Journal article |
- Sinje Neukirchen; Inês A C Pereira; Filipa L Sousa. "Stepwise pathway for early evolutionary assembly of dissimilatory sulfite
and sulfate reduction". The ISME Journal (2023): https://doi.org/10.1038/s41396-023-01477-y.
10.1038/s41396-023-01477-y
- "Modular structure of complex II: An evolutionary perspective". Biochimica et biophysica acta. Bioenergetics (2022):
https://doi.org/10.1016/j.bbabio.2022.148916.
10.1016/j.bbabio.2022.148916
- Sinje Neukirchen; Filipa L. Sousa. "DiSCo: a sequence-based type-specific predictor of Dsr-dependent dissimilatory sulphur
metabolism in microbial data". Microbial Genomics (2021): https://doi.org/10.1099/mgen.0.000603.
10.1099/mgen.0.000603
- "Energy at Origins: Favorable Thermodynamics of Biosynthetic Reactions in the Last Universal Common Ancestor (LUCA)". Frontiers
in microbiology (2021): https://europepmc.org/articles/PMC8710812.
10.3389/fmicb.2021.793664
- "Dissimilatory sulfate reduction in the archaeon ‘Candidatus Vulcanisaeta moutnovskia’ sheds light on the evolution of sulfur
metabolism". Nature Microbiology (2020): http://dx.doi.org/10.1038/s41564-020-0776-z.
10.1038/s41564-020-0776-z
- "Identification of the sirohaem biosynthesis pathway in
Staphylococcus aureus". The FEBS Journal (2020): http://dx.doi.org/10.1111/febs.15091.
10.1111/febs.15091
- "The Future of Origin of Life Research: Bridging Decades-Old Divisions". Life (2020): http://dx.doi.org/10.3390/life10030020.
10.3390/life10030020
- "Meet the relatives of our cellular ancestor". Nature (2020): http://dx.doi.org/10.1038/d41586-020-00039-y.
10.1038/d41586-020-00039-y
- "Metabopolis: scalable network layout for biological pathway diagrams in urban map style". BMC Bioinformatics (2019):
http://dx.doi.org/10.1186/s12859-019-2779-4.
10.1186/s12859-019-2779-4
- "Metagenomes from Coastal Marine Sediments Give Insights into the Ecological Role and Cellular Features of Loki- and Thorarchaeota".
mBio (2019): http://dx.doi.org/10.1128/mbio.02039-19.
10.1128/mbio.02039-19
- "Oxygen Reductases in Alphaproteobacterial Genomes: Physiological Evolution From Low to High Oxygen Environments". Frontiers
in Microbiology (2019): http://dx.doi.org/10.3389/fmicb.2019.00499.
10.3389/fmicb.2019.00499
- "An electrogenic redox loop in sulfate reduction reveals a likely widespread mechanism of energy conservation". Nature
Communications (2018): http://dx.doi.org/10.1038/s41467-018-07839-x.
10.1038/s41467-018-07839-x
- Sousa FL; Preiner M; Martin WF. "Native metals, electron bifurcation, and CO2 reduction in early biochemical evolution.".
Current opinion in microbiology (2018): http://europepmc.org/abstract/med/29316496.
10.1016/j.mib.2017.12.010
- "Staphylococcus aureus haem biosynthesis and acquisition pathways are linked through haem monooxygenase IsdG". Molecular
microbiology (2018): https://doi.org/10.1111/mmi.14060.
10.1111/mmi.14060
- "Serpentinization: Connecting Geochemistry, Ancient Metabolism and Industrial Hydrogenation". Life (Basel, Switzerland)
(2018): https://doi.org/10.3390/life8040041.
10.3390/life8040041
- Annalisa Abdel Azim; Christian Pruckner; Philipp Kolar; Ruth-Sophie Taubner; Debora Fino; Guido Saracco; Filipa L Sousa; Simon
K-M R Rittmann. "The physiology of trace elements in biological methane production". Bioresource Technology 241 (2017):
775-786. https://ucris.univie.ac.at/portal/en/publications/the-physiology-of-trace-elements-in-biological-methane-production(11234984-4d5f-4d54-8249-45c2acb43c58).html.
10.1016/j.biortech.2017.05.211
- Madeline C. Weiss; Sinje Neukirchen; Mayo Roettger; Natalia Mrnjavac; Shijulal Nelson-Sathi; William F. Martin; Filipa L Sousa.
"Reply to 'Is LUCA a thermophilic progenote?'". Nature Microbiology 1 12 (2016): https://ucris.univie.ac.at/portal/en/publications/reply-to-is-luca-a-thermophilic-progenote(3559e5f5-4693-4ffd-b6e0-555952d4063f).html.
10.1038/NMICROBIOL.2016.230
- William F. Martin; Madeline C. Weiss; Sinje Neukirchen; Shijulal Nelson-Sathi; Filipa L Sousa. "Physiology, phylogeny, and
LUCA". Microbial Cell 3 12 (2016): 451-456. https://ucris.univie.ac.at/portal/en/publications/physiology-phylogeny-and-luca(18398f95-ede8-48f5-a558-6c4fe1e9699e).html.
10.15698/mic2016.12.545
- William F. Martin; Sinje Neukirchen; Verena Zimorski; Sven B. Gould; Filipa L Sousa. "Energy for two". BioEssays: advances
in molecular, cellular and developmental biology 38 9 (2016): 850-856. https://ucris.univie.ac.at/portal/en/publications/energy-for-two(1d7899b7-30c0-440f-9085-b415c95e1bcc).html.
10.1002/bies.201600089
- Sousa, Filipa L.; Parente, Daniel J.; Hessman, Jacob A.; Chazelle, Allen; Teichmann, Sarah A.; Swint-Kruse, Liskin. "Data
on publications, structural analyses, and queries used to build and utilize the AlloRep database". Data in Brief 8
(2016): 948-957.
papers3://publication/doi/10.1016/j.dib.2016.07.006
- Martin, William F.; Sousa, Filipa L.. "Early Microbial Evolution: The Age of Anaerobes". Cold Spring Harbor Perspectives
in Biology 8 2 (2016): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000371181300005&KeyUID=WOS:000371181300005.
10.1101/cshperspect.a018127
- Sousa, Filipa L.; Parente, Daniel J.; Shis, David L.; Hessman, Jacob A.; Chazelle, Allen; Bennett, Matthew R.; Teichmann,
Sarah A.; Swint-Kruse, Liskin. "AlloRep: A Repository of Sequence, Structural and Mutagenesis Data for the Lacl/GaIR Transcription
Regulators". Journal of Molecular Biology 428 4 (2016): 671-678. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000372561800002&KeyUID=WOS:000372561800002.
10.1016/j.jmb.2015.09.015
- Sousa, Filipa L.; Nelson-Sathi, Shijulal; Martin, William F.. "One step beyond a ribosome: The ancient anaerobic core". Biochimica
Et Biophysica Acta-Bioenergetics 1857 8 (2016): 1027-1038. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000378179300002&KeyUID=WOS:000378179300002.
10.1016/j.bbabio.2016.04.284
- Weiss, Madeline C.; Sousa, Filipa L.; Mrnjavac, Natalia; Neukirchen, Sinje; Roettger, Mayo; Nelson-Sathi, Shijulal; Martin,
William F.. "The physiology and habitat of the last universal common ancestor". Nature Microbiology 1 (2016): 16116-16116.
- Martin, William F.; Neukirchen, Sinje; Zimorski, Verena; Gould, Sven B.; Sousa, Filipa L.. "Energy for two: New archaeal lineages
and the origin of mitochondria". BioEssays (2016):
- Sousa, Filipa L.; Neukirchen, Sinje; Allen, John F.; Lane, Nick; Martin, William F.. "Lokiarchaeon is hydrogen dependent".
Nature Microbiology 1 (2016): 16034-16034.
- de Vries, Jan; Sousa, Filipa L.; Boelter, Bettina; Soll, Juergen; Gould, Sven B.. "YCF1: A Green TIC?". Plant Cell
27 7 (2015): 1827-1833. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000359358600005&KeyUID=WOS:000359358600005.
10.1105/tpc.114.135541
- Ku, Chuan; Nelson-Sathi, Shijulal; Roettger, Mayo; Sousa, Filipa L.; Lockhart, Peter J.; Bryant, David; Hazkani-Covo, Einat;
et al. "Endosymbiotic origin and differential loss of eukaryotic genes". Nature 524 7566 (2015): 427-+. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000360069300029&KeyUID=WOS:000360069300029.
10.1038/nature14963
- Nelson-Sathi, Shijulal; Sousa, Filipa L.; Roettger, Mayo; Lozada-Chavez, Nabor; Thiergart, Thorsten; Janssen, Arnold; Bryant,
David; et al. "Origins of major archaeal clades correspond to gene acquisitions from bacteria". Nature 517 7532 (2015):
77-U185. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000347178400038&KeyUID=WOS:000347178400038.
10.1038/nature13805
- Sousa, Filipa L.; Martin, William F.. "Biochemical fossils of the ancient transition from geoenergetics to bioenergetics in
prokaryotic one carbon compound metabolism". Biochimica Et Biophysica Acta-Bioenergetics 1837 7 (2014): 964-981. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000338815000003&KeyUID=WOS:000338815000003.
10.1016/j.bbabio.2014.02.001
- Martin, William F.; Sousa, Filipa L.; Lane, Nick. "EVOLUTION Energy at life's origin". Science 344 6188 (2014): 1092-1093.
http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000336791200024&KeyUID=WOS:000336791200024.
10.1126/science.1251653
- Ku, Chuan; Roettger, Mayo; Zimorski, Verena; Nelson-Sathi, Shijulal; Sousa, Filipa L.; Martin, William F.. "Plastid origin:
who, when and why?". Acta Societatis Botanicorum Poloniae 83 4 (2014): 281-289. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000347215700003&KeyUID=WOS:000347215700003.
10.5586/asbp.2014.045
- Sousa, Filipa L.; Shavit-Grievink, Liat; Allen, John F.; Martin, William F.. "Chlorophyll Biosynthesis Gene Evolution Indicates
Photosystem Gene Duplication, Not Photosystem Merger, at the Origin of Oxygenic Photosynthesis". Genome Biology and Evolution
5 1 (2013): 200-216. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000314778600017&KeyUID=WOS:000314778600017.
10.1093/gbe/evs127
- Sousa, Filipa L.; Thiergart, Thorsten; Landan, Giddy; Nelson-Sathi, Shijulal; Pereira, Ines A. C.; Allen, John F.; Lane, Nick;
Martin, William F.. "Early bioenergetic evolution". Philosophical Transactions of the Royal Society B-Biological Sciences
368 1622 (2013): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000320105200014&KeyUID=WOS:000320105200014.
10.1098/rstb.2013.0088
- Sousa, Filipa L.; Alves, Renato J.; Ribeiro, Miguel A.; Pereira-Leal, Jose B.; Teixeira, Miguel; Pereira, Manuela M.. "The
superfamily of heme-copper oxygen reductases: Types and evolutionary considerations". Biochimica Et Biophysica Acta-Bioenergetics
1817 4 (2012): 629-637. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000301885600020&KeyUID=WOS:000301885600020.
10.1016/j.bbabio.2011.09.020
- Sousa, Filipa L.; Alves, Renato J.; Ribeiro, Miguel A.; Pereira-Leal, Jose B.; Teixeira, Miguel; Pereira, Manuela M.. "Heme-copper
oxygen reductases: Taxonomic profiling". Biochimica Et Biophysica Acta-Bioenergetics 1817 (2012): S112-S113. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000308525400280&KeyUID=WOS:000308525400280.
10.1016/j.bbabio.2012.06.303
- Perica, Tina; Marsh, Joseph A.; Sousa, Filipa L.; Natan, Eviatar; Colwell, Lucy J.; Ahnert, Sebastian E.; Teichmann, Sarah
A.. "The emergence of protein complexes: quaternary structure, dynamics and allostery". Biochemical Society Transactions
40 (2012): 475-491. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000304803900001&KeyUID=WOS:000304803900001.
10.1042/BST20120056
- Sousa, Filipa L.; Alves, Renato J.; Pereira-Leal, Jose B.; Teixeira, Miguel; Pereira, Manuela M.. "A Bioinformatics Classifier
and Database for Heme-Copper Oxygen Reductases". Plos One 6 4 (2011): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000290024700067&KeyUID=WOS:000290024700067.
10.1371/journal.pone.0019117
- Sousa, Filipa L.; Alves, Renato J.; Teixeira, Miguel; Pereira-Leal, Jose B.; Pereira, Manuela M.. "Heme-copper oxygen reductases
superfamily revisited". Biochimica Et Biophysica Acta-Bioenergetics 1797 (2010): 101-101. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000279662500285&KeyUID=WOS:000279662500285.
- Refojo, Patricia N.; Sousa, Filipa L.; Teixeira, Miguel; Pereira, Manuela M.. "The alternative complex III A different architecture
using known building modules". Biochimica Et Biophysica Acta-Bioenergetics 1797 12 (2010): 1869-1876. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000284788500005&KeyUID=WOS:000284788500005.
10.1016/j.bbabio.2010.04.012
- Brito, Jose A.; Sousa, Filipa L.; Stelter, Meike; Bandeiras, Tiago M.; Vonrhein, Clemens; Teixeira, Miguel; Pereira, Manuela
M.; Archer, Margarida. "Structural and Functional Insights into Sulfide:Quinone Oxidoreductase". Biochemistry 48 24
(2009): 5613-5622. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000267117900014&KeyUID=WOS:000267117900014.
10.1021/bi9003827
- Sousa, Filipa L.; Verissimo, Andreia F.; Baptista, Antnio M.; Soulimane, Tewfik; Teixeira, Miguel; Pereira, Manuela M.; Baptista,
Antonio M.. "Redox properties of Thermus thermophilus ba3: Different electron-proton coupling in oxygen reductases?". Biophysical
Journal 94 6 (2008): 2434-2441. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000253676200045&KeyUID=WOS:000253676200045.
10.1529/biophysj.107.122614
- Verissimo, Andreia F.; Sousa, Filipa L.; Baptista, Antonio M.; Teixeira, Miguel; Pereira, Manuela M.. "Thermodynamic Redox
Behavior of the Heme Centers in A-Type Heme-Copper Oxygen Reductases: Comparison between the Two Subfamilies". Biophysical
Journal 95 9 (2008): 4448-4455. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000260072600036&KeyUID=WOS:000260072600036.
10.1529/biophysj.108.139493
- Pereira, Manuela M.; Sousa, Filipa L.; Verissimo, Andreia F.; Teixeira, Miguel. "Looking for the minimum common denominator
in haem-copper oxygen reductases: Towards a unified catalytic mechanism". Biochimica Et Biophysica Acta-Bioenergetics
1777 7-8 (2008): 929-934. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000257696400053&KeyUID=WOS:000257696400053.
10.1016/j.bbabio.2008.05.441
- Verissimo, Andreia F.; Sousa, Filipa L.; Baptista, Antonio M.; Teixeira, Miguel; Pereira, Manuela M.. "Thermodynamic redox
behavior of the heme centers of cbb(3) heme-copper oxygen reductase from Bradyrhizobium japonicum (vol 46, pg 13245, 2007)".
Biochemistry 47 19 (2008): 5480-5480. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000255547600024&KeyUID=WOS:000255547600024.
10.1021/bi8005829
- Sousa, Filipa L.; Verissimo, Andreia F.; Baptista, Antonio M.; Teixeira, Miguel; Pereira, Manuela M.. "What can thermodynamics
tells us about haem-copper oxygen reductases: A comparison between families". Biochimica Et Biophysica Acta-Bioenergetics
1777 (2008): S68-S68. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000258037700257&KeyUID=WOS:000258037700257.
10.1016/j.bbabio.2008.05.267
- Verissimo, Andreia F.; Sousa, Filipa L.; Baptista, Antonio M.; Teixeira, Miguel; Pereira, Manuela M.. "Thermodynamic redox
Behavior of the heme Centers of cbb3Heme-Copper oxygen reductase from Bradyrhizobium japonicum". Biochemistry 46 46
(2007): 13245-13253. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000250960400001&KeyUID=WOS:000250960400001.
10.1021/bi700733g
- Fernandes, AS; Sousa, FL; Teixeira, M; Pereira, MM. "Electron paramagnetic resonance studies of the iron-sulfur centers from
complex I of Rhodothermus marinus". Biochemistry 45 3 (2006): 1002-1008. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000234988600036&KeyUID=WOS:000234988600036.
10.1021/bi0519452
- Pereira, MM; Sousa, FL; Teixeira, M; Nyquist, RM; Heberle, J. "A tyrosine residue deprotonates during oxygen reduction by
the caa3 reductase from Rhodothermus marinus". Febs Letters 580 5 (2006): 1350-1354. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000235597700024&KeyUID=WOS:000235597700024.
10.1016/j.febslet.2006.01.055
- Melo, AMP; Lobo, SAL; Sousa, FL; Fernandes, AS; Pereira, MM; Hreggvidsson, GO; Kristjansson, JK; Saraiva, LM; Teixeira, M.
"A nhaD Na+/H+ antiporter and a pcd homologues are among the Rhodothermus marinus complex I genes". Biochimica Et Biophysica
Acta-Bioenergetics 1709 1 (2005): 95-103. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000231346700008&KeyUID=WOS:000231346700008.
10.1016/j.bbabio.2005.06.003
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