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Select item 88968261.

Cellular assays identify barriers impeding iron-sulfur enzyme activity in a non-native prokaryotic host

Francesca D'Angelo, Elena Fernández-Fueyo, Pierre Simon Garcia, Helena Shomar, Martin Pelosse, Rita Rebelo Manuel, Ferhat Büke, Siyi Liu, Niels van den Broek, Nicolas Duraffourg, Carol de Ram, Martin Pabst, Emmanuelle Bouveret, Simonetta Gribaldo, Béatrice Py, Sandrine Ollagnier de Choudens, Frédéric Barras, Gregory Bokinsky

eLife. 2022; 11: e70936. Published online 2022 Mar 4. doi: 10.7554/eLife.70936

PMCID:: PMC8896826

Abstract Article PDF–2.7M

Select item 50311342.

Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics

Jasper J. Koehorst, Edoardo Saccenti, Peter J. Schaap, Vitor A. P. Martins dos Santos, Maria Suarez-Diez

Version 3. F1000Res. 2016; 5: 1987. Published online 2017 Jun 27. doi: 10.12688/f1000research.9416.3

PMCID:: PMC5031134

Abstract Article PDF–5.2M

Select item 42995203.

Genome-wide gene order distances support clustering the gram-positive bacteria

Christopher H. House, Matteo Pellegrini, Sorel T. Fitz-Gibbon

Front Microbiol. 2014; 5: 785. Published online 2015 Jan 20. doi: 10.3389/fmicb.2014.00785

PMCID:: PMC4299520

Abstract Article PDF–8.7M

Select item 34222174.

Meta-Analysis of General Bacterial Subclades in Whole-Genome Phylogenies Using Tree Topology Profiling

Thomas Meinel, Antje Krause

Evol Bioinform Online. 2012; 8: 489–525. Published online 2012 Aug 7. doi: 10.4137/EBO.S9642

PMCID:: PMC3422217

Abstract Article PDF–1.3M

Select item 33040155.

Biogenesis of cbb₃-type cytochrome c oxidase in Rhodobacter capsulatus

Seda Ekici, Grzegorz Pawlik, Eva Lohmeyer, Hans-Georg Koch, Fevzi Daldal

Biochim Biophys Acta. Author manuscript; available in PMC 2013 Jun 1.

Published in final edited form as: Biochim Biophys Acta. 2012 Jun; 1817(6): 898–910. Published online 2011 Nov 4. doi: 10.1016/j.bbabio.2011.10.011

PMCID:: PMC3304015

Abstract Article PDF–1.7M

Select item 30935446.

Phylogenetic Distribution and Evolutionary History of Bacterial DEAD-Box Proteins

Varinia López-Ramírez, Luis D. Alcaraz, Gabriel Moreno-Hagelsieb, Gabriela Olmedo-Álvarez

J Mol Evol. 2011; 72(4): 413–431. Published online 2011 Mar 25. doi: 10.1007/s00239-011-9441-8

PMCID:: PMC3093544

Abstract Article PDF–9.0M

Select item 30551547.

Molecular modelling of urease accessory interaction proteins of Helicobacter Pylori J 99 and predicting an interruption in interaction by Vigna radiata Defensins

Manivannan Paramasivan, Ganesan Sankaran, Naveenkumar Sethuraman, Daniel Selvakumar Devadoss, Sathiamoorthi Thangavelu, Muralitharan Gangatharan

Bioinformation. 2011; 5(10): 410–415. Published online 2011 Feb 15. doi: 10.6026/97320630005410

PMCID:: PMC3055154

Abstract Article PDF–840K

Select item 29746428.

Distribution Analysis of Hydrogenases in Surface Waters of Marine and Freshwater Environments

Martin Barz, Christian Beimgraben, Torsten Staller, Frauke Germer, Friederike Opitz, Claudia Marquardt, Christoph Schwarz, Kirstin Gutekunst, Klaus Heinrich Vanselow, Ruth Schmitz, Julie LaRoche, Rüdiger Schulz, Jens Appel

PLoS One. 2010; 5(11): e13846. Published online 2010 Nov 5. doi: 10.1371/journal.pone.0013846

PMCID:: PMC2974642

Abstract Article PDF–850K

Select item 27968179.

inGAP: an integrated next-generation genome analysis pipeline

Ji Qi, Fangqing Zhao, Anne Buboltz, Stephan C. Schuster

Bioinformatics. 2010 Jan 1; 26(1): 127–129. Published online 2009 Oct 30. doi: 10.1093/bioinformatics/btp615

PMCID:: PMC2796817

Abstract Article PDF–318K

Select item 226668110.

Characterization of a novel prokaryotic GDP dissociation inhibitor domain from the G protein coupled membrane protein FeoB

Edward T. Eng, Amir R. Jalilian, Krasimir A. Spasov, Vinzenz M. Unger

J Mol Biol. Author manuscript; available in PMC 2009 Jan 25.

Published in final edited form as: J Mol Biol. 2008 Jan 25; 375(4): 1086–1097. Published online 2007 Nov 19. doi: 10.1016/j.jmb.2007.11.027

PMCID:: PMC2266681

Abstract Article PDF–919K

Select item 185231611.

Transcriptional regulatory network discovery via multiple method integration: application to e. coli K12

Jingjun Sun, Kagan Tuncay, Alaa Abi Haidar, Lisa Ensman, Frank Stanley, Michael Trelinski, Peter Ortoleva

Algorithms Mol Biol. 2007; 2: 2. Published online 2007 Mar 30. doi: 10.1186/1748-7188-2-2

PMCID:: PMC1852316

Abstract Article PDF–707K

Select item 131687812.

Preferential attachment in the evolution of metabolic networks

Sara Light, Per Kraulis, Arne Elofsson

BMC Genomics. 2005; 6: 159. Published online 2005 Nov 10. doi: 10.1186/1471-2164-6-159

PMCID:: PMC1316878

Abstract Article PDF–381K

Select item 55231413.

Clustering the annotation space of proteins

Victor Kunin, Christos A Ouzounis

BMC Bioinformatics. 2005; 6: 24. Published online 2005 Feb 9. doi: 10.1186/1471-2105-6-24

PMCID:: PMC552314

Abstract Article PDF–286K

Select item 22295914.

The COG database: an updated version includes eukaryotes

Roman L Tatusov, Natalie D Fedorova, John D Jackson, Aviva R Jacobs, Boris Kiryutin, Eugene V Koonin, Dmitri M Krylov, Raja Mazumder, Sergei L Mekhedov, Anastasia N Nikolskaya, B Sridhar Rao, Sergei Smirnov, Alexander V Sverdlov, Sona Vasudevan, Yuri I Wolf, Jodie J Yin, Darren A Natale

BMC Bioinformatics. 2003; 4: 41. Published online 2003 Sep 11. doi: 10.1186/1471-2105-4-41

PMCID:: PMC222959

Abstract Article PDF–443K

Select item 12625115.

Pervasive properties of the genomic signature

Robert W Jernigan, Robert H Baran

BMC Genomics. 2002; 3: 23. Published online 2002 Aug 9. doi: 10.1186/1471-2164-3-23

PMCID:: PMC126251

Abstract Article PDF–288K

Select item 18664416.

Evidence That Plant-Like Genes in Chlamydia Species Reflect an Ancestral Relationship between Chlamydiaceae, Cyanobacteria, and the Chloroplast

Fiona S.L. Brinkman, Jeffrey L. Blanchard, Artem Cherkasov, Yossef Av-Gay, Robert C. Brunham, Rachel C. Fernandez, B. Brett Finlay, Sarah P. Otto, B.F. Francis Ouellette, Patrick J. Keeling, Ann M. Rose, Robert E.W. Hancock, Steven J.M. Jones

Genome Res. 2002 Aug; 12(8): 1159–1167. doi: 10.1101/gr.341802

Correction in:: Genome Res. 2002 Oct; 12(10): 1624.

PMCID:: PMC186644

Abstract Article PDF–175K

Select item 31096917.

Horizontal Gene Transfer in Bacterial and Archaeal Complete Genomes

Santiago Garcia-Vallvé, Anton Romeu, Jaume Palau

Genome Res. 2000 Nov; 10(11): 1719–1725. doi: 10.1101/gr.130000

PMCID:: PMC310969

Abstract Article PDF–226K

Select item 816627218.

Transfer RNA-Derived Fragments, the Underappreciated Regulatory Small RNAs in Microbial Pathogenesis

Zhongyou Li, Bruce A. Stanton

Front Microbiol. 2021; 12: 687632. Published online 2021 May 17. doi: 10.3389/fmicb.2021.687632

PMCID:: PMC8166272

Abstract Article PDF–821K

Select item 793812219.

Information theoretic perspective on genome clustering

Alaguraj Veluchamy, Preeti Mehta, K.V. Srividhya, Hirendra Vikram, M.K. Govind, Ramneek Gupta, Abdul Aziz Bin Dukhyil, Raed Abdullah Alharbi, Saleh Abdullah Aloyuni, Mohamed M. Hassan, S. Krishnaswamy

Saudi J Biol Sci. 2021 Mar; 28(3): 1867–1889. Published online 2020 Dec 31. doi: 10.1016/j.sjbs.2020.12.039