Filipa L Sousa

Filipa L Sousa

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Filipa L Sousa

Filipa L Sousa

Publications by authors named "Filipa L Sousa"

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Metabopolis: scalable network layout for biological pathway diagrams in urban map style.

BMC Bioinformatics 2019 Apr 15;20(1):187. Epub 2019 Apr 15.

Research Division of Computer Graphics, Institute of Visual Computing and Human- Centered Technology, TU Wien, Vienna, Austria.

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http://dx.doi.org/10.1186/s12859-019-2779-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6466808PMC
April 2019

Oxygen Reductases in Alphaproteobacterial Genomes: Physiological Evolution From Low to High Oxygen Environments.

Front Microbiol 2019 18;10:499. Epub 2019 Mar 18.

Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.

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http://dx.doi.org/10.3389/fmicb.2019.00499DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6431628PMC
March 2019

An electrogenic redox loop in sulfate reduction reveals a likely widespread mechanism of energy conservation.

Nat Commun 2018 12 21;9(1):5448. Epub 2018 Dec 21.

Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.

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http://dx.doi.org/10.1038/s41467-018-07839-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6303296PMC
December 2018

Staphylococcus aureus haem biosynthesis and acquisition pathways are linked through haem monooxygenase IsdG.

Mol Microbiol 2018 08 2;109(3):385-400. Epub 2018 Aug 2.

Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.

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http://dx.doi.org/10.1111/mmi.14060DOI Listing
August 2018

Native metals, electron bifurcation, and CO reduction in early biochemical evolution.

Curr Opin Microbiol 2018 06 12;43:77-83. Epub 2018 Jan 12.

Institute of Molecular Evolution, Heinrich-Heine-University, Universitätsstr. 1, 40225 Düsseldorf, Germany; Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.

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http://dx.doi.org/10.1016/j.mib.2017.12.010DOI Listing
June 2018

The physiology of trace elements in biological methane production.

Bioresour Technol 2017 Oct 2;241:775-786. Epub 2017 Jun 2.

Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, Universität Wien, Vienna, Austria. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S09608524173088
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http://dx.doi.org/10.1016/j.biortech.2017.05.211DOI Listing
October 2017

Reply to 'Is LUCA a thermophilic progenote?'

Nat Microbiol 2016 11 25;1:16230. Epub 2016 Nov 25.

Institute for Molecular Evolution, Heinrich-Heine University Düsseldorf, Universitätsstraβe 1, 40225 Düsseldorf, Germany.

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http://dx.doi.org/10.1038/nmicrobiol.2016.230DOI Listing
November 2016

Physiology, phylogeny, and LUCA.

Microb Cell 2016 Nov 25;3(12):582-587. Epub 2016 Nov 25.

Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.

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http://dx.doi.org/10.15698/mic2016.12.545DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5348977PMC
November 2016

Energy for two: New archaeal lineages and the origin of mitochondria.

Bioessays 2016 09 24;38(9):850-6. Epub 2016 Jun 24.

Institute of Molecular Evolution, Heinrich-Heine University, Düsseldorf, Germany.

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http://dx.doi.org/10.1002/bies.201600089DOI Listing
September 2016

Data on publications, structural analyses, and queries used to build and utilize the AlloRep database.

Data Brief 2016 Sep 9;8:948-57. Epub 2016 Jul 9.

The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160, USA.

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http://dx.doi.org/10.1016/j.dib.2016.07.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4961497PMC
September 2016

One step beyond a ribosome: The ancient anaerobic core.

Biochim Biophys Acta 2016 Aug 2;1857(8):1027-1038. Epub 2016 May 2.

Institute for Molecular Evolution, Heinrich-Heine Universität Düsseldorf, Universitätstrasse 1, 40225 Düsseldorf, Germany.

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http://dx.doi.org/10.1016/j.bbabio.2016.04.284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4906156PMC
August 2016

The physiology and habitat of the last universal common ancestor.

Nat Microbiol 2016 Jul 25;1(9):16116. Epub 2016 Jul 25.

Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany.

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http://www.nature.com/articles/nmicrobiol2016116
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http://dx.doi.org/10.1038/nmicrobiol.2016.116DOI Listing
July 2016

Lokiarchaeon is hydrogen dependent.

Nat Microbiol 2016 Apr 4;1:16034. Epub 2016 Apr 4.

Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany.

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http://dx.doi.org/10.1038/nmicrobiol.2016.34DOI Listing
April 2016

AlloRep: A Repository of Sequence, Structural and Mutagenesis Data for the LacI/GalR Transcription Regulators.

J Mol Biol 2016 Feb 25;428(4):671-678. Epub 2015 Sep 25.

Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2015.09.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4783282PMC
February 2016

Contact angles and wettability of ionic liquids on polar and non-polar surfaces.

Phys Chem Chem Phys 2015 Dec;17(47):31653-31661

CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.

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http://xlink.rsc.org/?DOI=C5CP05873B
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http://dx.doi.org/10.1039/c5cp05873bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5024753PMC
December 2015

Early Microbial Evolution: The Age of Anaerobes.

Cold Spring Harb Perspect Biol 2015 Dec 18;8(2):a018127. Epub 2015 Dec 18.

Institute for Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany.

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http://dx.doi.org/10.1101/cshperspect.a018127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4743081PMC
December 2015

Endosymbiotic origin and differential loss of eukaryotic genes.

Nature 2015 Aug 19;524(7566):427-32. Epub 2015 Aug 19.

Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany.

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http://dx.doi.org/10.1038/nature14963DOI Listing
August 2015

YCF1: A Green TIC?

Plant Cell 2015 Jul 27;27(7):1827-33. Epub 2015 Mar 27.

Molecular Evolution, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany

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http://dx.doi.org/10.1105/tpc.114.135541DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4531346PMC
July 2015

Autocatalytic sets in metabolism.

J Syst Chem 2015;6(1). Epub 2015 Apr 1.

Institute of Molecular Evolution, Heinrich Heine Universität, Düsseldorf, Germany.

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http://www.jsystchem.com/content/6/1/4
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http://dx.doi.org/10.1186/s13322-015-0009-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4429071PMC
April 2015

Release behavior of trans,trans-farnesol entrapped in amorphous silica capsules.

Results Pharma Sci 2012 11;2:52-6. Epub 2012 Aug 11.

CICECO, Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal.

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http://dx.doi.org/10.1016/j.rinphs.2012.07.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4166580PMC
March 2015

Origins of major archaeal clades correspond to gene acquisitions from bacteria.

Nature 2015 Jan 15;517(7532):77-80. Epub 2014 Oct 15.

1] Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany [2] Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.

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http://dx.doi.org/10.1038/nature13805DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4285555PMC
January 2015

Biochemical fossils of the ancient transition from geoenergetics to bioenergetics in prokaryotic one carbon compound metabolism.

Biochim Biophys Acta 2014 Jul 7;1837(7):964-81. Epub 2014 Feb 7.

Institute for Molecular Evolution,University of Düsseldorf, 40225 Düsseldorf, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.bbabio.2014.02.001DOI Listing
July 2014

Evolution. Energy at life's origin.

Science 2014 Jun;344(6188):1092-3

Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.

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http://dx.doi.org/10.1126/science.1251653DOI Listing
June 2014

Magnetically responsive dry fluids.

Nanoscale 2013 Aug 8;5(16):7229-33. Epub 2013 Jul 8.

Departamento de Química and CICECO, Aveiro Institute of Nanotechnology, Universidade de Aveiro, 3810-193 Aveiro, Portugal.

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http://dx.doi.org/10.1039/c3nr01784bDOI Listing
August 2013

Early bioenergetic evolution.

Philos Trans R Soc Lond B Biol Sci 2013 Jul 10;368(1622):20130088. Epub 2013 Jun 10.

Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany.

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http://dx.doi.org/10.1098/rstb.2013.0088DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3685469PMC
July 2013

The emergence of protein complexes: quaternary structure, dynamics and allostery. Colworth Medal Lecture.

Biochem Soc Trans 2012 Jun;40(3):475-91

MRC Laboratory of Molecular Biology, Hills Road, Cambridge, U.K.

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http://dx.doi.org/10.1042/BST20120056DOI Listing
June 2012

The superfamily of heme-copper oxygen reductases: types and evolutionary considerations.

Biochim Biophys Acta 2012 Apr 6;1817(4):629-37. Epub 2011 Oct 6.

Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal.

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http://dx.doi.org/10.1016/j.bbabio.2011.09.020DOI Listing
April 2012

A bioinformatics classifier and database for heme-copper oxygen reductases.

PLoS One 2011 Apr 29;6(4):e19117. Epub 2011 Apr 29.

Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019117PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3084760PMC
April 2011

The alternative complex III: a different architecture using known building modules.

Biochim Biophys Acta 2010 Dec 21;1797(12):1869-76. Epub 2010 Apr 21.

Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal.

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http://dx.doi.org/10.1016/j.bbabio.2010.04.012DOI Listing
December 2010

Vectorial growth/regulations in a {P8W48}-type polyoxotungstate compartment: trapped unusual molybdenum oxide acts as a handle.

Chem Commun (Camb) 2009 Dec 9(48):7491-3. Epub 2009 Nov 9.

Fakultät für Chemie, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany.

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http://dx.doi.org/10.1039/b917476aDOI Listing
December 2009

Supramolecular chemistry on a cluster surface: fixation/complexation of potassium and ammonium ions with crown-ether-like rings.

Angew Chem Int Ed Engl 2009 ;48(32):5934-7

Fakultät für Chemie, Universität Bielefeld, Postfach 100131, 33501 Bielefeld, Germany.

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http://dx.doi.org/10.1002/anie.200902137DOI Listing
October 2009

Structural and functional insights into sulfide:quinone oxidoreductase.

Biochemistry 2009 Jun;48(24):5613-22

Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal.

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http://dx.doi.org/10.1021/bi9003827DOI Listing
June 2009

Thermodynamic redox behavior of the heme centers in A-type heme-copper oxygen reductases: comparison between the two subfamilies.

Biophys J 2008 Nov 1;95(9):4448-55. Epub 2008 Aug 1.

Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal.

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http://dx.doi.org/10.1529/biophysj.108.139493DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2567927PMC
November 2008

Looking for the minimum common denominator in haem-copper oxygen reductases: towards a unified catalytic mechanism.

Biochim Biophys Acta 2008 Jul-Aug;1777(7-8):929-34. Epub 2008 May 26.

Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República - EAN, 2780-157 Oeiras, Portugal.

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http://dx.doi.org/10.1016/j.bbabio.2008.05.441DOI Listing
August 2008

Redox properties of Thermus thermophilus ba3: different electron-proton coupling in oxygen reductases?

Biophys J 2008 Mar 7;94(6):2434-41. Epub 2007 Dec 7.

Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2781-901 Oeiras, Portugal.

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http://dx.doi.org/10.1529/biophysj.107.122614DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2257904PMC
March 2008

Thermodynamic redox behavior of the heme centers of cbb3 heme-copper oxygen reductase from Bradyrhizobium japonicum.

Biochemistry 2007 Nov 27;46(46):13245-53. Epub 2007 Oct 27.

Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, Av. da República (EAN), 2781-901 Oeiras, Portugal.

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http://dx.doi.org/10.1021/bi700733gDOI Listing
November 2007

Reactions inside a porous nanocapsule/artificial cell: encapsulates' structuring directed by internal surface deprotonations.

Chem Commun (Camb) 2006 Aug 5(32):3396-8. Epub 2006 Jul 5.

Fakultät für Chemie der Universität, Postfach 100131, 33501, Bielefeld, Germany.

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http://dx.doi.org/10.1039/b604557jDOI Listing
August 2006

A tyrosine residue deprotonates during oxygen reduction by the caa3 reductase from Rhodothermus marinus.

FEBS Lett 2006 Feb 30;580(5):1350-4. Epub 2006 Jan 30.

Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa Av. da República, Apartado 127, 2781-901 Oeiras, Portugal.

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http://dx.doi.org/10.1016/j.febslet.2006.01.055DOI Listing
February 2006

Electron paramagnetic resonance studies of the iron-sulfur centers from complex I of Rhodothermus marinus.

Biochemistry 2006 Jan;45(3):1002-8

Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, Apartado 127, 2784-505 Oeiras, Portugal.

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http://dx.doi.org/10.1021/bi0519452DOI Listing
January 2006

A nhaD Na+/H+ antiporter and a pcd homologues are among the Rhodothermus marinus complex I genes.

Biochim Biophys Acta 2005 Aug;1709(1):95-103

Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, Apartado 127, 2781-901 Oeiras, Portugal.

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http://dx.doi.org/10.1016/j.bbabio.2005.06.003DOI Listing
August 2005

Structure at 1.3 A resolution of Rhodothermus marinus caa(3) cytochrome c domain.

J Mol Biol 2005 Feb 7;345(5):1047-57. Epub 2004 Dec 7.

Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Marie-Curie-Str. 15, D-60439 Frankfurt am Main, Germany.

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http://dx.doi.org/10.1016/j.jmb.2004.10.069DOI Listing
February 2005

Novel cerium(IV) heteropolyoxotungstate containing two types of lacunary Keggin anions.

Chem Commun (Camb) 2004 Dec 8(23):2656-7. Epub 2004 Oct 8.

Department of Chemistry, CICECO, University of Aveiro, 3810-193 Aveiro, Portugal.

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http://dx.doi.org/10.1039/b409034aDOI Listing
December 2004

Lanthanopolyoxotungstoborates: synthesis, characterization, and layer-by-layer assembly of europium photoluminescent nanostructured films.

J Nanosci Nanotechnol 2004 Jan-Feb;4(1-2):214-20

Department of Chemistry, University of Aveiro, CICECO, 3810-193 Aveiro, Portugal.

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August 2004