321, 2011.

J.M. Dantas, I.H. Saraiva, L. Morgado, M.A. Silva, M. Schiffer, C.A. Salgueiro, R.O. Louro, “Orientation of the axial ligands and magnetic properties of the hemes in the cytochrome c7 family from Geobacter sulfurreducens determined by paramagnetic NMR”, Dalton Trans., 40, 12713-12718, 2011.

V.G. Correia, V.D.B. Bonifácio, V.P. Raje, T. Casimiro, G. Moutinho, C. Lobato da Silva, M.G. Pinho, A. Aguiar-Ricardo, “Oxazoline-Based Antimicrobial Oligomers: Synthesis by CROP Using Supercritical CO2”, Macromol. Biosci., 11(8), 1128-1137, 2011.

S.B. Leite, A.P. Teixeira, J.P. Miranda, R.M. Tostões, J.J. Clemente, M.F. Sousa, M.J. Carrondo, P.M. Alves, “Merging bioreactor technology with 3D hepatocyte-fibroblast culturing approaches: Improved in vitro models for toxicological applications”, Toxicol. in Vitro, 25(4), 825-832, 2011.

P.H. Oliveira, K.J. Prather, D.M.F. Prazeres, G.A. Monteiro, “Mutation detection in plasmid biopharmaceuticals”, Biotechnol. J., 6(4): 378-391, 2011.

M. Soares da Silva, R. Viveiros, P.I. Morgado, A. Aguiar-Ricardo, I.J. Correia, T. Casimiro, “Development of 2-(dimethylamino)ethyl methacrylate- based molecular recognition devices for controlled drug delivery using supercritical fluid technology”, Int. J. Pharmaceutics, 416(1), 61-68, 2011.

M. Soares da Silva, R. Viveiros, F. Nóbrega, A. Aguiar-Ricardo, E.J. Cabrita, T. Casimiro, “Supercritical fluid technology-assisted development of molecularly imprinted co-polymers for controlled delivery of flufenamic acid”, J. Supercritical Fluids, 58(1), 150-157, 2011.

H. Vazão, R. Pires das Neves, M. Grãos, L.S. Ferreira, “Towards the characterization and maturation of smooth muscle cells derived from human embryonic stem cells”, PLoS One, 6(3), e17771, 2011.


T. Barroso, M. Temtem, A. Hussain, A. Aguiar-Ricardo, A.C.A. Roque, “Preparation and characterization of a cellulose affinity membrane for human immunoglobulin G (IgG) purification”, J. Membrane Science, 348( 1-2), 224-230, 2010.

D.F. Coutinho, S.V. Sant, H. Shin, J.T. Oliveira, M.E. Gomes, N.M. Neves, A. Khademhosseini, R.L. Reis, “Modified Gellan Gum hydrogels with tunable physical and mechanical properties”, Biomaterials, 31(29), 7494-7502, 2010.

M. de Rosa, D. de Sanctis, A.L. Rosario, M. Archer, A. Rich, A. Athanasiadis, M.A. Carrondo, “Crystal structure of a junction between two Z-DNA helices”, P. Natl. Acad. Sci. USA, 107, 20-24, 2010.

M.S. Fernandes, N.S. Dias, A.F. Silva, J.S. Nunes, S. Lanceros-Méndez, J.H. Correia, P.M. Mendes, “Hydrogel-based photonic sensor for a biopotential wearable recording system”, Biosens. Bioelectron., 26, 80-86, 2010.

B.J. Hackel, M.E. Ackerman, S.W. Howland, K.D. Wittrup, “Stability and CDR Composition Biases Enrich Binder Functionality Landscapes”, J. Mol. Biol., 401(1), 84-96, 2010.

B.J. Hackel, K.D. Wittrup, “The full amino acid repertoire is superior to serine/ tyrosine for selection of high affinity immunoglobulin G binders from the fibronectin scaffold”, Protein Eng. Des. Sel., 23(4), 211–219, 2010.

E. Leonard, P.K. Ajikumar, K. Thayer, W.H. Xiao, J.D. Mo, B. Tidor, G. Stephanopoulos, K.L. Prather, “Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction and selectivity control”, P. Natl. Acad. Sci. USA, 107, 13654-13659, 2010.

L.R.A. Markely, B.T. Ong, K.M. Hoi, G. Teo, M.Y. Lu, D.I.C. Wang, “A highthroughput method for quantification of glycoprotein sialylation”, Anal. Biochem., 407(1), 128-133, 2010.

P.H. Oliveira, K.J. Prather, D.M.F. Prazeres, G.A. Monteiro, “Analysis of DNA repeats in bacterial plasmids reveals the potential for recurrent instability events”, Appl. Microbiol. Biotechnol., 87, 2157–2167, 2010.

C.M. Paquete, I. Saraiva, E. Calçada, R.O. Louro, “Molecular basis for directional electron transfer”, J. Biol. Chem., 285, 10370-10375, 2010.

C.M. Paquete, R.O. Louro, “Molecular details of multielectron transfer: the case of multiheme cytochromes from metal respiring organisms”, Dalton Trans., 39, 4259-4266, 2010.

C.S.O. Paulo, M. Vidal, L.S. Ferreira, “Antifungal Nanoparticles and Surfaces”, Biomacromolecules, 11(10), 2810–2817, 2010.

S.C. Ribeiro, R. Mendes, C. Madeira, G.A. Monteiro, C. Lobato da Silva, J.M.S. Cabral, “A quantitative method to evaluate mesenchymal stem cell lipofection using real-time PCR”, Biotechnol. Progr., 26(5),1501-1504, 2010.

M. Soares da Silva, E.R. Vão, M. Temtem, L. Mafra, J. Caldeira, A. Aguiar-Ricardo, T. Casimiro, “Clean synthesis of molecular recognition polymeric materials with chiral sensing capability using supercritical fluid technology. Application as HPLC stationary phases”, Biosens. Bioelectron., 25(7), 1742-1747, 2010.

R.M. Tostões, S.B. Leite, J.P. Miranda, M.F.Q. Sousa, D.I.C. Wang, M.J.T. Carrondo, P.M. Alves, “Perfusion of 3D encapsulated hepatocytes – a synergistic effect enhancing long term functionality in bioreactors”, Biotechnol. Bioeng., 108(1), 41-49, 2010.


M. Ackerman, D. Levary, G. Tobon, B. Hackel, K.D. Orcutt, K.D. Wittrup, “Highly avid magnetic bead capture: an efficient selection method for de novo protein engineering utilizing yeast surface display”, Biotechnol. Progr., 25(3), 774-783, 2009.

Y. Astier, O. Uzun, F. Stellacci, “Electrophysiological Study of Single Gold Nanoparticle/a-Hemolysin Complex Formation: A Nanotool to Slow Down ssDNA Through the a-Hemolysin Nanopore”, Small, 5(11), 1273–1278, 2009.

T. Barroso, M. Temtem, T. Casimiro, A. Aguiar-Ricardo, “Development of pH-responsive poly(methylmethacrylate-co-methacrylic acid) membranes using scCO2 technology. Application to protein permeation”, J. Supercrit. Fluids, 51(1), 57-66, 2009.

Y. Du, J. Shim, M. Vidula, E. Lo, B.G. Chung, M.J. Hancock, J. Borenstein, D. Cropek, A. Khademhosseini, “Rapid generation of spatially and temporally controllable long range concentration gradients in a microfluidic device”, Lab Chip, 9, 761-767, 2009.

A.C.  Engler, H.I. Lee, P.T. Hammond, “Highly Efficient "Grafting onto" a Polypeptide Backbone Using Click Chemistry”, Angew. Chem. Int. Edit., 48(49), 9334-9338, 2009.

L.S. Ferreira, A. Zumbuehl, “Non-leaching surfaces capable of killing microorganisms on contact”, J. Mater. Chem., 19, 7796–7806, 2009.

G. Ivanova, E.R. Vão, M. Temtem, A. Aguiar-Ricardo, T. Casimiro, E.J. Cabrita, “High-Pressure NMR Characterization of Triacetyl-beta-Cyclodextrin in Supercritical Carbon Dioxide”, Magn. Reson. Chem., 47(2),133-141, 2009.

B.S. Kim, H.I. Lee, Y. Min, Z. Poon, P.T. Hammond, “Hydrogen-bonded multilayer of pH-responsive polymeric micelles with tannic acid for surface drug delivery”, Chem. Commun., 28, 4194-4196, 2009.

S.W. Lee, W.G. Lee, B.G. Chung, J.H. Park, A. Khademhosseini, “Rapid formation of acrylated microstructures by microwave-induced thermal crosslinking”, Macromol. Rapid Comm., 30(16), 1382–1386, 2009.

W.G. Lee, Y.G. Kim, B.G. Chung, U. Demirci, A. Khademhosseini, “Nano/microfluidics for diagnosis of infectious diseases in developing countries”, Adv. Drug Deliver. Rev., 62(4-5), 449-57, 2009.

W.G. Lee, D. Ortmann, M.J. Hancock, H. Bae, A. Khademhosseini, “A hollow sphere soft lithography approach for long-term hanging drop assays”, Tissue Eng. Part C: Methods, 16(2), 249-259, 2009.

N. Nezamoddini-Kachouie, L. Kang, A. Khademhosseini, “Arraycount, an algorithm for automatic cell counting in microwell arrays”, Biotechniques, 47(3), 351-357, 2009.

P.H. Oliveira, K.J. Prather, D.M.F. Prazeres, G.A. Monteiro, “Structural instabilities of plasmid biopharmaceuticals: challenges and implications”, Trends Biotechnol., 27(9), 503-511, 2009.

M. Temtem, D. Pompeu, T. Barroso, J. Fernandes, P.C. Simões, T. Casimiro, A.M. Botelho do Rego, A. Aguiar-Ricardo, “Development and characterization of a thermoresponsive polysulfone membrane using an environmental friendly technology”, Green Chem., 11, 638-645, 2009.

M. Temtem, D. Pompeu, G. Jaraquemada, E.J. Cabrita, T. Casimiro, A. Aguiar-Ricardo, “Development of PMMA membranes functionalized with hydroxypropyl-b-cyclodextrins for controlled drug delivery using a supercritical CO2-assisted technology”, Int.J. Pharm., 376, 110-115, 2009.

J.E. Toettcher, A. Loewer, G.J. Ostheimer, M.B. Yaffe, B. Tidor, G. Lahav, “Distinct mechanisms act in concert to mediate cell cycle arrest”, P. Natl. Acad. Sci. USA, 106, 785–790, 2009.

Y.L. Zhang, M.L. Radhakrishnan, X. Lu, A.W. Gross, B. Tidor, H.F. Lodish, “Symmetric signaling by an asymmetric 1 erythropoietin: 2 erythropoietin receptor complex”, Mol. Cell, 33(2), 266-274, 2009.


L. Fernandes, R. Rial-Otero, M. Temtem, C. Veiga de Macedo, A. Aguiar-Ricardo, J.L. Capelo, “Ultrasonic energy as a tool for sample treatment in the characterization of polymers through matrix assisted laser desorption ionization time-of-flight mass spectrometry”, Talanta, 77, 882-888, 2008.

B.J. Hackel, A. Kapila, K.D. Wittrup, “Picomolar Affinity Fibronectin Domains Engineered Utilizing Loop Length Diversity, Recursive Mutagenesis, and Loop Shuffling”, J. Mol. Biol., 381(5), 1238-5, 2008.

H.I. Lee, J.A. Lee, Z.Y. Poon, P.T. Hammond, “Temperature-triggered reversible micellar self-assembly of linear-dendritic block copolymers”, Chem. Commun., 32, 3726-3728, 2008.

S.L. Sazinsky, R.G. Ott, N.W. Silver, B. Tidor, J.V. Ravetch, K.D. Wittrup, “Aglycosylated immunoglobulin G1 variants productively engage activating Fc receptors”, P. Natl. Acad. Sci. USA, 105, 20167–20172, 2008.

M. Temtem, T. Casimiro, J.F. Mano, A. Aguiar-Ricardo, “Preparation of membranes with polysulfone/polycaprolactone blends using a high pressure cell specially designed for a CO2-assisted phase inversion”, J. Supercrit. Fluids, 43, 542-548, 2008.


Stem Cell, Tissue Engineering and Regenerative Medicine


R.F. Canadas, J.M.B.T. Cavalheiro, J.D.T. Guerreiro, Almeida, E. Pollet, C.L. da Silva, M.M.R. da Fonseca, F.C. Ferreira, Frederico Castelo ; 2014 ; "Electrospun fibers of bacterial polyhydroxyalkanoates produced from biodiesel-derived crude glycerol and their application in human mesenchymal stem cell cultivation". Biomacromolecules.


N. Monteiro, A. Martins, D. Ribeiro, S. Faria, N. A. Fonseca, J. N. Moreira, R. L. Reis, N. M. Neves. “On the Use of Dexamethasone Loaded Liposomes to Induce the Osteogenic Differentiation of Human Mesenchymal Stem Cells”. Journal of Tissue Engineering and Regenerative Medicine, 2013, doi -10.1002/term.1817. 


L. Bernardino, M.F. Eiriz, T. Santos, S. Xapelli, S. Grade, A.I. Rosa, L. Cortes, R. Ferreira, J. Bragança, F. Agasse, L. Ferreira, J.O. Malva, “Histamine Stimulates Neurogenesis in the Rodent Subventricular Zone”, STEM CELLS, 30(4), 773–784, 2012.

A.C. Lima , P. Batista, T.A. Valente, A.S. Silva , I.J. Correia, J.Mano, "Novel Methodology Based on Biomimetic Superhydrophobic Substrates to Immobilize Cells and Proteins in Hydrogel Spheres for Applications in Bone Regeneration", Tissue Eng Part A., doi:10.1089/ten.TEA.2012.0249., 2012

S.M. Mihaila, A.M. Frias, R.P. Pirraco, T. Rada, R.L. Reis, M.E. Gomes, A.P. Marques, “Human Adipose Tissue-Derived SSEA-4 SubPopulation Multi-Differentiation Potential Towards the Endothelial and Osteogenic Lineages”, Tissue Engineering Part A, doi:10.1089/ten.tea.2012.0092, 2012.

N. M. Nathaniel, H. Cheng,P.S.Hill, J.D.T.Guerreiro, T.T. Dang, M.Ma, S. Watson, H.Shanée, S. Nathaniel R. Langer, D.G. Anderson; 2012 ; "Localized delivery of dexamethasone from electrospun fibers reduces the foreign body response". Biomactomolecules. 13(10):30131.

R.B. Restani, P.I. Morgado, M.P. Ribeiro, I.J. Correia, A. Aguiar-Ricardo, V.D.B. Bonifácio, “Biocompatible Polyurea Dendrimers with pH-Dependent Fluorescence”, Angewandte Chemie International Edition, 51(21), 5162–5165, 2012.


P.Z. Andrade, C. Lobato da Silva, F. dos Santos, G. Almeida-Porada, J.M.S. Cabral, “Initial CD34+ cell-enrichment of cord blood determines hematopoietic stem/progenitor cell yield upon ex vivo expansion”, J. Cell. Biochem., 112(7), 1822-1831, 2011.

P.P. Carvalho, X. Wu, G. Yu, I.R. Dias, M.E. Gomes, R.L. Reis, J.M. Gimble, “Use of Animal Protein Free Products for Passaging Adherent Human Adipose-derived Stromal/Stem Cells (ASCs)”, Cytotherapy, 13(5), 594-597, 2011.

P.P. Carvalho, X. Wua, G. Yua, I.R. Dias, M.E. Gomes, R.L. Reis, J.M. Gimble, “The Effect of Storage Time on Adipose-Derived Stem Cell Recovery from Human Lipoaspirates”, Cells Tissues Organs, 194(6), 494-500, 2011.

E. Costa, J. de‐Carvalho, T. Casimiro, C. Lobato da Silva, M.T. Cidade, A. Aguiar‐Ricardo, “Tailoring  thermoresponsive  microbeads  in  supercritical  carbon  dioxide  for  biomedical  applications”, J. Supercrit. Fluids, 56(3), 292-298, 2011.

E. Costa, M. Coelho, L. Ilharco, A. Aguiar-Ricardo, P.T. Hammond, “Tannic Acid mediated suppression of PNIPAAm microgels thermoresponsive behavior”, Macromolecules, 44(3), 612–621, 2011.

F. dos Santos, P.Z. Andrade, M.M. Abecasis, J.M. Gimble, L.G. Chase, A.M. Campbell, S. Boucher, M.C. Vemuri, C. Lobato da Silva, J.M.S. Cabral, “Toward a Clinical-Grade Expansion of Mesenchymal Stem Cells from Human Sources: A Microcarrier-Based Culture System Under Xeno-Free Conditions”, Tissue Engineering Part C: Methods, 17(12), 1201-1210, 2011.

M.F. Eiriz, S. Grade, A. Rosa, S. Xapelli, L. Bernardino, F. Agasse, J.O. Malva, “Functional evaluation of neural stem cell differentiation by single cell calcium imaging”, Current Stem Cell Research & Therapy, 6(3), 288-296, 2011.

T.P. Kraehenbuehl, L.S. Ferreira, A.M. Hayward, M. Nahrendorf, A.J. van der Vlies, E. Vasile, R. Weissleder, R. Langer, J.A. Hubbell, “Human embryonic stem cell-derived microvascular grafts for cardiac tissue preservation after myocardial infarction”, Biomaterials, 32(4), 1102-1109, 2011.

T.P. Kraehenbuehl, R. Langer, L.S. Ferreira, “Biomaterials for the self-renewal and differentiation of human pluripotent stem cells”, Nature Methods, 8(9), 731-736, 2011.

J. Loureiro, P.Z. Andrade, S. Cardoso, C. Lobato da Silva, J.M.S. Cabral, P.P. Freitas, “Magnetoresistive Cytometer”, Lab Chip, 11, 2255-2261, 2011.

J. Loureiro, P.Z. Andrade, S. Cardoso, C. Lobato da Silva, J.M.S. Cabral, P.P. Freitas, “Spintronic chip cytometer”, J. Appl. Phys., 109(7), 07B311, 2011.

M. Ma, W.F. Liu, P.S. Hill, K.M. Bratlie, D.J. Siegwart, J. Chin, M. Park, J. Guerreiro, D.G. Anderson, “Development of cationic polymer coatings to regulate foreign-body responses”, Adv. Mater., 23, H189-94, 2011.

C. Madeira, S.C. Ribeiro, I.S.M. Pinheiro, S.A.M. Martins, P.Z. Andrade, C. Lobato da Silva, J.M.S. Cabral, “Gene delivery to human bone marrow mesenchymal stem cells by microporation”, J. Biotechnol., 151(1), 130-136, 2011.

M.J. Nunes-Pereira, I.F. Carvalho, J.M. Karp, L.S. Ferreira, “Sensing the Cardiac Environment: Exploiting Cues for Regeneration”, Journal of Cardiovascular Translational Research, 4(5), 616-630, 2011.

D.C.S. Pedroso, A. Tellechea, L. Moura, I. Fidalgo-Carvalho, J. Duarte, E. Carvalho, L.S. Ferreira, “Improved survival, vascular differentiation and wound healing potential of umbilical cord stem cells co-cultured with endothelial cells”, PLoS One, 6(1), e16114, 2011.

M.J. Pereira, I.F. Carvalho, J.M. Karp, L.S. Ferreira, “Sensing the cardiac environment: exploiting cues for regeneration”, J Cardiovasc Transl Res, 4(5), 616-30, 2011.

T. Rada, R.L. Reis, M.E. Gomes, “Distinct Stem cells subpopulations isolated from  human adipose tissue with different  chondrogenic and osteogenic differentiation potential”, Stem Cells Reviews and Reports, 7(1), 64-76, 2011.

T. Rada, M.E. Gomes, R.L. Reis, “A novel method for the isolation of subpopulations of rat adipose stem cells with different proliferation and osteogenic differentiation potentials”, Journal of Tissue Engineering and Regenerative Medicine, 5(8), 655–664, 2011.

T. Rada, T.C. Santos, A.P. Marques, V.M. Correlo, A.M. Frias, A.G. Castro, N.M. Neves, M.E. Gomes, R.L. Reis, “Osteogenic differentiation of two distinct subpopulations of human adipose-derived stem cells: an in vitro and in vivo study”, Journal of Tissue Engineering and Regenerative Medicine, 6(1), 1–11, 2011.

P.M. Rocha, V.E. Santo, M.E. Gomes, R.L. Reis, J.F. Mano, “Encapsulation of Adipose-derived Stem Cells and Transforming Growth Factor beta1 in Carrageenan-based Hydrogels as a New System for Cartilage Tissue Engineering”, Journal of Bioactive and Compatible Polymers, 26(5): 493–507, 2011.

C.A.V. Rodrigues, M.M. Diogo, C. Lobato da Silva, J.M.S. Cabral, “Microcarrier expansion of mouse embryonic stem cell-derived neural stem cells in stirred bioreactors”, Biotechnol. Appl. Bioc., 58(4), 231-242, 2011.

C.A.V. Rodrigues, T.G. Fernandes, M.M. Diogo, C. Lobato da Silva, J.M.S. Cabral, “Stem Cell Cultivation in Bioreactors”, Biotechnology Advances, 29(6), 815–829, 2011.


S. Aday, M. Gumusderelioglu, “Bone-like Apatite Coated Chitosan Scaffolds: Characterization and Osteoblastic Activity”, Polym. Composite., 31(8), 1418-1426, 2010.

P.Z. Andrade, F. dos Santos, G. Almeida-Porada, C.L. da Silva, J.M.S. Cabral, “Systematic delineation of optimal cytokine concentrations to expand hematopoietic stem/progenitor cells in co-culture with mesenchymal stem cells”, Mol. BioSyst., 6(7), 1207-1215, 2010.

F. dos Santos, P.Z. Andrade, J.B. Boura, M. Abecassis, C. Lobato da Silva, J.M.S. Cabral, “Ex vivo expansion of human mesenchymal stem cells: A more effective cell proliferation kinetics and metabolism under hipoxia”, J. Cell. Physiol., 22 3(1), 27-35, 2010.

G. Eibes, F. dos Santos, P.Z. Andrade, J.S. Boura, M. Abecasis, C. Lobato da Silva, J.M.S. Cabral, “Maximizing the ex vivo expansion of human mesenchymal stem cells using a microcarrier-based stirred culture system”, J. Biotechnol., 146(4), 194-197, 2010.

T.G. Fernandes, M.M. Diogo, A. Fernandes-Platzgummer, C. Lobato da Silva, J.M.S. Cabral, “Different stages of pluripotency determine distinct patterns of proliferation, metabolism and lineage commitment of embryonic stem cells under hypoxia”, Stem Cell Res., 5(1), 76-89, 2010.

T.G. Fernandes, A.M. Fernandes-Plaztgummer, C. Lobato da Silva, M.M. Diogo, J.M.S. Cabral, “Kinetic and metabolic analysis of mouse embryonic stem cell expansion under serum-free conditions”, Biotechnol. Lett., 32(1), 171-179, 2010.

T.G. Fernandes, S-J. Kwon, S.S. Bale, M-Y. Lee, M.M. Diogo, D.S. Clark, J.M.S. Cabral, J.S. Dordick, “Three-Dimensional Cell Culture Microarray for High-Throughput Studies of Stem Cell Fate”, Biotechnol. Bioeng., 106(1), 106-118, 2010.

A. Fernandes-Platzgummer, M.M. Diogo, R.P. Baptista, C. Lobato da Silva, J.M.S. Cabral, “Scale-up of mouse embryonic stem cell expansion in stirred bioreactors”, Biotechnol. Progr., 27(5), 1421-1432, 2010.

L.S. Ferreira, D.C.S. Pedroso, H. Vazão, R.S.M. Gomes, “Stem cell-based therapies for heart regeneration: what did the bench teach us?”, Cardiovascular & Haematological Disorders-Drug Targets, 10(3), 173-185, 2010.

S. Levenberg, L.S. Ferreira, L. Chen-Konak, T.P. Kraehenbuehl, R. Langer, “Isolation, differentiation and characterization of vascular cells derived from human embryonic stem cells”, Nat. Protoc., 5(4), 1115–1126, 2010.

C. Lobato da Silva, R. Gonçalves, F. dos Santos, P.Z. Andrade, G. Almeida-Porada, J.M.S. Cabral, “Dynamic cell–cell interactions between cord blood haematopoietic progenitors and the cellular niche are essential for the expansion of CD34+, CD34+CD38- and early lymphoid CD7+ cells”, J. Tissue Eng. Regen. M., 4(2), 149-158, 2010.

S.M. Luna, J.V. Araujo, M.E. Gomes, J.F. Mano, R.L. Reis, “Development of a novel cell encapsulation system based on natural origin polymers for tissue engineering applications”, Bioactive and Compatible Polymers, 25(4), 342-359, 2010.

C. Madeira, S. Ribeiro, M.Z. Turk, J.M.S. Cabral, “Optimization of gene delivery to HEK293T cells by microporation using a central composite design methodology”, Biotechnol. Lett., 32(10), 1393-1399, 2010.

C. Madeira, R.D. Mendes, S.C. Ribeiro, J.S. Boura, M.R. Aires-Barros, C. Lobato da Silva, J.M.S. Cabral, “Non-Viral GeneDelivery to Mesenchymal Stem Cells Using Cationic Liposomes for Gene and Cell Therapy”, J. Biomed. Biotechnol., ID:735349, 12pg, 2010.

J. Maia, T. Santos, S. Aday, F. Agasse, L. Cortes, J.O. Malva, L. Bernardino, L.S. Ferreira, “Controlling the neuronal differentiation of stem cells by the intracellular delivery of retinoic acid-loaded nanoparticles”, ACS Nano, 5(1), 97-106, 2010.

J.T. Oliveira, L. Gardel, L. Martins, T. Rada, M.E. Gomes, R.L. Reis, “Injectable gellan gum hydrogels with autologous cells for the treatment of rabbit articular cartilage defects”, Journal of Orthopedic Research, 28, 1193-1199, 2010.

A.R.B. Restani, V.G. Correia, V.D.B. Bonifácio, A. Aguiar-Ricardo, “Development of Functional Mesoporous Microparticles for Drug Delivery”, J. Supercrit. Fluids, 55(1), 333-339, 2010.

C.A.V. Rodrigues, M.M. Diogo, C. Lobato da Silva, J.M.S. Cabral, “Hypoxia Enhances Proliferation of Mouse Embryonic Stem Cell-derived Neural Stem Cells”, Biotechnol. Bioeng., 106(2), 260-270, 2010.

M. Serra, C. Brito, M.F.Q. Sousa, J. Jensen, R. Tostões, J. Clemente, R. Strehl, J. Hyllner, M.J.T. Carrondo, P.M. Alves, “Improving expansion of pluripotent human embryonic stem cells in perfused bioreactors through oxygen control”, J. Biotechnol., 148(4), 208‐215, 2010.

F.B. De Sousa; J. D.T. Guerreiro; M. Ma; D.G.Anderson; C.L.Drum; R.Sinisterra; R. Langer; 2010 "Photo-response behavior of electrospun nanofibers based on spiropyran-cyclodextrin modified polymer". Journal of Materials Chemistry. 20(44):9910; DOI: 10.1039/C0JM01903H


N. Annabi, J.W. Nichol, X. Zhong, C. Ji, S. Koshy, A. Khademhosseini, F. Dehghani, “Controlling the porosity and microarchitecture of hydrogels for tissue engineering”, Tissue Eng.: Part B Reviews, 16(4), 371-83, 2009.

M.D. Brigham, A. Bick, E. Lo, A. Bendali, J.A. Burdick, A. Khademhosseini, “Mechanically robust and bioadhesive collagen and photocrosslinkable hyaluronic acid semi-interpenetrating networks”, Tissue Eng. Part A, 15, 1645-53, 2009.

B.D. Cosgrove, B.M. King, M.A. Hasan, L.G. Alexopoulos, P.A. Farazi, B.S. Hendriks, L.S. Griffith, P.K. Sorger, B. Tidor, J.J. Xu, D.A. Lauffenburger, “Synergistic drug–cytokine induction of hepatocellular death as an in vitro approach for the study of inflammation-associated idiosyncratic drug hepatotoxicity”, Toxicol. Appl. Pharm., 237, 319-330, 2009.

Y. Du, M. Ghodousi, E. Lo, M.K. Vidula, O. Emiroglu, A. Khademhosseini, “Surface-directed assembly of cell-laden microgels”, Biotechnol. Bioeng., 105(3), 655-62, 2009.

T.G. Fernandes, M.M. Diogo, D.S. Clark, J.S. Dordick, J.M.S. Cabral, “High-throughput cellular microarray platforms: potential applications in drug discovery, toxicology and stem cell research”, Trends Biotechnol., 27(6), 342-349, 2009.

S.A. Hacking, A. Khademhosseini, “Applications of microscale technologies for regenerative dentistry”, J. Dent. Res., 88, 409-21, 2009.

J. He, Y. Du, J.L. Viua-Uribe, C. Hwang, D. Li, A. Khademhosseini, “Rapid generation of biologically relevant hydrogels containing long-range chemical gradients”, Adv. Funct. Mater., 20(1), 131–137, 2009.

C.M. Hwang, Y.D. Park, J.Y. Park, K. Sun, A. Khademhosseini, S.H. Lee, “Controlled cellular orientation on PLGA microfibers with different defined diameters”, Biomed. Microdevices, 11(4), 739-46, 2009.

Y.-S. Hwang, B.G. Chung, D. Ortmann, N. Hattori, H.-C. Moeller, A. Khademhosseini, “Microwell mediated control of embryoid body size regulates embryonic stem cell fate via differential expression of WNT5a and WNT11”, P. Natl. Acad. Sci. USA, 106(40), 16978-16983, 2009.

L. Kang, M.D. Brigham, M.J. Hancock, A. Khademhosseini, “Cell confinement in patterned nanoliter droplets in a microwell array by wiping”, J. Biomed. Mater. Res. A, 93(2), 547-57, 2009.

M. Khabiry, B.G. Chung, M.J. Hancock, H.C. Soundararajan, Y. Du, D.C. Cropek, W.G. Lee, A. Khademhosseini, “Cell Docking in Double Grooves in a Microfluidic Channel”, Small, 5, 1186-1194, 2009.

A. Khademhosseini, J. Vacanti, R. Langer, “Tissue Engineering: Next Generation Tissue Constructs and Challenges to Clinical Practice”, Sci. Am., 300(1), 64-71, 2009.

T.P. Kraehenbuehl, L.S. Ferreira, P. Zammaretti, J.A. Hubbell, R. Langer, “Cell-responsive hydrogel for encapsulation of vascular cells”, Biomaterials, 30, 4318–4324, 2009.

C. Lobato da Silva, R. Gonçalves, C.D. Porada, J.L. Ascenção, E.D. Zanjani, J.M.S. Cabral, G. Almeida Porada, “Differences amid bone marrow and cord blood hematopoietic stem/progenitor cell division kinetics”, J. Cellular Physiology, 220, 102-111, 2009.

C. Mirren, M. Textor, A. Khademhosseini, M.P. Lutolf, “Microwell arrays for biomedical research”, Integrative Biology, 1(5), 625-634, 2009.

B. Murtuza, J. Nichol, A. Khademhosseini, “Micro- and nanoscale control of the cardiac stem cell niche for tissue fabrication”, Tissue Eng. Part B: Reviews, 15(4), 443-54, 2009.

J. Nichol, A. Khademhosseini, “Modular tissue engineering: Engineering biological tissues from the bottom up”, Soft Matter, 5, 1312-1319, 2009.

A.P. Serro, C. Completo, R. Colaço, F. dos Santos, C. Lobato da Silva, J.M.S. Cabral, H. Araújo, E. Pires, B. Saramago, “A comparative study of titanium nitrides, TiN, TiNbN and TiCN, as coatings for biomedical applications”, Surface and Coatings Technology, 203, 3701-3707, 2009.

B.V. Slaughter, S. Khurshid, O.Z. Fisher, A. Khademhosseini, N.A. Peppas, “Hydrogels in Regenerative Medicine”, Adv. Materials, 21, 1-23, 2009.

Y.S. Song, R.L. Lin, G. Montesano, N.G. Durmus, G. Lee, S.-S. Yoo, E. Kayaalp, E. Hæggström, A. Khademhosseini, U. Demirci, “Engineered 3D tissue models for cell-laden microfluidic channels”, Anal. Bioanal. Chem., 395(1), 185-193, 2009.

M. Temtem, L.M. Silva, P.Z. Andrade, F. dos Santos, C. Lobato da Silva, J.M.S. Cabral, M.M. Abecasis, A. Aguiar-Ricardo, “Supercritical CO2 Generating Chitosan Devices with Controlled Morphology. Potential Application for Drug Delivery and Mesenchymal Stem Cell Culture”, J. Supercrit. Fluids, 48 (3), 269-277, 2009.


M.M. Diogo, D. Henrique, J.M.S. Cabral, “Optimization and integration of expansion and neural commitment of mouse embryonic stem cells”, Biotechnol. Appl. Biochem., 49, 105-112, 2008.

T.G. Fernandes, S.J. Kwon, M.Y. Lee, D.S. Clark, J.M.S. Cabral, J.S. Dordick, “On-Chip, Cell-Based Microarray Immunofluorescence Assay for High-Throughput Analysis of Target Proteins”, Analytical Chemistry, 80, 6633-6639, 2008.

L.S. Ferreira, T. Squier, H. Park, H. Choe, D.S. Kohane, R. Langer, “Human Embryoid Bodies Containing Nano- and Micro-Particulate Delivery Vehicles”, Adv. Materials, 20, 2285-2291, 2008.

L.S. Ferreira, J.M. Karp, L. Nobre, R. Langer, “New Opportunities: The Use of Nanotechnologies to Manipulate and Track Stem Cells”, Cell Stem Cell, 3, 136-146, 2008.

L.S. Ferreira, “Nanoparticles as Tools to Study and Control Stem Cells”, J. Cellular Biochemistry, 108, 746–752, 2008.

A.M. Frias, C.D. Porada, K.B. Crapnell, J.M.S. Cabral, E.D. Zanjani, G. Almeida-Porada, “Generation of functional natural killer and dendritic cells in a human stromal-based serum-free culture system designed for cord blood expansion”, Exp. Hematol., 36, 61-68, 2008.

J. Fuller, G. Zugates, L.S. Ferreira, H. Ow, N. Nguyen, U. Wiesner, R. Langer, “Intracellular delivery of coreeshell fluorescent silica nanoparticles”, Biomaterials, 29, 1526-1532, 2008.

A. Mahdavi, L.S. Ferreira, C. Sundback, J.W. Nichol, E.P. Chan, J.D. Carter, C. Bettinger, S. Patanavanich, L. Chignozha, E. Ben-Joseph, A. Galakatos, H. Pryor, I. Pomerantseva, P. Masiakos, W. Faquin, A. Zumbuehl, S. Hong, J. Borenstein, J. Vacanti, R. Langer, J.M. Karp, “A biodegradable and biocompatible Gecko-inspired tissue adhesive”, P. Natl. Acad. Sci. USA, 105(7), 2307-2312, 2008.


Computational Bioengineering, Genomics, Systems and Synthetic Biology


P. Maia, P. Vilaça, I. Rocha, M. Pont, J.F. Tomb, M. Rocha, “An integrated computational environment for elementary modes analysis of biochemical networks”, International Journal of Data Mining and Bioinformatics, 6(4), 382-395, 2012.


S. Carneiro, S. Villas-Bôas, E.C. Ferreira, I. Rocha, “Metabolic footprint analysis of recombinant Escherichia coli strains during fed-batch fermentations”, Mol. BioSyst., 7(3), 899-910, 2011.

R.S. Costa, D. Machado, I. Rocha, E.C. Ferreira, “Critical perspective on the consequences of the limited availability of kinetic data in Metabolic Dynamic Modeling”, IET Systems Biology, 5(3), 157-163, 2011.

A. Lourenço, S. Carneiro, M. Rocha, E.C. Ferreira, I. Rocha, “Challenges in integrating E. coli molecular biology data”, Brief. Bioinform., 12(2), 91-103, 2011.

A. Lourenço, S. Carneiro, J.P. Pinto, M. Rocha, E.C. Ferreira, I. Rocha, “A study of the short and long-term regulation of E. coli metabolic pathways”, Journal of Integrative Bioinformatics, 8(3), 183, 2011.

Z.I.T.A. Soons, E.C. Ferreira, I. Rocha, “Identification of minimal metabolic pathway models consistent with phenotypic data”, Journal of Process Control, 21(10), 1483-1492, 2011.

P. Vilaça, I. Rocha, M. Rocha, “A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/regulatory information”, Biosystems, 103(3), 435–441, 2011.


J.F. Apgar, D.K. Witmer, F.M. White, B. Tidor, “Sloppy models, parameter uncertainty, and the role of experimental design”, Mol. Biosyst., 6(10), 1890-1900, 2010.

S. Carneiro, S. Villas-Bôas, I. Rocha, E.C. Ferreira, “Applying a metabolic footprinting approach to characterize the impact of the recombinant protein production in Escherichia coli”, Advances in Soft Computing, 74/2010, 193-200, 2010.

R.S. Costa, D. Machado, I. Rocha, E.C. Ferreira, “Hybrid dynamic modeling of E. coli central metabolic network combining Michaelis-Menten and approximate kinetic equations”, Biosystems, 100(2), 150-157, 2010.

A. Lourenço, R. Carreira, D. Glez-Peña, J.R. Méndez, S. Carneiro, L.M. Rocha, F. Díaz, E.C. Ferreira, I. Rocha, F. Fdez-Riverola, M. Rocha, “BioDR: Semantic indexing networks for biomedical document retrieval”, Expert Syst. Appl., 37(4), 3444-3453, 2010.

M.L. Radhakrishnan, B. Tidor, “Cellular level models as tools for cytokine design”, Biotechnol. Progr., 26(4), 919-937, 2010.

I. Rocha, P. Maia, P. Evangelista, P. Vilaça, S. Soares, J.P. Pinto, J. Nielsen, K.R. Patil, E.C. Ferreira, M. Rocha, “OptFlux: an open-source software platform for in silico metabolic engineering”, BMC Syst. Biol., 4(45), 1-12, 2010.

P. Vilaça, P. Maia, I. Rocha, M. Rocha, “Metaheuristics for strain optimization using transcriptional information enriched metabolic models”, Lect. Notes in Computer Science, 6023, 205-216, 2010.


D.M. Bower, K.L.J. Prather, “Engineering of bacterial strains and vectors for the production of plasmid DNA”, Appl. Microbiol. Biotechnol., 82(5), 805-813, 2009.

B.M. King, B. Tidor, “MIST: Maximum information spanning trees for dimension reduction of biological data sets”, Bioinformatics, 25, 1165–1172, 2009.

A. Lourenço, R. Carreira, S. Carneiro, P. Maia, D. Glez-Peña, F. Fdez-Riverola, E.C. Ferreira, I. Rocha, M. Rocha, “@Note: a workbench for biomedical text mining”, J. Biomed. Inform., 42(4), 710-720, 2009.

D. Machado, R.S. Costa, M. Rocha, I. Rocha, B. Tidor, E.C. Ferreira, “A critical review on modelling formalisms and simulation tools in computational biosystems”, Lect. Notes in Computer Science, 5518, 1063-1070, 2009.

Z. Shi, N. Chen, Y. Du, A. Khademhosseini, M. Alber, “Stochastic model of selfassembly of cell-laden hydrogels”, Phys. Rev. E, 80, 061901, 2009.

A.K. Wilkins, B. Tidor, J.K. White, P.I. Barton, “Sensitivity analysis for oscillating dynamical systems”, SIAM J. Sci. Comput., 31(4), 2706–2732, 2009.


Biomedical Devices and Technologies: Hybrid Human - Machine Systems


E. Bicho, W. Erlhagen, L. Louro, E. Costa e Silva, “Neuro-cognitive mechanisms of decision making in joint action: a Human-Robot interaction study”, Human Movement Science, 30, 846–868, 2011.

E. Bicho, L. Louro, W. Erlhagen, “Integrating verbal and non-verbal communication in a dynamic neural field architecture for human-robot interaction”, Frontiers in Neurorobotics, 4, Art 5, 2011.

D. S. Ferreira, J. Mirkovic, R.F. Wolffenbuttel, J.H. Correia, M.S. Feld, G. Minas, “Narrow-band pass filter array for integrated opto-electronic spectroscopy detectors to assess esophageal tissue”, Biomedical Optics Express, 2(6), 1703-1716, 2011.

D. S. Ferreira, V.C. Pinto, J.H. Correia, G. Minas, “Spectroscopic Detection of Gastrointestinal Dysplasia using Optical Microsensors”, IEEE Transactions on Biomedical Engineering, 58(9), 2633-2639, 2011.


S. Monteiro, E. Bicho, “Attractor dynamics approach to robot formations: theory and implementation”, Autonomous Robots, Volume 29(3), 331-355, 2010.


Biosystems Innovation, Management and Policy


L.E. McCray, K.A. Oye, A. Petersen, “Planned Adaptation in Risk Regulation: A Review of US Environmental, Health, and Safety Regulation”, Technol. Forecast. Soc., 77(6), 951-959, 2010.


G. Mukunda, K.A. Oye, S. Mohr, “What Rough Beast? Synthetic biology, uncertainty, and the future of biosecurity”, Politics and the Life Sciences, 28(2), 2-26, 2009.


L.F. Lages, S.D. Jap, D. Griffith, “The role of past performance in export ventures: A short-term reactive approach”, Journal of International Business Studies, 39(2), 304-325, 2008.



Eiriz MF, Malva JO, Agasse F*, Bernardino L* (2014) Histamine in the neural and cancer stem cell niches. Stem Cells and Cancer Stem Cells 12, 3-17 Edited by Hayat MA; Springer.L.


De Anda, F.C., Rosario, A.L., Durak, O., Tran, T., Gräff, J., Meletis, K., Rei, D., Soda, T., Madabhushi, R., Ginty, D.D., Kolodkin, A.L., Tsai, L.-H., 2012. Autism spectrum disorder susceptibility gene TAOK2 affects basal dendrite formation in the neocortex. Nat. Neurosci. 15, 1022–1031. doi: 10.1038/nn.3141

L. Bernardino*, M.F. Eiriz *, T. Santos, S. Xapelli,  S. Grade, A.L. Rosa, L. Corte, R. Ferreira , J. Bragança,F. Agasse, L. Ferreira, J.O. Malva (2012) Histamine Stimulates Neurogenesis in the RodentSubventricular Zone. Stem Cells, 30: 773-784.

J. Goméz-Lobo,  M.F. Eiriz, T. Santos, I. Neiva, R. Ferreira and J. O. Malva (2012) Microglia: the bodyguard and the hunter of the adult neurogenic niche. Advances in Stem Cell Research, 245-79, Edited by Baharvand H; Springer

C.Rendeiro, J.D.T. Guerreiro, C.M. Williams,J.P.E. Spencer ; 2012; "Flavonoids as modulators of memory and learning: molecular interactions resulting in behavioural effects". The Proceedings of the Nutrition Society. 71(2):246.  doi: 10.1017/S0029665112000146


J.L. Chen, W.C. Lin, J.W. Cha, P.T. So, Y. Kubota, E. Nedivi, “Structural basis for the role of inhibition in facilitating adult brain plasticity”, Nat. Neurosci., 14, 587-594, 2011.

J.L. Chen, G.H. Flanders, W-C.A. Lee, W.C. Lin, E. Nedivi, “Inhibitory dendrite dynamics as a general feature of the adult cortical microcircuit”, J. Neurosci., 31, 12437-12443, 2011.

M. F. Eiriz, S. Grade, A. Rosa, S. Xapelli, L. Bernardino, F. Agasse, J. O. Malva (2011) Functional evaluation of neural stem cell differentiation by single cell calcium imaging. Current Stem Cell Research & Therapy, 6 (3): 288-96


J.L. Chen, E. Nedivi, “Neuronal Structure Remodeling: is it all about access?”, Curr. Opin. Neurobiol., 20(5), 557-562, 2010.

V. Ruta, S.R. Datta, M.L. Vasconcelos, J. Freeland, L.L. Looger, R. Axel, “A dimorphic pheromone circuit in Drosophila from sensory input to descending output”, Nature, 468 (7324), 686-690, 2010.


A. Holtmaat, T. Bonhoeffer, D. Chow, J. Chuckowree, V. De Paola, S.B. Hofer, M. Hubener, T. Keck, G. Knott, W.C.A. Lee, R. Mostany, T.D. Mrsic-Flogel, E. Nedivi, C. Portera-Cailliau, K. Svoboda, J. Trachtenberg, L. Wilbrecht, “Long-term, high-resolution imaging in the mouse neocortex through a chronic cranial window”, Nat. Protoc., 4(8), 1128-1144, 2009.


W-C.A. Lee, L.L. Chen, H. Huang, J.H. Leslie, Y. Amitai, P.T. So, E. Nedivi, “A dynamic zone defines interneuron remodeling in the adult neocortex”, P. Natl. Acad. Sci. USA, 105(50), 19968-19973, 2008.




J.M. Waldie, D.J. Newman, “A gravity loading countermeasure skinsuit”, Acta Astronautica, 68(7–8), 722–730, 2011.


R.A. Opperman, J.M. Waldie, A. Natapoff, D.J. Newman, J.A. Jones, “Probability of Spacesuit-Induced Fingernail Trauma is associated with Hand Circumference”, Aviat. Space Envir. Md., 81, 907-913, 2010.

L. Stirling, K. Willcox, D. Newman, “Development of a computational model for astronaut reorientation”, J. Biomech., 43(12), 2309-2314, 2010.

E.B. Wagner, N.P. Granzella, N. Saito, D.J. Newman, L.R. Young, M.L. Bouxsein, “Partial weight Suspension: A Novel Murine Model for Investigation Adaptation to Reduce Musculoskeletal Loading”, J. Appl. Physiol., 109(2), 350-357, 2010.


C.E. Carr, D.J. Newman, “Characterization of a lower-body exoskeleton for simulation of space-suited locomotion”, Acta Astronaut., 62, 308-323, 2008.